Protons, electrostatic interactions

If electrostatic interactions play a major role in the strength of anion binding, then it is natural to expect that the higher the polyammonium cation charge is the stronger the affinity for anions will be. This was found to be case with [24]aneN6 and [32]aneNg which possess 6 and 8 protons, respectively, at pH 7 (see Table 4)46). 

The second part of lanosterol biosynthesis is catalyzed by oxidosqualene lanosterol cyclase and occurs as shown in Figure 27.14. Squalene is folded by the enzyme into a conformation that aligns the various double bonds for undergoing a cascade of successive intramolecular electrophilic additions, followed by a series of hydride and methyl migrations. Except for the initial epoxide protonation/cyclization, the process is probably stepwise and appears to involve discrete carbocation intermediates that are stabilized by electrostatic interactions with electron-rich aromatic amino acids in the enzyme. 

In the original, elementary treatment governed by Eq. 4 above, one might initially expect contributions to the barrier from several sources. There is first the Coulomb integral Q, which will contain angle dependent terms from the electrostatic interaction of the electrons and protons ar the two ends of the molecule. In this treatment the only orbitals used are Is on each H atom and tetra-... 

Theoretical studies aimed at rationalizing the interaction between the chiral modifier and the pyruvate have been undertaken using quantum chemistry techniques, at both ab initio and semi-empirical levels, and molecular mechanics. The studies were based on the experimental observation that the quinuclidine nitrogen is the main interaction center between cinchonidine and the reactant pyruvate. This center can either act as a nucleophile or after protonation (protic solvent) as an electrophile. In a first step, NH3 and NH4 have been used as models of this reaction center, and the optimal structures and complexation energies of the pyruvate with NH3 and NHa, respectively, were calculated [40]. The pyruvate—NHa complex was found to be much more stable (by 25 kcal/mol) due to favorable electrostatic interaction, indicating that in acidic solvents the protonated cinchonidine will interact with the pyruvate. 

Figure 7-2. Properties of CAII active site in the COHH state (zinc-bound hydroxide and protonated His 64). (a) Superposition of a few key residues from two stochastic boundary SCC-DFTB/MM simulations with the X-ray structure [87] (colored based on atom-types) the two sets of simulations did not have any cut-off for the electrostatic interactions between SCC-DFTB and MM atoms but used different treatments for the electrostatic interactions among MM atoms group-based extended electrostatics (in yellow) and atom-based force-shift cut-off (in green). Extended electrostatics simulations sampled configurations with the protonated His 64 too close to the zinc moiety while force-shift simulations consistently sampled the out configuration of His 64 in multiple trajectories, (b) Statistics for productive water-bridges (only from two and four shown here) between the zinc bound water and His 64 with different electrostatics protocols...

Comparison of solution pH with the pKa of a side chain informs about the protonation state. A unique pKa, termed the standard or model pKa, can be experimentally determined for each ionizable side chain in solution when it is incorporated in a model compound, often a blocked amino acid residue [73] (Table 10-1). In a protein environment, however, the pKa value of an ionizable side chain can substantially deviate from the standard value, due to desolvation effects, hydrogen bonding, charge-charge, charge-dipole, and other electrostatic interactions with the... 

It is noted that (ip1)2 + ip2 k2. The symmetry is broken by separating the variables and this eliminates the quantum-mechanical equivalence of proton and electron. Only electrostatic interaction, V = 4pfoT remains in the electronic wave equation. 

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