Molecular models, comparing

The journal Quantitative Structure-Activity Relationships publishes, in addition to original contributions, every year about 500-600 detailed reviews on scientific papers in the fields of QSAR, 3D QSAR and molecular modeling (compare Table 1). 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Mosimann S, S Meleshko and M N G Jones 1995. A Critical Assessment of Comparative Molecular Modeling of Tertiary Structures of Proteins. Proteins Structure, Function and Genetics 23 301-317. 

These are all empirical measurements, so the model of the harmonic oscillator, which is pur ely theoretical, becomes semiempirical when experimental information is put into it to see how it compares with molecular vibration as determined spectroscopically. In what follows, we shall refer to empirical molecular models such as MM, which draw heavily on empirical information, ab initio molecular models such as advanced MO calculations, which one strives to derive purely from theory without any infusion of empirical data, and semiempirical models such as PM3, which are in between (see later chapters). 

Practice working with your Learning By Modeling software Construct molecular models of ethane ethylene and acetylene and compare them with respect to their geometry bond angles and C—H and C—C bond distances... 

Make a molecular model of each chair conformation of methylcyclohexane and compare their energies... 

Make molecular models of c/s and trans 1 2 dimethylcy clopropane and compare their strain energies... 

Make molecular models of (f) and (Z) cyclooctene and compare their H—C=C—H dihedral angles... 

Use molecular models to compare —C=CH —CH=CH2 and —CH2CH3 with respect to their preference for an equatonal onentation when attached to a cyclohexane nng One of these groups IS very much different from the other two Which one" Why" ... 

Mesitylene (13 5 trimethylbenzene) is the most stable of the tnmethylbenzene isomers Why2 Which isomer do you think is the least stable" Make a molecular model of each isomer and compare their calculated strain energies with your predictions Do space filling models support your explanation" ... 

Which one of the dichlorobenzene isomers does not have a dipole moment" Which one has the largest dipole moment" Compare your answers with the dipole moments calculated using the molecular modeling software in Learning By Modeling... 

Make a molecular model of dimethyl sulfide How does its bond angle at sulfur compare with the C—O—C bond angle in dimethyl ether"d... 

Newtonian behavior the rate of shear is small compared to the rate constant for the flow process. When molecular displacements occur very much faster than the rate of shear (7 < kj ), the molecules show maximum efficiency in dissipating the applied forces. When the molecules cannot move fast enough to keep pace with the external forces, they couple with and dissipate those forces to a lesser extent. Thus there is a decrease in viscosity from its upper, Newtonian limit with increasing 7/kj. The rate constant for the flow process is therefore seen to define a standard against which the rate of shear is to be judged large or small. In the next section we shall consider a molecular model in terms of which this rate constant can be analyzed. 

The purpose of these comparisons is simply to point out how complete the parallel is between the Rouse molecular model and the mechanical models we discussed earlier. While the summations in the stress relaxation and creep expressions were included to give better agreement with experiment, the summations in the Rouse theory arise naturally from a consideration of different modes of vibration. It should be noted that all of these modes are overtones of the same fundamental and do not arise from considering different relaxation processes. As we have noted before, different types of encumbrance have different effects on the displacement of the molecules. The mechanical models correct for this in a way the simple Rouse model does not. Allowing for more than one value of f, along the lines of Example 3.7, is one of the ways the Rouse theory has been modified to generate two sets of Tp values. The results of this development are comparable to summing multiple effects in the mechanical models. In all cases the more elaborate expressions describe experimental results better. 

S Mosimann, R Meleshko, MNG lames. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23 301-317, 1995. 

The most stable conformation of cyclohexane is the chair. Electron diffraction studies in the gas phase reveal a slight flattening of the chair compared with the geometry obtained when tetrahedral molecular models are used. The torsion angles are 55.9°, compared with 60° for the ideal chair conformation, and the axial C—H bonds are not perfectly parallel but are oriented outward by about 7°. The length of the C—C bonds is 1.528 A, the length of the C—H bonds is 1.119 A, and the C—C—C angles are 111.05°. ... 

Problem 1.8 concerned the charge distribution in methane (CH4), chloromethane (CH3CI), and methyllithium (CH3Li). Inspect molecular models of each of these compounds, and compare them with respect to how charge is distributed among the various atoms (carbon, hydrogen, chlorine, and lithium). Compare their electrostatic potential maps. 

Make a molecular model of the alkene in Problem 5.3, and compare the various C—C bond distances. 

How do the bond I distances of molecular models of propene and propyne compare with the experimental values ... 

Learning By Modeling contains molecular models of CH3CO2 (acetate) and CI3CCO2 (trichloroacetate). Compare these two ions with respect to the amount of negative charge on their oxygens. 

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