text:
Cheap but efficient disinfectant / biocide for home lab
EDIT
I am forced to reword my question about a chemical mixing ratio.
I have seen in Wikipedia that peroxide ($\ce{H2O2}$) and Acetic Acid can be mixed to Peracetic acid - this is an equilibrium.
I have also seen in Wikipedia that peracetic acid mixed with acetic acid will be explosive - in other words: If I don't get the mixing ratio just right then the "peracetic acid" will actually be "peracetic acid dissolved in acetic acid". I need to avoid this situation.
I have also read in Wikipedia that "thinning" the peracetic acid will shift the equilibrium and so this might end up in an explosive solution - I need to avoid this.
I have also seen at amazon.de that peressigsäure/alkohol is widely used as a disinfectant and I suppose the ratio of ethanol should be at 69% in order to kill most any microbes.
I need to mix a weak solution of $\ce{H2O2}$ and acetic acid and 69 % ethanol so that the peracetic equilibrium is held to be non explosive. And I also need to mix a more potent solution of $\ce{H2O2}$ and acetic acid and 69 % ethanol so that again, the peracetic equilibrium will fit and not be explosive.
As far as I understood it is not done by having the potent solution in the fridge at 0 degree Celsius and on demand simply thinning the potent solution to a weaker disinfectant - the peracetic equilibrium would then shift and it might become explosive.
Sorry, I am not really fit to calculate concentrations in Vals and Mols - but I could of course deal with any complex mathematical formula (on paper or on the calculator - or I could even code a small mixing calculator in java or c#).
So I would ask you to give me the right formula for my problem:
Component A = 12 % $\ce{H2O2}$
Component B = 20 % Acetic Acid
Component C = 98 % Ethanol
Component D = $\ce{H2O}$
AND I need 1 liter of mixture so that Alcohol appears with 69 VOL % and that peracetic acid appears with $x$ % ($x$ between 2 and 10) and no acetic acid will be in the mixture aside from the equilibrium.
I could then simply vary the $x$ (the conecntraction of peracetic acid) in the formula and mix as needed.
please, show me how to calculate the concentrations.
thanks!

I'm voting to close this question as off-topic because this belongs on biology SE or other site - it's not about chemistry

well the interactions between ehtanol and peroxide and acetic acid is definatly about chemistry - or should the mathemacician tell me how these chemicals will react?
please suggest where I should ask this. thanks

You may want to give https://biology.stackexchange.com/ a try. No guarantees (by the way, I really like the question, but unfortunately it's really off topic as it's more about how to kill living things)

it is not primarily about killing life - I know how to kill contaminations.
it is a question about the mixing rate so that peroxide and acecic acid will stay in the proposed equilibrium and that not highly explovives will happen by accident.
This is 100% a question about chemistry

Ok, I'll vote to reopen.

Mixing rate (how fast) or mixing ratio (how much)? Check out the MSDS for the product TM peracid 15 (English ; German). They don't use any alcohol, and have a whole range of substance that are incompatible.

With "mixing rates" I referred to the relative quantities. Yes, there is some information in the TM peracid 15 manual, it is not explosive but then a lower explosive conecntration and an upper explosive concentration is given.
Unfortunatedly this doesnt make it easier to develop the formula.

It should be simple once you know tha safety limits. Besides, are you sure that bleach won't be ok? Just to be sure you do not overshoot.

I did not succeed with my new lamina flow hood 20 years agao although I washed the plant samples with NaHypoChlorid Bleach and then washed these with H2O2 and then rinsed these with autoclaved water while the hood was cleaned with 85% Ethanol.
Some yeast and some bacteria survived.
Now I read in de.wikipedia that only Peracetic Acid will kill them all - virus, bacteria, yeast, spores and funghus.

The Amazon website gives the composition of Peressigsaure/Alkohol: Inhaltsstoffe pro 100g:
● 19g 2-Propanol
● 5g Ethanol
● <1% Wasserstoffperoxid
● <1% Peroxyessigsäure
● <1% Essigsäure
Working time 30 seconds, shelf life 12 months.
Don't expect that H2O2 plus acetic acid to give peroxyacetic acid. The full Wikipedia reference is:
Peracetic acid is produced industrially by the autoxidation of acetaldehyde:[2]
O2 + CH3CHO → CH3CO3H

It forms upon treatment of acetic acid with hydrogen peroxide with a strong acid catalyst:[3]
H2O2 + CH3CO2H ⇌ CH3CO3H + H2O

Making the peroxy acid can be done from acetic acid, but requires a strong acid catalyst (to generate CH3CO+).
So, you will have to get peroxyacetic acid from somewhere in some form, in addition to your other chemicals. Duplicating this formula requires more isopropanol than ethanol, but either alcohol should perform equally.
An overview document titled Chemical Disinfectants at https://www.cdc.gov/infectioncontrol/guidelines/disinfection/disinfection-methods/chemical.html mentions two chemical sterilants are available that contain peracetic acid plus hydrogen peroxide (i.e., 0.08% peracetic acid plus 1.0% hydrogen peroxide [no longer marketed]; and 0.23% peracetic acid plus 7.35% hydrogen peroxide. This document also lists the benefits of H2O2, peracetic acid, alcohol(s) and chlorine bleaches. And formaldehyde! About peracetic acid, it says: It is considered unstable, particularly when diluted; for example, a 1% solution loses half its strength through hydrolysis in 6 days, whereas 40% peracetic acid loses 1%–2% of its active ingredients per month.
As regards explosivity, a document of ECETOC at http://www.ecetoc.org/wp-content/uploads/2014/08/JACC-040.pdf gives the formulas of two cleaners as:
1: PAA 15%,H2O2 23%,HOAc 16%,H2O 45% and
2: PAA 15%,H2O2 14%,HOAc 25%,H2O 42%.
I gather from these two formulations that they and anything less in H2O2 or PAA would not even remotely be explosive. No alcohol was listed in these formulations.
Now if you could obtain either of these concentrated sterilants, you would have a reasonable ratio of peracetic acid, H2O2 and acetic acid. The only item missing would be the alcohol. Let's use ethanol, at 70% (or 69%, if you must). The peracetic acid cleaners would have a good shelf life because of their high concentrations. When you need to make up some sterilant, you could take ~800 grams of ethanol and add ~350 grams of the cleaner you choose to get 1 L of final sterilant (density ~1.150 g/cc), which will be 69-70% ethanol, 4.5% PAA, 4.3-7% H2O2, 7.6-4.9% HOAc, remainder H2O.
These levels are 5 or more times higher than the concentrations listed for Peressigsaure?Alkohol Pro, so you could consider adding much less of the peracid cleaner to get in the range of 1% PAA and H2O2.
Overall, it seems that H2O2 by itself is good at killing bacteria, and so is alcohol, by itself, and so is peracetic acid, by itself, but PAA is not stable for long at low concentrations (12 months at 1%??).
And perhaps it would be easier to buy the Peressigsaure/Alkohol Pro, or one of the other sterilants offered by that company, because it already comes in a spray bottle.


text:
Soil conductivity: How do I get a near equivalent between meq/100 g to mS/cm?
I have two soil reports, one that reports CEC as 45 meq/100 g and another that reports 6 mS/cm using 1:1 water soil.
I can see that the two are, if not apples and oranges, they are at best tangerines and grapefruit — the meq/100 g is the source for the ions in a water extract, but an equilibrium solution may not contain all the ions.
Can a meaningful conversion between meq/100 g and mS/cm be made?
E.g: few plants will grow in soil that has conductivity greater than 2.5 mS/cm and generally you start getting concerned at 1.  What is the equivalent measure in meq/100 g?
FWIW main ions of concern are $\ce{K+},$ $\ce{PO4^3-},$ $\ce{Mg^2+},$ $\ce{Ca^2+},$ $\ce{CO3^2-},$ $\ce{HCO2-}.$

The mineral ions (nutrients) in soil can be expressed as two ways: (i) Cation Exchange Capacity (CEC), which has units of $\pu{meq}$/$\pu{100 g}$; and (11)  Electrical Conductivity (EC), which has units of $\pu{mS/cm}$.
When the conductivity is measured in 1:1 mixtre of soil:water, it is called $\mathrm{EC_{1:1}}$ (This is a way of measuring electrical conductivity of soil water or $\mathrm{EC_{sw}}$).
According to USDA Publication, $\mathrm{EC_{1:1}}$ readings less than $\pu{1 dS/m}$ ($\pu{1 mS/cm}$), soil are considered non-saline and do not impact most crops. This publication also gives you a easy procedure for how to measure $\mathrm{EC_{1:1}}$ of your soil.
My best bet is you don't have to worry about your second soil sample, which has CEC of $\pu{45 meq}$/$\pu{100 g}$, because none of the cations (exchangeble cations in the soil) in concern is $\ce{Na+}$ (the given CEC is the sum of all exchangeable cations in equivalents). According to above publication, soils with a high concentration of sodium salts (sodic conditions) have given problems.
To my understanding, there is no direct relationship between $\pu{meq}$/$\pu{100 g}$ and $\pu{mS/cm}$. For more info on Cation Exchange Capacity (CEC) and units of $\pu{meq}$/$\pu{100 g}$, read:

J. P. Reganold, J. B. Harsh, “Expressing cation exchange capacity in milliequivalents per 1 100 grams and in SI units,” J. Agronomic Educ. 1985, 14(2), 84–90 (https://www.agronomy.org/publications/nse/archive/vol-14).

If I understand it well, then $\pu{1 meq}$ means 1 milimol equivalent.
Therefore, if we consider for illustration molar masses $M_{\mathrm{Ca}}=\pu{40 g/mol}$ and $M_{\mathrm{K}}=\pu{39 g/mol}$, then $\pu{1 meq K}=\pu{39 mg}$ and $\pu{1 meq Ca}=40/2=\pu{20 mg}$
The first step is to express molar amounts of involved ions, resp. molar equivalents, in the conventionally used representative ions or salts. As the same molar concentration of ions of different mobility have both different molar conductivity and different specific conductivity.
Second step is recalculation to soecific conductivity in $\pu{mS/cm}$.
The third step is determine the degree of extraction, experimentally ( extraction method versus total analysis e.g. by acidic extraction and AAS analysis) or by convention.
It is also possible that even meq/100g is related directly to the 1:1 extract. Then there would remain to determine tho representative, probably conventional salt for recalculation factor
As
$$\kappa=c\cdot \Lambda$$
Where
$\kappa$ is ( specific} conductivity
$c$ is concentration of mol equivalents per volume
$\Lambda$ is molar conductivity ( specific conductivity per unit of molar equivalent concentration.)

There is no universal conversion factor between $\pu{mS/cm}$ and $\pu{meq/100g}$. As suggested by Poutnik's thorough answer, you may need to know some additional details about how the data was compiled, which may be embedded in your reports. A scan through websites describing soil analysis suggests the following as a useful conversion:
$$CEC(\pu{mS/cm)} = (0.01f_{sat})^{-1} \times C(\pu{meq/100g})$$
with $f_{sat}$ the percent saturation of the soil (the water retention capacity of the soil as weight of water per dry weight soil, times 100). The expression makes certain assumptions:

$C(\pu{meq/100g}$) refers to the equivalent molar concentration of $\ce{NaCl}$ that would result in the conductivity observed in a saturated solution extracted from water-saturated soil.
the molar conductivity of $\ce{NaCl}$ is $\approx \pu{100 mS cm^{-1}M^{-1}}$

Note the molar conductivity of $\pu{100 mM}$ NaCl, according to the CRC Handbook of Chemistry and Physics, is $\pu{107 mS cm^{-1}M^{-1}}$ at $\pu{298 K}$.

source: Stack Exchange

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text:
Why is it easier to break a C-H bond of methane after another C-H bond has already been broken?
Bond energy explanations say the number given is often an average.
For instance, in methane, the $\ce{C-H}$ bond dissociation energy is the total energy required to remove all four hydrogens, divided by four. $(\pu{415.5 kJ/mol})$
But, removing the first hydrogen atom is harder than the second or third ($\pu{439 kJ/mol}$ for the first). Why?

Pardon me, I just read that removing the second hydrogen is harder than removing the first, not easier.  But the third is easier than the first two, and the fourth easiest of all.       But, I am still curious as to why....

What is your take? Let's hear that first.

I believe unpaired and/or 'nonbonding' valence electrons interfere somehow with the other bonds/electrons....

@KurtHikes Note that you can [edit] your question if you feel it needs to be corrected. For instance, you can convert your first comment into an edit.

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text:
Learning chemistry in a new language
I'm from Slovakia, 16 and like chemistry a lot. I want to pursue it in the future but there aren't any good universities here where you can get a Ph.D. in chemistry so I want to go abroad, preferably to America or the UK. But there's a problem: I don't even know how to name molecules in English. I want to prepare for the future so I want to learn that before I go to UNI. And there's another problem. I can't find a source that I can learn from. I just want to know the basics: oxides, salts, acids, and hydroxides. If anybody could send me a link to a site that I can learn it from I'd be very thankful.
P.S.
I don't know if it's done in English the same way, but we use oxidation numbers to get the chemical formula from the name and in reverse. That's what I want to know but in English.
EDIT: I just want to know the basics RN and I don't want to start off with organic chemistry and stuff like that. I just want to know how to take a simple molecule, for example, AlCl3 and know how to say its name. Is it aluminum (III) chloride or aluminum trichloride? Or something like SO4 and SO3. Is it sulfate and sulfane or what? I just want to know how to name molecules and write down their chemical formula.

You may want to start here

That of using oxidation numbers is a practice which is still used for some, long-known compounds (eg: perchlorate, chlorate, chloride, hypochlorite), which now is (luckily?) falling in disuse because of the internationally used IUPAC nomenclature.
My advice is that of reading some introductory books in english. One example of such books is Chemical Principles, by Atkins, Jones

I would not worry about substance names in different languages, I don't think it will be a big hurdle. Chemists all over the world read and write scientific publications in English, and substance names are easy to look up. If your background in chemistry is strong, switching languages when necessary is fairly easy.

Beside the resources for learning chemistry Poutnik indicated, you may learn some of the chemical names and concepts from wikipedia, too. Frequently, articles are available in more than one language and sometimes a version in an other language offers additional details, too.  You find the switch at the left side of the pages:

Typically, you find some references at the bottom of these pages which may be accessible by you without going to a university library.
As side note: You mention that you did not yet start to study chemistry at a university at all.  Hence, it is too early for you to judge if a Slovak (or Czech, given the language) university is good or bad for your aspiration of a PhD in chemistry; because you likely do not know yet which specialty will attract your interest, nor potential co-workers and supervisors.  Remain active to obtain a solid chemical education first -- a chemistry department with classes about 30--60 students per year may be more helpful for laying such a foundation, than a larger institution where you become "just a number".  Do not exclude smaller departments (and countries) just because they are smaller, or less frequently in the scientific media, than others when thinking about a move to an other institution is an opportunity.


text:
Nomenclature of simple molecules
I'm from Slovakia, 16, and I'm really confused about the English simple molecule (oxides, hydroxides, salts, acids) nomenclature. I guess we do it differently. To sum it up: we have suffixes from 1-8 to communicate the oxidation number of an element in a molecule. We put those suffixes at the end of the elements stem, combine it with the word for what kind of molecule it's forming (oxide, hydroxide, ...), and then we can determine from that name and the oxidation number of the other elements (if it's an oxide then oxygen if it's a hydroxide then the hydroxide anion and so on) what it's chemical formula is. Is it done the same way in English speaking countries? Do you just have to search for the oxidation number in a periodic table? If not then how?
Thanks!
Edit: we use these suffixes for oxidation numbers:

-ný/á
-natý/á
-itý/á
-ičitý/á
-ičný/ečný/á
-ový/á
-istý/á
-íčelý/á

(ý or á is based on gender of the word...)
They all represent the positive oxidation number of a part of a simple molecule, for example, Al2O3 would be "oxid hlin-ITÝ" because aluminum is hliník in Slovak and -itý means that the oxidation number of the aluminum is +3.
How would you write down $\ce{Al2O3}$ in English? And also how do you name salts, bases, and acids?
EDIT2(for Karsten Theis)
\begin{array}{|c|c|c|}
\hline
\text{Formula} &  \text{English name} & \text{Slovak name}  &\text{Oxidation #}  \\
\hline
\ce{FeCl2 }& \text{ferrous chloride, iron(II) chloride} &  \text{chlorid želez-natý}  & +2\\
\hline
\ce{FeCl3 }& \text{ferric chloride, iron (III) chloride} & \text{chlorid želez-itý} & +3\\
\hline
\ce{FeO }& \text{iron(II) oxide} &  \text{oxid želez-natý}  & +2\\
\hline
\ce{Fe2O3 }& \text{iron (III) oxide} & \text{oxid želez-itý} & +3\\
\hline
\ce{N2O}& \text{nitrous oxide} & \text{oxid dus-ný} &+1 \\
\hline
\ce{NO}& \text{nitric oxide} & \text{oxid dus-natý} &+2\\
\hline
\ce{HNO2}& \text{nitrous acid} & \text{kyselina dus-itá} &+3\\
\hline
\ce{HNO3}& \text{nitric acid} & \text{kyselina dus-ičná} &+5\\
\hline
\ce{NO2-}& \text{nitrite} & \text{dus-ita-n} &+3\\
\hline
\ce{NO3-}& \text{nitrate} & \text{dus-ičita-n} &+5\\
\hline
\ce{N^3-}& \text{nitride} & \text{nitrid} &-3\\
\hline
\ce{CrO}& \text{chromous oxide} & \text{oxid chróm-natý} &+2\\
\hline
\ce{CrO3}& \text{chromic oxide, chromium trioxide} & \text{oxid chróm-ový} &+6\\
\hline
\ce{Cr2O3}& \text{chromium (III) oxide} & \text{oxid chróm-itý} &+3\\
\hline
\ce{H2CrO4}& \text{chromic acid} & \text{kyselina chróm-ová} &+6\\
\hline
\ce{HCl}& \text{hydrochloric acid} & \text{kyselina chlóro-vodíková *} &-1\\
\hline
\ce{HClO}& \text{hypochlorous acid} & \text{kyselina chlór-na} &+1\\
\hline
\ce{HClO2}& \text{chlorous acid} & \text{kyselina chlor-itá} &+3\\
\hline
\ce{HClO3}& \text{chloric acid} & \text{kyselina chlor-ečná} &+5\\
\hline
\ce{HClO4}& \text{perchloric acid} & \text{kyselina chlor-istá} &+7\\
\hline
\ce{Al2O3}& \text{aluminum oxide} & \text{oxid hlin-itý} &+3\\
\hline
\ce{CaO}& \text{calcium oxide} & \text{oxid vápen-natý} &+2\\
\hline
\ce{Li2O}& \text{lithium oxide} & \text{oxid lít-ný} &+1\\
\hline
\end{array}
*(vodíková means that that acid only has hydrogen and not oxygen)

Can you show a few examples? My experience has been that I can understand "chemistry" in any romanic/germanic language without any problem.

Generally there are two types of simple (inorganic) names: Element-(oxidation number)-oxide/chloride (e.g. Cu-(II)-oxide, CuO), and less systematic names like carbondioxide.

There seems to be no better way than to practise chemical nomenclature like a language with rules (like grammar) and vocabulary; which equally depend a bit from the natural language, too.  From a search about oxides (https://glosbe.com/en/sk/oxide) interestingly Slovak -- in comparison to English, Lithuanian, German -- seems to regularly invert the order of "elements of meaning" (metal; oxide / sulfate) in a pattern like the romanic French, Spanish; and equally slavic Polish and Russian.  Just substitute "sk" by lt, ge, fr, sp, pl, ru.

Pavol, thanks for adding that table - it nicely illustrates how systematic the naming is. @Curt F. - thanks for the edits, I fixed them here too. I hope it is correct now, but if someone can check the Slovak language ones...

In English, French and German, the names are less systematic. Here are some examples from English:
\begin{array}{|c|c|c|}
\hline
\text{Formula} &  \text{Name} & \text{Oxidation #}  \\
\hline
\ce{FeCl2 }& \text{ferrous chloride, iron(II) chloride} &  +2\\
\hline
\ce{FeCl3 }& \text{ferric chloride, iron (III) chloride} &  +3\\
\hline
\ce{N2O}& \text{nitrous oxide} &  +1 \\
\hline
\ce{NO}& \text{nitric oxide} &  +2\\
\hline
\ce{HNO2}& \text{nitrous acid} &  +3\\
\hline
\ce{HNO3}& \text{nitric acid} &  +5\\
\hline
\ce{NO2-}& \text{nitrite} &  +3\\
\hline
\ce{NO3-}& \text{nitrate} &  +5\\
\hline
\ce{N^3-}& \text{nitride} &  -3\\
\hline
\ce{CrO}& \text{chromous oxide} &  +2\\
\hline
\ce{CrO3}& \text{chromic oxide, chromium trioxide} &  +6\\
\hline
\ce{Cr2O3}& \text{chromium (III) oxide} &  +3\\
\hline
\ce{H2CrO4}& \text{chromic acid} &  +6\\
\hline
\ce{HCl}& \text{hydrochloric acid} &  -1\\
\hline
\ce{HClO}& \text{hypochlorous acid} &  +1\\
\hline
\ce{HClO2}& \text{chlorous acid} &  +3\\
\hline
\ce{HClO3}& \text{chloric acid} &  +5\\
\hline
\ce{HClO4}& \text{perchloric acid} &  +7\\
\hline
\ce{Al2O3}& \text{aluminum oxide} &  +3\\
\hline
\ce{CaO}& \text{calcium oxide} &  +2\\
\hline
\ce{Li2O}& \text{lithium oxide} &  +1\\
\hline
\end{array}
I think this is what happens if names of substances were chosen before the concept of oxidation state (and electrons etc) existed. It would be nice to have something more systematic, but that would mess up all the older literature.
It would be fascinating (to me, at least) to see the Slovak names in another column of this table. Also, I am glad that chemical formulae exist that are universal in any language.

I'll try later today to make that table for you. And give you some insight in naming the acids and salts because thats the hardest.

@PavolKomlos Have a look at http://www.rsc.org/suppdata/c9/dt/c9dt00352e/c9dt00352e5.pdf (freely available supplementary informtion of https://pubs.rsc.org/en/content/articlelanding/2019/DT/C9DT00352E#!divAbstract) as a handy English guide.

English is certainly less systematic, but there is method to the madness.  "-ic" was assigned to the highest known oxidation state, then "-ous", then "hypo--ous" for lower known oxidation states. I think "per--ic" for an even higher state came later, but I'm not sure. The big difference from Slovak is that the English refers to relative oxidation states rather than absolute, ie -ic is always more oxidized than -ous, but it might be +5 or +3 or +2 depending on the element.

@Andrew - Great comment! Some method ... but often the oxidation state is different by two for "-ic" and "-ous". Sometimes they are correlated from acid to oxide, and sometimes not (nitrogen compounds). Sometimes, a compound with an oxidation state between "-ic" and "-ous" gets discovered after naming compounds (see chromium). It is a nice historical record, but pretty tough on learners (pre-internet, I guess).


text:
FMO analysis of the [3,3] Sigmatropic reaction regarding geometry. Is it accurate?
While studying the reasons behind the stereospecificity of [3,3] Sigmatropic reactions, I ran into an image portraying both possible transition states for the reaction: The Chair TS and Boat TS. The complete FMO orbitals were only drawn for the Chair TS and the final geometries of the products was shown for both transition states:

I find it a little bit hard sometimes to visualize the three dimensional transitions that result in a specific configuration, so I tried to complete the FMO analysis with the orbitals for the Boat TS and to draw the sigma-bond rotations necessary to create constructive overlap between the lobes. I came up with the following:

On the Chair TS we see the σ* shaded lobe is perpendicular to the shaded lobe of the π HOMO from the double bond next to it (having a 3D model would make it easier to see because in the drawing they seem aligned, but they are actually perpendicular). The sigma-bond would then have to rotate 90º inward for effective constructive interaction, "throwing" the R-Group outwards and resulting in the E-configuration seem in the product. The other σ* lobe also rotates 90º in the same direction (I forgot to draw the arrow there, but it would be the same as the one beside the shaded lobe), but for some reason this rotation result in the regular "cyclic-like" geometry for that double bond (Z-configuration?).
If it wasn't hard enough to visualize it on the Chair TS, it gets worse on the Boat TS. I came up with the orbital configuration as seem in the image. First, I got a little confused about the σ* shading, because the whole premise for the shading had to do with constructive overlap where the double bonds would occur. But there I had to draw opposite phases on the lower part. That, I believe, is because initially they were aligned with the same phases (as in the Chair TS), but the conformation twisting threw the constructive phases in opposite directions. Anyways, to reach constructive overlap the sigma-bond next to the substituted carbon would have to rotate close to 90º counter-clockwise, while the other sigma-bond would have to rotate almost 180º. That explains why this transition state is so unfavorable, but I'm still struggling a bit with the geometry. The 180º rotation sounds like it would result in the unsubstituted double bond pointing out of the "cyclic-like" shape as seem in the product. But I can't clearly see how the 90º rotation throws the R-Group inward in a Z-configuration geometry. Instead, I came up with another orbital configuration possible that might be the correct one:

In that orbital configuration the sigma-bond of the substituted carbon wouldn't have to rotate, and we would have the R-Group pointing inward like in the product.
Which orbital configuration is correct, if any? Is my reasoning about the sigma-bond rotations and the resulting products geometry correct? Do you have any tips when it comes to visualizing geometrical issues on more complicated molecules?

Remember that the p-orbitals of the double bonds are orthogonal to the plane of the carbon framework. The Cope rearrangement you show will be an equilibrium mixture of the E-isomer (major) and the starting material (minor) because the activation energy for the chair transition state is lower than for the boat. At more elevated temperature some "leakage" to the Z-isomer may be seen because the three dienes are in equilibrium with each other. Your best bet is to make a molecular model and traslate what you see to paper.

I see, it's just a little harder to visualize where the plane of the carbon framework is on those conformations, because the molecule as a whole doesn't have a single plane I guess. That makes me think the second Boat TS orbitals drawing is a little closer to reality than the first. Also makes me think the HOMO orbitals (blue) point outside of the "paper" plane, like the lobes where coming towards us.

For chair-like transition states the angle at which you draw your chair can make a significant difference to how easy it is to visualise stereoelectronic interactions. Sadly, there is no real way to know which is the best way to draw it, except by either trial and error, or prior experience (or leveraging on other people's experience, i.e. copying it from somebody else!).
If you rotate the chair a bit so that the forming bond is in front (as opposed to at the side), then you can have something like this:

You don't need to overthink how the sigma bond rotates; this is a sigmatropic rearrangement, not a electrocyclic reaction where there are conrotatory/disrotatory modes. The geometry at the substituted carbon definitely changes (from tetrahedral to trigonal planar), so there is some kind of "flattening" as the reaction proceeds, but all you really need to pay attention to is the relative disposition of the R substituent and the rest of the carbon chain: here they are clearly trans to one another, which is an (E)-alkene. This is stereospecific, so if you start with the conformation shown in the left, you will end up with a trans alkene. There isn't a different "rotation mode" that leads to the cis alkene.
The main way of getting a cis, or (Z)-alkene, is not actually via a boat TS, but rather via a chair TS with the R substituent axial instead of equatorial. Note that this is a different conformation from the previous image, so again it's not about which direction the sigma bond rotates in, but rather the original location of the substituent (axial/equatorial). The orbital diagram is exactly the same, so there's no need to redraw it, but it should be easy enough to see that this leads to the reverse stereochemistry.
The boat TS is trickier to draw. This is my preferred representation:

but I am not entirely sure which TS is higher in energy (i.e. whether the substituent prefers to point up or point down), even after consulting several references. I don't think it's a matter of great significance; after all, the boat TS usually only plays a very minor role, as far as I know.

Thanks, things are a bit clearer with your answer. I was wondering, considering the stereospecificity of the reaction, can I conclude that only the equatorial form of the Chair TS exists for that specific reactant (with a dashed bond to the R substituent)? Analogously, the Boat TS for that specific reactant would always be axial?

No, you can always redraw it such that it is axial in a chair TS. You need to flip the entire structure to do that.

Sorry, I think I'm still a bit confused, because the course material I have states the Chair TS leads to a trans product (stereospecificity). While the Boat TS would lead to a cis product, though this TS isn't favored due to the lack of constructive orbital overlap. If the substituent could be either in the axial or equatorial position wouldn't the final product be a mix of cis/trans conformations? Or maybe the equatorial TS is more stable and the course material is just not showing the axial TS because it's more unstable and thus unlikely to happen?

“The chair TS leads to the trans product” Not exactly; the chair TS with the substituent equatorial leads to the trans product. “Wouldn’t the final product be a mix of cis/trans”? Yes. “Not showing... because it’s more unstable” It is a minor product, but it will be formed in nonzero quantities. I also don’t entirely agree with the use of the word “stereospecific”, but I’ll leave it for now.

Thanks, I took a while to answer so I could research more. On the video explanation of the analysis there’s less ambiguity than the text I guess. It states clearly that the chair conformation can have the substituent in either position, but the equatorial is more stable one for the substituent resulting in the preferred isomer. I’ll look further on the subject but you made things much clearer!


text:
Williamson Ether and Carboxylic Acids
What would happen if you tried a Williamson Ether Synthesis on something that has both an alcohol and a carboxylic acid? Would both -OH groups be functionalized, where the alcohol would become an ether and the carboxylic acid become an ester?

Hi Tbl, welcome to Chemistry SE.  Have you tried to do any research on this on your own?  The products formed will likely depend heavily on the nature of reactants and the reaction conditions.

I’ve been trying to find the answer to this question for a while, even pulled out my old organic textbook to try and answer this question. The only things I’ve found have basically said that for Williamson Ether Synthesis, turn the carboxylic acid into an alcohol then run the reaction, but I don’t actually want the carboxylic acid to react. It would be awesome if it didn’t, and only the alcohol reacted.

There is a general principle known as “last in-first out” that I think applies here. If a molecule contains multiple acidic positions with significantly different pKa, you can selectively react on the least acidic position (in your case, the alcohol).
Specifically, I would try treating your molecule with 2 eq. Of strong base such as NaH or LDA. The first equivalent will deprotonate all of your acid to form the quite stable metal acetate. The second equivalent removes the alcohol hydrogen to generate a less stable alkoxide. If you add 1.0 eq. Of the electrophile it ought to react selectively on the more reactive alkoxide nucleophile, leaving the metal acetate unaffected, then you can just neutralise in work up.

Certainly true that the alkoxide is a better nucleophile than the carboxylate

In priciple this should work. If you dissolve your omega-hydroxycarboxylic acid in excess aqueous hydroxide (or hydrolyse the lactone) then add a reactive electrophile like MeI, I think you will get the ether you want. Any ester that forms will quickly hydrolyse back. I do not have database access to search for this, but perhaps someone else can find a reference.

Won’t this just give lots of methanol?

No, I don't think so otherwise Williamson synthesis of methyl ethers would not work

True, I wonder why? Heavier solvation of hydroxide vs alkoxide?


text:
Is water the most common multielemental compound?
Water is a very common substance, not just on Earth, but also in space. Although water usually occurs in space as a solid and occasionally as a gas and relatively rarely as a liquid, the most common compound is H₂. I believe based on the abundance of elements in the universe (ignoring helium because it is a noble gas) that water is the most common multielemental (having more than one type of element in its structure) compound. Are there more common ones, or is water the most common one?

Because space is so empty, there's a fair chance the most common compound has only two atoms. Things like $\ce{HO}$ and $\ce{CH}$ can last for a very long time if there's nothing else to react with.

Ignoring He isn't good idea. HeH+ cation is one of most common in the Universe.

Helium is not only a noble gas, but also the least reactive one. Mithoron might be right, but I am doubtful though I think it is a possibility.

Well. if you ask only about neutral molecules then OK, but $\ce{HeH+}$ is, along with $\ce{H3^+}$, very common in space, so I think you should decide whether the question should be less or more broad.

Related, though I can't make any guarantees about the source: https://www.reddit.com/r/askscience/comments/3mr1i7/is_water_the_second_most_common_molecule_in_the/

$\ce{H2}$ is not a compound, it is an element. It is a molecule rather than an atom, though.

It is worthy to note HeH+ is the strongest  known acid, able to protonize any anion, molecule or atom.

You are indeed correct that the elemental molecule $\ce{H2}$ is the most abundant molecular species in the universe by far.[1]. In order to answer your question

Is water the most common multielemental compound?

I only focus on neutral species, of which around $50\%$ are in molecular, i.e. multiatomic form.[2]
In this category, second only in total abundance to molecular hydrogen $\ce{H2}$ is carbon monoxide $\ce{CO}$.
This has become evident during the extensive work that has been conducted in the last few decades as large-scale $\ce{CO}$ surveys of the Milky Way galaxy and other galaxies have been performed, further corroborating $\ce{CO}$ as the second most abundant neutral species and technically[3] as most abundant interstellar compound.
To conclude, it might be interesting to realize how substantial the difference in mass is still between the two most abundant molecular species in interstellar space:[2]

Estimates of the galactic mass of $\ce{H2}$ and $\ce{CO}$ can now be given with reasonable accuracy $m(\ce{H2}) = 2 \cdot 10^9 \; M_\odot$, and $m(\ce{CO}) = 2 \cdot 10^6 \; M_\odot$.

So in order to estimate $m(\ce{H2})$ which constitutes the bulk of the gas mass, carbon monoxide $\ce{CO}$ is typically used as tracer or proxy for $\ce{H2}$, as further reading I suggest a very informative post on the physics.SE: Why is $\ce{CO}$ a good tracer for $\ce{H2}$? How are those molecules correlated?
The mass unit $M_\odot$ is commonly used in astrophysics and represents the mass of the Sun, i.e. $M_\odot \cong \pu{1.98E30 kg}$.
The water molecule $\ce{H2O}$ is probably next, i.e. in third place, of the most abundant molecular (neutral) species in the universe which can be directly underpinned by the fact that it made up of the first and third most abundant elements in the universe, hydrogen $\ce{H}$ and oxygen $\ce{O}$*[4]. But I am not aware of any reputable source that explicitly states or confirms this assumption.
Footnotes & References

vide, e.g. Why is $\ce{CO}$ a good tracer for $\ce{H2}$? How are those molecules correlated? or Wikipedia: List of interstellar and circumstellar molecules respectively

Winnewisser, G. The chemistry of interstellar molecules. Topics in Current Chemistry,Cosmo- and Geochemistry 1981, 39–71. DOI: 10.1007/3-540-10920-X_14.

vide ut supra, comment by Karsten Theis:

$\ce{H2}$ is not a compound, it is an element. It is a molecule rather than an atom, though.

van Dishoeck, E. F.; Herbst, E.; Neufeld, D. A. Interstellar Water Chemistry: From Laboratory to Observations. Chem. Rev. 2013, 113 (12), 9043–9085. DOI: 10.1021/cr4003177.

Hello! Chemical formulae should be typeset in upright, not italic. On Chemistry.SE this is most readily accomplished using the \ce{} macro provided by mhchem (see my edit for examples).

@orthocresol I see, thank you very much for your edit and leaving a comment! I inherently thought about 'emphasising' the molecular formulae somehow, which I attempted ad hoc with the math environment $...$. The \ce{} approach looks better and it still does set off the chemical formulae from the text itself. I'll apply it in future posts. I hope the rest of the layout does conform with any Chemistry.SE standards (as I was playing around with the 'References & Footnotes' section at the end.

May I ask @orthocresol how one can set text in the grey background as you have done in the first comment?

The rest of your layout is more than fine. The grey-background text can be done by surrounding text with backticks ```.


text:
What is a molecule’s smallest set of smallest rings?
It is been a while since I've studied chemistry. Now, I am reading the documentation of RDKit, where they mention the expression "smallest set of smallest rings" (SSSRs). I understand that a ring is a cycle in a molecule. I also understand that the SSSRs is, as the name suggest, the smallest set of smallest rings, but how do you determine what the smallest sets and rings are?  What is a molecule's smallest set of smallest rings? What is a SSSRs used for?

This is a tool to classify molecules with multiple rings. Here is an example from a PhD thesis:

So even though you can find six-membered and eight-membered rings in this structure, these are made up of multiple four-membered rings, and are thus not parts of the set of rings. As the picture illustrates, it is sufficient to choose five rings to show the connectivity of the atoms, so even though there are six four-membered rings, the SSSR includes only five of them. In this case, which five is ambiguous.

how do you determine what the smallest sets and rings are?

It turns out that this is ambiguous, so different software might get different results. In contrast, giving the size of all rings is unambiguous, but - according to the thesis I quoted - computationally more expensive and chemically less intuitive.

What is a SSSRs used for?

To classify cyclic molecules in cheminformatics. For a given software, two molecules are different if they have different SSSRs. Conversely, two identical molecules will have the same SSSR. This makes it easier to classify, sort, and search this class of molecules.

I think you mean "identify" instead of "classify". But I don't get this. If the SSSR is ambigous, that makes it rather useless for identification.

@Karl Yes, rather useless or worse: https://www.ics.uci.edu/~dock/manuals/oechem/pyprog/node123.html


text:
What is kekulization (in RDKit)?
It's been a while since I've studied chemistry. Now, I am reading the documentation of RDKit. At a certain point, the term "kekulization" is mentioned. What is kekulization (in RDKit, if this is not a standard chemical term)?

This is a method to generate alternate Lewis structures of the same molecule. Here are two examples from the cumulative dissertation by Sascha Urbaczek[1]:

If you were to search for the left molecule in panel (1) using an image search or a SMILES string, you might miss the right molecule in that panel.
According to the RDkit document cited in the question, the software routinely generates the alternate position of double bonds, and then (in a second step they call "aromatization") labels the ring as aromatic. In panel (2), there are three possible Lewis structures contributing to the actual structure (i.e. there is resonance), so the software would have to generate all three to be able to search for identical structures.

Urbaczek, Sascha. A consistent cheminformatics framework for automated virtual screening. Ph.D. Thesis, Universität Hamburg, August 2014. URL: http://ediss.sub.uni-hamburg.de/volltexte/2015/7349/; URN: urn:nbn:de:gbv:18-73491; PDF via Semantic Scholar

I do not really get the connection that led to the naming, but fwiw i suppose this is named after Kekulé? https://en.wikipedia.org/wiki/Kekul%C3%A9_Program

@bukwyrm Kekule of benzene structure fame. Alternate positions for double bonds, or delocalising the double bond electrons into hybrid orbitals.

SMILES also exist in kekulized and non-kekulized forms. The kekulized form makes the double bonds in aromatic rings explicit. Instead, the normal (canonical) SMILES omits the double bond symbol = in favor of lowercase characters to denote aromaticity. For example:
Canonical SMILES:
CC(C)(C)c1cc(O)ccc1O

Kekulized:
CC(C)(C)C1=CC(O)=CC=C1O


text:
How to dissolve calcium sulfate fast?
I would like to dissolve $\ce{CaSO4}$ in a hardened condition (e.g. gypsum board) as fast as possible. I have seen in posts about $\ce{CaSO3}$ that vinegar and sulfamic acid are able to dissolve it.
However, I would appreciate leads to reactants that are a little more active. Basically I am looking for a drop of something that would instantly create a hole.

Lead moving at 1000 fps will create a hole quickly.

A little known substance called drillium, maybe?

Substances instantly creating a hole in CaSO4 instantly create a hole in most of other stuff too. Like ClF3 or RDX or 239Pu.

Thanks to the commenters above, they are useful as they answer the question in a creative way.

Hi that is kind of a common industrial problem, however, some companies invented some effective Calcium Sulfate scale remover. May be the combination ATMP and other chemicals.

Woodchipper, great for all your disposal needs.

Mechanical methods and extreme chemistry aside, there is no instant method of dissolving bulky calcium sulfate (or its hydrates: $\ce{CaSO4 · 0.5 H2O}$ and gypsum $\ce{CaSO4 · 2H2O}$).
Soda-acid treatment
Since $\ce{CaSO4}$ is notably one of the reasons for permanent water hardness, industrial scale machinery using water heat exchangers or boilers are typically liberated from calcium sulfate by washing the insides with concentrated hot sodium carbonate solution for several hours, converting sulfate to less soluble carbonate, which is subsequently dissolved in inhibited acid solution (the process might take half a day or longer):
$$
\begin{align}
\ce{CaSO4(s) + Na2CO3(aq) &<=>> CaCO3(s) + Na2SO4(aq)}\\
\ce{CaCO3(s) + HCl(aq) &-> CaCl2(aq) + H2O(l) + CO2(g)}
\end{align}
$$
Complexing
There are numerous commercially available mixes for cleaning molds used for gypsum casting within hours.
Exact composition is usually classified as a trade secret; the majority of the manufacturers would list two main components:

Alkaline cleansing agents. To put it simply, any alkali, e.g. $\ce{NaOH}$.
Complexing agents. Most likely, these are disodium edetate $\ce{Na2H2EDTA}$ and sodium citrate $\ce{Na3C6H5O7}$.

The idea behind using EDTA salts is pretty simple: it makes insoluble metal salts soluble by making chelate complexes such as $\ce{CaNa2EDTA}$ which are stable (and well-soluble) in water.
Citrate may also complexate calcium, and alkaline medium promotes complex formation.
This method is widely used in analytical chemistry for the qualitative and quantitative determination of numerous cations (transition and rare-earth metals, actinoids).
Both of the above-mentioned methods may be significantly accelerated if the diffusion barrier is lowered, e.g. by using ultrasonic bath.

Unfortunately calcium sulphate, gypsum, $\ce{CaSO4}$, is depressingly stable and nothing non-deadly will dissolve it.
The other posts you have seen are about calcium carbonate, chalk/limestone/marble, $\ce{CaCO3}$, which acids will dissolve, although people do not in practice use that fact to make holes in it. One of the first difficulties would be to get the application of a liquid focused enough to make a hole-shaped hole.
If you ever did want to dissolve marble, I'd use hydrochloric acid, $\ce{HCl}$, because calcium chloride is nice and soluble. But check beforehand that it doesn't dissolve the gloves you intend to use.


text:
Sand grains and kinetic two-body processes in the gas phase
This question stems from a search for an answer to this other one regarding which molecules are most abundant in the universe (specifically which multielemental compound).
I found an article on the subject of interstellar water chemistry, which states in the introduction that

Molecules such as water form in localized regions of cold and dense gas and dust between the stars (see Figure 1). Typical densities in such interstellar clouds are $10^4$ hydrogen molecules per $cm^3$ and temperatures can be as low as 8 K (pressure∼10−14mbar). The clouds also contain small 0.001–0.1 μm sized solid dust particles or ‘grains’, consisting of amorphous silicates and carbonaceous material.  Grains are important because they absorb and scatter the ultraviolet(UV) radiation produced by stars and thereby protect molecules from dissociating photons. Reactions on the surfaces of the dust particles promote the formation of molecules, especially of H2 and other hydrogen-rich species like H2O. [emphasis mine]

But in the paragraph immediately following this statement it says that

Interstellar space is a gigantic ultrahigh vacuum laboratory with densities low enough that molecules can form only through kinetic two-body processes in the gas phase.

The process described in the first paragraph does not seem to comply with the statement in the second one. In particular, involvement of the surface of a sand particle would appear to define (at least) a "three-body process" and while exposure to the gas phase is important to bring reagents together, it would still not seem sufficient to call this a "gas-phase" reaction. Am I wrong? How to reconcile this apparent contradiction?

Reference
Interstellar water chemistry: from laboratory to observations. Ewine F. van Dishoeck,Eric Herbst, and David A. Neufeld. Chem. Rev. (2013), 113 (12), 9043-9085, https://doi.org/10.1021/cr4003177.


text:
Rate of reaction graph
An autocatalytic reaction is a reaction in which one of the products catalyses the reaction.
In general what will be the shape of curve if the rate of reaction was plotted against time for an autocatalytic reaction?
I think answer should be A (in image) as an autocatalyst should always increase rate of reaction until there is a limiting factor for example concentration but the answer is B.

Do you have a specific example in mind? How do you think it might be different from a "regular" reaction? Please show that you have invested some time into trying to figure this question out yourself, and tell us where you got stuck. With those edits, the chance of getting the question upvoted will increase, and it will be easier for folks to give a meaningful answer.

Reactants are consumed

My answer is very mathy, but if the curves represent rates, just note that A implies the rate will plateau and then stay at a largish positive value forever.  But even autocatalytic reactions can't go forever.  If the curves were to represent concentration, then A seems like a reasonable answer.  But that's not what you said.

Let's suppose the mechanism is:
$$\ce{A + B <=> (AB) -> B + B}$$
Here, A is decomposed catalytically by B into B through the formation of a transient (AB) complex.
We can decompose two-step process into two reactions:
$$\ce{A + B <=>[k_1][k_2] (AB)} $$
$$\ce{(AB) ->[k_3] B + B}$$
Supposing these are "elementary" reactions, then,
$$\frac{d}{dt}(AB) = k_1[A][B] - k_2 (AB) - k_3[B]$$
If we apply the pseudo-steady state hypothesis to (AB):
$$\frac{d}{dt}(AB) = k_1[A][B] - k_2 (AB) - k_3[B] = 0$$
$$(AB) = \frac{k_1[A][B] - k_3[B]}{k_2}$$
We can additionally eliminate [A] from this equation because by stoichiometry, $[A] + (AB) + [B] = C$, where C is a constant.  For simplicity, let's also suppose that (AB) will always be very low compared to [A] and/or [B].  But if (AB) is always low, we can approximate this by $[A] + [B] = C$.  If so, then $[A] = C - [B]$.  Substituting this into the equation above:
$$(AB) = \frac{k_1\left(C - [B] \right)[B] - k_3[B]}{k_2}$$
$$(AB) = [B]\frac{k_1\left(C - [B] \right) - k_3}{k_2}$$
Now, the rate of formation of [B] is what we are interested in.  The 2nd reaction gives us the rate:
$$\frac{d}{dt}[B] = 2 k_3 (AB)$$
We can sub in the equation for (AB) we got above:
$$\frac{d}{dt}[B] = 2 k_3 [B]\frac{k_1\left(C - [B] \right) - k_3}{k_2}$$
$$\frac{d}{dt}[B] = 2 \frac{k_3}{k_2} \left([B]k_1\left(C - [B] \right) - k_3[B]\right)$$
$$\frac{d}{dt}[B] = r_B = 2 \frac{k_3}{k_2} \left( \left(k_1 C -k_3\right)[B] - k_1 [B]^2 \right)$$
$$\frac{d}{dt}[B] = r_B = 2 \frac{k_3 k_1}{k_2} \left(- [B]^2 + \left(C - \frac{k_3}{k_1}\right)[B]  \right)$$
That factor in parenthesis is a quadratic in [B].  We can find when the rate will be a maximum by differentiating this term with respect to [B] and setting the result to zero.
$$-2 [B]_{maxrate} + (C - \frac{k_3}{k_1}) = 0$$
$$[B]_{maxrate} = \frac{1}{2}(C - \frac{k_3}{k_1})$$
This shows that the rate of formation of [B] will have a maximum.  (Well technically an extremum but if you take the 2nd derivative you will find the extremum we found is in fact a maximum.)
You indicated in your question that the curves you drew represented plots not of concentration, but of the reaction rate.  The only curve that has a maximum rate is curve B, therefore it must be the right answer.

As Curt F. has correctly showed that, in general, if the rate of reaction is plotted against time for an autocatalytic reaction, it would be the shape of curve B (in your question). Since Curt F. has already worked with the mathematical part, only I can do is show you some literature evidence. One of research on an epoxy resin composite hardening (Ref.1) state that:

Composite structures for aerospace applications are mainly made by the well-known prepreg technology. In order to achieve adequate prepreg processing schedules, and consequently maximum fiber strength utilization, one has to know in deep the cure kinetics of matrix, which held the fibers together. This work describes a procedure to study the cure kinetic and has as example how aromatic amine hardeners influence the cure kinetics of an epoxy resin used in advanced composites. The investigation was carried out by using the DSC technique and it was found that depending on the system used the cure kinetics of the formulation obeys order $n$ or autocatalytic order.

For Comprehensive details for autocatalyzation and review, see Ref.2 & 3.

References:

Michelle L. Costa, Luiz C. Pardini, Mirabel C. Rezende, “Influence of aromatic amine hardeners in the cure kinetics of an epoxy resin used in advanced composites,” Mat. Res. 2005, 8(1), 65–70 (http://dx.doi.org/10.1590/S1516-14392005000100012).
Donna G. Blackmond, “Asymmetric autocatalysis and its implications for the origin of homochirality,” Proc. Natl. Acad. Sci. USA 2004, 101(16), 5732–5736 (https://doi.org/10.1073/pnas.0308363101).
Andrew J. Bissette, Stephen P. Fletcher, “Mechanisms of Autocatalysis,” Angew. Chem. Int. Ed. 2013, 52(49), 12800–12826 (https://doi.org/10.1002/anie.201303822).


text:
If vibrational modes are quantised, why is infrared spectroscopy smooth looking?
I have heard that the vibrational energy level in a molecule is quantised. However, when looking at the infrared spectroscopy graph, the curves look highly continuous and smooth - not something I would expect from a quantised quantity.

The sharp pointy bits in the fingerprint region (on the right) make sense, given that only certain quantised frequencies would be absorbed - but the alcohol $\ce{OH}$ group seems to be able to absorb a very large range. So, why is the graph smooth when the vibrational energy is quantised?

Related: IR spectra and hydrogen bonds

Each vibrational level is in fact a bunch of rotational levels.

Consider that electronic transitions give rise to bands already. It should make easier to understand the vibrational ones.

You should first have a look at the gas phase spectrum of water to convince yourself that vibrational levels are indeed "discrete". The textbook treatment of vibrating molecules assumes that there is no molecule nearby and each and every unit is independent. Which state of matter is closest to these assumptions? The gas phase, the lower the pressure, the further the molecules are apart (large mean free paths). Therefore if you wish to see quantitization visually, it is better to look at the spectrum of gases (rotations, vibrations and electronic transitions). Recall you study atomic spectrum of hydrogen gas not of solid hydrogen or liquid hydrogen.
Now, you may ask, that water is a triatomic molecules with 3N-6= 3 vibrational modes. What are the rest of those lines? Recall that water can also rotate in the gas phase. Those very thin lines represent rotational energy transitions.

The story changes when you deal with liquids or solids. Now the vibrating molecules are so close to each other that they are no longer independent from each other's influence. The rotational structure is completely smeared. The vibrations are still quantized but now you see a collective behavior millions of close-by water molecules which are strongly interacting by hydrogen bond. If we had a very fancy ultra ultra high resolution infrared spectrometer, we might be able to see some structure in each broad band, but the smearing is so bad in solids and liquids that we all see a overall wide peak, which is just an envelope of all possible vobrational transitions by millions of molecules in different environments on the liquid and solid state.

Solvent molecules can have important effects on the internal vibrations in a number of ways, resulting for instance in "collisional broadening" of the spectral lines. Significant broadening can happen also in a gas if collisions are frequent due to high pressure, in which case it is not surprisingly referred to as "pressure broadening". Collisions shorten the lifetime of particular vibrational states, leading to uncertainty in the energy (and thereby frequency), which translates into broadening. A collisional model provides similar insight in a gas and a non-H-bonding solvent. An alternate useful model that illustrates the effect is that of a damped oscillator. The solvent "slows down" solute vibrations. In addition, since each solute molecule interacts slightly differently with the solvent, its frequency is altered to a different extent. This leads to both lifetime broadening and inhomogeneous broadening.
The solvent effect may also arise as a coupling between the vibrational modes of the solvent and those of the solute. This is particularly easy to understand if you have hydrogen bonds. A group in a molecule hydrogen-bonding to the solvent, being part of an extended and highly inhomogeneous bonding system (effectively akin to a large molecule which can change its configurations extensively), contains a continuum of vibrational energy levels, and therefore exhibits bands rather than narrow peaks. This explains why $\ce{O-H}$ peaks are broadened more often and extensively than $\ce{C-H}$ peaks, given that both are subject to rotational splitting. Another important feature of such hydrogen-bonded systems is that the broadened vibrational modes are "soft", that is, they occur at low relatively low energy (high wavenumber) which is consistent with more closely spaced energy levels. Resonance with soft collective modes involving the solvent is then relatively easy.

That broadening combined with the multiple peaks due to rotational levels (mentioned by Ivan Neretin in the comments to the question) results in the very broad features in solution. For a gas phase spectrum, see e.g. page 10 here

@KarstenTheis Yes but do rotational splittings explain differences say between the width of O-H and C-H bands?

No, I guess that is hydrogen bonding, see Orthocresol’s comment with link.

@KarstenTheis Yes, orthocresol's answer addresses h-bonding effects quite thoroughly, mentioning even the red-shifting effect. I play the tune slightly differently you might say :-)


text:
How to you show a 3-center 2-electron bond in a Lewis structure?
How would you write $\ce{PCl5}$ or other hyper-conjugate molecules as a Lewis structure that indicates 3-center 2-electron bonds?
I have seen depictions [1] for transition metal complexes but not for main group non-metals such as sulfur or phosphorous.

With dashed lines but in some structures I am puzzled, too.

I started writing an answer, but realized I was rambling, and it was probably better as a comment. My opinion is that Lewis structures are too focused on 2-center-2-electron bonds to easily depict anything else. I feel like in practice, you draw everything as a electron pair and rely on reader experience to detect when things are 3-center-2-electron bonds.

I had troubles to convey 3c-2e in TEMPO (in conjunction with a big number of hyperconjugation mesomers) to explain the long life of it in an old threat. And still have them.

@Alchimista - TEMPO? Oh, I see: https://chemistry.stackexchange.com/a/90993

As a general comment, it's clear that the conventions for Lewis structures that have accumulated over the years are are not internally consistent, but are so well-established that it's too late to change. For example, in second row oxides like $\ce{HNO3}$, octet rule wins over "minimize formal charge", but in the third row, expanded octet is preferred over adding formal charge, as in $\ce{H3PO4}$. For more complex bonding interactions like the two $\pi$ half-bonds in $\ce{O2}$, Lewis structures are completely inadequate.

If you stick to the original idea of Lewis diagrams, you are limited to 2e-2c bonds (no donor-acceptor-bonds, i.e. no arrows), and you should be. Then again, the concept of hypervalency is only necessary for these bonds, and a phosphorus bonded five times, or pi bonds within sulfate are fine. Since we know that is (at least partially) wrong, a different kind of representation has to be chosen, which must be more complex. @zhe said it best: rely on the experience of the reader, even when that makes it impossible for the beginner to understand. (meta: Ugh... a researchgate pdf, how ugly.)

There is an article in JChemEd suggesting a way to count electrons even in the presence of 3-center-2-electron bonds: https://doi.org/10.1021/acs.jchemed.9b00750

What about the probably "not so good" approach might be the bent bond as sometimes seen for diborane?

(source)
The latest recommendation by IUPAC I know, exemplified in rule "GR-1.9 Multi-center bonds":

(Brecher, Pure Appl. Chem., 80, 277-410, 2008; doi 10.1351/pac200880020277, open access)
stating:

"As a matter of convention, any such multi-center character is ignored
  when producing chemical structure diagrams, and regular bonds
  connecting pairs of atoms are used instead."

To accommodate Karsten Theis' comment on the initial form of this answer, I would like to add the perspective provided by Robert Grossmann's The Art of Writing Reasonable Organic Reaction Mechanisms.  Starting page 270 (2nd edition, 2003) the chapter introducing reactions with transition metals draws attention about "Conventions of Drawing Structures"; highlighting that there are field dependent conventions about what line and dash represent.  To quote:

"The conventions for drawing organometallic and inorganic compounds
  differ in subtle ways from those used to draw “ordinary” organic
  compounds. The most important difference is the way in which bonds are
  drawn. In organic compounds, one does not use a line to connect a bond
  to an atom. In organometallic and inorganic compounds, however, a line
  sometimes connects an atom and a  $\sigma$ or $\pi$ bond. In this
  case, the line indicates that the pair of electrons in the $\sigma$ or
  $\pi$ bond is shared with the metal also."

(loc. cit. p. 271)

"An even more confusing situation arises in complexes in which the
  electrons in a $\pi$ system spread over three or more atoms are used
  to make a bond to a metal. In this case, the usual convention is to
  use a curved line to indicate the $\pi$ system and a single line to
  connect the $\pi$ system to the metal, regardless of the number of
  electrons in the $\pi$ system (the organometallic chemists’
  convention). However, sometimes the curved line is omitted and single
  lines are used to connect the metal to each of the atoms in the $\pi$
  system (the crystallographers’ convention). The representation that
  would make the most sense to organic chemists, in which a single line
  represents a two-electron  bond and a dative bond is used to show
  two-electron bonds between each individual $\ce{C=C}$ $\pi$ bond and
  the metal, is simply never used."

(loc. cit., p. 271)

"Formal charges are usually omitted in inorganic and organometallic
  complexes. Only the overall charge on the complex is indicated. For
  example, formal charges are usually not assigned in Lewis acid–base
  complexes involving transition metals. The acid–base bond is sometimes
  indicated by an arrow pointing from the ligand to the metal, but more
  often it is indicated by an ordinary line."

(loc. cit., p. 271)
This precedes just the section about electron counting (specifically in organometallic compounds with transition metals). I speculate, however, Robert Grossman aiming to highlight differences between "organic" and "organometallic" convention meant does while accidentally deploying does not in the first paragraph.

For the diborane, if you count 2 electrons per line representing a bond, one structure has the correct electron count and the other (the IUPAC-preferred) doesn't. If you don't expect 2e-3c bonds, this might trip you up. I guess it's the same for coordination compounds.

@KarstenTheis  Thanks to your comment, the perspective provided by the answer was enlarged.


text:
Why should ether O be named as OXA in a bicyclo ring when it is a substituent?
I was asked to name the molecule below .
For the following molecule, since ether is a substituent here (keto is more prior group) my answer was:
3-methoxy-6-methy-7-oxy bicyclo[2.2.1]hept-5-en-2-one
.
My answer is wrong. The correct answer is
3-methoxy-6-methyl-7-oxabicyclo[2.2.1]hept-5-en-2-one
My point is, at C-3, ether is methoxy, but at 7 the same ether is OXA. Ether as substituent outside the bicyclo ring is alkoxy, but inside bicyclo compound it is OXA.
My question is, why should ether O be named as OXA in a bicyclo ring?

OXO is reserved for =O. https://goldbook.iupac.org/html/O/O04377.html

@user55119 ,Thank you,looked up at link provided.It is about keto group  when it is a substituent with another functionsl group carboxylic acid.

True, as in 4-oxocyclohexane-1-carboxylic acid.

The suggested name 3-methoxy-6-methyl-7-oxabicyclo[2.2.1]hept-5-en-2-one is correct. Indeed, the ketone is the principal characteristic group in this case; however, this is not the reason why the other oxygen is named as ‘oxa’. Already the unsubstituted parent structure is named 7-oxabicyclo[2.2.1]hept-2-ene.
According to the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book), such bicyclic heterocycles are named using skeletal replacement (‘a’) nomenclature (a system in which a heteroatom replaces skeletal atoms of a parent hydride).

P-31.1.4.4 Bi- and polycyclic von Baeyer heterocycles named by skeletal replacement (‘a’) nomenclature. In heterocyclic compounds formed using skeletal replacement (‘a’) nomenclature, low locants are assigned to heteroatoms, in accord with the fixed numbering of the system, then to unsaturated sites.

Nondetachable prefixes, called replacement (‘a’) prefixes representing the element being introduced, are used to designate the replacing skeletal atoms with their standard bonding number, for example ‘aza’ (N), ‘oxa’ (O), or ‘thia’ (S).


text:
Building an average model from MD snapshots
I am performing a molecular dynamics simulation, and I am taking "snapshots" of the system at regular intervals.
The aim is that of finding the preferred geometry of a molecule in solution.
Are you aware of any software capable of automating to some extent the superposition of different geometries, and maybe of building an "average" structure?

I think what you are asking is a fairly difficult and likely not automatable procedure as the details will vary a lot depending on what you are interested in and the system you are studying. The simplest (but not necessarily simple) thing to do is just define a set of internal coordinates and transform your cartesians to these and average over your snapshots.

I have also been a part of a project where we were interested in averaging over a particular coordinate that is sensitive to low frequency vibrations which themselves are sensitive to thermal fluctuations. So, we first performed a Fourier filtering over these low frequency vibrations and then averaged the ones we were actually interested in. I'm just trying to get across that doing this in a reliable manner can be highly non-trivial and is certainly not unique as the systems get bigger and which coordinates are good ones becomes less obvious.

Indeed, averaging the coordinates was my idea as well, but I hoped in a less time-consuming procedure :)

Ya, unfortunately defining coordinates is the bane of many computational chemists' existence. It is time-consuming and often has to be done by hand if you want to be able to easily interpret the chemical relevance of the coordinates. The actual transformation from one set to another isn't too bad, but you have to write the code to do it at least once. I don't know of any well-established code to do this, but maybe there's a github repo somewhere...

If you want to get really modern you could try to use some kind of unsupervised learning to pick out important motifs and then average over these somehow. See: Ceriotti, M. (2019). Unsupervised machine learning in atomistic simulations, between predictions and understanding. The Journal of chemical physics, 150(15), 150901.

For people interested, I have not tried it yet, but it looks like there is a script for PyMol (free for academic purpose). http://muralab.org/~cmura/PyMOL/pymol_mainFrame.html PyMol also allows alignment of different stuctures

GROmaps may be an option for you too GROmaps

This is possible with the Python package MDTraj. Assuming you have your trajectory saved as trajectory.dcd and topology in topology.pdb:
import mdtraj as md
from mdtraj.geometry.alignment import compute_average_structure

traj = md.load('trajectory.dcd', top='topology.pdb')
average = compute_average_structure(traj.xyz)

I believe it will RMSD align the trajectory first, but you may need to specify that explicitly first.
You might also want to check out MDAnalysis as well, it may have similar functionality. I've used both packages and both are still actively maintained.


text:
MOs of Benzene using group theory
I am trying to analyze the $\sigma$ orbitals of benzene molecule using group theory, doing the same thing that is done to the $\pi$ orbitals. The symmetry group of benzene is the $D_{6h}$; considering the $sp^{2}$ orbitals of the benzene:

and applying the symmetry operations to these orbitals, I can find the caracters of the representation with which they are transformed, and I can decompose this representation in the irreducible representation of the group. Doing this, I found
$$\Gamma = 2 A_{1g} \oplus 2E_{2g} \oplus B_{1u} \oplus B_{2u} \oplus 2E_{1u} $$
Now, I can construct the projection operators and with them I get the symmetrized orbitals for each representation. The molecular orbitals will be the linear combinations of these orbitals. My question is: In which function should I apply the projection operators? In the $sp^{2}$ function?

There's no reason to apply hybrids to this problem. You should pick an appropriate set of coordinates and use the atomic orbitals instead.

Then again, whatever happens next can be told in terms of $sp^2$ orbitals all right, as well as it can be told in any other terms. Also, like I said, it is not much fun.

Zhe, can you be more specific? So, can I choose any orbital (let's say, the $p_{x}$ orbital of Carbon) and apply the projectors to it? Ivan Neretin yes, I agree, but it's only  an educational problem.

Your decomposition is for the hybrid orbitals that point from carbon to carbon, omitting the ones that point out towards the hydrogens, so you really want to project starting from one of the hybrid orbitals. First off we correct your decomposition:
$$\Gamma=A_{1g}\oplus A_{2g}\oplus B_{1u}\oplus B_{2u}\oplus2 E_{1u}\oplus 2E_{2g}$$
We only need half the operations of $D_{6h}$ because all the hybrid orbitals transform the same under $\sigma_h$, so we write out the matrices for the group operations of the subgroup $D_6$ and a set of matrix representations for each irreducible representation and the result of each group operation acting on $\phi_1$, first half:
$$\begin{array}{c|cccccc}R&E&C_6&C_6^2&C_6^3&C_6^4&C_6^5\\\hline
A_{1g}&1&1&1&1&1&1\\
A_{2g}&1&1&1&1&1&1\\
B_{1u}&1&-1&1&-1&1&-1\\
B_{2u}&1&-1&1&-1&1&-1\\
E_{1u}&\begin{bmatrix}1&0\\0&1\end{bmatrix}&\begin{bmatrix}\frac12&-\frac{\sqrt3}2\\\frac{\sqrt3}2&\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\\frac{\sqrt3}2&-\frac12\end{bmatrix}
&\begin{bmatrix}-1&0\\0&-1\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\-\frac{\sqrt3}2&-\frac12\end{bmatrix}&\begin{bmatrix}\frac12&\frac{\sqrt3}2\\-\frac{\sqrt3}2&\frac12\end{bmatrix}\\
E_{2g}&\begin{bmatrix}1&0\\0&1\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\\frac{\sqrt3}2&-\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\-\frac{\sqrt3}2&-\frac12\end{bmatrix}
&\begin{bmatrix}1&0\\0&1\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\\frac{\sqrt3}2&-\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\-\frac{\sqrt3}2&-\frac12\end{bmatrix}\\
R\phi_1&\phi_1&\phi_3&\phi_5&\phi_7&\phi_9&\phi_{11}\end{array}$$
Ummm... yeah, I assume the $x$-axis points right in your illustration and the $y$-axis points up. Also I number the hybrid orbitals $1$ to $12$ counterclockwise starting with the one just above the $x$-axis in the first quadrant. I will label the dihedral $C_2$ rotation axes $a$ to $f$ with $a$ parallel to the $x$-axis counterclockwise in $30°$ increments. So now we can produce the second half of our table:
$$\begin{array}{c|cccccc}R&C_{2a}&C_{2b}&C_{2c}&C_{2d}&C_{2e}&C_{2f}\\\hline
A_{1g}&1&1&1&1&1&1\\
A_{2g}&-1&-1&-1&-1&-1&-1\\
B_{1u}&1&-1&1&-1&1&-1\\
B_{2u}&-1&1&-1&1&-1&1\\
E_{1u}&\begin{bmatrix}1&0\\0&-1\end{bmatrix}&\begin{bmatrix}\frac12&\frac{\sqrt3}2\\\frac{\sqrt3}2&-\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\\frac{\sqrt3}2&\frac12\end{bmatrix}
&\begin{bmatrix}-1&0\\0&1\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\-\frac{\sqrt3}2&\frac12\end{bmatrix}&\begin{bmatrix}\frac12&-\frac{\sqrt3}2\\-\frac{\sqrt3}2&-\frac12\end{bmatrix}\\
E_{2g}&\begin{bmatrix}1&0\\0&-1\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\\frac{\sqrt3}2&\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\-\frac{\sqrt3}2&\frac12\end{bmatrix}
&\begin{bmatrix}1&0\\0&-1\end{bmatrix}&\begin{bmatrix}-\frac12&\frac{\sqrt3}2\\\frac{\sqrt3}2&\frac12\end{bmatrix}&\begin{bmatrix}-\frac12&-\frac{\sqrt3}2\\-\frac{\sqrt3}2&\frac12\end{bmatrix}\\
R\phi_1&\phi_{12}&\phi_2&\phi_4&\phi_6&\phi_8&\phi_{10}\end{array}$$
Then it remains to apply projection operators:
$$\Gamma_j^{(\mu,i)}=\sum_{R\in G}D_{ij}^{(\mu)}\left(R^{-1}\right)R\phi_1$$
(Note the $R^{-1}$ in the above formula)
$$\Gamma_{A_{1g}}=\phi_1+\phi_3+\phi_5+\phi_7+\phi_9+\phi_{11}+\phi_{12}+\phi_2+\phi_4+\phi_6+\phi_8+\phi_{10}$$
$$\Gamma_{A_{2g}}=\phi_1+\phi_3+\phi_5+\phi_7+\phi_9+\phi_{11}-\phi_{12}-\phi_2-\phi_4-\phi_6-\phi_8-\phi_{10}$$
$$\Gamma_{B_{1u}}=\phi_1-\phi_3+\phi_5-\phi_7+\phi_9-\phi_{11}+\phi_{12}-\phi_2+\phi_4-\phi_6+\phi_8-\phi_{10}$$
$$\Gamma_{B_{2u}}=\phi_1-\phi_3+\phi_5-\phi_7+\phi_9-\phi_{11}-\phi_{12}+\phi_2-\phi_4+\phi_6-\phi_8+\phi_{10}$$
$$\Gamma_{E_{1u},x}^{(1)}=\phi_1+\frac12\phi_3-\frac12\phi_5-\phi_7-\frac12\phi_9+\frac12\phi_{11}+\phi_{12}+\frac12\phi_2-\frac12\phi_4-\phi_6-\frac12\phi_8+\frac12\phi_{10}$$
$$\Gamma_{E_{1u},y}^{(1)}=\frac{\sqrt3}2\phi_3+\frac{\sqrt3}2\phi_5-\frac{\sqrt3}2\phi_9-\frac{\sqrt3}2\phi_{11}+\frac{\sqrt3}2\phi_2+\frac{\sqrt3}2\phi_4-\frac{\sqrt3}2\phi_8-\frac{\sqrt3}2\phi_{10}$$
$$\Gamma_{E_{1u},x}^{(2)}=-\frac{\sqrt3}2\phi_3-\frac{\sqrt3}2\phi_5+\frac{\sqrt3}2\phi_9+\frac{\sqrt3}2\phi_{11}+\frac{\sqrt3}2\phi_2+\frac{\sqrt3}2\phi_4-\frac{\sqrt3}2\phi_8-\frac{\sqrt3}2\phi_{10}$$
$$\Gamma_{E_{1u},y}^{(2)}=\phi_1+\frac12\phi_3-\frac12\phi_5-\phi_7-\frac12\phi_9+\frac12\phi_{11}-\phi_{12}-\frac12\phi_2+\frac12\phi_4+\phi_6+\frac12\phi_8-\frac12\phi_{10}$$
$$\Gamma_{E_{2g},x^2-y^2}^{(1)}=\phi_1-\frac12\phi_3-\frac12\phi_5+\phi_7-\frac12\phi_9-\frac12\phi_{11}+\phi_{12}-\frac12\phi_2-\frac12\phi_4+\phi_6-\frac12\phi_8-\frac12\phi_{10}$$
$$\Gamma_{E_{1u},2xy}^{(1)}=\frac{\sqrt3}2\phi_3-\frac{\sqrt3}2\phi_5+\frac{\sqrt3}2\phi_9-\frac{\sqrt3}2\phi_{11}+\frac{\sqrt3}2\phi_2-\frac{\sqrt3}2\phi_4+\frac{\sqrt3}2\phi_8-\frac{\sqrt3}2\phi_{10}$$
$$\Gamma_{E_{1u},x^2-y^2}^{(2)}=-\frac{\sqrt3}2\phi_3+\frac{\sqrt3}2\phi_5-\frac{\sqrt3}2\phi_9+\frac{\sqrt3}2\phi_{11}+\frac{\sqrt3}2\phi_2-\frac{\sqrt3}2\phi_4+\frac{\sqrt3}2\phi_8-\frac{\sqrt3}2\phi_{10}$$
$$\Gamma_{E_{2g},2xy}^{(2)}=\phi_1-\frac12\phi_3-\frac12\phi_5+\phi_7-\frac12\phi_9-\frac12\phi_{11}-\phi_{12}+\frac12\phi_2+\frac12\phi_4-\phi_6+\frac12\phi_8+\frac12\phi_{10}$$

Thank you so much, you helped me a lot! The last functions we wrote are the symmetrized functions, right? Can I write them in function of the orbitals $s$, $p_{x}$ and $p_{y}$ of the Carbons? I would use the relations for the $sp^{2}$ orbitals: $$\phi_{1} = (1/\sqrt{3}) s + (2/\sqrt{6}) p_{x},$$ $$\phi_{2} = (1/\sqrt{3}) s - (1/\sqrt{6}) p_{x} + (1/\sqrt{2}) p_{y},$$ $$\phi_{3} = (1/\sqrt{3}) s - (1/\sqrt{6}) p_{x} - (1/\sqrt{2}) p_{y}.$$

My $$\phi_1=\frac1{\sqrt3}s_1-\frac2{\sqrt6}p_{1y}$$ $$\phi_2=\frac1{\sqrt3}s_1-\frac1{\sqrt2}p_{1x}+\frac1{\sqrt6}p_{1y}$$ $$\phi_3=\frac1{\sqrt3}s_2+\frac1{\sqrt2}p_{2x}-\frac1{\sqrt6}p_{2y}$$ I think you would be better off writing in terms of the $p$ orbitals parallel and perpendicular to the ring, $p_{i\parallel}$ and $p_{i,\perp}$ along with the $s_i$ orbitals, at least until you get the SALCs just to keep the algebra as simple as possible. The SALCs for the $p_{i\perp}$, $s_i$, and for the hydrogen $s_j$ orbital sets will be the same, so that makes your life easier.


text:
How dangerous is superglue?
A long time ago, when I used to make plastic models with glue, I never wore white gloves when gluing together the pieces, so I often got a lot of superglue on my hands. The superglue, which was very viscous and liquid, dried on my hands and later created small flakes in the process of coming off my skin.
At the time the back of the superglue container were listed instructions that read “in case of contact with skin, rinse with warm water until the glue is completely removed” or something similar.
My questions are

Is it okay to have ever had glue on my skin? Will it not create a lasting problem?
Is it okay that the flakes could have been spread on the bathroom towel when I wiped my hands, on the bedsheets, my clothes, the surface of the desk, the floor, and in other areas in the home?

I'm worried that the dust could have remained or been absorbed through the mouth, eyes or even nose (inhaled)?
*by glue I mean the type of glue that can be found on this link:
https://www.amazon.com/Tamiya-87038-Extra-Cement-Plastic/dp/B01F1S4N8U

Pretty dangerous if you drink it, or glue shut any of your body orifices. Short of that, not much to worry about.

Plastic models are not usually stuck together with cyanoacrylate superglue but with slower acting, more plastic-specific glues designed to glue polystyrene parts together. They are not very good at gluing body parts together (unlike cyanoacrylate glues) and are considerably safer and easier to use. The glue you link to is not a superglue and shouldn't be confused with one.

You should not regard this answer as medical advice. If concerned about your health consult a physician.
The glue you link to (TAMIYA  EXTRA-THIN  CEMENT, made by IKEGAMI PAINT INDUSTRY COMPANY), according to a material safety data sheet (MSDS) I was able to retrieve online, appears to be a 1:1 mixture of acetone and butyl acetate. Such a mixture works in a similar way to dihloromethane as a solvent to weld together plastic parts. Quoting the wikipedia,

Acetone is believed to exhibit only slight toxicity in normal use, and there is no strong evidence of chronic health effects if basic precautions are followed.

OSHA classifies acetone under the following health codes ("principal effect(s) of exposure to each substance [...] used in determining if a violation of an air contaminant standard is serious"):

HE16     Irritation-Eyes, Nose, Throat, Skin---Mild

OSHA classifies butyl acetate as follows:

HE8    Nervous System Disturbances---Narcosis
HE15   Irritation-Eyes, Nose, Throat, Skin---Moderate

For completeness, I include a screenshot from the beginning of the MSDS I found for the adhesive. For more on the GHS classification (divisions or categories) you can refer to the method employed in classifying substances.

Note that superglue has also surgery application, so it is not much dangerous.
The precautions are due possibility of local temporary skin/mucous irritation when exposed to cyanoacrylate monomer.
Other aspects are unpredictable effects of impurities of technical glues and  undesired glueing of body parts.

Superglue are Cyanoacrylates.They polymerise in presence of slight amounts of moisture that creates bonding between surfaces.Skin contains moisture which sets off polymerisation on contact with superglue$\ce{^1}$, giving a flaky appearance on skin.

Without force, however, the glue will spontaneously separate from the skin in time (up to four days). Separation can be accelerated by applying vegetable oil near, on, and around the glue. (Wikipedia)

The methods to remove superglue from skin include$\ce{^2}$

Soaking in warm, soapy water.
Nail polish remover or acetone.
Butter and oils, such as coconut or avocado oil, can help separate fingers that are stuck together with super glue.
Pumice stone
Lemon juice

References

https://www.compoundchem.com/2015/10/15/superglue/
https://www.medicalnewstoday.com/articles/323532.php


text:
Di-alpha-halogenation of ketones in acidic medium
I was studying alpha-halogenation of ketones from LibreTexts Chemistry,

Under acidic conditions the reaction occurs through the formation of an enol which then reacts with the halogen${^1}$.

1) Protonation of the carbonyl

2) Enol formation

3) SN2 attack

4) Deprotonation

It also says (look at the highlighted text):
Overreaction during base promoted α halogenation

The fact that an electronegative halogen is placed on an α carbon means that the product of a base promoted α halogenation is actually more reactive than the starting material. The electron withdrawing effect of the halogen makes the α carbon even more acidic and therefor promotes further reaction. Because of this multiple halogenations can occur. This effect is exploited in the haloform reaction discussed later. If a monohalo product is required then acidic conditions are usually used${^2}$.

Why can't we just reprotonate the monohalogen in the same way as the initial ketone to form a dihalo compound?
Referance
${^1}$:https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(McMurry)/Chapter_22%3A_Carbonyl_Alpha-Substitution_Reactions/22.03_Alpha_Halogenation_of_Aldehydes_and_Ketones
${^2}$:https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(McMurry)/Chapter_22%3A_Carbonyl_Alpha-Substitution_Reactions/22.03_Alpha_Halogenation_of_Aldehydes_and_Ketones

Is the question in the headling and the post same ? Reprotonation of halo ketone or is it poly halogenation of ketones ?

@ChakravarthyKalyan I'm asking if dihalo will form due to reprotonation?

Acid Catalysed Halogenation of ketone
In the halogenation of ketones, both in acidic and basic medium, enols are reactive intermediates. After addition of first halogen to double bond, deprotanation occurs immediately (Scheme 1). The second halogen does not add$\ce{^1}$.
Scheme 1

The introduction of second Bromine is slower then the first ,since cabocation is destabilized by the electron-attracting polar effect of two Bromines (**Scheme 2).
Scheme 2

Consequently, reprotonation of the monobrominated ketone does not occur.

Base Catalysed Halogenation of ketone
The mechanism of this reaction involves the formation of an enolate ion as a reactive intermediate. After mono bromination, the enolate ion of the alpha-bromo ketone is even more stable the enolate ion of the starting ketone.(Scheme 3). Consequently, a second bromination occurs$\ce{^2}$.
Scheme 3

As discussed above, in acid catalysed halogenation  the intermediate is unstable ,hence reprotonation to give dihalo products is less (If one equivalent of Bromine is taken).
Note$\ce{^3}$ :

Comparatively, in base calalysis the intermediate (Bromo enolate anion) is quite stable leading to di and tri bromination (provided acidic H is present).

Reference

Organic Chemistry, 5th Edition  by Prof. Marc Loudon
Organic Chemistry, 5th Edition by Prof. Marc Loudon
Organic Chemistry, 2nd Edition ,Jonathan Clayden , Nick Greeves ,Stuart Warren.

Of course the product can be protonated. It can also form an enol. It is just that the enol of the product is less prevalent than the enol of the starting material, and so if you only have a limited amount of bromine to react, the bromine will preferentially react with the SM. If you just put in a ton of bromine, then the excess bromine will still react with the product. cf. Clayden 2nd ed p 463

@orthocresol the question was aswered without assuming ton of Bromine .I have assumed conditions as given in the question and ventured an answer.However,excess usage pf Bromine will react .

Yes, but you claim that "reprotonation of the monobrominated ketone does not occur". That is not correct. It does not logically follow from "introduction of second bromine is slower than the first".

@orthocresol I will recorrect with the conditions discussed at the earliest, thankyou

@orthocresol I have removed my claim and have used 1 equivalent as suggested by  Clayden 2nd ed p 463 .


text:
What are the components of a labware setup for short-path distillation?
I've recently become interested in short-path distillation and have found that most kits are in the thousands of dollars. So I thought that I would compile the labware myself.
I understand the theory behind short path distillation, but do not know the actual names of the components. I do know I will be using a digital hotplate and labware grade pyrex labware.
So what is the (cheapest) "shopping list" needed to compile and assemble all the labware necessary to construct a short-path distillation apparatus?

Of course the answer depends a bit on the quantity to distill and the conditions (temperature and vacuum applied, difference in the boiling points of the components to separate).
There are about palm size short-path distillation heads, which may be connected easily directly to your round bottom flask and receivers like the following example:

(source)
At chemglass.com, this device (CG-1239) is listed for USS 178.95 and allows you to mount as usual thermometer, water-in and -out for the condenser, and the vacuum by an oil pump.  The efficiency of separation may be increased by mounting a vigreux column below the head, of course, which are available in different (shortened) lengths, too.  There are "jacketed versions" (e.g., CG-1240) which are more suitable if the head temperature to reach is quite elevated (say, 150 $^\circ\mathrm{C}$) already while applying vacuum, at a bit more elevated price tag, too.
Of course, the advantage of the Kugelrohr shortpath's design is that you may moderate the heat gradient better, because the bulb outside the oven may be cooled with a bath of acetone / dry ice, and the rotation reducing sudden evaporation.  The one by Buchi B-585 is more suitable for smaller quantities, while the ones by Aldrich obviously allow distillations out of a 250 mL flask, which truly are both considerably more expensive.  (The larger Aldrich ovens require more bench place, too.)
Do not forget that there are e-bay-like companies specialized in selling used but still working lab equipment, too, e.g. Richmond, LabX to mention two.


text:
Is it possible to create weaker version of guncotton by replacing cotton wool with wood chips or linen cloth?
If the cotton wool was replaced by wood chips or linen (flax) cloth, would the mixture of nitric and sulfuric acids still react with the cellulose in it to produce nitrocellulose?
If it would, would it be reasonable to assume that the power of such explosive would be (very approximately) proportional to the content of cellulose in your substitute for cotton wool?
Would such explosive produce smoke (as besides nitrocellulose it would contain other flammable substances and no oxygen source)?
Would hemicellulose go through a similar reaction with the acid mixture as cellulose?

You might check  https://en.wikipedia.org/wiki/Nitrocellulose for nitrocellulose prepration using lenin.(it was a accidental find).The post has very many questions(3),This can be taken ass TOO BROAD.You might want to edit the question part.

@Chakravarthy Kalyan If you are talking about the original discovery of nitrocellulose, it mentions a cotton apron while linen is made of flax.

I believe the first and last question are related enough to belong together. The questions about smoke and effectiveness might be split into another post, though not sure whether they should.

http://textilefashionstudy.com/chemical-composition-of-flax-fiber-linen-fiber-composition/ for lenin flux composition and http://textilefashionstudy.com/what-is-cotton-fiber-chemical-composition-of-cotton-fiber/ for celluclose (part of cotton) are interestingly very near .So we may endup with the same

I was looking for how much cellulose does flax contain but was not able to find it. Thanks for the link.

Regarding hemicellulose I found this article: link. Page 10, item 2: During the reaction, a large amount of lignin was oxidized and nitrated, and the hemicellulose was hydrolyzed by nitric acid. Though they were using a mixture of nitric acid with ethanol. My knowledge is not enough to say whether hemicellulose  would not be nitrated with a mixture of nitric acid and sulfuric acid either.

This article mentions hemicellulose from wood chips being hydrolyzed, not nitrated by a mixture of ethanol and nitric acid, while cellulose does get nitrated: Isolation of cellulose from poplar wood by nitric acid-ethanol treatment and its effect on the quality of films cast from ionic liquid
I also found a patent for Preparation of wood pulp cellulose for nitration which from the name alone suggests that cellulose from wood can be nitrated (the preparation described is purely physical, no chemicals applied).
Regarding linen and cotton fabric, they will work same as cotton wool. Cotton fabric is how nitrocellulose was first accidentally discovered (wikipedia article) and linen is made of cellulose fiber just like cotton (these fabrics have 94% and 95% cellulose respectively: flax, cotton).
Tldr:
Linen fabric, cotton fabric and cotton wool work equally well. It is possible to nitrate the cellulose in wood chips. Hemicellulose will (most likely) not get nitrated. No idea about smoke production and effectiveness so far though.


text:
How good is 2-Butoxyethanol as a replacement for acetone?
I have recently bought a bottle of acetone from my local hardware store. When I opened the bottle, I was surprised about the absence of the strong smell of acetone. Only then I discovered the smaller printed words "Eco replacement" on the label:

On the backside, the bottle indicates the constituents as:

2-Butoxyethanol
< 10 % anionic surfactants

I compared the chemical composition and characteristics of 2-Butoxyethanol and acetone. To the eyes of a non-chemist, they are very distinct substances. Both are very good solvents, 2-butoxyethanol seems less toxic than acetone. I am happy to believe that 2-butoxyethanol can replace acetone for very many applications, but I fail to find any application notes about 2-butoxyethanol as an acetone replacement.
My question is about the limits. Are there applications where 2-Butoxyethanol fails to replace acetone?
If this is too broad as a question, I would like to narrow it down to the two applications that I am really interested in:

use as a cleaner before applying glass fiber reinforced resins (epoxy or polyester). Acetone is usually used because it solves many polymers, but leaves polyester intact.
use to "rejuvenate" PEI (polyetherimide) coated heat beds for 3D printing. The materials to be removed from such heat beds are the printing materials (including PLA, PETG, and ABS), as well as glue stick residues, and body grease.

Is 2-Butoxyethanol a good choice for these uses?

You'll have to try it out. I'll say it seems likely. Your second point is surely uncritical, if it works, it works. Wether your resin sticks worse (or even better) after the replacement, your customers might find out in a year or ten. What would make me a bity wary are the tensides. They will stay on your surface.

I tried exactly this liquid: it does not work at all for smoothening ABS. Even after a few hours there is no smoothing visible. The smell of this stuff is very different, 'sweet' like glycol, as to 'sharp' for acetone. It's an other chemical, that 'replaces' acetone only in the sense that it can act as a solvent for certain materials (but not ABS). The label is misleading, and in the NL the company has been ordered to change the label, in 2016.