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Molecule News and Molecule of the Day
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The molecule of the day is: Sodium Chloride
Sodium chloride is common table salt. With two atoms bound
together by a strong ionic bond, it is perhaps a marvel that
such a simple molecule can cause such a powerful sensation of
taste. In water, the ionic bond is easily broken, so that
the individual ions can pass quickly through special channels in the
tissues of the tongue. This results in a depolarization of
the membrane, which signals the taste of salt to the nerve
endings nearby. It is also perhaps remarkable that such a
hard and brittle material is so easily disolved in water,
again due to its ionic character. Sodium flux can cause
an excitatory stimulus in a variety of tissues, not just
the tongue, and this is why a pinch of moderation is called
for in the use of this molecule.
Sodium Chloride related molecules gallery and structural archive
7647-14-5 Common salt Flexivial Gingivyl Halite Hyposaline Iodized salt NSC77364 Natriumchlorid Rock Salt SS Salt Saline Salt Sea salt Slow Sodium Sodium chloric Sodium chloride Sodium chloride (Na4Cl4) Sodium chloride (NaCl) Sodium chloride brine, purified Sodium chloride, hypertonic Sodium chloride, isotonic Sodium monochloride Table salt Trisodium trichloride WLN: NA G
related molecule names:
7647-14-5 Common salt Flexivial Gingivyl Halite Hyposaline Iodized salt
NSC77364 Natriumchlorid Rock Salt SS Salt Saline Salt Sea salt Slow Sodium
Sodium chloric Sodium chloride Sodium chloride (Na4Cl4) Sodium chloride (NaCl)
Sodium chloride brine, purified Sodium chloride, hypertonic Sodium chloride,
isotonic Sodium monochloride Table salt Trisodium trichloride WLN: NA G
227453-69-2 56172-57-7 7681-52-9 8007-59-8 AD Gel Antiformin B-K liquid CCRIS
708 Carrel-dakin solution Caswell No. 776 Chlorinated water (sodium
hypochlorite) Chloros Chlorox Cloralex Cloropool Clorox Clorox liquid bleach
Dakin's solution Dakins solution Deosan Deosan Green Label Steriliser Dispatch
EINECS 231-668-3 EPA Pesticide Chemical Code 014703 HSDB 748 Hospital Milton
Household bleach Hyclorite Hypochlorite sodium Hypochlorous acid, sodium salt
Hyposan and Voxsan Hypure Hypure N Javel water Javelle water Javex Klorocin
Milton Milton Crystals Modified dakin's solution Neo-cleaner Neoseptal CL
Parozone Purin B SODIUM HYPOCHLORITE Sodium hypochlorite (NaClO) Sodium
hypochlorite (NaOCl) Sodium hypochlorite [Hypochloride salts] Sodium
hypochlorite [USAN:JAN] Sodium hypochlorite
15189-51-2 16903-35-8 3145-90-2 8011-75-4 AURATE(1-), TETRACHLORO-, SODIUM
Aurate(1-), tetrachloro-, sodium, (SP-4-1)- EINECS 239-241-3 Gold chloride
sodium Gold sodium chloride Hydrochloroauric acid, sodium salt Natrium
tetrachloroauratum Sodium chloroaurate Sodium gold chloride Sodium gold(III)
chloride Sodium tetrachloroaurate Sodium tetrachloroaurate(1-) Sodium
tetrachloroaurate(3+) Sodium tetrachloroaurate(III) Tetrachloroaurate(1-)
sodium Tetrachloroauric(3+) acid, sodium salt
17108-96-2 37299-86-8 60-15-1 96332-84-2 Acid Red 388 Ethanaminium,
chloride, disodium salt RHODAMINE WT
66827-28-9 AMMONIUM, TETRAMETHYL-, CHLORIDE with SODIUM FLUOROACETATE Sodium
fluoroacetate with tetramethyl ammonium chloride TL 869
13840-33-0 142857-18-9 CCRIS 4023 Caswell No. 528A EINECS 237-558-1 EPA
Pesticide Chemical Code 014702 Hypochlorous acid, lithium salt Hypochlorous
acid, lithium salt, mixture with sodium chloride LITHIUM HYPOCHLORITE Lithium
chloride oxide Lithium hypochlorite [Hypochlorite salts] Lithium hypochlorite,
dry or lithium hypochlorite mixtures, dry [UN1471] [Oxidizer] Lithium
49658-21-1 CHLOROUS ACID, SODIUM SALT, TRIHYDRATE Sodium chloride trihydrate
Sodium chlorite trihydrate
6138-47-2 EINECS 228-120-0 LIOTHYRONINE SODIUM Liothyronine hydrochloride
NSC169535 Nucleic acid, deoxyribo-, sodium salt, compd with
DAUNOMYCIN, DIAMINOBUTYRYL- Diaminobutyral-daunomycin sodium chloride
Diaminobutyryl-daunomycin sodium chloride NSC332580
isoindole-2,6-diyl)bis(methylene) ester, compd. with D-gluconic acid and sodium
chloride (1:2:2) NSC608003
Daunorubicin hydrochloride DNA NSC169533 Nucleic acid, deoxyribo-, sodium salt,
Adriamycin-DNA hydrochloride NSC169534 Nucleic acid, deoxyribo-, sodium salt,
hydrochloride Nucleic acid, deoxyribo-, sodium salt, compound with
de, hydrochloride, (2S-cis)-, compd. with deoxyribonucleic acid sodium salt
10026-00-3 Disodium tetrachloroplatinate Disodium tetrachloroplatinate(2-)
NSC271964 Platinate(2-), tetrachloro-, disodium Platinate(2-), tetrachloro-,
disodium, (SP-4-1)- Platinous sodium chloride Sodium chloroplatinite Sodium
platinochloride Sodium tetrachloroplatinate
DAUNOMYCIN, LYSYL- Lysyl-daunomycin NaCl Lysyl-daunomycin sodium chloride
DAUNOMYCIN, DBU-LYS- DBU-LYS-Daunomycin sodium chloride Dbu-lys-daunomycin NaCl
compd. with sodium chloride (1:1) 5,12-Naphthacenedione,
(N-L-prolyl-L-lysyl)amino]-a-L-lyxo-hexopyranosyl]oxy]-, (8S-cis)-, compd. with
sodium chloride (1:1) DAUNOMYCIN, PRO-LYS- NSC332582 Pro-lys-daunomycin sodium
15189-51-2 AIDS-004144 AIDS004144 NaAu(III) chloride Sodium gold(III) chloride
7681-52-9 AIDS-006138 AIDS006138 Sodium hypochlorite Sodium oxychloride
compound with water (1:1), sodium chloride (5:1), and sodium bisulfate (5:1)
4-[[(4-amino-1-methyl-1H-pyrrol-2-yl)carbonyl]amino]- 208576-38-9 (DISODIUM
SALT) AIDS-058924 AIDS058924 NSC655720 (DISODIUM, HYYDROCHLORIDE SALT)
16904-96-4 Choline chloride O-(disodium phosphate) EINECS 240-953-1
101-77-9 21646-20-8 4,4'-Methylenebis(aniline), compound with sodium chloride
(3:1) Benzenamine, 4,4'-methylenebis-, compd. with sodium chloride (NaCl)(3:1)
EINECS 244-493-2 Sodium, chlorotris(4,4'-methylenedianiline)-
8022-63-7 Hartmann's solution Propanoic acid, 2-hydroxy-, monosodium salt,
mixt. with calcium chloride (CaCl2), potassium chloride (KCl) and sodium
chloride (NaCl) Ringer's injection, lactated Ringer's lactate Ringer-lactate
disodium salt 68092-44-4 Disodium
um chloride EINECS 268-457-0
61702-59-8 Disodium 1,1-bis(carboxymethyl)-4,5-dihydro-2-undecyl-1H-imidazolium
chloride EINECS 262-921-6
61702-60-1 EINECS 262-922-1 Sodium
1-Benzyl-3-carboxylatopyridinium sodium chloride
3-Carboxy-1-(phenylmethyl)pyridinium, chloride, sodium salt 68133-60-8
73470-03-8 EINECS 268-692-9 Pyridinium, 3-carboxy-1-(phenylmethyl)-, chloride,
sodium chloride 1,2-Methyl-5-(trifluoromethyl)-3-(3-sulfopropyl)benzimidazolium
chloride, sodium salt 1H-Benzimidazolium,
1,2-dimethyl-3-(3-sulfopropyl)-5-(trifluoromethyl)-, chloride, sodium salt
68413-90-1 EINECS 270-262-0
63467-35-6 Ethanesulfonic acid, 2-(methylamino)-, hydrochloride, monosodium
63815-66-7 Benzothiazolium, 6-methoxy-2,5-dimethyl-3-(4-sulfobutyl)-, chloride,
7784-16-9 Aluminium sodium tetrachloride EINECS 232-050-6 Sodium
y-2-oxoethyl)-3-(phosphonooxy)-, monosodium salt, trihydrochloride
12258-98-9 Disodium dichloride
84008-89-9 Disodium monochloride
95860-64-3 Sodium cesium monochloride
95860-65-4 Rubidium sodium monochloride
95860-66-5 Potassium sodium monochloride
71373-33-6 Morphinan-6-ol, 7,8-didehydro-4,5-epoxy-3-ethoxy-17-methyl-,
hydrochloride, (5alpha,6alpha)-, mixt. with
4))non-7-yl alpha-(hydroxymethyl)benzeneacetate hydrobromide and sodium
biphenyl selenium stylized
arginine highway stylized
infinite carbon chain stylized
Cysteine with hydrogens
RSS News Feed
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.
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
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Here is a link to the
Our founder is an X-ray laboratory admin for the
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We would like to build a community around this website, and we are looking for
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firstname.lastname@example.org, with gdmolecules in the subject line. Cheers!