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    The molecule of the day is: Vanillin

    Vanillin is the key flavor producing component of natural vanilla bean, and it is able to produce a strong vanilla flavor by itself. It is a member of the family of phenolic molecules, which includes polyphenols; such as resveratrol, flavanoids; such as anthocyanins, aspirin, and molecules of culinary interest such as; piperidine from black pepper, and capsaicin from hot peppers. It is very likely that vanillin is able to produce effects similar to health promoting benefits of these other molecules, but it is so typically served drenched with sugar and milk fats, that the health benefits are likely nullified. According to Wikipedia, synthetic vanillin is made from wood pulp, lignin, which is actually another good sign. It is probably worth looking into whether vanilla extract produces significant health benefits. It should be noted that the aldehyde moiety increases the reactivity of this molecule with respect to the other phenolic substances mentioned, so that it might form undesirable adducts, or even breaks in the DNA backbone. This again is another topic worth further investigation, although the effect is likely ameliorated by the oxygenase enzymes in the body. At any rate, it is probably not a bad idea to avoid vanilla until these things become settled, especially considering the fact that it is usually served in a high calorie snack of low nutritional value.

    Vanilla related molecules gallery and structural archive

    other names: 121-33-5 2-Methoxy-4-formylphenol 3-Methoxy-4-hydroxybenzaldehyde 4-Formyl-2-methoxyphenol 4-Hydroxy-3-methoxybenzaldehyde 4-Hydroxy-5-methoxybenzaldehyde 4-Hydroxy-m-anisaldehyde Benzaldehyde, 4-hydroxy-3-methoxy- Lioxin NSC15351 Protocatechualdehyde, methyl- VANILLIN Vanilla Vanillaldehyde Vanillic aldehyde WLN: VHR DQ CO1 Zimco m-Anisaldehyde, 4-hydroxy- p-Hydroxy-m-methoxybenzaldehyde

    SMILES: O(C)c1cc(C=O)ccc1O

    related molecule names:
    121-33-5 4-Hydroxy-3-methoxy-benzaldehyde 4-Hydroxy-3-methoxybenzaldehyde C00755 Vanillaldehyde Vanillin 306-08-1 C05582 Homovanillate Homovanillic acid 121-34-6 4-Hydroxy-3-methoxybenzoate 4-Hydroxy-3-methoxybenzoic acid C06672 Vanillate 121-32-4 3-Ethoxy-4-hydroxybenzaldehyde 4-Hydroxy-3-ethoxybenzaldehyde Benzaldehyde, 3-ethoxy-4-hydroxy- Bourbonal Ethavan Ethovan Ethyl Vanillin Ethylprotal Ethylvanillin NSC1803 Protocatechuic aldehyde ethyl ether Quantrovanil Vanilal Vanillal Vanillin, ethyl- Vanirom WLN: VHR DQ CO2 3-Methoxy-4-hydroxybenzoic acid, ethyl ester 4-Hydroxy-3-methoxybenzoic acid ethyl ester 617-05-0 Benzoic acid, 4-hydroxy-3-methoxy-, ethyl ester Ethyl 4-hydroxy-3-methoxybenzoate Ethyl vanillate NSC8513 Vanillic acid, ethyl ester WLN: 2OVR DQ CO1 m-Anisic acid, 4-hydroxy-, ethyl ester 121-33-5 2-Methoxy-4-formylphenol 3-Methoxy-4-hydroxybenzaldehyde 4-Formyl-2-methoxyphenol 4-Hydroxy-3-methoxybenzaldehyde 4-Hydroxy-5-methoxybenzaldehyde 4-Hydroxy-m-anisaldehyde Benzaldehyde, Vanilla Vanillaldehyde Vanillic aldehyde WLN: VHR DQ CO1 Zimco m-Anisaldehyde, 4-hydroxy- p-Hydroxy-m-methoxybenzaldehyde (4-Hydroxy-3-methoxyphenyl)acetic acid 3-Methoxy-4-hydroxyphenylacetic acid 306-08-1 4-Hydroxy-3-methoxybenzeneacetic acid 4-Hydroxy-3-methoxyphenylacetic acid Acetic acid, (4-hydroxy-3-methoxyphenyl)- Benzeneacetic acid, 4-hydroxy-3-methoxy- HMPA HVA Homovanillic acid NSC16682 Vanillacetic acid 2,6-Bis(4-hydroxy-3-methoxybenzylidene)cyclohexanone 2,6-Divanillidenecyclohexanone 2,6-Divanillylidenecyclohexanone 579-23-7 Beveno Curcumoid Cyclohexanone, 2,6-bis[(4-hydroxy-3-methoxyphenyl)methylene]- Cyclohexanone, 2,6-divanillylidene- Cyclohexanone, 2,6-vanillylidene- Cyclovalone Cycvalon Cyqualon DVC Divanil Divanillalcyclohexanone Divanon Flavugal NSC26727 Tsikvalon Vanilone WLN: L6YVYTJ AU1R DQ CO1& CU1R DQ CO1 149-17-7 4-Pyridinecarboxylic acid, [(4-hydroxy-3-methoxyphenyl)methylene]hydrazide Ftivazid Ftivazide Isonicotinic acid vanillylidenehydrazide Isonicotinic acid, vanillylidenehydrazide NSC31725 Phthivazid Phthivazide Vanicid Vanillaberon Vanizide 121-33-5 2-Methoxy-4-formylphenol 3-Methoxy-4-hydroxybenzaldehyde 4-Formyl-2-methoxyphenol 4-Hydroxy-3-methoxybenzaldehyde 4-Hydroxy-5-methoxybenzaldehyde 4-Hydroxy-m-anisaldehyde Benzaldehyde, 4-hydroxy-3-methoxy- Lioxin NSC48383 Protocatechualdehyde, methyl- VANILLIN Vanilla Vanillaldehyde Vanillic aldehyde WLN: VHR DQ CO1 Zimco m-Anisaldehyde, 4-hydroxy- p-Hydroxy-m-methoxybenzaldehyde 121-32-4 3-Ethoxy-4-hydroxybenzaldehyde 4-Hydroxy-3-ethoxybenzaldehyde Benzaldehyde, 3-ethoxy-4-hydroxy- Bourbonal Ethavan Ethovan Ethyl Vanillin Ethylprotal Ethylvanillin NSC67240 Protocatechuic aldehyde ethyl ether Quantrovanil Vanilal Vanillal Vanillin, ethyl- Vanirom WLN: VHR DQ CO2 3943-74-6 4-Hydroxy-3-methoxybenzoic acid methyl ester Benzoic acid, 4-hydroxy-3-methoxy-, methyl ester Methyl 3-methoxy-4-hydroxybenzoate Methyl 4-hydroxy-3-methoxybenzoate Methyl vanillate NSC74385 Vanillic acid methyl ester Vanillic acid, methyl ester 121-32-4 2-Ethoxy-4-formylphenol 3-Ethoxy-4-hydroxybenzaldehyde 3-Ethoxyprotocatechualdehyde 4-08-00-01765 (Beilstein Handbook Reference) 4-Hydroxy-3-ethoxybenzaldehyde AI3-00786 BRN 1073761 Benzaldehyde, 3-ethoxy-4-hydroxy- Bourbonal CCRIS 1346 EINECS 204-464-7 ETHYL VANILLIN Ethavan Ethovan Ethyl protal Ethylprotal Ethylprotocatechualdehyde-3-ethyl ether Ethylprotocatechuic aldehyde Ethylvanillin FEMA No. 2464 HSDB 945 NSC 1803 Protocatechuic aldehyde ethyl ether Quantrovanil Vanilal Vanillal Vanillin, ethyl- Vanirom Vanirome 121-33-5 2-Methoxy-4-formylphenol 3-Methoxy-4-hydroxybenzaldehyde 4-08-00-01763 (Beilstein Handbook Reference) 4-Formyl-2-methoxyphenol 4-Hydroxy-3-methoxybenzaldehyde 4-Hydroxy-5-methoxybenzaldehyde 4-Hydroxy-m-anisaldehyde 52447-63-9 8014-42-4 AI3-00093 BRN 0472792 Benzaldehyde, 4-hydroxy-3-methoxy- CCRIS 2687 EINECS 204-465-2 FEMA No. 3107 HSDB 1027 Lioxin Methylprotocatechuic aldehyde NSC 15351 Protocatechualdehyde 3-methyl ether Protocatechualdehyde, methyl- VANILLIN Vanilla Vanillaldehyde Vanillic aldehyde Vanillin (natural) Vanillin [USAN] Vanilline Zimco m-Anisaldehyde, 4-hydroxy- p-Hydroxy-m-methoxybenzaldehyde p-Vanillin 149-17-7 4-22-00-00598 (Beilstein Handbook Reference) 4-Pyridinecarboxylic acid, ((4-hydroxy-3-methoxyphenyl)methylene)hydrazide 4-Pyridinecarboxylic acid, ((4-hydroxy-3-methoxyphenyl)methylene)hydrazide (9CI) BRN 0234808 Ftivazid Ftivazida [INN-Spanish] Ftivazide Ftivazide [INN] Ftivazidum [INN-Latin] ISONICOTINIC ACID, VANILLYLIDENEHYDRAZIDE Isonicotinic acid vanillylidenehydrazide NSC 31725 Phthivazid Phthivazide Phthivazidum Phtivazid Phtivazide Vancide Vanicid Vanillaberon Vanizide 3-Methoxy-4-hydroxybenzoic acid diethylamide 304-84-7 4-10-00-01481 (Beilstein Handbook Reference) AI3-20163 Analepticon BRN 2694478 Benzamide, N,N-diethyl-4-hydroxy-3-methoxy- Cardiovamil Cardiovanil Corivanil Diethamivan Diethylamide de vanillique Diethylvanillamide EINECS 206-157-3 ETHAMIVAN Emivan Etamivan Etamivanum Etamivanum [INN-Latin] Ethamivan [USAN:BAN] N,N-Diethylvanillamide NSC 406087 Romecor Sevanil Sevinal Simaron Vandid Vanillamide, N,N-diethyl- Vanillic acid N,N-diethylamide Vanillic acid diethylamide Vanillinsaeure-diaethylamid [German] Ventilone (4-HYDROXY-3-METHOXYPHENYL)ACETIC ACID 3-Methoxy-4-hydroxyphenylacetic acid 306-08-1 4-Hydroxy-3-methoxybenzeneacetic acid 4-Hydroxy-3-methoxyphenylacetic acid Acetic acid, (4-hydroxy-3-methoxyphenyl)- (8CI) Benzeneacetic acid, 4-hydroxy-3-methoxy- EINECS 206-176-7 HMPA HVA Homovanillic acid NSC 16682 Vanillacetic acid 2,6-Bis((4-hydroxy-3-methoxyphenyl)methylene)cyclohexanone 2,6-Bis(4-hydroxy-3-methoxybenzylidene)cyclohexanone 2,6-Divanillidenecyclohexanone 2,6-Divanillylidenecyclohexanone 4-08-00-03586 (Beilstein Handbook Reference) 579-23-7 AI3-26016 BRN 2019082 Beveno Ciclovalona [INN-Spanish] Curcumoid Cyclohexanone, 2,6-bis((4-hydroxy-3-methoxyphenyl)methylene)- (9CI) Cyclohexanone, 2,6-divanillylidene- (8CI) Cyclohexanone, 2,6-vanillylidene- Cyclovalon Cyclovalone Cyclovalone [INN] Cyclovalonum [INN-Latin] Cycvalon Cyqualon DVC Divanil Divanillalcyclohexanone Divanon EINECS 209-438-9 Flavugal NSC 26727 Tsikvalon VANILONE (0)-Dehydroparadol (O)-Paradol, dehydro- 1080-12-2 2-08-00-00326 (Beilstein Handbook Reference) 3-BUTEN-2-ONE, 4-(4-HYDROXY-3-METHOXYPHENYL)- 3-Methoxy-4-hydroxybenzalacetone 4-(4-Hydroxy-3-methoxyphenyl)-3-buten-2-one 4-Hydroxy-3-methoxybenzylideneacetone 4-Hydroxy-3-methoxystyryl methyl ketone AI3-01934 BRN 2049660 Dehydro(O)-paradol Dehydrozingerone EINECS 214-096-9 FEMA No. 3738 Feruloylmethane MHSK Methyl-3-methoxy-4-hydroxy styryl ketone Methyl-3-methoxy-4-hydroxystyryl ketone NSC 26613 NSC 4019 NSC 44708 NSC 45411 NSC 5316 Vanillalacetone Vanillidene acetone Vanillylidene acetone Vanylidenacetone 3-10-00-01410 (Beilstein Handbook Reference) 3943-74-6 4-Hydroxy-3-methoxybenzoic acid methyl ester AI3-20212 BENZOIC ACID, 4-HYDROXY-3-METHOXY-, METHYL ESTER BRN 1369113 EINECS 223-525-9 Methyl 3-methoxy-4-hydroxybenzoate Methyl 4-hydroxy-3-methoxybenzoate Methyl vanillate NSC 74385 Vanillic acid, methyl ester Vanillic acid, methyl ester (8CI) 6746-48-1 VANILLATE ION (+-)-2'-(2-(1-Methyl-2-piperidyl)ethyl)vanillanilide (+-)-4-Hydroxy-3-methoxy-N-(2-(2-(1-methyl-2-piperidinyl)ethyl)phenyl)benzamide 3-Methoxy-O-demethylencainide 81329-71-7 82522-70-1 BENZAMIDE, 4-HYDROXY-3-METHOXY-N-(2-(2-(1-METHYL-2-PIPERIDINYL)ETHYL)PHENYL)-, ( BMY 40327 Benzamide, 4-hydroxy-3-methoxy-N-(2-(2-(1-methyl-2-piperidinyl)ethyl)phenyl)-, (+-)- MJ 14030 Modecainida [INN-Spanish] Modecainide Modecainide [USAN:INN] Modecainidum [INN-Latin] 3-Methoxy-4-hydroxybenzoic acid diethylamide 304-84-7 AIDS-130355 AIDS130355 Analepticon Benzamide, N,N-diethyl-4-hydroxy-3-methoxy- Cardiovamil Cardiovanil Corivanil Diethamivan Diethylamide de vanillique Diethylvanillamide Emivan Etamivan Etamivanum Ethamivan N,N-Diethyl-4-hydroxy-3-methoxybenzamide N,N-Diethylvanillamide NSC406087 Romecor Sevanil Sevinal Simaron Vandid Vanillamide, N,N-diethyl- Vanillic acid N,N-diethylamide Vanillic acid diethylamide Vanillinsaeure-diaethylamid Ventilone 121-33-5 2-Methoxy-4-formylphenol 3-Methoxy-4-hydroxybenzaldehyde 4-Formyl-2-methoxyphenol 4-Hydroxy-3-methoxybenzaldehyde 4-Hydroxy-5-methoxybenzaldehyde 4-Hydroxy-m-anisaldehyde Benzaldehyde, 4-hydroxy-3-methoxy- Lioxin NSC403658 Protocatechualdehyde, methyl- VANILLIN Vanilla Vanillaldehyde Vanillic aldehyde WLN: VHR DQ CO1 Zimco m-Anisaldehyde, 4-hydroxy- p-Hydroxy-m-methoxybenzaldehyde 3-Methoxy-4-hydroxybenzoic acid diethylamide 304-84-7 Analepticon Benzamide, N,N-diethyl-4-hydroxy-3-methoxy- Cardiovamil Cardiovanil Corivanil Diethamivan Diethylamide de vanillique Diethylvanillamide Emivan Etamivan Etamivanum Ethamivan N,N-Diethylvanillamide NSC406087 Romecor Sevanil Sevinal Simaron Vandid Vanillamide, N,N-diethyl- Vanillic acid N,N-diethylamide Vanillic acid diethylamide Vanillinsaeure-diaethylamid Ventilone WLN: 2N2 & VR DQ CO1 5348-74-3 Butyl vanillate EINECS 226-307-1 175796-50-6 Benzeneacetic acid, 4-hydroxy-3-methoxy-, (9a-(acetyloxy)-1a,1b,4,4a,5,7a,7b,9,9a-decahydro-4a,7b-dihydroxy-1,1,6,8-tetram ethyl-5-oxo-9-((phenylacetyl)oxy)-1H-cyclopropa(3,4)benz(1,2-e)azulen-3-yl)methy l ester, (1aR-(1aalpha,1bbeta,4abeta,7aalpha,7balpha,8alpha,9beta,9aalpha))- PPAHV Phorbol 12-phenylacetate 13-acetate 20-homovanillate 4-Hydroxy-3-methoxybenzoic acid hexyl ester 84375-71-3 Benzoic acid, 4-hydroxy-3-methoxy-, hexyl ester n-Hexyl vanillate 107512-56-1 4-Hydroxy-3-methoxy-N-9-octadecenylbenzeneacetamide (Z)- Benzeneacetamide, 4-hydroxy-3-methoxy-N-9-octadecenyl-, (Z)- NE 28345 Oleylhomovanillamide 126294-32-4 Benzoic acid, 3-hydroxy-4-methoxy-, hexylester, mixt. with 2-ethoxybenzoic acid Hexyl vanillate-2-ethoxybenzoic acid 2475-56-1 3-Methoxy-4-hydroxyphenyllactic acid Vanillactic acid Vanillylactic acid alpha,4-Dihydroxy-3-methoxybenzenepropanoic acid






    pdb file:151625.pdb
    directory:151625
    CAS: 121-33-5


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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.

    http://molecules.gnu-darwin.org/mod/Bisphenol-more.html

    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.

    Molecules@gnu-darwin.org 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. Molecules@gnu-darwin.org 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, molecules@gnu-darwin.org, with gdmolecules in the subject line. Cheers!