Systems with small molecules

Kawasumi M, Nghiem P. (2007) Chemical genetics elucidating biological systems with small-molecule compounds. JInvest Dermatol 127, 1577-84. 

Typical of polymer blends is that phase separation occurs when the temperature is increased to a certain lower critical solution temperature (LCST) (Fig. 4.19). The upper critical solution temperature (UCST) behaviour predominates in systems with small-molecule solvents (Fig. 4.19). The equation-of-state theories can relatively adequately describe the phase diagrams of polymer blends. 

For small molecules, the accuracy of solutions to the Schrodinger equation competes with the accuracy of experimental results. However, these accurate ab initio calculations require enormous computation and are only suitable for the molecular systems with small or medium size. Ab initio calculations for very large molecules are beyond the realm of current computers, so HyperChem also supports semi-empirical quantum mechanics methods. Semi-empirical approximate solutions are appropriate and allow extensive chemical exploration. The inaccuracy of the approximations made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. Indeed, semi-empirical methods can sometimes be more accurate than some poorer ab initio methods, which require much longer computation times. 

Our experiments so far have focused exclusively on reactions of isolated transition metal atoms with small molecules. Owing to their simplicity, these systems are attractive from a theoretical and experimental point of view. However, the absence of ligands makes these systems quite foreign to an inorganic chemist. In the near future, we plan to carry out studies of reactions involving partially-ligated species in crossed beams. We hope that this will provide an important link between reactions of isolated transition metal atoms and real transition metal complexes of interest to the inorganic and synthetic community. 

Bigeleisen J (1949) The relative velocities of isotopic molecules. J Chem Phys 17 675-678 Bigeleisen J (1955) Statistical mechanics of isotopic systems with small quantum corrections. I. General considerations and the rule of the geometric mean. J Chem Phys 23 2264-2267 Bigeleisen J (1998) Second-order correction to the Bigeleisen-Mayer equation due to the nuclear field shift. Proc National Acad Sci 95 4808-4809... 

Perhaps the simplest two-site cooperative systems are small molecules having two binding sites for protons, such as dicarboxylic acids and diamines. Despite their molecular simplicity, most of these molecules do not conform with the modelistic assumptions made in this chapter. Therefore, their theoretical treatment is much more intricate. The main reasons for this are (1) there is, in general, a continuous range of macrostates (2) the direct and indirect correlations are both strong and intertwined, so that factorization of the correlation function is impossible. In addition, as with any real biochemical system, the solvent can have a major effect on the binding properties of these molecules. 

The interaction of Fe(II) with small molecules has received much attention. The Fe(II)/ oxygen system must be one of the most studied chemical interactions. Since the Fe-porphyrin complex forms the core of the naturally occurring iron respiratory proteins myoglobin and... 

In order to test the small x assumptions in our calculations of condensed phase vibrational transition probabilities and rates, we have performed model calculations, - for a colinear system with one molecule moving between two solvent particles. The positions ofthe solvent particles are held fixed. The center of mass position of the solute molecule is the only slow variable coordinate in the system. This allows for the comparison of surface hopping calculations based on small X approximations with calculations without these approximations. In the model calculations discussed here, and in the calculations from many particle simulations reported in Table II, the approximations made for each trajectory are that the nonadiabatic coupling is constant that the slopes of the initial and final... 

For those systems we have studied so far, many classical ligand field features are successfully captured by LFMM e.g., the double hump variation of structural and thermodynamic properties due to the LFSE (73), o- (36,58,78) and -type (77) Jahn-Teller effects, the trans influence (21), and spin state effects (18,33,59). LFMM is equally at home with small molecules and large proteins and potential future coordination chemistry applications are enormous. 

The determination of these normal frequencies, and the forms of the normal vibrations, thus becomes the primary problem in correlating the structure and internal forces of the molecule with the observed vibrational spectrum. It is the complexity of this problem for large molecules which has hindered the kind of detailed solution that can be achieved with small molecules. In the general case, a solution of the equations of motion in normal coordinates is required. Let the Cartesian displacement coordinates of the N nuclei of a molecule be designated by qlt q2,... qsN. The potential energy of the oscillating system is not accurately known in the absence of a solution to the quantum mechanical problem of the electronic energies, but for small displacements it can be quite well approximated by a power series expansion in the displacements ... 

Superoxide radical anion, hydroxyl radical, and hydrogen peroxide are known as prooxidants, whereas substances that neutralize their effects are called antioxidants. Oxidative stress occurs when the prooxidant-antioxidant balance becomes too favorable to the prooxidants. The effects of prooxidants can be neutralized by their direct reaction with small-molecule antioxidants, including glutathione, ascorbate, and tocopherols. In addition, oxidizing radicals are scavenged from a living system by several enzymes, including peroxidase, superoxide dismutase, and catalase. Oxidative lesions on DNA may be repaired by DNA repair enzymes. 

Summarizing macroporous systems can be done in any desired pore size range. They are of inestimable value if we deal with large molecules. In using them as polymeric supports for reactions with small molecules or a stepwise synthesis we are still faced with the problem of an appropriate surface structure. 

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