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Basic
Protonation
Partitioning
Charge
Isomers
Geometry
Other
Molecule
Names and identifiers
The name of the compound according to the International Union of Pure and Applied Chemistry nomenclature. The commonly used trivial or traditional name is also shown if available.
Elemental Analysis
- Formula: chemical formula of the molecule
- Isotope formula: chemical formula of the molecule listing isotopes separately
- Composition: elemental composition (w/w %)
- Isotope composition: elemental composition listing isotopes separately (w/w %)
- Mass: molecular mass
- Exact mass: molecular mass calculated from the most frequent natural isotopes of the elements
pKa
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
The major protonation form of the molecule at a specified pH.
Isoelectric Point
Net charge of an ionizable molecule is zero at a certain pH. This pH is called the isoelectric point, also referred to as pI. Isoelectric point plugin calculates gross charge distribution of a molecule as function of pH.
logP
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.
logD
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.
Charge
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
Polarizability
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
Orbital Electronegativity
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
Tautomerization
Tautomers are organic compounds that are interconvertible by tautomerization. Tautomerization reaction results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond. Commonly, the catalysts of these reactions are acids or bases. In solution a chemical equilibrium of the tautomers will be reached. Some types of tautomers: ketone-enol, amid-imidic acid, lactam-lactim, enamine-imine.
Dominant tautomer distribution is calculated, and the first 6 most likely tautomers displayed.
Dominant tautomer distribution is calculated, and the first 6 most likely tautomers displayed.
Stereoisomers
The number of possible stereoisomers is calculated, duplicates (mesomers) are filtered. All chiral centers and double bonds are considered.
Topology Analysis
- Platt index: sum of the edge degrees of a molecular graph
- Randic index: harmonic sum of the geometric means of the node degrees for each edge
- Balaban index: the Balaban distance connectivity of the molecule, which is the average distance sum connectivity
- Harary index: half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule
- Hyper Wiener index: a variant of the Wiener index
- Szeged index: The Szeged index extends the Wiener index for cyclic graphs by counting the number of atoms on both sides of each bond (those atoms only which are nearer to the given side of the bond than to the other), and sum these counts
- Wiener index: the average topological atom distance (half of the sum of all atom distances) in the molecule
- Wiener polarity: the number of 3 bond length distances in the molecule
Geometry
- Dreiding energy: the energy value of the most stable conformer predicted by Dreiding force field. Dreiding force field is the simplest generic force field suitable for providing accurate geometries of organic, biological, and main-group inorganic molecules.
- Volume: The van der Waals volume of the conformer. Learn more on wikipedia.org
- Minimal projection radius: the radius of the circumscribed circle (green) of the minimal projection of the current conformer.
- Maximal projection radius: the radius of the circumscribed circle (yellow) of the maximal projection of the current conformer.
- Min z length: the extent (green arrow) of the conformer perpendicular to its minimal projection area.
- Max z length: the extent (yellow arrow) of the conformer perpendicular to its maximal projection area.
Polar Surface Area
Polar surface area is formed by polar atoms of a molecule. It is a descriptor that shows good correlation with passive molecular transport through membranes, and so allows estimation of transport properties of drugs. Results in Å2.
Molecular Surface Area
The solvent accessible surface area of the molecule is calculated.
H-bond Donor/Acceptor
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.
Huckel Analysis
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.
Refractivity
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)
Structural Frameworks
Bemis-Murcko framework is calculated by removing side chains from the input and generalizing atom/bond types.
Lipinski-like filters
These filters are used in drug discovery and drug development to narrow down the scope of molecules. They provide estimation on solubility and permeability of orally active compounds considering their physical and chemical properties. The filter is valid, when all of the examined properies of the molecule meet the criteria. The examined properties are:
- Lipinski's rule of five:
(mass() <= 500) && (logP() <= 5) && (donorCount() <= 5) && (acceptorCount() <= 10) - Bioavailability:
(mass() <= 500) + (logP() <= 5) + (donorCount() <= 5) + (acceptorCount() <= 10) + (rotatableBondCount() <= 10) + (PSA() <= 200) + (fusedAromaticRingCount() <= 5) >= 6 - Ghose filter:
(mass() >= 160) && (mass() <= 480) && (atomCount() >= 20) && (atomCount() <= 70) && (logP() >= -0.4) && (logP() <= 5.6) && (refractivity() >= 40) && (refractivity() <= 130) - Lead likeness:
(mass() <= 450) && (logD('7.4') >= -4) && (logD('7.4') <= 4) && (ringCount() <= 4) && (rotatableBondCount() <= 10) && (donorCount() <= 5) && (acceptorCount() <= 8) - Muegge filter:
(mass() >= 200) && (mass() <= 600) && (ringCount() <= 7) && (atomCount('6') >= 5) && ((atomCount() - atomCount('6') - atomCount('1')) >= 2) && (rotatableBondCount() <= 15) && (donorCount() <= 5) && (acceptorCount() <= 10) && (logP() >= -2) && (logP() <= 5) && (PSA() <= 150) - Veber filter:
(rotatableBondCount() <= 10) && (PSA() <= 140)
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Similar Structures
