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    The molecule of the day is: Oxygen

    Molecular oxygen, O2, is love to me, and it is a substance that life must treat in a delicate way. For most multicellular organisms, it is an absolute requirement for continuing survival. In too great a portion it is too reactive and toxic, but if there is not enough, the organism suffers hypoxia and survival is threatened. This is clearly true for humans, as anyone knows who hyperventilates or holds their breathe too long. Experimentation beyond that point may possibly be unheathful. Cells use clever chemistry to capture the energy in the O2 double bond and oxidize nutrients for energy as well. It is clever because the dangers posed by molecular oxygen are minimized in various ways, so that the cell can survive in conditions where oxygen levels vary somewhat. Oxygen is clearly an essential molecule and indispensible for most of us. Most agree that it looks fine in red, as shown at right ;-}. There are some interesting examples of oxygen chemistry in the gallery, so be sure to check it out.

    Oxygen related molecules gallery and structural archive

    other names: 1338-93-8 14797-70-7 7782-44-7 80217-98-7 80937-33-3 CCRIS 1228 EINECS 231-956-9 HSDB 5054 Hyperoxia LOX Liquid oxygen Molecular oxygen OXYGEN Oxigeno [Spanish] Oxygen (liquid) Oxygen molecule Oxygen, compressed [UN1072] [Nonflammable gas] Oxygen, liquified Oxygen, refrigerated liquid (cryogenic liquid) [UN1073] [Nonflammable gas] Oxygen-16 Oxygene [French] Oxygenium Oxygenium medicinale Pure oxygen Sauerstoff UN1072 UN1073


    related molecule names:
    10-Deoxygeniposide tetraacetate C11664 10-Deoxygeniposidic acid C11672 1156-78-1 2',4',5,7-Tetrahydroxyisoflavone 2'-Hydroxygenistein C12134 7782-44-7 C00007 O2 Oxygen 3-Oxo acid 3-Oxy acid 3-Oxygen acid C01656 1-Bromohenicosafluorodecane 307-43-7 AF0144 Component of AF0144 Component of Oxygent EINECS 206-201-1 Oxygent PERFLUORODECYL BROMIDE Perflubrodec Perflubrodec [INN] 1-Bromoheptadecafluorooctane 1-Bromoperfluorooctane 423-55-2 EINECS 207-028-4 Imagent GI LiquiVent Long's compound OCTANE, 1-BROMOHEPTADECAFLUORO- Octane, 1-bromo-1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-heptadecafluoro- Oxygent Perflubron Perflubron [USAN:INN] Perfluoroctyl bromide Perfluorooctyl bromide 961-22-8 AZINPHOSMETHYL OXYGEN ANALOG Azinphosmethyl oxon Phosphorothioic acid, O,O-dimethyl S-((4-oxo-1,2,3-benzotriazin-3(4H)-yl)methyl) ester 5598-15-2 BRN 1545755 CCRIS 7774 Chloropyrifos oxon Chloropyrifos oxygen analog Chlorpyrifos oxon Diethyl-2,5,6-trichloro-2-pyridinol Diethyl-3,5,6-trichloro-2-pyridyl phosphate Dursban oxygen analog Dursbanoxon Fospirate-ethyl O,O-Diethyl O-3,5,6-trichloro-2-pyridyl phosphate PHOSPHORIC ACID, DIETHYL 3,5,6-TRICHLORO-2-PYRIDYL ESTER Phosphoric acid, diethyl 3,5,6-trichloro-2-pyridinyl ester (9CI) 1338-93-8 14797-70-7 7782-44-7 80217-98-7 80937-33-3 CCRIS 1228 EINECS 231-956-9 HSDB 5054 Hyperoxia LOX Liquid oxygen Molecular oxygen OXYGEN Oxigeno [Spanish] Oxygen (liquid) Oxygen molecule Oxygen, compressed [UN1072] [Nonflammable gas] Oxygen, liquified Oxygen, refrigerated liquid (cryogenic liquid) [UN1073] [Nonflammable gas] Oxygen-16 Oxygene [French] Oxygenium Oxygenium medicinale Pure oxygen Sauerstoff UN1072 UN1073 7783-41-7 Difluorine monoxide Difluorure d'oxygene [French] Difluoruro de oxigeno [Spanish] EINECS 231-996-7 FLUORINE MONOXIDE Fluorine (di-)oxide Fluorine oxide HSDB 2525 Oxydifluoride Oxygen difluoride Oxygen difluoride, compressed [UN2190] [Poison gas] Oxygen fluoride Oxygen fluoride (OF2) UN2190 10028-15-6 74087-86-8 CCRIS 4503 EINECS 233-069-2 HSDB 717 OZONE Oxygen, mol (O3) Ozon [Polish] Ozone heavy work Ozone heavy, moderate, or light workloads (<2 hours) Ozone light work Ozone moderate work Triatomic oxygen 14816-17-2 3,5-Dioxa-6-aza-4-phosphaoct-6-ene-8-nitrile, 4-ethoxy-7-phenyl-, 4-oxide (9CI) Bayer 10050 GLYOXYLONITRILE, PHENYL-, OXIME, DIETHYL PHOSPHATE NSC 132981 Phenylglyoxylonitrile oxime diethyl phosphate Phoxim, O,O-diethyl phosphate Phoxim, oxygen analog 25006-32-0 AI3-27872 BRN 2947938 Leptophos OA Leptophos oxon Leptophos oxygen analog Leptophosoxon Leptophoxon PHOSPHONIC ACID, PHENYL-, 4-BROMO-2,5-DICHLOROPHENYL METHYL ESTER Phenylphosphonic acid 4-bromo-2,5-dichlorophenyl methyl ester Phosvel oxon Velsicol VCS O-analog 92047-76-2 Ancloximex Animexan Oxilium Oxocebron Oxoferin Oxomexan Oxovasin Oxovir Oxoviron Ryoxon TCDO Tetrachlorodecaoxide Tetrachlorodecaoxygen WF 10 8063-77-2 CARBON DIOXIDE MIXED WITH OXYGEN Carbogen Carbon dioxide and oxygen mixtures, compressed [UN1014] [Nonflammable gas] UN1014 2600-69-3 4-01-00-03090 (Beilstein Handbook Reference) BRN 1708515 Diethyl S-eththiomethyl thiophosphate O,O-Diethyl S-eththiomethyl phosphorothioate Phorate oxygen analog Phoratoxon Phosphorothioic acid, O,O-diethyl S-(ethylthio)methyl ester 3983-45-7 Dimethyl (2,4,5-trichlorophenyl) phosphate Dimethyl 2,4,5-trichlorophenyl phosphate Dowco 101 Fenchlorphos-oxon NSC133018 O,O-Dimethyl O-2,4,5-trichlorophenyl phosphate Phosphoric acid, dimethyl 2,4,5-trichlorophenyl ester Ronnel oxon Ronnel oxygen analog Ronnoxon Ronoxon WLN: GR BG DG EOPO&O1&O1 6552-21-2 Dasanit O Dasanit O analog Dasanit O-analog Dasanit oxygen analog NSC133045 O,O-Diethyl O-[p-(methylsulfinyl)phenyl] phosphate Phosphoric acid, diethyl 4-(methylsulfinyl)phenyl ester Phosphoric acid, diethyl p-(methylsulfinyl)phenyl ester WLN: OS1&R DOPO&O2&O2 92047-76-2 AIDS-004703 AIDS004703 Oxoferin (TM) TCDO Tetrachlorodecaoxygen anion complex WF10 3983-45-7 4-06-00-00993 (Beilstein Handbook Reference) AI3-24682 BRN 1987935 Dimethyl 2,4,5-trichlorophenyl phosphate Dowco 101 EINECS 223-624-7 Fenchlorphos-oxon NSC 133018 Phosphoric acid, dimethyl 2,4,5-trichlorophenyl ester Ronnel oxon Ronnel oxygen analog Ronnoxon Ronoxon 6552-21-2 BRN 2138839 Dasanit O Dasanit O analog Dasanit O-analog Dasanit oxygen analog NSC 133045 O,O-Diethyl O-(p-(methylsulfinyl)phenyl) phosphate Phosphoric acid, diethyl 4-(methylsulfenyl)phenyl ester Phosphoric acid, diethyl 4-(methylsulfinyl)phenyl ester (9CI) Phosphoric acid, diethyl p-(methylsulfinyl)phenyl ester (Dioxygen)bis(triphenylphosphine)platinum 15614-67-2 EINECS 239-692-6 17650-76-9 BAY 62944 BRN 4501136 Dicapthon oxygen analogue Dicapthon-oxon Dicapthoxon Dimethyl 2-chloro-4-nitrophenyl phosphate Phosphoric acid, dimethyl 2-chloro-4-nitrophenyl ester 2-Hydroxygentamicin C(sub 1) 60609-40-7 60802-56-4 BRN 1333493 D-Streptamine, O-2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)-alpha-D-ribo-heptopyranosyl-(1-4)-O-(3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl-(1-6))- Gentamicin C1, 2-hydroxy- 12185-07-8 58238-79-2 Dioxygen Dioxygenyl ion 54510-89-3 Anesoxyn-50 Entonox Eutonal Nitralgin Nitrogen oxide (N2O), mixt. with oxygen Nitronox 37291-87-5 GHM 8 Gas hypoxic mixture (nitrogen with oxygen) Ghm 10 Hypoxic gas mixture Nitrogen, mixt. with oxygen Nitrox 25476-48-6 AI3-24965 Demeton-O-methyl sulfone Dimethyl 2-ethsulfonylethylthionophosphate Disulfoton oxygen analog sulfone Methylsystox sulfone O,O-Dimethyl O-(2-ethylsulfonylethyl)phosphorothioate Phosphorothioic acid, (2-(ethylsulfonyl)ethyl) O,O-dimethyl ester (6CI) Phosphorothioic acid, O,O-dimethyl O-(2-(ethylsulfonyl)ethyl) ester Phosphorothioic acid, O-(2-(ethylsulfonyl)ethyl) O,O-dimethyl ester (8CI,9CI) Phosphorothioic acid, S-(2-(ethylsulfonyl)ethyl) O,O-dimethyl ester 7783-44-0 Fluorine dioxide Oxygen fluoride ((O2)F2) Perfluoroperoxide 58933-55-4 Heliox, hyperbaric Heliox,hyperbaric Helium, mixt. with oxygen heliox 15499-23-7 Dioxygen monofluoride 20243-59-8 4H-1-Benzopyran-4-one, 2-(3,4-dihydroxyphenyl)-5-hydroxy-7-methoxy- Hydroxygenkwanin 22756-17-8 BRN 2146189 Ethion dioxon Ethion oxygen analog Ethyl methylene phosphorothioate ((EtO)4(CH2S2)P2O2) PO-Ethion Phosphorothioic acid, S,S'-methylene O,O,O',O'-tetraethyl ester 12061-70-0 Oxygen fluoride 27270-89-9 7-Oxabicyclo(4.1.0)hept-3-ene-2,5-dione, 3-(hydroxymethyl)-, (1R)- Epoxygentisylquinone Phyllostine 89210-11-7 Helium, mixt. with nitrogen and oxygen Trimix 84128-91-6 Carbon dioxide, mixt. with nitrogen and oxygen Pneumoxide 13539-27-0 3-(4-Hydroxyphenyl)-5,7,8-trihydroxy-4H-1-benzopyran-4-one 4H-1-Benzopyran-4-one, 3-(4-hydroxyphenyl)-5,7,8-trihydroxy- 5-18-05-00314 (Beilstein Handbook Reference) 8-Hydroxygenistein BRN 1294503 Isoflavone, 4',5,7,8-tetrahydroxy-

    pdb file:167037.pdb
    CAS: 1338-93-8

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    Molecule News

    updated Thu Sep 11 22:33:51 EDT 2008

    We continue to get encouragment to provide coordinate files with improved geometry, although this is a computationally intensive task which is down the road still. Meanwhile, a few supurb 3-dimensional structures are already found in the archive, and two of them have been featured in the right sidebar today. If you rummage around in the MOD galleries, you are likely to find more 3D coordinate files, as well as some very interesting 2D representations! In our opinion, many of the most interesting molecules have planar geometry, so that the current files are quite useful. In due course, we plan to provide a comprehensive collection of coordinate files with good stereochemical geometry, all in the selfsame spirit of free and open source software and public access. We welcome any and all input.

    updated Wed Sep 10 20:28:49 EDT 2008

    Our new directory style was featured in a the right sidebar of the Jasmone MOD page today. Just click the directory link from the top page or in any of the recent galleries to view this new feature. These pages typically include links to the source databases, which often have chemical diagrams or useful additional information about the molecules. A smiley code is currently featured at the bottom of each page. Smile.

    updated Thu Sep 4 22:28:57 EDT 2008

    Added quick navigation links to the left side bar. The site has reached 111 GB, and a massive backup is underway. We are still just getting started.

    updated Thu Sep 4 13:30:20 EDT 2008

    Added developer links to the left side bar.

    updated Wed Sep 3 12:05:13 EDT 2008

    I have automated the process to make molecule galleries, which I am finding very useful to my research, so I thought that I would share the opportunity and take requests. It is quick and easy. I did a bisphenol search today, and as I expected, the search turned up a few stilbenes, which is the same molecular family as resveratrol. Strikingly, Bisphenol A is a noted teratogen, which shows that care must be taken when using such molecules during pregnancy, nursing, and development. Here is a link to the bisphenol gallery.

    If you would find it useful, I am definitely interested in taking requests for molecule galleries. Just send me the name of your favorite molecule. As you may be able to tell, we have access for galleries to about 1% or 0.5 million structures, in the total archive thus far, but it is already quite useful. The automated jobs are underway to fill in the rest. The next milestone is the capability to index and make galleries for the remaining millions of molecules for which we have pdb files already, which would be 5-10% complete. Any comments or suggestions are also welcome.

    updated Tue Sep 2 14:10:15 EDT 2008

    A terminal screenshot has been added to the right sidebar, in order to show the kind of code that is being used to generate the Molecules directory indices. All inquiries and suggestions are welcome.

    updated Fri Aug 29 14:39:14 EDT 2008

    Reaction to our website has been quite positive and encouraging, but people are anxious to see structures with improved stereochemistry. We have received many suggestions about how to make that happen faster. For the time being, we are experiencing the best structure viewing results with RasMOL. Name extraction and structure file linking jobs are underway, which is an indication that we are still in a preliminary phase. Google spiders more almost everyday, and past experience indicates that the search capability will become very useful indeed! Here is some secret mumbo jumbo. I'm afraid that my Japanese or Korean is broken at best ;-}. Enjoy!

    updated Wed Aug 27 21:38:32 EDT 2008

    An RSS News Feed has been added to the right side bar.

    updated Tue Aug 26 19:27:29 EDT 2008

    Several new indices have been added to our sidebar, notably; current index by name, and gallery by name. These are large indices, but also vastly incomplete, and work is underway to improve them. A list of bloggers who have mentioned the site, with links in their blogs, is now in the front sidebar, although only one is known thus far. Due to the vastness of the scale, many of these things will be divided out and buried a little deeper eventually, but they can be showcased now, and they are a good survey.

    updated Tue Aug 19 19:45:09 EDT 2008

    Some facts: The Molecules website contains more than 4 million small molecule structure files in pdb format, and molecular graphics representations. About 50 million molecules are still in the pipe, and they are expected to appear here over the course of the next few weeks and months. The pdb format is readable by common FOSS molecule viewer software, such as RasMol and PyMOL. In due course, we plan to provide high quality structures via energy minimization refinement, and additional resources. is founded in the spirit of free software, open source, and public access. It is hoped that access to these files will be a wonderful community resource for science education, research, and entertainment as well. We are looking for investment, funding, or sponsorship in order to expedite and expand this work, and lead the field, with an eye towards an advanced, complete, synthetic, structural, and informatical bioorganome. Meanwhile, the site is already an exceptional lab resource, and molecular catalog, providing the means and building blocks towards additional novel structures. We aim to be the best.

    The structural biology, protein crystallography, and molecular graphics talent that is building the Molecules archive is available to work for you in a contract or consulting arrangement. Wide-ranging expertise is available. is built entirely with FOSS, free and open source software, GNU-Darwin OS, and it is under the aegis of The GNU-Darwin Distribution. Here is a link to the Distribution résumé. Our founder is an X-ray laboratory admin for the Department of Biophysics and Biophysical Chemistry of Johns Hopkins University School of Medicine. You can also read his CV. We would like to build a community around this website, and we are looking for volunteers and collaborators to help. Regarding any aspect of the work of this site, please feel free to contact us,, with gdmolecules in the subject line. Cheers!

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