Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

doi:10.1016/j.gca.2006.04.023

Cited by 60 publications

(47 citation statements)

References 58 publications

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“…An example is flexible organic molecules that can have a continuum of different possible conformational possibilities, such as during sorption to a mineral. [43] In these cases, there are many different configurations of the molecule and it is difficult to isolate the contribution of their conformal structure to the intrinsic reactivity. However, we are optimistic that much can be learned from computational work in biochemistry where complex, flexible structures are endemic.…”

Section: The Tricks Of the Tradementioning

confidence: 99%

Geochemical reaction mechanism discovery from molecular simulation

Stack

Kent

2015

Environ. Chem.

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Environmental context. Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique's overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems.Abstract. Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. Some common methods are summarised that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and their strengths and weaknesses are also discussed. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The effect that molecular simulation has had on our understanding of geochemical reactivity is highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models. Introduction -why molecular simulation?Current and future needs for geochemistry include the capacity to assess the risk and effect of anthropogenic activities. Examples include the certification of the long-term fate and transport of contaminants during nuclear waste disposal, caprock integrity and extent of mineral trapping during geologic carbon sequestration, provenance and treatment of flowback water during hydraulic fracturing, and other critical needs for society. Our ability to assess risk and effects could improve with better, more quantitative, estimates of the rates and mechanisms of geochemical processes. Molecular simulation might be able to help us improve that predictive capability, but how it will do so is not necessarily self-evident. After all, when these subjects are applied, it is often in 'muddy boot' settings in the field, e.g. collecting pore water, core or sediment samples from monitoring wells or waste stream effluent. It is difficult to make the Andrew G. Stack is a Senior R&D Staff Member in the Geochemistry and Interfacial Sciences Group, Chemical Sciences Division at Oak Ridge National Laboratory. He is a geochemist who specialises in understanding the kinetics and mechanisms of mineral reactions, and how these inherently molecular-level processes manifest themselves at larger scales. Reactions he has examined include mineral grow...

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Section: The Tricks Of the Tradementioning

confidence: 99%

Geochemical reaction mechanism discovery from molecular simulation

Stack

Kent

2015

Environ. Chem.

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“…A recent review paper outlines current understanding of the important effect of cation bridging in NOM aggregation [87]. Indeed, molecular modeling studies of NOM-mineral interfacial systems indicates that cation bridging between NOM and surface sites predominates over direct interactions between NOM functional groups and the surface [88,89], although humic substances can adsorb directly to clay surfaces in confined interlayer environments [90]. In a recent review of soil humic substances, Sutton and Sposito concluded that NOM consists of a "supramolecular association" of small organic molecules linked by short-range interactions dominated by amide-amide interactions [91].…”

Section: Simulations Of Natural Organic Matter (Nom) and Nom-mineral mentioning

confidence: 99%

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

2014

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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.

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“…We assume that the polysaccharides adsorb preferentially onto particular surfaces of the calcite crystal. Polysaccharides are generally believed to control the biomineralization process of calcite crystal [38][39][40]. The biological role of polysaccharides in controlling the calcite crystallization has been studied extensively.…”

Section: Effects On Crystal Morphologymentioning

confidence: 99%