texts: I have a 1922 silver half dollar with scotch tape on it.  The tape has been on it 50 years plus.  It’s dried out and totally adhered to the coin.  I’ve soaked it in lemon essential oil and googone but still a lot of tape left, adhered to coin.  Impossible to get off. What will melt tape but not damage silver coin?


texts: What are Mulliken atomic charges, and how are they computed?

texts:
I was reading about the self-consistent extended Hückel method (SC-EHT), and stumbled upon various formulae for the diagonal elements of the Hamiltonian matrix. I noticed that many formulae depend on either the gross atomic population or Mulliken atomic charges. I know the formula for the Mulliken population analysis, but what is the Mulliken atomic charge and how can I evaluate it?

Thanks!


texts: Why does free chlorine in the stratosphere lose its ozone-depleting potential after about 100,000 reactions?

texts:
Free chlorine ($\ce{Cl}$) in the stratosphere can deplete ozone ($\ce{O3}$)  as follows:
$$\ce{Cl + O3 -> ClO + O2}$$

The chlorine atoms can then react with oxygen and return to the beginning of the cycle:
$$\ce{ClO + O -> Cl + O2}$$

The EPA estimates the ozone-depleting potential of a single chlorine atom:

  It is estimated that one chlorine atom can destroy over 100,000 ozone molecules before it is removed from the stratosphere.

From the equations above, it seems that each chlorine atom returns to its original form. Why, after about 100,000 cycles, does it lose its ozone-depleting potential?

As a side question, how is this estimated?


texts: I am a bit confused about the lewis structure of $\ce{NO}$ The answer from my worksheet is $\ce{N=O}$ with nitrogen having a free radical. But I drew the structure as N triple bonded to $\ce{O (:N#O:)}$ and oxygen has the free radical. I am confused as to why my answer is not the case


texts:
What is the bond energy of H-O? Wikipedia disagrees with itself:

On English Wikipedia:
467 kJ/mol

On French Wikipedia:
366 kJ/mol

What is the right value?


texts: The Combining of Carbon Dioxide and Hydrogen

texts: How does this work exactly? Does it need some sort of kick in order to come together, or does it come together when put in a pressurized chamber?


texts: Why is quinone mono oxime more stable than 4-nitrosophenol?

texts:
When we do nitrosation of phenols, we get para-nitrosophenol as the major product, which tautomerises to quinone mono oxime. This article states that it largely exists in the quinonoid form.
My question is, why? I know that nitroso form is less stable than the oxime form, and enol is less stable than keto, but on the other hand we are losing the aromaticity also. Why is being non aromatic getting more favourable than being aromatic in this case?
I read the post shared by @Safdar in the comments, but this answer there says that both forms are aromatic. Is this true?


texts: What compounds exist in the bitter peel of specific fruits?

texts:
Actually, my original question was: What makes a pith of pomegranate so bitter?
Then I decided to be more generic. You'll hardly find someone that consumes pomegranate and doesn't nag about the bitter taste the white pith has! Additionally, when I was a kid, my parents taught me not to eat the bitter peel of an orange, which I later learned that is basic. So, since the evolution of these kind of fruit trees has unanimously been altogether, the chemical species that cause the bitterness of their fruits' piths can be of the same group.
I have a hunch what I seek is the "family" of phenols, but that is nothing more than a hunch. Answer in detail please.


texts: Gases produced by bacterial decomposition of human urine

texts:
I know that when urine (more specifically, the urea within) is metabolised by bacteria, ammonia is released. However, because of the high solubility of ammonia, I assume it simply dissolves into the water.

A container of urine will develop gases inside. What are they?


texts: Why is europium used in Euro bank notes?

texts:
Europium is apparently used as an anti-counterfeiting measure in Euro bank notes because of its fluorescence under UV light.

Is there any reason why it is specifically $\ce{Eu}$ and not any of the other lanthanides that fluoresce as well?

Is it because $\ce{Eu}$ is relatively rare and expensive so it's harder to fake? Is it because it has a very characteristic fluorescence? Is it because they just thought it's funny to use $\ce{Eu}$ in Euros?


texts: Hydrochloric acid substitute in an Iron-gall ink solution

texts:
Recently I started experimenting with making my own ink to be used in fountain pens.

I was wondering if hydrochloric acid in an iron-gall ink is used to prevent sediment ONLY by lowering the pH of the solution or if it also does something else that I don't know.
The recipes found on Wikipedia call for varying amount of hydrochloric acid to be added [3-5cm^3 in 1000ml solution]; however I am quite sceptical of adding it to my ink because of its corrosive nature. I even spoke with one manufacturer of modern iron-gall inks and they said they do not use said acid in theirs; they also said it shouldn't really be a problem since its in such a small concentration.
However I am still reluctant to use it honestly.

I've made couple of test batches with citric acid as a replacement, i added 2 and 5 grammes of it but after about half a day I noticed some sediment forming on the bottom of the container (which I assume is the iron). The ink works alright although I would like the ink to be more stable and predictable.

Here is the recipe I was following, however I cut the water to 500mls:

11.7 g tannic acid
3.8 g gallic acid C6H2(OH)3COOH
15 g iron(II) sulfate
3 cm3 hydrochloric acid (used to prevent sediment forming)
1 g carbolic acid (phenol) C6H5OH (biocide)
3.5 g china-blue aniline dye (water-soluble)
1000 cm3 distilled water

As you can probably see I am no chemist at all, I do not got much clue about it, but it would be lovely if you could tell me if and what I could replace the hydrochloric acid with in order to keep the solution under pH 3. I hope this makes sense.


texts:
Consider 5-cyano-2,2-dimethylpentyl 4-methylbenzene-1-sulfonate:

What would it yield by a Lemieux-Johonson oxydation ($\ce{OsO4}$, $\ce{NaIO4}$)?

My first guess would have been that $\ce{OsO4}$ was likely to attack any of the bonds in the cycle (since they are delocalized); but would it stop here, or attack the remaining bonds? Or would something even different happen?


texts: I have a flask of silica gel connected to a flask that contains a bit of water, so when I heat the silica gel the water absorbed gets evaporated and I want it to move to the other flask, but it always condenses on the roof of the first flask, so is there any way to force the vapour to move flasks?


texts: Are the p orbitals of the biradical dioxo compound in the HOMO perpendicular to the plane?

texts:
I tried to draw the frontier molecular orbitals of the following biradical structure:

(A) At the top I've drawn the HOMO and LUMO, because I know that the reaction coordinate belongs to the $\ce{C_{$2v$}}$ point group. These two orbitals of the HOMO (green) lies in the O-C-O plane. In each $p$ orbital I would locate one electron (triplett state is favoured because of Hunds rule). Oxygen has six  valence electrons, so I must bring four electrons in orbitals of each oxygen. I can place two electrons in a $p$ orbital perpendicular to the greenish depicted orbital. Then I would place the other two electrons in a $sp$ hybrid orbital.

(B) In the second possibility (at the right at the bottom) I also used a $sp$ hybridization for the oxygen atom. The two radicals are placed in the $p$ orbital perpendicular to the O-C-O plane. I guess the structure is less favoured than the first possibility (with the two radical in the O-C-O plane) because there are unfavoured filled-filled interactions between pink-pink and green-green while above there is onyl a pink-pink destabilizing interaction.

(C) As a third possibility I've used a $sp^2$ hybridization of the oxygen. The radicals are now perpendicular to the plane. Without exact calculation of the hybrid orbitals I would predict that 4 electrons in $sp^2$ hybrid orbitals plus one electron in a $p$ orbital is lower in energy as case (A) (3 electrons in $p$ orbital and two electrons in a $sp$ hybrid orbital). However the green lobes (both two electrons and hence repulsive interaction) here in the case (C) in the $sp^2$ hybrid orbitals seems to come closer (120°) than the two electrons in the orthogonal $p$ orbitals (also filled-filled) in case (A).

Are these reasons why the HOMO is best described by case (A)>(C)>(B)?

Probably this question has similiarties to the hybridization in a previous question (please note I'm a novice concerning hybridization)
Why allene cannot be described with an allyl system?


texts: Removal of tetrabutylammonium from an organic reaction

texts:
I need to synthesize some organic compound for my Ph.D. research. Everything went OK during the synthetic route but got messed up at the very end. In my final step (once the final compound has been obtained) I remove a silyl protecting (TBS) group using TBAF. The problem comes when I try to purify the reaction. No matter how carefully I run my flash column (FCC, flash column chromatography), I always obtain my compound with traces of TBA.

I've tried other deprotection procedures (mainly acidic ones) but they hydrolyze my final compounds since they are sensitive to acidic conditions.
Does anyone know of an alternative purification technique (or reaction) that would remove the TBA?


texts: Atmospheric Humidity Effects on Non-water Evaporation

texts: Does evaporation of non-water liquids into the atmosphere vary with atmospheric humidity?


texts: Number of optically active isomers of [Co(NH3)2Cl2(NO)(OH)]?

texts:
My Attempt:

Since Compound is of the form M[a2b2cd]

I got three optically active isomers of the form M[(ab)(ab)(cd)] , M[(ab)(ac)(bd)] , M[(ab)(bc)(ad)]
and since NO is a bidentate ligand, total number of optically active isomers should be multiplied by 2 due to linkage isomerism.

Hence i was getting the answer as 2*3=6 but answer given was 4.

Can you please help me with this?


texts: I wanted to decompose formic acid into $\ce{CO2}$ and $\ce{H2}$ for a school experiment. I was wondering what would be a suitable catalyst to use?


texts: Selectivity of olefin cross-metathesis reaction

texts:
I'm looking at the reaction shown below which uses a ruthenium catalyst:

I am confused because the ruthenium catalyst which is used in the reaction should be Z selective due to the features on the catalyst because the adamantyl group favours the side bound pathway i.e. the Z isomer and the di-iso-propyl phenyl group blocks the path to the E alkene.


texts: Which ion of iron is produced in a reaction between iron and copper(II) sulfate?

texts:
Using these equations:
\begin{aligned}
\text{(Fe2):}&&\ce{ Fe + CuSO4 &-> FeSO4 + Cu}\\
\text{(Fe3):}&&\ce{ 2Fe + 3CuSO4 &-> Fe2(SO4)3 + 3Cu}
\end{aligned}
Beginning with $\pu{0.78 g}$ of iron, the theoretical yields of copper are $\pu{0.89 g}$ (with $\ce{Fe^{2+}}$) and $\pu{1.33 g}$ (with $\ce{Fe^{3+}}$), and the actual yield was $\pu{0.78 g}$ of copper. I know to find of the ratio of the moles of iron used to the moles of copper formed (88% for $\ce{Fe^{2+}}$, 58% for $\ce{Fe^{3+}}$), and so the clear choice would be that this reaction formed $\ce{Fe^{2+}}$ ions.
But my teacher said this would form $\ce{Fe^{3+}}$ ions, but why is that? Shouldn't it have formed $\ce{Fe^{2+}}$? The reaction formed $\pu{0.12 mol}$ of copper, compared to the $\pu{0.14 mol}$ in the theoretical yield, and the other $\pu{0.02 mol}$ could have just been lost somewhere along the reaction process.


texts: How is (SO4)^2- Charged if S and O all are Neutral Themselves?

texts:
As far as I understand $\ce{SO4^2-}$ structure,  sulfur makes two coordinate bonds with two oxygen atoms and two double bonds are formed with oxygen after sulfur expands it's valance shell to 6. At this point calculating formal charge of those two coordinate bonded oxygen gives total formal charge of −2 and the formal charge on $\ce S$ and the double bonded $\ce O$ is zero. Thus the minus 2 charge on $\ce{SO4^2-}$ can be shown but initially all the atoms were neutral. While making bonds electrons were shared only.

How did excess 2 negative charge pop up?

Please help, I am certainly making some mistakes


texts: In naming of compound, for example in strong base; KOH and $\ce{Ca(OH)2}$ have different formula, in potassium hydroxide, one hydroxyl group is attached while in calcium hydroxide two hydroxyl group are present, but both named hydroxide, please explain.


texts:
What's the difference between $G$, $\Delta G$, $\Delta G^\circ$, and $\Delta_\mathrm r G^\circ$?

I've seen the first two used interchangably, and seen $G$ specifically referred to as change in Gibbs Free energy. Is this common? Are there cases where $G$ refers to absolute Gibbs Free Energy?

For those with the circle ($^\circ$), I've seen that referred to as "standard", and this means that they are in reference to standard pressure or concentration. Does this make their use noticably different?


texts: Why do you need a strong base for a titration

texts: For a titration, if you want to know the concentration of an acid you use a strong base such as $\ce{NaOH}$. My question is; why you can't use a weak base for this purpose? Is it because the calculation would be tougher? Is it because you'd need more of the base?


texts:
I noticed that the enthalpy of the products of an exothermic reaction (bonds formed are stronger than bonds broken) is lower than the enthalpy of the reactants. Enthalpy equals internal energy plus $PV$. In a constant pressure environment, change in enthalpy equals to change in internal energy as $PV$ in constant. Internal energy consists of $E_k$ (kinetic energy) of particles and $E_p$ (potential energy) of bonds between particles. When stronger bonds are formed, $E_p$ is bigger. And the energy of the heat released to environment equals to the energy gained in form of potential energy, so why is the internal energy lower?
It would be helpful if someone shows me my mistake :)


texts: To model early fluid flow which types of pumps should be used?

texts: I have I microchannel test rig , I want to push a 150-300 ml/hr from water in my test , I would like to know which pump type i can use ?


texts:
In one of the exams I saw it was written that dehydration of 1-methyl-cyclobutanol yields cyclobutylmethylene (double bond outside the ring) which is the anti Zaitzev product, instead of methylcyclobutene.
Why?
Thanks!


texts: What happens to the first ionization potential when a hydrogen-like atom captures a particle?

texts:
This is a textbook problem from Resonance DLPD Physical Chemistry, Page #83:

  The mass of a proton is $1836$ times the mass of an electron. If a subatomic particle of mass $207$ times the mass of an electron is captured by the nucleus, what happens to the first ionization potential of H?

My answer is that it may either increase or decrease depending on the charge of the captured particle.

However, the correct answer according to my book is that the ionization potential increases.

How do I arrive at this solution?


texts:
I am learning Chemistry from a book Heterocyclic compounds and I have bumped onto a following image with given tasks:

What is the balanced reaction?
What is the RMM of thiazole?
What is the fuel-air mass ratio?
What is the oxygen depletion?
What is the yield of CO2?
What is the yield of H2O?
What is the yield of N2?
For ideal combustion, what is the yield of carbon-monoxide?

Now, from this I can see that aformentioned product is Thiazole( checked on wiki ) and that products of combustion are carbon dioxide, water, hydrogen sulphide (H2S) and nitrogen. Now how can I solve this matter having in mind following data that air is consisted of 21% O2 and 79% of N2.


texts: What does the reaction of hydrogen and iodine to hydrogen iodide look like?

texts:
The reaction, $\ce{H2 + I2 <=> HI}$ is often used as an example for equilibrium reactions. It is however a difficult reaction to show in a school laboratory: we are not equipped to work with flammable gas at $\pu{450 ^\circ C}$ and high pressure.

It would be great if I could show my students what this process looks like in real life. I have a description, with drawings, by Max Bodenstein, from 1896 -- slightly dated.

Does anyone have pictures or videos of the gases involved and of the equipment used to make $\ce{HI}$ from the elements and to measure reactants and products?


texts: Is it possible for Cytosine and Hypoxantine to make three hydrogen bonds?

texts:
I think the O from Hypoxanthine can bond with one of the Hs in NH2 from Cytosine and the H that is connected to N in Hypoxanthine with the N in Cytosine but is it possible also for the H connected to C in Hypoxanthine to bond with the O in Cytosine?

[Hypoxantine]

[Cytosine]

I have almost the same question between Xanthine and Adenine.(please note that I'm not talking about Xanthine and Adenine inside RNA, I know they can't bind at all in RNA because of their sizes)


texts: Stoichiometry reactions for water clarification

texts:
If ferric chloride was added to a water sample which had calcium bicarbonate alkalinity present, would the reaction be a ‘stoichiometry reaction’ or a ‘limiting reagent reaction’?

For example, if 1 g of ferric chloride was added, how much precipitate would form [$\ce{Fe(OH)3}$] and what type of reaction (mentioned above) would happen?

$$\ce{2FeCl3(aq) + 3Ca(HCO3)2(aq) ->2Fe(OH)3(s) + 3CaCl2(aq) + 6CO2(g)}$$


texts: Is it possible to raise pH in RO water without Na, Mg, K, Ca, S addition?

texts:
Maybe the question in the title is simple (=stupid) and the answer is 'simple No' but I have the urge to ask.

Some background, I have an aquarium which I use RO water and I use some portions of $\ce{KHCO3, MgSO4, CaSO4}$ to raise my GH and KH and in result, I get also an amount of $\ce{K, Mg, S, Ca}$ + (bi)carbonates in the water in a specific $\pu{ppm}$ quantity and ratio between them which I want to keep it stable.

Still, after the additions of the compounds above, I get something like 1 KH, 3 GH and pH of 6.4 but I need to raise it around 7.

Is there any other way to do it without another compound? (preferable no baking soda or soda ash)

Thanks!


texts: pH of CH3COOH + HCl solution (shouldn't be a buffer)

texts:
$\pu{0.05 L}$ of a solution containing $\pu{0.3 M}$ acetic acid $(\ce{CH3COOH}$, $K_\mathrm{a} = \pu{1.8e-5})$ are added to $\pu{75 mL}$ of a solution containing $\pu{0.02 M}$ hydrochloric acid ($\ce{HCl}$, a strong acid). Calculate the $\mathrm{pH}$.

Can I simply find the $[\ce{H+}]$ released by the reaction of $\ce{CH3COOH}$ with water and add them to the $[\ce{H+}]$ released by $\ce{HCl}$, add the two concentrations and then calculate $\mathrm{pH}$ that way? Or does some reaction happen that I'm not aware of?


texts: Find product of the oxidation of 2-methylnaphthalene with chromium trioxide

texts:
This is a question from an organic chemistry book.
I did not understand the solution given in that book.
Here's the solution given in that book,

I know that CrO3 oxidizes methyl group of toluene, but here
Why are alpha positions more reactive and alpha positions of which functional group have they mentioned?


texts:
How do we know that one mole of an ideal gas occupies (exactly) 22.4 Liters? Why is it so precise a value? Many other constants/conversions in science have multiple decimal places, so why is this conversion terminated so soon?

Yes, I have googled it, and searched it up on StackExchange, and flipped though my chemistry textbook. I just want a nice clear explanation for the exact value of the the mol/liter conversion.

Finally, please don't use the ideal gas constant $\ce{R=8.314 J/K\cdot mol}$ to justify your answer, because we get $R$ by using this conversion fact.

Thank you for any information or insights!

EDIT: This has been suggested as a duplicate of What volume does one mole of an ideal gas occupy?, which does not answer my question because it derives the liter/mol conversion from the ideal gas constant.


texts:
I operate in a wastewater treatment plant laboratory and I use respirometric method for BOD5 measurement (hach direct plus). Recently I am obtaining high value for BOD (biological oxygen demand) for example BOD5 581 mg/L when the COD (chemical oxygen demand) of the same sample 895 mg/L. I did multiple assays on another sample and I obtained different values for the same sample using the same initial volume (209 mg/L and 586 mg/L while COD 630 mg/L).
I thought that some sensors are not functioning properly. I want to know if these pressure sensors can be calibrated, anyone can help please??


texts: Does the pre-exponential factor (Arrhenius constant) depend on temperature?

texts:
I was taught that the the pre-exponential factor $A$ in the Arrhenius equation \eqref{arrhenius} does not increase with temperature.

$$k = A\cdot\mathrm \exp\left(-\frac{E_\mathrm a}{RT}\right)\tag1\label{arrhenius}$$

But, a component of the pre-exponential factor is the number of collisions, which presumably increases with temperature. Should the pre-exponential factor therefore not increase with temperature as well?


texts: How to calculate the start concentration for a first order reaction?

texts:
The half-life of the first order reaction, A → products, is 33.8 s. What was the original concentration, [A]O in mol/L, if after 2.5 minutes, the concentration of A is 0.0796 mol/L? Round your answer to three significant figures.

I think the formular is 1/(A)t = kt + 1/(A)0

So I tried 1/33.8s = (0.0796)

so it = 1/0.0796.

I know this is not correct, but I think I'm using the right formula.  I looked back at my notes and nothing is really making any sense, but this formula.


texts: Organometallic Synthesis: Cp2Ti(I)Me from TiCl4

texts:
I've been working on this synthesis question for a couple days but I'm a little stuck. The question is:

  Using only $\ce{TiCl_{4}}$, $\ce{NaCp}$, $\ce{PhLi}$, $\ce{MeI}$, and $\ce{EtMgBr}$, synthesize $\ce{Cp_{2}Ti(I)Me}$. (should take 4 to 6 steps)

But it seems to me the synthesis can be done in 2 steps like so:

$\ce{TiCl_{4} + 2NaCp -> Cp_{2}TiCl_{2}}$

$\ce{Cp_{2}TiCl_{2} + MeI -> Cp_{2}Ti(I)Me}$

Which doesn't match the question's "4-6 steps" note, so I'm not sure what I'm missing.


texts:
I am not now nor have I ever been a chemist.

I'm practicing by drawing molecules in the Chemspider structure search tool. Today I drew buckminsterfullerene, in order also to test my 3D spatial awareness. I chose to draw the double bonds on the hexagonal rings only - the resulting symmetry making this the intuitive choice, I thought.

Chemspider recognised my sketch as C60 right enough, but in its own 3D rendering has the double bonds placed differently, with some in the pentagonal rings, so of course I run to Google to see what is up with that, and learn the following from Wikipedia :

  C60 tends to avoid having double bonds in the pentagonal rings, which
  makes electron delocalization poor, and results in C60 not being
  "superaromatic".

So according to this my intuition was correct, but I guess Chemspider just has a different version stored for some reason?

So:

Q0: Any guess as to WHY Chemspider has different configuration?

Q1: Is the extract above actually true? (If you can imagine for a moment a world where Wikipedia might not be 100% accurate and authoritative)

Q2: If so, why? As I said, the more maximally symmetric arrangement seems intuitive. I guess the charge of the mutually repelling (repulsive?) electrons would be more evenly distributed this way, and so this is how it would self-organise, like a soap bubble.

Q2: In the context of the extract, does electron delocalization being 'poor' mean that there is a lot of it (this is my instinct), or not so much?

Q3: Either way, why is the degree of delocalization contingent upon where the double bonds are? My first guess would be that the positively charged nuclei in the hexagons keep the electrons in a less vice-like grip than in the more tightly convex pentagons.

Q4: Are the bonds static? Once you have a C60 molecule with its bonds a certain way, do they stay that way, or do they jump about arbitrarily?

Q5: Does it matter? Does the geometry of the bonds affect the chemistry, or indeed physics, of C60 that much?

If your answer is 'go read a book/paper on C60' then that's fine, if you could recommend a good one for a beginner. There's a lot out there.

Cheers MD.


texts: When surface area of electrodes is increased, why does the current in the galvanic cell increase?

texts:
I did a lab in galvanic cells where I changed the surface area. As a result, the current increased, but I don't really understand why. I guessed it was because more are means that more ions from the anode are oxidized and more ions from the cathode reduced, more electrons are transferred and taking into account that current is the flow of electrons per unit time, the current increases.

Is that even correct?

Thank you all


texts: Mathematical model for reaction rate in fixed volume

texts:
Is there a way to find the rate of reaction of a chemical reaction inside a closed container that is fixed in volume as a function of time?

Can the answer provide an example reaction (such as baking soda + vinegar $\rightarrow$ carbon dioxide + "the other stuff")?


texts: What does the 1H NMR spectroscopy coupling pattern look like for the hydrogen attached to the carbon that the blue arrow is pointing to? There is a $\ce{CH2}$ attached to ether side of the carbon, but each of those carbons is in a different chemical environment from the other. Does that mean that it is a doublet of doublets? Or just a doublet?


texts: What do you chemists need from a periodic table?

texts:
I am developing a website and later on an app with the periodic table. The reason I started was that I thought almost all the other periodic tables was awfully ugly.
I do not only want to make it a well-looking periodic table, but I want to make it easy and smart to use combined with the design.

My question to you:
Which features do you require and want from an online periodic table?
I am also asking for the smallest features you can come up with. The more the better!

Features I already have got:

The periodic table view with number, symbol, name, and type of element (like noble gas)
Detailed information on an element on a specific page for each element including:

Number, name, and symbol
Discovery, etymology, and meaning
Electron configuration
Electronegativity
Density
Melting and boiling point
Phase at room temperature

I hope you chemists can help me. By the way, the service will be free of charge to use when it is developed.

Right now it looks like this:

and when you click on one of the elements:


texts: Euclidean distance between atoms using RDKit

texts:
I'm trying to find the Euclidean distance between two atoms in the molecule with SMILES representation O=CC1OC12CC1OC12 using the rdkit package. Looking online, I have converged to the following code.

import numpy as np
from rdkit import Chem

mol = Chem.MolFromSmiles('O=CC1OC12CC1OC12')

conf = mol.GetConformer()
at1Coords = np.array(conf.GetAtomPosition(bond_i.GetBeginAtomIdx()))
at2Coords = np.array(conf.GetAtomPosition(bond_i.GetEndAtomIdx()))
print(np.linalg.norm(at2Coords - at1Coords))

But I get the error

conf = mol.GetConformer()
ValueError: Bad Conformer Id

I was wondering how to fix the issue. Thanks!


texts: Why doesn't Delta S total = 0 for this reversible process?

texts:
My textbook (Engel Physical Chemistry 3rd Edition) says:

For any irreversible process in an isolated system, there is a unique direction of spontaneous change: $\Delta S > 0$ for the spontaneous process, $\Delta S < 0$ for the opposite or nonspontaneous direction of change, and $\Delta S = 0$ only for a reversible process. In a quasi-static reversible process, there is no direction of spontaneous change because the system is proceeding along a path, each step of which corresponds to an equilibrium state.

It is my understanding that when a system is broken up into a system and the surroundings, $\Delta S + \Delta S_\text{surroundings} = \Delta S_\text{total} = 0$ for a reversible process.
I was doing the following question when I got stuck:

An ideal gas sample containing $\pu{2.50 mol}$ for which $C_{V,m} =3/2R$ undergoes the following reversible cyclical process from an initial state characterized by $T = \pu{450 K}$ and $P = \pu{1.00 bar}$:
a. It is expanded reversibly and adiabatically until the volume doubles.
b. It is reversibly heated at constant volume until $T$ increases to $\pu{450 K}$.
c. The pressure is increased in an isothermal reversible compression until $P = \pu{1.00 bar}$.
Calculate $q, w, \Delta U, \Delta H, \Delta S, \Delta S_\text{surroundings}$, and $\Delta S_\text{total}$ for each step in the cycle, and for the total cycle. The temperature of the surroundings is $\pu{300 K}$.

I was attempting the process denoted in question b, and my answers matched the books answers:

However, when I thought about the values, I was confused as to why $\Delta S_\text{total}$ is negative. Isn't it true that in the reversible process, $\Delta S_\text{total} = 0$?


texts: Entropy as the driving force for osmosis

texts:
How is entropy responsible for osmosis and is movement of solvent possible from its higher concentration to lower concentration?

By concentration, I will be referring to the concentration of solvent molecules below.

I understand that the entropy of the universe tends to increase. But I do not understand how this principle applies to osmosis. Basically, in osmosis the solvent moves from its higher concentration  to lower concentration. Here, it appears that the entropy of the lower concentration side is increasing and the entropy of the higher concentration of solvent side is decreasing. How can we claim that the net change is increase in entropy?

Also, is the reverse process i.e. movement of solvent molecules from  lower concentration side to their higher concentration side ever possible (= thermodynamically favorable) without the presence of external driving forces?


texts:
What is the lowest temperature tungsten starts sublimating at? I've tried to search in Google but without any luck.

For example, $\ce{WO3}$ starts sublimating roughly at $\pu{550 °C}$, according to the paper Growth of epitaxial tungsten oxide nanorods.


texts:
I have a question regarding the hybridization of $\ce{NCl3}$.
From what I've understood, hybridization occurs when electrons belonging to different orbitals mix.
For example an electron belonging to the orbital 's' moves to one of the 'p' orbitals creating a certain number of hybrid orbitals. This occurs when more individually occupied orbitals are needed in order to complete the bonds and form the molecule.

Now, considering the fact that in $\ce{NCl3}$, nitrogen already has three individually occupied 'p' orbitals, it doesn't need to hybridise these orbitals in order to create three bonds with chlorine.
So why does $\ce{NCl3}$ utilise sp3 hybridization?


texts: What is the exact definition of the radial distribution function?

texts:
I have been very confused by the radial distribution function which is often used in chemistry to predict the probability of finding an electron at a distance from the nucleus.

From Atkins' Physical Chemistry:

  Now consider the total probability of finding the electron anywhere between the two walls of a spherical shell of thickness $\mathrm dr$ at radius $r$. The... volume of the shell... is now $4\pi r^2 \mathrm dr$. ... The probability that the electron will be found within the inner and outer surfaces of the shell is the probability density at the radius $r$ multiplied by volume... i.e $|\psi|^2\times 4 \pi r^2 \mathrm dr$. $$P(r) = 4\pi r^2|\psi(r)|^2$$ The function $P(r)$ is called the radial distribution function (in this case, for an s orbital).

Immediately after this, I find:

  It is also possible to devise a more general expression which applies to orbitals that are not spherically symmetrical. ... $$P(r)=r^2R(r)^2$$

From Housecroft and Sharpe's Inorganic Chemistry:

  A useful way of depicting the probability density is to plot the radial distribution function ... $$\text{Radial distribution function} = 4\pi r^2R(r)^2$$

Again, from this page, the probability density turns out to be (for the 1s orbital) $$P(r)=4\pi r^2|R(r)|^2$$ However, the integral that the answerer calculated $\bigg(\int \limits _{\theta =0}^{\pi }\int \limits _{\varphi =0}^{2\pi }|Y(\theta ,\varphi)|^2\sin \theta \,\mathrm {d} \theta \,\mathrm {d} \varphi \bigg)$ to get $4\pi$ (for 1s orbital) is calculated to be 1 (for all orbitals) in Atkins', as "the spherical harmonics are normalized" (I don't know what that signifies).

My confusion is compounded by the fact that there is another function called the probability density which is $|\psi|^2$. This function is maximum at the nucleus and falls exponentially (for an 1s orbital). The radial distribution function, however, is maximum at a certain distance from the nucleus.

So, my questions are:

What is the physical significance of probability distribution and that of radial distribution function?

There is a similar question here but the answer does not satisfy me. If there is no physical difference between these two functions, then why do we use the second to find out where the electron is most likely present? Why not the first function?

What is the correct expression for calculating radial distribution function?

Which begs the question, what is the definition of radial distribution function?


texts: Conceptual understanding of solution / solute in a question

texts:
6.853g of sodium cyanide was dissolved in water and brought to volume in a 100ml volumetric flask. The final mass of the solution was found to be 107.166g

My understanding -

A solution is understood when I put a solute into a solvent (water) and dissolves it.

So in this case, if I wanted to find the composition of solution expressed as moles,
I must take mass multiply by the molecular weight of Sodium Cyanide, do I use the mass of the solution or the mass of solute ?

With this then I can go on to find molarity, normality as well as weight percent (mass of solute/mass of total solution) and weight/volume percent (mass of solute/volume of total solution).


texts: Tetragonal (z-in/z-out) in tetrahedral complexes?

texts: Is it possible to have tetragonal distortion in tetrahedral complexes? Because distortions in octahedral complexes take place along the C4 axis to reduce the symmetry to D4h, but there is no C4 operation in the Td point group, I was inclined to think there cannot be z-in/z-out as such?


texts:
I am trying to run nucleation simulations of glycine in water. To generate a supersaturated solution, a solution that will crystallize, I need to know the solubility. Luckily for me, this data exists. Now at 1 atm, 324 K, glycine's solubility is 0.338 g/ml water.

My question is how to determine the appropriate box size for a given simulation, if I specific the number of glycine molecules. I posted a question similar to this before,in the CCL mailing list, and was told to just assume ml water is ml of simulation box. For instance, if I want 1024 glycine molecules, whose molecular weight is 75.066 g/mol,

  (1024/6.0223*10^(23))*(75.066) = weight = 1.27*10^(-19) g
  weight/0.338 = ml simulation box = 3.78*10^(-19) ml
  box = ml simulation box^(1/3) = 72.28 angstroms

I guess my first question is if this procedure appears to be correct. Specifically, all experimental data for solubility is clearly gathered at 1 atm pressure. However, if I fix the pressure, my understanding is that there is only one equilibrium concentration that the MD will take me to. If I think of the number of DOF's here, temperature is fixed, pressure is fixed, and the mol fraction is fixed, so I don't get to choose the box and hence the solubility. If I work in the NVT ensemble, which I am leaning towards, I don't know if I will actually be supersaturated because the simulation is no longer ran at 1 atm. Is there another definition of solubility that I should be using for MD?

The above scenario is more confusing to me when I think of simulating a "bulk" crystal. If I were to simulate a glycine crystal consisting of 1024 molecules, the above method would tell me a simulation box of 72.28 angstroms and a temperature of 294 K would mean the crystal wouldn't dissolve (assuming  nanoscale stability is similar to bulk stability). However, if I am simulating a bulk crystal, why would the box size matter to the crystal? It should always see a "sea" of solvent, and I thought I should only be concerned with making sure the box is large enough to prevent the cluster from seeing its own periodic images.


texts: How does iodide replace bromide when the latter is more basic?

texts: The following reaction follows the $S_N2$ pathway: $$\ce{CH3CH2CH2-Br + I- (presence of DMSO) -> CH3CH2CH2I + Br-}$$ I found this reaction in my textbook and according to me this reaction should not even take place. $\ce{Br-}$ is a stronger base than $\ce{I-}$ and keeping in mind, stronger the base, lesser is the leaving ability, why will $\ce{I-}$ replace $\ce{Br-}$ in the first place?


texts: Thermodynamics: Solving for Entropy, Gibbs and Helmholtz

texts:
A reversible melting of $32.0\ \mathrm g$ of ice at $0\ \mathrm{^\circ C}$ and $1\ \mathrm{atm}$. Solve for $\Delta G, \Delta S_\text{universe}$, and $\Delta A$

I'm also given latent heat of fusion/vaporization, heat capacity at constant pressure, ($C_p$) and the densities of water and ice at the appropriate temperature and pressure,

Solving for $\Delta S_\text{universe}$

from equation sheet: $$\Delta S_\text{vap} = \frac {q_{p,\text{vap}}}{T_\mathrm b}$$ Which is for vaporization and I assume I can transform that into $$\Delta S_\text{melt}= \frac {q_{p,\text{fus}}}{T_\mathrm m}$$
So solving for $\Delta S_\text{system}$ I get
$$\Delta S_\text{system}=\Delta S_\text{melt}= \frac {q_{p,\text{fus}}}{T_\mathrm m}$$

But the question asked for $\Delta S_\text{universe}$ not $\Delta S_\text{system}$. I know that $$S_\text{universe}=S_\text{surroundings}+S_\text{system}$$, so $\Delta S_\text{universe}$ must be $$\Delta S_{universe}=\Delta S_\text{surroundings}+\Delta S_\text{system}$$ But I'm given no information on the surroundings. How can I solve this? Is it possible that the change in entropy in the surroundings constant such that $\Delta S_\text{universe}=\Delta S_\text{system}$?

Solving for $\Delta A$ $$A=U-TS$$
 $$\Delta A = \Delta U -T\Delta S_\text{sys}$$
$$\Delta A = (q-P\Delta V)  -T\Delta S_\text{sys}$$
$$\Delta A = (q-P[\rho_\text{water}m-\rho_\text{ice}m])-T\Delta S_\text{sys}$$

But I don't know how to solve $q$ for this problem. Additionally, I'm not sure if the ice melted completely, so perhaps the change in Volume is less that what I wrote in the equation.

Solving for $\Delta G$
$$\Delta G = \Delta H-T\Delta S_\text{sys}$$
$$\Delta G = \Delta U+P\Delta V-TS_\text{sys}$$
$$\Delta G = (q-P\Delta V)+P\Delta V-TS_\text{sys}$$
$$\Delta G = q-TS_\text{sys}$$

But same as before I don't know how to solve for $q$.


texts: Why is 3-chloro-5-(1-methylethenyl)cyclopenta-1,3-dien-1-ol named so?

texts: I'm afraid I can't find an image for this organic compound, but when applying lowest locant rule in the numbering (1-methylethenyl) gets 2 and Cl gets 4. (2,4) is less than (3,5). Why then is lowest locant rule not applied here? Also here (1-methylethenyl) is an alkene, and isn't priority order of alkenes before halogens which have no priority?


texts: Colour intensity of transition metal complexes

texts: Even though they are both $\mathrm{d^7}$ complexes, the colour of $\ce{[Co(H2O)6]^2+}$ is pale whereas that of $\ce{[CoCl4]^2-}$ is more intense. Does the octahedral or tetrahedral geometry matter in determining the molar absorption coefficient of the two species?


texts: Calculating the zero-point energy for the C2N2 molecule

texts:
I shall calculate the zero-point energy for the $\ce{C2N2}$ molecule in the $^{1}\Sigma_{g}^{+}$ electron ground state with the following vibrational wavenumbers (symmetries in parentheses) which were found in IR and Raman spectra:

$v_1 = 2330~\mathrm{cm}^{-1}$ ($\sigma_g$)
$v_2 = 854~\mathrm{cm}^{-1}$ ($\sigma_g$)
$v_3 = 2158~\mathrm{cm}^{-1}$ ($\sigma_u$)
$v_4 = 507~\mathrm{cm}^{-1}$ ($\pi_g$)
$v_5 = 233~\mathrm{cm}^{-1}$ ($\pi_u$)

I have no clue about how to do it - maybe somebody can help me.


texts: One-piece short distillation glassware - worth it?

texts:
Does anyone have any experience using one-piece short distillation setups similar to this: https://www.hornik.eu.com/en/3-985_distillation-bridges/8216-distilling-link-for-short-path-distillation-duran-cones-ns1423-socket-ns1423.html?
I've been struggling with a tricky distillation recently and was wondering whether something like the above would help. I wanted to hopefully get some opinions before shelling out.
Cheers


texts: What is the stochiometric equation of the sucrose and potassium chlorate reaction with sulfuric acid?

texts:
I am researching this reaction for my chemistry assessment. Various sources I have dug up state different answers and opinions on what the stoichiometry is and what the products are, sometimes giving no answer at all.

In one source, sulfuric acid is a catalyst that speeds up the reaction while in another source, sulfuric acid is one of the reactants, and is therefore part of the stochiometry. The final products also vary from source to source, and include pure carbon or potassium chloride in addition to carbon dioxide and water.

Can anyone clarify the subject for me?


texts: Name of the substance on which water cannot stay?

texts:
There is a show on discovery, 'You have been warned.'. In that show, once I remember seeing an unusual substance, when, on water was poured in it, even on a perfectly straight (non-slanting) table, water just didn't stay on it. It "rushed" in random directions and then when it was not in contact of the substance, it stopped. I don't remember the episode, nor the substance.

What could this substance be, or if they're a class of compounds, what are their properties?
Can anybody also  point out that episode?


texts: Which of these reactants will not generate this racemic amine?

texts:
I understand that in E there is no electrophile the amine can attack, however, I do not understand why A is an answer as well. The amine in A can perform an intramolecular attack on the aldehyde and form the product below. Why can it not?

Also, how does the oxygen leave anyway?


texts: Why Does Adding Catalyst Slow Down My Reaction?

texts: I currently did a lab where I was meant to identify factors that increase the rate of the reaction. I reacted Glucose with Potassium Permanganate and used Sulfuric Acid as a catalyst. But in my recordings I found that the more catalyst I added to my mixture, the slower the reaction took to reach its endpoint. Is there any reason why a reaction may take longer to reach endpoint when more catalyst is added?


texts: Show that decomposition of AsH3 follows first order kinetics

texts:
The decomposition of $\ce{AsH3}$ into solid $\ce{As}$ and $\ce{H2}$ is given in terms of pressure of the gas in a closed vessel from time to time.
$$\ce{2AsH3 -> 2As + 3H2} $$

Show that this reaction follows first order kinetics.

My attempt :

So to prove that the reaction follows first order kinetics, I tried finding the relation between pressure in the vessel and the time taken.

I assumed the initial concentration of $\ce{AsH3}$ (which is the pressure of the whole vessel at $t=0$) as '$2a$'. Assuming the dissociation factor to be $\alpha$, at any time $t$, the composition of the vessel can be :
$$\ce{AsH3} \rightarrow (2a - 2\alpha)$$
$$\ce{As} \rightarrow 2\alpha$$
$$\ce{H2} \rightarrow 3\alpha$$
(We are working with gases so the concentration of solid As can be assumed to be constant and have no effect on the pressure of the vessel)

Assuming all gases to be ideal.

So I was able to pull through till here. Assuming temperature to be constant, $a$ can found out:
$$2a = {\frac{P}{RT}} \Rightarrow a = {\frac{733.22} {2 \cdot 0.081 \cdot  T}} = {\frac{4465.4}{T}}$$

I am not able to move forward after this.


texts: Why does only one $\ce{Br+}$ ion get generated in a non-polar solvent (such as $\ce{CS2}$), while more $\ce{Br+}$ ions are generated in aqueous or polar solvent (such as $\ce{H2O}$)?


texts: How did Joseph-Louis Proust know what gases weighed?

texts:
Proust's work led him to conclude that compounds always contain the same ratio, by weight, of their constituent elements. How did he know (or deduce?) what gases weighed?

Precise answers appreciated - I can find nothing on the net that explains how the weight of gases was measured at that time - all accounts of Proust & Dalton's work skip over this & other accounts just refer to modern tech.

I am not a chemist - I just want to know this.


texts:
I had prepared the sample of Cav2O6 using solid-state reaction route. I had done XRD, SEM-EDS which all matched with the previous results. There was something strange when I did the PL analysis. I saw that most of the vanadates gave the yellow-orange spectra but my sample was giving dark blue. I was not able to find anything related to that in previous researches.
So, I thought that CaV2O6 must also have the properties of CaO as (CaV2O6=CaO-V2O5). I searched the PL studies of CaO and the results were matching closely. So, can I conclude that at a particular excitation wavelength, the properties of CaO component of my sample are more prominent.


texts: Constructing an equation for the precipitation of a salt

texts:
I was asked to write a balanced equation, as well as the net ionic equation, for the formation of $\ce{CaCO3}$ by precipitation. The equations should also include state symbols.

Unfortunately, I am not familiar with the concept of precipitation. Could anybody please show me a method for constructing these equations?


texts: Aetiology of the word "fullerene" in Chemistry

texts:
I am a mathematician and not a chemist, and I am trying to understand the historical relationship and current usage of the word "fullerene" across Mathematics and Chemistry.

I apologise in advance if I say chemically-ridiculous things, but I am genuinely interested in understanding this.

I will assert some things that loosely describe my understanding of the situation, but which may be chemically wrong. Constructive correction is welcomed.

MY UNDERSTANDING FROM MATHEMATICS

(1) In graph theory (my area of Mathematics) a "fullerene graph" or simply "fullerene" is usually defined to be a 3-regular planar graph, where by "graph" we mean a combinatorial graph with vertices and edges (i.e. abstractions of atoms and bonds).

(2) The standard example of a fullerene is a 60-vertex planar graph, whose faces are arranged as in a standard soccer ball, and of course this is the famous geodesic dome structure or buckyball.

[Actually, mathematicians will also use the dodecahedron as a standard example of a fullerene graph because it has just 12 pentagonal faces and no hexagonal faces. This is fine for a mathematician because 0 hexagons is a perfectly sensible number of hexagons but perhaps it is chemically nonsensical.]

(3) This structure and its name arises from the carbon molecule $C_{60}$ which was first synthesised by Kroto et al., which has this spherical shape, and which they named buckminsterfullerene after Buckminster Fuller.

(4) Mathematics writings on fullerene graphs that attempt to explain the relationship to chemical fullerenes then usually say something like:

an actual physical fullerene must have a molecular structure (atoms and bonds) that is a 3-valent planar graph with pentagonal and hexagonal faces
there are lots of mathematically possible fullerenes, but only a minuscule fraction actually physically exist.
to determine whether or not a mathematical structure might be physically realised, we compute the spectrum of the adjacency matrix and magically believe it relates to a mysterious chemistry thing called the HOMO-LUMO gap.

[In addition, some authors insist that to qualify as a fullerene graph, the pentagons must be separated from each other.]

[I guess that as carbon atoms are 4-valent, there must be a pile of double bonds floating around that us mathematicians have just totally ignored!]

MY QUESTIONS REGARDING THE CHEMISTRY

(1) When did the very specific term "buckminsterfullerene" get relaxed to "fullerene" and by whom?

(2) To exactly what class of carbon molecules does the term "fullerene" apply?

[I have learned that other forms of carbon include diamond where all atoms are 4-valent, then graphite, then fullerenes but I am hazy on the precise mathematical or chemical distinction.  Then I am further confused by the fact that some sources distinguish tube structures (nano-tubes) from spherical structures and only call the latter fullerenes]

Sorry for the ridiculously long first question, but all clarification is gratefully received!


texts: What is the chemical composition of the grignard reagent?

texts: What is the actual chemical composition of the grignard reagent and what is the method of preparation? Can it be prepared in college laboratories?


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

texts:
In the book "Quantum Chemistry" by Ira Levine I found a plot of the radial probability distribution function of argon:

The figure appears in the context of the following section:

  Electron densities calculated from Hartree–Fock wave functions are quite accurate. Figure 11.1 compares the radial distribution function of argon (found by integrating the electron density over the angles θ and φ and multiplying the result by r2) calculated by the Hartree–Fock method with the experimental radial distribution function found by electron diffraction. (Recall from Section 6.6 that the radial distribution function is proportional to the probability of finding an electron in a thin spherical shell at a distance r from the nucleus.) Note the electronic shell structure in Fig. 11.1. The high nuclear charge in 18Ar makes the average distance of the 1s electrons from the nucleus far less than in H or He. Thus there is only a moderate increase in atomic size as we go down a given group in the periodic table. Calculations show that the radius of a sphere containing 98% of the Hartree–Fock electron probability density gives an atomic radius in good agreement with the empirically determined van der Waals radius. [See C. W. Kammeyer and D. R. Whitman, J. Chem. Phys., 56, 4419 (1972).]

Source: Ira N. Levine. Quantum Chemistry 7th ed.; Pearson, 2014; page 294.

What kind of chemical software allows one to do this?

It is possible to do with Gaussian, and, of course, how is it possible?


texts: Does adding prefixes to SI units make them no longer SI units?

texts:
Our chemistry professor said that "mg for mass, g/m3 for density, ms for time are all SI units".

I want to make sure now, even if we added a prefix to the unit, will it still be an SI unit?


texts: How to interpret spectroscopic data to obtain the structural formula?

texts:
I am currently struggling with an assignment question regarding structural determination using both $\ce{^1H}$ and $\ce{^{13}C}$ NMR data.

The first thing I have done is calculate my double bond equivalences which I believe is 3. I believe the IR data corresponds to a $\ce{C=O}$ bond which is supported by the number of DBEs. As it states this is a cyclic compound I believe that the there is a ring containing a double bond and a carbon double bonded to an oxygen which accounts for the 3 DBEs.

Putting together this information which I believe to be correct with the spectroscopic data above is where I am really struggling.

I am quite confident in saying that the 6.8 triplet is due to an aromatic carbon with two hydrogens on the adjacent carbons so I have a fragment there that I believe is correct but I cannot get anything more than that.


texts: What is the smell of a glass of water in contact with fresh air?

texts:
When you pour water into a clean glass in a small confined room with no or little fresh air circulation, the only smells you perceive are those of the glass and the water (or the impurities from both of them).

However, expose that very glass to a bit of fresh air, and voilà, it starts to smell different, a bit like the (wet) shells of mollusks in the sea or from a sweetwater source (it is not a "fishy" smell in the sense that is smells like fish but rather one reminding of the sea, lakes or rivers).

I found this smell with wet glass, ceramics, porcelain, but apparently not really or not at all with plastic or metal (maybe the smell of metal somehow obstructs perception, or maybe it alters or destroys the chemical compounds).

So what is this smell actually?
What chemicals are there causing this smell?

Why does it apparently need contact with fresh air (maybe oxygen radicals or something) to emerge? And it seems to be volatile so that the smell weakens with time (or maybe you just get used to it).

I hope at least some here know what I am talking about... if not, maybe try it out.

Some people are apparently more susceptible to this smell than others (a friend of mine is very susceptible to it while others have no idea what this fuss is all about).

It also works when you get the glass hot and fresh from a dishwasher, though it is recommended to try with a non-scented detergent.

And you absolutely have to try it with non-chlorinated water.

Update:
I've come across two substances that may be related to the phenomenon, Trimethylamine and Dimethyl sulfide, however, I don't know how they smell, so I can't really say if any of these are responsible for the odors, but from the Wikipedia articles, trimethylamine sounds more fishy than "mollusky" while dimethyl sulfide is described to be cabbage-like.


texts: Why is cell potential defined as E0[Reduction]-E0[Oxidation] and not the reverse?

texts:
Why is the cell potential defined as:

$$ E^\circ_{cell} = E^\circ_{cathode} - E^\circ_{anode} $$

or
$$ E^\circ_{cell} = E^\circ_{reduction} - E^\circ_{oxidation} $$

as opposed to
$$ E^\circ_{cell} = E^\circ_{anode}  - E^\circ_{cathode} $$

or
$$ E^\circ_{cell} = E^\circ_{oxidation} - E^\circ_{reduction} $$

A few definitions which relate to the problem:

  Cell potential is the measure of the potential difference between two half cells in an electrochemical cell

  The potential difference is caused by the ability of electrons to flow from one half cell to the other

  The difference between the potential for the reducing agent to become oxidized and the oxidizing agent to become reduced will determine the cell potential.   (Chem.Libretexts)

But why is this the case?

Also, why does it then say here that
$ E^\circ_{cell} = E^\circ_{reduction} +  E^\circ_{oxidation} $ rather than $ E^\circ_{cell} = E^\circ_{reduction} -  E^\circ_{oxidation} $


texts: Extracting iron oxide from ceramics waste

texts:
In my ceramics class, we use iron oxide in our glazes, but a lot of it goes to waste. We have a bucket full of scrap glaze which contains quite a lot of iron oxide, but is also mixed in with silica, alumina, titanium dioxide, tin oxide, and other substances.

Is there any way to extract the iron oxide or other metal oxides from the scrap bucket?


texts: Why do phosphorus and sulfur have variable valences?

texts:
I have learnt that phosphorus and sulfur have valences 3, 5 and 2, 4, 6 respectively because of vacant d orbitals. But how?
Phosphorus' configuration is $\mathrm{[Ne]3s^23p^3}$. There are 3 unpaired electrons that can get paired with bonds, so 3 makes sense (similar to nitrogen) and a similar argument for 2 with sulfur (similar to oxygen), but how do the vacant d orbitals help in giving valence 5?
Do 2 electrons from the s orbitals go to the d orbitals and then there are 5 unpaired electrons available for bonding and similarly for sulfur?


texts: How to simulate phase separation in a discrete system using LAMMPS?

texts:
I would like to simulate phase separation in LAMMPS and need advice what kind of two particle systems and interactions will yield phase separation.

For example, a meta stable phase separation is achieved with a continuous phase flow model governed by Cahn–Hilliard equation, where $c$ is the concentration, $\mu$ is the chemical potential, and $\gamma$ is a constant:
$$\begin{align}
\frac{\partial c}{\partial t} &= D\nabla^2\mu&
\mu &= \left(c^3-c-\gamma\nabla^2 c\right)\\
\end{align}
$$

I tried to use a discrete two atom system in LAMMPS. The first type of the particles has an inter-LJ interaction and the second type has an inter-soft-potential interaction. Between the distinct two types there is also a soft potential:

Initial configuration (interleaved lattice of the two particles):

Steady state configuration at $T=0.1$ (reduced LJ units):

Configuration file:

units lj

timestep 0.001

dimension 2
boundary p p p
atom_style atomic
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no

variable temp equal 0.1

lattice hex 0.5
region simbox block 0 50 0 25 -0.1 0.1
create_box 2 simbox

lattice hex 0.5
create_atoms 1 region simbox

lattice hex 0.5 origin 0.5 0.5 0
create_atoms 2 region simbox

mass 1 1
mass 2 1.0

velocity all create ${temp} 1234567 dist gaussian
pair_style hybrid lj/cut 2.5 soft 0.5
pair_coeff 1 1 lj/cut 2.0 0.8 4.0

pair_coeff 1 2 soft 0.5
pair_coeff 2 2 soft 0.5

fix 1 all nvt temp ${temp} ${temp} 0.1

dump 1 all atom 500 out/dump_temp_${temp}.lammpstrj
write_data data.all
thermo 500
run 500000

How do I make my system to look more similar to the continuous model suggested by Cahn and Hiliard? I want to get a more prominent phase separation like in the continuous model. I am not sure how to calibrate my system/interactions.
Is there a different simple system I could use to simulate phase separation?
If you think Matlab could be more suitable to simulate phase separation, please elaborate.


texts: Flow rate of the fuel consisting of ethanol and water burning in air of a given flow rate

texts:
I hope that someone could give me some hints or tips on how to approach this question, even though these types of questions are usually closed off as homework.

A burner is run by a fuel mixture of $\pu{90 mol.\%}$ ethanol and $\pu{10 mol.\%}$ water. Assume a complete combustion with air ($\pu{79 mol.\%}$ $\ce{N2}$, $\pu{21 mol.\%}$ $\ce{O2}$). The whole process takes place at $\pu{100 kPa}$.
Calculate the inlet flow rate of the fuel given that the flow rate of air is $\pu{100 mol s-1}$ and that the excess of air is $20\%$.

The answer key only gives the answer $\pu{6.48 mol s-1}$ of the fuel without explaining the calculations.
My attempt at the question was:
$$\ce{C2H5OH + H2O + 3O2 -> 2CO2 + 4H2O}$$
Knowing that we have $20\%$ excess in air, we could calculate the theoretical moles needed.
$${\text{fractional excess} = (n_\mathrm{feed} - n_\mathrm{theo})/n_\mathrm{theo}}$$
$$\to n_\mathrm{theo} = \pu{83.3 mol}$$
I then used the molar ratio from the reaction to calculate how much ethanol and water was needed. I just don't see how the answer becomes $\pu{6.48 mol s-1}$. Any help is greatly appreciated!


texts: Does concentration remain constant in an electrochemical cell's half cells?

texts:
We have from Nernst equation:

$\mathrm{E_{cell} = E^\circ - \dfrac{RT}{nF} \ln Q_c}$

But I was wondering that in a simple cell like Daniel cell if concentration of $\ce{Zn^{2+}}$ keeps increasing and that of $\ce{Cu^{2+}}$ keeps decreasing, won't the value of $\mathrm{Q_c}$ keep increasing?  In that case, won't that lead to a decreasing emf? If it does, then what's the use of such a cell that yields decreasing emf?


texts: Why does heating transform the aquacomples of slightly acidified cobalt(II) chloride solution to the chlorido complex?

texts:
There is a famous demonstration where, if you mix a $\ce{CoCl2}$-solution with the right amount of $\ce{HCl}$ you will end up with the pink $\ce{[Co(H2O)6]^2+}$ complex but when heating it to boiling temperatures it will change to blue as the $\ce{[CoCl4]^2-}$ complex is formed. This reaction is reversible as the mixture is cooled again. Now literature always describes that this works because that shift towards $\ce{[CoCl4]^2-}$ is endothermic, but why is this the case?

What causes one to be more stable here than the other one but being substituted when heated?

I have some ideas but I can't really compare them:

First of all there should actually be an entropic advantage towards the chlorido-side, as 6 water ligands leave, meaning that the exothermic step here is against the natural direction of the entropy(?).
Second, perhaps the chlorido ligand is the better leaving group. I know usually $\ce{H2O}$ is a good leaving group in organic molecules but then its usually a $\ce{H2O+}$. So perhaps chloride is the better leaving group here.
Maybe there is a kinetic effect, that it is harder to displace 6 ligands than just four ligands
Or, as much more water is present it just shifts towards the water side because of the huge excess of water?
Chloride is a weaker ligand than water. But on the other hand the iron-fluorido complex is quite stable in water and towards other ligands.
So could it be due to the different ligand fields? The splitting in the tetrahedron is much smaller than in the octahedron. Although I don't know how this actually affects the stability.

So those were the ideas I had but I can't really find a common thing among them besides the excess of water which often causes an equlibrium to shift.

By the way $\ce{[Cu(H2O)6]^2+}$ and $\ce{[CuCl4]^2-}$ do the exact same thing.

Does anyone have an idea why this reaction is endothermic?


texts:
I have just managed to understand the difference between oxidation and reduction. So basically if A oxidises B, then B loses electrons, right? But what does this formulation mean: "A is oxidized on B"? What is this "on" suppose to mean? That A is losing electrons to B or vice-versa?

Sorry if this sounds like a very stupid question, but I'm really confused by presence of "on something"

EDIT:
If you search for this

  "Carbonate-based electrolytes commonly used in Li-ion batteries are
  reduced on negative electrodes"

on Google, you will find the first paper and this specific formulation.

And here you can find the paper: http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b01727?journalCode=jpclcd


texts:
The IUPAC name of $\ce{K4[Fe(CN)6]}$ is:
A. Potassium hexacyanido ferrate(II)
B. Potassium hexacyanido ferrate(4-)
C. Tetrapotassium hexacyanoferrate
D. All are correct

Actually I had been going through the IUPAC exercise of my book when I encountered just this question.
I know that the correct answer is option A but in the answer key the answer is given as option D.
Can this really happen ? Can a compound have more than one IUPAC name?
Our teacher told that whichever name can be used to deduce the structure of the coordination compound can be termed as the IUPAC name of that compound but I am not at all convinced with this fact.


texts: Which is most stable conformation of optically inactive butane-2,3-diol?

texts:
The most stable conformation of optically inactive butane-2,3-diol is:

(A)
(B)
(C)
(D)

I chose C as the correct answer but, in the answer key it is given to be B. C is the staggered form and the most stable one. It can also have hydrogen bonding between -OH and -H groups. B can also have hydrogen bonding but there would be repulsion between the two Me groups. So, which one is correct?


texts:
How to balance this redox reaction (using half reaction method):

$$\ce{Cu + HNO3 -> Cu(NO3)2 + NO + NO2 + H^2O}$$

My attempt:

$$\ce{Cu -> Cu(NO3)2 + 2e-}$$
$$\ce{3e- + HNO3 -> NO}$$
$$\ce{e- + HNO3 -> NO2}$$

So we multiple Cu half reaction by 2 to balance electrons and we get:-

$$\ce{2Cu + 2HNO3 -> 2Cu(NO3)2 + NO + NO2}$$

I would have solved further but the correct answer happens to be different.

Correct answer: $\ce{2Cu + 6HNO3 -> Cu(NO3)2 + NO + NO2 + H2O}$


texts: Why was Avogadro's number chosen to be the value that it is?

texts:
I understand that the mole is an extremely useful way of measuring and understanding atomic quantities. I did find some history of the number in its wikipedia article, but I did not find an answer to the question "Why is the number chosen to be what it is?".
I understand that it is not necessary to know the history of the number in order to apply it, but it would seem to me that the number wasn't chosen arbitrarily. Why is it, then, that Avogadro's number was chosen as $6.022\times10^{23}$?


texts: Why does 1,2-dihydroxybenzene have higher boiling point than monohydroxybenzene?

texts: I studied that any kind of  dihydroxybenzene has higher boiling point than monohydroxybenzene, and among the dihydroxybenzenes, I understood that because of inter molecular hydrogen bonding they have more boiling point. But in 1,2-dihydroxybenzene shouldn't it do intramolecular H-bonding and hence have the least attraction with other molecules?


texts:
For a chemical reaction
$$\ce{2 A + 2 B -> C + D}$$
the order of reaction is one with respect to $\ce{A}$ and one with respect to $\ce{B}$. The initial rate of the reaction is $\pu{4e-2 mol L-1 s-1}.$ When $50\%$ of the reactants are converted into products, the rate of the reaction would become
(A) $\pu{2e-2 mol L-1 s-1}$
(B) $\pu{1e-2 mol L-1 s-1}$
(C) $\pu{4e-2 mol L-1 s-1}$
(D) $\pu{2e-1 mol L-1 s-1}$

This is the first time I am attempting kinetics problems. Is the question asking the concentration when the system has reached its half-life?
Could I use the half-life formula here?
My attempt at a solution:
I used the rate law which I equated to the definition of rate.
I have serious conceptual issues which I hope to clear up. So is this this right?
$$\frac{1}{c(t)} - \frac{1}{c_0}  = kt$$
Would this formula solve the above problem?


texts: What happens if you make a gas of magnetic particles

texts:
I was reading todays SMBC which asked what happens if you make a gas of magnetic particles

So what does happen if you make a gas of magnetic particles?


texts: Which metals with high density do not react with mercury?

texts:
I would like to know the highest density material between 10-17 g/mol range that is less than mercury and does not react with mercury.

Also would I like to know the highest density metal that is in solid form naturally.

Which ones are easily available and are highly dense?


texts: What is the use of "pyro" in the naming of organic compound?

texts:
Recently I asked a question on the naming of polyhydroxy phenols. One of them was pyrogallol (1,2,3-Trihydroxybenzene) which is  synthesized from gallic acid  obtained from oak galls. (BEWARE- not a compound of gallium).

But why "pyro"? Pyro is usen in naming inorganic acids like pyrosulfuric acid ($\ce{H2S2O7}$) or pyrophosphoric acid ($\ce{H4P2O7}$). It is also observed that the carboxylic acid derivative is gallic acid not pyrogallic acid and the hydroxy derivative is pyrogallol not gallol. Why is it so?


texts: Is it safe to lyophilize/Freeze-dry a chelated compound?

texts:
I have a compound that consists of a metal ion chelated by a linear organic structure with assorted moieties in aqueous medium. I'd like to dehydrate this mixture fully to get solid product, but heating is out of question due to unwanted repercussions on aforementioned "assorted moieties". If I lyophilize the compound, will it remain chelated or is there a risk of the metal ion unbinding?

I lyophilized my sample and redissolved a portion of it and confirmed chelation by verifying the presence of the absorption peak of the Lanthanide I was chelating and using Beer's Law.

Thanks for your help.


texts:
What are the oxidizing and reducing agents in the reaction?
  $$\ce{Pb(s) + PbO2(s) + 2H^+ + 2HSO_4^- -> 2PbSO4(s) + 2H2O(l)}$$

I thought that, since the solid lead is going from $0$ to $2+$ it is being oxidized, and in the half reaction it works with the $\ce{HSO4^-}$, so the $\ce{HSO4^-}$ would be the oxidizing agent.


texts: When mixing lye and citric acid, which citrate will form?

texts:
I'm trying to combine precise amounts of citric acid and lye to get sodium citrate with minimal amount of reacted acid/base. I'm not so sure how stochiometry works, but I could sure learn that from some web article.

What's the real problem is, that I don't know which of three sodium citrates will form. Depending on the number of $\ce{Na}$ molecules, the amounts of $\ce{NaOH}$ greatly differs.

Which forms and why?


texts: Estimating the absolute entropy of water at room temperature

texts:
I thought it would be fun to get an idea of how enormously large $W$ in $S = k\ln W$ is. I'd specifically like to estimate this for a mole of water at $\pu{1 atm}$ and $\pu{298 K}$.  To do this, I need an estimate of the absolute molar entropy of water at those conditions, enabling me to calculate W using:
$$W= e^{S/k} $$

Are there tables of absolute (as opposed to standard) molar entropies of water at various temperatures?  I searched, and was unable to find one.

Alternately, is there an expression (or series of expressions) that provides an estimate for $C_p(T)$ of ice at $\pu{1 atm}$, between $\sim\pu{0 K}$ and $T_\mathrm{fus}$?  If there were, I could use this to estimate the absolute entropy of ice at $\pu{1 atm}$ and $\pu{273.15 K}$ by substituting it into the following:

$$ S_T-S_0=\int_0^T \frac{C_p(T)}{T}\mathrm{d}T$$

It would then be an easy matter to add the difference in entropy between ice at $T_\mathrm{fus}$ and water at $\pu{298 K}$.


texts: Finding mass percent through molality of potassium nitrate solution

texts:
Question

An aqueous $\ce{KNO3}$ solution has a molality of $\pu{4.16 m}$ and a density of $\pu{1.08 g/mL}$.  Calculate the percentage by mass $\ce{KNO3}$ of the solution.

My Approach
I know that molality ($b$) is defined as:
$$b = \frac{n_\mathrm{solute}}{m_\mathrm{solvent}}$$
In order to the mass of solution I multiplied $\pu{(1.08 g/mL)}\times\pu{1 mL}$, since, $m_\mathrm{solution} = m_\mathrm{solvent} + m_\mathrm{solute}$
However, I don't know where to use this information. I am also not sure what I to do with the $\pu{4.16 m}$ since I don't have moles of solute or mass of solvent. I am thinking that I have to assume some number here, but I might be wrong about this. Any help will be appreciated.


texts: How to rationalise the protonation state of amino acids

texts:
I am learning about amino acids in various $\ce{pH}$ environments and how their groups are protonated or deprotonated in these environments.
I don't need to mention a specific acid for my question, I will just use the generic form of one:
$$\ce{H2N-CH(R)-COOH}$$

The $\ce{H2N}$ group has a $\mathrm{p}K_a$ of $8$, I believe, and the acid has a $\mathrm{p}K_a$ of $3.1$.

If I drop these into a solution with $\ce{pH} = 12$, the $\ce{COOH}$ will donate it's hydrogen ion, but the $\ce{H2N}$ will not. It will only add another hydrogen ion if it is basic compared to the solution to become $\ce{H3N+}$. Why is it, that it won't donate its hydrogen ion like $\ce{COOH}$, when it is acidic compared to the solution, to become $\ce{HN-}$?


texts: first-order binding kinetics with multiple identical binding sites

texts:
I have beads in solution at concentration $B$ which have $N$ independent binding sites for a single target molecule at concentration $T$. $T$ is small compared to $B$, so most beads will probably not have anything bound at all. The on and off rates for a single target binding a single site on the bead are $k_{on}$ and $k_{off}$.

I want to determine the equilibrium distribution of the number of bound targets per bead. I expect it to be a Poisson distribution (right?) with an average binding count that depends on the parameters above.

Define $B_n$ to be the concentration of beads with $n$ bound targets. First order kinetics suggest we should have the coupled system of equations:

$\frac{dB_n}{dt}=k_{on}T(B_{n-1}-B_n)+k_{off}(B_{n+1}-B_n)$,

$\frac{dT}{dt}=\sum_{n=0}^{N-1}\left(-k_{on}TB_n+k_{off}B_{n+1}\right)$

with $B_{-1}\equiv 0\equiv B_{N+1}$

First question: is there an analytical solution for this system of equations? I am perfectly happy to simulate it, but if there is a way to avoid that, it would be nice.

Second question: the wikipedia page for Dissociation Constant has some ambiguous wording suggesting that even if the receptors are all identical, the rate constants will be dependent on $n$ as well, via

$K_d(n) =K_d \frac{n}{N-n+1}$

where $K_d=\frac{k_{off}}{k_{on}}$

How does that play here? Are my equations in need of modification, to something like:

$\frac{1}{k_{on}}\frac{dB_n}{dt}=T(B_{n-1}-B_n)+K_d \frac{n}{N-n+1}(B_{n+1}-B_n)$.

If so, could someone explain where that modification comes from?

EDIT: it seems that this is probably due to the fact that there is a higher change of dissociation if a bead has many targets bound since there is an equal probability for each target to unbind. However, it seems that the fraction presented is 1 for $n=N$, which suggests that the dissociation constant is defined in terms of a fully bound bead and not on a per-site basis. Could someone show me the derivation?


texts: Does steam from nuclear reactor does work on the system or to the system?

texts: I was doing research on nuclear reactors and was wondering when the steam from the fission pushes the steam turbine does it do work on the system or to the system?


texts: Bond strength of pi acceptors and metals with filled d(pi) orbitals

texts:
I was reading in The Organometallic Chemistry of the Transition Metals (Robert Crabtree) that lewis acids like BF3 often accept electrons from d(pi) orbitals. Is this generally true for all pi acceptor ligands? That is, do metals with filled d(pi) orbitals form thermodynamically stable bonds with pi acceptor ligands? I would imagine that d(pi) electrons would only be available for donation if said metal was in a low oxidation state. Correct me if I'm wrong.

If this post merits two different question threads, I'd be happy to separate them.


texts: Does Finkelstein's reaction proceed through an SN2 mechanism?

texts: I was dealing with a question whose answer was justified only when it was assumed that the Finkelstein reaction proceeds through an $\mathrm{S_N2}$ mechanism. So, does it really follow an $\mathrm{S_N2}$ mechanism or is there some other mechanism at play?


texts: Reactivity of chlorobenzene and benzene in electrophilic substitutions

texts:
As we know, chlorobenzene is a deactivating substituent and benzene has a stable structure. Now I'm confused.

My question is — considering electrophilic aromatic substitution is chlorobenzene or benzene more reactive?


texts:
I have a summer job as a custodian and one cleaner I use is called Goof Off, which is pretty much just acetone. Another is a disinfectant which is mostly water.

Why is it that whenever I put the acetone on my rag, it is always colder than when I use another cleaner or plain water?

The acetone also seems to stay cold longer than water does. Both cleaners are left in the open so they are both the same temperature.


texts:
How and under what circumstances can cations form a lattice structure?
Would they not repel each other?


texts: Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?

texts:
I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the activated form of vitamin B6).

A significant similarity is that both have an "offshoot chain" (Topiramate's sulfamate taking the place of PLP's phosphate) where PLP's phosphate is what binds it to enzymes in the first place, and both have a more electronegative element in the middle of what would otherwise be a six-carbon ring, apparently important in the typical PLP enzyme reaction.

I have been wondering if Topiramate supplants PLP in the enzyme glutamate decarboxylase, changing the reaction into a deamination. This would deplete glutamate, causing the pill's migraine relief, and the deamination could even cause Topiramate hyperammonemia.
If it does the same or similar to serine hydroxymethyltransferase, which is also PLP dependent, it could cause glycine deficiency, thus collagen deficiency - and this would even explain Topiramate hair loss.
When you look at it this way, it's frankly hard to imagine the mechanism of action is anything different. Have I stumbled upon it? Or has this been suggested already?


texts: why are simple organic molecules usually white?

texts: I have heard that it is because they absorb electronically in the ultraviolet range, if this is true, why is it true. What is it about the nature of organic molecules that make them absorb in the ultraviolet range.


texts: Does acid and base react directly, or do they react first with water?

texts:
If an acid $\ce{AH}$ reacts with a base $\ce{B}$ in aqueous solution, in textbook they write

  $$\ce{AH + B -> A- + BH+}\label{rxn:1}\tag{1}$$

But first I add acid to water and then base, so why we don't write the equations like this:

When I add acid to water:
$$\ce{AH + H2O -> A- + H3O+}$$
When I add base to the acidic solution:
$$
\begin{align}
\ce{B + H2O &-> BH+ + OH-}\\
\ce{B + H3O+ &-> BH+ + H2O}
\end{align}
$$

So the equation $\eqref{rxn:1}$ isn't true because the base doesn't react directly with the acid, but with $\ce{H3O+}$ formed by the acid reaction with water. Is what I have written true?


texts: How to liquefy or extract water from superabsorbent polymer

texts: I am finding a good way to liquefy or extract water from superabsorbent polymer. From what I remember it was salt that can liquefy it. Since salt when dissolve will have sodium cation and there for naturalize the polymer chain making it contract.  Is that true?. Thank very much.


texts: Disambiguate molecule's bonds, angles or dihedral angles selection

texts:
I am working on a project where one of the goals is to store data from computational quantum chemistry calculations for later retrieval.
Currently, we are trying to store the outcomes of simple bond (or angle or dihedral angle) "scan jobs". The main problem we have is in finding a way to represent the scan coordinate that would be independent of the order of the atoms in a molecule.
As an example, given a simple $\ce{C-C}$ bond scan in $\ce{CH3CH2CH2CH3}$ molecule, we may define the scan coordinate using atom labels and their order in the molecule (where the order may be taken as the order of atoms in an xyz coordinate file) so that we know which $\ce{C-C}$ bond has been scanned.
However, that would only work if the order of atoms is kept the same. What if there are other scan jobs on the same molecule and the same $\ce{C-C}$ bond, but with different order of atoms. How could we define that $\ce{C-C}$ bond in an unambiguous way?
Our goal is to store the scan jobs in a distributed way and access them via a simple query that would define the molecule and the bond (or angle or dihedral angle) we want the scan data for.
I was thinking that maybe SMARTS strings would allow us to somehow describe the scan coordinate pattern we want to retrieve (e.g. two atoms for a bond or three atoms for an angle or four atoms for a dihedral angle). However, it is not yet clear how could I do that with SMARTS.
Another problem is that sometimes to disambiguate which bond (angle/dihedral) has been scanned one needs to provide extra context information about the bond chemical environment(certain functional groups near the bond atoms etc.). Any advice on how to define such scan coordinates will be welcome.


texts: Reduction of 2-cyclohexenone to cyclohexanol

texts:
Is $\ce{NaBH4}$ a suitable reducing agent for the conversion of 2-cyclohexenone to cyclohexanol?

In Clayden (page 506, second edition), I have found the reduction of cyclopentenone to cyclopentanol using $\ce{NaBH4}$ in $\ce{Et-OH}$. (99% yield!). First NaBH4 performs 1,4 addition and then 1,2 addition to give the product.

However, I am unable to find a reference for reduction of cyclohexenone to cyclohexanol.

I found this in Smith:

I don't understand why it can't reduce the double bond through Michael addition in case of cyclohex-2-enone as well. What is the reason behind it?


texts: Ionic reaction between lithium and chlorine

texts: I got a weird question in my chemistry book. It says Li and Cl react to form LiCl an ionic compound. Cl has .... electrons in its outermost occupied shell and the answer of the book is 6 electrons . How?


texts: Addition v/s elimination with double bond and OH together

texts:
If a compound has both an hydroxyl group and a double bond and we add $\ce{HBr}$ to it,
(a) substitution reaction to the hydroxyl group can take place, or
(b) an addition reaction of a double bond can happen.

How to decide which one will occur?
What kind of conditions favour which type? Eg : How are the products affected by different conditions like solvent medium , Temperature, Structure , etc


texts: To model early earth chemical reactions which types of reactions should be included?

texts:
I'm currently working on building a simulator for the early earth to examine the spontaneous occurrence of food generated autocatalytic sets. No one in my group is a chemist, so the bottle neck for the project is implementing some sort of realistic chemistry in our model.

We are considering using the software outlined in this paper:
http://arxiv.org/abs/1304.1356

This will allow us to create a reaction network from an initial set, based on a set of general rules. The paper demonstrates well how the formose reactions are executed, which we intend to include. What other reaction groups would it be important to include? Our initial set of molecules would be comprised of the food molecules for each set of reaction rules included, we don't intend to start from H,O,N,C for example, so fundamental chemical rules should not be too crucial, as they should be generalised into the major reaction groups we will use.


texts: Relationship between normality and molarity

texts:
I found this formula for calculating the normality from the molarity:
$$\text{Normality} = n \cdot \text{Molarity}$$

with
$$n = \frac{\text{Molecular weight}}{\text{Equivalent weight}}$$

But in one book I found that if equivalent weight is equal to half of the molecular weight then
$$2N = M$$

Under the given condition, I am confused if the above statement is true.

Am I following a factually correct book for solving problems on volumetric analysis?


texts: What chemical reactions could ancient people use to propel projectiles?

texts: Are there reactions other than burning of gunpowder that ancient people could perform that would produce gas from non gaseous substances, so that it could have been used for propulsion of projectiles had they thought of it? An example would be CaO + H2O reaction, as upon mixing in a closed container this mixture would pressurize the container, and at some pressure the cord tying the projectile to the chamber would rip and projectile would be propelled


texts: Is sedimentation coefficient constant and why?

texts:
Biochemistry by Voet writes the sedimentation rate of a macromolecule in a  centrifuge this way:
$$s=\frac{v}{\omega^2r}=\frac{M(1-\bar{V}_\rho)}{Nf}$$
where $\omega$ is the angular velocity of the rotor, $r$ is the position of the macromolecule with respect to the rotational axis, $M$ is its molar mass, $\bar{V}_\rho$ its partial specific volume, $N$ the number of moles, and $f$ the frictional coefficient.

The book further discusses the uses of $s=M(1-\bar{V}_\rho)/(Nf)$ and the information it reveals. Since they haven’t discussed any changes to $s$, it seems to me that they are holding it constant, but why should that be? If $s$ is a function of $r$, and $r$ changes, then $s$ should change too. Is my reasoning wrong? Is $s$ considered to be constant and, if so, why?


texts: Monosaccharides configurations (alpha beta, D L) identification

texts:
I am really finding it difficult to identify the correct configuration(s) of a given monosaccharide, in fact my friends and I have been trying to solve this, much to our annoyance.

In one of our classes, our teacher said, in cyclic form:

  If $\ce{CH2OH}$ is below the ring its configuration is  L, and if its above the ring its D.
   If $\ce{C1}$'s $\ce{OH}$ is below the ring its alpha configuration and if its above its beta configuration .

My friends seem to agree with the above explanation, however my understanding is:

  If all groups of $\ce{OH}$ and $\ce{-CH2OH}$ is reversed from D form, its L.
  If $\ce{C1}$'s $\ce{OH}$ is on the same side of the ring as $\ce{-CH2OH}$ its beta else its
  alpha.

So I want to know if these assumptions are right:

D and L in linear form:

If the last chiral carbon's OH (one before the last carbon) is on the right its D and if its on the left its L. so if you want to make for example L glucose from D, you should reverse ALL groups.

D and L in cyclic form:

It's hard mainly but can be deduced by making linear form into cyclic and cyclic into linear and comparing them or reversing all carbon branches.

Alpha and Beta in cyclic form:

If the carboxyl carbon's $\ce{OH}$ is on the same side of last ring carbons branch ($\ce{CH2OH}$ in glucose, $\ce{COO-}$ in glucoronate) it's neta, else it's alpha. So in D form, if $\ce{OH}$ is above it's beta else it is alpha. In L form, if $\ce{OH}$ is above its alpha else its beta.

Also when i see 3D linear form of Glucose it doesn't match with 2D at all: 2D view of this site isn't like what I find in books I can't find the match between 2D and 3D view neither.

I'm still confused because of following examples:

1-Alpha-L-Glucose

2-Alpha-D-Glucose

3-Beta-D-Glucuronate

4-Beta-L-Iduronic Acid

these just don't match.

also Harper biochemistry image is this:

but lehningers is this:


texts: Comparing nucelophlicity order of acetate anion with different nucelophiles

texts:
We have hydroxide anion, methoxide anion, bisulfide anion , triphenyl phosphine,  azide anion , 1-pyrrolidine cyclohexene.
We want to tell which of the above species are better nucleophiles than acetate  anion.
We know that good nucleophile  is a weak base, (I know there might be exceptions like cyanide anion), so hydroxide anions, bisulfide anions, methoxide anions are much more basic than acetate ion, so acetate ion should be better nucelophiles than these. However, my question is that whether the rule of  good base   implies a bad nucleophile  will imply here? Also, I'm not sure which criterion do we use to decide for the other three species.
Thanks.


texts: Electron affinities of the chalcogens and halogens

texts:
Here are the electron affinities of the 16th and 17th groups.

The general trend for electron affinity down the group is that it decreases because of the increase in atomic radius.The exception of $\ce{Cl}>\ce{F}$, I can understand is because fluorine has a high electron density and it is unfavourable to add more electrons as it would only increase the electron -electron repulsion.

The same reasoning can be applied to $\ce{S}>\ce{O}$. But oxygen's electron affinity is lesser than all the elements down group 16. Why is this so? And how is it so different from group 17 or why doesn't group 17 have $\ce{F}$ being less than the rest?.

I tried to apply the reasoning that the electron-electron repulsion in oxygen is so much that it is less favourable for $\ce{O}$ than any other element in group 16 to gain an electron. But in that case $\ce{F}$ is an even smaller atom hence with even more repulsion. So why are these two groups so different?


texts: Why am I getting higher conversion values of isopropanol dehydration over a zeolite catalyst than n-propanol dehydration?

texts:
The two process are run separetly but under the same condition, same activation of the catalyst, same reaction temperature, same flow.
The initial conversion of n-propanol is ~50% and isopropanol ~70%.
My expections was lower conversion values of isopropanol, because of it's branched structure it has a more contrained diffusion to the acid sites of the zeolite.


texts: Positive or Negative Anode/Cathode in Electrolytic/Galvanic Cell

texts:
In a galvanic (voltaic) cell, the anode is considered negative and the cathode is considered positive. This seems reasonable as the anode is the source of electrons and cathode is where the electrons flow.

However, in an electrolytic cell, the anode is taken to be positive while the cathode is now negative. However, the reaction is still similar, whereby electrons from the anode flow to the positive terminal of the battery, and electrons from the battery flow to the cathode.

So why does the sign of the cathode and anode switch when considering an electrolytic cell?


texts: pH Testing Without Cabbage/Disposal of Ferric Chloride

texts: I have a year old bottle of ferric chloride in my basement for PCB etching that I realized that I was never going to use. What is the best way to make sure that it is neutralized without pH paper or cabbage for testing?


texts: Introduction to modeling chemical reactions

texts: I am looking for introduction to modeling of chemical reactions. I think there is the base approach, where concentrations of chemical species are given, plus ratios of each possible reaction / outcome. Is there a paper lightly explaining internal mechanics of such reactions, and their modeling via system of differential equations?


texts:
Is the concept of orbital hybridisation an accurate description of a physical process that actually occurs in bonding atoms, or is it, like VSEPR, a heuristic tool to reason about the characteristics of classically infeasible chemical bonds? Forgive the naivete of my question: I ask this because I am not actually acquainted with the bulk of the underlying theory of chemical bonds, but only with a somewhat flimsy and superficial description that seems inadequate and overly contorted to me.

Thanks in advance for any answers!


texts:
A full FAQ post has been written on meta.chem.SE, explaining the premise of synthesis golf and the 'rules'. Please take a look at this before answering (if you haven't already).

This fourth round of golf concerns the synthesis of plaunotol, a peptic ulcer treatment:

InChI=1S/C20H34O2/c1-17(2)8-5-9-18(3)10-6-12-20(16-22)13-7-11-19(4)14-15-21/h8,10,13-14,21-22H,5-7,9,11-12,15-16H2,1-4H3/b18-10+,19-14+,20-13-

In a departure from previous rounds of synthesis-golf, no stereocentres to worry about (hopefully easier for even more people to get involved), though several challenging alkenes for which the geometry must be controlled.

You may start from anything commercially available in the Sigma Aldrich catalogue, but to make this 'simple' challenge a bit harder, you must make each of the C=C bonds (i.e. no buying in the alkenes that form the product, but you may use an alkene if it is not preserved into the product).


texts: Can more than 1 mol of gas dissolve in 1 mol of H2O?

texts:
$\pu{1176 mL}$ of ammonia can dissolve in $\pu{1 mL}$ of water at $\pu{0℃, 1 atm}$, according to wikipedia. Equivalently, about $\pu{0.94 mol}$ of $\ce{NH3}$ dissolve in $\pu{1 mol}$ of $\ce{H2O}$.
I wonder that is there any gas such that more than $\pu{1 mol}$ of the gas can dissolve in $\pu{1 mol}$ of $\ce{H2O}$.


texts:
I am working the following USNCO problem (#41 from 2002). Based on this question and answer Deriving a reduction potential from two other reduction potentials, it seems that $\Delta G$ must be calculated and then added. However, when I do this, I get an answer that is not one of the given choices.

The problem is:

  Use the given standard reduction potentials to determine the reduction potential for this half-reaction:
  $$\ce{MnO4- + 3e- +4H+ -> MnO2 + 2H2O}$$

  The given reactions are:

  $$\begin{align}
\ce{MnO4- + e-} &\rightarrow \ce{MnO4^2-} & E &= +0.564~\mathrm{V} \\
\ce{MnO4^2- + 2e- + 4H+} &\rightarrow \ce{MnO2 + 2H2O} & E &= +2.261~\mathrm{V}
\end{align}$$

  The possible answers are: $1.695~\mathrm{V}$, $2.825~\mathrm{V}$, $3.389~\mathrm{V}$, and $5.086~\mathrm{V}$.

The correct answer is A. Using $\Delta G$, I got $E = 1.928$, but this is not a choice. Am I doing the math wrong, or is my method incorrect? Thanks!


texts:
I need to draw the Lewis formula for $\ce{CN}$. However, I am not sure how to draw the single free electron.
My idea would be as follows:

$$\Large\ce{\llap{·}C#N\rlap{:}}$$

Does that make sense?


texts: Chemical Reaction for making Acetic Acid from Glycerol inside Fermenter

texts:
I have been trying to find a chemical reaction for the formation of acetic acid from glycerol. I have been searching different literature, but apparently the reaction can not be found. I was hoping maybe anyone here would know the reaction.

$$\ce{C3H8O3 + X -> C2H4O2 + X}$$

Some Background

I am working on producing Succinic Acid (SA) from Glycerol (GLA) inside a fermenter. I know that inside the fermenter, the GLA is converted into succinic acid, water and acetic acid. I have been able to find a reaction for the formation of succinic acid, which is given by the following,

$$\ce{C3H8O3 + CO2 -> C4H6O4 + H2O}$$

But I can not seem to find a reaction for the acetic acid. I need an equation because I want to know the stoichiometric relation between the GLA and AA.

Additional Question

Another thing is the buffer solution reaction required to keep the $\mathrm{pH}$ constant inside the fermenter. I have been studying that either ammonia or $\ce{Ca(OH)2}$ can be used. I know the chemical reaction,

Calcium Hydroxide + Succinate -> Calcium Succinate + Water.

The calcium succinate can be reacted with conc. sulfuric acid in order to crystallize the SA crystals, since sulfuric acid can release the free succinic acids. I understand the theory behind these reactions, but I can not seem to find chemical reactions, from where I can see the stoichiometric coefficients.


texts: how to separate gamma-butyrolactone from N-methyl-2-pyrrolidone

texts: Since these two chemicals have different freezing temps (pyrrolidone is $-11~\mathrm{^\circ F}$ [$-24~\mathrm{^\circ C}$] and $\unicode[Times]{x3b3}$-butyrolactone freezes (also called melting) at $-46~\mathrm{^\circ F}$ [$-43~\mathrm{^\circ C}$]), could a person wanting to separate these just immerse them in liquid nitrogen (or something else?) to get the desired chemical to freeze, then filter off the unfrozen butyrolactone? Other routes seem quite difficult for a non chemist. Any objections or other routes? Anything you can add? Even a step by process will be much appreciated.


texts: How do these restrictions on the wavefunction logically arise?

texts:
My lecturer notes that the following restrictions on the wavefunction (in addition to it being a solution to the Schrodinger equation) are logical:

i) Continuous (mathematical definition of a continuous function)

ii) Single-valued (every x input has precisely one y output)

iii) Have a continuous derivative i.e. can define the gradient at every point

Why are these restrictions necessary?


texts: Identify the structure of compound with C₉H₁₀ formula using IR and NMR data

texts:
Use IR and NMR data to define the structure of the molecule, the formula of the given structure $\ce{C9H10}.$

On what basis do we conclude that its structure is that (the answer) only? On what points can we identify the structure of this molecule?
I have found out that since its frequency is just less than $\pu{3000 cm-1}$ it is an alkane. Also, the approximate value of the chemical shift is near $7.2,$ hence it is aromatic.
But what I did not get was the meaning of two peaks at $7.2$ and the shifts at $2.9$ and $2.1.$


texts: Why does hydrogen bonding in salicylic acid make it more acidic?

texts: When salicylic acid deprotonates (losing the proton from the carboxyl group) it forms a hydrogen bond with between the oxygen in the carboxylate anion and the hydrogen in the alcohol group. However, surely there will be a steric clash between these groups which would surely be make more significant by the long hydrogen bond? Could the hydrogen bond still form with the carboxyl group twited out of the plane? Also, why doesn't it hydrogen bond intramolecularly before deprotonation which would disfavor the loss of a proton?


texts: Why is CH4 a gas at room temperature but CH3Cl a liquid?

texts:
I cannot figure out a question on my review sheet. The full question is:

  Methane ($\ce{CH4}$) is a gas at room temperature but chloroform ($\ce{CH3Cl}$) is a liquid. Explain why changing just one $\ce{H}$ atom for a $\ce{Cl}$ atom changes the compound's state at room temp.

I thought about it, and I think it does have to do with $\ce{CH4}$ is non polar, so it does not tend to stick to each other (gas state), while $\ce{CH3Cl}$ is polar, so it does stick, such as like $\ce{H2O}$, which is liquid and is cohesive, so $\ce{CH3Cl}$ would be as well. Is anyone able to tell me if I am on the right path?


texts: How are related the electrons magnetic dipole moments in atomic orbitals?

texts: I wondering, has somebody ever try to take in account the electrons magnetic dipole moment for the shapes of the probability distribution in atom? Does this magnetic dipole moment play any role in the inner bounds of molecules?


texts: Directional nature of the acetamido group in electrophilic substitution reaction

texts:
Here, in $\ce{CH3CONH2 -}$ group, the nitrogen has a lone pair and can thus activate the benzene ring along with having an ortho-para directive effect in the following manner:

However at the same time, both nitrogen and oxygen are electronegative. Hence, they should attract (roughly speaking) the electron cloud of the ring to deactivate the ring and may result in a meta directive effect in the following manner:

So which effect is applicable here and why?


texts: What is Sodium Chloride like in gas state?

texts: Since sodium chloride is sodium and chlorine atoms bonded as a lattice and there are no discrete molecules, doesn't that mean in gas state, sodium chloride is simply sodium and chlorine atoms separate from each other, resulting in a mixture of sodium gas and chlorine gas?


texts:
However, the concentration of hydronium and hydroxide ions will be very, very small; in fact, the equilibrium that's established in solution lies so far to the left, that only 18 in 1010 molecules of water will undergo autoionization.

What does "to the left" mean in the extract above? Does it mean the left side of the chemical equation?


texts: I've always wondered why clouds can have flat bottoms, and have debated to myself whether it was a difference in atmospheric pressures, or some water molecule tendency? Could someone shed light?


texts: I am finding great difficulty in understanding the differences between stereospecific, stereoselective, regiospecific and regioselective nature of reactions. Can you explain it in simple terms without mixing them with each other?