texts: Understanding two-electron integrals in Gaussian 09

texts:
I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in including the factors coming from permutational symmetry ("redundancy factors").

Here I use water as an example, with the Huzinaga minimal basis set taken from bse.pnl.gov for consistency (built-ins in some packages had different primitive terms or number of decimal places).

\begin{array}{|c|c|}\hline
O&0.0&0.0&0.1173\\\hline
H&0.0&0.7572&-0.4692\\\hline
H&0.0&-0.7572&-0.4692\\\hline
\end{array}

I assumed no spatial symmetry (xyz coordinates) and used cartesian functions (not that it makes a difference with Huzinaga, but for later changes).

After the runs, the easiest one to understand was the output from GAMESS (option NPRINT=4) which left the integrals uncorrected for redundancy.  Molpro (INT,SPRI=2) printed some numbers that are off by factors of 2, 4, 8 but otherwise agree with GAMESS.
But I fail to understand the output from Gaussian (SCF(Conventional) IOp(3/33=6) ExtraLinks=L316 Symmetry=None).  Some of the numbers are off by factors of 2 or 4 (but not in the same entries as in Molpro) and some other numbers seem completely unrelated, even having opposite signs.

Q: Does anyone know the reason for this and how to read it correctly (to confirm agreement with other packages)?

Here are my outputs: GAMESS (line ~292), Molpro (line ~187), Gaussian 09 (line ~4810)
The indices of $[ij|k\ell]$ are in "canonical" order, ie. $i\ge j$, $k \ge \ell$, and ${i\choose2} + j \ge {k\choose 2} + \ell$.


texts: Bond length increase when replacing nitrogen with phosphorus for NH3 and NF3

texts: There is an increase in bond length of about $40\rm~pm$ from $\ce{NH3}$ to $\ce{PH3}$, but only by about $20\rm~pm$ from $\ce{NF3}$ to $\ce{PF3}$. I understand that the bond length will increase with the larger $\ce{P}$ atom, but I cannot see why the changes are so different when the atom is changing in the same way.


texts: What is the mechanism of AChE inhibition by Onchidal?

texts:
A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below:

How and why does Onchidal act as an AChE inhibitor? What does the adduct of Onchidal with AChE look like? Why is the inhibition of AChE by Onchidal irreversible?


texts: I faced a question where I had to find the amphoteric oxides among some given oxides. The answer key says $\ce{Cr2O3} $ is amphoteric but $\ce{CrO}$ isn't. But why is that?


texts: Why do we use glacial acetic acid in lidocaine synthesis?

texts:
The lab sheet says the following :

  This reaction is carried out in glacial (anhydrous) acetic acid as the
  solvent. The acetic acid reacts with 2, 6-dimethylaniline to establish
  an equilibrium between it and its acetate salt.

What is the purpose of establishing an equilibrium between 2,6-dimethylaniline and its salt here?

EDIT:
This is the source of the quoted text & the procedure to synthesize lidocaine : https://tigerweb.towson.edu/jdiscord/www/332_lab_info/summer2016chem332labs/webexpt_lidocaine_a.pdf


texts: When dispensing liquid nitrogen, why does the surface get wet rather than frozen?

texts:
When I go to dispense liquid nitrogen after someone else has just used it (say in the last 30 minutes or so), the copper pipe used to transfer the liquid is covered in frost/ice.

This makes sense, as the pipe gets incredibly cold, condenses water out of the air which freezes extremely quickly due to the vast difference in temperature (77K for liquid nitrogen vs. water freezing at around 273K).

What I find confusing is that once I start dispensing the nitrogen, this frost/ice appears to 'melt' into a liquid, this seems less intuitive to me. My first thought is that so much new water is condensing out of the air that the frost/ice gets 'wet', however I'd expect this to freeze very quickly and the ice to eventually get so thick that this issue of wetting became irrelevant. Alternatively, one could imagine condensing something else out of the air which is indeed a liquid at these temperatures such as oxygen, but in this case I don't observe the characteristic blue colour.

  An example of the type of dewar in question


texts: Except pure alloys, are there any compounds with more metal elements proportion of atoms than nonmetal elements in proportion of atoms?

texts:
Except pure alloys, are there any compounds with more metal elements in proportion of atoms than nonmetal elements in proportion of atoms?

For example, Aluminium oxide has 2 metal elements & 3 nonmetal elements. Do we have a compound with X metal elements & Y nonmetal elements, where Y is more then X.


texts: How can I pass this concentration to ppm?

texts:
So the exercise gave us the concentration of a solution (1,5 x 10^-3 M) and the volume (10 mL).

The 1st part of the exercise was to calculate the amount of volume we need from a more concentrated solution (0,010 M). I calculated the volume which is 1,5 mL.

The solution is from CoCl2.6H2O.

Now they want us to pass the concentration of our prepared solution to ppm. How can I do that? Thanks!


texts: What is the structural formula of alkali hypohalite: MOX or MXO?

texts:
There seems to be an inconsistency in the formula. Somewhere it is written as MOX and in some places, it is written as MXO. This is what Google gives when you search sodium hypochlorite:

I think the formula of alkali hypohalite should be MOX because since the negative charge bears over the oxygen atom, it accepts the electron coming from the alkali metal ion and forms a duplet  thus forming ionic bond.

Is my assumption correct? What is the correct formula of alkali hypohalite?


texts: Anitaromatic compounds: Why do they have lower stability?

texts:
What is the cause for some compounds like cyclobutadiene to be antiaromatic?

I know they don't satisfy Huckle's rule but I don't understand why that leads to the decrease in stability of the compound. Whenever we analyse stability we look at steric hindrance, delocalization, etc. Delocalization of electrons does take place, then why does the stability decrease?


texts: Basicity comparison of ammonia derivatives (and guanidine)

texts:
Arrange the following in decreasing order of basicity:

  $\ce{N(CH3)3}$
  Guanidine
  $\ce{N(C6H5)3}$
  $\ce{NH(CH3)2}$

My answer - 2 > 1 > 4 > 3

Option '2' due to equivalent resonance structures on protonation. Then option
 '1' due to thrice +I effect. Followed by option '4' having +I effect twice which causes the lone pair electrons to be repelled from the nitrogen atom. Finally option '3', because lone pair electrons are delocalised on three rings.

Is my logic for the question correct or not? I am not sure if my answer is correct.


texts: Relation between number of conjugated double bonds and absorbance?

texts: I observed the absorbance on Phenolphthalein in acidic and basic medium, and I know that the absorbances differ due to the number of conjugated double bonds, but I am not sure exactly why this happens. I believe it has something to do with the delocalised electrons, which causes lower energy differences, but I am unable to establish a solid link between the concepts. Why does this happen?


texts: $$\mathrm{molarity} = \frac{\text{amount of solute}}{\text{volume of solution}} $$ and amount of substance is based on quantity (larger mass means larger amount), so how come it is an intensive property. Shouldn't it be an extensive property?


texts: I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as the Berny algorithm. I understand that this algorithm uses the idea of updating the Hessian matrix, a matrix of 2nd order derivatives of the energy with respect to spatial coordinates, with past gradient history, something similar to the conjugate gradient method. My mathematical understanding is not that advanced so I would prefer if the answer uses a step-by-step approach. An overview of the approach in laymen terms would also be appreciated.


texts: Why does sodium citrate in water turn black when blueberries are added?

texts:
I recently started making oral rehydration therapy for someone I'm taking care of who developed POTS after COVID-19 infection. (ORT was recommended by their doctor.) I use the standard ingredients of ORT: sodium chloride, sodium citrate, potassium chloride and dextrose/glucose. To add some flavor, I tried blending in some frozen blueberries, but when I did the solution instantly turned black. The water became cloudy and opaque as well. By trying to recreate the reaction methodically, making four different solutions of blueberries and one of the other chemicals in water, I determined that this was a reaction between the sodium citrate and something in the blueberries.
Despite its off-putting color, the solution still tastes fine. However, I'm hesitant to serve it to the person I'm caring for without knowing for sure if it's safe to drink! What causes this reaction, and is it safe?


texts:
This is my interpretation of an MRI:
There's an external magnetic field and most of the hydrogen nuclei will align themselves with that field (which is the lower energy state) but some are not aligned (which is the higher energy state). A chemist can then direct a wide range of radio waves with different wavelengths. The specific wavelength that causes the hydrogen nuclei to go from their lower energy aligned state to their higher energy unaligned state can be determined by the wavelength of the energy emitted by the photon when the hydrogen nuclei return to its ground state. And that wavelength determines the environment. Is this accurate?


texts:
I need help with the reaction between fluorescein and blood in the method of detecting latent blood stains.

I find it hard to find any literature on this subject.
As far as I am concerned, the fluorescein is reduced into fluorescin in a stock solution with powdered zinc, distilled water and sodium hydroxide pellets.
$\ce{Fe^2+}$ (found in the latent blood) is oxidized into $\ce{Fe^3+}$ with hydrogen peroxide.
When fluorescin is reacting with iron ions in the haemoglobin, it will be oxidized back to fluorescein.

Can anyone help me with this? Maybe even on a molecular level.


texts:
In talking about Raman spectroscopy, one finds the Stokes line is simply the difference between the energy of an incoming photon and an emitted photon. This energy corresponds to a vibrational transition in terms of energy. Yet, the light sent at the molecule is usually much higher energy than that vibrational transition (or else we would just be doing IR).

The explanation I've heard is that the state which holds all that energy in between the ground vibrational state and decaying back to the first vibrationally excited state is a virtual state.

From doing some reading, I have gathered that a virtual state is called virtual not because it's imaginary, but because it's not an eigenfunction of the hamiltonian of the system.

Where does this state come from? I've heard that it drops out of some perturbation theory. Because Raman is intricately connected with polarizabilities, I imagine this might be perturbations to the time-dependent Schroedinger equation.

So, to put some actual questions out there:

What is meant by "virtual state"? In what sense is it virtual?

Can anyone show me the perturbation theory where this comes from? Even if it is just a reference, that would be greatly appreciated.

I have also seen this is somehow connected with Feshbach Resonance which I know nothing about, so an answer which addresses that point would be a good one.


texts: In terms of electronegativity, from what I understand electronegativity increases going across the period, so surely this should mean that zinc less readily loses its outer shell electrons than copper? Zinc has a greater nuclear charge but the outer shell electrons are in the same shell, so should the outer shell electrons in zinc not experience a stronger attraction to the nucleus? I have a feeling that this has something to do with which sub shells the electrons are removed from in copper and zinc...


texts: How to buy 1g of enzyme that is sold in units/mg?

texts: I am trying to buy 1g of horseradish peroxidase. On sigma-aldrich, it is sold as units/mg. I am confused as to what this unit is. It comes in 50-150, 150-250, and 250-330 u/mg. The way I currently understand it is if I buy 25 KU (kilo-units?) of 50-150 u/mg, than I should have  at minimum 167 mg of the peroxidase. Is this a correct understanding? The price of 25 KU of horseradish peroxidase is $95, so it seems ridiculous to pay that for only 1 2/3g.


texts: What is the difference between "primary quantum yield" and quantum yield?

texts:
The definition of the primary quantum yield given in Atkins textbook Physical chemistry as "The primary quantum yield, φ, is defined as the number of photophysical or photochemical events that lead to primary products divided by the number of photons absorbed by the molecule in the same interval."
And from Wiki: The general definition of the quantum yield (Φ) of a radiation-induced process - it is the number of times a specific event occurs per photon absorbed by the system.
And both sources use the same equation for Φ:
$$\displaystyle Φ=\frac{Number~of~events}{Number~of~photons~absorbed}$$
Is there any special use for term "Primary quantum yield" (I haven't found the explanation in literature)?


texts: What's the meaning of wavefunction being finite?

texts: I know ,in quantum mechanics it's important that the wavefunction has to be finite everywhere , including infinity. It's a criteria for acceptable wavefunction . What exactly does this statement mean ? And how it's associated with square integrability ?


texts: How would you go about solving this pH problem?

texts:
What is the $\mathrm{pH}$ of a $0.24\ \mathrm M$ solution of benzylammonium chloride ($\ce{C6H5CH2NH3Cl}$)?
  $K_\mathrm b$ for benzylamine is $2.2\times10^{-5}$
  Your answer must be within $\pm 0.4\ \%$

I was able to determine that $[\ce{H3O^+}]=-1.8\times10^{-5}\ \mathrm M$ using $K_\mathrm b$. Then I used the formula $\mathrm{pH}=-\log[\ce{H3O^+}]$ to determine that the $\mathrm{pH}$ is $0.0000414465$. However, this answer keeps being marked as incorrect.

What am I doing wrong?


texts: Synthesis of ZnO by wet chemical method and reducing particle size by ball milling

texts:
I synthesized bulk $\ce{ZnO}$ which is pure white in colour, but after high energy ball milling colour changes from white to yellow, why?

Figure 1: Zinc oxide (courtesy of Wikipedia).


texts:
Is law of equivalence valid for partial displacement reactions?

【I found this in my textbooks:
According to the law of equivalence, whenever two substances react, the equivalents of one will be equal to the equivalents of other and the equivalents of any product will also be equal to that of the reactant.】

If I consider this reaction, then the law of equivalence holds good:
$$\ce{H2SO4 + 2NaOH -> Na2SO4 + 2H2O}$$
Here, number of gram equivalents of each of the reactants and products are equal.

But, if I consider this reaction:
$$\ce{H2SO4 + NaOH -> NaHSO4 + H2O}$$
Here, 2 equivalents of $\ce{H2SO4}$
react with 1 equivalent of $\ce{NaOH}$ to produce 1 equivalent of $\ce{NaHSO4}$ and 1 equivalent of $\ce{H2O}$ .

Here, the law of equivalence does not hold true.

Similarly,
$$\ce{HC#CH ->[1eq  of NaNH2] NaC#CH}$$
The law of equivalence does not hold true for this.

Please explain the limitations of law of equivalence, if any.


texts: What does the dissociative mechanism for cis/trans interconversion of [Mo(CO)4(PPh3)2] look like?

texts:
All I can find in the literature is that the cis→trans interconversion proceeds via dissociation of one of the PPh3 ligands resulting in a square-pyramidal Cs intermediate, with the remaining PPh3 in an axial position.

I assume it proceeds via either dissociation of the CO trans to the PPh3, followed by PPh3 and CO binding again to form the trans isomer; or via a Berry pseudorotation-like conversion of the square pyramidal intermediate, however considering that the former seems unlikely due to the CO being a more strongly binding ligand than PPh3 and the latter would require quite a bit of energy, neither of these make sense to me.


texts:
I would like to know what precautions should be taken when handling liquids like trichloroethylene, tetrachloroethylene, dichlormethane, and mercury. Of these, which is most toxic?

I have seen people handle mercury in rooms without fume hoods. I don't have access to a fume hood, so is it adequate protection if I wear a suitable mask when handling mercury?

Also, I am interested in the conditions in which mercury vapor is formed. Why is it formed when its gaseous temperature is high?


texts:
The Casimir effect makes two close metal plates in a vacuum attract.
I was pondering and figured out that two close molecules should experience the same effect, as they are close and between molecules there is nothing. Maybe even stronger as they are usually way closer than metal plates can be.
So, is there any theoretical work on this? Is the Casimir "force" considered one of the van der Waals forces? Am I talking nonsense?
Also, could the attraction between the plates result from van der Waals interactions and not from the quantum field stuff? How is it known that this is not the case?


texts: Why does capillary action occur better in narrow tubes than in wide tubes?

texts: We all have seen the meniscus of a small graduated cylinder in the lab. The reasons for the occurrence of capillary action are clear, but why does it occur more profusely in smaller-rimmed containers?


texts:
How do I tell which one is cis/trans? I know the definitions: cis is same side; trans is across; but

1) What am I comparing here.

2) How do I compare/visualize?


texts: What are the products of the thermal decomposition of potassium cyanate with carbon at elevated temperature?

texts:
What are the products of the thermal decomposition of potassium cyanate ($\ce{KOCN}$) with carbon ($\ce{C}$) at elevated temps ($\ce{300^\circ C - 1300^\circ C}$)?

I guess some of the nitrogen is lost and forms something. I'm trying to find out the full equation, but a google search brings up nothing concerning reduction of potassium cyanate with carbon.


texts:
Considering that $\ce{Zn^2+}$ is $\mathrm{d}^{10}$, $\ce{Fe^3+}$ is $\mathrm{d^5}$, and $\ce{O^2-}$ is a weak field ligand, the CFSE values of both the normal and inverse spinel structures should be $0$.

Why is it then that the normal spinel, with $\ce{Zn^2+}$ in tetrahedral holes and $\ce{Fe^3+}$ in octahedral holes, is formed?


texts: HOMO Odd, LUMO Even: Why does the affected orbital change depending on the carbon? How are carbons numbered?

texts:
While looking at how substituents affect the absorption spectra of molecules, I came across this:

  Substituents alter the emitted wavelengths of these molecules by affecting the electron densities. Electron Withdrawing Groups (or EWGs) withdraw electron density, thereby making the arrangement more stable. The energy level of the orbital affected subsequently lowers, causing a typically-noticeable red shift in the maximum wavelength. Alternately, Electron Donating Groups (EDGs, for short), add to the electron densities of the molecule. This causes the affected orbital to be less stable, and requires more energy to obtain. The orbital affected depends on the placement of the substituent. A useful mnemonic device in this matter is HOLE: HOMO Odd, LUMO Even. This explains that the affected orbital alternates between odd and even placements.

Why does the orbital affected depend on the placement of the substituent? I thought substituents that caused bathochromic shifts just extended conjugation and hence reduced the HOMO-LUMO gap? Is this odd-even rule only applicable to azulene, or can it be applied to other chromophores?

Also, why are the carbons numbered the way they are? Here's a picture with the numbering.

Shouldn't the carbons with the question mark also be counted?


texts: What materials for a boiler, if any, do not require a deaerator?

texts:
I'm imagining a portable boiler/turbine unit that burns wood and creates steam for a turbine, generating electricity.

I was planning on using freshwater from a river or lake. (A simple filter will remove particulate matter and minerals.)

But then I came across something called a Deaerator.

Basically, the deaerator removes oxygen and carbon dioxide from the water. Those substances often dissolve in the water and, in a boiler, can cause metal corrosion.

So I'd like to choose a material that doesn't require this, if possible. Titanium? Bronze? Carbon-carbon? Iron-Nickle like they use in jet engines?

Edit: For the curious, this question arose from studying old steam trains. Pretty sure they did not de-aerate the feedwater there and just let boiler lifetime suffer. I'm wondering if some modern "miracle" material, maybe carbon composites, can eliminate the need for de-aeration.


texts: What happens to the crystal structure of ice as it gets colder and colder

texts:
Not sure if this belongs on Chemistry or Physics stackexcahnge.

As water freezes into ice, it turns into a solid, and expands as it forms a crystal structure.  But what happens to this crystal structure as it continues to cool?  For example, if you take ice and cool it down to -50C, how does the crystal structure alter?  -100C?

I would assume that it contracts, similar to any other crystal as it cools.

I'm familiar with the different phases of ice, which require different amounts of pressure and such to create.  For my example above, I'm talking about taking a cup of water, and slowly freezing it over time with roughly no change to the pressure in the room.


texts: How to explain the excited states in the dinitrogen cation?

texts:
The $\ce{N2^+}$ molecule has the molecular orbitals
$$\ce{\sigma(1s)^2\; \sigma^*(1s)^2\; \sigma(2s)^2\; \sigma^*(2s)^2\; \pi(2p_x)^2 \; \pi(2p_y)^2 \; \sigma(2p_z)^1,}$$
which can be seen on the following picture:

So, the ground state has $\mathrm{A_g}$ symmetry in $D_\mathrm{2h}$ point group, i.e. $\Sigma_\mathrm{g}^+$ in $D_\mathrm{\infty h}$.

But what will the excited states look like?

I'd expect, that the first excited electrons will be the ones, which "need" the smallest amount of energy to get into a higher state.

So, the first electron will be excited from $\ce{\pi(2p_x)}$ or $\ce{\pi(2p_y)}$ orbitals to $\ce{\sigma(2p_z)}$ like this:

The first excited state will have $\mathrm{B_{3u}}$ or $\mathrm{B_{2u}}$ symmetry in $D_\mathrm{2h}$.

The second excited state would be

I.e. it would have the $\mathrm{B_{3g}}$ or $\mathrm{B_{2g}}$ symmetry.

Is my expectation correct or will the electrons be excited in a different order? And what will the 3rd and 4th excited states look like?


texts: How can one calculate the pH of a solution?

texts:
So, I have 1 litre of acetate buffer, and 0.1 mol of oxonium ions/$\ce{H3O+}$ is added. The task is to calculate the pH of this solution.

What I was thinking:

$$\ce{CH3COOH + H2O <=> CH3COO- + H3O+}$$
$$\mathrm{pH} = \mathrm{p}K_\mathrm{a} + \log\frac{c(\ce{Ac-})}{c(\ce{HAc})} = \mathrm{p}K_\mathrm{a} + \log\frac{n(\ce{Ac-})}{n(\ce{HAc})}$$
$$\mathrm{pH} = 4.74 + \log\frac{n(\ce{Ac-}) - 0.1\ \mathrm{mol}}{n(\ce{HAc}) + 0.1\ \mathrm{mol}}$$

But neither $c(\ce{Ac-})$ nor $c(\ce{HAc})$ (which should, in theorey, be equal) is given. The only thing I know (or I think I know) is this: $$\frac{c(\ce{Ac-})}{c(\ce{HAc})} = \frac{1}{1} = 1$$

So, is it possible to calculate the pH from that? Am I missing something?


texts: How should I think about potential energy surfaces for reactions of complex systems?

texts:
I've recently started doing some computational chemistry, studying the reaction dynamics of some moderately complex organic and inorganic reactions. I'm doing things like finding maxima, minima, TS's, saddle points, geom. optimizations, and finding conformational isomers of all of the above. I'm really enjoying myself.

One thing I would like to better understand, though, is how to think of the potential energy surface (PES) of these sorts of systems. The way I see it, a PES is just a potential energy profile (PEP) with one or more dimensions beyond energy and reaction coordinate. I understand that you cannot really compute a complete PES for a complex system. Most of the PES's I've seen are for simple systems like this solvent study of an SN2 reaction:

(R. Otto et al. 2011, Nature Chemistry 4, 534-538)

This is simple enough to understand. They have added the dihedral angle as another dimension of their picture of the reaction dynamics. But what about a large system, especially a non-rigid one? Since there are so many more possible ways the system can move, does that mean its 'true' PES is polydimensional? I like to think of these mechanistic studies of big reactions as us 'exploring the PES', even though we cannot see the whole thing. How should I think about this surface? Am I understanding this concept properly?


texts: Usage of TFA in Pfitzner-Moffat oxidation and Collins vs Jones oxidation

texts:
Is the addition of TFA in Pfitzner-Moffat oxidation to protonate the DCC to form a positive carbocation for the alcohol to attack? Or is there more to it? Why is TFA used and not other acids? Are other acids to weak for this?

Lastly for the Collins vs Jones oxidation, the only discernible differences are the solvent: $\ce{H2SO4}$ vs DCM, and that the Collins oxidation makes use of a pyridin chlorochromate, does this complex dampen the oxidative effect of chromium? So much so that the Collins oxidation can not directly oxidise a alcohol to a carboxylic acid, whereas Jones reagent with $\ce{H2SO4}$ and $\ce{CrO3}$ can?


texts: Potassium permanganate (VII) + glucose + sodium hydroxide =?

texts:
I saw this experiment many times but still can't explain why.

The experiment is first prepare two solutions. The first one is to dissolve potassium permanganate crystal into distilled water to form potassium permanganate (VII) while the second one is to put sodium hydroxide and glucose (sugar) into distilled water.

Secondly, I pour the second solution into the first one. My observation is the purple solution will slowly turn into blue, then slowly turn into green and lastly turn into yellowish orange.

So, what really happen in the solution?


texts: Coordination compound nomenclature for [Cu(acac)(bpy)]BPh4

texts:
The title says it all really.
I thought it would be acetylacetonatobipyridinecopper(II) tetraphenylborate. Is this correct? I feel as though it looks a bit clumsy and wasn’t sure if I was supposed to include as (2,2-bipyridine)? Is it ok to use brackets like this for naming a coordination compound the IUPAC way or is my first naming correct?


texts:
There is a reduction reaction of phenol with zinc dust which is found in many books.

$\ce{Ph-OH + Zn -> Benzene + ZnO}$

However, a simple google search fails to explain anything about the reaction. So, I put forth my questions:

  1) What is the name of the reaction and who invented it?

I have already done a google search, but it yields no results. My textbook also mentions nothing about the inventor of the reaction, or any name of the reaction. I understand that every reaction might not have a name, but at least it must have an inventor. You can't say that the reduction of phenol by distilling it with zinc dust is known from time immemorial. Can you?

  2)What is the reaction mechanism of the reaction?

This and this page writes about a mechanism of the reaction. If drawn, I suppose it would look like this:

It would certainly explain the formation of biphenyl and hydrogen ( if they are indeed formed). But the problem is that no reference is given in the answers. There is at least one book or paper which wrote about the mechanism.

So, if you answer, please add a reference if possible. If you think that the above mechanism might be incorrect, then also add an answer. I want your insights on this problem.

[Note: There is another question at Reaction of phenol with Zinc dust which is similar. But I have already drawn a mechanism and I am asking a different question here. So I don't think this question is a duplicate.]


texts: Reduction potential and electron affinity

texts:
Why is it that fluorine has a much greater reduction potential than chlorine, despite the fact fluorine has a lower electron affinity than chlorine?

I understand that fluorine has a lower electron affinity than chlorine due to fluorine's compact size and higher negative charge density.

So what makes fluorine a good oxidizing agent - one better than chlorine?

Could it be that the reduction potentials are referring to diatomic fluorine rather than elemental fluorine? And similarly diatomic chlorine rather than elemental chlorine?


texts: Nuclear equations for the decay of radon-222 to lead-206

texts:
I have to answer this on my worksheet. I understand nuclear chemistry equations a bit, as well as the process of alpha decay and somewhat about what happens when an atom changes its number of protons and neutrons, I understand the gamma symbol and the m symbol meaning the element is high-energy state but this has me stumped. It's an 8 step question. It reads:

  The inhalation of radon-222 and its decay to form other isotopes poses a health hazard.
  Write balanced nuclear equations for the decay of radon-222 to lead-206 in eight steps.
  Show step 1 below, and show steps 2-8 are on the next page.

  a. Step 1: radon-222 decays by alpha emission.

  b. Step 2: the daughter product in part a decays by alpha emission and is in a high energy state.

  c. Step 3: the high energy daughter product in part b decays by beta and gamma emissions and is in a high energy state.

  d. Step 4: the daughter product in part c decays by beta and gamma emissions and is in a high energy state.

  e. Step 5: the high energy daughter product in part d decays by beta emission.

  f. Step 6: the daughter product in part e decays by alpha emission and is in a high energy state.

  g. Step 7: the high energy daughter product in part f decays by beta and gamma emissions and is in a high energy state.

  h. Step 8: the high energy daughter product in part g decays by alpha and gamma emissions.


texts: Explaining hypervalency in the framework of molecular orbital theory

texts:
In preparing for teaching duties in an introductory course in inorganic chemistry, I seem to have made a digression into how we understand the hypervalent molecules.

Just to re-iterate what this concept is (most likely a bad definition, correct me if this is bad): We say that a molecule is hypervalent if an atom has more than its maximum number of valence electrons participating bonding, as drawn in Lewis structures. Three examples are $\ce{PCl5}$, $\ce{SF6}$, and $\ce{XeF2}$.

When reading up on this, it seems to me that mostly the valence bond framework is used to explain hypervalent molecules. There is talk of ionic configurations accounting for the majority of the energy, that of single electrons localized on the ligands preventing the "octet rule" from breaking.

But how do we explain this with concepts from molecular orbital theory? If I run a high level calculation of $\ce{SF6}$, my computer does not explode (presumably, I have not tried it).

Assuming that d-electrons do not participate in bonding to any significant extent, then we only have the valence electrons. If I add up the partial occupancies of the orbitals surrounding the central atom, will I then get a number very close to 8? So only 8 electrons will participate in bonding? The "remaining" electrons could then occupy nonbonding orbtils?

Is "hypervalent molecules" a non-issue in molecular orbital theory?


texts: Is it possible to achieve a level of "truly zero" concentration?

texts: If we take some aqueous solution and dilute it further and further, will the concentration of the solution ever get to zero? I would say no, simply because total dilution implies that all the molecules of the solute have literally disappeared. But, the fact that I am unable to figure out where the molecules have gone doesn't make my argument compelling at all. I am led to believe that there is a far better answer and/or explanation to my questionUPDATE: While it is true that this question closely resembles the linked one, the answer provided in this question is a lot better as it gives a much deeper insight into the dilution process.


texts: Can you model intermolecular interactions by using the Born-Oppenheimer approximation to get a potential function for nuclei?

texts:
Here is a claim about the modeling of chemical systems. I can’t remember if it’s true or not:

Suppose we have a bunch of molecules and we want to know how they interact. Eg we want to look at the physics of two $\ce{CO_2}$ molecules bumping into each other. We can do this by treating the nuclei as classical particles moving in a potential function determined by the ground state electronic wavefunction for a given configuration of nuclei.

Eg, we want to know how hydrogen molecules bounce off each other. We do this by modeling it as two protons with momentums and positions, and we iterate forward through time using a Hamiltonian where the potential energy operator uses the Hartree-Fock method or something to calculate the electronic potential.

This approximation obviously ignores some important things, for example the momentum of electrons. But that’s small compared to the momentum of the nuclei and plausibly doesn’t matter.

Is this approximation good? Is it commonly used?


texts:
I've been struggling for a few days with the cleaning of a fridge that was left off for a few weeks with raw chiken meat in the freezer compartment. When I found it, the meat had turned liquid with the smell you'd expect, spread in the entire fridge. I started cleaning thoroughly with bleach with little effect and then vinegar after stumbling on this piece of advice. But there is still a noticeable smell lingering.

My question is then: Is it possible that the plastic of the fridge has absorbed the cadaverine and/or putrecine that I assume are responsible for the smell? And if so will any amount of vinegar (or some other household acid) be able to remove the remaining smell?


texts: How do I understand exactly how hazardous a material is based on SDS?

texts:
I work with a lab occasionally and get asked often if a chemical is safe to breathe, how hazardous is it if it lands on skin, etc. For the most part, I'll try to go to an SDS and look it up. The pictograms and diamond are what I search for, so I try to give a general answer based on that. I'm never entirely confident in what I suggest, though.
We had a lab supervisor who could tell us something like, "You don't want that on your skin for a long time, but if it falls on you, don't worry about it too much, just wash your hands thoroughly when you can." I'd like to be able to give answers like that without going over the top.
Do you have any suggestions, or could you point me to some other sources that go more in depth?


texts: Interpreting Infrared Spectroscopy (IR) Spectra

texts: I have already attempted to interpret some of the peaks. Please tell me if they are correct/incorrect and anything that I have missed.


texts: What does a number in brackets after another number mean? I.e. 21(1)cm-1

texts:
What does the number in brackets mean in these two examples?

$$21(1)\ \mathrm{cm^{-1}}$$

and

$$1.0(3)\times10^{-7}$$


texts:
On this Wikipedia page, the electrical conductivity of various materials are given in the third column ($\sigma \text{ (S/m) at 20}^\circ \text{C}$).  I am interested in the entry for Carbon (graphite):

$2$ to $3 \times 10^5 \text{ S/m} \perp \text{basal plane}$
$3.3 \times 10^2 \text{ S/m} \parallel \text{basal plane}$

Why is conductivity lower parallel to the plane than in the direction perpendicular to the plane?

I am surprised by the relative magnitudes of these $\sigma$ values because I thought that one of the amazing things about graphene -- an atomic layer of graphite -- was that its conductivity in the plane (i.e., parallel to the basal plane) is very high.  I would expect a similar trend parallel to the basal plane in graphite.

Do you have any suggestions for reading that I can do to understand this?


texts: Can a refractometer adequately measure sugar content in fruit pulp?

texts:
I am trying to measure the sugar content in mango pulp (used for food processing).

Using a hydrometer to measure specific gravity is not adequate because the pulp thickness prevent the hydrometer from adjusting its level as expected. As a work around I am diluting the pulp to a 1:1 ratio of water and mesure the gravity which I then multiply by 2, though strongly doubting this is an accurate methodology.

I am considering measuring the same with a refractometer, reading a proposed methodology suggesting to squeeze the pulp through a fine filter (cheese cloth) and using the extracted liquid to measure sugar content.

So I have few concerns:

How much solid is too much so as to skew the measurement with a refractometer?
Assuming the extracted liquid is not polluted by solids, how to ascertain this liquid is representative of the sugar content of the pulp (and that solids do not trap more sugar that would be omitted in the measurement)?


texts: How is it Possible to Measure Electrode Potential?

texts: It is known that potential difference on metal/electrolyte or any kind of interphase can't be measured since voltmeter needed to measure it is made of metal which would in contact with metal and solution develop its own potential difference at interphase and as such affect the measurement. To solve this problem, potential is measured with respect to SHE. What I don't understand is that if you want to measure the electrode potential with respect to SHE, voltmeter needs to come in contact with two metal electrodes (one is electrode which potential you want to measure and the other is SHE) which will again create potential difference between the electrodes and voltmeter since two different metals in contact create potential difference between them. Can you explain?


texts: Why are antibonding orbitals higher in energy?

texts:
I found an explanation on Quora.com

https://www.quora.com/Why-are-antibonding-orbitals-more-destabilized-or-higher-energy-when-theyre-between-two-atoms-of-very-different-electronegativities

I wasn't satisfied with their reason about electrons being inside the two nuclei region.

Why exactly does electrons being shared between atoms reduce the energy? What's the quantum mechanical and mathematical argument? What's the quantum mechanical and mathematical explanation of the octet rule?

Electrons being shared sounds like repulsion forces would increase. Anti bonding sounds like a way to reduce electron repulsion by the coulomb force.


texts: Chemical equation that can be balanced in infinite number of ways?

texts:
When I was studying for my chemistry test, I found an equation that illustrates how to get water gas (carbon monoxide + hydrogen) out of methane. It is stated like this:
$$\begin{align}\ce{2CH4 + CO2 + H2O &->[\space \Delta ] 3CO +5H2}\tag{1}\\
\end{align}$$

First, I tried to balance it by myself in order not to memorize it but I ended with this equation:
$$\begin{align}\ce{3CH4 +CO2 +2H2O &->[\space \Delta] 4CO +8H2}\tag{2}\\
\end{align}$$
Then, I noticed that if we make the coefficient Of CO2 one, we can get infinite number of ways to balance the equation by changing the coefficient of CH4

We can make a third trial:
$$\begin{align}\ce{4CH4 +CO2 +3H2O &->[\space \Delta] 5CO +11H2}\tag{3}\\
\end{align}$$
Have you seen the pattern? I can conclude my observations in this equation:
$$\begin{align}\ce{nCH4 +CO2 +(n -1)H2O &->[\space \Delta] (n +1)CO +(3n -1)H2}\tag{4}\\
\end{align}$$
I am confused. Which one is true? If all of them are true, why my textbook mentions only one of them? What really happens in reality? Is equation $2$ just a simplification of more complicated equations? Does this have to do anything with the reaction mechanism?

I need to get more intuition about what is happening and the causes of this special feature.


texts: In the photoelectric effect, why we use momentum to calculate kinetic energy?

texts:
If we know the wavelength of an ejected electron, why do we use the momentum equation ($E_\mathrm k=\frac{p^2}{2m}$, $\lambda = h/p$). Why can't we use $\frac{1}{2}mv^2$ instead, using $c/\lambda = v$?

Does it have something to do with particle-like or wave-like behavior?


texts: Why are the acidities for H-CH3 and H-OH so different?

texts:
I was comparing the acidity of H-CH3 and H-OH, and a lot of things weren't making sense. Generally, the process of turning H-X into $H^{+}$ and $X^{-}$ can be broken into 2 hypothetical steps: 1.) Homolytic cleavage of the H-X bond, followed by 2.) Electron donation from H to X. The energy required for step 1 is correlated with bond length, while the energy released by step 2 is correlated with electronegativity of X.

The way I see it, electronegativity comes as a DIRECT consequence of atomic size. Adding an electron to smaller element means the electron is added to an orbital that's relatively close to the nucleus, which is more stable. Thus, smaller elements are generally more electronegative, particularly across a row in the periodic table.

Now we consider H-CH3 and H-OH. Oxygen, being smaller than carbon, will be more electronegative; thus, $OH^{-}$ is more stable than $CH3^{-}$ and step 2 will be more favorable for H-OH. But oxygen being smaller than carbon also means the O-H bond length is smaller than the C-H bond length, and thus harder to homolytically break. Overall, I'd expect these two steps to roughly cancel, and their acidities to be at least in the same ballpark. Yet the pKa for H-OH is 15.7, while the pKa for H-CH3 is approximately 55!

How can I make sense of this? What are other factors that impact electronegativity and homolysis that I am not considering? Or are there other aspects to this problem that I am not considering entirely?


texts: Shouldn't enthalpy be constant measured at constant volume?

texts:
Shouldn't enthalpy be measured at constant volume? Then the work done on and by the gas is 0 meaning that the temperature change is caused solely by heat released or absorbed by the system. You'd be able to calculate
$$\mathrm dQ = \mathrm dT \cdot C_\mathrm s$$
(specific heat).
However, since enthalpy is at constant pressure the substance will do or have work done on it and thus there is no easy way to relate the enthalpy change to the change in temperature. Am I mistaken somehow?


texts: Why is sodium chloride edible whereas both sodium and chlorine are highly reactive?

texts:
Sodium chloride is edible. But elemental sodium and chlorine are highly reactive and poisonous. What is the difference?

Also, is there any difference in eating sodium chloride in powder form and after dissolving in water? It gets ionized, correct?


texts: DCC coupling of N-hydroxysuccinimide and 2,2-dimethoxyacetic acid

texts:
I am forming N-hydroxysuccinimide ester (1) by DCC coupling with N-hydroxysuccinimide and 2,2-dimethoxyacetic acid using distilled THF as solvent.

What I see on $\ce{^1H}$-NMR is three major singlets:
$\delta~\pu{4.840 ppm}~(1\ce{H}),$ $\delta~\pu{3.432 ppm}~(7.26\ce{H}),$ $\delta ~\pu{2.731 ppm}~(6.36\ce{H})$ and some impurities.
While the chemical shifts are well-aligned with theoretical predictions (in my opinion), integration ratios do not quite make sense. I wish I could purify it to have a clearer NMR spectrum and see whether I actually have the desired product, but I don't think my ester will stay stable in silica in column chromatography. Any suggestions?


texts: Thought experiment for evaluating total energy

texts:
Atomization Energy ΔHat is the energy required to disintegrate a molecule into isolated atoms that are infinitely away from each other. The question is about atomization energy and its relation to the total energy (E) in Schrodinger equation (Eψ=Hψ).

If we disintegrate a molecule one step further to isolated electrons and nuclei, will the overall energy spent be equal to negative of the total energy of Schrodinger equation? I am assuming an energy reference will come into play as well as thermal energy. So let's say we are conducting the thought experiment of disintegration at 0 K (zero Kelvin) and we correct the values by assuming a reference energy point. Then, is the total Energy E equal to disintegration energy of the molecule into isolated electrons and nuclei?


texts:
I recently came across a practice problem in my textbook asking me to name a few compounds using -ic and -ous endings. The exact wording is:

Write the name of each of the following ionic substances, using -ous and -ic endings to indicate the charge of the cation.

The first one was $\ce{CoCl2}$. However, cobalt has more than just two oxidization states (3, 2, 0, and -1).

So if it is one of the states in the middle, how do I decide whether to use -ous or -ic


texts: AChE Aging time of organophosphorus compounds containing hydroxyl groups

texts:
Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated in time, a second reaction occurs, whereby one of the alkyl groups on the OP molecule is hydrolyzed off, giving the alcohol and the phosphorylated serine residue. The hydrolysis reaction also protonates the nearby Histidine-447 at the active site of AChE, forming a salt bridge between the OP and the enzyme. This is called "Aging", and makes the inhibited enzyme resistant to activation even by oximes. Depending on the OPC in question, the aging reaction can take between a few minutes (In the case of Soman) to several hours (In most cases). Here is a figure explaining the reaction:

Sources:

  https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&uact=8&ved=2ahUKEwi0r7T4g8jnAhXCK80KHfFCBIEQFjAGegQICRAB&url=https%3A%2F%2Fwww.mdpi.com%2F1420-3049%2F22%2F9%2F1464%2Fpdf&usg=AOvVaw0WTpEABL2j3q-kXjlvKdQM

  https://www.ncbi.nlm.nih.gov/pubmed/8250487

The part which I have circled in red depicts the aging reaction. Firstly, is the information which I have found thus far correct?
Secondly, If an organophosphorus AChE inhibitor which already contained a hydroxyl group, such as EA-2192

or (Presumably) fluoro(methyl)phosphinic acid

were to inhibit AChE, how long would the "Aging" reaction take? My guess is that aging would occur even faster (Seconds to minutes) due to the OPC itself being capable of acting as a proton donor, and thus leading to the formation of the salt bridge without any additional hydrolysis needing to take place beforehand. However, I have not been able to find any information on this particular matter, and so that is just pure speculation. Has any research been conducted into this? Is my speculative guess likely to be correct?


texts: What is the liquid in Mathmos lava lamps?

texts:
How can I identify the liquid in Mathmos lava lamps?
I have two of them with broken caps, I need to get rid of them. Can I flush the stuff down the toilet?

It smells funny.


texts: I am trying to picture how electrons move around in atomic orbitals

texts:
Are they thought to continuously pop in and out of existence at various points inside the orbital defined by probabilities or do they follow definite paths that are made fuzzy by the Heisenberg uncertainty principle?
I sometimes find myself as thinking of the electron cloud as a gas with varying charge density corresponding to the shape of the atomic orbital.


texts: What is the role of the sulfuric acid in a titration between potassium permaganate and iron ammonium sulphate solution?

texts: So basically my titration was of finding the concentration of potassium permaganate against an iron ammonium solution. In the iron ammonium sulphate solution it consisted of water, iron ammonium sulfate and sulfuric acid. Im not sure about the role of sulfuric acid in this case so if someone could explain it to me that'd be great!


texts:
I was solving questions on the MSU website on organic nomenclature.
Out of the following questions, I got only the first and last one right.
Where am I going wrong with the others?Hints would suffice.

EDIT:I got the second one correct as well.

(2)----7,7-Dichloro-4-ethyl-3,3,8-trimethyl-4-propyldecane


texts: What are the components of and how would one go about making polyester casting resin?


texts:
Why do reactions with oxygen produce flame (i.e. light), heat and hence a lot of energy? I mean, why only oxygen, why not any other element like nitrogen? What is special about the electronic configuration/arrangement or molecular geometry that confers it with this property?

Maybe you
will cite examples of other reactions involving a lot of energy and producing flame, but I am sure there is nothing as familiar to mankind (in terms of the frequency in their occurance) as the reactions involving this compound. Reactions with oxygen are so ubiquitous and vital to life and thus they were classified under a separate category, i.e. combustion.


texts:
I am thinking on an alternative synthesis of pPDA, in which I need counsel. I was thinking about these easy reactions, and I want to ask if it can be done, or maybe you can hint me some reference. I am trough the reading of nitration and reduction of aniline, or from 4-nitrochlorobenzene or the DuPont synthesis.

The first route smells a bit fishy, but I think with enough heat, and molar ratios it can be done.

The second reaction is more promising for me since it is made from economic reagents, I'm fairly sure the ascorbic acid reduces the imine to the amine form. The only problem that could occur is with the reaction of 1,4-benzoquinone with ammonia. Can you validate my thoughts? I see no reason why it should not work.

Please if you have any suggestions or help, I gladly welcome it.

EDIT 1:

The comment from Waylander in wich he/she states the step from 1,4-benzoquinone to the imine form is probably not achievable. Howered i found also an another route from benzoquinone, wich is to react it with hydroxil-amine forming the oxime. *1 Then the question left behind is the step from oxime to amine, maybe the ascorbic acid still can do the job, however i dont find any source for it, but my assumption is that it still works.


texts: Where did the acac come from in Cr(acac)₃ synthesis by CrCl₃ reagent?

texts:
Those are the reactions:

$$\ce{(H2N)2CO + 3 H2O -> CO2 + 2 NH4+ + 2OH-}$$
$$\ce{CH3COCH2COCH3 + OH- -> acac- + H2O}$$
$$\ce{CrCl3.6H2O -> Cr3+ + 3Cl- + 6H2O}$$
$$\ce{Cr3+ + 3acac- -> Cr(acac)}3$$

I don't get from where comes the $\ce{C5H8O2}$ in reaction #2!


texts: I was wondering if we could break a bond by applying a big magnetic field on a molecule. The magnetic would just cause the spin of cores of the atoms making the molecule to be aligned , raising the energy of molecular bonding orbital in the same energy of the antibonding molecular orbital allowing an electron to hop from the molecular bonding orbital to the molecular antibonding orbital destroying the molecule.


texts: An unconventional decarboxylation to form bullatenone

texts:
I recently had an assessment which required me to draw the mechanism of decarboxylation of a $\beta$-ketoacid. However, it is slightly peculiar because there is the presence of $\alpha$, $\beta$-unsaturation. If the normal mechanism was drawn, then there would be an $\ce {sp}$-hybridised carbon in the enol intermediate after the $\ce {CO2}$ leaves. The hydrolysis and decarboxylation steps are similar to these shown in a publication by Takeda, Tsuboi  & Sakai (1973). The only difference being that the question I attempted specified that the acid used to effect decarboxylation is $\ce {H2SO4}$.

To make it seem more logical, after the ester hydrolysis, I included an additional protonation step at the start of the decarboxylation, which involves protonating the double bond and forming an oxonium ion. Then, the normal decarboxylation mechanism proceeded. After which, there is tautomerisation back to the keto form, with shifting of the two double bonds to generate the bullatenone. Would that be the likely mechanism that is operating?

Out of curiosity, I would also like to ask if the decarboxylation would still take place without the $\alpha$ oxygen atom or the $\ce {Ph}$ group. I believe it could still take place but it is much less likely since it will now involve the formation of a secondary carbocation with no resonance stabilisation.

Reference

Takeda, S.; Tsuboi, K.; Sakai, T. A new synthesis of bullatenone. Chem. Lett. 1973 , 2, 425-426.


texts: Does this freezing point depression problem make sense?

texts: The solvent is water. Pure water has a freezing point of 0 degrees Celsius. How come, in this problem, the addition of solute results in an elevation of the freezing point from 0 to 0.46 degrees C? Is this possible? Or is this question just flawed?


texts: Understanding how the definitions of pH and activity are compatible

texts:
At $T=\pu{25 ^\circ C}$ and $P=\pu{1bar}$, the density of water is $\pu{0.997 kg L-1}$.

Neglecting nonideality of the mixture $\ce{H2O(l), H+}$ and $\ce{OH-}$ (all activity coefficients are close to $1$), we have the following for $\ce{H+}$:

amount concentration (molarity): $C =\pu{1 \times 10^{-7} mol L-1}$.
mole fraction: $x = 1.807 \times10^{-9}$

An old definition for pH is $\mathrm{pH} = −\log_{10}(C)$, which gives the familiar $pH=7$ for pure water.

A more modern definition is $\mathrm{pH} = -\log_{10}(a)$, where $a$ is activity.

This definition would make sense if the activity of a component in an ideal solution were equal to its molarity. However, isn't the activity defined as

$a = \exp\left(\frac{\mu - \mu_0}{RT}\right)$,

where $R$ is the gas constant, $T$ the thermodynamic temperature, $\mu$ the chemical potential and $\mu_0$ the standard chemical potential of reference, in which case it is equal the mole fraction in an ideal solution?

My impression is that the definition of $\mathrm{pH}$ was changed in order to incorporate the effect of nonideality, in which case I would expect it to be redefined as $\mathrm{pH} = -\log_{10}(\gamma C)$, where $\gamma$ is the activity coefficient. Maybe there is an alternative definition for activity such that $a = \gamma C$.


texts: Highly concentrated NaOH solution at high temperature vs borosilicate glassware and cellulose?

texts:
I've read here on stack-exchange that NaOH will react with glass through the following reaction:

4 NaOH + SiO2 ⤑ Na4SiO4 + 2 H2O

I would like to briefly heat a highly concentrated NaOH solution to 140-200C over the course of a few minutes just to pass it through a filter.

Beside safety concerns, several questions come up to my mind:

1) Do I need to worry that an NaOH solution at 140-200C could dissolve more than say max 0.5ppm Boron, Aluminium and Na4SiO4 from the glassware to my solution over the course of less than 10 minutes? or is that too short of a time to be a cause of concern?

2) Could it cause problems with my glass-joints over such a short period of time?

3) I think that cellulose doesn't chemically react with NaOH. As for the temperature, wikipedia reads "whereas starch undergoes a crystalline to amorphous transition when heated beyond 60–70 °C in water (as in cooking), cellulose requires a temperature of 320 °C and pressure of 25 MPa to become amorphous in water." In light of that and of the aforementioned reaction between NaOH and glass, am I right to assume a cellulose filter would be better than fritted glass disk or fiber glass filter and suitable for the operation or would the solution risk burning or dissolving my filter?

4) I plan on keeping my filtering apparatus around 90-110C thanks to a steam bath until right before proceeding with the filtration to minimise the incremental dissipation that will occur upon contacting the solution. Wikipedia reads "The temperature differential that borosilicate glass CAN withstand before fracturing is about 165 °C (329 °F)."  From this, is it reasonable to assume my filtration apparatus made of borosilicate glass WILL take the remaining temperature difference without cracking? (there might be up to max 120C difference)

5) I have an A2B2E2K2P3 cartridge for my full face mask. Does the P3 part protect against NaOH fumes?

6) Would you have any advice with respect to this prospective operation? (other than comments such as "don't do it" or the like)


texts: Why mass spectra of 2-methylbutane do not show big peak at 71 coming from tertiary carbocation?

texts:
Mass spectra of 2-methylbutane show strong peak at 57 by loss of methyl radical to give secondary carbocation while a loss of hydrogen radical from 2-position would form tertiary carbocation with m/z = 71 peak.

Since rules suggest that it is the stability of carbocation that determines the fragmentation pattern.So this process must be more favorable process still we do not get base peak at 71 instead we get a small peak at 71.

Same pattern is observed in case of 2-methylpentane where M-1 peak is almost absent. Other compounds also do not favor loss of hydrogen radicals to give M-1 peak.

I had read about this somewhere that it had something to do with energy of overall process but not able to recall. Kindly help me to explain the reason behind this phenomenon.


texts: Deriving the absorption coefficient from state transitions

texts:
This source states that the absorption coefficient $\gamma$ is proportional to the difference in particle number density $\Delta n$ per unit volume between the initial and the final rotational state and also proportional to the dipole moment $\mu_T$
$$\gamma \propto \Delta n\cdot \mu_T$$
According to the Beer-Lambert Law the absoprtion coefficient is also equal to:
$$\gamma=\log_{10}\bigg(\frac{I_0}{I}\bigg)\cdot \frac{1}{c\cdot l}$$
Where $I_0$ and $I$ are the incidental and transmitted intensity, $c$ is the concentration of the solution and $l$ the traveled length through the solution by the incidental beam.
From this Beert-Lambert law I woud deduce that the absorption coefficient is in terms of per 1 unit length and per 1 unit concentration.
I would assume that the difference in number density $\Delta n$ is analogous to the concentration of a solution.
But how is $\gamma$ then proportional to the $\Delta n$ if it should be per 1 unit of $\Delta n$ just as it is per 1 unit of sample concentration?


texts: Composition of Portland Cement before Hydration

texts:
I recently came across a question-

Which of following chemicals is NOT found in Portland Cement?
A. Di-calcium silicate
B. Tri-calcium silicate
C. $\ce{CaSiO3}$
D. $\ce{Ca3(PO4)2}$

I answered D. $\ce{Ca3(PO4)2}$. But according to the examiner the answer is C. $\ce{CaSiO3}$
I strongly doubt that. Any pointers to credible sources/books settling this please!!


texts: How can I remove water vapor from an airstream without a cold trap?

texts:
I'm trying to perform vacuum distillation at home with a rotary vane vacuum pump.

In order to not ruin my vacuum pump, solvent vapor (in my case, water) should be removed from the air before it reaches the pump inlet. The only method that I've encountered for accomplishing this, is using a cold trap to chill the air below $\mathrm{-50^\circ C}$ to deposite the water. To this end, the cold trap is filled with a cryogenic liquid such as liquid nitrogen.

Unfortunately I do not have access to liquid nitrogen, dry ice, etc. Is there any other affordable way to remove water vapor from the air before it reaches the pump?

Could I use a container filled with crushed silica beads or a liquid to absorb the water in the air? Or would using a very hydrophobic membrane work?


texts: What reaction would take place on an electrode in a secondary cell if it were charged and the other electrode removed?

texts:
I'm reading a book that covers the basics of electrical theory and I'm at a chapter that discusses the concept of a secondary cell. The author includes the redox reactions that take place in a primary cell when it is charging/discharging.
The secondary cell is comprised of an anode (composed of PbO2) and a cathode (composed of Pb) submerged in a solution of H2SO4. As it discharges both electrodes are plated with PbSO4 until they are fully covered, at which point the reactions that produce a charge for the battery cease and the original H2SO4 is now diluted with H2O.
My question focuses on the charging aspect of it not the discharging (because I have an easier time framing my question from this perspective) but I want to preface this aspect with two quotes the author said earlier in the chapter:
First quote: "From previous information, we found that H2SO4, when charging or discharging a cell, dissociates into hydrogen H+ ions and sulfate SO4= ions."
Second quote (this quote comes from a section describing a different cell): "The zinc element or electrode, when immersed in the acid, starts to dissolve, leaving its electrons behind and the zinc goes into solution as Zn++ ions. This action stops very shortly, as the zinc plate becomes negative and ceases to throw off positive ions. The amount of zinc thus dissolved is very minute. If the negative zinc plate is connected externally by a wire to the copper plate, an electrical current will flow from the negative zinc plate through the external wire to the copper plate (positive). As the negative charge of the zinc plate is thus removed, more Zn++ ions go into the solution"
As the original secondary cell I mentioned recharges the PbSO4 plating reverts to the composition of it's respective electrode and the diluted H2SO4 reverts to it's original solution. The reactions that take place when the cell is recharging as quoted from the book:
Negative Plate: PbSO4 + 2H+ + 2e --> Pb + H2SO4
Positive Plate: PbSO4 + SO4= - 2e --> Pb(SO4)2
I presume that each plate is a half reaction; the negative plate is a reduction half reaction; the positive plate is an oxidation half reaction; I believe these half reactions can be combined into the full reaction: 2PbSO4 + 2H+ + SO4= --> Pb(SO4)2 + Pb + H2SO4. Please correct me if I'm wrong about what these half reactions are or about how I combined them; I have only just recently learned about redox reactions in order to better understand this chapter.
Now for the question this has all been building up to; if the positive plate were removed during the recharge process would the half reaction that takes place on the negative plate become the half reaction: PbSO4 + 2H+ + SO4=  --> Pb + H2SO4 + SO4= for a short period of time until the solution becomes negative with SO4= anions and ceases to throw off H+ cations (similar to what happens in the second quote and considering what happens in the first quote)?
If this is the case, then I don't know how the difference of charge between the reaction and product side is possible. The only thing I can imagine is that the SO4= is just a spectator and does not participate in the actual reaction.


texts: During the development of aspartame, why was the methyl ester chosen?

texts: One frequent argument against the safety of the synthetic sweetener aspartame is that it can be hydrolyzed, with one of the hydrolysis products being methanol, which is known to be toxic. Of course, usually not much aspartame is added in food anyway to yield a sufficient amount of methanol or its oxidation product formaldehyde, but this does beg the question: why wasn't, say, the ethyl ester chosen to be developed as an artificial sweetener? Is there a structure-activity relationship between the alcohol used to esterify the dipeptide and the sweetness of the product?


texts: Inorganic chemistry for condensed matter physicists

texts:
I'm a theoretical condensed matter physicist, on a field of magnetism research. I wonder if any of you could recommend a concise and well-written textbook on inorganic chemistry to learn concepts of the ligand field theory, coordination of transition metal complexes and their magnetic states, etc.

During my work, I just look up the periodic table and see the electronic configurations, but the oxidization of the transition metal complexes depends on ligands, and it's frustrating as I don't seem to understand a general principle.

I'm quite familiar with solid state physics, and a bit of quantum chemistry. It would be great if you could recommend me textbooks or materials on inorganic chemistry for "solid state physics" or "material science".


texts: Is it blueish, perfect white or some other color? I am interested because some celestial bodies are said to be covered with methane ice.


texts: Numerical simulation and calculations of pH

texts:
a. Reaction of $\ce{CO2}$ addition in water is as follows:

$\ce{CO2}$ + $\ce{H2O}$ $\ce{->}$ $\ce{H2CO3}$

b. Then, pH of $\ce{H2CO3}$ solution is increased to 12 by addition of 1M $\ce{NaOH}$.

So, the reaction would be:

$\ce{2NaOH(aq)}$ + $\ce{H2CO3(aq)}$ $\ce{->}$ $\ce{Na2CO3(aq)}$ + $\ce{2H2O}$

c. This new solution at pH 12 is added to $\ce{CaCl2}$ solution; the final reaction of the system would be:

(  $\ce{Na2CO3(aq)}$ + $\ce{2H+}$ + $\ce{2OH-}$  ) + $\ce{CaCl2}$ $\ce{->}$ $\ce{CaCO3(s)}$ + $\ce{2 NaCl}$ + $\ce{2H2O}$

My questions are:

1. Is the final chemical reaction correct?

2. By setting the pH of step c equal to 12, which is ( $\ce{Na2CO3(aq)}$ + $\ce{2H+}$ + $\ce{2OH-}$ ), and addition of 50 ml of that to $\ce{CaCl2}$ solution, is it possible to make some sort of pH calculations?

$\ce{[H+]} = 10^{-12} M$

$\ce{[OH-]} = 10^{-2} M$

$\ce{[CO3]}$ = assuming 0.05 M in 50 ml

3. Overall, is it possible to do a numerical simulation (e.g., MATLAB) of change in the overall solution pH? OR, predict the final pH by calculations?

Thanks and Best Regards,


texts: How to control pH in a fermenter based on the acid produced by mircoorganism

texts:
I have got a bioreactor with an aqueous medium which produces biomass (yeast; S.cerevisiae) after inoculation.
 I am observing and collecting data over the whole process via probes/etc. on different process parameters such as pH, temperature, offgas of $\ce{O_2}$ and $\ce{CO_2}$, base uptake ($\ce{NaOH}$), weight of bioreactor and some little more like stirrer speed and so on.

How can one calculate or make a model on adding base to control pH based on the produced acid  (for now I've got no information on which one that is exactly) of the yeast or other factors?
(Is there a mechanistic or only a deterministic solution?)

Thanks in advance!


texts: Conversion of carboxylic acid to alcohol

texts:
Is it feasible to convert carboxylic acids to alcohols? I know the reverse is done during the oxidation of alcohols (e.g. in the production of vinegar), but is it possible to do it the other way round?

For example: the conversion of methanoic/formic acid ($\ce{HCOOH}$) to methanol ($\ce{CH3OH}$)?


texts: Is there any effect on bonds formation and reactants due to a reaction in adiabatic calorimeter

texts: Is there any effect on reactants and bond formation due to a reaction going on a adiabatic calorimeter.We know enthalpy of a reaction should be measured at constant temperature but in adiabatic calorimeter every second the temperature of the chemical solution keeps on changing.


texts: Could someone help me please (preferably talk me through not just provide the answer) with the IUPAC name of phthalic anhydride?  I'm sorry for not posting attempts but I'm afraid I have absolutely no idea how to begin here...


texts: Intrinsic Reaction Coordinate - What does 'Connectivity' really mean?

texts:
I am currently in the process of connecting transition state (TS) structures to other minima in order to determine a reaction pathway.  Now I understand the basic concepts of this method.  You start with your TS, run an IRC in both the Forward and Reverse directions, then you optimize the final structure in the successful IRC run.

My question is, what constitutes connectivity between a TS and a minimum energy structure?

Examples

1.) I run an IRC and I take the last resulting structure and optimize it. The optimization takes 4 steps and the geometry barely changed.  Is this structure connected to the TS?

2.) I run an IRC and I take the last resulting structure and optimize it.  The optimization takes 20 steps and the geometry changed fairly appreciably, however, connectivity of the atoms remains the same.  Is this structure connected to the TS?

3.) I have a TS where a water is being formed next to some other molecule.  I run the IRC and following the pathway shows you that the water forms and is being moved away from the molecule.  The IRC successfully finishes so I take the last structure and optimize it.  The optimization brings the water back towards the molecule to some particular spot where H-bonding occurs with the molecule.  Is this structure connected to the TS?

Note

These examples were purposely laid out in order to determine at what point TS->Minima are or are not connected.


texts: Why is the compound called 5-Chloro-2-Methylphenol rather than 2-Chloro-5-methylphenol? The occurence of the highest number 5 is exactly the same, so are they both correct?


texts: How does chloroform react with cyclopentadiene in base?


texts: Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group

texts:
I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation of a peptide bond).
How come there are two variations? And also, if the starting amino acid has three hydrogens in its amino group, what is the mechanism for the part that the nitrogen bonded to the carbonyl ends up having one hydrogen attached to it?
I worked up the mechanism on the former condition, but starting with three hydrogens, I don't quite get it. I hope you someone can enlighten me.


texts: Is polymeric ethylene glycol conductive?

texts:
The other day, when we were doing the chapter Polymer Chemistry my teacher mentioned that Polymeric Ethylene Glycol (PEG) is conductive.

[EDIT- By 'conductive', I guess my teacher meant, "sufficiently conductive, so that it can permit a significant amount of current"...Now I really don't want to go and elaborate on "significant"]

Naturally I was taken aback, having lived all my life believing anything even remotely related to plastics could possibly conduct electricity. So I Googled it, but that endeavor wasn't particularly fruitful. I ended up getting links to articles like these: http://www.sciencedirect.com/science/article/pii/S001346861101190X

As I wasn't able to get my hands on any piece of scientific literature, that definitively puts my question to rest, I resolved to have a look at the chemical structure of PEG:

But I wasn't able to identify anything that could possibly impart conductor-like properties to PEG. No free ions or any delocalized electrons that could facilitate conduction. Nothing ._.

However, I was able to discern something about possibly 'altering' PEG, via a method that's akin to doping. At any rate, I'm getting no where here.

Would anyone happen to know if PEG really is conductive in the pure state? Or is it somehow 'modified' to impart conductive properties to it? If so, then how is it modified?

A good reference would be appreciated.


texts: Is this calculation of the amount of required hydrogen gas correct?

texts:
I was a bit hesitant to post this question for it may appear like a "homework help" type of question. But upon rethinking it felt like a genuine question. I was studying stoichiometry with my son (from the OpenStax Chemistry 2e book) and suddenly I had an idea to use these calculations in a real chemistry experiment that I am going to perform at home (of course, I truly believe in a "safety first" approach). I wrote it all up here on GitHub, but reposting here to keep it all at one place:
A practical problem: It was decided to inflate a common latex balloon to 5cm radius by the hydrogen gas produced during a single-displacement reaction:
$$\ce{2HCl(aq) + Zn(s) -> ZnCl2(s) + H2(g)}$$ that uses an N/10 i.e. 0.1M HCl solution (available in many drugstores, typically in $\pu{200ml}$ bottles). How much reactants are needed?
Solution: We need to inflate the balloon to about $\pu{5cm}$ radius. Assuming the balloon to be a sphere gives us the volume of balloon, $V_b$, as:
$V_b = \frac{4}{3}\cdot \pi r^3 = \pu{523.599cm^3}$.
Assuming the density of hydrogen at STP as 0.0000899 $\pu{g/cm^3}$, the mass of hydrogen is $\pu{523.599 \times \space 0.0000899 g} = \pu{0.0471 g}$. Since 1 mol $\ce{H_2(g)}$ has a mass of $\pu{2 \times \space 1.008 g} = \pu{2.016 g}$, we need
$\pu{\frac{0.0471}{2.016} mol} = \pu{0.0233 mol}$ $\ce{H_2(g)}$.
Balancing the reaction, we see that to produce 1mol $\ce{H_2(g)}$ we need 2 mol HCl(aq) and 1 mol Zn(s).
This means that to produce 0.0233 mol $\ce{H_2(g)}$ we need $2 \times 0.0233 = \pu{0.0466 mol}\ \ce{HCl(aq)}$. We have a 0.1M HCl (aqueous) solution which means that $\frac{\text{mol of solute}}{\text{litres of solution}} = 0.1$. Clearly, we need $\frac{0.0466}{0.1} = \pu{0.466 L}$ or $\pu{466 ml}$ HCl.
The amount of zinc needed = $0.0233 \times \text{molar mass of zinc} = 0.0233 \times 65.38 = \pu{1.523 g}$.


texts: Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

texts: As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, would the interactions between 33-SN and AChE differ in any way from those between 33-SN+ and AChE? Also, would the phosphoryl-thiocholine analog of Soman have different interactions with AChE compared to Soman itself? In short, would a set of organophosphate AChE inhibitors which only differ in whether the leaving group during the process of AChE inhibition is a fluorine, dialkylaminothiolate, or thiocholine, interact differently with AChE??


texts: Maximum (Z) to (E) ratio in the photoisomerization of azobenzene?

texts:
Considering the photoswitching of azobenzene, I was told the following argument: Considering that the photoexcited state of azobenzene has a about 50% to 50% chance of yielding either the (E)- or (Z)-isomer, the maximum (Z)/(E) ratio achievable should be 1:1.

However, I have seen UV-VIS spectra where the (Z)-isomer seems to be in excess. So I figured that the above argument must be wrong. I would analyze the situation in the following way:

In this picture, the fact that the photoexcited state has about equal probability to yield (E) or (Z), i.e. $k_{-1} = k_2$.

So wouldn't the overall (Z) to (E) ratio be given by the expression
$\frac{k_1\cdot k_2}{k_{-1}\cdot k_{-2}}$?

I would then argue that in many cases, the cis isomer exhibits lower absorption at the wavelength of excitation, meaning that $k_{-2} << k_{1}$, which would explain that in many cases, an excess of the cis isomer is obtained.
By this reasoning, the initial argument would be completely wrong, as in principle an infinite excess of the cis isomer could be obtained if $k_{-2}$ is sufficiently smaller than $k_{1}$.

Is this analysis correct or am I overlooking something?


texts: If I add some KOH, where will the reaction shifts?

texts:
I just got a final test and one of the question is:

$\ce {Ni^2+}$ + 6$\ce{NH_3}$ $\ce {<=>}$ $\ce{[Ni(NH3)6]^2+}$
If we add some aqueous $\ce{KOH}$ after the reaction reach equilibrium, where will the reaction shifts?


texts: Determine whether the tank will overflow with mass flowrate

texts:
Hydrocarbon mixture ($\pu{20 mol\%}$ $\ce{CH4}$ and the balance is $\ce{C2H6}$) enters a tank at a velocity of $\pu{1 m/s}$ and is withdrawn at a rate of $\pu{2 kg/s}$. The tank is initially one quarter full. The diameter of the pipe is given as $\pu{15 cm}$ and the height of the tank is $\pu{2 m}$. Density of $\ce{CH4}$ is $\pu{422.36 kg/m^3}$ and density of $\ce{C2H6}$ is $\pu{543.83 kg/m^3}$. The volumetric flowrate of the hydrogen mixture entering the tank is $\pu{6361.56 m^3/h}$

Determine the mass flowrate ($\pu{kg/h}$) of hydrocarbon entering the tank and determine how long ($\pu{s}$) does the tank take to overflow or to be emptied.

As for determining the mass flow rate, of the inlet, I used the densities of the component to help me get the total mass flowrate. This is what I have done:

$$\text{Density} = \frac{\text{Mass flowrate}}{\text{volumetric flowrate}}$$

For $\ce{CH4}$:
$$\text{Mass flowrate} =  (422.36)(6361) = \pu{2686868.482 kg/h}$$

For $\ce{C2H6}$:
$$\text{Mass flowrate} = (543.83)(6361) = \pu{3459302.63 kg/h}$$

Therefore, total mass flowrate into the tank is $\pu{6146171.112 kg/h}$.

Now I'm stuck on the question to determine how long does it take for the tank to overflow or be emptied.
Should I use the mass flowrate to determine or the volumetric flowrate?
I assumed is the mass flowrate, but I am unsure how to start.


texts:
Basically, what are some mistakes that you can make while using the downward displacement of water method and how to fix them? This is actually a homework question and I'm not too sure what it means either. The original question:

  State and explain Dalton’s Law of Partial Pressures. Why is it necessary to correct the pressure of a gas that is collected over water? {Background: Gases formed in a chemical reaction are collected using a technique called the downward displacement of water, feel free to research this technique before you respond to this question}


texts: When a thin lead sheet is hammered, what happens to internal energy, does it increase, decrease or remains the same or first increases and then decreases?


texts: Order of reactivity of carbonyl compounds towards nucleophilic addition

texts:
Arrange the following according to reactivity towards nucleophilic addition reaction:

I have already seen this post regarding the reactivity. It helped me to some extent.

$\ce{Cl}$ increases the positive charge on the carbonyl carbon increasing its reactivity.

So (B) > (A) > (the remaining 3)

Further, aldehydes are more reactive than ketones. But I should also consider steric factors. In compounds (C), (D), and (E), compound (D) has highest carbocation stability but also has highest steric hinderance.

Compound (C) has lowest steric hinderance but low carbocation stability as well. How can I arrance (C), (D), and (E)?

To all those who say steric effects dont play a role: This is taken from page 147 of organic chemistry book by Clayden:

  The same structural features that favour or disfavour hydrate formation are
  important in determining the reactivity of carbonyl compounds with other
  nucleophiles, whether the reactions are reversible or not. Steric hindrance and
  more alkyl substituents make carbonyl compounds less reactive towards any
  nucleophile; electron-withdrawing groups and small rings make them more reactive


texts: Molarity of hydrogen gas in standard hydrogen electrode

texts:
I am unable to understand the folowing statement of Wikipedia it is about standard hydrogen electrode :

  The concentration of both the reduced form and oxidised form is maintained at unity. That implies that the pressure of hydrogen gas is 1 bar.

But why if I apply ideal gas equation then I am getting molarity of nearly 0.004M .this is condradiction to the statement in Wikipedia. N/V=P/RT THEREFORE M=N/V~0.004


texts:
Does anisole undergo friedel-crafts reaction or does the oxygen atom complex with Lewis acid?

We know that yields of this reaction are reduced in case of phenol but does the same happen in anisole?


texts:
If I understand correctly, when we go from a keto to an enol form, we simply abstract an alpha proton and thereby create a double bond to a carbon-bearing the hydroxyl functional group.

When evaluating the stabilities of the two enol forms, it appears that the enol derivative of 2,4-pentadione is more stable because of intramolecular hydrogen bonding. Both have long-range conjugation, so that cannot be a factor. The only difference really is the hydrogen bonding ... and of course ring strain (a 5-membered ring with two double bonds can't be very stable).


texts: What should I do to prevent cellulose from turning black?

texts:
In my research on producing ethanol from grass, I have boiled 4g of grass in a beaker on a Bunsen burner with 30ml of sulfuric acid (bottle of 1 mol/l). However, within a few minutes the solution turned black and thus was burnt with release of smoke.

In my next attempt to try out this experiment this Monday, I want to make a 2.5 % sulfuric acid solution using a bottle of sulfuric acid with a concentration of 1 mol/l and add it to 4g of grass and boiling it for one hour.

What is your advice on this? Should I add a larger volume of sulfuric acid solution, and if so, how much?


texts: Why mixture turns brown upon heating, during esterification with H2SO4?

texts: In the lab I was synthesising an ester with sulphuric acid as a catalyst. However the mixture turned brown and my teacher said I had burnt the acid, but what does this actually mean?


texts: How to quickly predict the group of elements with atomic numbers 117 and 120?

texts:
The elements Z (atomic number) = 117 and 120 have not yet been discovered. In which group would you place these elements?

I tried to write their electronic configurations but it was too tedious and I do not remember the Aufbau principle to that extent ($\ce{5g, 6f}$...).

Is there any quicker way to solve this question?


texts: Why does the barium ion in barium titanate move in its tetragonal crystal structure?

texts:
Barium titanate is known in the materials science world to be a great dielectric. This is known to be because the $\ce{Ba^2+}$ ion sits off center in the middle of the tetragonal crystal structure.

How does this $\ce{Ba^2+}$ ion, or even the crystal structure itself, move in order to accompany a larger amount of charge? How much freedom of movement does this ion have in a solid crystalline structure? Additionally, does the $\ce{Ba^2+}$ ion naturally sit off-center in this configuration, or does it only behave that way when introduced to a charge?


texts: What is the significance of the downward arrows in energy level diagrams in organic chemistry?

texts:
The following text is from Solomons, Fryhle and Snyder Organic Chemistry Third Edition, chapter 1 "The Basics: Bonding and Molecular Structure", page 13, topic 1.5 "Resonance Theory", sub topic 1.5B "Schematic Energy Level Diagrams of Some Mesomeric Molecules/Ions":

Energy level diagrams of some resonating structures are given as follows. (Note: The downward arrow marks the conventional mesomeric energies and indicates energy level).

It is given that the downward arrows in examples 1, 2, 3, and 4 mark the conventional mesomeric energies. What is meant by "conventional mesomeric energy"? I searched for this word on Google as well as on this site, but I couldn't find any relevant information.
What is the purpose of the downward arrows in the above energy level diagrams? Is that to depict the structure with least energy or the one which is the most stable? I thought this was the reason until I saw example 5. The arrow goes from the structure which has the highest stability to the one which has the least stability. Is there any specific reason for this upward arrow or is it just a misprint? I was unable to see any other energy level diagrams with these arrows, so is this an outdated convention followed by the book?


texts:
I have been trying to find out the bond angle of $\ce{H2O}$, but every site I visit has a different answer.

So far, I have found the following angles listed:

Site 1: 104.4º
Site 2: 107.5º OR 104.5º, depending on where you are in the article.
Site 3: 104.5º


texts: Help understanding the pressure's effect on equilibrium and Le Chatelier's principle

texts:
So let's say we have a closed system in the following reaction:

$\ce{N2O4 -> 2 NO2}$

The only way to increase the system's pressure without adding any mole of gas and keeping temperature constant is reducing the system's volume. Once we increase the pressure by reducing the total volume, formation of $\ce{N2O4}$ is observed.

In many text books, the explanation for this is that 2 moles of $\ce{NO2}$ occupy a bigger volume than 1 mole of N2O4, thus the equilibrium is restablished when more $\ce{N2O4}$ is formed. What doesn't make sense for me is that both the substances are contained in the same volume, so how 1 mole of $\ce{N2O4}$ would occupy less volume than 2 moles of $\ce{NO2}$? It only makes sense to think about partial pressures, not partial volumes, right?

I'm trying to use entropy and energy microstates to solve this problem, because it seems more fundamental than this mantra in the general chemistry textbooks. From quantum mechanics, I know (can't explain, just know; need further studying on this subject) that translational energy states become closer when a gas expands in a bigger volume, so I'm assuming that in the reaction above, with a bigger pressure (and thus a smaller volume) these energy states will be more spaced between each other. With energy states more far apart, why are there more possible energy microstates when $\ce{N2O4}$ is formed?

I can't get past this! Why does this implies in the formation of the substances with less gaseous coeficients? How are the energy states of reactants and products and their changes on pressure related with that?

Edit: to make myself clearer, I'll use this example from this textbook I'm reading:

Chem1 Virtual Textbook, Stephen Lower, link

In the endothermic reaction H–H (g) ⟶ 2 H (g), you only get hydrogen atoms at very high temperatures, because you'll have a higher distribution of populated states on the 2 H side, thus you favor the products at higher temperatures for endothermic reactions. I can completely understand the effects of themperature in Le Chatelier's principle, and I'm trying to understand an analogous thought for changes in pressure in the microscopic point of view.


texts: In molecular orbital theory, why does s-p mixing in the dinitrogen molecule not effect the 1σᵤ orbital?

texts:
s-p mixing in $\ce{N2}$ causes the $1\sigma _g$ orbital to decrease in energy, the $2 \sigma _g$ orbital to increase in energy (to higher than the $1 \pi _u$) yet the $1 \sigma _u$ is left unchanged by the interaction. Why is this?

My lack of understanding may be as a result of the fact that I am unclear as to what exactly it is that is mixing. Clearly they are the s and p orbitals but is this within the atom or is the s orbital on one atom interacting with the p on the other?

Some clarification as to why the $1\sigma _g$ orbital to decreases in energy, the $2 \sigma _g$ orbital to increases in energy would also be much appreciated.


texts: How long will it take for a measurable change in mass (corrosion) in an iron copper corrosion cell to happen?

texts: I am planning to do an experiment, in which I will test the affect of salt concentration on corrosion rate. Would there be a relationship? How long would it take for rust to form, that could be scrapped off and corrosion rate measured?


texts:
This question arises because: by giving classes in thermodynamics, I have observed that students are often confused between the different definitions (or applications) of the enthalpy concept.

The enthalpy expression is obtained as follows:

From the first law of thermodynamics:
\begin{align*}
 U=Q+W
\end{align*}
Recalling the definition of work:
\begin{align*}
    W=-PV
\end{align*}
Variations added:
\begin{align*}
 \delta U=Q - \delta (PV)
\end{align*}
Its obtained that:
\begin{align*}
 \delta U&=Q-(V\delta P+P\delta V)
\end{align*}
Constant volumen:
\begin{align*}
 \delta U=Q-V\delta P
\end{align*}
Constant pressure:
\begin{align*}
 \delta U=Q-P\delta V
\end{align*}
Variations enlarged:
\begin{align*}
 (U_f-U_i)&=Q-P(V_f-V_i)\\
 (U_f-U_i)&=Q-(PV_f-PV_i)\\
         Q&=(U_f-U_i)+(PV_f-PV_i)\\
         Q&=(U_f+PV_f)-(U_i+PV_i)\\
         Q&=H_f-H_i
\end{align*}
Therefore, the definition of enthalpy is:
$$
    H = U - W
$$

Is this properly proposed?


texts: Determining structure factors for crystals from lattice and motif

texts:
I understand that the structure factor for a crystal is given by:

$$F_{hkl} = \sum_r f_{r} e^{2{\pi}i(hx_{r}+ky_{r}+lz_{r})} $$

My textbook (''Structures of crystals'', Glazier) suggests that you can calculate structure factors if you know the lattice type and motif of the crystal, simply by finding the product of the lattice and the motif structure factors.

Can this method be used generally, and if so, do you need to define the motif relative to a centre of symmetry in order to get real structure factors for centrosymmetric crystals ?


texts: What compound does this chemical formula represent?

texts:
I recently saw this:

What chemical does this formula represent?


texts: What are the isomers of a complex having a structure of M(AB)2C2?

texts: Our instructor have us answer an isomerism problem of a crystal structure that has a form of $\ce{M(AB)2C2}$. I keep getting 9 isomers, which includes the optically inactive isomer, and my peers and I have different answers.


texts: What's the difference between the two equations for work?

texts: I'm studying thermochemistry and I don't get this. What's the difference between  $w = Fd$ and $w = -p \Delta V$?


texts: Calculating the heat of reaction for Mg metal and HCl

texts:
Adding $\pu{2.00g}$ $\ce{Mg}$ metal to $\pu{95.0 mL}$ of $\mathrm{1.00 M}$ $\ce{HCl}$ in a coffee-cup calorimeter leads to an increase of $\pu{9.2 ^\circ C}$. If the molar heat capacity of $\pu{1.00 M }$ $\ce{HCl}$ is the same as that for water $(\pu{C_p = 75.3 J mol-1 K-1)}$, what is the heat of reaction?

Two relevant equations are: $${\Delta H_{(rxn)} = -q}\\
{q = n \times C_p \times \Delta \mathrm T}$$

The answer given is $\pu{-44.4 kJ mol-1}$. I wonder if I'm not way off the mark here by using the wrong equations, because the answer I got was $\pu{122.83 J mol-1 \; ( 0.1773 mol \times 75.3 J \times 9.2)}$.

note: The heat of reaction = $\Delta H_{(rxn)}$


texts: An equal amount of hydrogen gas is dissolved in a 1L vessel and a 2L vessel, both filled with water. Which vessel has higher entropy?

texts: This question came up in our chemistry class and we could not determine which would have the higher entropy. Clearly, Vessel 2 has a larger volume, but Vessel 1 has a higher concentration of $H_2$. How do we resolve this?


texts:
I am currently stuyding electrochemistry, and recently I've stumbled upon a problem where one is supposed to calculate the concentration of Fe3+ ions after a solution containing Fe2+ was titrated using acidified permanganate, but I obtained an unrealistic result and I became confused.

What I first did was write the half-reactions involved within the voltaic cell:
Anode (-): 5Fe2+(aq) ⇌ 5Fe3+(aq) + 5e- ε01= -0.77 V
Cathode (+): MnO4-(aq) + 8H+(aq) + 5e- ⇌ Mn2+(aq) + 4H2O(l) ε02= 1.5 V
Notice the fact that I obtained the first reaction, the oxidation, by reversing the equation for the reduction of Fe3+.
By combining both half-cell reactions, one can obtain the equation for the whole process:
5Fe2+(aq) + MnO4-(aq) +  8H+(aq) ⇌ 5Fe3+(aq) + Mn2+(aq) + 4H2O(l) E0= 0.73 V

A positive standard potential will yield a negative value for the Gibbs free energy, so the reaction is product-favoured. The problem is concerned with calculating the concentration at equillibrium, corresponding to the equivalence point of our titration, so the overall Gibbs free energy will be 0, just as the non-standard potential, which we can calculate using the Nernst equation (considering 298.15 K of temperature and 1 atm of pressure). I'm also assuming that the reaction quotient is equivalent to the equilibrium constant, since we are at the equivalence point.

\begin{align*}
    E=E^{0}-\frac{0.0592}{5}\log{K}
\end{align*}
\begin{align*}
    E=0, E^{0}=\frac{0.0592}{5}\log{K}
\end{align*}
I then obtained the mathematical expression for the equilibrium constant:
\begin{align*}
    K=10^{\frac{5E^{0}}{0.0592}}
\end{align*}
I then entered the values, and calculated K (substantially larger than 1):
\begin{align*}
    K=4.523*10^{61}
\end{align*}
However, this is the hurdle I have yet to overcome. I didn't quite understand what activities are in the Nernst equation (afaik they are not equilibrium concentrations), so I assigned a formula for K based on the equilibrium reaction:

\begin{align*}
    K=\frac{[Fe^{3+}]^{5}[Mn^{2+}]}{[Fe^{2+}]^{5}[MnO4^{-}][H^{+}]^{8}}
\end{align*}

The problem mentions the following concentrations for the titration:
Fe2+:0.1 N (I assumed it was 0.1/5=0.02 M)
H2SO4: 1N (probably 0.1M for H+)
KMnO4: 1N (0.2M MnO4- following the same steps)

In my conception, the activities of the reagents in the equilibrium constant were their initial concentrations, and the activities of the products were their equillibrium concentrations. I then made an ice table, considering a concentration of x. By replacing those values into the equilibrium constant, I obtained:
\begin{align*}
    K=\frac{5x^{5}*x}{0.02^{5}*0.2*0.1^{8}}
\end{align*}
X was supposed to be the concentration of Fe^{2+}, however the answer I got is definitely not the right one.
\begin{align*}
    x=6726501.235
\end{align*}

Where did I go wrong?


texts:
Is  the (200) plane of fcc crystal structure(the plane parallel to the face of unit cell and passing through the body centre of it) a close packed plane?

A close packed palne is a plane where the neighbouring atoms touch each other.
Eg: (100) of simple cubic
(111)of fcc

But in thiscase when i draw the plane, i got four half circles on the middle edges of the square, touching the atoms on each side. But, they donot touch the atom infront.
So, i have a doubt whether it is close packed?
Please explain.


texts: Gaussian parameters for IP and EA calculation

texts:
I have already calculated ionization potentials (IP) and electron affinities (EA) for a whole bunch of organic molecules (from around 20 to 25 heavy atoms, mostly carbon atoms, just a few oxygen or nitrogen atoms here and there). A few molecules are actually a little smaller (6 heavy atoms). I have scrupulously checked the geometry of each and every molecule using the following DFT parameters in gaussian 09:

# freq=noraman cphf=noread b3lyp/6-31g(d) geom=connectivity
 integral=grid=ultrafine scf=maxcycle=1000

and made sure that I got the stationary point in every case.

Then I follwed a published paper in which they applied Koopman's thoerem approximation using HOMO and LUMO energies as IP and EA values, respectively. My results look pretty reasonable in terms of comparing the molecular structures between themselves, and also in terms of the obtained experimental results from a biological system. However, I understand that one can always question the accuracy of a chosen computational method...

I would like to ask you if it would make sense for me to double check the computational results I got with a potentially more accurate method (basis set, functionals), and which one would you recommend in this case? It just so happens that I will have access to a pretty decent cluster (12 cores, RAM 12 GB, HDD 500 GB) with like 1000 hrs/core computation time.

Thanks in advance for any help you can offer.


texts: When you heat $\ce{NH4Cl}$ it decomposes into $\ce{NH3 + HCl}$ gases. My question is why does it decompose into ammonia and hydrogen chloride gases on the molecular level. Is it because in the $\ce{N-(HCl)}$ bond, The $\ce{N-H}$ bonds breaks easily since it requires only $\pu{390 kJ/mol}$ and $\ce{H-Cl}$ requires far more heat energy? Thus the $\ce{N-H}$ bonds breaks first?


texts:
I was under the impression that differences between the various long range electrostatic algorithms, ewald, PME, PPPM, to name a few, lied solely in their treatment of the reciprocal space term. Specifically, I thought all methods looped over a particles neighbor and summed q(i)*q(j)erfc(alphar)/r for the real space calculation. However, this is my impression, which I have yet to validate with others. I became confused when I recently read "Ewald summation techniques in perspective: a survey" whose equation 22 seems to have suggested a different way to calculate the short range potential. Could anyone else chime in here, and either tell me where I am wrong, or I am correct?

Thanks!


texts:
Will there be a hydride shift to form a tertiary carbocation or will it proceed as secondary carbocation?

My text book shows that it would proceed as secondary carbocation
But tertiary carbocation is more stable. I am a bit confused here.
Will someone please clarify?


texts: Magnetic moment of coordination complexes?

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To understand the commonly quoted magnetic values of coordination complexes (central ion) we use
$$m_l=\sqrt{n(n+2)} \text{BM where BM}=\frac{e\hbar}{2m_e}\text{JT}^{-1}$$
$n$=number of unpaired electrons.

How did we derive this equation?

I know the orbital angular momentum of electron is given by $\sqrt{l(l+1)}\hbar$, spin angular momentum is given by $\sqrt{s(s+1)}\hbar$ and the gyromagnetic ratio for electron is $$\vec \mu_B=\frac{-e}{2m_e}\vec L$$. There is also the "total" angular momentum given by $n_0\hbar$.

I fail to see how these magnetic moments and angular momentums are
 related, and how they can be added or related to get the corresponding
 values for an entire atom or a complex?.

I have also heard that the Lande g-factor is relevant here.

Key:-

$n_0$=principal quantum number, $l$=azimuthal quantum number,$s$=spin (half for an electron), $\hbar=\frac{h}{2\pi}$, $S=\Sigma s+1$(spin multiplicity), $\vec L$=angular momentum, $\vec \mu_B$=Magnetic moment.


texts: discover of the neutron, what happen to 2+ charge

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James Chadwik found the neutron by shoot α rays to a Beralium foil. α rays are equal to the He²⁺ and he saw that particles without a charge is out from that. He understood the neutrons are those particles without the charge.

But my question is this.

This is the equation that the chadwik found.

Be + He²⁺= C +neutron

In this equation the left side has a 2+charge, but in right there is no any charge. So, What happen to the 2+ charge when this reaction occurs?


texts:
Where did the description that acids are sour and bases are bitter come from? With Arrhenius definition, those descriptions may have fit acids and bases, but with the Lewis definition, I guess they would not really apply.

For example, $\ce{AlCl3}$, a known Lewis acid, does not taste sour but rather "gives water a bitter astringent taste" as stated by PubChem in this link.