Thermodynamic Information and Molecules

The preceding chapters focused on thermodynamic state points, both individually and in collections assembled by fluctuations and pathways. The present chapter considers state points at the microscopic level. These points link with the statistical structure presented by molecules and their communication in thermal environments. It is this structure that determines information at the Angstrom scale. 

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Thermodynamic information can also be obtained from simulations. Currently we are measuring the differences in chemical potential of various small molecules in dimethylimidazolium chloride. This involves gradually transforming one molecule into another and is a computationally intensive process. One preliminary result is that the difference in chemical potential of propane and dimethyl ether is about 17.5 kj/mol. These molecules are similar in size, but differ in their polarity. Not surprisingly, the polar ether is stabilized relative to the non-polar propane in the presence of the ionic liquid. One can also investigate the local arrangement of the ions around the solute and the contribution of different parts of the interaction to the energy. Thus, while both molecules have a favorable Lennard-Jones interaction with the cation, the main electrostatic interaction is that between the chloride ion and the ether molecule. 

Mass spectrometric studies yield principally three types of information useful to the radiation chemist the major primary ions one should be concerned with, their reactions with neutral molecules, and thermodynamic information which allows one to eliminate certain reactions on the basis of endothermicity. In addition, attempts at theoretical interpretations of mass spectral fragmentation patterns permit estimates of unimolecular dissociation constants for excited parent ions. 

DD can be monitored by a variety of experimental techniques. They involve thermodynamic, dilatometric, and spectroscopic procedures. Molecular dynamics (MD) simulations also become applicable to self-assembled systems to some extent see the review in Ref. 2. Spectroscopic methods provide us with molecular parameters, as compared with thermodynamic ones on the macroscopic level. The fluorescence probing method is very sensitive (pM to nM M = moldm ) and informs us of the molecular environment around the probes. However, fluorescent molecules are a kind of drug and the membrane... 

The strategy in a molecular dynamics simulation is conceptually fairly simple. The first step is to consider a set of molecules. Then it is necessary to choose initial positions of all atoms, such that they do not physically overlap, and that all bonds between the atoms have a reasonable length. Subsequently, it is necessary to specify the initial velocities of all the atoms. The velocities must preferably be consistent with the temperature in the system. Finally, and most importantly, it is necessary to define the force-field parameters. In effect the force field defines the potential energy of each atom. This value is a complicated sum of many contributions that can be computed when the distances of a given atom to all other atoms in the system are known. In the simulation, the spatial evolution as well as the velocity evolution of all molecules is found by solving the classical Newton equations of mechanics. The basic outcome of the simulation comprises the coordinates and velocities of all atoms as a function of the time. Thus, structural information, such as lipid conformations or membrane thickness, is readily available. Thermodynamic information is more expensive to obtain, but in principle this can be extracted from a long simulation trajectory. 

Acrylonitrile (C3H3N, mol wt = 53.064) is an unsaturated molecule having a carbon-carbon double bond conjugated with a nitrile group. It is a polar molecule because of the presence of the nitrogen heteroatom. Tables 1 and 2 list some physical properties and thermodynamic information, respectively, for acrylonitrile. 

The methods are well established, and are supported by a well-defined theory, and the equipment used is relatively inexpensive for obtaining information concerning molecules in solution, thermodynamic data and insight in kinetics of reactions. 

Statistical mechanics provides a bridge between the properties of atoms and molecules (microscopic view) and the thermodynmamic properties of bulk matter (macroscopic view). For example, the thermodynamic properties of ideal gases can be calculated from the atomic masses and vibrational frequencies, bond distances, and the like, of molecules. This is, in general, not possible for biochemical species in aqueous solution because these systems are very complicated from a molecular point of view. Nevertheless, statistical mechanmics does consider thermodynamic systems from a very broad point of view, that is, from the point of view of partition functions. A partition function contains all the thermodynamic information on a system. There is a different partition function... 

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