Models dynamic aqueous systems

Molecular level computer simulations based on molecular dynamics and Monte Carlo methods have become widely used techniques in the study and modeling of aqueous systems. These simulations of water involve a few hundred to a few thousand water molecules at liquid density. Because one can form statistical mechanical averages with arbitrary precision from the generated coordinates, it is possible to calculate an exact answer. The value of a given simulation depends on the potential functions contained in the Hamiltonian for the model. The potential describing the interaction between water molecules is thus an essential component of all molecular level models of aqueous systems. 

Dyer, J.A., Predicting trace-metal fate in aqueous systems using a coupled equilibrium-surface-complexation, dynamic-simulation model, in Underground Injection Science and Technology, Tsang, C.F. and Apps, J.A., Eds., Elsevier, New York, February 2007. 

The substitution and protonation behavior of the rcms-dioxotetra-cyanometalate complexes of Re(V), Tc(V), W(IV), Mo(IV), and Os(VI) have been extensively investigated in the past decade and selected aspects have been reviewed (1, 2). Previous studies demonstrated the use of oxygen-17 NMR in different metal systems (3), including the complex oligomeric Mo(IV) aqueous systems (4), and therefore, since these oxocyano complexes contain an even wider range of nuclei such as 13C, 15N, 170, "Tc, and 183W, they are attractive model complexes to study by multinuclear NMR. Thus, detailed studies on the dynamics therein have been investigated in the past few years (5-8). 

Laboratory simulations of aqueous-phase chemical systems are necessary to 1) verify reaction mechanisms and 2) assign a value and an uncertainty to transformation rates. A dynamic cloud chemistry simulation chamber has been characterized to obtain these rates and their uncertainties. Initial experimental results exhibited large uncertainties, with a 26% variability in cloud liquid water as the major contributor to measurement uncertainty. Uncertainties in transformation rates were as high as factor of ten. Standard operating procedures and computer control of the simulation chamber decreased the variability in the observed liquid water content, experiment duration and final temperature from 0.65 to 0.10 g nr3, 180 to 5.3 s and 1.73 to 0.27°C respectively. The consequences of this improved control over the experimental variables with respect to cloud chemistry were tested for the aqueous transformation of SO2 using a cloud-physics and chemistry model of this system. These results were compared to measurements made prior to the institution of standard operating procedures and computer control to quantify the reduction in reaction rate uncertainty resulting from those controls. 

Johnson RG Jr. (1988) Accumulation of biological amines into chromaffin granules a model for hormone and neurotransmitter transport. Physiol Rev 68 232-307 Jorgensen AM, Tagmose L, Jorgensen AM, Bogeso KP, Peters GH (2007a) Molecular dynamics simulations of Na-l-/Q(-)-dependent neurotransmitter transporters in a membrane-aqueous system. ChemMedChem 2 827- 40... 

McAvoy. T. J. "Dynamic Modelling of pH in Aqueous Systems, in Proceedings of AIChE Workshop in Industrial Process Control, 1979, p. 35-39 (1979). 

The UV radiation disinfects germs in an aqueous system, which can be operated as plug flow, continuous flow, or other modes. The killing efficiency is controlled by many factors, which can be classified into two aspects disinfection kinetics and flow dynamics. Like many other processes in both chemical and environmental engineering, the mathematical modeling of the UV disinfection can be started from simulation of distribution of flow velocity together with definition of suitable kinetic model(s). The disinfection effect in terms of survival of pathogens as a function of operational conditions such as time and dose can then be estimated. Since the mathematical models involve many unknown parameters that must be experimentally determined, they are mainly... 

FIGURE 7.10 Side view models showing the system and protocol adopted for the reactive molecular dynamics simulation of the interaction of chloride ions with passivated copper surfaces. Left Cu(l 11) slab covered by CU2O thin films with O-deficient (top) and O-enriched (bottom) terminations after thermal relaxation at 300 K. Middle filling the gap with 20 M Cl" aqueous solution (pH 7). Right complete system after relaxation for 250 ps at 300 K showing preferential interaction of the chlorides ions with the O-deficient surface. Periodic boundary conditions apply along the x-, y-, and z-directions.Adapted from Jeon et al. [135], 1229, with permission from the Ameriean Chemical Society. 

However, despite of the great importance of quantum mechanical potentials from the purely theoretical point of view, simple effective two-body potential functions for water seem at present to be preferable for the extensive simulations of complex aqueous systems of geochemical interest. A very promising and powerful method of Car-Parrinello ah initio molecular dynamics, which completely eliminates the need for a potential interaction model in MD simulations (e.g., Fois et al. 1994 Tukerman et al. 1995, 1997) still remains computationally extremely demanding and limited to relatively small systems N < 100 and a total simulation time of a few picoseconds), which also presently limits its application for complex geochemical fluids. On the other hand, it may soon become a method of choice, if the current exponential growth of supercomputing power will continue in the near future. 

The need to validate the model for halogens in aqueous media using spectroscopic predictions makes necessary an accurate description of the electronic structure of the halogen and its environment or at least, the effect the latter has on the solute. The dynamic and thermal effects of the aqueous system also need to be captured in a realistic way. For these reasons, designing an accurate model for these systems is a true challenge. Furthermore, a well-suited model for this system requires attributes such as ... 

Ab initio molecular dynamics and/or Car-Parrinello-type simulations seem a promising option to model the physical chemistry of halogens in aqueous systems due to their robustness, and the fact that they might be useful to simulate spectroscopic properties and reactivity. However, the size of the systems needed to... 

The use of film theory to describe solution mass transfer phenomena in pressure-driven membrane processes has a proven track record for aqueous systems. Under the flow conditions encountered in nanofiltration, the simplified film theory description of mass transfer has an accuracy close to solutions obtained by computational fluid dynamics (CFD) modeling (Zydney, 1997). The film theory, for component i, gives, for the total volumetric flux [see Peeva et al. (2004) for details] ... 

While experiment and theory have made tremendous advances over the past few decades in elucidating the molecular processes and transformations that occur over ideal single-crystal surfaces, the application to aqueous phase catalytic systems has been quite limited owing to the challenges associated with following the stmcture and dynamics of the solution phase over metal substrates. Even in the case of a submersed ideal single-crystal surface, there are a number of important issues that have obscured our ability to elucidate the important surface intermediates and follow the elementary physicochemical surface processes. The ability to spectroscopically isolate and resolve reaction intermediates at the aqueous/metal interface has made it difficult to experimentally estabhsh the surface chemistry. In addition, theoretical advances and CPU limitations have restricted ab initio efforts to very small and idealized model systems. 

A model of blending aqueous salt buffers for chromatography has been developed.1 The model assumed full miscibility, low mixing enthalpy and low volume change. It reproduced experimental S-curves of buffer strength produced by a Pharmacia P3500 dual piston system equipped with a model 24 V dynamic mixer with 0.6 mL internal volume as well as those produced by a BioSepra ProSys 4-piston system equipped with two dynamic mixers of 1.2 mL internal volume. 

It is important to propose molecular and theoretical models to describe the forces, energy, structure and dynamics of water near mineral surfaces. Our understanding of experimental results concerning hydration forces, the hydrophobic effect, swelling, reaction kinetics and adsorption mechanisms in aqueous colloidal systems is rapidly advancing as a result of recent Monte Carlo (MC) and molecular dynamics (MO) models for water properties near model surfaces. This paper reviews the basic MC and MD simulation techniques, compares and contrasts the merits and limitations of various models for water-water interactions and surface-water interactions, and proposes an interaction potential model which would be useful in simulating water near hydrophilic surfaces. In addition, results from selected MC and MD simulations of water near hydrophobic surfaces are discussed in relation to experimental results, to theories of the double layer, and to structural forces in interfacial systems. 

As pointed out by Warshel and co-workers, the derivation of the important relation (14) is based on the assumption of non-saturation of the dielectric medium, which does not necessarily applies in the case of a macromolecule in solution [43]. These authors have shown that the validity of relation (14) could be directly tested by simulating the dipole motions through molecular dynamics models [43, 44, 45]. Detailed numerical calculations were carried out for the selfexchange reaction of cytochrome c [43], and for the electron transfer between two benzene-like molecules in water [45]. A similar approach was recently developed for the system (Fe " ", Fe ) in aqueous solution [46]. From these calculations, it was concluded that relation (14) applies provided that X is evaluated from a microscopic model. 

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