Structural modeling in humic acids

Jansen, Susan A.; Malaty, M.; Nwabara, Sarah; Johnson, Ernestine; Ghabbour, Elham A.; Davies, Geoffrey; Varnum, James M.

doi:10.1016/s0928-4931(96)00151-8

Cited by 55 publications

(56 citation statements)

References 6 publications

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“…2,3,[26][27][28] The TNB model fragment used in our simulations contains three carboxylic groups, three carbonyl groups, two phenolic groups, two amine groups, and four other R-OH alcohol groups and has a total molecular weight of 753 Da. [38][39][40] The size, composition, molecular weight, degree of aromaticity, and total charge density of this model are in good agreement with available experimental characterization of NOM 26,27,29 , the results of computer assisted 3-D structure elucidation, 42 and stochastic biogeochemical modeling. 33 The composition of the TNB model is also quite close to the composition of Suwannee River NOM, which is often used experimentally.…”

Section: Computational Methods and Detailssupporting

confidence: 80%

“…37 Despite the well recognized uncertainties of the NOM composition and structure, such methods have been successfully used over the last decade to investigate NOM in molecular-scale detail. [38][39][40][41][42][43][44][45][46][47] The TNB (Temple-Northeastern-Birmingham) model of an NOM molecular fragment [38][39][40] used in our work provides a good structural and compositional analog of the Suwannee River NOM commonly used in experimental studies. [43][44][45] Carboxylic groups are the most important interaction sites for metal binding to these molecules, as they are for many other organic and bioorganic molecules.…”

Section: Introductionmentioning

confidence: 99%

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Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

Iskrenova-Tchoukova¹,

Kalinichev²,

2010

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Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation.Computational molecular dynamics (MD) study of the interactions of Na + , Mg 2+ , and Ca 2+ with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent separated ion pair coordination, and Na + and Ca 2+ show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca 2+ ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na + ion is only between 0.02 and 0.05 ns. The average residence times of a Ca 2+ ion in a bidentate coordinated contact ion pair vs. a monodentate coordinated contact ion pair are about 0.5 ns and about 0.08 ns, respectively. On the 10-ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca 2+ but not Na + or Mg 2+ . These results agree with previous experimental observations and are explained 3 by both Ca 2+ ion-bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.4

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Section: Computational Methods and Detailssupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

Iskrenova-Tchoukova¹,

Kalinichev²,

2010

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“…The TNB model of an NOM molecular fragment used in all three simulations discussed below has a molecular weight of 753 Da and contains three carboxylic groups, three carbonyl groups, two phenolic groups, two amine groups, and four other R-OH alcohol groups (Jansen et al, 1996;Davies et al, 1997;Sein et al, 1999). The size, composition and molecular structure of the TNB model of NOM fragment is illustrated in Figure 1.…”

Section: Molecular Dynamics Simulations Of Ca-nom Systemsmentioning

confidence: 99%

Effects of Ca2+ on supramolecular aggregation of natural organic matter in aqueous solutions: A comparison of molecular modeling approaches

et al. 2011

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“…The Temple-Northeastern-Birmingham (TNB) model [7,86,98] of a NOM fragment is an average structure based on spectroscopic and analytical data. It is a good computational analog of the Suwannee River NOM often used in experimental studies [99][100][101].…”

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

confidence: 99%

“…Structurally, NOM is extremely complex with a three-dimensional macromolecular structure and consisting of a diverse group of organic molecules [7]. At the moment, there is no consensus on the primary binding mechanism holding the aggregated molecules that comprise NOM in place.…”

Section: Introduction To Natural Organic Matter-mineral Systemsmentioning

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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Structural modeling in humic acids

Cited by 55 publications

References 6 publications

Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

Effects of Ca2+ on supramolecular aggregation of natural organic matter in aqueous solutions: A comparison of molecular modeling approaches

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

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