Marvin contains a framework for integrating chemical computations into the drawing/viewing application environment. These tools - called plugins - are loaded dynamically upon request. ChemAxon provides various tools for calculating charge, pKa, logP, etc. The available calculator plugins are located in the Tools menu. The corresponding calculation parameters can be set in the parameter panel accessible from the Options submenu.
Some plugins (Charge, Polarizability, Polar Surface Area and Hydrogen Bond Donor-Acceptor) optionally perform their computation on the physiological microspecies of the input molecule taken at a specified pH. This option together with the corresponding pH can also be set in the parameter panel.
Basic molecular values related to the elemental composition of the molecule are displayed by the Elemental Analysis plugin.
Mass: molecular mass
Exact mass: molecular mass calculated from the most frequent natural isotopes of the elements
Formula: chemical formula of the molecule
Composition: elemental composition (w/w %)
By default, molecules are handled separately if more than one molecules are drawn in the sketcher. However, sometimes a single molecule consists of more fragments (e.g. salt molecules), in which case the fragments should be treated as one molecule. This behavior can be reached by switching off the "Single fragment mode" option in the corresponding Options panel.
Most molecules contain some specific functional groups likely to loose or
gain proton under specific circumstances. Each ionization equilibrium between
the protonated or deprotonated forms of the molecule can be described with a
constant value called pKa. The pKa plugin
calculates the pKa values of all proton gaining or loosing
atoms on the basis of the partial charge distribution.
Learn more about how the plugin calculates pKa.
The chart shows the microspecies distribution curves by pH. The microspecies images are shown in the legend. When clicking on an image, the corresponding microspecies molecule is displayed in the upper-left viewer. The viewer can be detached from the chart panel by double clicking in it, or else by selecting Open Viewer from the View menu. The original molecule with the pKa values is shown when clicking on the chart outside of the legend image areas, or else when selecting pKa Values from the View menu.
The logP plugin calculates the octanol/water partition coefficient,
which is used in QSAR analysis and rational drug design as a measure of
molecular hydrophobicity. The calculation method is based on the publication
of Viswanadhan at al.1 The logP value of
a molecule is composed of the increment values of its atoms. Though,
logP is generally calculated for the neutral molecule forms only, this
plugin is able to handle ionic species as well, owing to the improved
Learn more about how the plugin calculates logP.
The panel on the right shows the logP increments for each atom. The numbers in brackets refer to the logP increment sums of implicit H atoms. This panel is displayed if Increments is selected from the Type listbox on the logP Options pane (this pane can be accessed by selecting logP from the Options submenu in the Options menu).
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 coefficient2,
logD represents the compounds at any pH value.
Learn more about how the plugin calculates logD.
The chart shows the logD(pH) curves for each molecule drawn in the sketcher. The molecule images are shown in the legend. When clicking on an image, the corresponding molecule is displayed in the upper-left viewer. The viewer can be detached from the chart panel by double clicking in it, or else by selecting Open Viewer from the View menu. The reference logD values originally shown can be restored by either clicking on the chart outside of the legend image areas, or else by selecting logD at reference pH-s from the View menu.
Polar surface area (PSA) 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. Estimation of topoligical polar surface area (TPSA) is based on the method given in 4. The method provides results which are practically identical with the 3D PSA, while calculation time of TPSA is approximately 100-times faster. This method is more suitable for fast bioavailability screening of large virtual libraries.
The partial charge distribution determines many physico-chemical properties
of a molecule, such as ionization constants, reactivity and pharmacophore
pattern. Use Charge plugin to compute the partial charge value of each atom.
Total charge is calculated from sigma and pi charge components, any of these
three charge values can be displayed.
Learn more about how the plugin calculates the partial charge.
The numbers in brackets refer to the charge sums of implicit H atoms.
Localization energies L(+) and L(-) for electrophilic and nucleophilic attack at an aromatic center are calculated by the Hückel 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.
Theoretical background is given in Neil S. Isaacs5.
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 physiological microspecies at a given pH). The weighted average hydrogen bond donor and acceptor multiplicities taken over the microspecies with proportions of their occurrences are computed for different pH-s and displayed in a chart.
Determines the major microspecies at a specified pH.
The pH can be set in the Options panel, the default pH is
The electric field generated by partial charges of a molecule spread through intermolecular cavities and the solvent that the molecule is solved within. The induced partial charge (induced dipole) has a tendency to diminish the external electric field. This phenomenon is called as polarizability. The more stable each ionized site is the more its vicinity is polarizable. This is why atomic polarizability is an important factor in the determination of pKa and why it is considered in our pKa calculation plugin. Atomic polarizability is altered by partial charges of atoms. Our calculation is based on 3, and takes into account the effect of partial charge upon atomic polarizability
Our calculation is based on the atomic method proposed by Viswanadhan at al.1. 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 numbers in brackets refer to the refractivity sums of implicit H atoms.
The topology analysis plugin provides characteristic values related to the topological structure of a molecule.
Atom count: number of atoms in the molecule inluding hydrogens.
Aliphatic atom count: number of atoms in the molecule having no aromatic bond (excluding hydrogens).
Aromatic atom count: number of atoms in the molecule having aromatic bonds.
Bond count: number of bonds in the molecule including hydrogens.
Aliphatic bond count: number of non-aromatic bonds in the molecule (excluding bonds of hydrogen atoms).
Aromatic bond count: number of aromatic bonds in the molecule.
Ring atom count: number of ring atoms.
Ring bond count: number of ring bonds.
Chain atom count: number of chain atoms (non-ring atoms excluding hydrogens).
Chain bond count: number of chain bonds (non-ring bonds excluding bonds of hydrogen atoms).
Rotatable bond count: number of rotatable bonds in the molecule. Those single bonds are considered rotatable, which are not connected to hydrogens, nor to terminal atoms (atoms having maximum one non-hydrogen adjacent). Amides, sulphonamides and single bonds connecting two hindered aromatic rings (having at least three ortho substituents) are also considered non-rotatable.
Ring count: number of rings in the molecule. This calculation is based on SSSR (Smallest Set of Smallest Rings).
Aliphatic ring count: number of those rings in the molecule, which have non-aromatic bonds (SSSR based).
Aromatic ring count: number of aromatic rings in the molecule. This number is calculated from the smallest set of smallest aromatic rings (SSSAR), which might contain rings which are not part of the standard SSSR ring set. As a consequence, the sum of the aliphatic ring count and the aromatic ring count can sometimes be greater the the ring count value. The difference is the sign of a macroaromatic ring system.
Hetero ring count: number of those rings in the molecule, which contain hetero atoms (SSSR based).
Heteroaromatic ring count: number of aromatic heterocycles in the molecule (SSSAR based).
Fused ring count: number of fused rings in the molecule (having common atoms). This calculation is based on SSSR (Smallest Set of Smallest Rings).
Fused aliphatic ring count: number of fused aliphatic rings in the molecule (having common atoms, SSSR based).
Fused aromatic ring count: number of fused aromatic rings in the molecule (having common atoms, SSSAR based).
Smallest ring size: size of the smallest ring in the molecule (SSSR based).
Largest ring size: size of the largest ring in the molecule (SSSR based).
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