Thermodynamics of Macromolecular Systems

At the moment there exist no quantum chemical method which simultaneously satisfies all demands of chemists. Some special demands with respect to treatment of macromolecular systems are, the inclusion of as many as possible electrons of various atoms, the fast optimization of geometry of large molecules, and the high reliability of all data obtained. To overcome the point 4 of the disadvantages, it is necessary to include the interaction of the molecule with its surroundings by means of statistical thermodynamical calculations and to consider solvent influence. 

In some cases, when the polymerization appears, the energy distribution of micropores is negligible in comparison with the energy of polymerization. That is possible when the temperature of the treatment of the primary material (if this one can be polymerized, e.g., silica, alumina) is low (less 300-350 °C). In such cases, traditional methods of nonequilibrium thermodynamics are not effective, and the micropore formation can be considered as the result of the polymerization process which is described by methods of polymer science. However, models of macromolecular systems do not always give enough information about micropores as the empty space between polymers. For such systems, the application of fractal methods can allow us to obtain additional information, while one has to take into account the fact that they cannot be applied to very narrow pores (ultramicropores which are found, for instance, in some silica gels). 

The thermodynamics of macromolecular solutions with small molecules is described in Sect. 7.1. A term frequently used to describe solutions of macromolecules is blend. The word is obviously derived from the mixing process and should only be used when the resulting system is not fully analyzed, i.e., one does not know if a dissolution occurred or the phases remained partially or fully separated. The term blend should best be used only if a phase-separated system has changed by vigorous mixing to a finer subdivision, containing micro- or nanophases. The differences between nanophase separation and solution can be rather subtle, as is seen, for example, in the thermodynamic description of block copolymers (see Sect. 7.1). Micro- and nanophase-separated systems can often be stabilized by compatibilizers that may be block copolymers of the two components. Their properties can be considerably different from macrophase separated systems or solutions and, thus, of considerable technical importance. 

Thermodynamics and statistical mechanics of macromolecular systems / Michael Bachmann. 

Equations (4.98) and (4.102) are the backbone of a method describing thermodynamic properties of macromolecular systems akin to the van der Waals approach to low molecular weight systems. The lattice approach outlined here was pioneered independently by Staverman and van Santen (Stavermann and van Santen 1941), Huggins (Huggins 1941,1942) and Flory (Paul John Flory, Nobel prize in chemistry for his work on the physical chemistry of macromolecules, 1974) (Flory 1941,1942 Koningsveld and Kleintjens 1988). 

A mechanism of action describes the molecular sequence of events (covalent or non-covalent) that lead to the manifestation of a response. The complete elucidation of the reactions and interactions among and between chemicals, include very complex and varied situations including biological systems (macromolecular receptors, physical phenomena (thermodynamics of explosions) or global systems (ozone depletion). Unfortunately, this level of mechanistic detail is often unavailable but recent advances in molecular toxicology and others hazards, at the molecular level, have provided valuable information that elucidates key steps in a mechanism or mode of action. ... 

Ota, N. Stroupe, C. Ferreira da Silva, I.M.S. Shah, S.A. Mares-Guia, M. Brunger, A.T., Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems relative free energy of binding of trypsin to benzamidine and benzylamine, Proteins 1999, 37, 641-653... 

Application to Macromolecular Interactions. Chun describes how one can analyze the thermodynamics of a particular biological system as well as the thermal transition taking place. Briefly, it is necessary to extrapolate thermodynamic parameters over a broad temperature range. Enthalpy, entropy, and heat capacity terms are evaluated as partial derivatives of the Gibbs free energy function defined by Helmholtz-Kelvin s expression, assuming that the heat capacities integral is a continuous function. 

The evaluation of the thermodynamic properties of the optically active macromolecular systems starting from the temperature coefficient of rotation, is therefore very complicated however a preliminary attempt (69) to perform a calculation of this type was made by Luisi, by adoptingthe Volkenstein and Ptitsyn theory (759). It was thus shown that the difference in the average free energy between monomeric units included in spiraled sections of different screw sense (17) should be about 300—500 eal/mol for highly isotactic optically active poly-a-olefins. 

The preceding analysis shows that there is a distinct lower bound for the size of the simulation cell. Below this bound, finite size artifacts heavily bias the thermodynamics and kinetics of ion accumulation. Therefore, it seems unadvisable to design simulations using neutralizing counterions alone, especially if the objective is to understand ion-mediated conformational transitions or to understand how ions interact with a macroion. The minimal number of excess ions needed to simulate 800 mm excess monovalent salt was nearly identical 800 pairs) for all of the systems studied (32 nt A-RNA, B-DNA, and the Tar—Tar RNA kissing-loop complex), indicating a simple dependence on net macroion charge. For other macromolecular solutes or other concentrations of excess salt, a box-size... 

---