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

Natural organic matter (NOM) represents a complex molecular system that cannot be fully characterized compositionally or structurally in full atomistic detail. This makes the application of molecular modeling approaches very difficult and significantly hinders quantitative investigation of NOM properties and behavior by these otherwise very efficient computational techniques. Here we report and analyze three molecular dynamics (MD) simulations of Ca2+ complexation with NOM in aqueous solutions in an attempt to quantitatively assess possible effects of model- and system size-dependence in such simulations. Despite some obvious variations in the computed results that depend on the size of the simulated system and on the parameters of the force field models used, all three simulations are quite robust and consistent. They show Ca2+ ions associated with 35-50% of the NOM carboxylic groups at near-neutral pH and point to a strong preference for the stability of bidentate-coordinated contact ion pairs. The degree and potential mechanisms of NOM supramolecular aggregation in the presence of Ca2+ ions in solution are also assessed on a semi-quantitative level from two larger-scale MD simulations

Optimal trapping wavelengths of Cs2_2 molecules in an optical lattice

The present paper aims at finding optimal parameters for trapping of Cs$_2$ molecules in optical lattices, with the perspective of creating a quantum degenerate gas of ground-state molecules. We have calculated dynamic polarizabilities of Cs$_2$ molecules subject to an oscillating electric field, using accurate potential curves and electronic transition dipole moments. We show that for some particular wavelengths of the optical lattice, called "magic wavelengths", the polarizability of the ground-state molecules is equal to the one of a Feshbach molecule. As the creation of the sample of ground-state molecules relies on an adiabatic population transfer from weakly-bound molecules created on a Feshbach resonance, such a coincidence ensures that both the initial and final states are favorably trapped by the lattice light, allowing optimized transfer in agreement with the experimental observation

Theory and applications of atomic and ionic polarizabilities

Atomic polarization phenomena impinge upon a number of areas and processes in physics. The dielectric constant and refractive index of any gas are examples of macroscopic properties that are largely determined by the dipole polarizability. When it comes to microscopic phenomena, the existence of alkaline-earth anions and the recently discovered ability of positrons to bind to many atoms are predominantly due to the polarization interaction. An imperfect knowledge of atomic polarizabilities is presently looming as the largest source of uncertainty in the new generation of optical frequency standards. Accurate polarizabilities for the group I and II atoms and ions of the periodic table have recently become available by a variety of techniques. These include refined many-body perturbation theory and coupled-cluster calculations sometimes combined with precise experimental data for selected transitions, microwave spectroscopy of Rydberg atoms and ions, refractive index measurements in microwave cavities, ab initio calculations of atomic structures using explicitly correlated wave functions, interferometry with atom beams, and velocity changes of laser cooled atoms induced by an electric field. This review examines existing theoretical methods of determining atomic and ionic polarizabilities, and discusses their relevance to various applications with particular emphasis on cold-atom physics and the metrology of atomic frequency standards.Comment: Review paper, 44 page

Molecular dynamics simulation of humic substances

© 2014, Orsi. Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research on HS has been traditionally carried out by conventional experimental approaches, over the past 20 years complementary investigations have emerged from the application of computer modeling and simulation techniques. This paper reviews the literature regarding computational studies of HS, with a specific focus on molecular dynamics simulations. Significant achievements, outstanding issues, and future prospects are summarized and discussed

Metal cation complexation with natural organic matter in aqueous solutions: molecular dynamics simulations and potentials of mean force

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+, Mg2+, and Ca2+ 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 metalâˆ'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 Ca2+ show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca2+ 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 Ca2+ ion in a bidentate coordinated contact ion pair vs a monodentate coordinated contact ion pair are about 0.5 and 0.08 ns, respectively. On the 10 ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca2+ but not Na+ or Mg2+. These results agree with previous experimental observations and are explained by both Ca2+ ion bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOMâˆ'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