Mechanism-free model

Consider a simplified illustration of the foregoing QSAR examples. Consider a list of normal alkanes together with their water solubility and boiling points. A plot shows that solubility (in logarithmic form) is linear with number of carbon atoms and that boiling point is nonlinear. Such a relation is a QSAR based on the simple structure feature, number of carbon atoms. A linear equation captures all the structure information available in this data set. (The structure information could, of course, be represented in other ways, such as number of methylene groups, number of hydrogen atoms, number of carbon-carbon bonds, etc.) It is important to note here that no assumption has been made about the relation between water solubility and number of carbon atoms. This is an example of what Adamson has called a mechanism-free model. 

Shirts, M. R. Pande, V. S., Solvation free energies of amino acid side chain analogs for common molecular mechanics water models, J. Chem. Phys. 2005,122, 134508. 

Giesen, D. J., Storer, J., Cramer, C. J. and Truhlar, D. J. General semiempirical quantum mechanical solvation model for nonpolar solvation free energies, n-hexadacane., J.Am. Chem.Soc., 117 (1995), 1057-1068... 

Positrons emitted for a radioactive source (such as 22Na) into a polymeric matrix become thermalized and may annihilate with electrons or form positronium (Ps) (a bound state of an electron and positron). The detailed mechanism and models for the formation of positronium in molecular media can be found in Chapters 4 and 5 of this book. The para-positronium (p-Ps), where the positron and electron have opposite spin, decays quickly via self-annihilation. The long-lived ortho positronium (o-Ps), where the positron and electron have parallel spin, undergo so called pick-off annihilation during collisions with molecules. The o-Ps formed in the matrix is localized in the free volume holes within the polymer. Evidence for the localization of o-Ps in the free volume holes has been found from temperature, pressure, and crystallinity-dependent properties [12-14]. In a vacuum o-Ps has a lifetime of 142.1 ns. In the polymer matrix this lifetime is reduced to between 2 - 4 ns by the so-called pick-off annihilation with electrons from the surrounding molecule. The observed lifetime of the o-Ps (zj) depends on the reciprocal of the integral of the positron (p+(rj) and electron (p.(r)) densities at the region where the annihilation takes place ... 

A General Semiempirical Quantum Mechanical Solvation Model for Nonpolar Solvation Free Energies. n-Hexadecane. 

D. J. Giesen, C. J. Cramer, and D. G. Truhlar,/. Phys. Chem., submitted for publication. A Semiempirical Quantum Mechanical Solvation Model for Solvation Free Energies in All... 

Despite all the problems inherent to QM/CM approaches, some extremely interesting and perceptive work has been described in the literature recently in which all sorts of approaches have been used, improvements introduced and results obtained ([351, 372] and references therein). The study of enzyme catalysed reaction mechanisms, the calculation of relative binding free energies of substrates and inhibitor, and the determination of proton transfer processes in enzymatic reactions, are all good examples of enzyme-ligand interactions studies. Even though Warshel s EVB method [349] probably remains the most practical QM/CM approach for the study of enzyme catalysis, very useful work has been reported on enzyme catalysed reactions ([381] for an excellent review-[238, 319, 382-384]). This is a consequence of the accuracy of QM to treat the active site and inhibitor/substrate and the viability of classical mechanics to model the bulk of the enzyme not directly involved in the chemical reaction. 

Free-Wllson model (12) quantum mechanically based models (13, 14) and pattern recognition methods (8,15). Reviews are cited that describe the progress made using each of the approaches. 

Thirdly, the discrete model was extended to mechanical models, multi-link mechanism (kinematic model) and deformable objects (dynamic model) to consider design parameters and boundary condition of the gels. If one side of the gel is fixed, the former kinematic model is selected. If both sides of the gel are free... 

Cooke, I. R., and Desemo, M. 2005. Solvent-free model for self-assembling fluid bilayer membranes Stabilization of the fluid phase based on broad attractive tail potentials. J. Chem. Phys. 123 224710. de Gennes, P. G. 1980. Conformations of polymers attached to an interface. Macromolecules 13 1069. Espanol, R, and Warren, P. 1995. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 30 ... 

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