logD is a log of partition of a chemical compound between the lipid and aqueous phases. The most popular lipid phase is octanol. LogP is equivalent to logD for non-ionisable compounds and represents the partition of the neutral form for ionizable compounds (and, hence, is a virtual, unmeasurable, property). LogD/logP are used as meaurable, though imperfect, proxies of an illusive and unmeasurable concept of hydrophobicity. They are particularly useful in drug discovery and development.
In short, during HPLC method development, the analyst is setting up a concentration partition of the molecule(s) of interest between the mobile phase(s) and the stationary phase or column. While logD is helpful information, it is not required.
logD refers the the water:octanol partition coefficient at a specific pH, normally pH 7.4. For ionizable compounds (acids and bases), logD would be altered by pH because the distribution of charged and uncharged forms would change, and the uncharged form is more hydrophobic.
Log D = 0 if the substance partitions equally between water and octanol (ratio =1, hence log D = 0) at the specified pH (usually 7.4). There is nothing unusual about this. Caffeine has a log D7.4 very close to zero.
A molecule that has no ionizable groups, i.e. a neutral molecule, has the same log D at every pH, equal to the log P. Caffeine is one such molecule, approximately. The measured log P is -0.07. (It could be protonated under extremely acidic conditions, however, that are not physiologically relevant.)
Log D is a distribution coefficient widely used to measure the lipophilicity of ionizable compounds, where the partition is a function of the pH. For non-ionizable compounds Log P = Log D throughout pH range, whereas for ionizable compounds Log D takes into account the partition of both ionized and non-ionized forms. Log D is more convenient for practical measurements, as it takes into account solution pH, which is important for the analysis of the drug candidate properties in various biologic media with different pH values.