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Minerals
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Computational Methods in Mineralogy and Geochemistry
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Computational Methods in Mineralogy and Geochemistry

A special issue of Minerals (ISSN 2075-163X).

Deadline for manuscript submissions: closed (15 February 2019) | Viewed by 38865

Special Issue Editor

Dr. Raffaella Demichelis

E-Mail Website
Guest Editor
Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), and Department of Chemistry, Curtin University, Perth, WA 6845, Australia
Interests: nucleation and crystal growth; biomineralization; surface chemistry; modelling; mineral-fluid interface; nanotubes; Density Functional Theory; Force fields; vibrational spectroscopy

Special Issue Information

Dear Colleagues,

Computational methods and virtual experiments are increasingly playing a main role in revealing the fundamental science underpinning complex geochemical phenomena and in predicting mineral structures, properties, formation and reactivity. In particular, during the past two decades, the rapid development of supercomputing facilities and of new algorithms exploiting these growing hardware capabilities has lead computational techniques to become a complementary tool to both interpret and direct experiments. Indeed, major advances in predicting and interpreting polymorphism, optical properties, surface reactivity, phase stability, nucleation pathways, dissolution and crystal growth mechanisms (to mention only a few) have been achieved through a variety of ab initio, classical, and semi-empirical methods that allow accessing accurate electronic and atomic scale information.

This Special Issue aims to bring together studies from all these areas, and, more generally, from the broad fields of computational mineralogy and geochemistry. We welcome theoretical studies, as well as combined experimental-theoretical investigations. We solicit studies employing novel methodological approaches, as well as applications of state-of-the-art techniques to characterize crystalline and amorphous minerals and mineral-based (hybrid) materials (structure, morphology, properties, formation, chemical reactivity), and to interpret and/or predict geochemical phenomena.

The hope is that this Special Issue will serve to showcase the current capabilities, the advantages, and possibly the future perspectives of computational techniques in the context of mineralogy and geochemistry.

Dr. Raffaella Demichelis
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Minerals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Combined experimental-theoretical studies
  • First principle methods
  • Classical methods
  • Semi-empirical methods
  • Method development
  • Mineral characterization
  • Surface morphology and reactivity
  • Crystal, quasi-crystal and amorphous phases
  • Hybrid mineral-based materials
  • Nucleation, dissolution, and crystal growth
  • Mineral-fluid interaction
  • Other geochemical processes

Published Papers (8 papers)

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Research

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17 pages, 7014 KiB  
Article
Understanding Cement Hydration of Cemented Paste Backfill: DFT Study of Water Adsorption on Tricalcium Silicate (111) Surface
by Chongchong Qi, Lang Liu, Jianyong He, Qiusong Chen, Li-Juan Yu and Pengfei Liu
Minerals 2019, 9(4), 202; https://0-doi-org.brum.beds.ac.uk/10.3390/min9040202 - 27 Mar 2019
Cited by 47 | Viewed by 4822
Abstract
Understanding cement hydration is of crucial importance for the application of cementitious materials, including cemented paste backfill. In this work, the adsorption of a single water molecule on an M3-C3S (111) surface is investigated using density functional theory (DFT) calculations. The [...] Read more.
Understanding cement hydration is of crucial importance for the application of cementitious materials, including cemented paste backfill. In this work, the adsorption of a single water molecule on an M3-C3S (111) surface is investigated using density functional theory (DFT) calculations. The adsorption energies for 14 starting geometries are calculated and the electronic properties of the reaction are analysed. Two adsorption mechanisms, molecular adsorption and dissociative adsorption, are observed and six adsorption configurations are found. The results indicate that spontaneous dissociative adsorption is energetically favored over molecular adsorption. Electrons are transferred from the surface to the water molecule during adsorption. The density of states (DOS) reveals the bonding mechanisms between water and the surface. This study provides an insight into the adsorption mechanism at an atomic level, and can significantly promote the understanding of cement hydration within such systems. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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17 pages, 4101 KiB  
Article
Thermo-Elasticity of Materials from Quasi-Harmonic Calculations
by Maurizio Destefanis, Corentin Ravoux, Alessandro Cossard and Alessandro Erba
Minerals 2019, 9(1), 16; https://0-doi-org.brum.beds.ac.uk/10.3390/min9010016 - 26 Dec 2018
Cited by 24 | Viewed by 4294
Abstract
An effective algorithm for the quasi-harmonic calculation of thermo-elastic stiffness constants of materials is discussed and implemented into the Crystal program for quantum-mechanical simulations of extended systems. Two different approaches of increasing complexity and accuracy are presented. The first one is a quasi-static [...] Read more.
An effective algorithm for the quasi-harmonic calculation of thermo-elastic stiffness constants of materials is discussed and implemented into the Crystal program for quantum-mechanical simulations of extended systems. Two different approaches of increasing complexity and accuracy are presented. The first one is a quasi-static approximation where the thermal dependence of elastic constants is assumed to be due only to the thermal expansion of the system. The second one is fully quasi-harmonic, takes into account thermal expansion, and explicitly computes Helmholtz free energy derivatives with respect to strain. The conversion of isothermal into adiabatic thermo-elastic constants is also addressed. The algorithm is formally presented and applied to the description of the thermo-elastic response of the forsterite mineral. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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15 pages, 1865 KiB  
Article
Multiple Kinetic Parameterization in a Reactive Transport Model Using the Exchange Monte Carlo Method
by Ryosuke Oyanagi, Atsushi Okamoto and Noriyoshi Tsuchiya
Minerals 2018, 8(12), 579; https://0-doi-org.brum.beds.ac.uk/10.3390/min8120579 - 08 Dec 2018
Cited by 5 | Viewed by 3699
Abstract
Water–rock interaction in surface and subsurface environments occurs in complex multicomponent systems and involves several reactions, including element transfer. Such kinetic information is obtained by fitting a forward model into the temporal evolution of solution chemistry or the spatial pattern recorded in the [...] Read more.
Water–rock interaction in surface and subsurface environments occurs in complex multicomponent systems and involves several reactions, including element transfer. Such kinetic information is obtained by fitting a forward model into the temporal evolution of solution chemistry or the spatial pattern recorded in the rock samples, although geochemical and petrological data are essentially sparse and noisy. Therefore, the optimization of kinetic parameters sometimes fails to converge toward the global minimum due to being trapped in a local minimum. In this study, we simultaneously present a novel framework to estimate multiple reaction-rate constants and the diffusivity of aqueous species from the mineral distribution pattern in a rock by using the reactive transport model coupled with the exchange Monte Carlo method. Our approach can estimate both the maximum likelihood and error of each parameter. We applied the method to the synthetic data, which were produced using a model for silica metasomatism and hydration in the olivine–quartz–H2O system. We tested the robustness and accuracy of our method over a wide range of noise intensities. This methodology can be widely applied to kinetic analyses of various kinds of water–rock interactions. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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11 pages, 2935 KiB  
Article
[Au(CN)2]—Adsorption on a Graphite (0001) Surface: A First Principles Study
by Xianhai Li, Qin Zhang, Jun Xie and Zhihui Shen
Minerals 2018, 8(10), 425; https://0-doi-org.brum.beds.ac.uk/10.3390/min8100425 - 27 Sep 2018
Cited by 7 | Viewed by 4158
Abstract
Gold is mainly present in the form of [Au(CN)2]− during the cyanide leaching process, and this [Au(CN)2]− can be adsorbed by graphite in carbonaceous gold ore resulting in preg-robbing gold. In order to clarify the adsorption mechanism [...] Read more.
Gold is mainly present in the form of [Au(CN)2]− during the cyanide leaching process, and this [Au(CN)2]− can be adsorbed by graphite in carbonaceous gold ore resulting in preg-robbing gold. In order to clarify the adsorption mechanism between the [Au(CN)2]− and graphite, the interaction between the [Au(CN)2]− and graphite (0001) surface was studied using density functional theory (DFT). The distance between [Au(CN)2]− and graphite (0001) decreased from (4.298–4.440 Å) to (3.123–3.343 Å) after optimization, and the shape of [Au(CN)2]− and graphite (0001) obviously changed from straight to curved, which indicated that the [Au(CN)2]− had been adsorbed on the graphite (0001) surface. A partial densities of state (PDOS) analysis revealed that there was little change in the delocalization and locality of the PDOS on the graphite (0001) surface after adsorption. However, the valence bands of the Au 5d orbital, C 2p orbital, and N 2p orbital near the Fermi level moved slightly towards lower energy levels; therefore, the adsorption configuration was stable. An analysis of the Mulliken charge population indicated that the Au, N, and C in [Au(CN)2]− obtained 0.26, 0.18, 0.04 electrons after adsorption, respectively, while C(surf) lost 0.03 electrons. [Au(CN)2]− changed to a conductor from an insulator after adsorption. Taking into account the surface electrical properties of [Au(CN)2]− and graphite (0001), there was still a slight electrostatic adsorption between them. The analysis of adsorption energy, electronic structure, PDOS, electron density, Mulliken charge population, and Mulliken bond population revealed that [Au(CN)2]− could be adsorbed to the graphite (0001) surface; the adsorption was a type of physical adsorption (including electrostatic adsorption) and mainly occurred on the two C≡N. These results contributed to the understanding of the mechanisms involved in preg-robbing gold formation by graphite and the optimization of this process during cyanide leaching. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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14 pages, 2772 KiB  
Article
Combined DFT and XPS Investigation of Cysteine Adsorption on the Pyrite (1 0 0) Surface
by Xingfu Zheng, Xuan Pan, Zhenyuan Nie, Yi Yang, Lizhu Liu, Hongying Yang and Jinlan Xia
Minerals 2018, 8(9), 366; https://0-doi-org.brum.beds.ac.uk/10.3390/min8090366 - 23 Aug 2018
Cited by 15 | Viewed by 5556
Abstract
The adsorption of cysteine on the pyrite (1 0 0) surface was evaluated by using first-principles-based density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) measurements. The frontier orbitals analyses indicate that the interaction of cysteine and pyrite mainly occurs between HOMO of [...] Read more.
The adsorption of cysteine on the pyrite (1 0 0) surface was evaluated by using first-principles-based density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) measurements. The frontier orbitals analyses indicate that the interaction of cysteine and pyrite mainly occurs between HOMO of cysteine and LUMO of pyrite. The adsorption energy calculation shows that the configuration of the -OH of -COOH adsorbed on the Fe site is the thermodynamically preferred adsorption configuration, and it is the strongest ionic bond according to the Mulliken bond populations. As for Fe site mode, the electrons are found transferred from cysteine to Fe of pyrite (1 0 0) surface, while there is little or no electron transfer for S site mode. Projected density of states (PDOS) is analyzed further in order to clarify the interaction mechanism between cysteine and the pyrite (1 0 0) surface. After that, the presence of cysteine adsorption on the pyrite (1 0 0) surface is indicated by the qualitative results of the XPS spectra. This study provides an alternative way to enhance the knowledge of microbe–mineral interactions and find a route to improve the rate of bioleaching. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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25 pages, 5944 KiB  
Article
Multiscale Computational Simulation of Amorphous Silicates’ Structural, Dielectric, and Vibrational Spectroscopic Properties
by José Ángel Martínez-González, Javier Navarro-Ruiz and Albert Rimola
Minerals 2018, 8(8), 353; https://0-doi-org.brum.beds.ac.uk/10.3390/min8080353 - 15 Aug 2018
Cited by 7 | Viewed by 6071
Abstract
Silicates are among the most abundant and important inorganic materials, not only in the Earth’s crust, but also in the interstellar medium in the form of micro/nanoparticles or embedded in the matrices of comets, meteorites, and other asteroidal bodies. Although the crystalline phases [...] Read more.
Silicates are among the most abundant and important inorganic materials, not only in the Earth’s crust, but also in the interstellar medium in the form of micro/nanoparticles or embedded in the matrices of comets, meteorites, and other asteroidal bodies. Although the crystalline phases of silicates are indeed present in nature, amorphous forms are also highly abundant. Here, we report a theoretical investigation of the structural, dielectric, and vibrational properties of the amorphous bulk for forsterite (Mg2SiO4) as a silicate test case by a combined approach of classical molecular dynamics (MD) simulations for structure evolution and periodic quantum mechanical Density Functional Theory (DFT) calculations for electronic structure analysis. Using classical MD based on an empirical partial charge rigid ionic model within a melt-quenching scheme at different temperatures performed with the GULP 4.0 code, amorphous bulk structures for Mg2SiO4 were generated using the crystalline phase as the initial guess. This has been done for bulk structures with three different unit cell sizes, adopting a super-cell approach; that is, 1 × 1 × 2, 2 × 1 × 2, and 2 × 2 × 2. The radial distribution functions indicated a good degree of amorphization of the structures. Periodic B3LYP-geometry optimizations performed with the CRYSTAL14 code on the generated amorphous systems were used to analyze their structure; to calculate their high-frequency dielectric constants (ε∞); and to simulate their IR, Raman, and reflectance spectra, which were compared with the experimental and theoretical crystalline Mg2SiO4. The most significant changes of the physicochemical properties of the amorphous systems compared to the crystalline ones are presented and discussed (e.g., larger deviations in the bond distances and angles, broadening of the IR bands, etc.), which are consistent with their disordered nature. It is also shown that by increasing the unit cell size, the bulk structures present a larger degree of amorphization. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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10 pages, 1274 KiB  
Article
(10.4) Face of Ordered and Disordered Dolomite, MgCa(CO3)2: A Computational Study to Reveal the Growth Mechanism
by Marco Bruno and Erica Bittarello
Minerals 2018, 8(8), 323; https://0-doi-org.brum.beds.ac.uk/10.3390/min8080323 - 27 Jul 2018
Cited by 7 | Viewed by 3525
Abstract
In this study, the stability of the (10.4) face of dolomite was systematically investigated. The surface energies at 0 K of the different (10.4) surfaces resulting from the cut of both ordered and disordered bulk structures were determined and compared, to establish how [...] Read more.
In this study, the stability of the (10.4) face of dolomite was systematically investigated. The surface energies at 0 K of the different (10.4) surfaces resulting from the cut of both ordered and disordered bulk structures were determined and compared, to establish how different atomic configurations (surface terminations) can affect the stability of the investigated face. To study the thermodynamic behavior of a surface, a 2D periodic slab model and the ab initio CRYSTAL code were adopted. The surface energies of the (10.4) faces of calcite and magnesite were also calculated in order to compare them with those of the different terminations of the (10.4) face of dolomite. Our calculations showed that the bulk of the dolomite crystal must have an ordered structure to reach the minimum of the energy, whereas the (10.4) surface is more stable when its structure is disordered. A growth model of the (10.4) face has been proposed: the peculiarity of this model consists in the existence of some disordered layers forming at the interface crystal/solution, which arrange in an ordered structure once covered by others disordered layers resulting by the spiral steps propagation. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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Review

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20 pages, 4461 KiB  
Review
Quantum Mechanical Modeling of the Vibrational Spectra of Minerals with a Focus on Clays
by James D. Kubicki and Heath D. Watts
Minerals 2019, 9(3), 141; https://0-doi-org.brum.beds.ac.uk/10.3390/min9030141 - 27 Feb 2019
Cited by 17 | Viewed by 5849
Abstract
We present an overview of how to use quantum mechanical calculations to predict vibrational frequencies of molecules and materials such as clays and silicates. Other methods of estimating vibrational frequencies are mentioned, such as classical molecular dynamics simulations; references are given for additional [...] Read more.
We present an overview of how to use quantum mechanical calculations to predict vibrational frequencies of molecules and materials such as clays and silicates. Other methods of estimating vibrational frequencies are mentioned, such as classical molecular dynamics simulations; references are given for additional information on these approaches. Herein, we discuss basic vibrational theory, calculating Raman and infrared intensities, steps for creating realistic models, and applications to spectroscopy, thermodynamics, and isotopic fractionation. There are a wide variety of programs and methods that can be employed to model vibrational spectra, but this work focuses on hybrid density functional theory (DFT) approaches. Many of the principles are the same when used in other programs and DFT methods, so a novice can benefit from simple examples that illustrate key points to consider when modeling vibrational spectra. Other methods and programs are listed to give the beginner a starting point for exploring and choosing which approach will be best for a given problem. The modeler should also be aware of the numerous analytical methods available for obtaining information on vibrations of atoms in molecules and materials. In addition to traditional infrared and Raman spectroscopy, sum-frequency generation (SFG) and inelastic neutron scattering (INS) are also excellent techniques for obtaining vibrational frequency information in certain circumstances. Full article
(This article belongs to the Special Issue Computational Methods in Mineralogy and Geochemistry)
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