GeoScienceWorld

Abstract

Somewhere between the ideas that we can calculate everything about chemical systems and that everything coming out of a computer is nonsense, lies the truth about molecular modeling. In essence, we might be able to calculate everything, if we could solve the Schrödinger equation for macroscopic size systems. However, numerous approximations to the full Schrödinger equation are generally made in even the most sophisticated quantum mechanical calculations. Furthermore, the size of simulated systems does not even approach one mole of a substance, to say nothing of a complex geochemical system of solution and minerals. Limitations, such as these, should not discourage the use of molecular modeling techniques in geochemistry, soil science, catalysis or other disciplines interested in clay structure and chemistry. Judicious choice of model systems and techniques allow a great deal of useful information to be extracted from a "computer experiment." In this volume we outline a variety of techniques that can be employed to address different types of chemical questions and demonstrate through examples what types of answers we can expect.

  1. Page 1
    Abstract

    Somewhere between the ideas that we can calculate everything about chemical systems and that everything coming out of a computer is nonsense, lies the truth about molecular modeling. In essence, we might be able to calculate everything, if we could solve the Schrödinger equation for macroscopic size systems. However, numerous approximations to the full Schrödinger equation are generally made in even the most sophisticated quantum mechanical calculations. Furthermore, the size of simulated systems does not even approach one mole of a substance, to say nothing of a complex geochemical system of solution and minerals. Limitations, such as these, should not discourage the use of molecular modeling techniques in geochemistry, soil science, catalysis or other disciplines interested in clay structure and chemistry. Judicious choice of model systems and techniques allow a great deal of useful information to be extracted from a “computer experiment.” In this volume and short course, we hope to outline a variety of techniques that can be employed to address different types of chemical questions and demonstrate through examples what types of answers we can expect.

  2. Page 26
    Abstract

    This chapter summarizes some important concepts in using molecular modeling methods for geochemical problems, with emphasis on chemistry as opposed to physics. Rather than summarize the most reliable ways of predicting crystal structures or physical properties and the equations of state of minerals, the chapter focuses on studies addressing problems associated with chemical reactivity. The development of a molecular-level understanding of low-temperature geochemical problems is theoretically challenging. Many of the most interesting questions are concerned with chemistry at the mineral-water interface (Lasaga, 1990), and involve complex phenomena including hydrogen-bonding, the presence of an aqueous phase, minerals which may be spin polarized, and electron and proton transfer. In general, these systems are (at present) too computationally difficult for a purely first-principles approach. For example, only recently have ab initio electronic structure methods satisfactorily dealt with the binding energy and structure of the water dimer (Feyereisen et al., 1996)1. Because of this computational complexity, it is often useful to couple theoretical and empirical modeling methods.

  3. Page 101
    Abstract

    The aim of this chapter is to acquaint the reader with the general principles of both Monte Carlo and molecular dynamics simulations, and to describe the application of these techniques to interlayer fluids in clay minerals. The main focus will be on the properties of water and aqueous solutions in swelling clays such as smectites and vermiculites. Modelling of these systems is now providing detailed understanding of the interlayer region and the microcopic mechanisms of clay swelling.

    Statistical mechanical computer simulations provide a direct link between the microscopic properties of particles, such as their masses and interactions, and the observable properties of macroscopic systems, such as the average structure and transport coefficients. This chapter takes the reader through the simulation cycle, as illustrated in figure 1. We begin with a discussion of clay-fluid interactions, and the specific molecular models that are currently used in computer simulations of interlayer fluids in clays. Next we introduce some of the general concepts required to study macroscopic systems (e.g. periodic boundary conditions, treatment of long-range and short-range interactions, minimum- and all-image conventions, choice of statistical ensemble). Two methods of molecular simulation, Monte Carlo and molecular dynamics, are then discussed, using as examples recent research into clay-water-cation systems. In addition to highlighting the successes of this research, attention will also be drawn to the pitfalls and limitations. The chapter concludes by identifying some challenges and opportunities for the future.

  4. Page 143
    Abstract

    Containment of radionuclide and chemical wastes in the environment is linked intimately to the ability of subsurface materials to attenuate and immobilize contaminants by chemical sorption and precipitation processes. Our ability to evaluate these complex processes at the molecular scale is provided by a few experimental and analytical methods such as X-ray absorption and NMR spectroscopies. However, due to complexities in structure and composition of clays and clay minerals, and the inherent uncertainties of the experimental methods, it is critical to apply theoretical atomistic models for an improved understanding and interpretation of these phenomena. The cryptocrystalline nature of clay materials and the associated difficulty of obtaining quality X-ray structural refinements also direct a need for theoretical analysis of the bulk structure of clays. Combined with recent advances in high-performance computing, molecular modeling may help provide a sound basis for designing efficient methods for waste treatment and improved immobilization of contaminants.

  5. Page 195
    Abstract

    The general properties of humic substances are summarized, emphasising features most relevant to ion-binding. The results of experimental determinations of proton and metal binding are summarized and interpreted. The modelling of ion-binding by humic matter to date has been concerned mainly with the parameterization of thermodynamically-based equations. The two most advanced current models are Humic Ion-Binding Model VI, which uses a discrete-site description, and the NICA-Donnan model, which treats site heterogeneity as a continuous distribution. These two models provide similar predictions, and show promise in applications to field situations. Some efforts at predictive modelling have been made, in which ion-binding is simulated on the basis of known or assumed properties of humic substances. Possible future developments in this area are discussed.

Purchase Chapters

Recommended Reading