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Chemosynthesis
International Hazard
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I think most people on the forum are happy to help you learn chemistry out of curiosity and genuine interest as long as we don't think it will harm
others or contribute to regulations which would impact hobby chemistry, which the forum is based on. I am also pretty sure that at least most of us
would enjoy having you as a member, and probably that within time, you can feel comfortable contributing. I think some of the confusion and suspicion
is that you are trying to do many things at once that are not necessarily related, or taught as related.
You definitely posted in an appropriate subforum for learning or re-learning these things. I think you should seek out an introductory text or website
to assist you as well, and the way courses are typically oriented in a highschool-to-college/university-to-graduate progression build on each other
through much trial and error. You may have noticed this thread with additional resources: https://www.sciencemadness.org/whisper/viewthread.php?tid=66...
Where exactly are you stuck? There are two points of stoichiometry, and a bridge between them:
1. You have a theoretical, idealized, balanced equation. This has no limiting reagent because there is no waste. Everything reacts in the most
efficient manner possible. This gives you theoretical yield, which is what you asked about. It's abstracted from how reality actually works, but we
use it as a limitation or ceiling for how efficient a reaction can possibly be. Try and conceptually separate this from any experimentation. To
reiterate, the theoretical yield, which is what you asked about, is built on a balanced equation. You have to have a concept of the equation first.
This doesn't tell you about whether the equation is accurate for your reaction conditions, if it proceeds to the right or the left with a particular
favorability, what the yield of an experiment is, etc. It doesn't show what happens in terms of energy or much in terms of three dimensional
structure. These are all generally taught later, and build upon stoichiometry.
Bridge: You have data. You have data from the amount of reactants you started with, and then you have data on your reactants: the actual
empirical/experimental yield. This is just a measurement. No stoichiometry necessary here.
2. Now, in theory, you could measure out exact, flawless amounts of reagent to match your balanced equation. In practice, this doesn't happen, and you
have one reagent which limits your reaction, while the other(s) is/are in excess, and have zero bearing on the theoretical yield since they would be
left unchanged when they ran out of partner reactants. This means you have to perform another round of stoichiometry to compare with the theoretical
yield you already have.
Now you have percent yield. You determined how efficient your reaction was in reality versus how efficient it could possibly have been, taking into
the real quantities of material you reacted.
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Darkstar
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No problem. Just to make it clear, though, the exact mechanism for these hypochlorite oxidations isn't actually known. The only thing for certain is
that they tend to work much better under acidic conditions, suggesting that it's actually hypochlorous acid that's doing the oxidizing (or at least
playing a significant role in it), and don't appear to involve any sort of free-radical mechanism.
| Quote: | | However, Im still at a loss as to what the stoichiometry would look like. Are the THF and the Ca(OCl)2 both 1 and 1? |
If you look back at Turd's original post, you'll see the balanced equation:
According to this, in theory, one equivalent of Ca(ClO)2 will oxidize one equivalent of THF, producing one equivalent of GBL,
CaCl2 and H2O in the process. If you look at the mechanism I proposed, you'll see the same thing as well.
| Quote: | | Id like to understand and see how the acetonitrile and acetic acid play a role in the reaction. |
The acetonitrile functions as a solvent and the acetic acid catalyzes the reaction by protonating hypochlorite and activating it for nucleophilic
attack on its chlorine by THF's oxygen. The calcium acetate initially produced is eventually neutralized by the aqueous HCl, regenerating acetic acid
and producing CaCl2 instead.
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Chemosynthesis
International Hazard
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Yes, you may have missed that balanced equation because it wasn't there originally, RelativeEffectiveness. It's amazing what one can edit into a post
after they claim to have defined variables and were asked to point it out.
I'd like to add another possible mechanism at play here as well, not to detract from Darkstar's post.
I don't have any chemical drawing software on this computer, but I might draw an alternative tomorrow. Luckily, it is very similar to Darkstar's first
mechanism, and converges with the second oxidation.
What I would propose as also reasonable as a competing reaction mechanism is the protonation of THF at the oxygen (as opposed to the chlorination
shown in Darkstar's first reaction), forming a different oxonium intermediate. Resonance structure of the oxygen withdrawing electrons from a
proximate carbon, very similar to Darkstar's third step in the same mechanism, but instead of water, the attack is from hypochlorite. Ketone formation
between the carbon and new oxygen, with loss of hydrogen and chlorine, respectively. Hydrogen joins free acetate anion deprotonated to activate the
THF at the start of reaction, reforming the catalyst, and chlorine is evolved. Proceed with second oxidation in an identical fashion to Darkstar's
proposal.
Edit- | Quote: | | Are the THF and the Ca(OCl)2 both 1 and 1? |
Oh, are you asking about how to balance the stoichiometry of the equation for theoretical yield calculation? Here is where you keep track of your
atoms on both sides of the equation and use linear algebra so as not to violate conservation of matter. Empirical formulas make this simple to keep
track of explicitly, but you can derive this from the mechanisms Darkstar drew since the bond line notation is understood to represent each atom, just
with some more structural information. How much detail you show can vary, and it's important to figure out notation you prefer and what speaks to you.
For example, if you take the dissociated hypochlorite as a reactant and ignore the calcium as a spectator ion, you will see 2 hypochlorite polyatomic
ion for each molecule of THF. Adjust accordingly when necessary, as the valence and normality of reagents will not always follow.
You do need to keep track of your atoms. Once you hit aldol condensations, I see students mysteriously lose a carbon all the time. It's very easy to
do, and it's also very wrong. Don't be that person! One of whole points of a mechanism is to be able to use pictures to represent the math for you,
and also to give you a little more spatial information than an empirical formula, with more interactive information than a condensed formula.
It makes mathematical operation a bit more intuitive this way, but you still need to understand that what is on the left doesn't vanish from existence
on the right. As with the equation 1+7, the commutative property shows you can also have 7+1 mean the same thing. THF+calcium hypochorite is
indistinguishable from calcum chlorite+THF. In the real world, the rate of addition and order matter, but not here because it is using mathematical
operation.
Subtraction is not commutative. 7-1=/=1-7. Similarly, Ca(OCl)2- Ca2+ (dissociating) is not Ca2+-Ca(OCl)2.
Hopefully that doesn't warp anyone's brain reading this.
[Edited on 19-2-2015 by Chemosynthesis]
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Darkstar
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No problem at all. I'm completely open to alternative mechanisms. I welcome it, in fact. To be honest, I tend to believe there's more than one
mechanism at play as well. I also suspect there's more than one active oxidizing species, too. While I'd like to think it's the hypochloronium ion, it
could also be ClO-, HOCl, Cl2, AcOCl or even something like a free chloronium ion. Since the reaction produces chloride ions that can be
oxidized by H2OCl+, Cl2 may very well play some kind of role in the oxidation.
Which is why I've always found these hypochlorite oxidations rather interesting, as no one honestly knows how the hell they actually work.
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Chemosynthesis
International Hazard
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Excellent points. It is fascinating to me how we can know so much about a product, yet so much less about how exactly it was produced, even with all
the fancy equipment and techniques out there.
Kind of rambling for the rest of this.
I remember when I was first shown an attempt at reaction monitoring with a Raman spectroscope instead of TLC, or a transition state analog diagram,
and how these were kind of hyped by the person showing me... And someone else in the lab or office or wherever chimes in with methodological critiques
and signal-to-noise sensor limitations. Mental whiplash.
For related reasons, I can't help but get excited at things like tabletop NMRs and gel electrophoresis kits for home use. Kids of the future will be
able to analyze their vinegar volcanoes in ways that would elicit my jealousy if it's all they can do!
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CuReUS
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Quote: Originally posted by gdflp  | | Quote: Originally posted by turd |
| Quote: | | No one will help you make drugs |
Who gives you the authority to speak for everyone? Stop being a prick.
[Edited on 17-2-2015 by turd] |
You're right, I phrased that wrong. Everyone who values their equipment and doesn't want to face the small chance of being charged as an accomplice
will not help you make drugs. I apologize.
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surely you are not serious.So suppose someone makes a drug from the instructions in an article or journal,than the author of that article can be
summoned to court and be charged as an accomplice ?
also,the accomplice could just say that he/she had no idea what the other guy was up to,because the OP has not clearly stated what chemical he is
after.
| Quote: Originally posted by RelativeEffectiveness |
In the synthesis, solution A is added dropwise to solution B allowing for an ether to transform into an ester to for use of the 1deg alcohol oxidation
into a lactone.
Solution A: (CH2)4O + CH3CN + CH3CO2H
Solution B: Ca(ClO)2 + H2O
If you understand this equation then you'll almost certainly understand its ultimate purpose as it has limited use for anything else.
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I think what turd is trying to convey is right.Organic chemistry cannot be completely explained using equations,unlike inorganic(its like trying to
give a reaction mechanism for say,a displacement reaction)
suppose there is a reaction,HCl +NaOH>>>NaCl+H2O ,I am sure of the products formed,so I can now balance it and find out yields
but an organic reaction does not go like that
as turd gives an example: | Quote: Originally posted by turd |
E.g. you cook phenylacetone from phenylacetic acid in acetic anhydride. You use a huge excess of acetic anhydride, because you know that you will get
biaryl product otherwise. Say 20 g PAA in 800 ml AA. You can calculate yield based on PAA without knowing how much AA reacts with PAA.
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like he says,along with phenylacetone,you will get other compounds.So you are not certain of your products
then how can you make an equation,when you don't even know all the different products that could form ?
anyways,the best thing to do would be to calculate the yield based on turd's and chemo's idea and check with this
http://winter.group.shef.ac.uk/chemputer/reaction-yields.htm...
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Chemosynthesis
International Hazard
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| Quote: Originally posted by CuReUS |
surely you are not serious.So suppose someone makes a drug from the instructions in an article or journal,than the author of that article can be
summoned to court and be charged as an accomplice ? |
I don't mean to speak for gdflip, Or what it takes to be considered an accomplice, accessory, civil asset forfeiture, etc. for any particular locale,
but the law can be completely irrational. http://www.theverge.com/2014/11/11/7193391/italy-judges-clea...
published scientists scientists have actually discussed this very topic in relation to pharmacologically active compounds, potency, animal modeling,
syntheses, etc. I doubt anyone quit their jobs over it, but I also thought this was a parody news story from The Onion. The law can be completely
irrational in both how it is written and how it is interpreted/applied.
http://theweek.com/speedreads/443383/irs-seizes-womans-entir...
Some people even quit hobby chemistry for these underlying reasons. Everyone has to decide for themselves what is an appropriate level of concern for
their own unique situation. I wear a seatbelt, but I don't strap on a trauma plate when I drive even though they are attributed dramatically increased
car crash survivability odds in some circumstances.
| Quote: |
Organic chemistry cannot be completely explained using equations,unlike inorganic(its like trying to give a reaction mechanism for say,a displacement
reaction) |
I would be very careful about saying that as an absolute. From a reductionist approach, building
a quantum model of anything requires approximations. From a larger scale perspective, no inorganic solid lattice is considered free of defects.
In terms of explaining the theoretical yield, like the thread title, yes, a theoretical equation of perfect efficiency is formulated and balanced.
What else would we possibly use to normalize yield to in order to cross-compare samples?
The reaction equation itself never explains unreacted starting material to any degree of confidence without an empirical determination, just as real
chemical byproducts must also be measured. And even then, measurements have associated error. You can never be 100% certain your reagents are pure
down to the last molecule. Even if you assume them pure, UPLC solvents are not free from degradation over time, either. You have radioactive decay,
which can transmute atoms and break bonds with recoil energy.
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