Molecular dynamic simulations of fulvic acid clusters in water

Porquet, Alain; Bianchi, Laurent; Stoll, Serge

doi:10.1016/s0927-7757(02)00557-5

Cited by 11 publications

(9 citation statements)

References 7 publications

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“…Kubicki & Apitz (1999) used this model to compare relative structures computed by classical molecular mechanics and quantum (semi‐empirical and Hartree‐Fock) calculations and to test the effect of computational methodology on the predicted structure. This model was also used by Porquet et al (2003) to study hydrogen bonding and clustering of neutral fulvic acid in aqueous solution. The Temple‐Northeastern‐Birmingham (TNB) model of an NOM building block was derived by Davies et al (1997) from an earlier model of Steelink (1985) and was then successfully used in the conformational modelling study (Sein et al , 1999).…”

Section: Introductionmentioning

confidence: 99%

“…Cygan et al, 2001). However, these techniques have only rarely been applied to the investigation of NOM and its interaction with aqueous solutions and mineral surfaces (Schulten & Schnitzer, 1997;Leenheer et al, 1998;Kubicki & Apitz, 1999;Sein et al, 1999;Shevchenko et al, 1999;Diallo et al, 2003;Porquet et al, 2003;. Classical molecular computer simulations are typically performed for a relatively small system of 100 < N < 100 000 particles (atoms, ions, and/or molecules) confined in a box with so-called 'periodic boundary conditions'.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dynamics simulation of cationic complexation with natural organic matter

Kirkpatrick

2007

European J Soil Science

167

170

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Molecular computer modelling of natural organic matter (NOM) and its interactions with metal cations in aqueous solution is a highly effective tool for helping to understand and quantitatively predict the molecular mechanisms of metal-NOM complexation. This paper presents the results of molecular dynamics (MD) computations of the interaction of NOM with dissolved Na þ , Cs þ , Mg 2þ and Ca 2þ . They show that Na þ forms only very weak outer-sphere complexes with NOM, whereas Cs þ interacts somewhat more strongly, but also mainly via outer-sphere association. Mg 2þ interacts little with NOM due to its strongly held hydration shell. Ca 2þ has the strongest association with NOM and forms inner-sphere complexes with NOM carboxylate groups. This last result supports the idea of supramolecular, Camediated NOM aggregation. Cation-NOM binding occurs principally with carboxylate groups, and to a lesser extent with phenolic and other -R-OH groups. The contributions of other NOM functional groups are minimal. The diffusional mobility of NOM-bound cations is ;20% (NOM-Na þ outersphere complex) to ;95% (NOM-Ca 2þ inner-sphere complex) less than in aqueous solutions without NOM. The MD simulation results are in good agreement with NMR spectroscopic measurements for Cs-NOM solutions.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation of cationic complexation with natural organic matter

Kirkpatrick

2007

European J Soil Science

167

170

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“…Similarly, despite decades of widespread use of computational molecular dynamics (MD) and Monte Carlo (MC) methods (e.g., Allen and Tildesley, 1987;Cygan and Kubicki, 2001;Schlick, 2002), these techniques have been rarely applied to the investigation of NOM and its interaction with aqueous solutions and mineral surfaces (Schulten and Schnitzer, 1997;Leenheer et al, 1998;Kubicki and Apitz, 1999;Sein et al, 1999;Shevchenko et al, 1999;Diallo et al, 2003;Porquet et al, 2003;Sutton et al, 2005). Classical molecular computer simulations are typically performed for systems containing 10 3 -10 6 particles (atoms, ions, and/or molecules) and can thus effectively capture longer range and cooperative behavior of the simulated systems.…”

Section: Introductionmentioning

confidence: 99%

133Cs and 35Cl NMR spectroscopy and molecular dynamics modeling of Cs+ and Cl− complexation with natural organic matter

Kalinichev

Kirkpatrick

2006

Geochimica et Cosmochimica Acta

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“…This model was also later used in the molecular simulation of hydrogen bonding and clustering of neutral FA fragments in aqueous solution [39].…”

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confidence: 99%

Molecular models of natural organic matter and its colloidal aggregation in aqueous solutions: Challenges and opportunities for computer simulations

Kalinichev

2012

Pure and Applied Chemistry

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Natural organic matter (NOM) is ubiquitous in soil and groundwater and its aqueous complexation with various inorganic and organic species can strongly affect the speciation, solubility and toxicity of many elements in the environment. Despite significant geochemical, environmental and industrial interest, the molecular-scale mechanisms of the physical and chemical processes involving NOM are not yet fully understood. Recent molecular dynamics (MD) simulations using relatively simple models of NOM fragments are used here to illustrate the challenges and opportunities for the application of computational molecular modeling techniques to the structural, dynamic, and energetic characterization of metal-NOM complexation and colloidal aggregation in aqueous solutions. The predictions from large-scale MD simulations are in good qualitative agreement with available experimental observations, but also point out to the need for simulations at much larger time and length scales with more complex NOM models in order to fully capture the diversity of molecular processes involving NOM

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Molecular dynamic simulations of fulvic acid clusters in water

Cited by 11 publications

References 7 publications

Molecular dynamics simulation of cationic complexation with natural organic matter

Molecular dynamics simulation of cationic complexation with natural organic matter

133Cs and 35Cl NMR spectroscopy and molecular dynamics modeling of Cs+ and Cl− complexation with natural organic matter

Molecular models of natural organic matter and its colloidal aggregation in aqueous solutions: Challenges and opportunities for computer simulations

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