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Advances in Low-temperature Computational Mineralogy

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

Deadline for manuscript submissions: closed (15 December 2013) | Viewed by 75752

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Special Issue Editor

Prof. Dr. Udo Becker

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Guest Editor

Department of Earth and Environmental Sciences, University of Michigan, 1100 North University Avenue, 2534 CC Little, Ann Arbor, MI 48109-1005, USA

Special Issue Information

Dear Colleagues,

The aim of this special issue is to show the breadth and underlying theory of computational methods in low-temperature and environmental applications, with focus on the mineral-liquid interface. The roles of atomistic methods in this field are manifold, from supporting and analyzing experimental methods, to complementing these, and to provide information on the structure, thermodynamics, reaction mechanisms and kinetics, and physical properties of interface features that would be difficult to obtain otherwise. Not only the evolution of computer power but also the development of the careful design of software and, maybe most importantly, of models that are a good representation of larger-scale phenomena have helped for this discipline becoming a more and more important part in understanding low-temperature processes in a fundamental way. This has led to developing models that have a sound physicochemical basis and are less black-box oriented. We hope that this issue will be helpful to the experienced modeler as well as for graduate students that are new to the field in gaining a broad understanding of the opportunities in this field.

Prof. Dr. Udo Becker
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

interface processes
adsorption and desorption of aqueous species
atomistic simulations
crystal growth and dissolution
redox processes
thermodynamics; kinetics; and reaction mechanisms of low-temperature processes

Published Papers (6 papers)

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Research

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2521 KiB

Open AccessArticle

Quantum-Mechanical Methods for Quantifying Incorporation of Contaminants in Proximal Minerals

by Lindsay C. Shuller-Nickles, Will M. Bender, Sarah M. Walker and Udo Becker

Minerals 2014, 4(3), 690-715; https://doi.org/10.3390/min4030690 - 14 Jul 2014

Cited by 26 | Viewed by 8439

Abstract

Incorporation reactions play an important role in dictating immobilization and release pathways for chemical species in low-temperature geologic environments. Quantum-mechanical investigations of incorporation seek to characterize the stability and geometry of incorporated structures, as well as the thermodynamics and kinetics of the reactions themselves. For a thermodynamic treatment of incorporation reactions, a source of the incorporated ion and a sink for the released ion is necessary. These sources/sinks in a real geochemical system can be solids, but more commonly, they are charged aqueous species. In this contribution, we review the current methods for ab initio calculations of incorporation reactions, many of which do not consider incorporation from aqueous species. We detail a recently-developed approach for the calculation of incorporation reactions and expand on the part that is modeling the interaction of periodic solids with aqueous source and sink phases and present new research using this approach. To model these interactions, a systematic series of calculations must be done to transform periodic solid source and sink phases to aqueous-phase clusters. Examples of this process are provided for three case studies: (1) neptunyl incorporation into studtite and boltwoodite: for the layered boltwoodite, the incorporation energies are smaller (more favorable) for reactions using environmentally relevant source and sink phases (i.e., ΔE_rxn(oxides) > ΔE_rxn(silicates) > ΔE_rxn(aqueous)). Estimates of the solid-solution behavior of Np⁵⁺/P⁵⁺- and U⁶⁺/Si⁴⁺-boltwoodite and Np⁵⁺/Ca²⁺- and U⁶⁺/K⁺-boltwoodite solid solutions are used to predict the limit of Np-incorporation into boltwoodite (172 and 768 ppm at 300 °C, respectively); (2) uranyl and neptunyl incorporation into carbonates and sulfates: for both carbonates and sulfates, it was found that actinyl incorporation into a defect site is more favorable than incorporation into defect-free periodic structures. In addition, actinyl incorporation into carbonates with aragonite structure is more favorable than into carbonates with calcite structure; and (3) uranium incorporation into magnetite: within the configurations tested that preserve charge neutrality (U⁶⁺ → 2Fe³⁺_oct/tet or U⁴⁺ → Fe²⁺_oct), uranium incorporation into magnetite is most favorable when U⁶⁺ replaces octahedral Fe³⁺ with charge balancing accomplished by an octahedral Fe³⁺ iron vacancy. At the end of this article, the limitations of this method and important sources of error inherent in these calculations (e.g., hydration energies) are discussed. Overall, this method and examples may serve as a guide for future studies of incorporation in a variety of contexts. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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2333 KiB

Open AccessArticle

Arsenic Adsorption onto Minerals: Connecting Experimental Observations with Density Functional Theory Calculations

by Heath D. Watts, Lorena Tribe and James D. Kubicki

Minerals 2014, 4(2), 208-240; https://doi.org/10.3390/min4020208 - 27 Mar 2014

Cited by 56 | Viewed by 10575

Abstract

A review of the literature about calculating the adsorption properties of arsenic onto mineral models using density functional theory (DFT) is presented. Furthermore, this work presents DFT results that show the effect of model charge, hydration, oxidation state, and DFT method on the structures and adsorption energies for As^III and As^V onto Fe³⁺-(oxyhydr)oxide cluster models. Calculated interatomic distances from periodic planewave and cluster-model DFT are compared with experimental data for As^III and As^V adsorbed to Fe³⁺-(oxyhydr)oxide models. In addition, reaction rates for the adsorption of As^V on α-FeOOH (goethite) (010) and Fe³⁺ (oxyhydr)oxide cluster models were calculated using planewave and cluster-model DFT methods. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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3077 KiB

Open AccessArticle

Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

by Abdullah Ozkanlar, Morgan P. Kelley and Aurora E. Clark

Minerals 2014, 4(1), 118-129; https://doi.org/10.3390/min4010118 - 04 Mar 2014

Cited by 11 | Viewed by 7899

Abstract

Intermolecular chemical networks defined by the hydrogen bonds formed at the α-quartz|water interface have been data-mined using graph theoretical methods so as to identify and quantify structural patterns and dynamic behavior. Using molecular-dynamics simulations data, the hydrogen bond (H-bond) distributions for the water-water and water-silanol H-bond networks have been determined followed by the calculation of the persistence of the H-bond, the dipole-angle oscillations that water makes with the surface silanol groups over time, and the contiguous H-bonded chains formed at the interface. Changes in these properties have been monitored as a function of surface coverage. Using the H-bond distribution between water and the surface silanol groups, the actual number of waters adsorbed to the surface is found to be 0.6 H₂O/10 Å², irrespective of the total concentration of waters within the system. The unbroken H-bond network of interfacial waters extends farther than in the bulk liquid; however, it is more fluxional at low surface coverages (i.e., the H-bond persistence in a monolayer of water is shorter than in the bulk) Concentrations of H₂O at previously determined water adsorption sites have also been quantified. This work demonstrates the complementary information that can be obtained through graph theoretical analysis of the intermolecular H-bond networks relative to standard analyses of molecular simulation data. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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2524 KiB

Open AccessArticle

A Density Functional Theory Study of the Adsorption of Benzene on Hematite (α-Fe₂O₃) Surfaces

by Nelson Y. Dzade, Alberto Roldan and Nora H. De Leeuw

Minerals 2014, 4(1), 89-115; https://doi.org/10.3390/min4010089 - 14 Feb 2014

Cited by 112 | Viewed by 22472

Abstract

The reactivity of mineral surfaces in the fundamental processes of adsorption, dissolution or growth, and electron transfer is directly tied to their atomic structure. However, unraveling the relationship between the atomic surface structure and other physical and chemical properties of complex metal oxides is challenging due to the mixed ionic and covalent bonding that can occur in these minerals. Nonetheless, with the rapid increase in computer processing speed and memory, computer simulations using different theoretical techniques can now probe the nature of matter at both the atomic and sub-atomic levels and are rapidly becoming an effective and quantitatively accurate method for successfully predicting structures, properties and processes occurring at mineral surfaces. In this study, we have used Density Functional Theory calculations to study the adsorption of benzene on hematite (α-Fe₂O₃) surfaces. The strong electron correlation effects of the Fe 3d-electrons in α-Fe₂O₃ were described by a Hubbard-type on-site Coulomb repulsion (the DFT+U approach), which was found to provide an accurate description of the electronic and magnetic properties of hematite. For the adsorption of benzene on the hematite surfaces, we show that the adsorption geometries parallel to the surface are energetically more stable than the vertical ones. The benzene molecule interacts with the hematite surfaces through π-bonding in the parallel adsorption geometries and through weak hydrogen bonds in the vertical geometries. Van der Waals interactions are found to play a significant role in stabilizing the absorbed benzene molecule. Analyses of the electronic structures reveal that upon benzene adsorption, the conduction band edge of the surface atoms is shifted towards the valence bands, thereby considerably reducing the band gap and the magnetic moments of the surface Fe atoms. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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Review

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1331 KiB

Open AccessReview

Interaction of Natural Organic Matter with Layered Minerals: Recent Developments in Computational Methods at the Nanoscale

by Jeffery A. Greathouse, Karen L. Johnson and H. Christopher Greenwell

Minerals 2014, 4(2), 519-540; https://doi.org/10.3390/min4020519 - 06 Jun 2014

Cited by 47 | Viewed by 11583

Abstract

The role of mineral surfaces in the adsorption, transport, formation, and degradation of natural organic matter (NOM) in the biosphere remains an active research area owing to the difficulties in identifying proper working models of both NOM and mineral phases present in the environment. The variety of aqueous chemistries encountered in the subsurface (e.g., oxic vs. anoxic, variable pH) further complicate this field of study. Recently, the advent of nanoscale probes such as X-ray adsorption spectroscopy and surface vibrational spectroscopy applied to study such complicated interfacial systems have enabled new insight into NOM-mineral interfaces. Additionally, due to increasing capabilities in computational chemistry, it is now possible to simulate molecular processes of NOM at multiple scales, from quantum methods for electron transfer to classical methods for folding and adsorption of macroparticles. In this review, we present recent developments in interfacial properties of NOM adsorbed on mineral surfaces from a computational point of view that is informed by recent experiments. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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689 KiB

Open AccessReview

Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces

by Krishnamoorthy Arumugam and Udo Becker

Minerals 2014, 4(2), 345-387; https://doi.org/10.3390/min4020345 - 24 Apr 2014

Cited by 56 | Viewed by 13948

Abstract

Applications of redox processes range over a number of scientific fields. This review article summarizes the theory behind the calculation of redox potentials in solution for species such as organic compounds, inorganic complexes, actinides, battery materials, and mineral surface-bound-species. Different computational approaches to predict and determine redox potentials of electron transitions are discussed along with their respective pros and cons for the prediction of redox potentials. Subsequently, recommendations are made for certain necessary computational settings required for accurate calculation of redox potentials. This article reviews the importance of computational parameters, such as basis sets, density functional theory (DFT) functionals, and relativistic approaches and the role that physicochemical processes play on the shift of redox potentials, such as hydration or spin orbit coupling, and will aid in finding suitable combinations of approaches for different chemical and geochemical applications. Identifying cost-effective and credible computational approaches is essential to benchmark redox potential calculations against experiments. Once a good theoretical approach is found to model the chemistry and thermodynamics of the redox and electron transfer process, this knowledge can be incorporated into models of more complex reaction mechanisms that include diffusion in the solute, surface diffusion, and dehydration, to name a few. This knowledge is important to fully understand the nature of redox processes be it a geochemical process that dictates natural redox reactions or one that is being used for the optimization of a chemical process in industry. In addition, it will help identify materials that will be useful to design catalytic redox agents, to come up with materials to be used for batteries and photovoltaic processes, and to identify new and improved remediation strategies in environmental engineering, for example the reduction of actinides and their subsequent immobilization. Highly under-investigated is the role of redox-active semiconducting mineral surfaces as catalysts for promoting natural redox processes. Such knowledge is crucial to derive process-oriented mechanisms, kinetics, and rate laws for inorganic and organic redox processes in nature. In addition, molecular-level details still need to be explored and understood to plan for safer disposal of hazardous materials. In light of this, we include new research on the effect of iron-sulfide mineral surfaces, such as pyrite and mackinawite, on the redox chemistry of actinyl aqua complexes in aqueous solution. Full article

(This article belongs to the Special Issue Advances in Low-temperature Computational Mineralogy)

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