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Basic
Protonation
Partitioning
Charge
Isomers
Geometry
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Logarithmic measure of the acid dissociation constant, -log10Ka. This dissociation constant is a quantitative measure of the strength of an acid in solution.
Major microspecies at pH=7.4:
The major protonation form of the molecule at a specified pH.
logP: 4.22
The partition coefficient is a ratio of concentrations of an un-ionized compound in the two phases of immiscible solvents (water and n-octanol) at equilibrium. logP is the 10-base logarithmic measure of the coefficient.
Compounds having ionizable groups exist in solution as a mixture of different ionic forms. The ionization of those groups, thus the ratio of the ionic forms depends on the pH. Since logP describes the hydrophobicity of one form only, the apparent logP value can be different. The octanol-water distribution coefficient, logD represents the compounds at any pH value.
Partial charges are introduced due to the asymmetric distribution of electrons in the chemical bonds between atoms having different electronegativity.
The calculation of partial charges is based on the partial equalization of the orbital electronegativity of atoms. The numbers presented in parentheses belong to the relevant implicit hydrogen. Learn more at chemaxon.com
Molecular polarizability: 41.54
The electric field generated by partial charges of a molecule spreads through intermolecular cavities and the solvent. The induced partial charge (induced dipole) has a tendency to diminish the external electric field. This phenomenon is called polarizability. The more stable the ionized site is the more its vicinity is polarizable. Calculation method based on Miller, K. J.; Savchik, J. A., J. Am. Chem. Soc., 1979, 101, 7206-7213; doi
Partial charge distribution of the molecule is governed by the orbital electronegativity of the atoms contained in the molecule.
The definition of orbital electronegativity of atoms in molecules was first given by Mulliken in this equation:
Where
is the orbital electronegativity of the atom
Iv is the ionization potential of the atom
Ev is the electron affinity of the atom
Where
is the orbital electronegativity of the atomIv is the ionization potential of the atom
Ev is the electron affinity of the atom
Hydrogen Bond Donor/Acceptor calculates atomic hydrogen bond donor and acceptor inclination. Atomic data and overall hydrogen bond donor and acceptor multiplicity are displayed for the input molecule (or its microspecies at a given pH). The weighted average hydrogen bond donor and acceptor multiplicities taken over the microspecies and the proportions of their occurrences are computed for different pHs and displayed in a chart.
pi energy = 52.15
Localization energies L(+) and L(-) for electrophilic and nucleophilic attack at an aromatic center are calculated by the Huckel method. The smaller L(+) or L(-) means more reactive atomic location. Order of atoms in E(+) or in Nu(-) attack are adjusted according to their localization energies. The total pi energy, the pi electron density and the total electron density are also calculated by the Hückel method. Depending on the chemical environment the following atoms have optimal Coulomb and resonance integral parameters: B, C, N, O, S, F, Cl, Br, I. All other atoms have a default, not optimized parameter.
Molecular refractivity: 108.736
Molar refractivity is strongly related to the volume of the molecules and to London dispersive forces that has important effect in drug-receptor interaction. The calculation is based on the atomic method proposed by Viswanadhan et al. (Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K., J. Chem. Inf. Comput. Sci., 1989, 29, 163-172; doi)
Bemis-Murcko framework
Bemis-Murcko framework is calculated by removing side chains from the input and generalizing atom/bond types.
