Molecular Notebook for the Mac desktop

Content creation for chemistry: draw molecules and reactions, assemble them into collections with data. Create beautiful graphics and keep your data ready to share and use.

Product Overview

Molecular Notebook.

A desktop app to draw chemical structures and reactions, and to organise your data in convenient spreadsheet-like files. The Molecular Notebook is designed from the ground up to leverage the macOS platform, integrating seemlessly and making presentation quality graphics just one drag away.

  • Molecules

    Built in sketcher interface for drawing molecules perfectly, and quickly, with finely tuned ergonomics. Get started immediately with the familiar toolbar, then learn the power user command actions and keyboard shortcuts.

  • Reactions

    Edit multi-step chemical reactions with full control over stoichiometry and quantities. Rendering and layout is done automatically, as detailed and complete information about the balanced reaction scheme is filled out.

  • Collections

    View and edit collections of molecules with a familiar spreadsheet-like interface. Use the aspect plugins for more complex datatypes such as experiments, assay data and scaffold fragments, each of them with their own editors.

  • Platform

    Uncompromisingly native to macOS: built from the ground up using the Swift programming language, integrated with the natural workflow - not ported as an afterthought.

  • Diagrams

    Rendered diagrams are exported preferentially using vector graphics formats, so when you drag a picture into your presentation app, it will be just as excellent when you zoom in or print it out.

  • Integrity

    Any chemistry data you create is self describing, and is a faithful representation that can be used by software. With most other tools, it's just just a picture (though it can be that, too!)

Features

The Molecular Notebook is a regular Mac app that works like any other app for opening documents: double click on a datasheet file, or create a new one from the menu, and you'll be editing a spreadsheet-like table which happens to include molecules.

It looks like a spreadsheet, but it's chemistry.

Unlike a regular spreadsheet, the columns have names and types. Numbers and text can be edited as you would expect, while molecules have a sophisticated editor.

Molecule editing is done inline: the cell expands to fill the window, and editing controls appear.

Starts out familiar, becomes more powerful with use.

Sketching atoms and bonds is simple. Positioning is automatic, and can be finely controlled when necessary for unusual geometries. Templates are provided, with sophisticated grafting algorithms. Bulky groups can be turned into inline abbreviations (which store the corresponding fragment), and exotic bond types such as resonance paths and arenes can be layered on top of a molecular sketch, allowing it to be rendered how chemists want to see it, while also preserving the true composition of the molecule.

Chemical reactions are made up of steps, each of which has reactants, reagents and products.

Assemble the reaction scheme one component at a time.

The scheme editor allows components to be sketched, pasted or selected from various sources. The visual layout is computed automatically, and the overall diagram can be used for presentation. Stoichiometry can be controlled, and used to balance the reaction. Atoms can be mapped, quantities can be provided, molarity calculations are done automatically, and green chemistry metrics are calculated.

Sometimes a datasheet needs more context, which is provided by aspects.

More complex metadata can be added.

For example, capturing information about assays can be improved by storing information about the corresponding property in the datasheet header. The aspect also gathers together the assay measurement into what looks like a single entry field, for capturing value, experimental error, units and relation, which removes all the guesswork from adhoc data entry.

Some aspects impart special properties to the molecules, such as scaffolds and fragments.

Fragments are glued to scaffolds automatically.

Filling out the scaffolds and each of the fragments provides enough information to recreate an entire molecule by connecting them together based on R-group labels. This makes it possible to quickly build the kinds of tables that are encountered so often in the literature, except that it is no longer necessary to painstakingly check that the fragments and the assembled molecule are the same, because the assembly is done automatically.

Technology

The Molecular Notebook is based on proprietary technology, built from scratch using the latest version of Apple's Swift programming language and the macOS core API. The codebase is closely related to that of other technologies from Molecular Materials Informatics used to build mobile apps, webapps and back-end cheminformatics processing capabilities.

AppStore

The Molecular Notebook can be purchased on the AppStore for one account at a time. Follow the instructions using your Mac and Apple account. Once purchased, the current and all future versions will be available in perpetuity, on any computers for which you are using the same Apple account.

The app is also available outside of the AppStore by special arrangement. See the contact details below to ask for more information.