Mamadou S. Diallo

Calculation of Solvation Free Energies of Charged Solutes Using Mixed Cluster/Continuum Models

We derive a consistent approach for predicting the solvation free energies of charged solutes in the presence of implicit and explicit solvents. We find that some published methodologies make systematic errors in the computed free energies because of the incorrect accounting of the standard state corrections for water molecules or water clusters present in the thermodynamic cycle. This problem can be avoided by using the same standard state for each species involved in the reaction under consideration. We analyze two different thermodynamic cycles for calculating the solvation free energies of ionic solutes: (1) the cluster cycle with an n water cluster as a reagent and (2) the monomer cycle with n distinct water molecules as reagents. The use of the cluster cycle gives solvation free energies that are in excellent agreement with the experimental values obtained from studies of ion-water clusters. The mean absolute errors are 0.8 kcal/mol for H(+) and 2.0 kcal/mol for Cu(2+). Conversely, calculations using the monomer cycle lead to mean absolute errors that are >10 kcal/mol for H(+) and >30 kcal/mol for Cu(2+). The presence of hydrogen-bonded clusters of similar size on the left- and right-hand sides of the reaction cycle results in the cancellation of the systematic errors in the calculated free energies. Using the cluster cycle with 1 solvation shell leads to errors of 5 kcal/mol for H(+) (6 waters) and 27 kcal/mol for Cu(2+) (6 waters), whereas using 2 solvation shells leads to accuracies of 2 kcal/mol for Cu(2+) (18 waters) and 1 kcal/mol for H(+) (10 waters).

Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

Development and validation of a ReaxFF reactive force field for Cu-cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases

To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis.

Computational Study of Copper(II) Complexation and Hydrolysis in Aqueous Solutions Using Mixed Cluster/Continuum Models

We use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of the hydrated Cu(II) complexes [Cu(MeNH(2))(H(2)O)(n-1)](2+) and [Cu(OH)(x)(H(2)O)(n-x)](2-x) (x = 1-3) as a function of metal coordination number (4-6) and cluster size (n = 4-8, 18). The small clusters with n = 4-8 are found to be the most stable in the nearly square-planar four-coordinate configuration, except for [Cu(OH)(3)(H(2)O)](-), which is three-coordinate. In the presence of the two full hydration shells (n = 18), however, the five-coordinate square-pyramidal geometry is the most favorable for Cu(MeNH(2))(2+) (5, 6) and Cu(OH)(+) (5, 4, 6), and the four-coordinate geometry is the most stable for Cu(OH)(2) (4, 5) and Cu(OH)(3)(-) (4). (Other possible coordination numbers for these complexes in the aqueous phase are shown in parentheses.) A small energetic difference between these structures (0.23-2.65 kcal/mol) suggests that complexes with different coordination numbers may coexist in solution. Using two full hydration shells around the Cu(2+) ion (18 ligands) gives Gibbs free energies of aqueous reactions that are in excellent agreement with experiment. The mean unsigned error is 0.7 kcal/mol for the three consecutive hydrolysis steps of Cu(2+) and the complexation of Cu(2+) with methylamine. Conversely, calculations for the complexes with only one coordination shell (four equatorial ligands) lead to a mean unsigned error that is >6.0 kcal/mol. Thus, the explicit treatment of the first and the second shells is critical for the accurate prediction of structural and thermodynamic properties of Cu(II) species in aqueous solution.

Solubilization of nonaqueous phase liquid hydrocarbons in micellar solutions of dodecyl alcohol ethoxylates.

Results of an experimental investigation of hydrocarbon solubilization in 0.01 M micellar solutions of dodecyl alcohol ethoxylates at 25 o C are presented. The effects of surfactant hydrophile-lipophile balance (HLB) and hydrocarbon molar volume and polarity on the molar solubilization ratios (MSRs) and micelle-water partition coefficients of 11 nonaqueous phase liquid (NAPL) hydrocarbons are examined. The MSRs of the alkanes (n-dodecane, n-decane, n-hexane, and cyclohexane), which sharply decrease and asymptotically approach zero with increasing HLB, are shown to depend on micellar core volume and hydrocarbon molar volume and affinity for the micellar core

Interactions of poly(amidoamine) dendrimers with human serum albumin: binding constants and mechanisms.

The interactions of nanomaterials with plasma proteins have a significant impact on their in vivo transport and fate in biological fluids. This article discusses the binding of human serum albumin (HSA) to poly(amidoamine) [PAMAM] dendrimers. We use protein-coated silica particles to measure the HSA binding constants (K(b)) of a homologous series of 19 PAMAM dendrimers in aqueous solutions at physiological pH (7.4) as a function of dendrimer generation, terminal group, and core chemistry. To gain insight into the mechanisms of HSA binding to PAMAM dendrimers, we combined (1)H NMR, saturation transfer difference (STD) NMR, and NMR diffusion ordered spectroscopy (DOSY) of dendrimer-HSA complexes with atomistic molecular dynamics (MD) simulations of dendrimer conformation in aqueous solutions. The binding measurements show that the HSA binding constants (K(b)) of PAMAM dendrimers depend on dendrimer size and terminal group chemistry. The NMR (1)H and DOSY experiments indicate that the interactions between HSA and PAMAM dendrimers are relatively weak. The (1)H NMR STD experiments and MD simulations suggest that the inner shell protons of the dendrimers groups interact more strongly with HSA proteins. These interactions, which are consistently observed for different dendrimer generations (G0-NH(2)vs G4-NH(2)) and terminal groups (G4-NH(2)vs G4-OH with amidoethanol groups), suggest that PAMAM dendrimers adopt backfolded configurations as they form weak complexes with HSA proteins in aqueous solutions at physiological pH (7.4).

Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model

The hydrated structure of the Cu(II) ion has been a subject of ongoing debate in the literature. In this article, we use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of [Cu(H2O)n](2+) clusters as a function of coordination number (4, 5, and 6) and cluster size (n = 4-18). We find that the most thermodynamically favored Cu(II) complexes in the gas phase have a very open four-coordinate structure. They are formed from a stable square-planar [Cu(H2O)8](2+) core stabilized by an unpaired electron in the Cu(II) ion d(x(2)-y(2)) orbital. This is consistent with cluster geometries suggested by recent mass-spectrometric experiments. In the aqueous phase, we find that the more compact five-coordinate square-pyramidal geometry is more stable than either the four-coordinate or six-coordinate clusters in agreement with recent combined EXAFS and XANES studies of aqueous solutions of Cu(II). However, a small energetic difference (approximately 1.4 kcal/mol) between the five- and six-coordinate models with two full hydration shells around the metal ion suggests that both forms may coexist in solution.

Thermodynamic properties of asphaltenes: a predictive approach based on computer assisted structure elucidation and atomistic simulations

Publisher Summary This chapter describes a new methodology used in the estimation of the thermodynamic properties of asphaltenes. This methodology combines computer assisted structure elucidation (CASE) with atomistic simulations. To illustrate this new approach, quantitative and qualitative structural data is used as an input to a CASE program (SIGNATURE) to generate a sample of ten model asphaltene structures for a Saudi crude oil (Arab Beni). Molecular mechanics (MM) calculations and molecular dynamics (MD) simulations to estimate selected volumetric and thermal properties of the model structures are also carried out. The estimated values are in good agreement with the available experimental data. The results of this study suggest that CASE can be combined with atomistic simulations to obtain adequate estimates of the thermodynamic properties of petroleum geomacromolecules such as asphaltenes. The precipitation of asphaltene aggregates can cause problems as reservoir plugging and wettability reversal. The adsorption of asphaltene aggregates at oilwater interfaces has been shown to cause the steric stabilization of (W/O) petroleum emulsions.

Microalgae recovery by ultrafiltration using novel fouling-resistant PVDF membranes with in situ PEGylated polyethyleneimine particles.

In this article, we report the preparation, characterization and microalgae recovery potential of a new family of fouling-resistant polyvinylidene fluoride (PVDF) ultrafiltration (UF) membranes embedded with hydrophilic and PEGylated polymeric particles. To optimize membrane performance for microalgae harvesting, we investigate the effects of three hydrophilic additives (Pluronic F-127, polyvinylpyrrolidone and polyethylene glycol) on the morphology, pore size, bulk composition, surface composition, wettability and surface charge, flux and fouling resistance of the mixed matrix PVDF membranes with in situ PEGylated polyethyleneimine (PEI) particles. Our filtration experiments show that a mixed matrix PVDF membrane with PEGylated PEI particles and Pluronic F-127 additive (PNSM-1) has an algae retention of 100% with a permeate flux of 96 L/m(2)/hr that is larger (by ∼50%) than that of a commercial and hydrophilic PVDF UF membrane with a molecular weight cut-off of 30 kDa using a suspension of Chlorella sp. KR-1 microalgae with 1.2-1.4 g/L of dry biomass. The algae and water flux recovery rates of our new PNSM-1 are equal to∼ 94% and 100%, respectively, following a simulated membrane wash with deionized water and two subsequent water and microalgae filtration cycles.

Two-Electron Three-Centered Bond in Side-On (η2) Uranyl(V) Superoxo Complexes

Theoretical calculations suggest a novel two-electron three-atom bonding scheme for complexation of O 2 with U(V) compounds, leading to the stabilization of superoxo complexes in the side-on (eta (2)) configuration. This binding motif is likely to play an important role in the oxidative processes involving trans-uranium compounds having valence 5f phi electrons.