Molecular structure

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Standards and instructions

In order to maintain consistency across the wiki, images of molecular structures should be produced in a standardized format rather than obtained from a variety of external sources. ChemDraw has a simple interface for production of molecular diagrams and is available for both Windows, Mac, and Linux.

Please draw the bond angles and depth of molecular structures as accurately as possible, using existing images for reference. Element labels should be set to use the font Arial at size 12.

Atoms should be colored as follows:

  • H, C = Black
  • O = Red
  • N = Blue
  • F, Cl = Green
  • Br, I = Purple
  • S = Yellow
  • P = Orange
  • R = Violet

Step1-Chemdraw.png

Pixels are a function of energy, which is a function of time, and as we all know; time is money. So pixels are money. Use as few as possible. Lines should be around 1px in width with some anti-aliasing. Unfortunately, ChemDraw doesn't support exporting to specific line weight, but the design preview (without altering any of the application's display settings), is about right. We can extract this representation using the print screen key and modifying the image in Photoshop or some other graphic editor.

Crop the image, leaving 1px of white space surrounding the molecule as a buffer between the image and MediaWiki's thumbnail border. Now the size is correct, the white background can be made transparent in Photoshop by selecting Select > Color Range, using the settings defined below and clicking on a white area of the image to set the sample color. Press OK to apply the selection, then delete to remove the background. You may have a mysterious "Background" layer behind the now transparent top layer; make sure you delete this.

Step3-Photoshop.png Step2-Photoshop.png

Once the image is complete, it should be exported using Save for Web or similar. Molecular structures should be saved at full quality and size, using PNG-24 format. Please upload the file giving some description of who and when designed the molecule for later reference. Please keep hold of any ChemDraw documents you create in case we ever modify the standards.

Step4-Photoshop.png

Gallery

Neurotransmitters

Amino acids

Monoamines and biogenic amines

Other

Hallucinogens

Psychedelics

Dissociatives

Deliriants

Miscellaneous


Entactogens

Stimulants

Depressants

Sedative/hypnotics

Opioids

Antipsychotics

Nootropics

Cholinergics

Choline Sources

Eugeroics

Others

References

References for molecular structures can be found all over the internet:

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