Force-Energy Generators

Molecular Mechanics uses an analytical, differentiable, and relatively simple potential energy function, V(R), for describing the interactions between a set of atoms specified by their Cartesian coordinates R. 

Each molecular mechanics method has its own functional form MM+, AMBER, OPES, and BIO+. The functional form describes the analytic form of each of the terms in the potential. Eor example, MM+ has both a quadratic and a cubic stretch term in the potential whereas AMBER, OPES, and BIO+ have only quadratic stretch terms. The functional form is referred to here as the force field. Eor example, the functional form of a quadratic stretch with force constant Kj. and equilibrium distance rQ is  

Each force field includes a set of atom types. Consider the quadratic stretch term shown above. In principle, every different bond in every molecule would have its own parameters rg and Kj.. This 

Einally, each force field may have multiple parameter sets (the values ofrg and Kj., for example). The AMBER force field and AMBER 

These ideas plus others related to the molecular mechanics options of HyperChem are discussed in this chapter. 

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The theory and methods discussed in this book are HyperChem s two fundamental force-energy-generator modules one for molecular mechanics and one for quantum mechanics. Molecular mechanics and quantum mechanics are described in subsequent chapters as modules capable of delivering an energy, or derivatives of the energy. Other chapters describe the uses for these energies and their derivatives in more generic parts of HyperChem. 

The energies generated by forces among ideal gas molecules are negligible compared with molecular kinetic energies. 

A gas will obey the ideal gas equation whenever it meets the conditions that define the ideal gas. Molecular sizes must be negligible compared to the volume of the container, and the energies generated by forces between molecules must be negligible compared to molecular kinetic energies. The behavior of any real gas departs somewhat from ideality because real molecules occupy volume and exert forces on one another. Nevertheless, departures from ideality are small enough to neglect under many circumstances. We consider departures from ideal gas behavior in Chapter if. 

The electromotive force (EMF) generated by electrochemical cells can be used to measure partial Gibbs energies which, like vapour pressure measurements, distinguishes these methods from other techniques that measure integral thermodynamic quantities. Following Moser (1979), a typical cell used to obtain results on Zn-ln-Pb is represented in the following way ... 

The compartmentalization of energy generation provides a mechanism for the increased efficiency of high energy bond transfer to form the ultimate cellular fuel ATP, and has been the driving force behind the evolution of the mitochondrion. This viewpoint is supported by studies of the mitochondrial proteome, which have demonstrated that proteins of eubacterial origin predominantly... 

We noted before that some fields are not used in static (5c) separations because the forces they generate are so weak. We see that a weak force, -dfixt/dx, leads to a small structuring energy -AfMx which is inadequate to provide values of N or nc large enough for practical use. 

Mechanical force is generated by the cyclic interaction of myosin heads with actin and the energy supplied from the hydrolysis of ATP (Fig. 5-33). Each myosin head can bind a single molecule of ATP. Myosin is an ATPase. The ATPasc activity is constitutive but can be increased up to 200-fold in the presence of actin. 

We can summarize the HDA example as follows. The process converts 132 kmobh of toluene. If it were possible to extract all the work contained in the reactants we could generate 1.58 MWT of electric power at standard conditions. When forced to generate power from steam we would obtain much less than 0.65 MW of electric power. When none of the reaction energy is converted to work we need to dissipate about 1.55 MW of heat to utilities. On the separation side we need 0.52 MW of mechanical power at standard conditions. If ideal heat-driven separation devices were... 

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