MedChem Designer™

Chemical Structure Drawing and Property Prediction

MedChem Designer™ – free chemical structure drawing program


A few drugs, approved in 2015, displayed in MedChem Designer. The user interface includes pulldown menus, quick access icons, and controls for various sketching functions. Predicted properties that are available with the free version are shown at the bottom.

MedChem Designer 3.0 is a free chemical structure drawing program.  MedChem Designer can open SMILES, SDF, MOL, CSK, and RXN file types.  Up to 32 compounds can be displayed in one window.  Images can be exported in SMILES, SD, MOL, CQF, bitmap, JPG, or PNG formats.  Various properties e.g., logP, logD, topological polar surface area (TPSA), can be quickly and easily computed. Additionally, structure images and predicted properties can be exported in Excel format.  One can also copy a SMILES string e.g., from the Wikipedia page for aspirin, and paste it into MedChem Designer. Reactions can be sketched and converted to SMIRKS strings or saved as RXN files for use in other programs.  The optical structure recognition tools allows one to copy an image into MedChem Designer.



Predicted Properties
MedChem Designer with free computed properties

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The properties below can be predicted with the free version of MedChem Designer:

  • S+logP – predicted log of the octanol/water partition coefficient using the Simulation Plus ANNE model
  • S+logD –  predicted logD at pH 7.4 using the Simulation Plus ANNE model
  • MlogP – predicted logP using Moriguchi’s model
  • MWt – Molecular weight
  • M_NO – count of nitrogen and oxygens
  • T_PSA – topological polar surface area, as defined by P. Ertl, et al.
  • HBDH – number of OH and NH hydrogen bond donor protons
  • DiffCoef – Hayduk and Laudie’s estimation of diffusion coefficients
  • RuleOf5 – number of Lipinski’s rule of 5 violations
  • RuleOf5 Code – a list of the Lipinski rule violations

The figure on the right shows a few anti-depressants and their computed properties.




Sketching molecules is easy with MedChem Designer’s drawing tools

  • Extend structure with a single bond
  • Hoover over an atom and type a letter, e.g. “N” to change the atom type
  • Change formal charge by hoovering over atom and typing – (minus) or + (plus)
  • Wedge bonds display atoms in front or back of the canvas
  • Long straight or “hex” (for creating macrocycles) bonds
  • Aromatic and saturated ring templates
  • Ability to create custom templates, e.g. glucuronic acid
  • Ability to modify bond and torsional angles of side chains
  • Convenient structure-cleanup feature with the option to keep one or more regions of a structure fixed
  • Eraser removes individual atoms or drag to remove multiple atoms
  • Double click to delete molecule when using eraser tool
Edit and Export

Below are a couple examples of editing the geometry of the molecule.  Exporting in Excel format is also discussed.

Torsional bond rotation tool

The torsion bond rotation tool will “flip” a torsional bond.  Either side of the bond can be be moved.  A red line will appear on the bond that is being modified.  The portion of the molecule on the same side of the red line will be relocated.


Rotatable bond tool

Cleanup tool

The cleanup tool will modify bond lengths and angles of a selected portion of the molecule or the whole molecule.  This can be used to maintain the geometry of the scaffold.


The clean up tool only affects the highlighted atoms.

Export in Excel format

Structures and property data in MedChem Designer can be exported in Excel format.  The figure below shows the exported file displayed in Excel.

Structures and properties exported and displayed in Excel










Reaction Mapping Tool

You can sketch chemical reactions in MedChem Designer and map the atoms in the reactant to their corresponding atoms in the product.  The reaction can be copied as a SMIRKS string or exported as a RXN file.  These formats can then be used in other programs to specify reactions for enumeration.  For example, the SMIRKS string can be pasted into MedChem Studio’s “Combinatorial Reaction…” command to enumerate a combinatorial chemistry reaction.

The figure below illustrates the Pictet-Spengler reaction in which an ethylbenzylamine reacts with an aldehyde to form a tetrahyrdoisoquinoline (THIQ).

Illustration of reaction mapping tool

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The reaction is shown in the top panel.  The next panel shows how the reaction mapping tool is used.  One simply clicks on a reactant atom and then drags the cursor onto the corresponding atom in the product.

The reaction mapping tool is smart! One only needs to map the carbonyl carbon in the aldehyde to its corresponding atom in THIQ and the program maps the rest of the atoms.  The atom mapping of the whole reaction is shown in the bottom panel.

OSR Tool
OSR tool can be used to “copy” image into MedChem Designer

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The Optical Structure Recognition (OSR) tool allows you to extract chemical structures from displayed images in journal articles, Word documents, PowerPoint slides, web pages, etc.

Simply position the transparent window over the image of interest and click the “Convert Image” button.  The chemical structure will be retrieved automatically and displayed in MedChem Designer (note: paid license to ADMET Predictor or MedChem Studio is required).


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