Acidity parameter

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Figure 3-3 illustrates well the different influence of acid concentration on the rates of diazotizations in regions B and C, i. e., on either side of the maximum. In region B this influence corresponds to Scheme 3-14, i.e., to a linear dependence on the acidity parameter h0. In region C the slope is steeper, in 57-61 % HC104 the rate corresponds to Scheme 3-25 (Challis and Ridd, 1960).

The satisfactory correlations between Kamlet-Abraham s acidity parameters and H-bond donor free energy factors, and between Kamlet-Abraham s basicity parameters and H-bond acceptor free energy factors for many sets of compounds [26] deserve particular mentioning ... 

Among the reported parameters the only one which shows some degree of linear correlation with the redox potential is the acidity parameter t(30), Figure 7. 

One may question the need for a four parameter enthalpy equation, i.e., whether describing an acid or base by two parameters each is redundant. The following simple matrix algebra shows the conditions whereby a four parameter model reverts to a less redundant two parameter equation. Letting A be the transformation matrix, E and C represent the parameters for the four parameter model, and a represent the acid parameters for the two parameter model, the following equation results ... 

For an organic compound (Q) in dipolar aprotic solvents, the half-wave potential ( 1/2) of the first reduction step tends to shift to the positive direction with an increase in solvent Lewis acidity (i.e. acceptor number). This is because, for the redox couple Q/Q, the reduced fonn (Q ) is energetically more stabilized than the oxidized fonn (Q) with increasing solvent acidity. The positive shift in E1/2 with solvent acceptor number has been observed with quinones [57 b], benzophenone [57 a, c] and anthracene [57 c], With fullerene (C60), the positive shift in E1/2 with solvent acidity parameter, ET, has been observed for the reductions of C60 to Qo, Qo to Clo, and Cf)0 to Cli, [54c], However, the positive shift in E1/2 is not apparent if the charge in Q is highly delocalized, as in the cases of perylene and fluoren-9-one [57 c]. 

N 055 "Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. IX. Glutamic Acid Parameters from Random... 

An acidity scale has been proposed in which the difference in the acidity parameters. (aB — aA), of a metal oxide and a nonmetal oxide is the square root of the enthalpy of reaction of the acid and base.4 Thus for reaction 9.5, the enthalpy of reaction is —8fikJ mol-1 and so the a values of CaO and SiO, differ by about 9 units. Selected values are fisted in Table 9.1. Although based on the Lux-Flood concept, the values are obviously of more general interest. The most basic oxide, as expected, is cesium oxide, amphoteric oxides have values near zero (water was chosen to calibrate the scale at a value of 0.0). and the most acidic oxide is CLO,. the anhydride of perchloric acid. 

Selected acidity parameters, a, for acidic, basic, and amphoteric oxides0... 

Plot I he acidity parameters, a. from Table 9 I vs. I he p Kh values in Table 9.3 for those metals that occur in both tables. Interpret your plot. 

What is required is a value of pA extrapolated to water (pAH2°). Fortunately, the dependences of the relevant equilibrium constants on the composition of the acidic medium are well described by free energy relationships. This means that an unknown pAa (or pAR) can be obtained from measurements in concentrated acidic solutions by plotting values against known pAas for the protonation of a reference base.52,53 In practice, medium acidity parameters, XQ = pKa — pAaH2°, are conveniently defined for a family of structurally... 

It was suggested earlier in this section that oxoacid salts such as CaC03 could be viewed as products of reactions between basic oxides (containing O2- discrete ions) and covalent (molecular/polymeric) oxides in which oxide ions are transferred to form oxo-anions. Analysis of the thermochemistry of such reactions has led to the formulation of a numerical scale of acidity for oxides. In Table 9.1 the acidity parameter a is listed for the most important binary oxides. Highly-negative values indicate a basic oxide, while acidic oxides have positive values. 

Fig. 7 Hydrogen bond acidity and vertical pK. Vertical pA a values show a reasonable correlation with Abraham s hydrogen bond acidity parameter, while the equilibrium pKa values show much more scatter. ( ) Points used in the least squares fit, ( ) vertical pATa values for carboxylic acids not used in the least squares fit, and ([>) equilibrium pK.A values not used in the least squares fit.

An amino acid scale refers to a numerical value assigned to each amino acid such as polarity, hydrophobicity, accessible/buried area of the residue, and propensity to form secondary structures (e.g., amino acid parameter of AAIndex). For example, selecting (clicking) ProtScale from the list of ExPASy Proteomics tools opens the query page with a list of predefined amino acid scales. Paste the query... 

In situ performic acid Parameter In situ peracetic acid Parameter... 

Table 6 Oleic Acid Parameters Calculated from the Term hoo for a DPPC/OA Monolayer on a Water Subphase...

This strength only becomes manifest in the presence of a suitable base or proton acceptor, in which case appropriate values of such acidity parameters as Hammett s Ho can be measured. In rather simplistic terms one could draw a parallel between the Ho values and the relative ease with which a given monomer would be protonated if dissolved in the pure acids. Unfortunately, this protonation capacity is not a sufficient criterion to establish the potential usefulness of a Br nsted acid as initiator in cationic polymerisation, although it does represent an important parameter. Other factors, such as the solubility of the acid in the common solvents used, its inertness towards them, the relative stability of the ions formed in the protonation reaction against their collapse to the corresponding ester, etc., can play a major role in determining the real qualities of these possible initiators. 

The data collected by Gritzner [79] and his analysis led him to the conclusion that different interactions of hard and soft cations with donors cannot be accounted for by using only one parameter. Gritzner [79] also tried other correlations. No correlation was found with the acceptor number and the other Lewis acidity parameter, x, introduced by Dimroth and Reichardt [19, 83]. Only those parameters which represent donor properties of solvents are correlated with the change of E /2 potentials for the electroreduction of cations. 

The change in the Lewis acidity parameter, Ej with the mixed solvent composition is either monotonie or exhibits a maximum with an value higher than those found for the pure solvents [266]. 

TT is the dipolarity/polarizability parameter, a is the solvent HBD (acidity) parameter. 

Considering the mechanism involved, it is somewhat surprising that neither o-p" nor crj were superior to the benzoic acid parameters in describing a tighter range. 

There are five adjustable parameters per molecule X, the dispersion parameter q, the induction parameter x, the polarity parameter a, the hydrogen-bond acidity parameter and p, the hydrogen-bond basicity parameter. The induction parameter q often is set to a value of 1.0, yielding a four-parameter mcdel. The terms fi and are asymmetry factors calculated from the other parameters. A database of parameter values for 150 compounds, determined by regression of phase equilibrium data, is given by Lazzaroni et al. [Ind. Eng. Chem. Res., 44(11), pp. 4075-4083 (2005)]. An application of MOSCED in the study of liquid-liquid extraction is described by Escudero, Cabezas, and Coca [Chem. Eng. Comm., 173, pp. 135—146 (1999)]. Also see Frank et al., Ind. Eng. Chem. Res., 46, pp. 4621-4625 (2007). 

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