Sciencemadness Discussion Board

Nonspecific Descriptions Found in Chemistry Procedures

BromicAcid - 7-7-2007 at 16:54

I found a list titled "Nonspecific Descriptions Found in Chemistry Experimental Procedures" while reading "Practical Process Research and Development" [Neal G. Anderson, 2000 Academic Press, USA]. And decided that maybe some of the members here conveying their experimental adventures might be able to benefit from this list. I admit I have and still will use a number of these slightly vague terms, one can usually infer proper technique from them but there is the potential for misunderstanding, particularly when working with a sensitive/dangerous reaction. But it was interesting to read them and realize they can be a little ambiguous. Any additions would be welcome to this thread.
Quote:

Added Slowly
Added Dropwise
To a dilute solution
Added in portions
Added to a cold solution
Was run overnight
Added at -78 C (Was the temperature kept constant during the addition?)
With a slight exotherm
At room temperature (Colder in England, hotter in the tropics)
Excess Reagent
Vigorous Agitation
Worked up in the usual way
Gave a white solid
Sufficiently pure
Yields given with out consideration of product quality

absramarao - 7-7-2007 at 18:00

May be it is a Patent culture. One wants to say something and at the same time does not convey completely/fully/clearly.It is up to us to conduct number of experiments ,changing one parameter at a time.May be, you may come up with a still better procedure/yield during this process or simplify things.

not_important - 7-7-2007 at 18:56

I don't think it's patent related, such vague terms were more common a hundred years ago than now.

In some cases the term is acceptable, "Sufficiently pure" works in the context of making a precursor for some other compound where a minor amount of impurities aren't important in that next reaction but would mess up melting point, colour, and so on.

Similarly "Worked up in the usual way" is shorthand when there's a standard workup for the reaction and class of compound, and that workup gave no difficulties. I've seen it used in cases where most of the starting materials worked with a standard workup, but a few didn't; the description used "usually way except for X Y Z, which were isolated in the following manner..." Why waste paper re-describing something well known, at least to researchers in the field, better to concentrate on the new stuff.

Sauron - 7-7-2007 at 20:33

I've been working with preps containing all or most of those terms all my life and do not find them bothersome at all.

But then I'm not a process engineer. Perhaps for the purposes of that specialty more precision and better communication is mandatory. I do not think that is the case for bench scale.

BromicAcid - 7-7-2007 at 21:24

I'm not saying that these are incredibly disruptive unspecific statements. But they are things that could be misconstrued, that people might assume something different than the author intended. For example, 'Worked up in the usual way' is something I have seen in preps that are specific to a field (both online and professionally) but those people without the expertise in the field might not be directed to the 'usual way' and then have to attempt to find this all encompassing resource that would explain what this baseline method entails.

And again, I have used these expressions before and will likely continue to use them. Just mentioning this because when I read thought them I realized the ambiguity of some of the statements. My favorite example on the list though is "Was Run Overnight" which is a statement I have seen a lot but honestly gives no sense of time, some people sleep 9 hours after all, some like me sleep 4 and then there is the assumption weather or not the reaction was stopped as soon as they woke up, or if they ate breakfast first or went to school....

Sauron - 7-7-2007 at 21:52

The last time I saw "was run overnight" was rather recently in an article from the 1920s. However the author did go on to specity the reaction time at 20 hrs.

If he had not done so I would have assumed that the reaction was started in the afternoon and left unattended overnight, and completed in the morning so the reaction time could have been c.18 hours give or take a few. In many cases I doubt the uncertainty would have made the difference between success and failure. At most it would likely mean a less than optimum yield for a less than optimum expenditure of energy.

In a process development and control environment small efficiencies mean big money but not usually so on the lab bench. A lot of procedures get published without optimizing anything much less everything.

Dropwise is only meaningful if it is associated with either a transfer rate (ml/min for example) or in case of an exotherm, a restriction on upper temperature reached. For example, "dropwise such that the temperature of the well stirred mixture never exceeds 25 C".

Drop size will vary, drops per unit time will vary unless you are using a constant-addition funnel, which are not especially common as they are costly. Even if the author specifies a constant addition funnel by brand and model number, it isn't very realistic to expect these to be consistent from specimen to specimen and they are intended to be calibrated by the user. In a process environment you are more likely to be working with flow controllers and flowmeters, pumps etc. You can transfer some of that to the bench with say, syringe pumps and peristaltic pumps which can deliver very precise liquid flow rates. But these are not encountered all that often outside of formal CE process development labs.

BromicAcid - 7-7-2007 at 22:02

Again though, although this little quote was taken from a book on process development I meant for us at home chemists to read it and take it into account (not necessarily the specific examples stated here) when they are writing up the outcome of a procedure that they have attempted, after all, small details can often help in diagnosing some of the problems that can occur in a reaction.

Pyridinium - 7-7-2007 at 22:28

Those terms can be fine where precision isn't critical... for example, "an excess of reagent" would be meaningful where a reaction requires any excess of reagent, although it would be not enough info when the reaction was sensitive to e.g. a 0.1 molar excess of reagent vs. a 5-molar excess.

A "white solid" is good enough to tell one not to look for e.g. a yellow, oily liquid that separates on top of the reaction, but it would be useless if a person were, for instance, interested in whether there'd be a fine mass of tetragonal crystals or a flocculent, amorphous precipitate that took 48 hours to settle.

It's certainly better when actual quantities are used, and occasionally I have found papers where I'd really wished they'd bothered to type that extra bit to clear things up. I agree with you about the small details- sometimes that makes a great difference.

I don't think it's news to any of us here, but sometimes in scientific papers the glossing-over of certain details isn't shorthand; it's that the writer(s) didn't know something or (gasp!)actually skipped that part but assumed it would go that way.

not_important - 7-7-2007 at 22:44

One other thing to consider when looking at older texts - the purity of the reagents. If you read journals and lab methods books from far enough back, there's a fair amount dedicated to purifying compounds that we don't worry about the purity of. The questionable purity could make exact measurements less useful, because if you were going to be making a lot of compound Z, you'd want to do smaller scale runs to calibrate for the reagents you had.

Pyridinium - 7-7-2007 at 23:16

Quote:
Originally posted by not_important
One other thing to consider when looking at older texts - the purity of the reagents. If you read journals and lab methods books from far enough back, there's a fair amount dedicated to purifying compounds that we don't worry about the purity of.


Makes me think of Krauchs' Chemical Reagents (1902). Lots of useful tests there (more on testing than on actual purification though), which would at least tell you if the reagent would make the grades of "C.P.", "Purum", or perhaps even "Puriss".

Probably better than vagueries such as "reasonably pure". Example... "reagent passed the tests for nitrate according to Krauch, 1902".

And many of the tests are within the reach of mad-science majors. Come to think of it, if you look at the label of modern lab reagents you'll often see "passes test" for some of the impurities. Some things haven't changed :-D

Nicodem - 8-7-2007 at 02:55

Added slowly

I use this when denoting that the reagent needs to be added slowly due to following reasons:
- exothermicity of the reaction (in which case it is preferable to use carefully added or added in portions);
- because this assures a more or less constant concentration over the entire reaction mixture without local build up;
- the reagent is added at such a speed as to allow its rapid consumption to minimize side reactions (in which case it is preferable to use added dropwise when a liquid).

To a dilute solution

Depends on the context, but it usually requires from the chemist to understand what he is doing and how the delineated reaction or workup works. It's certainly no phrase for cooks.

Added to a cold solution

Means that the addition is exothermic and thus it is best to cool the solution during the addition. If the temperature is not specified it can only mean that it is not particularly important and the cooling is required only to prevent the heat building up or the solvent boiling.

Was run overnight

This is a phrase I would like to often use yet neither the boss nor some referees are happy about it. If I set a reaction and the TLC shows its over in a couple of hours, for example, but I do not want to stay in the lab till evening, I will rather leave it running overnight and do the work up next morning. This phrase does not necessarily mean the reaction requires a lot of time! It only means chemists are humans and can not work 24 hours a day.
Another reason for leaving it overnight is for one of the reagents to get quenched before working up. For example, if I benzylate with BnBr, I rather leave the reaction run overnight, even though the benzylation is TLC fished much earlier, since I don't want to get the BnBr in my eyes during the work up.

Added at -78 °C

Means the reaction was performed under standard dry ice / acetone bath conditions. As long there is solid CO2 in the bath the temperature is at constant -78 °C (which does not mean the reaction mixture will be at constant temperature since this is actually the bath and not reaction mixture T).

With a slight exotherm

The reaction temperature rose for a couple of K during the operation.

At room temperature

The room temperature is sometimes defined in the experimental introduction, just like the instruments and chemicals used. If it is not, then it means anything from 20-30°C and nearby… or it is simply not that crucial.

Excess reagent

The [amount of] reagent added that is above the stoichiometry of the reaction or [the amount] that failed to be consumed during the reaction.

Worked up in the usual way

Worked up as described earlier in the same paper or otherwise known from the literature.

Gave a white solid

The product was not colored. This says nothing if it is crystalline or amorphous, just that there are no colored impurities.

Sufficiently pure

Sufficiently pure to use in its further application.

Yields given with out consideration of product quality

Never saw this one, but it looks to me like an alternative to the yields given on crude product or variations thereof.

YT2095 - 8-7-2007 at 04:49

one that I`m occasionally guilty of (and I`m not alone) is the Spatula add "half a spatula" or "a Heaped spatula".

not exactly Scientific is it ;)

Ozone - 8-7-2007 at 05:45

Nicodem is dead-on, especially re. "left-overnight", which of course usually means, "chemist was tired and decided to finish up the next day".

The only one of these that has given me problems is the old "mixture reacted for xxx time at rt". rt varies quite a bit and can have a profound effect. For example, a reaction run in the old days (without AC) could have been proceeding at 30°C. I try the reaction today, and it sits there like a rock at my lab 'rt' which is ~22.4 °C. Heating to 30 makes it go... For this reason I agree that maybe, we could be sufficiently motivated to keep a lab thermometer for purposes of recording 'rt' in our papers.

Heck, most papers *neglect* to mention, say, a very exothermic event which occurs on the addition of a reagent. These events should always (regardless of editors ruthless with print copy) be included in the technical citations. It only takes once for this one to tick-you-off (btw, dihydropyran and benzyl alcohol *will* erupt when mixed, then treated with toluenesulfonic acid--add the TOSYL to the benzyl alcohol then add, dropwise, your DHP;)).

so, how about "added dropwise"?

Cheers,

O3

Blind Angel - 8-7-2007 at 06:26

A little add-on, we usually learn that when you use reagent in excess you add 10% more than what you calculated, if it's a solution you add 10%m/v, if it's a mass you add 10%weight. Might help.

12AX7 - 8-7-2007 at 07:14

"Dropwise"

Approximately (+/- 30%) 0.05ml drop at a time, administered at a rate of less than two drops per second.

"Slowly" would be in the range of five seconds or more between drops.

See also: "Added slowly".

Tim

[Edited on 7-8-2007 by 12AX7]

Sauron - 8-7-2007 at 07:28

If I may digress just a little, I suggest reading the sixth Harry Potter book, in particular all the scenes in the Potions class, and if that doesn't remind you of an organic teaching lab then maybe nothing will.

Back on topic, I think those terms are more of a problem for the inexperienced and less of a problem for the old wet lab hands.

pantone159 - 8-7-2007 at 10:34

Returning to digression...

I also find that the Harry Potter books remind me very much of chemistry. Now, when I look at 'Advanced Inorganic Chemistry by Cotton & Wilkinson', I have to think 'Advanced Potion Making by Libatius Borage', and vice-versa.

End of digression...

Rosco Bodine - 8-7-2007 at 17:59

My favorite disagreeable ambiguity is that phrase

"known to those skilled in the art" ......

the plain inference being ,

( as for the rest of you dullards who might need to ask about the undisclosed details , well .... you are just SOL ! Whaddaya expect , a spoonfeeding ya big baby , so go back to school and get skilled and stop being a zero :P )

evil_lurker - 8-7-2007 at 18:09

Quote:
Quote:
Added Slowly

Add slowly, but proceed with caution.

Added Dropwise

Dropwise is dropwise. Means you set your separatory funnel to where it goes in drop by drop... I personally take it to where it means as long as individual drops and not a stream.

To a dilute solution

I consider dilute solutions to mean 5 or 10% solution, per weight.

Added in portions

Means don't dump the shit in all at once. 1-5g or 1-5ml added at a time until your confident that it won't go runaway.

Added to a cold solution

Cold solution is usually 0ºC under ice bath conditions.

Was run overnight

Means the synth took a long time and the researcher got tired and decided to hang it up for the evening.

Added at -78 C (Was the temperature kept constant during the addition?)

I take it to mean that the reagent was added to a solution held at -78ºC under dry ice/acetone bath.

With a slight exotherm

It means that if you attempt to scale up, expect massive runaway.

At room temperature (Colder in England, hotter in the tropics)

22-25ºC no special heating or cooling added.

Excess Reagent

Means not all will react. I usually consider excess reagent to mean an extra 10 molar per cent.

Vigorous Agitation

Overhead stirring, vortexing with slight shearing action.

Worked up in the usual way

Could mean several things...you should already know what the fuck your doing, we are too lazy to tell you how we did it, or we don't want you trying to duplicate our work because the entire synth is a crock of shit.

Gave a white solid

Crystaly powder! Yay!

Sufficiently pure

At least 92-95% pure and/or does not contain sufficiant other chemicals that would interfere with most other reactions or intended usages.

Yields given with out consideration of product quality

Means they were too lazy to seperate out the crude product, but the think it its OK.

sparkgap - 16-7-2007 at 02:51

In the same vein as YT's contribution, "a pinch of..." carries with it some ambiguity. :)

sparky (~_~)

DrP - 16-7-2007 at 05:20

I think dropwise addition is pretty standard for chemists. But that's it really isn't it - if your a chemist - you'll know what these terms mean - if not, then it probably doesn't matter anyway.

12AX7 - 16-7-2007 at 14:15

A pinch is actually somewhat specific. Look up cooking measures ;)

Tim

sparkgap - 16-7-2007 at 22:39

Actually, over the years, I've considered "a spatula tip of ____" and "a pinch of ____" to be effectively synonymous. ;)

sparky (~_~)

Sauron - 17-7-2007 at 00:26

Yeah, but Rosco as you know perfectly well "skilled in the art" is a phrase that has meaning only to patent attorneys, and by extension, inventors, assignees of patents, etc.

It's THE phrase that patent lawyers use to fudge up the issue of complete disclosure as required by the law.

To be precise, the invention must be nonobvious to those skilled in the art. And skilled in the art means skilled in the specific specialized art concerned not just "chemistry" or "organic synthesis". As the science and technology become more complex the size of the set of those skilled in the art concerned in a particular patent tends to shrink to a rather small number, doesn't it?

In short I would argue that this is an anachronism in the law held over from the 18th or early 19th century. However the patent community seems to be rather complacent about it, I see no great groundswell of support for any sort of patent reform.

Rosco Bodine - 17-7-2007 at 07:53

Indeed , there is some fudging of disclosure encountered in *some* patents , where the verbal description of examples is not the best illustration of the highest performance embodiment of the invention ....which is undisclosed by any general description , but rather is something of a parallel which is covered more precisely
within ranges of variables described in the claims .

It is like the patent doesn't give you the production blueprint , but only a summary artists impression ,
and then the claims cover some broader range of
variables which includes the undisclosed precise quantities .....that remain undisclosed . So a patent
may serve as a backup legal protection for a trade secret
or secrets , which is kept undisclosed in its most precise details , yet covered within the ambiguity of ranges of variables that are claimed to apply to the invention .

It can be something like patenting the combination for your combination lock , where you say the first number
is between zero and nine , as are the next five numbers
in the combination , entered by turning the dial either
clockwise or counter clockwise in some sequence , in
a fashion known to those who are skilled in the art :P

The_Davster - 17-7-2007 at 20:14

I had never noticed anything I considered too non-specific until the other day.
"and to this was added 10mL of sulfuric acid and 20mls of formaldehyde with stirring at 5-10C"

Rather ambigious whether both are added separatly simultaneously, as a mixture, or one after another. Adding one after the other makes more sense, but the wording is unclear.

12AX7 - 17-7-2007 at 20:26

Ah, well, ambiguous wording plagues all written media. :(

sparkgap - 20-7-2007 at 07:01

Oh yeah, I remember now, I have seen the word "several" in many a lab procedure, e.g. "several aliquots" or "washed several times with solvent X".

sparky (~.~)

12AX7 - 20-7-2007 at 13:20

I take that to mean two or three, non-critically.