The ionization of bioactive molecules impacts many ADME-relevant physicochemical properties, in particular, solubility, lipophilicity, and permeability. Ampholytes contain both acidic and basic groups and are distinguished as ordinary ampholytes and zwitterions. An influential review states that zwitterions only exist if the acidic p<i>K</i>_a is significantly lower than the basic p<i>K</i>_a. Through concordance of measured and calculated p<i>K</i>_a and log <i>P</i>, we show that the zwitterionic behavior of several marketed drugs and natural products occurs despite a low or negative Δp<i>K</i>_a. These nonclassical zwitterions are characterized by a weak acidic and basic p<i>K</i>_a and conjugation through an extended aromatic system, often including pseudorings via intramolecular hydrogen bonds. In contrast to most classical zwitterions, nonclassical zwitterions can exhibit excellent permeability. As permeability and lipophilicity are typically correlated, the combination of low lipophilicity and high permeability makes nonclassical zwitterions an attractive design principle in medicinal chemistry.

Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life. Amino acids can be classified according to the locations of the core structural functional groups (alpha- (α-), beta- (β-), gam The common natural forms of amino acids have a zwitterionic structure, with −NH+3 (−NH+2− in the case of proline) and −CO−2 functional groups attached to the same C atom, and are thus α-amino acids, and are the only ones found in proteins during translation in the ribosome. In aqueous solution at pH close to neutrality, amino acids are energetically favored in their zwitterionic form, with a deprotonated CO−2 group and a protonated NH+3 group, because the high dielectric constant of water and its hydrogen-bonding network effectively stabilize separated charges. Thus, the overall structure is NH+3−CHR−CO−2, and the so-called "neutral forms" −NH2−CHR−CO2H are not present to any measurable degree at physiological pH. A zwitterion has a net charge of zero, but because it contains both positively and negatively charged sites, it is misleading to describe it as "uncharged." In contrast, in low-dielectric hydrophobic environments such as organic solvents or cell membrane interiors, charge separation is poorly stabilized and proton transfer tends to yield a neutral form, while in the gas phase, where there is essentially no dielectric screening or solvation, spectroscopic and computational studies show that the lowest-energy structures of most amino acids are also neutral unless specific intramolecular interactions or stepwise hydration provide sufficient stabilization of the zwitterion. In strongly acidic conditions (pH below 3), the carboxylate group becomes protonated and the structure becomes an ammonio carboxylic acid, NH+3−CHR−CO2H. This is relevant for enzymes like pepsin that are active in acidic environments such as the mammalian stomach and lysosomes, but does not significantly apply to intracellular enzymes. In highly basic conditions (pH greater than 10, not normally seen in physiological conditions), the ammonio group is deprotonated to give NH2−CHR−CO−2. Although various definitions of acids and bases are used in chemistry, the only one that is useful for chemistry in aqueous solution is that of Brønsted: an acid is a species that can donate a proton to another species, and a base is one that can accept a proton. This criterion is used to label the groups…