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Every IUPAC Systematic name I have come across, I have understood up until now. This is Carminic Acid ($\ce{C22H20O13}$):

(source: chemspider.com)
This is the IUPAC Systematic Name for Carminic Acid:
(1S)-1,5-Anhydro-1-(7-carboxy-1,3,4,6-tetrahydroxy-8-methyl-9,10-dioxo-9,10-dihydro-2-anthracenyl)-D-glucitol
I have 3 main questions:

I do not understand the numbering system inside the brackets. The numbering system implies that the numbers assigned to the carbon atoms is the following:

I would have thought the numbers assigned to the carbon atoms would be the following:

Why is the numbering system the way it is? (Why does the numbering system not go around the molecule, in a normal cycle, counting off each carbon?, Why is the number 10 carbon opposite the number 9 carbon?, Why are 4 carbons [circled in the picture below] left out in the numbering system?)

I also do not understand why Carbons 9 and 10 in the anthracene group are referred to as '9,10-dioxo-9,10-dihydro'. Surely, they only need to be referred to as '9,10-dioxo'? And what is a '-hydro' group?

Doesn't '1,5-Anhydro...-D-Glucitol' imply the following: Hexan-2,3,4,6-tetrahydroxy-1-yl, a chain, and NOT a ring structure of: Oxan-3,4,5-trihydroxy-6-hydroxymethyl-2-yl, considering D-Glucitol (shown below). Also, as well as '1,5-Anhydro...-D-Glucitol' not accounting for the ring structure of that section of the molecule, it also doesn't account for the Oxygen.


texts: Ring contraction in pinacol rearrangement of cyclohexane-1,2-diol

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I came across this question in three different textbooks.

The question was: What is the major product obtained on dehydration (treatment with concentrated $\ce{H2SO4}$) of cyclohexane-1,2-diol.

I figured it would undergo a pinacole-pinacolone rearrangement. I expected the product to be cyclohexanone but to my surprise the answer was 1-cyclopentylmethanal.

What can be the driving factor for the ring to preferentially contract? Shouldn't the intermediate carbocation be stable in a six membered ring rather than a five membered ring?


texts: Titration curve of strong acid with strong base

texts: I have a question regarding the titration curve for $\ce{HCl}$ titrated with $\ce{NaOH}$. Why does it look like it does, with a steep slope near the equivalence point and a flat slope at the beginning and end?


texts: Under what circumstances would azeotrope exist in non ideal solutions? (when would the dew point curve and the bubble point curve meet?)

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[solved. For anyone who's interested in this topic, please view MaxW's comment under his/her answer. A thousand thanks to Poutnik and MaxW.]
I looked up several books on thermodynamics, and they all states that for non ideal solutions, the dew point curve and the boiling point curve sometimes meet at some point. Azeotropes forms there.
What I couldn't figure out was, under what circumstances would the two curves meet? Do they always meet if both of them have a local minimum? What is the logic under this phenomenon?


texts: Any way to guess what these crystals are?

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Is there any way to guess from these crystals what minerals formed them?  They came from ordinary tap water.

I was cleaning out a room humidifier which hasn't been used since last year when I noticed lots of little crystals in the bottom of it.  Most of them are square, which would suggest halite (NaCl) but some of them appear to have a pyramidal, or inverted pyramidal, shape.  This picture was taken with a cell phone and the largest crystals in the picture are probably 1/8".    Soaking them in warm water for an hour dissolved them.  The color - a pale brownish-yellow in the picture is accurate.


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I'm on the email list of an Organic Chemistry help website, and they sent out this problem:

http://orgomadesimple.com/june-9-email-practice-problem/

This got me thinking:

What if the nitrogen here was replaced with another oxygen atom?
Would it still be $sp^2$ hybridized?
Can oxygen molecules hybridize?

Thanks in advance for your help!


texts: Is there a way to determine the orientation of a benzene-ring ethyl group in synthesis reactions?

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On my study guide for synthesis reactions (specifically for the synthesis of disubstituted benzene derivatives), two of the problems look extremely similar.

The question on the guide asks us to synthesize each of these by using benzene as a starting material.

They appear to be the same molecule, just with a different orientation of the ethyl group. And in the solutions section of the guide, both have the same exact synthesis reaction listed.

Is there actually a way to determine the orientation of the substituent that isn't being explained by my study guide? Perhaps something done during the Friedel-Crafts acylation step? Or is this simply an effort to try and trip me up by asking the same question twice?


texts: Biomolecular energy functions and entropy

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From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions like AMBER, Charmm, etc. don't model entropy. They are however able to identify the native fold within a few angstroms (i.e. the minimum energy structure per the force fields is not more than a few angstroms away from the native structure) (http://onlinelibrary.wiley.com/wol1/doi/10.1002/jcc.20720/full).

If entropic changes are the primary driver of folding, then how is it that energy functions that don't even model entropy are still able to get close in terms of identifying the native structure (in particular, the burying of hydrophobic residues as well)? Is the entropic information incorporated in the solvent models?


texts: Steady State Approximation final integral proof $\frac{d[P]}{d t}=k_{a}[A]$ yielding $[P]=\left(1-e^{-k_{a} t}\right)[A]_{0}$

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I want to ask a question about the Steady State Approximation integral.

I understand the steady state integral works in Leyman's terms as the intermediate is formed as fast as it is consumed so the intermediate's concentration is really low and nearly always the same.

If I had a reaction:

$$\ce{A->I->P}$$

Then essentially,

$$\frac{d[I]}{d t} \approx 0$$

and therefore using this information and previous knowledge of rate

$$\begin{array}{l}{\frac{d[I]}{d t}=k_{a}[A]-k_{b}[I]} \\ {\frac{d[I]}{d t}=k_{a}[A]-k_{b}[I] \approx 0}\end{array}$$

which results after rearrangement:

$$[I] \approx \frac{k_{a}[A]}{k_{b}}$$

and hence $$\frac{d[P]}{d t}=k_{b}[I] \approx k_{b} \frac{k_{a}[A]}{k_{b}} \approx k_{a}[A]$$

The trouble is, I couldn't understand how:

$$\frac{d[P]}{d t}=k_{a}[A]$$

can be solved to give

$$[P]=\left(1-e^{-k_{a} t}\right)[A]_{0}$$

I recognise from previous work that:

$$\frac{d[A]}{d t}=-k_{a}[A]$$ gives

$$A =[A]_{0}e^{-k_{a} t}$$

from my final year at school, but I couldn't seem to apply this understanding to the final step of the integral above.

How can this be shown?


texts: Reactions which are impossible theoretically

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Take an example of reaction like :

Burning of carbon in air to form Carbon dioxide, say heat required is 100 joule (assume so)
And we provide the system say 20 joule heat
Theoretically it would be not possible. But the alone C atoms present near heat source will absorb their required heat (which would be very very small indeed) and get converted into co2
Hence, there will be small value of reactants which are converted into products then how can we say reaction is not possible. Thus at room temperature is it true that there is some concentration of products in any reaction.


texts: Why does the keto tautomer of guanine have lower energy?

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Looking at the keto and enol forms of guanine, it would seem as if the enol form is more stable, due to the fact that aromaticity is established with the enol form. However, according to a question on Chem.SE here: LINK there is a $\pu{8.7 kcal/mol}$ free energy difference between the enol and keto forms in aqueous solution.

Why is this? Shouldn't the enol form be much more stable due to aromatic stabilization?


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If there is a change in dipole moments such as absorption spectroscopy,  there are infrared absorptions (and/or transmittance) corresponding to them. Is the reason change in dipole moments are in infrared frequency simply because of the size of the molecules or scale of wavelength?   Or are the dipole moments producing particular frequencies simply because of their sizes just like in antenna? If not, why are they mostly in IR?

(Note: image from https://en.wikipedia.org/wiki/Electromagnetic_spectrum)


texts: New York Times Crossword: Is "electrically balanced" in chemistry "apolar" (given), "neutral," or something else entirely?

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As a lifelong New York Times crossword puzzler, I was baffled by clue 38-Across in today's puzzle (Saturday, May 22, 2021). The solution is a 6-letter word, and the clue is:

Electrically balanced, in chemistry

The word that comes to my mind is "neutral." The accepted answer is "apolar," a word I've never heard or muttered in my life. I would have gone with "non-polar" long before I hit "apolar," and I'd be in trouble due to the fine print around "non-polar" and "electrically neutral."
The Webster's Third New International Dictionary has this definition for "apolar":

having no poles - used esp. of nerve cells formerly believed to lack processes

My go-to text for historical chemistry - M. P. Crosland's Historical Studies in the Language of Chemistry - yields no answers. From the definition above, it might be something one would encounter in biology, specifically in regards to cellular biology.
Is "apolar" an accepted or commonly-used word in chemistry as a synonym for "electrically neutral," and if so, in what context has this appeared?


texts: Have Mossbauer spectroscopy on 67Zn ever been used to study Zinc containing enzymes?

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Have Mossbauer spectroscopy with 67Zn as absorber and 67Ga as emitter ever been used to study zinc containing enzymes?
The perfect answer will contain link to article/book where example of 67Zn usage is given or article/book where author tells that there is no such thing yet.


texts: Are compounds containing active methylene groups positive for the haloform test?

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Are compounds containing active methylene groups (e.g. 1,3-diketones) positive for the haloform test? Support your answer with a suitable explanation.

I was stuck on a certain question wherein a diketone was formed and I had to tell whether or not it shows the haloform test. It is clearly mentioned in my class notes that active methylene compounds don't show the haloform test; but in this problem the solution says that the diketone shows positive haloform just because it has an active methylene group. Please help!

Here's a possible mechanism that I came up with. Don't know if its correct. Sorry that it's handwritten; I don't know how to type chemistry.


texts: What does it mean to equilibrate a column in size exclusion chromatography and why is a buffer used?

texts: I'm reading a procedure on size exclusion chromatography and it says that the first step is to equilibrate the column with buffer. What does this mean?


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Due to electronegativity differences, the iodine will be electrophilic and the chloride nucleophilic. Correct me if I am wrong here.
My question is one of regioselectivity: will it proceed through an iodinium ion (like a bromonium ion which is observed when Br2 is added) where the iodine and Me groups are on opposite faces. Then, chloride attack at the most substituted carbon? Or would it be a more akin to a planar tertiary carbocation, so attack at either face almost equally probable? **chlorine should be "back" in first structure


texts: What is the correct way to verify a structure's geometry, for example for benzene?

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My goal is to compare a calculated bond length with experimental data. Benzene is obviously common enough to expect sufficient experimental data to be available for it on the internet.

I have found two sources for the C-C bond length in benzene, and the numbers differ very slightly. This source says 140 pm for benzene, while this source says 139 pm for benzene. Both claim their number comes from x-ray diffraction.

Is the discrepancy possibly attributable to a difference in solvent? Is a difference of 1 pm even significant? What is a good way to know for sure which quantity is correct?


texts: What chemical can be used for getting rid of hard water spots on cars?

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Most water spot removers available on Amazon or automotive stores are just fine abrasives which remove a small amount of your car's clearcoat every time you use them.

I'm looking for a chemical which can dissolve the water spots made out of limestone, chalk and gypsum.

Any acids suggested should not be strong enough to damage clearcoat (diluted), should not be abrasive.
Obviously I will not leave it on my car for very long, just apply, maybe rub around and rinse off with water.

I've not had any success with vinegar.


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I'm aware that there is a similar question here but it didn't really answer my specific questions.
I understand that steam distillation is used to separate an insoluble liquid from an aqueous solution, due to passing steam through the reaction mixture so they both evaporate etc...

I don't however understand what is so significant about this. If we started with a mixture of, let's say, 50% lavender oil and 50% water, wouldn't we also end up with a mixture of lavender oil and water, if both are evaporating below their boiling point? How is that useful - aren't we just ending up with what we started with? Or is it that the distillate will contain a greater proportion of oil? eg 60% to 40% - but then I don't see how that works, as shouldn't water should be more easily evaporated than the oil?

Furthermore, surely the two immiscible liquids form two seperate layers that can be put into a separating funnel and poured into separate containers?


texts: Why does water vapour deviate much more from ideal gas behaviour as it is cooled compared to nitrogen gas?

texts: My guess is that it is something to do with the difference in boiling point between the two aforementioned molecules. But I can seem to come up with a logical explanation to why this is the case.


texts: Combining Lead pipe with Zinc or Copper pipes in a domestic water installation

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Grateful if someone assists in explaining this example that appears on a high school text book. The problem can be summarized as follows:
"Old water networks supply water to a residential area via Pb lead pipes. A user wants to fit his own  installation with pipe made out of either Zn or Cu.  The intent is to reduce the lead presence in the water. Condition: the lead pipe of the municipality will remain unchanged up to the water gauge/meter at the house input.
Account for the presence of O2 in the water and give an explanation on your choice Zinc or Copper."
The solution suggested in the book shows Cu pipes, and excludes the use of Zn.
I would chose Zn. Reason would be that O2 would preferentially oxidize Zn instead of Pb. Thus preventing the formation of Pb oxide/hydroxides and consequent leaching in the water.
Thought I overlooked something and looking for an explanation to the book' choice which I assume is correct.. thanks for your support


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Why does the %s character increase on the orbital with electropositive atom?
I do not seem to properly grasp this concept. Is this rule based on observation or is there any proof to it? If there is a proof can you guys explain it to me in simple terms? I currently have knowledge of basic quantum mechanics and chemical bonding.


texts: What happens when potassium iodide is added to a copper (II) salt?

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$$\ce{Cu^2+ + KI -> ??}$$

I thought of this reaction:

$$\ce{Cu^2+ + 2KI -> CuI2 + 2K+}$$

But since $\ce{CuI2}$ doesn't exist, the $\ce{I-}$ ions must reduce $\ce{Cu^2+}$ to $\ce{CuI}$ and simultaneously get oxidised to $\ce{I2}$ and thus it will proceed the following reaction:-

$$\ce{2Cu^2+ + 4KI → 2CuI + I2 + 2K+}$$

I gave this reaction to my teacher and he gave me an another version of the reaction:

$$\ce{2Cu^2+ + 5KI -> 2CuI + KI3}$$

He says that he performed the reaction experimentally and obtained a white salt ($\ce{CuI}$) in a brown solution ($\ce{KI3}$).

Now, I started wondering what will happen if I alter the reaction and add sodium/lithium iodide instead of potassium iodide. Will it form sodium/lithium triiodide. Definitely not/ Or maybe, it will form.

  Two questions:

  What is the correct reaction?
  What will happen if we add sodium/lithium iodide instead of potassium iodide?

Related questions:

Why is NaCl3 possible?
What reaction takes place when potassium iodide is added to a tetraammine copper(II) complex?
Why triiodide ion does not form ionic bond with cation having +2 charge?
Why Cu+ is unstable in aqueous medium?


texts: What's the least common element in the universe? And what is its frequency measured in Hertz?


texts: How do we know a nerve agent is tasteless?

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According to the BBC, the nerve agent sarin is a tasteless liquid. How do we know that this liquid has no taste, given that anyone to have (not) tasted it in any meaningful quantity presumably died shortly thereafter.
Can the taste be inferred from its chemical properties?


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This is the article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611670/
I'm not a Chemist, so I can't understand the article very well.

The conclusion states that the molecules tested should not be called "piezolytes". Is this a nomenclature issue only? My only question is: does the presence of such molecules in deep sea organisms help in keeping proteins in their naturally folded state, resistant to denaturation due to high pressure or not?


texts: Activated complex theory vs. consecutive reactions

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Activated complex theory, tells us that due to the collision between the molecules of the reactants, they form a transition specie before the product is formed, which is called active complex. On the other hand we have consecutive reactions on which is also formed a intermediate product before forming the actual product we're interested on. My question is :

Where is the difference between the activated complex and the intermediate product, since they are both formed before  the actual product ?


texts:
I wonder what the name is of the following structure is:

I think it's something like 3-hyrodxypentanoic diacid
However, I wasn't able to find how to name a side chain if it contains a $\ce{COOH}$ group.

Maybe I'm completely wrong, I hope someone can tell me how to name this structure.


texts: 4-Bromo, 2,4-di-methylhexane and 3-Bromo, 3,5-di-methylhexane are the same thing?

texts: Came across the following question. The answer only says that option 3 is incorrect which is I agree to but dont you think option 4 is also incorrect. As per IUPAC rules isnt it the Halide that should get lowest possible number (in this case number 3 instead of 4) or is it both are same ? I am confused please help.


texts: Does increasing concentration of copper sulfate decrease or increase its conductivity?

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I am a high school student and for my chemistry lab, I did an electrolyis experiment on how the changing concentration of electrolyte (copper sulfate) will change the rate at which the copper is deposited on the cathode.

My hypothesis was that as the concentration is increased, so will the rate of electrolysis. However, my results are completely opposite. When I use 0.1 M solution, loads of copper is deposited on the cathode but as I increase the concentration, the amount of copper deposited becomes progressively less and less. With 1 M solution, there was almost no copper being deposited.

This makes no sense to me. Could somebody explain what is going on? Am I doing something wrong?

I used both copper electrodes. I did not use distilled water, just normal tap water. I used 12 V power supply.

EDIT:

I tried adding a little sulfuric acid (making the pH around 3) to the copper sulfate but it did not make any difference on electrolysis.

I tried to observe the electrolysis very closely today and noticed that there was some sort of oily liquid falling off from the anode. Also, I noticed that initially some flaky brown/black substance fell off from the anode (which may or may not be copper)and soon there was a silvery layer formed on the anode.

Also, I checked using Hanna checker that the overall pH of the solution was around 3 but the pH near the anode read between 9 and 14.

Also, I noticed that when I used a higher concentration, the copper deposition on the cathode was brown and clearly copper. But when I used lower concentration, even though the amount of deposit was a lot more, the substance was probably not pure copper as I had assumed earlier. It was black and flaky. It was certainly different to the deposit I observed when I used higher concentration of copper sulfate.

Does anybody know now what is happening? Is there anything that I can do to fix the problem?


texts: Is readily available ammonia a substitute for ammonia water?

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I am an artist attempting to duplicate a recipe for a painting medium.  The source says I can use powdered ammonia or ammonia water.  The recipe is from the 1940-50 and I am no chemist.

So, my question is can I use the readily available ammonia in place of "ammonia water" ... are they the same thing?


texts: Bandgap of a semiconductor for photocatalytic water splitting

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I'm reading a review article on photocatalytic water splitting (using semiconductors) and I came across the following:

"To achieve photocatalytic water splitting using a single photocatalyst, the bandgap of the semiconductor must straddle the reduction and oxidation potentials of water, which are +0 and +1.23 V vs the normal hydrogen electrode (NHE) at pH =0".

I have a few questions about this statement:

What exactly does it mean when you say that the bandgap has to "straddle" the reduction and oxidation potentials? Does it mean that you need an electron/hole with energy at least equal to 1.23 eV for oxidation/reduction to take place. So, the bandgap has to be greater than 1.23 eV in order to ensure that. Is my understanding accurate?
When using a single photocatalyst, I assume the oxygen and hydrogen evolution take place on the same material. If you had separate oxygen evolution and hydrogen evolution catalysts, what would the condition on the bandgaps of these semiconductors be?

Thanks! Sorry if these questions are too basic, I have little training in chemistry.


texts: Why is it necessary to consider infinitesimal changes in p,V,T for H,U and G given that they're state functions?

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State functions such as $G$ only depend on the state of the system and are not dependent on the "path" that took the system to that state (which would be the case for work, for example, which is not a state function.

We know that:

$$\mathrm{d}G=V\mathrm{d}p-S\mathrm{d}T$$

So…

$$\mathrm{d}G=\left(\frac{\partial G}{\partial p}\right)_T\mathrm{d}p+\left(\frac{\partial G}{\partial T}\right)_p\mathrm{d}T$$
Consequently, by comparing coefficients:

$$V=\left(\frac{\partial G}{\partial p}\right)_T$$ and $$-S=\left(\frac{\partial G}{\partial T}\right)$$

Just taking the equation involving $V$ now to save time and space:
$$\int_{p_1}^{p_2}V\mathrm{d}p=\int_{p_1}^{p_2}\left(\frac{\partial G}{\partial p}\right)_T\mathrm{d}p$$

Using the perfect gas equation and integrating leaves the result:

$$G(p_2)-G(p_1)=n\mathcal{R}T\ln\left(\frac{p_2}{p_1}\right)$$

But if $G$ is independent of the path taken to get to the final state, why shouldn't I use the equation

$$\Delta G=V(p_2-p_1)?$$


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I have issues understanding the spontaneity for these processes:

Which of the following processes are spontaneous:

(c) alignment of iron filings in a magnetic field;

(d) the reaction of sodium metal with chlorine gas to form sodium chloride;

The answer given for both (c) and (d) is that the entropy of the system decreases.

This has me puzzled because I don't think that even answers the question.
Clearly I would think both (c) and (d) are spontaneous processes.  For (c), the iron will naturally align itself in the magnetic field. For (d), I know the reverse reaction is non-spontaneous (table salt does not normally disassociate), so the forward reaction must be spontaneous.

Assuming I am correct, how do I reconcile this with the book answer?

The entropy of the universe increases for any spontaneous process.  If we assume the entropy of the system is negative (like the book does) then the entropy of the surroundings must be positive and greater.  I don't know what that would mean in this context.

I agree that it makes sense that the entropy of the system is negative.  The iron filings are moving to a more ordered state in (c).  For (d) there are more micro-states originally since there were more moles of reactants.


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This is theoretical scheme for preparing $\ce{KHSO4}$:
$$\ce{K2CO3 + 2H2SO4 -> 2KHSO4 + CO2 +H2O}$$
using 1 eq $\ce{K2CO3}$ and 2 eq of $\ce{H2SO4}$ in approx 10 eq of $\ce{H2O}$ one gets $\ce{K2SO4}$ instead. How is it possible that $\ce{H2SO4}$ completely dissociated despite $\ce{HSO4-}$ is very weak acid in water? Does $\ce{K+}$ ion somehow influence the acidity of that anion? You have to use double the amount of sulfuric acid (4 eq) to get desired product.
Also when using 1 eq $\ce{K2CO3}$ and 1 eq of $\ce{H2SO4}$ what product would you expect? Mixture of $\ce{KHCO3}$ and $\ce{KHSO4}$?


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Hello Folks

I am not now nor have I ever been any kind of chemist.

My question is, how is the formula for Cerin, C30H50O2, consistent with this diagram taken from Chemspider?

I can count the 30 Carbon atoms, assuming that each vertex of a hexagon is a single C. I can obviously see the two Oxygen atoms. But when I count the Hydrogens, I can only get to 28. Where are the other 22?

Thank you for your patience.


texts:
The metal carbonyls (and similar organometallic compounds) involve a combination of a $\sigma$-bond, a $\pi$-bond and backbonding. The bond strengths under consideration are the metal-carbon bond and the carbon oxygen bond. Here is the original question:

  Predict the order of $\ce{C−O}$ bond strength in the following:
  I) $\ce{[Mn(CO)6]+}$
  II) $\ce{[Cr(CO)6]}$
  III) $\ce{[V(CO)6]-}$

All of these are isoelectronic, and hence whatever the difference of bond strengths, must arise from the difference in the resultant nuclear force of attraction. Since $\ce{Mn+}$ has the highest charge density, I would assume that the $\ce{M−C}$ bond strength of the manganese compound is the strongest (vanadium being the weakest) and therefore, the $\ce{C-O}$ bond strength must follow the opposite order, as the strengthening of the metal carbonyl bond should weaken the carbon oxygen bond.

But the answer given is $\mathrm{III<II<I}$, exactly the opposite of my prediction. Why is it so? A relevant factor which I didn't consider is the back bonding, but I am unsure of how to integrate that into my prediction. Also, how would we make a prediction if the given compounds were not isoelectronic?


texts:
I have a short question: Which among Methanol and water will be a better nucleophile for a reaction carried out in some polar protic solvent .
Searching over the internet suggests that methoxide ion may be more nucleophilic than hydroxide ion, is that true? If it is, does that automatically imply methanol being more nucleophilic than water?
Also, on what precise factors does it depend?


texts: Why are metal oxides basic and non-metals' acidic or neutral

texts:
Recently I came across the fact: Metal oxides basic and non-metals' acidic or neutral.

Searching for it, partly my query is solved, as I found:

Metal oxides or $\ce{O2-}$ forms $\ce{OH-}$ after hydrolysis in the following reaction so metal oxides are basic in aqeous solutions.
$$\ce{O2- + 2H2O->4OH-}$$

I think this might happen as metal form ionic compunds and non-metals form covalent and some of them may not even react tus neutral.

I've got only a little $5\%$ of the exact reason, therefore I wish if someone could explain the whole process/fact. I considered Arhenius concept.

Note My question is partly answered here, but is not satisfactory.


texts: Questions about intramolecular interactions in AMBER forcefield

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I am trying to run a molecular dynamics simulation with AMBER forcefield. However, it's the first time I use is, and while I know the form of the various intra- and intermolecular energy terms, some details are not clear to me. So, for the AMBER forcefield:

What pairs are excluded in the summation of intramolecular Lennard-Jones interactions? Typical choices are “excluding bonded atoms”, “excluding 1-2 and 1-3 pairs”, “excluding 1-2 and 1-3, applying a factor 1/2 to 1-4 pairs”, and “excluding 1-2, 1-3 and 1-4 pairs”.
For torsion potentials, is the potential scaled by the number of such torsions? (as is done in the DREIDING forcefield, to ensure a constant torsional barrier for the central bond)


texts: When and how in anaerobic digestion is water dissociated?

texts:
Anaerobic digestion and methanisation of organic feedstocks is a complex series of processes that result in biogas. One way to look at this is a very top-down, stochiometric approach as in the Buswell equation

$$\ce{C_aH_bO_c + \left($a - \frac{b}{4} - \frac{c}{2}$\right)H2O -> \left($\frac{a}{2} + \frac{b}{8} - \frac{c}{4}$\right)CH4 + \left($\frac{a}{2} - \frac{b}{8} + \frac{c}{4}$\right)CO2}$$

There's also a Buswell-Boyle equation that takes nitrogen and sulfur into account, but right now I just want to understand one aspect.

During the process, at some point, water is dissociated. When does this happen (hydrolysis, acidification, ...), what role does the water play and what are sample reactions that illustrate this?


texts:
A soft species is typically large, polarizable and has a low charge (magnitude). The silver cation is not highly charged (this supports softness) however, it is anomalously small due to high nuclear charge and poor shielding by the d-orbitals. Consequently, shouldn't it also be less polarizable?

It does have a tendency to form bonds that are significantly covalent in nature which backs up the assertion that $\ce{Ag^+}$ is soft; however, I don't understand why.


texts: Is there any reason why halogenation of substituted alkanes wouldn't occur through free radical substitution?

texts: Say for example, you have isopropyl alcohol. Is there any reason why if you react it with bromine that it won't form a radical, as one of the bromines removes one of the protons adjacent to the hydroxyl group on the alkane, and then propagate into 2-bromo,2-propanol?


texts: Why do Magnesium and Lithium form *covalent* organometallic compounds?

texts:
Lithium and magnesium are Group 1 and Group 2 elements respectively. Elements of these groups are highly ionic, and I've never heard of them forming significantly covalent inorganic compounds.

Yet these elements form a variety of organometallic compounds ($\ce{PhLi}$, the whole family of Grignard reagents, etc). Organometallic compounds have significant covalent character (i.e., the bond can be called covalent)  in the carbon–metal bond.

What's so special about carbon that makes these elements form covalent bonds?


texts: atomic orbital probability graph for p and s orbitals

texts:
In the probability density graphs of s and p and even other orbitals start from nucleus as shown in the picture given below

they all start from nucleus i.e. there is good probability of electrons of the particular orbitals being there.

my doubts:

there is proper energy variation and differences of energies of electrons being in particular orbital, example, energy of 2p will be greater than 2s etc. and as i think energy of electron is due to its position with respect to nucleus. as in the diagram probability regions of 1s 2s and 2p is same {though value of y coordinate is small}
then how can there energies be different?
don't the electron clouds of 1s , 2s , 2p intermix? moreover electron cloud- a 3D SPACE which must be wide enough to get electrons at different distances from nucleus doesn't violate the rule that electron has one constant energy in one orbital.


texts: Why when deriving the Clapeyron equation can you assume that dH = dq, as surely the pressure is not constant?

texts: Part of the Clapeyron equation involves replacing $\Delta S$ with $\Delta H/T$. I can see the step from $\Delta S$ to $\Delta q/T$ but I'm not sure why you can replace $\Delta q$ with $\Delta H$. From my understanding $\mathrm dH = \mathrm dq_V +V\mathrm dp$ when assuming no work other than $pV$ work is done. I don't understand how you can substitute $\Delta H$ for $\Delta q$ without assuming that the pressure is constant?


texts: Is the quantum number $L$ a combination of the azimuthal and magnetic quantum numbers $(\ell, m_\ell)$?

texts:
Somehow, I am getting confused about this...
In the $J=L+S$ equation about total angular momentum, which of the four quantum numbers used to describe the electrons and their states is included in the $L$?
And does the $J$ include the first, principal quantum number?


texts: The effect of lactose monohydrate on acid-base extraction of tolterodine tartrate

texts:
I am doing an organic chemistry project for school in the form of an acid-base extraction of tolterodine tartrate (Detrol) in ammonium hydroxide (or sodium hydroxide, haven't decided yet) and dissolving the freebase in benzene.

I am planning on crushing up the tablets, and dissolving them in water. Almost all the inactive contents of the tablets are not soluble in water except for lactose monohydrate. Will the presence of lactose monohydrate effect the reaction of the acid base extraction when I add the hydroxide?


texts:
So I was going through the Schrödinger wave equation to determine the shapes of orbitals. We know that an orbital is nothing more than a region where probability of finding an electron is maximum.
Further, we know that the probability of finding a 2s electron in 1s orbital is just too low! Why do 1s orbital and 2s orbital intersect? I mean both the orbitals have the same shape and the radial function of 2s orbital is more than that of 1s which clearly means that 1s orbital lies inside 2s orbital!
But as it's impossible to find a 2s orbital electron in 1s orbital, shouldn't the shape of 2s orbital be something like a hollow sphere with thick walls instead of a complete sphere?


texts: Calculating the volume of 1 mole of liquid water

texts:
I am doing some rough calculations to test my understanding of elementary chemistry. In what follows, I calculate the volume of one mole of liquid water at about $\pu{4 ^\circ C}$ and $\pu{1 atm}$:

Method 1: Using the molar mass and density of water

The molar mass of water is $\pu{18 \times 10^-3 kg mol-1}$, and the density is $\pu{1 \times 10^3 kg m-3}$. Hence, the volume should be

$$V = \frac{(\pu{1 mol})(\pu{18 \times 10^-3 kg mol-1})}{\pu{1 \times 10^3 kg m-3}} = \pu{1.8 \times 10^-5 m3}.$$

Method 2: Using the size of an individual water molecule

If we model the mole of water as a cube, since there are $6.022 \times 10^{23}$ water molecules, each side of the cube would have $8.44 \times 10^{7}$ molecules.

Using the water data page on Wikipedia, I used trigonometry to calculate the H–H distance as being approximately $\pu{150 \times 10^-12 m}$. I would think the dimensions do not change too much when there are many molecules.

From this, I find that the volume is

$$V = [(8.44 \times 10^7) \times (\pu{150 \times 10^-12 m})]^3 = \pu{2.05 \times 10^-6 m3}$$

which is an order of magnitude smaller than Method 1.

What is the reason for this discrepancy?


texts: Can you electrolyse a single H2O molecule?

texts:
I don't know why I'm asking or why you'd want to but I'm just curious.

Every resource I read about electrolysis says the reaction is $\ce{2H_2O (l) \rightarrow 2H_2 (g) +O_2 (g)}$.

Can you electrolyse a single molecule?


texts: What is the reaction mechanism between boric acid and 2-ethyl-1-hexanol

texts:
Here is a photo from an article, Hydrometallurgy 2016, 160, 129–136

This indicates the reaction mechanism as esterification. However, the written reaction equation ($\ce{H3BO3 + nROH -> H3BO3.nROH}$) suggests the mechanism as solvation.
Shouldn't the reaction be $\ce{H3BO3 + ROH -> H2RBO3 + H2O}$ or something like that based on the scheme?


texts: Elimination of hydroxyl group while deprotecting acetal

texts: Regarding this reaction, other than de-protecting the acetal, will we have an elimination reaction for the alcohol or no?


texts: Alkyl chain substituent has higher preference than benzyl substituent?

texts:
The compound in question, and the name generated by ChemSketch:

I have looked at relevant (outdated) documentation for naming of substituted amines. I understand tertiary amines are named as: $\text{N-alkyl}_1\text{N-alkyl}_2\text{alkyl}_3\text{amine}$.

Now, I am confused at the first point: when we have to select the parent carbon chain. For this compound, I would have selected "benzylamine" as the parent chain, as it obviously has more number of carbon atoms and more unsaturation than both methyl and propyl. Thus, my preferred IUPAC name would have been "N-methyl-N-propylbenzylamine".

But, for some reason "propane" is the main carbon chain here instead. So, what is the logical reasoning for the naming these tertiary amines?


texts:
What happens to the surface tension of a solvent, say, water when we mix a solute in it?
For the sake of concrete discussion, the examples that I encountered in a test were sodium chloride $(\ce{NaCl}),$ methanol $(\ce{MeOH}),$ and sodium alkyl sulphates $(\ce{ROSO3Na}).$

My guess is that since the surface tension can be defined as the force per unit length on a line drawn on the surface of the liquid, if the solute attracts $\ce{H2O}$ more than another $\ce{H2O}$ molecule, then the surface tension should increase.

Using this logic, I predict the following:

Addition of methanol should decrease the surface tension because $\ce{MeOH}$ forms lower number of hydrogen bonds than pure water.
Sodium chloride addition should increase the surface tension because ion dipole interactions are stronger than dipole dipole interactions or H-bonds.
The $\ce{ROSO3Na}$ kind of confused me. I assume they intended for me to perceive it as detergent and I know that decreases the surface tension. They actually asked to recognize the appropriate plot of variation in surface tension with concentration and the graph I guessed attained a constant value after a certain concentration. I thought it might be due to micelle formation.

If anyone can confirm or deny my intuition, or point me in the direction of any data that would be helpful.


texts: Calculate the energy in the form of heat (in kJ) required to convert 325 grams of liquid water at 20.0 °C to steam at 115 °C

texts:
Calculate the energy in the form of heat (in kJ) required to convert 325 g of liquid water at 20.0 °C to steam at 115 °C. Assume that no energy in the form of heat is transferred to the environment. (Heat of fusion = 333 J/g; heat of vaporization = 2256 J/g; specific heat capacities: liquid water = 4.184 J/(g K), steam = 1.92 J/(g K)

Here is what I did:

$$Q=mcT$$

$$\begin{align}Q &= 325 ( 4.184) (100 - 20)\\
&= 325 ( 4.184 ) ( 80)\\
&= 108784\ \mathrm J\end{align}$$

$$\begin{align}Q&= ml\\
Q&= 325 ( 2256)\\
&= 733200\ \mathrm J\end{align}$$

$$\begin{align}Q &= 325 (1.92) ( 115 - 100)\\
&=325 (1.92) ( 15)\\
&= 9360\ \mathrm J\end{align}$$

$$(108784+733200+9360) \mathrm{J}= 851\ \mathrm{kJ}$$

But the correct answer is $735\ \mathrm{kJ}$

Do you know the right way to do it?


texts: Determine reaction rate constant from the reaction time?

texts:
I was doing some research and I came across an experiment similar to mine (potassium iodate with sodium bisulfite) from the University of Massachusetts (http://www.chem.umass.edu/genchem/chem122/122_Experiment_4.htm), but with the reaction of potassium permanganate with oxalic acid.

The rate equation is given as:
Rate = k[KMnO4][H2C2O4].

It was stated that the value of k could be determined by dividing the concentration of the potassium permanganate [KMnO4] by the reaction time to find the rate and then dividing the rate by [KMnO4] multiplied by the concentration of the oxalic acid [H2C2O4] to find the reaction rate constant.

They provide the following equations:

Rate = [KMnO4]/t

k = Rate/([KMnO4][H2C2O4])

Would this be applicable to my reaction (potassium iodate with sodium bisulfite), because this would allow me to find the activation energy without performing trials to find k experimentally?


texts: How does zinc become oxidized when it's not in direct contact with copper ions in a galvanic cell?

texts:
Whenever a galvanic cell is explained in textbooks/videos, it usually starts by showing that if you put a piece of $\ce{Zn}$ in a $\ce{Cu^{2+}}$ ion solution, the $\ce{Zn}$ will become oxidized and transfer $\ce{2e-}$ to the $\ce{Cu^{2+}}$ ion, so the $\ce{Cu^{2+}}$ becomes a neutral $\ce{Cu}$ metal.

I understand this, but in a galvanic cell, the $\ce{Zn}$ never actually touches the $\ce{Cu^{2+}}$ ions, the $\ce{Zn}$ and $\ce{Cu}$ are only connected with wires. I don't understand how the $\ce{Zn}$ can be oxidized and transfer ions through the current.


texts: Does tetrachlorodibenzo-p-dioxin (2,3,7,8) have a nonzero dipole moment?

texts:
I've looked at and drawn the structure, and I originally felt that it would be nonpolar - as I believe all the dipoles would cancel out, but I'm not 100% sure. I might be too dependent on the fact that it looks symmetric.

Also, is it true that the overall molecule shape would be planar? And is the hybridization of the oxygen atoms sp3 like I think they are?

Edit: Thanks to a commenter, I have changed the question to ask about the dipole moment in hopes of being more clear. I'd also like to add that this is a homework question that I am stuck on (for general chemistry l) and the teacher hasn't been the most thorough which is why I am here trying to teach myself.


texts: When aluminium is ignited in atmosphere, will it form only aluminium oxide or also aluminium nitride?

texts: We know when lithium is burnt in air, it forms lithium nitride and lithium oxide. I am wondering if this applies to aluminium (other metals) also?


texts:
If I have a pure substance which may be cholesterol can I test that by polarimetry? In other words the idea would be to dissolve the sample in dichloromethane or ethanol, then test the rotation using a polarimeter.

My concern is that I read that cholesterol will not actually dissolve, only form a colloid, so that may invalidate the possibility of a test.


texts:
I'm working on a project in which I'll be dealing with pressure vessels. As of now I've drawn/conceptualized everything on theory basis. The diagrams are made on the basis of theory, but then I came through a situation where I'll require to heat water under high pressure at around 300-350 Celsius. So then I decided to use pressure vessels and to use LPG gas for heating it (LPG has flame temperature of around 1100 Celsius, but please note that I want to heat the water kept in vessel at just 300-350 Celsius)

Now, I'm stuck in thinking that how do you heat pressure vessels? Are there any special port/connections provided to heat them/the content inside them? Or are any special type of heaters used to heat them? Would be great if you can tell everything you know about heating it

Optional to read(this could be wrong): Are we supposed to directly heat them on flame? Just like cooking your food on the gas-stove running using LPG? If this is so, then won't it take too much time because the walls of vessels would be very thick?


texts: Oxidation numbers of atoms in Ti(SeO3)2?

texts: What are the oxidation numbers of atoms in $\ce{Ti(SeO3)2}$? I'm having trouble figuring this out since I don't know the charge for either $\ce{Ti}$ or $\ce{Se}$.


texts:
For example, silver chloride, silver sulfide, and silver oxide are three exceedingly stable silver salts in water solution.

Why is it that silver forms such stable salts?

Does this have to do with charge density of the component ions? This doesn't seem to hold water because we know that silver oxide is much more soluble than silver sulfide, and the oxide anion is obviously a lot smaller than the sulfide ion, so the oxide ion should have a much higher negative charge density.

So simple charge density rationalizations go out the window. I've Googled, I've looked in books, etc., but I can't find an explanation.

On the other hand, can a Lewis acid/base model be used to rationalize the stability of the silver compounds? For example, the sulfur, by nature of being less electronegative than oxygen, is a better Lewis base/electron pair donor/nucleophile; the sulfide ion is more willing to "donate" its electrons. Also the sulfide ion should be bigger and has empty 3d valence orbitals which may or may not be accessible to a great extent. Nonetheless, metals, by nature of possessing a large number of valence d-electrons, may be able to increase the stability of the sulfide ion by populating its d-valence.

This Lewis acid/base model seems to get a lot of mileage. I also know that silver is a good Lewis acid, as are many metal cations, because of the poor shielding afforded by the d electrons. Also, the silver cation has an empty 5s orbital. Thus, we can form a sulfide-to-cation sigma coordinate covalent bond.

We may also form a pi-type coordinate covalent bond as the far-away d-electron density "drifts" to empty 3d valence orbitals on the sulfide anion, making the sulfide anion now more nucleophilic than ever.

Let me know if my rationalizations are incorrect or if there are better explanations of silver salt stability.


texts: Why does some compound as given in the image below change from low spin to high spin above a particular transition temperature?

texts: Magnetic moment sudden increase at a particular temperature is explained by CFT. But why does it happen at all?


texts:
Given
$$\ce{10KClO3 + 3P4 -> + 3P4O10 + 10KCl}$$

If 52.9 grams of $\ce{10KClO3}$ reacts with excess $\ce{P4}$, what mass of $\ce{3P4O10}$ could be produced? How many moles of $\ce{KCl}$ could be produced?

I am not sure if I have to calculate the excess mass of $\ce{P4}$ and then find the mass of $\ce{3P4O10}$ or if it is just telling me that $\ce{P4}$ is excess reactant. If it is calculating the excess mass, how would I do it if I do not know the original mass of  $\ce{P4}$?


texts: Dissociation of silver chloride in a solution

texts:
When silver chloride is exposed to light it can dissociate to silver metal and atomic chlorine. It might be a silly question, but could the chlorine go back into the solution as chloride ions ? if so is this likely to occur? does the outcome change if the solution is being boiled?
Thanks!


texts:
$1.25~\mathrm g$ of a sample of bleaching powder is dissolved in $100\ \mathrm{mL}$ of water. $25\ \mathrm{mL}$ of it are treated with $\ce{KI}$ solution. The iodine so liberated required $12.5~ \mathrm{mL}$ of $\frac{\mathrm{M}}{25}$ hypo solution ($\ce{Na2S2O3}$) for complete titration. Find percentage of available chlorine from the sample of bleaching powder.

My attempt:

In $25~\mathrm{mL}$ sample:

mEq of $\ce{Cl2}$ in bleaching powder $=$ mEq of $\ce{I2}$ liberated $=$ mEq of hypo solution

$\mathrm{mEq}$ of Hypo $= NV = \left(1\times\frac{1}{25}\right)\times12.5 = 0.5$

This is where I have a problem, if we are to go by the solution provided in my book, then the n-factor for the hypo solution is 1, whereas, when I write the balanced redox reaction, that is,

$\ce{2S2O3^2- -> S4O6^2- +2e^-}$

You can see that n-factor should be $2$.


texts: Mixing 1 cubic meter of HCl and NaOH: Temperature rise of a metal container?

texts:
Say I (perfectly) mix $1\ \mathrm{m^3}$ of 1 M $\ce{HCl}$ with $1\ \mathrm{m^3}$ of 1 M $\ce{NaOH}$ at standard air pressure and room temperature within a metal vessel. Heat of neutralization for strong acids and bases is $-55.8\ \mathrm{kJ/mol}$ (is that actually just the bond enthalpy of an $\ce{H-OH}$ bond?).

So the $2\ \mathrm{m^3}$ of $\ce{H2O}$ amount to around $2 \cdot 10^6\ \mathrm{mol}$ of water ($M(\ce{H2O}) \overset{\wedge}{=} 20\ \mathrm{g\ mol^{-1}}$). Therefore, $\Delta_\mathrm n H$ is around $2 \cdot 10^6 \times 55.8\ \mathrm{kJ/mol}$, around $110 \cdot 10^6\ \mathrm{kJ}$.

I would now like to calculate the temperature rise.

The heat released is $Q = m c_p \Delta T$, where $m$ is the mass of the solution ($2000\ \mathrm{kg}$), $c_p$ is the specific heat capacity of the solution and $\Delta T$ ist the change in temperature. But that's exactly what I'm trying to find. So unless I know $Q$, I can't find $\Delta T$. Therfore, how do I find $Q$?


texts: What type of glass are Pasteur pipettes made of? And at what temperature do they need to be heated to create a micro-pycnometer?


texts: Phantom Material: why formaldehyde doesn't rise my jelly melting point?

texts:
Just to be clear, I'm not a chemical but only a electronic engineer which want create a "phantom material" to reproduce the electrical characteristic of epidermis for the analysis of electrodes impedance.

I found this paper which explain very well the process to create the phantom. As described, the use of formaldehyde is very useful to rise up the melting point of jelly to menage the final product even at room temperature. The quantity I need to fill my container is 285 ml so I scaled the doses in Table 3 at pg. 31 in the paper. I got

285 ml distilled water
8.55 g of gelatine foil (in the paper is used the powder but I found only the foils. The product says 12, or 20 g, foils for 1 litre of water but I rised this dose to get a more solid jelly)
0.96 ml of formaldehyde (37%)
0 g of NaCl (I need the lower conductive type)
0 g of ethyl 4-hydroxybenzoate (I haven't found this product)

I dissolved the gelatine foils in hot distilled water, then added the formaldehyde and, after the temperature of mixture has dropped, putted all in the fridge.

Now the problem is that the my phantom melts even at room temperature. It seems the formaldehyde doesn't his job.

Did I do something wrong?


texts: Identifying nucleophiles and electrophiles in an acid-base reaction

texts:
Is ammonia a nucleophile and hydrogen the electrophile in the Brønsted-Lowry acid-base reaction of acetic acid with ammonia?
$$\ce{CH3COOH + NH3 <=> CH3COO- + NH4+}$$

I say that ammonia is the nucleophile because I drew a curved arrow from the lone pair on the ammonia to the ionizable hydrogen on acetic acid, and I drew a curved arrow from the bonding pair in the hydroxyl group to the oxygen in the hydroxyl group of acetic acid. It seems that ammonia is the nucleophile because it is attacking the hydrogen proton (a bare proton) and that hydrogen is the electrophile because it likes the lone pair on ammonia.
So if the above is right, this would make ammonia a Lewis base and the hydrogen proton a Lewis acid? Or do we say the entire acetic acid molecule is a Lewis acid?


texts: How much calcium hydroxide will precipitate after addition of sodium hydroxide into saturated calcium hydroxide solution?

texts:
Below was question 34 in the USNCO 2017 exam:

  If $\pu{0.10 mol}$ of solid $\ce{NaOH}$ is added to $\pu{1.00 L}$ of a saturated solution of $\ce{Ca(OH)2}$ $(K_\mathrm{sp} = \pu{8.0 \times 10^-6})$, what percentage of the calcium hydroxide will precipitate at equilibrium?

  (A) Roughly 50%
  (B) Roughly 75%
  (C) Roughly 95%
  (D) Over 99%

My solution is as follows:

Find concentration of $\ce{Ca^2+}$ $(\pu{0.02 M})$ and $\ce{OH-}$ $(\pu{0.04 M})$ ions from dissolved calcium hydroxide using $K_\mathrm{sp}$.
Add hydroxide ion concentration from sodium hydroxide (assuming full dissolution) to get total hydroxide concentration of $\pu{0.14 M}$
Find reaction quotient $Q = 0.02 \times 0.14^2 = 3.92 \times 10^{-4}$
Find amount of calcium $(x)$ and hydroxide ions $(2x)$ that will precipitate at equilibrium by using algebraic equation:
$$
(0.02 - x)(0.14 - 2x)^2 = 8.0 \times 10^{-6}, x = \pu{0.019 M}$$
Find percentage of calcium hydroxide precipitated:
$$\frac{0.019}{0.02} \times 100\% = 95\%,$$
hence (C)

I am unsure about step 4, where a cubic equation appears, and would not be able to be solved in exam conditions (use of graphing calculator is not permitted).

Is there a simpler method?


texts:
I'm planning on an Iodination reaction of a 2-aminothiazole derivative. Specifically, 2-aminothiazole, with two Boc groups on the amine.

What practical advice do you have for recrystallising NIS? Literature recommends dissolving in hot dioxane and then adding $\ce{CCl4}$ to precipitate out the NIS.
If I do not have access to $\ce{CCl4}$ would $\ce{CHCl3}$ suffice?
Do NIS and NBS (I've previously used NBS for this reaction in $\ce{CHCl3}$) have similar solubilities in $\ce{CHCl3}$?


texts: Weak buffers and accuracy when mixing acid and base

texts:
What is the weakest buffer possible - that is, what has the lowest buffer capacity possible?

I would just assume that the lower the concentrations of $[\ce{A-}]$ and $[\ce{HA}]$, the lower the capacity is, but it seems like the question is looking for a specific solution?

Also, how precise do you have to be when mixing a strong acid and base to get a pH value of 7 and not 6? since $[\ce{H+}] = 10^{-7}$ and  $[\ce{OH-}] = 10^{-7}$ at $\mathrm{pH} = 7$, while $[\ce{H+}] = 10^{-6}$ and $[\ce{OH-}] = 10^{-8}$ at $\mathrm{pH} = 6$, does this imply you can at most be off by a factor of $10^{-2}$ mol/L?


texts: Is there a treatment for distilled water to become drinkable?

texts:
It is my understanding that, drinking distilled water may not be recommended. Its not recommended indeed. Or maybe its not not recommended... Maybe not not indeed........ Anyway....

Well, apparently, in some places, they actually acquire distilled water from various sources (desalinization, atmospheric moisture, etc), and sell for people to drink.

My question is: What are the methods used to treat distilled water, such that it becomes more like the "tap water" we drink? (or, perhaps, drinkable/safer in the sense of the not-recommended-links (that is, assuming such links are true ofc)).


texts: Reduced Graphene Oxide (RGO) Conductivity vs Everything Else

texts:
Reduced Graphene Oxide (RGO), is the reduced version of Graphene Oxide (GO). Both RGO & GO are easily manufactured when compared to the complex process used to manufacture the 'atom-thick' Graphene. And because RGO & GO are arranged in the same fashion as graphene, they keep similar properties; but nothing in comparison. Nevertheless, it is worth taking a look into the characterization of these properties because we can manufacture them quite easily.

But here's my problem, is it a waste of time to create thin sheets of RGO if there is a material that is more conductive?

So I arrive at my question, is a small sheet RGO's conductivity greater than that of, say, a small sheet of Copper? I have tried researching this every where but have not came up with a solid answer.


texts: Can HI/P reduction be used to reduce nitroalkanes and nitroarenes to alkyl amines and aryl amines?

texts:
Can $\ce{HI/P}$ reduction be used to reduce nitroalkanes and
  nitroarenes to alkyl amines and aryl amines ?

I learnt from my textbook that heating the nitroalkanes and nitroarenes with $\ce{H2}/\ce{Pt}$ is sufficient for the above conversion. But I am not sure whether $\ce{HI}$ and red $\ce{P}$ reduction will give the same products. Also, I could not find related information about this on the Internet.


texts: How to remove paraffin wax drop from cam lense glass?

texts:
When I put a my cellphone on a table for charging, some drops of paraffin wax were laying there which I couldn't see.  After some time during charging, heat melted the paraffin wax and it stuck on the rear camera lens of my Lenovo k6 Power.

I tried to wipe the lens with a special cloth especially used for cleaning my glasses, but it couldn't remove all the scratches/stains.

Please suggest any solutions.


texts:
I have to suggest a method in order to produce $\ce{F2}$. It also says that I should consult the redox potential values. I know that there is a way to produce fluoride which is:

$$\ce{K2[MnF6] + 2 SbF5 -> 2 K[SbF6] + MnF2 + F2}$$

I also know that it can be produced by the electrolysis of non-aqueous halides ($\ce{KF}$).

Why do I have to check the values of redox potential? I know that $\ce{F2}$ can't be produced by the electrolysis of aqueous solutions because it oxidizes water.

Is this method correct?

\begin{align}
\ce{2 K+ + 2 e- &-> 2 K} \\
\ce{2 F- &-> F2 + 2 e-} \\
\hline
\ce{2 K+ + 2 F- &-> F2 + 2 K}
\end{align}


texts: Constructing a reactivity series, magnesium more reactive than sodium?

texts:
I reacted about $0.25 \,\mathrm{g}$ of magnesium, sodium and lithium in $20 \,\mathrm{ml}$ of $2 \,\mathrm{M} \,\ce{HCl}$ at room temperature. This was all done in a $100 \,\mathrm{mL}$ beaker.

I found the biggest temperature change in the reaction mixture with lithium, followed by the reaction mixture with magnesium and finally sodium.

I measured the temperature change over the course of the reaction with a Vernier temperature probe and accounted for the heat loss by interpolating a fitted line based on the heat loss signature after the reaction has completed.

I calculated the heat of the reaction and divided by the number of moles and get this:

Li reaction: $120 \,\mathrm{kJ/mol}$
Mg reaction: $91 \,\mathrm{kJ/mol}$
Na reaction: $33 \,\mathrm{kJ/mol}$

I did notice the evolution of a lot of gas when reacting $\ce{Na}$ with the $\ce{HCl}$. As expected a flame was produced with the sodium reaction.

My questions are:

Why is it that the reaction that apparently seemed to be the most vigorous produced the least temperature change?

I was initially thinking that the sodium had a lower temperature change as it reacted so vigorously that the hydrogen gas produced had more kinetic energy, and as it leaves the system, the temperature of the system does not change by much. But I figured this explanation to be incomplete as lithium is supposed to be more reactive than sodium, so if this was the case I would have an even lower temperature change for lithium?

Why is it that some reactivity series have lithium at the very top while others just omit it entirely or put it below sodium and potassium? Who is right?

I guess what I am really asking is for ideas on where I went wrong, because this data does not seem to be right.


texts:
I can't manage to find any information about the recycling process and the chemistry behind it. The only thing I see everywhere on the internet - is a guide like this:

Step 1 - Discharge the battery.
Step 2 - Store at room temperature.
End of the article.

I have a DELL XPS15 battery, slightly swollen. And when I asked local repair service about recycling - they said: "nobody recycling Li-Pol here" (in my city).
So I decided to investigate this topic. Any idea where I can start?


texts: Clear definition of a 'non-oxidizing acid'?

texts:
From the Beryllium article in Wikipedia:

  Beryllium dissolves readily in non-oxidizing acids, such as $\ce{HCl}$ and diluted $\ce{H2SO4}$, but not in nitric acid or water as this forms the oxide.

I think it would be helpful to have a definition of 'non-oxidizing acid'. Is it an established term in chemistry? Am I right to understand that it is an acid that can only act through its $\ce{H+}$ moiety, and not by the reduction of its conjugate base part (as in the reaction between $\ce{HNO3}$ and $\ce{Cu}$)?

There's a little obscure page titled oxidizing acid on Wikipedia.

The trouble is, until I came across this term, I imagined all acids to be oxidizing by definition. It's not very intuitive.

P.S.

Related: Weird Wikipedia Section on Oxidizing Acids


texts: How to calculate n factor for salts in this reaction?

texts:
My source says : For  salts which react such that no atom undergoes change in oxidation state ,
n-factor for such salt is the total moles of cationic /anionic species replaced in 1 mole of the salt .

For Example $$\ce{Na3PO4 + BaCl2  -> NaCl + Ba3(PO4)3}$$

N factor of $$\ce { Na3PO4} $$ is 3.

Please can anybody give more examples and explain that to me ?


texts:
I know that because Schrödinger equations solution for probability of that region is 0, but I was looking for an intuitive explanation.

How can you intuitively explain the existence of nodes in an orbital?


texts: How can you predict a double displacement reaction with no precipitate?

texts: Is it possible to predict a double displacement reaction between two ions where the products remain in aqueous solution? I see how you can predict precipitation reactions if you know whether the product(s) is/are soluble, but that doesn't apply to all possible double displacement reactions.


texts: Invisible spin allowed transitions in Tanabe-Sugano diagrams

texts:
In class we are looking at Tanabe-Sugano diagrams, more concretely at transitions for a d2 complex.
I understand that the only spin allowed transitions are those that have a triplet state, therefore that there are 3 spin allowed transitions
3T1g (P) <- 3T1g (F)
3A2g (F) <- 3T1g (F)
3T2g (F) <- 3T1g (F)
These can be seen in the diagram. In addition, were are given the orbital occupancies for each energetic state some of which I have attached for clarity.

From the  occupancy image, it can be seen that the 3A2g state corresponds to both d electrons being in the high energy eg orbitals. Hence my question is what process can lead to both electrons being in such an excited state? Is it possible for a photon to excite both electrons at the time? Which I had never heard of before, or is it that in order to achieve the 3A2g excited state, 2 photons need to be absorbed in rapid succession, going through an intermediate excited state?
If two photons need to be absorbed does that effectively make the 3A2g state "impossible" to reach and thus the absorption band isn't seen?
Thanks for your help.


texts: Can racemic compounds be found at the local drug store non-prescription? Where might one be found most readily/cheaply? Only one chiral center is needed. More may actually be unhelpful. The purpose here is to practice separating enantiomers.


texts:
I keep a bottle of hand sanitizer on my desk at work, as I touch a lot of things throughout the day. When I used it yesterday, a bit must've been left in the pump track or opening. So I was about to use it and I see that in the opening it looks opaque, kind of like lotion. I press the pump and it releases the opaque portion followed by the normal, gooey sanitizer.

What caused this chemical change? The air conditioning in our building is still on, but at about 6 p.m., the HVAC is turned off. Our lowest temps at night are between the 40s and the 50s.

Please clarify what is going on, particularly if something is wrong with this sanitizer and I need to throw it away.


texts: Calculating the Ionic strength of sodium acetylsalicylate

texts:
With the addition of aqueous NaOH to an aspirin solutions in water the reaction will yield products of sodium acetylsalicylate and water. I would like to measure the amount of sodium apsirin formed that is disolved in water right after the NaOH reaction.

Attempt for the solution:
Given that sodium acetylsalicylate dissociates in water to form sodium ions and salicylate ions, I can consider finding the ionic strength i.e. ion concentration. However in order to calculate the ionic strength I need the molality which require the amount of solutes disolved, which is basically what I am trying to find in the first place.

Is there a recorded value for the Ionic strength of of sodium acetylsalicylate, which would intern allow me to calculate the mass of the solute or I'm going the wrong way about this?

Is there any other way I can use to algebraic calculate the mass of the sodium acetylsalicylate dissolved?

Any help will be greatly appreciated!


texts: Phophorine seems aromatic as it has 6 conjugated electrons. But the answer given is that it is not. This seems odd since pyridine has a similar structure and is also aromatic. Thus I ask is phospohrine aromatic or not?


texts: Solubility of ortho- and para-nitrophenol in benzene

texts: Which one between o-nitrophenol and p-nitrophenol is more soluble in benzene? And what is the reason? If the solvent had been polar, hydrogen bonding would have provided a lot of explanation, but what about non polar solvents?


texts:
According to wikipedia, a chalcogenide is a chemical compound consisting of at least one chalcogen anion and at least one more electropositive element. In the same sense does transition metal chalcogenides mean atleast one chalcogen and one transition metal. If I have three classes of materials
$\ce{CrSbX_3}$
$\ce{BaVX_3}$ and
$\ce{Ba_2MnX_3}$ where $\ce{(X}$ = $\ce{S, Se)}$
Can I address them under a common term transition metal chalcogenides?
If not what might be a good term to address them together?
Update:
The common factor between these compounds is that they are all quasi-one dimensional. The $\ce{CrSbX3}$ structure consist of infinite chains of edge sharing $\ce{CrX_6}$. $\ce{BaVX_3}$ is made up of infinite chains of face sharing $\ce{VX_6}$ octahedara. $\ce{Ba_2MnX_3}$ consists of infinte chains of corner sharing $\ce{MnX_4}$ tetrahedra. Also this review has considered $\ce{BaVX_3}$ and $\ce{Ba_2MnX_3}$ among transition metal chalcogenides.


texts: Gibbs of vaporization of a substance at a non-standard temperature

texts:
I'm trying to solve for the gibbs energy of vaporization of ethanol at a temperature lower than its boiling point. I am given the heat capacities of liquid and gaseous ethanol, the standard enthalpy of vaporization, and the standard boiling point of ethanol.

I start with the form:

$\ce{dH=(C_{p,g}-C_{p,l})dt}$

Following integration, I get the form:

$\ce{\Delta H=\Delta H_{vap} +\Delta T(C_{p,g}-C_{p,l})}$

This form gives me the new enthalpy of vaporization at a non-standard temperature. However, When I try to enter this into the form:

$\ce{\Delta G=\Delta H - T\Delta S}$, with $\ce{\Delta S=\frac{\Delta H}{T}}$

This solution always results in an answer of zero (equilibrium). Intuitively, I understand that phase changes are typically reversible, however using another representation:

$\ce{\Delta G=-RTln(K)}$, with $\ce{K=\frac{P}{P_{0}}}$, the ratio of vapor pressure to standard pressure of the liquid (liquid activity = 1).

My question is, why do these formulas apparently conflate?


texts: Why does F have a higher ionization energy than O?

texts: The book I'm working from says F has a higher ionization energy than O because the nucleus has more protons so there is a higher attraction on the electrons. Isn't that balanced out by the higher number of electrons or is it because the atomic size is smaller?


texts: Will a strong acid still dissociate "completely" even in the presence of a stronger acid?

texts: For example, nitric acid or sulfuric acid in an equal-molar solution of perchloric acid. Won't perchloric protonate a significant concentration of nitrate ions?


texts:
I have learnt that you can test if a reaction is thermodynamically feasible by testing if the cell voltage $E_\mathrm{cell}$ is greater than $0$. Surely, if a reaction is feasible, then the $E_\mathrm{cell}$ of the reverse reaction is negative, and so not thermodynamically feasible; in which case, how can a cell be recharged? Taking the following example:

$$
\begin{align}
\ce{Li+ + CoO2 + e- &<=> LiCoO2} &\quad &\pu{+0.60 V}\tag{1a}\\
\ce{Li+ + e- &<=> Li} &\quad &\pu{-3.00 V}\tag{1b}\\
\end{align}
$$

$$
\begin{align}
\text{In use:} &\quad &\ce{CoO2 + Li &<=> LiCoO2} &&\tag{2a}\\
\text{Charging:} &\quad &\ce{LiCoO2 &<=> CoO2 + Li} &\quad \mathrm{EMF}&= \pu{+3.60 V}\tag{2b}\\
\end{align}
$$

Is it the case that putting an EMF against the EMF makes the reaction feasible? In this case, could any reaction be made thermodynamically feasible by putting a potential difference across it?


texts:
One of le chateliers principle is effect of concentration change :

  When the concentration of any of the reactants or products in a reaction at equilibrium is changed , the composition of equilibrium mixture changes so as to minimize the effect of concentration of changes.

So to get more products we need to decrease concentration of products. For decreasing concentration of products can we do it by adding something(example water) because it will also decrease"concentration". But I have not seen like this in my book. So can we?


texts: Cannizaro Reaction, Hydride Shift Reason?

texts:
In Cannizaro reaction when concentration of OH- is less in the rds step hydride shift occurs, though it is very difficult for hydride ion to shift yet the reaction proceeds but what is the driving force here??

My teacher told me that this mechanism was proposed because the hydride shift occurs but there must be some reason as to why the hydride shift?


texts:
The reaction is as follows, with (i) being my answer, and (ii) being the correct answer in the book.

My question is why is the product (ii) formed here and elimination not favoured here? I think that the first structure is more stable(has extended conjugation) whereas the latter is relatively unstable. I do understand that the carbocation formed during the formation of (ii) is highly stable (cyclopropyl carbocation and has extended conjugation with phenyl), but is this the reason why (ii) is the major product?


texts: Why exactly are standard potentials additive?

texts:
I don't really study chemistry so while my question may be very obvious, its not obvious to me. If we take an electrochemical reaction like

$$\ce{2Fe^2+ + Au^3+ -> 2Fe^3+ + Au+}$$

we can find its standard potential and standard Gibb's energy by summing half reactions whose are known, and can be consulted in tables.

It's intuitive for me that the standard Gibb's energy will be given by a sum of the corresponding reactions, and that I can multiply a reaction by minus one, or whatever, and use that to construct my complete reaction.

The reason I see Gibbs energy as intuitive is because you're essentially just taking

$$\sum_{\mathrm{products}} \mu_{\mathrm{products}} - \sum_{\mathrm{reactants}} \mu_{\mathrm{reactants}}$$

and this will prove the additive property of "summing up reactions".

But I don't see any reason for additivity being true when considering standard potentials. I don't even see why inverting the reaction should invert my potential if my half cell is in equilibrium and is a kind of "whole" that is compared to the standard hydrogen electrode and should therefore have the same potential no matter how I write it.

How am I screwing up here? Why can we add up potentials?


texts: Estimating magnitude of percentage and absolute error

texts: Can someone at least give me a hint to push me in the right direction of how to estimate the magnitude of the absolute and percentage errors when using a smaller amount in mL of a substance for a lab measurement?


texts:
We made a solution of Tetrakis Copper(I) hexafluorophosphate and the usual color is yellowish. As it oxidizes to Cu(II), it should turn blue.

However, our current mixture has an off color that is pink. Looking up alternative copper colors, there will be copper rose. What would cause that color?


texts:
I am a martial artist who uses fire weapons in my shows. I am wondering how I can get the flames to be different colors.

I've done some research about it, and have found that the salts of some metals can be used for the intended purpose (for instance, copper sulphate burns green).

However, I use kerosene as my fuel and am wondering if it is advisable to mix the chemicals with it (kerosene) without burning myself. Also, I would like to know how to obtain the chemicals and what amounts should be added to a given volume of fuel.


texts: How to construct NMR spectra from chemical shift tensors?

texts: If I know the chemical shift tensor (from ab initio methods), $\sigma$, for each atom in my structure, is it possible to construct an NMR spectra for my system? If yes, how and what mathematical implementations do I need?


texts: How to obtain the radial probability distribution function of a given orbital from a quantum chemical calculation?

texts: I know that a very similar question has already been asked here and a very competent and useful answer has been provided (see here). However, that previous question was related to the total electron density whereas I am interested in plotting the radial probability distribution function of a given single orbital. Can I also use MultiWFN tool and Gaussian output to do this?


texts: Why can we know a materials properties by knowing its ground state at 0K - DFT

texts:
I have had this doubt ever since I was introduced to DFT. For what I gathered whatever results you obtained with DFT (by using VASP, quantum expresso or any other software) you can say those properties are it, even for temperatures beyond 0K.

I don't understand why. For instance if DFT says it's ferromagnetic at 0K then why would you assume its ferromagnetic properties would stay sufficiently close to the ground state for T>0 as to state that.

I haven't read a theorem that says that excited states are close to the ground state. Does such theorem exist?

Thanks!

Edit:
Quoting the book "A chemist's Guide to DFT" at the end of the section about the first Hohenberg-Kohn theorem **

  One should note at this point that the ground state density uniquely
  determines the Hamilton operator, which characterizes all states of
  the system, ground and excited. Thus, all properties of all states are
  formally determined by the ground state density (even though we would
  need  functionals other than ∫ρ(r)V dr + F [ρ], which is the
  functional constructed to deliver E0 but not properties of
  electronically excited states).

I don't follow it. Seems pretty basic cuz everyone just brushes over but I don't follow it. Why would the ground state characterize excited states?

** The first theorem basically says that the hamiltonian can be defined by the electronic density and can be made a unique functional of it.


texts:
Which of the following compound has highest enol content?

The answer is an option (c) and I think the reason behind it is that there are two phenyl groups attached to it, hence there will be a good conjugation. Also, since phenyl is an electron-withdrawing group, it will provide stability to the structure (as the $\ce{C-C}$ double bond formed after tautomerism will have π-electrons). But I am not quite sure about my logic and I don't know the reasons to eliminate other options.


texts: Molecular Orbital Mixing to get the Molecular Orbitals of a large molecule

texts:
I am trying to get the molecular orbital for arbitrarily placed nuclear centres (identical). In other words , I am trying to solve the following one electron hamiltonian.
$$h=-\dfrac{1}{2}\nabla^{2}-\sum_{i=1}^{N}\dfrac{1}{|\vec{r}-\vec{R_{i}}|}$$

I assumed the charge on each nuclear centre is one and to solve the problem I took the following linear combination as the trial function.

$$\psi(\vec{r})=\sum_{i=1}^{N}\alpha_{i}1s(\vec{r}-\vec{R_{i}})+\sum_{j=1}^{N}\beta_{j}2p_{x}(\vec{r}-\vec{R_{j}})+\sum_{k=1}^{N}\gamma_{k}2p_{y}(\vec{r}-\vec{R_{k}})+\sum_{m=1}^{N}\delta_{m}2p_{z}(\vec{r}-\vec{R_{m}})$$

of course, I start with s orbitals and then I proceeded with the above linear combination. My question is that if there are some symmetries in the structure. Does variational principle take care of that and gives the right $$ \alpha, \beta,\gamma,\delta$$, the coefficients of the trial wave functions? Do I need to impose the symmetry of the molecule (if there is any) on the trial wavefunctions? Does it give totally wrong answer if I take the above trial wave functions without worrying about the symmetry of the molecule?Can someone throw some light on it? Also, I am curious to know how do I apply MO theory for polymer like chain molecules? Please suggest some good reference to understand that


texts: Ring contraction in a carbocation due to ring strain and back bonding

texts: Today our teacher told us that the following carbocation rearrangement occurs due to back bonding. I could not really follow what he meant. Can someone please explain what is actually happening during the following carbocation rearrangement, and why it happens?


texts: The mathematical condition for a complete complexation reaction

texts:
I'm being asked to find the volume of a $\ce{NH3}$ solution ($0.1\ \mathrm{M}$) to be added to $10\ \mathrm{mL}$ of a $\ce{AgNO3}$ solution ($0.1\ \mathrm{M}$) to assure the 'complete formation of $\ce{[Ag(NH3)2]+}$'. Both constants of formation are given:

\begin{align*}
\beta_1 &= \frac{\ce{[Ag(NH3)+]}}{\ce{[Ag+][NH3]}} =10^{3.3} \\
\beta_2 &= \frac{\ce{[Ag(NH3)2+]}}{\ce{[Ag+][NH3]^2}} =10^{7.2}
\end{align*}

As far as I know, a complete complexation would mean that $[\ce{Ag+}]<10^{-5}$. I tried working it out with the common method of solving those kind of complex equilibria, but the equations I get seem pretty much impossible to solve because of the volume that I have to find, which gets incorporated in them.

\begin{align*}
\dfrac{\beta_2}{\beta_1} &= \dfrac{\ce{[Ag(NH3)2+]}}{\ce{[Ag(NH3)+][NH3]}} \\
\ce{[Ag+]_0} &= \ce{[Ag+]} + \ce{[Ag(NH3)2+]} + \ce{[Ag(NH3)+]} \\
\ce{[NH3]_0} &= \ce{[NH3]} +2\ce{[Ag(NH3)2+]} + \ce{[Ag(NH3)+]}
\end{align*}

$\ce{[Ag+]_0}$ and $\ce{[NH3]_0}$ can be expressed with respect to the volume of the $\ce{NH3}$ solution, but the equations I get are really complicated...

What approximations should I go for besides $\ce{[Ag+]} << (\ce{[Ag(NH3)2+]}+\ce{[Ag(NH3)+]})$?

Their solution is really weird, but much simpler; they invoke this mathematical condition, which makes the problem easily solvable:

$$\dfrac{\ce{[Ag(NH3)2+]}}{\ce{[Ag(NH3)+]}}>10^2$$

Starting from this, I can find $[\ce{NH3}]$ present in the solution, therefore the volume.

Where did it come from?


texts:
DC Cell + Copper Wire + Ground Water produces bubbles from wire and water turns rust red gradually? What is happening?

I can see something is settling down...


texts: Spin coat of Graphene oxide on glass slides

texts: I would like to spin coat Graphene oxide on the glass slides and intend to have a thickness of 100nm/0.1micrometre. May I know what is the amount of Graphene oxide to be poured onto the glass slides, spin time, spin speed and time for it to develop to obtain the optimized and desired thickness of 100nm?


texts: We know that ice has a lower density than water despite both having the same [molecular] mass. I know that as water turns to ice, it expands. As far as I was taught, I know that it has something to do with hydrogen bonding. I would like to know in terms of hydrogen bonding, why ice actually expands?


texts: How many stereoisomers are present in octahedral complexes of type MA3B2C?

texts: Does $\ce{MA3B2C}$ type have optical isomerism or just geometric isomerism? I was told that it has three isomers, two cis and one trans. Are the two cis isomers optically active?


texts: Why is picric acid more explosive than TNT?

texts:
I've recently read that trinitrophenol (picric acid - relative effectiveness factor $1.20$) is more explosive than trinitrotoluene (TNT - relative effectiveness factor $1.00$).

Personally, I think that the mesomeric effect of the oxygen's lone pairs in picric acid should keep the nitro groups 'happy', because of the increase in electron density on them. This should enhance the overall stability of the molecule, and reduce the relative effectiveness factor. However, this is not the case. Why is this? My guess is that the electron withdrawing nature of oxygen somehow causes this.


texts: How to calculate the standard Gibbs energy at equilibrium?

texts:
Given that $K_c = 1.7 \times 10^{-13}$, calculate $\Delta G^{\circ}$ for this equilibrium mixture at $\pu{298 K}$.
$$\ce{N2O (g) + \frac{1}{2}O2 (g) <=> 2 NO (g)}$$

I've calculated:
$$
\begin{align}
\Delta G^{\circ} &= -RT \ln K \\
  &= -\pu{8.314 J mol-1 K-1}\cdot\pu{298 K}\cdot\ln (1.7 \times 10^{-13}) \\
  &= \pu{72.8 kJ mol-1}
\end{align}
$$
The result I'm expecting is $\pu{68.9 kJ mol-1}$. Where have I gone astray?


texts: Carbon/silicon pentacovalent intermediate during substitution

texts: During SN2 reaction with a silicon compound, a pentacovalent intermediate is formed, while there is no such intermediate formed with carbon compounds (only a pentacovalent transition state). Why is it so? I need an MO explanation (no d orbitals involved).


texts:
After having parked my car in a newly constructed airport parking garage, I came back to find something had dripped through a crack in the ceiling of the structure and left considerably thick film on my car.  On a glass window surface, I tested soap and water, mineral spirits, two types of latex paint remover (i.e. goof off), and household chlorine bleach.  None were effective.  But plain white 5% vinegar dissolved the film if I let it soak or scrubbed on it with a cloth.

My question: is an acid of the strength of vinegar a risk to automotive "paint" (the top layer is probably "clear coat").


texts: Acid Catalyzed Hydration of an Alkene Synthesis Problem

texts:
Devise syntheses of the following three compounds, starting in each case with any alkene that contains four carbons or fewer. You do not have to write mechanisms, although at this point it may be very helpful for you to do so.

$\ce{(CH3)3COH}$

$\ce{(CH3)2CHOH}$

$\ce{CH3CH2CHOHCH3}$

This is the question I'm trying to tackle. I'm having a bit of trouble with the third part of it, which is the synthesis of butan-2-ol. The text solutions says that I should use but-2-ene, which I can understand but I don't quite understand why my answer is also not plausible. Can someone help me out with this?


texts:
The $K_\mathrm{a}$ or $K_\mathrm{b}$ values provide an idea of how likely a specific step is to happen.
However, how do you specify one acid just being stronger than another, as in the case of $\ce{H2CO3}$ $(\mathrm{p}K_\mathrm{a1} = 3.6,$ but $\mathrm{p}K_\mathrm{a2} = 10.32)$ and phenol $(\mathrm{p}K_\mathrm{a} = 9.95)?$ How do you compare them?


texts: Predicting a route to use chloride as a reducing agent for titanium dioxide under UV

texts:
In my lab we are deadlocked on a seemingly simple problem.  We would like to find some reaction where $\ce{Cl-}$ can be used as a reducing agent on $\ce{TiO2}$ in a UV photosynthesis.  We ideally want a reaction like the following, but without using a metal

$\ce{Cl- + reactants -> products + e-}$

Then a hole in the TiO2 combines with the electron...

$\ce{TiO2+ + e- -> TiO2}$

As a secondary restriction, we need any extra reactants added to be unable to reduce $\ce{H2PtCl6}$.

What methods can be used to approach this problem, we are fairly certain something should work as its possible to do using ethylene glycol, but this can actually directly reduce the H2PtCl6.  This seems like an issue very similar to metal half reactions, but we are unable to use any metals.


texts: Which is the least stable trihalide of nitrogen?

texts:
Which is the least stable trihalide of nitrogen and why?
I have two conflicting theories, one is that fluorine-fluorine electron repulsion will make $\ce{NF3}$ least stable and another is steric reasons of iodine which give $\ce{NI3}$ as the answer.

Which is correct?


texts: What does the first $1$ mean in $\ce{Li}_2 1 ^1\Sigma_g^+: (1s\sigma_g)^2(1s \sigma_u)^2(2s \sigma_g)^2$?

texts:
I am trying to learn the nomenclature behind molecular states and in (Demtröder, 2010) I came across this expression:
 $$\ce{Li}_2 \color{red}{1} ^1\Sigma_g^+: (1s\sigma_g)^2(1s \sigma_u)^2(2s \sigma_g)^2$$
now I can explain the origin of every term except the $1$ which I have put in red. What does this 1 mean?


texts: Why are magnesium chloride and calcium chloride more soluble than sodium chloride?

texts:
I read that $\ce{MgCl2}$ and $\ce{CaCl2}$ are more soluble than $\ce{NaCl}$ in water. Solubility of $\ce{MgCl2}$ is $\pu{543 g/L}$ and that of $\ce{NaCl}$ is $\pu{360 g/L}$ (both at $20^{\circ} \pu{C}$).

I think that $\ce{NaCl}$ should be more soluble due to its higher ionic nature. $\ce{Mg^{2+}}$ and $\ce{Ca^{2+}}$ are more polarizing and have more covalent nature and thus should be less soluble.

I want to know the reason for why the opposite is happening.


texts: Freely available software for generating 3D coordinates of molecules

texts:
As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?

I was able to settle on the following constraints: freely available, or at least free for academic users; can be run on the command line (either Windows or *nix); and, can handle small to medium-sized molecules (I.e. I am not expecting the software to handle oligopeptides or other sizable biomolecules).

The input could be any of 1. a MOL file without 3D information; or 2. line notation like SMILES or InChI. I was envisioning doing tests for at least those formats, unless I am missing anything.

If there is no such list, would you be able to recommend any software for this task?

I am already using OpenBabel and RDKit to generate coordinates, so I got the idea to look for other software to compare with it.

(Survey papers that have previously done comparisons of this sort would also be welcome and appreciated, so that I can see what hasn't already been covered by previous researchers.)


texts: I am trying to find the $K_\mathrm{b}$ for 50 g of glucose dissolved in 1 kg of ethanol, given the change in boiling point is $\pu{2.2 °C}$. The molality is therefore 0.278. But what is the ionic factor $(i)$? I was told it is the number of ions, so I tried 24, but the answer did not match up with the accepted value.


texts: Terminology: what's the difference between "monomer" and "protomer"?

texts:
Using definitions from Wikipedia, a protomer is defined as:

the structural unit of an oligomeric protein. It is the smallest unit composed of at least two different protein chains that form a larger heterooligomer by association of two or more copies of this unit.

In terms of proteins, the term monomer may refer to the amino acid components. However, an oligomeric complex with one subunit can be called a monomer (according to the page on protein quarternary structure).
Are these two terms interchangeable?


texts:
I am writing an essay on the origin of life and I was reading an article on hydrothermal vents. (Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life).

It appears that (Ni,Fe)S has played an important role in protein synthesis, but I wanted to know more about the substance its self. It is a compound, a group of chemicals? Or is it simply nickel, iron, and sulfur individually? I'm not very clued up when it comes to chemistry and I haven't come across that sort of notation before.


texts: Should the volume of a solute be factored into the volume of a solvent when preparing a substance of a certain molarity?

texts: Upon being asked to prepare a solution of a given molarity from a solution with high concentration I was confused whether or not I should factor in the volume taken from the high concentration substance into the volume of the solvent. I think that an example could illustrate what I am asking more appropriately. Lets say I have to prepare a 5 M substance in 50 ml of water. The substance is in a container that is 10 M so I must calculate the number of moles and then the amount of solute to extract from the 10 M container.  $$M = {m\over{L}} $$ $$5 M = {m\over{.05}} $$ $$moles = .25$$ given that the solution's concentration is 10 M $$10M={.25\over{L}}$$ $$L = .025$$ Now in order to achieve the 5 M in the 50 ml of water, do I pour 25 ml of water and then the 25 ml, which then adds to 50 ml? or do I pour the 50 ml of water and then the 25ml resulting in a total volume of 75 ml?


texts:
Consider the following reaction:

Our interest is the second step. Notice that after protonation of oxygen, the water molecule attacks in an S$_{\text{N}}2$ fashion.
My question is, why does this reaction follow S$_{\text{N}}2$ mechanism? A protonated oxygen is an excellent leaving group. Therefore it must result in a carbocation formation. In other words, the reaction must follow S$_{\text{N}}1$ mechanism.
What am I missing here?

Source: Chapter-9, Organic chemistry by David Klein


texts: Why doesn't the Bessemer process oxidize the iron?

texts: The Bessemer process for making steel involves blowing air or oxygen thru hot iron. Impurities and carbon oxidize away. Why does the iron itself not oxidize?


texts: How do I calculate the density of propane assuming an ideal gas?

texts:
Assuming an ideal gas, calculate the density in $\mathrm{g/cm^3}$ of propane, $\ce{C3H8}$ at $0.000~^\circ\mathrm{C}$ and $1.000~\mathrm{atm}$. (3 significant figures)

I have figured out that I need this formula:
$$\frac{n}{V} = \frac{p}{RT}$$

I have a total of $44.09562~\mathrm{g/mol}$

I am stuck at this point.


texts: Simple experiments involving enantiomer synthesis

texts:
I want to do an experiment to investigate factors affecting the synthesis of chiral molecules. The only problem is, my institution doesn't have much money, and it seems like the chemicals required for any experiment involving chiral molecules are very expensive!

My initial research found an experiment based on the Bürgi-Dunitz trajectory (see Addition to Carbonyl Double Bonds), but with the use of L-Selectride it isn't the cheapest. I then researched the Diels-Alder reaction, but the conjugated dienes are also relatively expensive, or are only available in large quantities!

I am only an amateur in the field of chemistry, and much of the interesting material is very hard to find unless one knows the specific terms to use. Now I come to you for help - are there any cheap experiments involving the synthesis of enantiomers? Other than cost, the constraints are:

Equipment: standard laboratory equipment is available, but nothing too fancy
Aim: the experiment needs to investigate something, for example factors affecting the synthesis of L and D enantiomers. Two different chiral auxilliaries or catalysts would do well here.


texts: Are there any compound lists searchable by elemental content?

texts:
As I say in the question, I am looking for lists of compounds that I can search based on elemental content. Essentially, I want to find candidate compounds for boron doping liquid scintillator, we have a few likely candidates already but we want to see the available chemical space and see if there are better/cheaper candidates. I want to avoid high electron densities, so essentially I want to find compounds that only have boron, carbon, and hydrogen. I will filter later for hazard/reactivity/flammability.

Does such a list / service exist? If not, is there a general list of compounds with their formulas that I could then parse with a python script or something?


texts:
Consider [(1S,2S,4S)-bicyclo[2.2.1]hept-5-en-2-yl]acetic acid:

(Source: http://www.chemspider.com/Chemical-Structure.22823922.html)

According to the chemspider nomenclature, this has three S stereocenters.  However, when I perform the CIP both manually and computationally, the center labeled ? comes up as R.  I am trying to figure out if I am misunderstanding CIP (particularly the expansion part for handling double-bonds) or if the literature is wrong in this case. I would greatly appreciate if some chemist here could work out this example to give me another data point.


texts: Testing thermite for chemical properties

texts:
I'm writing a movie in which a bunch of military explosive ordnance experts destroy a turbine with thermite and the local fire chief has to work out whether it is plain $\ce{Fe2O3}$ and aluminium powder thermite or military-grade thermite with other stuff in it.

How would he test for these ingredients and better be able to discern between the two?
And what sort of language would he use to translate his finding?


texts:
I have seen several of my (rich) friends and teachers having glasses that are colorless indoors, but take up a darker shade when exposed to sunlight.

Upon searching for the chemistry of this, I did find out that silver was being reduced in the sunlight, and reverted back to silver ions indoors.

If silver was getting reduced, what's getting oxidized? And how is it that indoor lights (fluoroscent tubes etc.) do not affect the lens?


texts: Is cis-1,2-dimethylcyclohexane a meso compound?

texts:
I was watching a video lecture today on hydrocarbons and came across this. The instructor says that, as there is a plane of symmetry, cis-1,2-dimethylcyclohexane is a meso-compound:

However, the cyclohexane ring is never planar as it adopts a chair conformation. I cannot find any plane of symmetry in chair form. Like this:

Is the compound meso or not?


texts: What other molecules can methane plasma transform into?

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Imagine a sealed chamber with electrodes or an RF coil to turn gases inside into a plasma. Into the chamber we will put methane. There would be only methane inside, no other gas would be present.

Then the methane will be turned into plasma by the electric current. Will it turn into other stable molecules? If yes, how many? For example will it only turn into ethane and ethane will not turn into anything, so the total number of hydrocarbon molecule types will be 2,or will it dissociate the methane into individual hydrogen and carbon atoms and from this create every possible hydrocarbon in existence given long enough time?


texts:
Please help me figuring out what is going on with my RP-HPLC protocol.

I am purifying a small peptide out of E.coli Culture, heat stable enterotoxin, its amino acid sequence is:

N-T-F-Y-C-C-E-L-C-C-N-P-A-C-A-G-C-Y.

I am collecting culture supernatant and using amberlite XAD2 to concentrate and desalting the peptide in 80% and 99% methanol fractions. These fractions were subjected to flash evaporation. Then I am using on MCI gel CHP20P (glass column) for further concentration and removing unwanted proteins (polar and less hydrophobic ones) using stepwise elution with 20%, 40%, 60%, 80% and 100% methanol fractions. Each fraction is subjected to flash evaporation. A sample (1 ml) from each fraction (60, 80 and 100%) was then loaded to RP-HPLC using xbridge C8 preparative column (19x25 mm,10 micron, 130 angstrom) on a gradient system (solvent A: water/ solvent B: 80%methanol) initial-5 minutes 100 A, 5-10 minute 30% B, 10-65 minute 100% B, 65-80 minute 100% B at flow rate 2 ml/minute. The chromatogram showed a single large peak (3 AUF) at 25 minutes, B solvent around 45-50%.

I am wondering that the retention time is lower than that was reported before, 35 minute at 55-60% B (I followed almost the same protocol 5 years ago except using MCIgel methacrylate resin and Vaydc C8 column instead of mci gel CHP20P and xbridge C8 column). It is also very frustrating that I loaded 0.5 ml of the collected peak on Waters analytic C8 coulumn, 5 micron particle size and it  elutes very early at 5-6 minutes (almost in the mobile phase A: water). My frustration comes from that I am using highly hydrophobic resin particle (MCI gel CHP20P) to capture hydrophobic molecules and loaded these fractions (60%, 80% and 100% methanol MCI gel) on C8 column and eluted so early.

I am sorry for this long message but I rely on your understanding. Any answer would be highly appreciated. Thank you in advance


texts: Stability of cuprous iodide in aqueous solution

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An aqueous solution of $\ce{Cu+}$ is usually unstable, but $\ce{CuI}$ is stable. Explain. $E^\circ(\ce{Cu^2+/Cu+}) = \pu{0.153 V}$ and $E^\circ(\ce{Cu+/Cu}) = \pu{0.521 V}.$

I found this question while solving a paper and I am confused as to how I should answer. For the first part at least the disproportionation of $\ce{Cu+}$ into $\ce{Cu^2+}$ and $\ce{Cu}$ explains why it is unstable in aqueous solution. (since it is neither oxidised nor reduced by water)
$$\ce{2Cu+ <=> Cu^2+ + Cu}$$
However, for the stability of $\ce{CuI}$ which remains as a precipitate in aqueous solution, I do not understand what reasoning I should provide for its stability in reference to redox reactions and electrode/formal potentials.


texts: What role does the node play in determining broadly the relative stability of various types of atomic orbitals with the same principal quantum number?


texts: Why do different alcohols have different effects on the brain?

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I've been trying to understand why different alcohols have different effects on the brain.

Methanol is obviously poisonous, apparently because it's converted to formic acid. Because the body seems to cut organic substances in two's, any odd-numbered alcohol would seem to yield methanol, and therefore be poisonous. But why is 1-butanol (according to certain sites) more toxic than ethanol? Does it have a different effect on the receptors in the brain? And if so, why? Same with other simple even-numbered alcohols: why are their effects different from ethanol?


texts: How to explain the selectivity between methanol and methanethiol in an SN1 reaction with an halogenated hydrocarbon?

texts:
Consider the SN1 reaction shown below:

Would different products be formed if $\ce{CH3SH}$ was an additional reagent?

Superimpose both energy diagrams on top of each other.

For the first question, yes, two products would be formed. I'm confused about the second question though.  I know The rate determining step would remain unchanged, as the rate depends on the concentration of the substrate not the nucleophile (SN1 is unimolecular). However, methanethiol is a better nucleophile than methanol. Would the activation energy for the second transition state be less for methanethiol?