Base pairs strength

Figure 15.1 Conjugate acid-base pair strengths.

As an introduction to the method of calculating the melting curves for various periodic DNA molecules let us first consider the case of a molecule composed of a sequence of identical base pairs, say poly d(A) poly d(T) with no complication such as slippage or hairpin loops. The base pair strengths in this case are all the same and are defined as... 

The base pair strength Z,- for theyth base pair will be given by... 

The statistical weights gpg(J) and fp,(m) will determine OT and hence the djf. For poly d(A-C)-poly d(T-G) we have three parameters the correlation parameter between stacked base pairs = J(C7,4 + U j), the averaged base pair strength parameter + Ln), and M. ... 

Backbone (protein), 1028 Backside displacement. reaction and.363-364 von Baeyer, Adolf, 113 Baeyer strain theory, 113-114 Bakelile, structure of, 1218 Banana, esters in, 808 Barton, Derek, H. R., 389 Basal metabolic rate, 1169 Basal metabolism. 1169-1170 Base, Bronsted-Lowry, 49 Lewis, 57, 59-60 organic, 56-57 strengths of, 50-52 Base pair (DNA), 1103-1105 electrostatic potential maps of. 

To use the above expression for measuring the strength of an acid, a standard acid-base pair, say A2-B2, must be chosen, and it is usually convenient to refer acid-base strength to the solvent. In water the acid-base pair H30 + -H20 is taken as the standard. The equilibrium defining acids is therefore ... 

To express the relative strengths of an acid and its conjugate base (a conjugate acid-base pair ), we consider the special case of the ammonia proton transfer equilibrium, reaction C, for which the basicity constant was given earlier (Kb = [NH4+l[OH ]/ NH3]). Now let s consider the proton transfer equilibrium of ammonia s conjugate acid, NH4+, in water ... 

TABLE P a 10.3 Conjugate Acid-Base Pairs Arranged by Strength Acid name Acid formula Base formula Base name PKb... 

Some studies have been made with bases of the type ArO , as this allows study of the effects of variation in basic strength (by introduction of p-substituents in C HsO ) without concomitant change in the steric requirements of the base. With a given base, transfer from a hydroxylic solvent, e.g. HjO or EtOH, to a bipolar aprotic one, e.g. HCONMej (DMF) or MejS —O (DMSO), can have a very pronounced effect as the strength of the base, e.g. OH, OR, is enormously increased thereby. This arises because the base has, in the latter solvents, no envelope of hydrogen-bonded solvent molecules that have to be stripped away before it can act as a base (c/ effect on nucleophilicity in S, 2, p. 81). Such change of solvent may result in a shift of mechanistic pathway from E1 to E2 for some substrate/base pairs. 

Conversely, if a. para substituent stabilizes the conjugate base of an acid-base pair rather more than it stabilizes the benzoate ion, more positive substituent constants are required to achieve linearity in Hammett plots. Examples of this are acid dissociations of phenols and anilinium ions, where mesomerically electron-withdrawing substituents (Y = —NO2, —C N) are more effective in enhancing acid strength than they are in benzoic acid, because charge delocalization of the type [15] is not possible in the benzoate anion. 

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