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Molecular structure: Difference between revisions

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=Standards and instructions=
=Standards and instructions=
In order to maintain consistency across the wiki, images of molecular structures should be produced in a standardised format rather than obtained from a variety of external sources. [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ '''ChemDraw'''] has a simple interface for production of molecular diagrams and is available for both Windows, Mac and Linux. It is available for free via [http://proxybay.info popular torrent trackers].
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. [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ '''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'''.
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 coloured as follows:
Atoms should be colored as follows:
*H, C = Green
*H, C = Black
*O = Red
*O = Red
*N = Blue
*N = Blue
*P, Cl = Green
*F, Cl = Green
*Br, I = Purple
*S = Yellow
*S = Yellow
*Br, I = Purple
*P = Orange
*R = Violet


[[File:Step1-Chemdraw.png|250px]]
[[File:Step1-Chemdraw.png|250px]]
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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.
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 colour. 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.
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.


[[File:Step3-Photoshop.png|250px]]
[[File:Step3-Photoshop.png|250px]]
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[[File:Step4-Photoshop.png|250px]]
[[File:Step4-Photoshop.png|250px]]


=To do list=
Below is a checklist of molecular structures which require production; please add to this list any molecules which do not yet comply with our image standard as described above.
*Neurotransmitters
*Entactogens?
*Etc
=Gallery=
=Gallery=


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</gallery>
</gallery>


<gallery caption="[[Substituted phenethylamines|Phenethylamines]]">
<gallery caption="[[Phenethylamine|Phenethylamines]]">
     File:SubstitutedPhenethylamine.png|link=Substituted phenethylamine|[[Substituted phenethylamine]]
     File:SubstitutedPhenethylamine.png|link=Substituted phenethylamine|[[Substituted phenethylamine]]
     File:2C-B2.png|link=2C-B|[[2C-B]]
     File:2C-B2.png|link=2C-B|[[2C-B]]
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     File:DOI.png|link=DOI|[[DOI]]
     File:DOI.png|link=DOI|[[DOI]]
     File:DOM3.png|link=DOM|[[DOM]]
     File:DOM3.png|link=DOM|[[DOM]]
    File:5-MAPB.png|link=5-MAPB|[[5-MAPB]]
     File:MDA.png|link=MDA|[[MDA]]
     File:MDA.png|link=MDA|[[MDA]]
     File:MDMA2.png|link=MDMA|[[MDMA]]
     File:MDMA2.png|link=MDMA|[[MDMA]]
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</gallery>
</gallery>


<gallery caption="[[Substituted tryptamines|Tryptamines]]">
<gallery caption="[[Tryptamine|Tryptamines]]">
     File:SubstitutedTryptamine.png|link=Substituted Tryptamine|[[Substituted tryptamine]]
     File:SubstitutedTryptamine.png|link=Substituted Tryptamine|[[Substituted tryptamine]]
     File:AMT2.png|link=alpha-Methyltryptamine|[[alpha-Methyltryptamine|α-MT]]
     File:AMT2.png|link=alpha-Methyltryptamine|[[alpha-Methyltryptamine|α-MT]]
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     File:Psilacetin.png|link=Psilacetin|[[Psilacetin]] (''4-AcO-DMT'')
     File:Psilacetin.png|link=Psilacetin|[[Psilacetin]] (''4-AcO-DMT'')
     File:4-AcO-MET.png|link=4-AcO-MET|[[4-AcO-MET]]
     File:4-AcO-MET.png|link=4-AcO-MET|[[4-AcO-MET]]
    File:4-HO-MET.png|link=4-HO-MET|[[Metocin]] (''4-HO-MET'')
     File:4-HO-DET.png|link=Ethocin|[[Ethocin]] (''4-HO-DET'')
     File:4-HO-DET.png|link=Ethocin|[[Ethocin]] (''4-HO-DET'')
     File:Psilocin2.png|link=Psilocin|[[Psilocin]] (''4-HO-DMT'')
     File:Psilocin2.png|link=Psilocin|[[Psilocin]] (''4-HO-DMT'')
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     File:Arylcyclohexylamine.png|link=Arylcyclohexylamine|[[Arylcyclohexylamine]]
     File:Arylcyclohexylamine.png|link=Arylcyclohexylamine|[[Arylcyclohexylamine]]
     File:3-MeO-PCP.png|link=3-MeO-PCP|[[3-MeO-PCP]]
     File:3-MeO-PCP.png|link=3-MeO-PCP|[[3-MeO-PCP]]
    File:3-MeO-PCE.png|link=3-MeO-PCE|[[3-MeO-PCE]]
     File:4-MeO-PCP.png|link=4-MeO-PCP|[[4-MeO-PCP]]
     File:4-MeO-PCP.png|link=4-MeO-PCP|[[4-MeO-PCP]]
     File:Ketamine3.png|link=Ketamine|[[Ketamine]]
     File:Ketamine3.png|link=Ketamine|[[Ketamine]]
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<gallery caption="[[Antihistamine]]s">
<gallery caption="[[Antihistamine]]s">
  File:Diphenhydramine.png|link=Diphenhydramine|[[Diphenhydramine]]
    File:Diphenhydramine.png|link=Diphenhydramine|[[Diphenhydramine]]
File:Doxylamine.png|link=Doxylamine|[[Doxylamine]]
    File:Doxylamine.png|link=Doxylamine|[[Doxylamine]]
</gallery>
</gallery>


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<gallery caption="[[Synthetic cannabinoid]]s">
<gallery caption="[[Synthetic cannabinoid]]s">
     File:5F-AKB-48.png|link=5F-AKB-48.png|[[5F-AKB-48]]
     File:5F-AKB48.png|link=5F-AKB48.png|[[5F-AKB48]]
     File:5F-PB-22.png|link=5F-PB-22.png|[[5F-PB-22]]
     File:5F-PB-22.png|link=5F-PB-22.png|[[5F-PB-22]]
     File:AB-FUBINACA.png|link=AB-FUBINACA.png|[[AB-FUBINACA]]
     File:AB-FUBINACA.png|link=AB-FUBINACA.png|[[AB-FUBINACA]]
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==[[Entactogen]]s==
==[[Entactogen]]s==
<gallery caption="[[Entactogen]]s">
<gallery caption="[[Phenethylamine|Substituted Phenethylamines]]">
     File:Methylone.png|link=Methylone|[[Methylone]] (''βk-MDMA'')
     File:Ethylphenidate.png|link=Ethylphenidate|[[Ethylphenidate]]
    File:2C-B2.png|link=2C-B|[[2C-B]]
    File:2C-I.png|link=2C-I|[[2C-I]]
    File:25B-NBOMe.png|link=25B-NBOMe|[[25B-NBOMe]]
    File:25C-NBOMe2.png|link=25C-NBOMe|[[25C-NBOMe]]
    File:25I-NBOMe2.png|link=25I-NBOMe|[[25I-NBOMe]]
</gallery>
 
<gallery caption="[[Amphetamine|Substituted Amphetamines]]">
    File:4fa.png|link=4-FA|[[4-FA]]
    File:4-MTA.png|link=4-MTA|[[4-MTA]]
    File:MMA2.png|link=MMA|[[MMA2]]
    File:Mephedrone.png|link=Mephedrone|[[Mephedrone]] (''4-MMC'')
    File:5-APDI.png|link=5-APDI|[[5-APDI]]
     File:5-APB.png|link=5-APB|[[5-APB]]
     File:5-APB.png|link=5-APB|[[5-APB]]
    File:5-APDB.png|link=5-APDB|[[5-APDB]]
    File:6-APDB.png|link=6-APDB|[[6-APDB]]
     File:6-APB.png|link=6-APB|[[6-APB]]
     File:6-APB.png|link=6-APB|[[6-APB]]
    File:Methylone.png|link=Methylone|[[Methylone]] (''βk-MDMA'')
     File:MDAI.png|link=[[MDAI]]|[[MDAI]]
     File:MDAI.png|link=[[MDAI]]|[[MDAI]]
     File:MDMA2.png|link=MDMA|[[MDMA]]
     File:MDMA2.png|link=MDMA|[[MDMA]]
    File:MDA.png|link=MDA|[[MDA]]
    File:MDEA.png|link=MDEA|[[MDEA]]
    File:MBDB.png|link=MBDB|[[MBDB]]
    File:Bk-MBDB.png|link=bk-MBDB|[[bk-MBDB]]
    File:5-MAPB.png|link=5-MAPB|[[5-MAPB]]
</gallery>
<gallery caption="[[Tryptamine|Substituted Tryptamines]]">
    File:AMT2.png|link=AMT|[[AMT]]
    File:AET.png|link=AET|[[AET]]
    File:5-MeO-MiPT.png|link=5-MeO-MiPT|[[5-MeO-MiPT]]
    File:5-MeO-DiPT.png|link=5-MeO-DiPT|[[5-MeO-DiPT]]
</gallery>
<gallery caption="[[Others]]">
    File:GHB.png|link=GHB|[[GHB]]
    File:GBL.png|link=GBL|[[GBL]]
    File:150px-Tert-pentyl-alcohol-2D-skeletal.png|link=2-methyl-2-butanol|[[2-methyl-2-butanol]]
    File:1,4B.png|link=1,4-Butanediol|[[1,4-Butanediol]]
</gallery>
</gallery>


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     File:Methamphetamine.png|link=Methamphetamine|[[Methamphetamine]]
     File:Methamphetamine.png|link=Methamphetamine|[[Methamphetamine]]
     File:Methylphenidate.png|link=Methylphenidate|[[Methylphenidate]]
     File:Methylphenidate.png|link=Methylphenidate|[[Methylphenidate]]
    File:Ethylphenidate.png|link=Ethylphenidate|[[Ethylphenidate]]
    File:4-Fluoromethylphenidate.png|link=4F-MPH|[[4F-MPH]]
</gallery>
</gallery>


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     File:Caffeine.png|link=Caffeine|[[Caffeine]]
     File:Caffeine.png|link=Caffeine|[[Caffeine]]
     File:Xanthine.png|link=Xanthine|[[Xanthine]]
     File:Xanthine.png|link=Xanthine|[[Xanthine]]
File:Theacrine.png|link=Theacrine|[[Theacrine]]
    File:Theacrine.png|link=Theacrine|[[Theacrine]]
</gallery>
</gallery>


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     File:Cocaine.png|link=Cocaine|[[Cocaine]]
     File:Cocaine.png|link=Cocaine|[[Cocaine]]
     File:Nicotine.png|link=Nicotine|[[Nicotine]]
     File:Nicotine.png|link=Nicotine|[[Nicotine]]
File:Bromantane.png|link=Bromantane|[[Bromantane]]
    File:Bromantane.png|link=Bromantane|[[Bromantane]]
</gallery>
</gallery>


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     File:Pentobarbital.png|link=Pentobarbital|[[Pentobarbital]]
     File:Pentobarbital.png|link=Pentobarbital|[[Pentobarbital]]
     File:Secobarbital.png|link=Secobarbital|[[Secobarbital]]
     File:Secobarbital.png|link=Secobarbital|[[Secobarbital]]
</gallery>


<gallery caption="[[Quinazolinone|Quinazolinones]]">
    File:Methaqualone.png|link=Methaqualone|[[Methaqualone]]
    File:Diproqualone.png|link=Diproqualone|[[Diproqualone]]
    File:Etaqualone.png|link=Etaqualone|[[Etaqualone]]
</gallery>
</gallery>
<gallery caption="[[GABA-A receptor|GABAergics]]">
<gallery caption="[[GABA-A receptor|GABAergics]]">
     File:1-4-Butanediol.png|link=1,4-Butanediol|[[1,4-Butanediol]]
     File:1-4-Butanediol.png|link=1,4-Butanediol|[[1,4-Butanediol]]
Line 328: Line 367:
     File:GBL.png|link=GBL|[[GBL]]
     File:GBL.png|link=GBL|[[GBL]]
     File:GHB.png|link=GHB|[[GHB]]
     File:GHB.png|link=GHB|[[GHB]]
    File:150px-Tert-pentyl-alcohol-2D-skeletal.png|link=2-methyl-2-butanol|[[2-methyl-2-butanol]]
     File:Phenibut.png|link=Phenibut|[[Phenibut]]
     File:Phenibut.png|link=Phenibut|[[Phenibut]]
     File:Pregabalin.png|link=Pregabalin|[[Pregabalin]]
     File:Pregabalin.png|link=Pregabalin|[[Pregabalin]]
</gallery>
<gallery caption="Others">
     File:Ethanol.png|link=Alcohol|[[Alcohol]] (Ethanol)
     File:Ethanol.png|link=Alcohol|[[Alcohol]] (Ethanol)
</gallery>
</gallery>
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     File:Quetiapine.png|link=Quetiapine|[[Quetiapine]]
     File:Quetiapine.png|link=Quetiapine|[[Quetiapine]]
</gallery>
</gallery>


==[[Nootropic]]s==
==[[Nootropic]]s==
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===[[Acetylcholine|Cholinergics]]===
===[[Acetylcholine|Cholinergics]]===
<gallery>
<gallery>
File:Piracetam.png|link=Piracetam|[[Piracetam]]
    File:Piracetam.png|link=Piracetam|[[Piracetam]]
File:Aniracetam.png|link=Aniracetam|[[Aniracetam]]
    File:Aniracetam.png|link=Aniracetam|[[Aniracetam]]
File:Phenylpiracetam.png|link=Phenylpiracetam|[[Phenylpiracetam]]
    File:Phenylpiracetam.png|link=Phenylpiracetam|[[Phenylpiracetam]]
File:Noopept.png|link=Noopept|[[Noopept]]
    File:Noopept.png|link=Noopept|[[Noopept]]
</gallery>
 
===[[Acetylcholine|Choline Sources]]===
<gallery>
    File:Choline with Variable Counteranion X.png|link=Choline|[[Choline]]
    File:Choline Bitartrate.png|link=Choline bitartrate|[[Choline bitartrate]]
    File:Alpha-GPC.png|link=Alpha-GPC|[[Alpha-GPC]]
    File:CDP-Choline.png|link=CDP-Choline|[[CDP-Choline]]
</gallery>
</gallery>


===[[Eugeroic|Eugeroics]]===
===[[Eugeroic|Eugeroics]]===
<gallery>
<gallery>
File:Modafinil2.png|link=Modafinil|[[Modafinil]]
    File:Modafinil.svg|link=Modafinil|[[Modafinil]]
File:Armodafinil.png|link=Armodafinil|[[Armodafinil]]
    File:Armodafinil.svg|link=Armodafinil|[[Armodafinil]]
File:Adrafinil.png|link=Adrafinil|[[Adrafinil]]
    File:Adrafinil.svg|link=Adrafinil|[[Adrafinil]]
File:Hydrafinil.png|link=Hydrafinil|[[Hydrafinil (9-Fluorenol)]]
    File:N-methylbisfluoromodafinil.svg|link=N-Methylbisfluoromodafinil|[[N-Methylbisfluoromodafinil]]
    File:Hydrafinil.png|link=Hydrafinil|[[Hydrafinil]] (9-Fluorenol)
</gallery>
</gallery>


===Others===
===Others===
<gallery>
<gallery>
File:L-Theanine.png|link=L-Theanine|[[L-Theanine]]
    File:L-Theanine.png|link=L-Theanine|[[L-Theanine]]
File:Tianeptine.png|link=Tianeptine|[[Tianeptine]]
    File:Sulbutiamine.png|link=Sulbutiamine|[[Sulbutiamine]]
File:Withanolide.png|link=Withanolide|[[Withanolide]]     
    File:Acetylcarnitine.png|link=Acetylcarnitine|[[Acetylcarnitine]] (ALCAR)
File:Bacoside.png|link=Bacoside|[[Bacoside]]
    File:Tianeptine.png|link=Tianeptine|[[Tianeptine]]
    File:Withanolide.png|link=Withanolide|[[Withanolide]]     
    File:Bacoside.png|link=Bacoside|[[Bacoside]]
</gallery>
</gallery>


=References=
=References=
References for molecular structures can be found all over the internet:
References for molecular structures can be found all over the internet:
*[http://isomerdesign.com/Cdsa/posterGateway.php IsomerDesign.com - Controlled Drugs and Substances Act] - A comprehensive list of scheduled molecular structures
*[http://isomerdesign.com/Cdsa/posterGateway.php Isomer Design - Controlled Drugs and Substances Act] - A comprehensive list of scheduled molecular structures
*[http://www.google.com Google] - Google image search is an effective way of confirming the molecular structure of a specific chemical.
*[http://www.google.com Google] - Google image search is an effective way of confirming the molecular structure of a specific chemical.

Latest revision as of 09:55, 15 September 2022

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

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.

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.

Gallery

Monoamines and biogenic amines

Other

Miscellaneous


Others

References

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