Molecules is an application for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. These structures can be viewed in both ball-and-stick and spacefilling visualization modes.

New molecules can be downloaded from either the RCSB Protein Data Bank (, an international repository of biological molecules and their 3-D structures, or NCBI's PubChem (, a public database of compounds. Molecules can be downloaded directly to your handheld device and stored there for later viewing.

Custom molecular structures can be downloaded to the application via iTunes file sharing, or through the use of custom URL formats. For more details, please visit our website.

Molecules is a BSD-licensed open source project.

What’s New

Version 2.1

- Added support for the new Retina iPad to the rendering engine and artwork.
- Added a color key for elements to iPad interface.
- Slightly improved rendering fidelity on iPhone 4S and iPad 2.
- Fixed a few minor rendering glitches.

Ratings and Reviews

3.6 out of 5
166 Ratings

166 Ratings

Futile123 ,

What happened?

Still not fixed as of June, 2013. It cannot even use files previously saved via iTunes! Anyone have a viable replacement to suggest?

This worked great on the iPad 2 two months ago. The PubChem access is awful: e.g., ethanol is there, but this app cannot even find it! Finding simple substances like water, methane, ammonia, formaldehyde, hexane, ethanol, and so on worked great before. Now they either do not show up at all or are hidden as bizarre numbers that make no sense even to a chemist. And you cannot even add the common name if you get lucky and find the molecule you want. As a chemist, I am very disappointed with this serious decline in capability. I will be looking for a substitute. Please fix this screwup!

Almost worthless now. Please fix the blunders and make this usable again!

neutrinos4all ,

Structural annotation

I'm a high school chemistry teacher, and this app would be a lot more awesome if you guys could add some sort of structural annotation key (i.e., what are all of these atoms we're looking at?) and/or a chemical formula to the page. Surely that information is stored on the database pages your app pulls from, and so could be integrated into the GUI? It looks like all of the same sorts of atoms are of similar color across models, which is great, so now all we need is a little guide people (e.g., students) could reference at will to remind them what the atoms are.

Otherwise, this is a fantastic app! Great work!

AL223304 ,


Love this app but it needs some features updated and bug fixes badly. Needs iPhone 5 larger screen format. Needs a bug fix for small black bar at top of app that causes bottom of the molecules list to partly cut off from view.
Needs double, single and triple bonds to be shown as 1, 2 or 3 bars in the atom and stick model mode.
Needs much better at searching for new molecules.
Needs an element color key and/or option to have atoms labeled in the models.
Needs to be able to search for enzymes and biological molecules like ATP by their common abbreviations.
Needs to have a place in the app where you can see the chemical formulas for small molecules in your list and the amino acid sequence for proteins and enzymes in your list. Also would be cool if it could represent proteins with ribbon models.


Brad Larson
1.1 MB

Requires iOS 4.2 or later. Compatible with iPhone, iPad, and iPod touch.


English, French

Age Rating


  • Family Sharing

    With Family Sharing set up, up to six family members can use this app.

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