Hydrogen protonic state

Therefore, electrons adjust their state to any instant position of the proton and solvent polarization in both the initial (hydroxonium ion) and final (adsorbed hydrogen atom) states. The proton in the hydroxonium ion sees an average electron cloud but feels any instant configuration of solvent polarization. 

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... 

Fig. 3. Customization of the receptor description file. Chains allows specification of the chains present in the protein that have to be included (grayed out if only one chain is present) Templates to add specific metals, cofactors, and/or water molecules or determine protonation state of Asp, Cys, Glu, His, Ser Torsions allows setting of the dihedral angle of the terminal hydrogen atom of the specified residue.

There are numerous cases, where identical bases, mismatched bases, and even complementary bases in protonated states are involved in hydrogen bonding. Examples are as follows Protonated adenine (HA+) has been observed in DNA mismatches as well as in RNA in pairs such as HA 1 (antl) G(syn) and HA+(anti) C(anti) (70). Poly(A) forms HA+ HA+ self-pairs in a parallel strand fashion at pH <4 (21). Protonated cytosine (HC+) exists in hemiproto-nated polyC (i-motif) (32), in HC+(anti) G(syn) (71), in a HC+ C RNA... 

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