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aonomus
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To me, the point of the arguement for better posting standards is twofold.
1. Have readers exert less effort while reading posts and attempting to aid people
2. Have posters exert more effort so that they are more likely to get answers to their questions
For the most part, I like to see people actually exert effort. In many cases I won't even bother replying whether or not I know the answer because I
feel I shouldn't bother exerting effort for someone else who demonstrably failed to do so. Non-English speakers aside, people who come from English
speaking countries are the main issue at hand.
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gsd
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Quote: Originally posted by Magpie  |
I get this same feeling when I see someone wearing a baseball cap backwards. It immediately knocks their IQ down by 20 points.
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Well Magpie how many IQ points your will knock-out for this fellow? 
gsd
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Magpie
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That guy would get a loud pro-longed belly laugh from me. That's a classic.
The single most important condition for a successful synthesis is good mixing - Nicodem
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Ephoton
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at least his neck is not sun burnt ;P
e3500 console login: root
bash-2.05#
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unionised
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I presume this
"All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on
summary pages and in HTML titles."
was included in the first post for the benefit of those who enjoy irony.
HTML (hyper text markup language)
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arsphenamine
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| Quote: Originally posted by unionised | I presume this
"All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on
summary pages and in HTML titles."
was included in the first post for the benefit of those who enjoy irony.
HTML (hyper text markup language)
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Agreed.
HTML is an FLA (as distinct from the ubiquitous TLA, although 'FLA' is a TLA, but I digress).
The original point, though, was that it would help if folks were less prolix
using DMG instead of dimethylglyme (or glyoxime) prior to explication.
HTML is a well-recognized four letter acronym (FLA) while DMG is not.
I can somewhat forgive DNPH since dinitrophenylhydrazine approaches
the territory where the Principle Of Maximum Laziness holds sway.
One unmentioned point is that few here seem to use chemistry drawing
tools. Often, a simple picture can take the place of verbiage.
[Edited on 10-12-2010 by arsphenamine]
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hissingnoise
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Hmmm, you haven't changed a bit since I saw you last . . .
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arsphenamine
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*blush!*
You think so?
Check out the model shots under my stage name, salvarsan.
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madscientist
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It would indeed be nice to see more use of quality drawings.
http://www.symyx.com/downloads/downloadable/
You have to register, but it's worth it - their product "Symyx Draw" (based on ISIS Draw) is free and of high quality. It's much easier than trying to
scratch out crappy drawings in MS Paint, or posting huge IUPAC names for others to decipher.
I weep at the sight of flaming acetic anhydride.
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arsphenamine
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Freeware chemical drawing programs
ACD/labs ChemSketch
http://www.acdlabs.com/resources/freeware/chemsketch/
ChemAxon MarvinSketch
http://www.chemaxon.com/download/marvin/
Both of them require registration. If you can prove university affiliation,
you can get academic license discounts on their commercial products.
ChemSketch's authors have a close affiliation with IUPAC so their built-in
structure-to-name applet is the industrial standard.
I favor MarvinSketch for its cleaner user interface and ability
to export/import in many different formats, and for the ease with which you
can express reaction roadmaps. It can generate names from structures
as well, but gets confused when you draw chemically valid but non-
existent compounds. Theoretical chemists, take note.
It's easy to cruft up a structure and name it in formal IUPAC
({3-[2-(dimethylamino)ethyl]-1H-indol-4-yl}oxy)phosphonic acid
or, if you need to do online searches, as a SMILES string:
CN(C)CCc1c[nH]c2cccc(OP(O)(O)=O)c12
or traditionally as psilocybin.
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Nicodem
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| Quote: Originally posted by unionised | I presume this
"All abbreviations should be spelled out in full at least once before they are used, especially in subject lines that open new threads and appear on
summary pages and in HTML titles."
was included in the first post for the benefit of those who enjoy irony.
HTML (hyper text markup language)
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In my field of organic chemistry we do use lots of abbreviations and acronyms and I agree that this can be a source of confusion. However, some
abbreviations became so natural that those who use them either believe that everybody even closely affiliated to chemistry knows what they mean or
that they can have no other meaning to other people. For example, most if not all, would know that "Me" stands for methyl, but when it comes to "Ar"
or "Ac" (which to organic chemists means just aryl and acetyl), you will hardly find an organic chemist which consciously realizes these are also
symbols for elements. Yet, an inorganic chemist will first think of these being element symbols rather than a shorthand for a structural moiety.
Some acronyms are so generic that it is hard to believe that there is any chemist who does not know its meaning. Thus most chemists use acronyms for
solvents and this become so natural that you will see the naming of THF, DMF, DMSO, etc. in some articles without them ever being spelled out with the
full name.
Anyway, here is list of acronyms and abbreviations for organic chemistry: http://www.chem.wisc.edu/areas/reich/handouts/acronyms.pdf
And here you can search for acronyms and abbreviations in general: http://www.acronymfinder.com/
…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being
unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their
scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)
Read the The ScienceMadness Guidelines!
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watson.fawkes
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I think we might to transcribe our own list of well-known abbreviations,
particularly because we get so many beginners on the board. At the very least, it would be a designated place to point people to, and some might even
find it themselves.
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arsphenamine
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| Quote: Originally posted by watson.fawkes | | I think we might to transcribe our own list of well-known abbreviations,
particularly because we get so many beginners on the board. At the very least, it would be a designated place to point people to, and some might even
find it themselves. |
+1
For this level of intellectual inbreeding, a scorecard is essential and
a sense of humor helps.
Programmers have 0xDEADBEEF and OrgSyn chemists have DEADCAT.
You have to respect a field that creates such world class
mnemonics/acronyms as TOSMIC and LICKOR.
The latter is notable since "Lithium-potassium alkoxide reagents"
has no 'C' anywhere.
Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu.
Also, Tf derives from "triflate," itself derived from "Trifluoro sulfonate" --
a lexical second derivative with regard to etymology.
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turd
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What a terrible, unwieldy way of naming the phosphoric acid ester of 4-hydroxy-N,N-dimethyltrypramine.  Apart from historic interest and a few journals demanding it, has the formal IUPAC nomenclature any relevance to the
modern chemist? I see the point of a 1:1 molecule to name relation in times before the dawn of electronic databases. But nowadays, do they still annoy
students with this? Seems like a waste of time. And it's probably not even useful as an internal representation in electronic databases.
| Quote: | | For example, most if not all, would know that "Me" stands for methyl, but when it comes to "Ar" or "Ac" (which to organic chemists means just aryl and
acetyl), you will hardly find an organic chemist which consciously realizes these are also symbols for elements. Yet, an inorganic chemist will first
think of these being element symbols rather than a shorthand for a structural moiety. |
Sadly, most inorganic and especially analytic chemists I know seem to believe that Ac stands for acetate(sic!), as in NaAc for sodium acetate. The
mind boggles when the same people label their acetic acid bottles with "AcOH" instead of "AcH". 
| Quote: | Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu. |
Hear, hear. Are you into quasi-crystals or "simply" magnetism?
Edit: Should have googled before - AlNiCo is an iron alloy and has nothing to do with quasi-crystals.
[Edited on 12-12-2010 by turd]
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arsphenamine
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| Quote: | ({3-[2-(dimethylamino)ethyl]-1H-indol-4-yl}oxy)phosphonic acid
What a terrible, unwieldy way of naming the phosphoric acid ester of 4-hydroxy-N,N-dimethyltrypramine. Apart from historic interest and a few journals demanding it, has the formal IUPAC nomenclature any relevance to the
modern chemist? |
I have felt that pain, often in the gluteous maximus.
[mode="wizard"]
If you know its true name, you can conjure with it.
[/mode]
Chemical modeling and searching need unambiguous names if you want to share your knowledge quickly.
From IUPAC, we get 1,4,7,10,13,16-hexaoxa cyclooctadecane when we knew all along it was 18-crown-6.
In school, they told us that its oxygens like to fit around a K+ ion.
With a quick Avogadro draft or SMILES cut-and-paste, you can
run a few 1000's of force field iterations and watch it happen.
Two honking huge organizations like unambiguous naming for compound
searches in their PubChem and ChemSpider online databases. The IUPAC
naming, godawful as it is, is still more readable than the SMILES, SMART,
and InChI specifier grammars.
These specifiers allow you to construct a model on which you can perform all manner of calculations since the software is getting cheap enough for the
hobbyist. For example, it is possible to get useful estimates of 3D visualization, pKa, NMR spectra, conformational analysis in different solvents,
electron field topologies, vibrational energies/modes/frequencies ... and that's just the free stuff.
If BigPharma bankrolls you, drug simulation and pharmacokinetics simulation are just two that come to mind.
The good news is that you don't have to know it all.
You can sharpen your existing knowledge with some very good
freeware such as Avogadro and GAMESS.
| Quote: | | Quote: | Reminds me of AlNiCo III, which contains copper instead of cobalt,
but nobody wanted to call it AlNiCu. |
Hear, hear. Are you into quasi-crystals or "simply" magnetism?
Edit: Should have googled before - AlNiCo is an iron alloy and has nothing to do with quasi-crystals. |
Last I heard, but not read, Alnico is a mix of two co-aligned metallic crystals, one with low field-high coercivity, and one with high field-low
coercivity. I'd love to know more but more urgent things await.
[Edited on 12-12-2010 by arsphenamine]
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turd
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| Quote: Originally posted by arsphenamine | Two honking huge organizations like unambiguous naming for compound
searches in their PubChem and ChemSpider online databases. The IUPAC
naming, godawful as it is, is still more readable than the SMILES, SMART,
and InChI specifier grammars. |
Wow, that's stone-age.  In Beilstein/Gmelin/Crossfire and CA/SciFinder you
typically use a structure drawing applet which is much more flexible. You can do things like putting an arbitrary alkyl-chain at this and that
position. With IUPAC nomenclature this is impossible, since an alkyl-chain may completely change the canonical name of the molecule.
| Quote: | | Last I heard, but not read, Alnico is a mix of two co-aligned metallic crystals, one with low field-high coercivity, and one with high field-low
coercivity. I'd love to know more but more urgent things await. |
Magnetic structure and symmetry is very interesting. Unfortunately you need good neutron diffraction data, which means either huge crystals or powder
data, which limits you to simple structures. And of course few amateurs have access to a neutron source.
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arsphenamine
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| Quote: Originally posted by turd |
Wow, that's stone-age. In Beilstein/Gmelin/Crossfire and CA/SciFinder you
typically use a structure drawing applet which is much more flexible. You can do things like putting an arbitrary alkyl-chain at this and that
position. With IUPAC nomenclature this is impossible, since an alkyl-chain may completely change the canonical name of the molecule.
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If you haven't been to the IUPAC site, hold your criticism.
To be fair, they let you upload your model file in one of the common formats.
And, to be pragmatic, you can cut and paste a SMILES string very conveniently if the molecule isn't too large.
And, though it rankles to admit it, organic chemistry is itself "stone-age."
For proof, you need look no farther than the merging of chemistry and
biochemistry departments at many universities. It is much the same with
electrical engineering and computer science.
If you wanted to put a thumbnail image of a compound on this forum, what
would you use?
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turd
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I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form
O2N-CH=CH-R --> H2N-CH2-CH2-R
where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the
structure plugin of Scifinder.
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watson.fawkes
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| Quote: Originally posted by turd | | Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the structure plugin of Scifinder.
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You've inadvertently hit the nail on the head, IUPAC names are created for the express purpose of being
canonical names, that is, to provide common and unambiguous names of reference for communication between two chemists, and in particular, between a
chemist author and reader. For this purpose, you're going to get one kind of naming structure. Such a naming structure should not be expected to be
universal across all purposes. Different representations, different purposes. The subgraph-matching problem you pose needs a different representation
than an IUPAC name, sure, but this doesn't diminish in any way the value of such names as reference names.
On the other hand, your purpose has "R" notation in it, and it might behoove IUPAC to make canonical names for "compounds with unknowns", by analogy a
kind of algebraic expression for chemistry.
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arsphenamine
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| Quote: Originally posted by turd | I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form
O2N-CH=CH-R --> H2N-CH2-CH2-R
where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the
structure plugin of Scifinder. |
Well...um...yeah.
An arbitrary analog is not an unambiguously specified == unique compound.
A custom tailor job doesn't belong in the one-size-fits-all bin.
The SMILES method is worth a little examination,
particularly since many chemical sketch/draw/ model applications let you
paste in a SMILES string.
Searching for analogs requires, to my limited knowledge, either a SMART
string (a regular expression language) or Markush Structure queries.
There are undoubtedly many more query schemes.
Have a look at PubChem to see if any of their options are familiar or
conventient to your work. http://pubchem.ncbi.nlm.nih.gov/
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turd
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| Quote: Originally posted by watson.fawkes | | You've inadvertently hit the nail on the head, IUPAC names are created for the express purpose of being canonical names, that is, to provide common
and unambiguous names of reference for communication between two chemists, and in particular, between a chemist author and reader.
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Yes, but exactly in this context I don't understand the usefulness of a canonical naming. On the
contrary, I think it hurts. Of course naming has to be unambiguous (i.e. the relationship connecting names and compounds should be a
function). Of course the nomenclature should be able to name any thinkable compound (i.e. the function should be surjective). But
IUPAC also specifies rules to make the function injective and therefore bijective. Two reasons I don't think this is useful in the context of
author-reader:
With a non-canonical naming, we can emphasize certain aspects of our compound. E.g. we can emphasize the amine
(2-hydroxyethylamine) or the alcohol (2-aminoethanol).
A canonical naming will invariably in some cases become very unwieldy. Take for example the naming arsphenamine has given for psylocybin. If I
had to read something like this in a paper, the first thought that would cross my mind is "asshole". Publications should be clear and easy to read and
never cryptic. Never should I have to sit half an hour to work out what molecule the author is talking about. So the only reason for a canonical
naming I can come up with is for indexing in reference works (and of course a raison d'être for committees). But with Scifinder et. al., this seems
to be of less and less relevance to the modern chemist. That was my point - nothing more, nothing less.
PS: Actually, I think for brievety it's also useful soften the function part. Chloroethanol could designate Cl-CH2-CH2-OH or CH3-CHClOH, but as
chemists, we know which one the author is talking about.
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watson.fawkes
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| Quote: Originally posted by turd | But IUPAC also specifies rules to make the function injective and therefore bijective. [...]
With a non-canonical naming, we can emphasize certain aspects of our compound. [...]
A canonical naming will invariably in some cases become very unwieldy. [...] So the only reason for a canonical naming I can come up with is
for indexing in reference works (and of course a raison d'être for committees). |
I agree that the properties
of canonical names aren't good for either of the cases you list. The social norm to use canonical names, therefore, should not be to use them
exclusively. The relationship between a colloquial name and a canonical name is very much like that between a name and its abbreviation or acronym.
When you a colloquial name for the first time, you should identify it with a canonical name. Thereafter, use of the canonical name in the context of
that particular writing is unambiguous. For academic writing, this could be done once in the abstract (if needed) or body, since a "paper" represents
a clear boundary for creating a disambiguation context.
The purpose of this practice aligns with the self-interest of an author to draw attention to their work, because doing an exhaustive search for a
compound will always find its canonical name but be less successful in finding synonyms. It's for exactly this reason that IUPAC bijective naming is
the right thing, because it supports this important purpose. It's not the only purpose, though, and canonical naming is not a universal solution.
Tracking synonyms is certainly useful, necessary even for historical work, but is practically incapable of yielding 100% reliability as canonical
names are.
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Nicodem
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| Quote: Originally posted by turd | I'm not criticizing, I'm wondering. To give an example: I want to search all reactions of the form
O2N-CH=CH-R --> H2N-CH2-CH2-R
where R is an arbitrary organic rest. Canonical IUPAC names do not seem very helpful for this search, whereas it is trivially performed with the
structure plugin of Scifinder. |
Actually there exists a nomenclature equivalent of Markush structures. In the above case it would be "transforming beta-substituted nitroethenes to
beta-substituted ethylamines". You can narrow it further to beta-alkyl, beta-aryl, beta-heteroatom substituted, beta-dialkylamino, beta-alkoxy, etc...
This is a valid way to describe general transformations in the literature, however you will only find pertaining references if the authors ever wrote
these in the text. Similarly, you will ever find references using structure search if the reactions were properly abstracted, which is not always the
case (just compare reaction search hits between SciFinder and Beilstein, and you will see what I mean). As annoying as the formalism of IUPAC
nomenclature is, it is still the best there is, and to those who don't have proper access to CA and Beilstein, it also represents an efficient way to
find references by using publisher's ever more efficient keyword based search engines by searching for a specific compound using proper IUPAC
nomenclature.
…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being
unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their
scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)
Read the The ScienceMadness Guidelines!
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Ephoton
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I do love diagrams will do thanx arsphenamine.
Nicodem you are always miles beyond me 
I can only wish to rise to such hights alas I am going to be a thorn in
vultures foot for ever.
sigh to be disabled
[Edited on 18-12-2010 by Ephoton]
e3500 console login: root
bash-2.05#
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madscientist
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Something I forgot to mention - use the < sub>< /sub> tags (minus the spaces). They make posts a lot more pleasant to read.
Ph2C=CHCH2CH(CO2CH3)2
vs
Ph<sub>2</sub>C=CHCH<sub>2</sub>CH(CO<sub>2</sub>CH<sub>3</sub> <sub>2</sub>
It's not necessary, but it certainly is nice.
[Edited on 20-12-2010 by madscientist]
I weep at the sight of flaming acetic anhydride.
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