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    The molecule of the day is: Carbon Dioxide

    Like oxygen, Carbon dioxide (CO2) is toxic to most living systems above certain concentrations, but it is also essential to life. As an end product of our metabolism of oxygen and carbon chains, carbon dioxide is a product of a very large number of diverse enzymatic reactions, which demonstrates the elegance of our systems for harvesting the energy from the carbon bond. Likewise, in a similarly elegant system of reactions, plants utilize this molecule to produce the food structures that we eat. I find it interesting that the juxtaposition of a carbon atom within molecular oxygen renders a raw material of metabolism into an end product. The two molecules are not entirely dissimilar chemically. The representation at right illustrates a problem with the current iteration of our website. Carbon dioxide has co-linear carbon-oxygen bonds opposed at an angle of 180 degrees. Readers of this site may remember the similar geometry of silicon dioxide. I have included one representation in ball and sticks with the correct linear bond angle. The geometry of some of our molecules is simply wrong, and it is something that we have in our sights for future development. Finally, it should be noted that carbonated beverages sometimes derive their fizz from this molecule. This should obviously not be interpreted as an endorsement.

    Carbon Dioxide related molecules gallery and structural archive

    other names: 124-38-9 C00011 CO2 Carbon dioxide


    related molecule names:
    1(2H)-Quinolinecarboxylic acid, 2-ethoxy-, ethyl ester 16357-59-8 2-Ethoxy-1(2H)-quinolinecarboxylic acid, ethyl ester BC 681 EEDQ NSC147831 WLN: T66 BN CHJ BVO2 CO2 1,2,4-Thiadiazole, 5-ethoxy-3-(trichloromethyl)- 2593-15-9 3-(Trichloromethyl)-5-ethoxy-1,2,4-thiadiazole 5-Aethoxy-3-trichlormethyl-1,2,4-thiadiazol 5-Ethoxy-3-(trichloromethyl)-1,2,4-thiadiazole Aaterra Banrot ETMT Echlomezol Echlomezole Etcmtb Ethazol Ethazole Ethazole (fungicide) Etridiazol Etridiazole Koban NSC524929 OM 2424 OM 2425 Olin Mathieson 2,424 Terrachlor-super X Terracoat Terracoat L21 Terrazole Truban WLN: T5NS DNJ CO2 EXGGG NSC722780 trans-[Pt(II)(CH3CO2)2(thiazole)2] trans-bis(acetato)bis(thiazole)platinum(II) NSC722781 trans-[Pt(II)(CH3CO2)2(NH3)(pyridine)] 148-18-5 Carbamic acid, diethyldithio-, sodium salt Carbamodithioic acid, diethyl-, sodium salt Cupral DDC DEDC DEDK DTC Diethyl dithiocarbamate sodium salt Diethyl sodium dithiocarbamate Diethylcarbamodithioic acid, sodium salt Diethyldithiocarbamate, sodium Diethyldithiocarbamic acid sodium salt Diethyldithiocarbamic acid, sodium Diethyldithiocarbamic acid, sodium salt Dithiocarb Dithiocarbamate GS 694A N,N-Diethyldithiocarbamic acid, sodium salt NCI Co2835 NSC4857 Sodium DEDT Sodium N,N-diethyldithiocarbamate Sodium N,N-diethyldithiocarbmate Sodium diethylaminocarbodithioate Sodium diethylaminodithioate Sodium diethyldithiocarbamaate Sodium diethyldithiocarbamate Sodium salt of N,N-diethyldithiocarbamic acid Thiocarb Usaf ek-2596 WLN: SUYSHN2 & 2 &-NA- 148-18-5 Carbamic acid, diethyldithio-, sodium salt Carbamodithioic acid, diethyl-, sodium salt DDC DEDC DEDK DTC Diethyl dithiocarbamate sodium salt Diethyl sodium dithiocarbamate Diethylcarbamodithioic acid, sodium salt Diethyldithiocarbamate, sodium Diethyldithiocarbamic acid, sodium Diethyldithiocarbamic acid, sodium salt Dithiocarb Dithiocarbamate GS 694A NCI Co2835 NSC38583 Sodium DEDT Sodium N,N-diethyldithiocarbamate Sodium N,N-diethyldithiocarbmate Sodium diethylaminocarbodithioate Sodium diethyldithiocarbamaate Sodium diethyldithiocarbamate Sodium salt of N,N-diethyldithiocarbamic acid Thiocarb Usaf ek-2596 WLN: SUYSHN2 & 2 &-NA- 811-54-1 Formic acid, lead(2+) salt LEAD FORMATE Lead diformate Lead formate (Pb(HCO2)2) Lead formate Pb(O2CH)2 Lead(2+) formate NSC112233 1600-27-7 Acetic acid, mercury(2+) salt Diacetoxymercury Mercuriacetate Mercuric acetate Mercuric diacetate Mercury acetate Mercury acetate (Hg(CH3CO2)2) Mercury diacetate Mercury(2+) acetate Mercury(II) acetate Mercuryl acetate NSC215199 WLN: QV1 &QV1 &-HG- 4-Hydroxy-2,6-bis(phenylmethyl)-N,N'-bis[2-[(2-quinolinylcarbony)amino]cyclohexy l]heptanediamide, [1-S-[1.alpha.[2S*,6S*,7(1R*,2R*)]2.beta.]] AIDS-005962 AIDS005962 HepdiCO2N, Quin, c-Hex deriv. 4-Hydroxy-2,6-bis(phenylmethyl)-N,N'-bis[2-[(2-pyridinylcarbonyl)amino]cyclohexy l]heptanediamide, [1-S-[1.alpha.[2S*,6S*,7(1R*,2R*)]2.beta.]] AIDS-005963 AIDS005963 HepdiCO2N, Pyrid, c-Hex deriv. 4-Hydroxy-2,6-bis(phenylmethyl)-N,N'-bis[2-[(3-pyridinylcarbonyl)amino]cyclohexy l]heptanediamide, [1-S-[1.alpha.[2S*,6*,7(1R*,2R*)]2.beta.]] AIDS-005964 AIDS005964 HepdiCO2N Pyrid c-Hex deriv. 4-Hydroxy-2,6-bis(phenylmethyl)-N,N'-bis[2-[(4-pyridinylcarbonyl)amino]cyclohexy l]heptanediamide, [1-S-[1.alpha.[2S*,6S*,7(1R*,2R*)]2.beta.]] AIDS-005965 AIDS005965 HepdiCO2N Pyrid c-Hex deriv. 3PyrrCO2H 1,4diPh deriv. 4-(4-Chlorophenyl)-1-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009517 AIDS009517 1,4-Bis(4-chlorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009518 AIDS009518 3PyrrCO2H 1,4diPh deriv. 4-(4-Chlorophenyl)-1-(4-fluorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009519 AIDS009519 1-(4-Bromophenyl)-4-(4-chlorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009520 AIDS009520 3PyrrCO2H 1,4diPh deriv. 4-(4-Bromophenyl)-1-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009521 AIDS009521 3PyrrCO2H 1,4diPh deriv. 4-(4-Bromophenyl)-1-(4-chlorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009522 AIDS009522 3PyrrCO2H 1,4diPh deriv. 4-(4-Bromophenyl)-1-(4-fluorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009523 AIDS009523 1,4-Bis(4-bromophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009524 AIDS009524 3PyrrCO2H 1,4-diPh deriv. 4-(4-Fluorophenyl)-1-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid AIDS-009525 AIDS009525 1-(4-Chlorophenyl)-4-(4-fluorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009526 AIDS009526 1,4-Bis(4-fluorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009527 AIDS009527 1-(4-Bromophenyl)-4-(4-fluorophenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H diPh deriv. AIDS-009528 AIDS009528 1,4-Bis(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009529 AIDS009529 1-(4-Chlorophenyl)-4-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009530 AIDS009530 1-(4-Fluorophenyl)-4-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4diPh deriv. AIDS-009531 AIDS009531 1-(4-Bromophenyl)-4-(4-methylphenyl)-2-methyl-1H-pyrrole-3-carboxylic acid 3PyrrCO2H 1,4-diPh deriv. AIDS-009532 AIDS009532 AIDS-028258 AIDS028258 N,N',N-Tris(3-carboxy-4-hydroxy-5-sulfonyloxy)-1,3,5-benzenetrisulfonamide Ph(SO2N)3 2OH-3SO3-PhCO2H deriv. 2',3'-Dideoxy-2',3'-dideoxythymidine-5'-[phenyl-(benzyl,-L-alaninyl)]phosphate 5'-(PhPhCO2Ala)d4TMP AIDS-031531 AIDS031531 Phenyl benzyl-L-alaninyl-d4TMP derivative, So730 (5S)-5-((2S)-2-{(2S)-2-[(2S)-2-((2S)-2-Amino-3-carboxypropanoylamino)-4-carboxyb utanoylamino]-3,3-diphenylpropanoylamino}-3-carboxypropanoylamino)-3-amino-3-(3, 3-difluoropropyl)-6-cyclohexyl-2,4-dioxohexanoic acid AIDS-105129 AIDS105129 Ac-D-E-Dif-D-Cha-Dfab-COCO2H (S)-NHCO2OMe-Rapamycin AIDS-121921 AIDS121921 Rapamcyin deriv 367-64-6 Butyl trifluoroacetate CF3CO2(n-C4H9) EINECS 206-699-0 (Ch3)3co2 3395-62-8 Ethyldioxy, 1,1-dimethyl- tert-Butyldioxy tert-Butylperoxy (2-Carboxy-2-oxoethyl)hydroxyphosphinecarboxylic acid oxide 144705-36-2 CO2HPPA Carboxyphosphinopyruvic acid Phosphinecarboxylic acid, (2-carboxy-2-oxoethyl)hydroxy-, 1-oxide, trisodium salt Trisodium carboxyphosphinopyruvate 129118-73-6 Bmaa-alpha-nco2 L-Alanine, N-carboxy-3-(methylamino)- N-Carboxy-3-(methylamino)-L-alanine alpha-N-Carboxy-beta-N-methylaminoalanine 129118-74-7 3-(Carboxymethylamino)-L-alanine Bmaa-beta-nco2 L-Alanine, 3-(carboxymethylamino)- beta-(N-Carboxy-N-methyl)aminoalanine 132639-68-0 17-Ethoxycarbonyloxy-3-oxoandrost-4-ene-17-carbonitrile 17alpha-Ethoxycarbonyloxy-3-oxoandrost-4-ene-17-carbonitrile EtOCO2-OACN 4-CO2H-2-Nbba 4-Carboxy-2-nitrobenzeneboronic acid 85107-54-6

    pdb file:3260.pdb
    CAS: 124-38-9

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    Prized Arginine!

    directory: 587105

    Cysteine with hydrogens

    directory: 588600

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    Molecule News

    updated Wed Sep 17 23:56:32 EDT 2008

    Added Molscript graphics and MOD desktop image to the right sidebar. The theme is infinite carbon chain. The code is in infrastructure. The other main molecular graphics programs in use at this time are RasMol, Rester3D, PyMOL, and PovChem. The viewer is xzgv, and ImageMagick for touch up; mainly mogrify and convert. Please feel free to send any questions along.

    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!