ChemBrain IXL - Molecule Datasheet, Gateway to Molecular Descriptors

The molecule datasheet contains all the data that are related to the molecule and is the starting point for any further representations and calculations concerning this molecule.

In the graphics window the datasheet shows the 3-dimensional molecular structure (see screenshot). Like all the graphical representations in ChemBrain this structure can be rotated freely by means of the mouse cursor. (Beyond this, the molecule datasheet also optionally enables animated rotation.) Moving the mouse cursor over a specific atom shows the net charge of this atom, calculated by means of a fast EHMO algorithm.

Below the graphics screen you see the structure representation code in the form of a radial distribution function (RDF), a function which is rotation- and translation-invariant. This function is used for similarity search (explained elsewhere) and in artificial neural network calculations. ChemBrain allows you to apply various structure representation codes based on the atomic mass (as shown), charge, polarizability, electronegativity or even Van-der-Waals' volume by just double-clicking on the RDF.

Besides the graphics window a list of single-value properties, also called molecular descriptors, is shown. Several of them, namely the heats of combustion, formation, solvation, sublimation, vaporization and fusion, the phase-change entropies, the heat capacities of organic liquids and solids, the molar refractivity, the molecular electronic polarization by internal continuum (EPIC), the molecular polarizability, the partition coefficient log P, the solubility log S, the activity coefficient at infinite dilution in water, the aqueous toxicity, the viscosity, the molecular and molar volumes, the molecular surface, the polar surface area (PSA) and the solvent-accessible surface area (SASA), are optionally calculated automatically at the time of addition of a molecule to the database. However, you can add them individually by clicking the Calculate molecular descriptors button and/or add any further property by simply clicking the Add new property value button. On the other hand, provided that the structure database contains a series of molecules with a specifically known property and on condition that - among these - ChemBrain found a large enough number of structures similar to the query molecule, it delivers, upon clicking the Predict single-value property button, an "educated guess" of this property for the query molecule based on various, selectable architectures of an artificial neural network.

For molecules containing double, triple or aromatic bonds, ChemBrain enables you to immediately calculate the electronic absorption spectrum and colour (if it has any) in an artificial dilution series, by simply clicking the corresponding button on the molecule datasheet. The spectrum and further information are presented in a separate window (see screenshot).

You can at a single mouse-click (on the Suggest preparative methods button) have ChemBrain provide you with a list of potentially useful chemical reactions, sorted by relevance, which could give you an idea for the last synthetic step to obtain the present molecule. A double-click on one of these reaction suggestions opens the respective reaction datasheet with references (see screenshots).

On clicking the Notes button, ChemBrain opens a separate text window where you can add any textual information concerning the present molecule.

A very useful tool for users working synthetically opens on clicking the Elemental analysis button: it produces the molecular formula, weight and the composition in percent of the present molecule. As is often the case, a compound might be too sensitive for complete drying after purification and still contain traces of water. Therefore, in the elemental analysis window, you can add any amount of water in order to fit the resulting composition with measured data.

Finally, the molecule datasheet provides the gate to a great space-filling graphics tool which is opened by clicking on the corresponding button. In a separate window it then shows the present molecule in a variety of space-filling shapes explained elsewhere.