Molecules, thermodynamic properties

A quantitative theory of rate processes has been developed on the assumption that the activated state has a characteristic enthalpy, entropy and free energy the concentration of activated molecules may thus be calculated using statistical mechanical methods. Whilst the theory gives a very plausible treatment of very many rate processes, it suffers from the difficulty of calculating the thermodynamic properties of the transition state. 

Two simulation methods—Monte Carlo and molecular dynamics—allow calculation of the density profile and pressure difference of Eq. III-44 across the vapor-liquid interface [64, 65]. In the former method, the initial system consists of N molecules in assumed positions. An intermolecule potential function is chosen, such as the Lennard-Jones potential, and the positions are randomly varied until the energy of the system is at a minimum. The resulting configuration is taken to be the equilibrium one. In the molecular dynamics approach, the N molecules are given initial positions and velocities and the equations of motion are solved to follow the ensuing collisions until the set shows constant time-average thermodynamic properties. Both methods are computer intensive yet widely used. 

Verlet L 1967 Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules Phys. Rev. f59 98-103... 

Verlet, L. Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 165 (1967) 98-103. Ryckaert, J.-P., Ciccotti,G., Berendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints Molecular dynamics of n-alkanes. Comput. Phys. 23 (1977) 327-341. 

Verlet, L. Computer Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review 159 (1967) 98-103 Janezic, D., Merzel, F. Split Integration Symplectic Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 37 (1997) 1048-1054 McLachlan, R. I. On the Numerical Integration of Ordinary Differential Equations by Symplectic Composition Methods. SIAM J. Sci. Comput. 16 (1995) 151-168... 

Investigations to find such additive constituent properties of molecules go back to the 1920s and 1930s with work by Fajans [6] and others. In the 1940s and 1950s lhe focus had shifted to the estimation of thermodynamic properties of molecules such as heat of formation, AHf, entropy S°, and heat capacity, C°. 

Lsc th e force fields th at have dern on strated accuracy for particu lar molecules or simulations. For example, CiPLS reproduces physical properties in liquid simulations extremely well. MM+ reproduces the structure and thermodynamic properties of small, nonpolar molecules better than AMBER, BIO+, and OPLS. 

In some cases the atomic charges are chosen to reproduce thermodynamic properties calculated using a molecular dynamics or Monte Carlo simulation. A series of simulations is performed and the charge model is modified until satisfactory agreement with experiment is obtained. This approach can be quite powerful despite its apparent simplicity, but it is only really practical for small molecules or simple models. 

One may wonder why it is important to distinguish between and keep track of these two energies and Dq, when it seems that one would do. Actually, both are important. The bond energy Dg dominates theoretical comparisons and the dissociation energy Dq, which is the ground state of the real molecule, is used in practical applications like calculating thermodynamic properties and reaction kinetics. 

Completely ah initio predictions can be more accurate than any experimental result currently available. This is only true of properties that depend on the behavior of isolated molecules. Colligative properties, which are due to the interaction between molecules, can be computed more reliably with methods based on thermodynamics, statistical mechanics, structure-activity relationships, or completely empirical group additivity methods. 

Monte Carlo simulations are commonly used to compute the average thermodynamic properties of a molecule or a system of molecules, and have been employed extensively in the study of the structure and equilibrium properties of liquids and solutions. Monte Carlo methods have also been used to conduct conformational searches under non-equilibrium conditions. 

The earliest hint that physics and information might be more than just casually related actually dates back at least as far as 1871 and the publication of James Clerk Maxwell s Theory of Heat, in which Maxwell introduced what has become known as the paradox of Maxwell s Demon. Maxwell postulated the existence of a hypothetical demon that positions himself by a hole separating two vessels, say A and B. While the vessels start out being at the same temperature, the demon selectively opens the hole only to either pass faster molecules from A to B or to pass slower molecules from B to A. Since this results in a systematic increase in B s temperature and a lowering of A s, it appears as though Maxwell s demon s actions violate the second law of thermodynamics the total entropy of any physical system can only increase, or, for totally reversible processes, remain the same it can never decrease. Maxwell was thus the first to recognize a connection between the thermodynamical properties of a gas (temperature, entropy, etc.) and the statistical properties of its constituent molecules. 

When an ionic solution contains neutral molecules, their presence may be inferred from the osmotic and thermodynamic properties of the solution. In addition there are two important effects that disclose the presence of neutral molecules (1) in many cases the absorption spectrum for visible or ultraviolet light is different for a neutral molecule in solution and for the ions into which it dissociates (2) historically, it has been mainly the electrical conductivity of solutions that has been studied to elucidate the relation between weak and strong electrolytes. For each ionic solution the conductivity problem may be stated as follows in this solution is it true that at any moment every ion responds to the applied field as a free ion, or must we say that a certain fraction of the solute fails to respond to the field as free ions, either because it consists of neutral undissociated molecules, or for some other reason ... 

The influence of barriers on thermodynamic properties must have importance in determining the rates of various chemical reactions. It seems certain that the activated complex for many reactions will involve the possibility of restricted rotation and that the thermodynamic properties of the complex will therefore be in part determined by the magnitude of the barriers. Whereas at the moment there is no direct way of determining such barriers, any general principles obtained for stable molecules should ultimately be applicable to the activated state. One might then hope to be able to estimate the barriers and the reaction rates a priori. 

In Chapter 10, we will make quantitative calculations of U- U0 and the other thermodynamic properties for a gas, based on the molecular parameters of the molecules such as mass, bond angles, bond lengths, fundamental vibrational frequencies, and electronic energy levels and degeneracies. 

Statistical thermodynamics provides the relationships that we need in order to bridge this gap between the macro and the micro. Our most important application will involve the calculation of the thermodynamic properties of the ideal gas, but we will also apply the techniques to solids. The procedure will involve calculating U — Uo, the internal energy above zero Kelvin, from the energy of the individual molecules. Enthalpy differences and heat capacities are then easily calculated from the internal energy. Boltzmann s equation... 

The values given are for a molecule that corresponds to the natural abundance of each isotope since these average values" will give the thermodynamic properties of a mole of the naturally occurring substance. ... 

Tables 10.1, 10.2, and 10.3e summarize moments of inertia (rotational constants), fundamental vibrational frequencies (vibrational constants), and differences in energy between electronic energy levels for a number of common molecules or atoms/The values given in these tables can be used to calculate the rotational, vibrational, and electronic energy levels. They will be useful as we calculate the thermodynamic properties of the ideal gas.

We are now ready to relate the thermodynamic properties of the ideal gas to Z. We start with U - Uq. where Uq is the energy when all the molecules are at zero... 

Calculation of Thermodynamic Properties We note that the translational contributions to the thermodynamic properties depend on the mass or molecular weight of the molecule, the rotational contributions on the moments of inertia, the vibrational contributions on the fundamental vibrational frequencies, and the electronic contributions on the energies and statistical weight factors for the electronic states. With the aid of this information, as summarized in Tables 10.1 to 10.3 for a number of molecules, and the thermodynamic relationships summarized in Table 10.4, we can calculate a... 

Under most circumstances the equations given in Table 10.4 accurately calculate the thermodynamic properties of the ideal gas. The most serious approximations involve the replacement of the summation with an integral [equations (10.94) and (10.95)] in calculating the partition function for the rigid rotator, and the approximation that the rotational and vibrational partition functions for a gas can be represented by those for a rigid rotator and harmonic oscillator. In general, the errors introduced by these approximations are most serious for the diatomic molecule." Fortunately, it is for the diatomic molecule that corrections are most easily calculated. It is also for these molecules that spectroscopic information is often available to make the corrections for anharmonicity and nonrigid rotator effects. We will summarize the relationships... 

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