texts: Predicting 260/280 of DNA or RNA from sequence?

texts:
I asked this in biology, but I think they don't want to deal with the chemistry behind UV-Vis.

My question has to do with the Poly A tails on mRNA. I've been doing in vitro transcription and tailing for a while now and have noticed that the untailed RNA has a 260/280 of about 2.0, like you'd expect, but successful tailing results in ratios from 2.15 to 2.45, with higher ratios correlating to better band shifts on agarose gels, implying a longer tail. I suspect the reason for this is because the adenine has a much higher 260/280 than the other bases, so if you add a lot of adenines to the 3' end of the RNA you add much more 260 absorbance than 280 absorbance.

After seeing this I tried to come up with a mathematical method to estimate tail length based on 260/280, since gels are annoying, while I can get the ratio directly from the nanodrop.

I started by using the 260/280 for each nucleotide, A: 4.50, G: 1.15, C: 1.51, U: 4.00, T: 1.47 source here: 1. I then took the sequence for the Luciferase gene I'm using for mRNA and counted the nucleotides, 449 A, 566 C, 470 G, 374 U. I tried to get the weighted average of the 260/280 for my RNA.

A: 449 x 4.50 = 2020.50
C: 566 x 1.51 =  854.60
G: 470 x 1.15 =  540.50
U: 374 x 4.00 = 1496.00
Sum:            4911.60

Nucleotides: 449 + 566 + 470 + 374 = 1859
Sum / Nucleotides : 4911.60 / 1859 = 2.64

2.64 is clearly not 2.0. Even accounting for the potential effect of pH and ionic strength on RNA 260/280 ( acidic solutions have lower ratios ) I can't explain why the calculated ratio is so high. Even if we assumed an RNA with 25% of each base, the weighted average is still (1.15 + 4.50 + 1.51 + 4.00)/4 = 2.79, even higher than for my real sequence.

Doing the same calculation for DNA, (1.15 + 4.50 + 1.51 + 1.47)/4 = 2.16.

So why don't my calculated ratios for RNA and DNA 260/280 match the "ideal" ratios of 2.0 and 1.8? It probably has something to do with base stacking interactions, but I don't enough to compensate for it.


texts: Electroplating boat hulls with ceramic like material containing copper oxide to prevent barnacles from sticking?

texts:
Calcium bentonite can be electroplated onto steel. After it is electroplated on to steel it has a rough and porous like surface that is very hard and tough.

If you were to electroplate a thin layer of calcium bentonite onto steel then brush on a thin coating of copper oxide. The copper oxide would stick to the surface and fill some voids because the calcium bentonite that was electroplated on to the steel is porous. Is it then possible to electroplate more calcium bentonite over top this copper oxide layer? And repeat the process so that you have layers that start with steel then calcium bentonite then copper oxide then calcium bentonite then copper oxide then calcium bentonite etc. The final layer could be smoothed out by sanding/grinding.

I know that most paint for boats use copper oxide to keep barnacles from forming but thot what if there were a more permanent or tougher/longer lasting solution to that problem that causes ships to waste massive amounts of fuel due to drag.


texts: How to calculate molecular dipole moment from a known wavefunction?

texts:
Say I have a molecular wavefunction as a set of molecular orbitals and want to calculate the molecule's dipole moment, but don't know how! I searched a lot but couldn't find any practical example.

$$\psi _i=\sum ^N_{i=1}C_i\mathrm e^{-\alpha _ir^2}$$


texts:
For a small group of small organic molecules, I would like to use Avogadro to display short intermolecular contacts directing their packing patterns; separately from normal Hydrogen bonding pattern.  For example, to indicate intermolecular C(aryl)-H interactions.

It is known to me that this may be achieved with the freely accessible software Mercury by the CCSD (described here), too.  Yet, both for the sake of consistency with other drawings already prepared, as well some curiosity if Avogadro equally may provide this, I whish to address the question here.  The sole contribution in the software's mailing list partially relevant to this topic (here), dating back 2013, exludes even the indication of non-classical H-bonds.

To solve this problem, both the "classical version" (currently 1.2.0), as well as the more recent version Avogadro² (1.90.0) were accessed.


texts: What are the molecular orbitals of the hypothetical linear H₃⁺ molecule?

texts:
What would be the wave function of the lowest energy molecular orbital of a hypothetical linear H3+ molecule?
According to the LCAO method, I feel the lowest energy MO will be 1s(A) + 1s(B) + 1s(C).
Where 1s(A) is the wave function of the 1s orbital of one of the Hydrogen atoms.
This has 0 nodes and has the lowest energy.

Isn't this correst?


texts: Why any other element except fluorine wouldn't take electrons from oxygen?

texts:
My teacher said that fluorine is more electronegative than oxygen thus it will take electrons of oxygen.

But now, why won't other Group 17 elements, like chlorine, bromine, iodine, would take electrons from oxygen? They too have just 7 electrons in their valence shells.

Technically, they should but yet they have lesser electronegativity and this is something that I'm not able to digest.


texts: When it rains, it puddles. Spilled salt cycles between wet and dry with humidity. Is this akin to a phase change?

texts:
I have some spilled un-iodized table salt (NaCl). It is very humid where I live, and when it gets very humid for a few days, the salt absorbs so much water that it becomes a puddle of (probably) saturated salt water. When the humidity drops for a few days, the water evaporates and I have dry salt crystals again. This is repeatable.

My questions about this process are:

What is this process called exactly? As far as I understand "deliquescence" is a property and not a process. Does the exchange of water between my pile of salt and the air have a specific terminology? Something that would go along with terms like evaporation, sublimation, condensation, etc.? Perhaps some mash-up of adsorption and dissolution?
Is this process akin to a phase change in some way? For example, if I had a sealed box of air with a dish of salt and a beaker of water, and I could ramp the  temperature slowly enough, would I see a plateau at a certain humidity as the salt hit a threshold and started absorbing water until saturated?

Some may be familliar with the Morton Salt logo and slogan "When it rains, it pours" meaning that other moisture-absorbing materials in the package will keep the sodium chloride as table salt from absorbing too much water and becoming stuck and un-pourable:

Source


texts: Sigma and pi symbols in molecular orbital theory

texts: In molecular orbitals diagram, sigma ($\sigma$) and pi ($\pi$) symbols are used. What do these symbols really mean?


texts: How to calculate the cation exchange resin capacity?

texts:
If I have a cation exchange membrane and need to remove 2 g/L of sodium, how much resin would I need.

I used the amount of substance of $\ce{Na}$ to calculate the amount of substance of $\ce{SO3H-}$ needed for complete sodium removal. But this will not give me the correct mass since the resin is a polymer with that functional group attached. However I haven't been able to find any kind of complete structures for a cation resin.


texts: POCP: How many ozone molecules can be created by one ethene molecule?

texts:
One ethane molecule can create two molecules of ozone, one ethanol molecule can create one molecule of ozone:

In the following table the POCP is twice as high for ethene than for propane:

From this fact I expect four molecules of ozone from ethene, but in my own formulated reaction mechanism I get only three ozone molecules:

How many ozone molecules can be created by one ethene molecule and if my proposed mechanism is wrong what is the correct one?


texts: Rationalise the Relative Reactivity of Borane and DIBAL as Reductants

texts:
In Clayden's Organic Chemistry (Second Edition) it is written that borane is useful in chemoselectively reducing the most nucleophilic carbonyl to its corresponding alcohol. It is later said that DIBAL reacts similarly and is useful in reducing esters to aldehydes, but that they will not proceed to the alcohol.

How are these differences in reactivity rationalised? I tried to draw analogies from the comparison of $\ce{LiAlH4}$ and $\ce{NaBH4}$ but since $\ce{LiAlH4}$ is the stronger reductant, I would have expected DIBAL to be the more reactive species!


texts:
I'm trying to compare the relative stability of two carbocations:
$$\ce{CH3-\overset{+}{C}H-Cl}\quad\text{vs}\quad\ce{CH3-\overset{+}{C}H2}$$
Does the $\ce{Cl}$ exert a +M effect to stabilise the carbocation, or does it exert a −I effect to destabilise it?


texts: Find the boiling point of a compound given a pressure

texts:
I need to find the boiling point (in degrees centigrade) of ethanol on a day when the atmospheric pressure is $780\text{ torr}$.

I know that the molar mass of ethanol is $46.07\text{ g/mol}$ but I have no idea how to continue. Can you tell me what equations should be used or how is it solved, please?

Thanks!


texts:
I'm currently studying the temperature dependence of the following cell: $\ce{Cu_{(s)} + 2Ag^{+}_{(aq)} <=> 2Ag_{(s)} + Cu^{2+}_{(aq)}}$ ($E^⦵ = \pu{+0.46 V}$)

Experimentally, I recorded the initial temperature of the cell at $\pu{273 K}$, before increasing the temperature of the cell and recording its potential each time. This nicely followed the equation:
$$E^⦵ = T\frac{\Delta S^⦵}{nF} - \frac{\Delta H^⦵}{nF}$$
Which apparently can be used to describe cell temperature dependence. It's worth noting that the activities of all species was 1.

The issue is that in retrospect, the entire experiment seemed kind of pointless, as it doesn't appear to actually tell me anything at all. Consider the following logic:

In a 'normal' equilibrium reaction, e.g. the Haber process, the reaction will proceed until it gradually reaches equilibrium, giving an equilibrium constant; let's call it $K_{1}$. Changing system temperature will shift the equilibrium until a new equilibrium is formed, with a new equilibrium constant $K_{2}$... And so on for each temperature change.

In a cell, this is not what happens. If we consider that $E^⦵$ is a 'guide' to equilibrium position, and assumed that the above was true, then changing temperature would've caused a new value of $E^⦵$ to equilibrate each time. However, we know it doesn't do this, as by definition equilibrium in a cell is when $E^⦵ = \pu{0 V}$. Therefore, this seems to me as though a cell will naturally reach equilibrium  with the same equilibrium constant at any temperature.

Thus, apart from giving me rather accurate, experimentally derived values for $\Delta H^⦵$ and $\Delta S^⦵$ (assuming that these parameters aren't temperature dependent, I know), what does the experiment actually tell me? I mean, the cell is predisposed to run to equilibrium and thus have an $E^⦵$ value of $\pu{0 V}$ regardless of temperature, so where does the temperature dependence come into it?

Furthermore, this makes it confusing to study how the reaction quotient (and equilibrium constant) varied with temperature:

It's logical to extrapolate the graph and find the temperature at which equilibrium is apparently achieved; but as discussed, it doesn't work like that.
It's also logical to calculate both parameters at each temperature (which appears to fit nicely as my calculations show that $\log K$ decreases with temperature, vice versa for $\log Q$) and finding the point where $\log K = \log Q$ would surely give me the temperature at equilibrium; but again, as discussed it doesn't work like that, mainly because 'equilibrium' results in $E^⦵ > 0$

So is there any simple way to determine how the reaction quotient changed with temperature?


texts: How can you predict relative Rf values of cis-trans isomers in thin layer chromatography?

texts:
This is a "homework" question.

I'm writing up a lab in which we synthesized 1,4-diphenyl-1,3-butadiene. We analyzed the products using TLC with 4:1 Hexane:Ethyl Acetate as the solvent.

One of the isomers has a larger Rf value than the other (0.83 and 0.95).

I'm having trouble understanding how to figure out which of the isomers is which on the TLC. I know more polar compounds are going to have a lower Rf, like cinnamaldehyde.

My best guess is that, although the all the double bonds are conjugated, the phenyl rings have a higher electron density than the rest of the molecule. Since the trans,trans isomer is essentially symmetrical, it has little or no molecular dipole. The cis,trans isomer has a small molecular dipole because it is asymmetric. Therefore the cis-trans isomer has more affinity for the stationary phase (giving it the Rf value of 0.83).

Am I on the right track here?


texts: Why is ligand substitution only partial with copper(II) ions and ammonia?

texts:
When studying ligand substitution (at UK year 13 level), the following example has been given:

\begin{align}
\ce{[Cu(H2O)_6]^2+ + 2NH3 &<=> [Cu(OH)_2(H2O)_6] + 2NH4^+}\\
\ce{[Cu(OH)_2(H2O)_4] + 4NH3 &<=> [Cu(NH3)_4(H2O)_2]^2+ +2OH- +2H2O}\\
\end{align}

There has been no explanation given of why the substitution is only partial, whereas the substitution of, say, $\ce{[Co(H2O)_6]^2+}$ is complete.

To me, it seems that this partial substitution wouldn't be favourable, as it produces a slightly distorted octahedral shape, which is less stable than a regular octahedral shape, surely? Moreover my textbook states ammonia is a better ligand than water, so why would $\ce{NH3}$ not replace those final two aqua ligands?


texts: How to remove wash anthracene oil/creostae oil from stainless steel tanker?

texts:
I once loaded anthracene oil/creosate Oil in my stainless steel tanker and I had to transport it to some factory. The material was inside the tanker for throughout the journey that was of around 8 days.

The material got unloaded at the said factory. However I had another order to load Formaldehyde from the same city. I took my truck to the usual tanker service station to wash the tank with Detergents/water/diesel/scrubbing and everything which is quiet a normal procedure after and before any other liquid chemical.

However I have never had trouble with washing any other material as much as I am having with anthracene oil/creosote oil. It just doesn't seem to come off , the servicing person had severe respiratory problem when he went inside the tank.

Even after washing with several detergents, fast water streams and other things... the chemical is just not leaving the surface of my tank. One more thing, I think the service would have been much easier if the fumes/gas inside the tanker weren't so strong and scorching to the skin of the service person. He straight away told us to never come back with the same material.

Kindly let me know how to make sure to remove the essence of the gas/fumes left in the tank due to 8 days of material in the tank, how to remove the material from the surface of the tank and how to make this process well by using any other chemicals.


texts: Why do some chemical reactions lead to less stable state?

texts: If the universe is always trying to find a more stable energy state, then how do reactions take place that lead to a less stable state e.g. the formation of ammonia from extremely stable diatomic $\ce{N2}$ molecules?


texts:
I am attempting to interpret an experimental section on a scientific paper. The paper calls for 0.51 mmol of 3,5-dimethoxy phenol, 1.0 mmol of 3-methyl-3-butenal, 5 mol% of phenylboronic acid, 20 mol% of benzoic acid, and 2.5 mL of heptane. I am trying to figure out what is meant by mole% in this case. There are many different interpretations of this I have seen online, including mole percent being based on a fraction of the limiting reagent (the phenol in this case), the mole percent being based on the fraction of all of the total moles of reactant and catalyst (most fitting of the definition of mole percent), and the mole percent being based on all of the moles of reactant, catalyst, and solvent. It makes most sense that the mole percent for this protocol would be based on the limiting reagent, but I included the calculations based on the total moles of reactants and catalysts for reference. Does anyone know what the term "mole percent" would appropriately based on in this case?

0.51 mmol (phenol der.) + 1.0 mmol (aldehyde) + x mol PhB(OH)2 + y mol PhCOOH = z total mol

0.2 z (total mol) = y mol PhCOOH
0.05 z (total mol) = x mol PhB(OH)2

0.51 mmol (phenol der.) + 1.0 mmol (aldehyde) + 0.2z + 0.05z = z total mol
0.75z = 1.51
z = 2.013

0.2 (2.013) = 0.40 mol benzoic acid
0.05 (2.013) = 0.10 mol phenyl boric acid

If the mole percent was based on the moles of the LR, the moles of catalyst would be as follows:
0.10 mol benzoic acid and 0.026 mol of phenyl boric acid


texts: If hydrogen bonds are chemical bonds, and these bonds are broken when water changes phases, why doesn't this classify as a "chemical" change?

texts: This is more of a terminology question. How are phase changes considered a physical property, not a chemical property when hydrogen bonds break. A chemical property can only be observed during a chemical change. Aren't hydrogen bonds a type of chemical bond, and those bonds are being broken during a phase change from ice to liquid water, for example. I understand that no intramolecular bonds are being broken. Water molecules remain intact. But we teach that a chemical bond has to break during a chemical change, but phase changes are considered to be physical.


texts: Why are the concentrations in the equilibrium constant multiplied?

texts:
$$\alpha\,\mathrm{A}+\beta\,\mathrm{B}+\cdots\rightleftharpoons \rho\,\mathrm{R}+\sigma\,\mathrm{S}+\cdots$$
The equilibrium constant for this reaction can be calculated using the following formula:

$$\mathrm K_c = \frac{{{[\mathrm{R}]}}^\rho {{[\mathrm{S}]}}^\sigma ... } {{{[\mathrm{A}]}}^\alpha {{[\mathrm{B}]}}^\beta ...}$$

In this formula for the equilibrium constant of a reaction, why are the quantities R and S (and likewise A and B) multiplied?

I understand the equilibrium constant to be a ratio of the amounts of the products and the amounts of the reactants. But if this is the case, wouldn't a formula like $\mathrm K_c = \frac{[\mathrm{R}] + [\mathrm{S}] ... }{[\mathrm{A}] + [\mathrm{B}] ...}$ make more sense? I think this question is really a result of not understanding the meaning of the equilibrium constant.


texts: Do all metal nitrates give nitrogen dioxide on decomposition?

texts:
Some metal nitrates decompose to give nitrites: $\ce{2MNO3 -> 2MNO2 + O2}$

whereas some metal nitrates decompose to give $\ce{NO2}$. A possible reaction is $\ce{M(NO3)2 -> MO + NO2 + O2}$
Based on my observation my question is that, is it true that all metals (including transition metal) nitrates decompose to $\ce{NO2}$ apart from $\ce{[Na , K, Rb, Cs]}$ (alkali metals which give nitrites instead) ?


texts:
How easy is it to produce kevlar?

What are/is the chemical recation/-s to produce kevlar, and which chemical compounds are required?


texts:
Can $\ce{PCl5}$, phosphorus pentachloride, react with an amide?

I saw a reaction where the corresponding cyanide was formed in this process. What other reagents could do the same?


texts: Steady state approximation rate equation for an E1cB reaction

texts:
Is anyone able to explain why species 'D' is not included in the steady state approximation derivation for this E1cB reaction?
The correct rate equation in the image has been derived first and then I have added in the line I am confused about below
Thanks!


texts:
Discussing an article with friends we began discussing whether a protein complex that punches holes in cells (membrane attack complex) would be considered a machine.

Now, my friends are biochemistry students while I am a computer science student so this is far from my expertise. In my imagination this would be a mechanical action, hence the definition of a machine found on Wikipedia.
My friends counter argument is more of an emotional one, saying it feels wrong to call it a machine but also couldn't come up with a better word.

So:
Is it a machine? Is it something else? Or is a complex just a complex?
Does chemistry/biology have its very own definitions for things that do stuff in coordination without being "alive"?


texts: Is sulfuric acid still hazardous after it dries?

texts:
One of our housemates decided to pour battery electrolyte (which is 30-40% sulfuric acid) into a motorcycle battery on our back porch next to our laundry washer and dryer.  He did so extremely sloppily, and we don't know exactly what he might have spilled the acid on.

Is the acid safe to touch after it dries, or is it still a safety hazard?

If it isn't safe when dry, what can we do to neutralize the acid?  I know baking soda can neutralize acid, but I'm not really sure how to easily coat an entire porch in baking soda.

My boyfriend suffers from severe, debilitating OCD with a chemical contamination obsession, so this is an absolute nightmare for him.  Thank you in advance for any help you may have!


texts: How to write the last cell reaction for the following cell?

texts:
Consider the following electrochemical cell:
$$\ce{Zn|Zn^{2+}}(0.1~\mathrm{M})||\ce{Zn^{2+}}(0.01~\mathrm{M})\ce{|Zn}$$ How should I write the overall cell reaction for this cell? I can identify the oxidation and reduction reactions but when they are added, all the species cancel out, leaving my with no overall equation.

Anode: $\ce{Zn -> Zn^{2+} + 2e}$

Cathode: $\ce{Zn^{2+} + 2e -> Zn}$


texts: Why will a strong base neutralize as much acid as a weak base?

texts: I don't understand how the volume of 0.200 M NaOH needed to neutralize 250.0 mL of 0.010 M HCl (0.0125 mL) is the same volume of 0.200 M NH3 that would be needed to neutralize 250.0 mL of 0.010 M HCl.


texts: Best oxidizing and reducing agents: Na, Zn^2+, Ba, Ba^2+, and Ag?

texts:
Which is the best oxidizing agent and the best reducing agent from the species listed below?

$\ce{Na,~Zn^2+,~Ba,~Ba^2+,~Ag}$

I determined that oxidizing agent as $\ce{Zn^2+}$ because it appears on the table with the most positive reduction potential and determined that $\ce{Ba^2+}$ as the best reducing agent because it has the most negative reduction potential. I am not sure of my answer.


texts: Why do the protons in pentacarbonylmethylmanganese show up at –0.21 ppm?

texts:
The $\ce{^1H}$ NMR of $\ce{Mn(CO)5CH3}$ shows a resonance at –0.21 ppm, which has to be due to the methyl group. Why are the protons so shielded?

I would have thought that all the pi backdonation from the Mn to the carbonyl would reduce the electron density on the $\ce{CH3}$, hence increasing the chemical shift.


texts: Redox reaction with hydrogen peroxide with potassium iodide

texts:
I think I've managed to write down the correct reaction:

$$\ce{H2O2 + KI + H2SO4 -> K2SO4 + I2 + H2O}$$

Now I need to balance this using the ion-electron method in an acidic environment.

Normally this is no problem, but I'm a bit confused on how to work with the reduction of $\ce{O}$ from $\ce{-I}$ to $\ce{-II}$ and I'm not sure how to write down the total ionic equation. I've tried the following:

$\ce{2H^{+1} + O_2^{-2} + K^{+1} + I^{-1} + 2H^{+1} + SO_4^{-2} -> 2K^{+1}  +SO_4^{-2} + 2I^{} + 2H^{+1} + O^{-2}}$

But I'm not sure if that is correct, and if it is correct, I'm not sure what to do from here.

After this reaction and after diluting (with water?), I also need to know what will happen if I add a few drops of a starch-solution (I will actually have to perform this experiment so if it's merely something visible and not necessarily related to the reaction, then this part is less important.)

The final question is "what property of $\ce{H2O2}$ is demonstrated here?" and I suppose the answer to that is it's function as an oxidizer?


texts:
There was an exercise in my textbook asking to compare the dipole moments of 1,1-dibromoethene and 1,2-dibromoethene(Z). The answer in the textbook says that the dipole moment of 1,1-dibromoethene is greater than that of 1,2-dibromoethene.

This seems counter-intuitive as the angle between the dipole moments of the two $\ce{C-Br}$ bonds in 1,1-dibromoethene is $120°$ and that in 1,2-dibromoethene(Z) is $60°$. A little physics tells us that the net dipole moment of 1,2-dibromoethene should be greater than that of 1,1-dibromoethene which contradicts the answer in the textbook. I want to know whether I am correct or not.


texts: Molar enthalpy vs Enthalpy of formation?

texts:
(Note I've refocused a previous unanswered question into a more general question. You can find the original much more specific question here)
There seems to be two main ways of looking at the enthalpy of substances: molar enthalpy and heat of formation. What are the differences/advantages and disadvantages of each and are either one or more or less suitable for different purposes?


texts: Oxidizing properties of sulfuric acid: can it oxidize hydrochloric acid to chlorine?

texts:
Can $\ce{H2SO4}$ oxidize $\ce{HCl}$ to $\ce{Cl2}$? I know that $\ce{KMnO4}$ can do it, but my question is considering $\ce{H2SO4}$. In sulfuric acid, sulphur is in +6 oxidation state and in $\ce{KMnO4}$, manganese is in +7 oxidation state. But sulphur is more electronegative than manganese, so I guessed that, $\ce{H2SO4}$ should be equally good oxidizing agent as $\ce{KMnO4}$.
However, I got to know that $\ce{KMnO4}$ can oxidising $\ce{HCl}$ to $\ce{Cl2}$ but $\ce{H2SO4}$ can't. Why it is so? I would also like to know which one has more oxidizing power and why?


texts:
Can Tert-butoxide displace bromide via SN2 reaction? I read that Tert-butoxide is bulky and has steric hindrance, even with primary substrates. How is this reaction (picture below) possible?

Source: Levy, Arrow pushing in Organic Chemistry


texts: Dissociation rates: trans-effect rule in square planar complexes

texts:
In lecture, the trans-effect was described.

A ligand $L^t$ with a higher trans-effect as $L$ (cis to $L^t$) leads to a faster dissociation of ligand $L^d$ (trans to $L^t$). I would expect that the attacking ligand $B$ is needed to make a stronger bond as the leaving ligand $L^d$ did.

In order to see if these assumptions are always valid in planar quadratic systems I've set up following problem according to the given trans-effect order:

$\ce{CO}$ has a stronger trans-effect as $\ce{CH3-}$ and therefore the ligand trans to $\ce{CO}$ will be exchanged faster as trans to the $\ce{CH3-}$. But the leaving group $\ce{I-}$ would also have a higher trans-effect as $\ce{Cl-}$ so I wouldn't expect a substitution in b). Are these statements correct?


texts: When to use iso and sec while naming compounds in alkyl halides?

texts: I am having confusion on when to use iso- or sec- while naming the alkyl halides?


texts:
My current understanding of orthogonal wavefunctions is: two wavefunctions that  are perpendicular to each other and must satisfy the following equation: $$\int\psi_1\, \psi_2\, \mathrm{d}\tau =0$$

From this, it implies that orthogonality is a relationship between 2 wavefunctions and a single wavefunction itself can not be labelled as 'orthogonal'. They must be orthogonal with respect to some other wavefunction. However I have seen some textbooks refer to single wavefunctions as being orthogonal.

Am I missing some crucial thing in my definition of orthogonal wavefunctions? Could anyone provide me with a more complete definition of orthogonal wavefunctions from a chemistry point of view?


texts: Why does the test tube face downwards in gas production?

texts: In the preparation of $\ce{NH3}$ from $\ce{NH4Cl}$ and $\ce{Ba(OH)2}$, my teacher said that when heating the test tube, the test tube faces downwards as opposed to upwards. Why is this so? Wouldn't the solid just fall out?


texts: How to apply the Heisenberg Uncertainty Principle in calculations on the movement of bacteria?

texts:
In this problem, I know the formula, but I get confused with all the steps and how to use what I got, to get to what I need.

A student is examining a bacterium under the microscope. The E. coli bacterial cell has a mass of $m = \pu{0.100 fg}$ (where a femtogram, $\pu{fg}$, is $\pu{10^{−15} g}$) and is swimming at a velocity of $v = \pu{9.00\mu m/s}$, with an uncertainty in the velocity of  $9.00\%$. E. coli bacterial cells are around $\pu{1 \mu m}$ ($\pu{10^{−6} m}$) in length. What is the uncertainty of the position of the bacterium?

I used the formula $$\Delta x \Delta p \geq \hslash/2$$
I plugged in these numbers:

Mass of bacteria $(m) = \pu{0.100 fg} = \pu{0.1 \times 10^{-15} g} = \pu{10^{-16} g}$
Velocity of bacteria $(v) = \pu{2 m/s}$
Uncertainty in velocity = 9.00

I am getting this answer $1.67\times10^{-9}$, and it is wrong. I don't know what I am doing wrong.


texts: Standard Gibb's Free energy change, standard state and equilibrium

texts:
I just want to confirm if I am right in thinking that:

statement: When a reaction in standard state is in equilibrium, then equilibrium constant K=1

Reason: since in a equilibrium, $Q=K$ and $ΔG=0$. Now since compounds are in their standard states $ΔG^{0}=0$ too, so by $ΔG=ΔG^{0}+RT\ln K$ → K=1.

statement: If a reaction is in equilibrium but compounds are not in their standard states, then $ΔG^{0}≠0$. Thus, $K≠1$ always.

Please confirm this thought-process.


texts: Who figured out that different isotopes have different numbers of neutrons?

texts: I reasearched about the history of the discovery of neutrons and couldn't find who found out that isotopes are a change in the number of neutrons. Can you please tell me who it was that made this discovery?


texts: Can the hydroxyl group of 4-hydroxybenzoic acid react with phosphorus pentachloride?

texts:
I learned that, a phenol will not react (or react very slowly) with $\ce{PCl5}$ due to its stabilized structure.

How about the $\ce{-OH}$ group on the benzene ring of 4-hydroxybenzoic acid? Will that $\ce{-OH}$ group react with $\ce{PCl5}$? If the answer is yes, is it anything to do with the $\ce{-COOH}$ group?


texts: How do we calculate the partition coefficient (including titration)

texts:
In a separating funnel we add $\pu{25.0 mL}$ of $\pu{8.5 M}$ $\ce{HCl}$ solution. We also add $\pu{25.0 mL}$ of a tributyl phosphate solution. We shake the funnel for 1 minute and then after the two phases have separated we remove the lower phase.

We add in the same separating funnel $\pu{23.0 mL}$ of the same $\pu{8.5 M}$ $\ce{HCl}$ solution and we also add $\pu{2.00 mL}$ of $\pu{0.5 M}$ $\ce{ZnCl2}$ solution. We shake the funnel again and we remove the lower phase. Now the biggest concentration of zinc is in the organic phase.

We add in the separating funnel $\pu{20.0 mL}$ of deionized water. We shake the funnel and now the zinc comes back again the aqueuous phase. After the two phases have separated, we transfer the aqueous phase to a volumetric flask. We repeat the previous step 2 more times and we collect the aqueuous phase in the same volumetric flask. In a conical flask, we add $\pu{25.00 mL}$ of the volumetric flask, we add $\pu{75 mL}$ of deionized water and $\pu{3 mL}$ of a buffer and also drops of an indicator. We titrate this with EDTA solution.

Now we want to calculate the partition coefficient using these formulas;
$D_\ce{Zn}$ is the distribution coefficient.
$C_\ce{{Zn}_{org}}$ and $C_\ce{{Zn}_{aq}}$ are the concentrations of zinc in the organic and aqueous phases respectively.

$D_\ce{Zn}=\dfrac{C_\ce{{Zn}_{org}}}{C_\ce{{Zn}_{aq}}}$

If $n$ denotes amount, then

$n_\ce{{Zn}_{org}}=\pu{0.0100 mmol//mL}\times V_\mathrm{EDTA}\times 4$

$n_\ce{{Zn}_{total}}=\pu{0.0100 mmol//mL}\times V_\mathrm{{EDTA}_{total}}\times 4$

$n_\ce{{Zn}_{aq}}=n_\ce{{Zn}_{total}}-n_\ce{{Zn}_{org}}$

I get confused about what the difference between the $V_\mathrm{EDTA}$ and the $V_\mathrm{{EDTA}_{total}}$ is.


texts: Most stable resonating structure of 1-nitro-4-nitrosobenzene

texts:
The most stable resonating structure of 1-nitro-4-nitrosobenzene is:

In my view since in each case we have 4 charges and except in case 1 all have complete octets, so 1 is neglected. However, I am facing difficulty in eliminating other two in order to get the desired answer. I noticed that in case 3 it is in conjugation (alternating single and double bonds).


texts: Starch gelatinization, retrogradation and disgestability

texts:
Over on the sub-reddit on prebiotics we're a bit stumped on figuring out the process for turning raw potato starch (mainly containing R2 resistant starch) into R3 via retrogradation/gelatinization. The best thing we have found so far on the topic is this article, which is quite a bit too technical for us (e.g. what's melting enthalpy?) and doesn't fully answer our questions.

I myself had a haphazard go at it, boiling water with potato starch for an extended period of time (sorry, don't have exact ratios or times) and then leaving it in the fridge for 3 days. The end result was large chunks of a milky-clear substance of soft-gummybear consistency (can be picked up and lightly squeezed without loosing form or oozing) that will not disolve in water. My personal question is: what is the substance described here and what's could be assumed its digestibility?

For the r/prebiotics reddit in general, the question is what process should be be used by a layman to turn raw potato starch powder into either gelatinized and or retrograded starch (assuming here they're different). I presume the variables we need are water/starch ratio, mixing technique, heating temperature, lenght of heating, cooling temperature and cooling time.

Thank you in advance and for your time.


texts: Why is chloroethene said to be a conjugated system?Is it because of p orbitals present in chlorine or something?


texts:
One mole of benzene at $\pu{20^\circ C}$ is adiabatically mixed with 2 moles of toluene at $\pu{40^\circ C}$. The heat capacity of benzene is $\pu{84 J K-1 mol-1}$ and the heat capacity of toluene is $\pu{96 J K-1 mol-1}$. If benzene and toluene form an ideal solution, compute the entropy change for the process.

I tried to use

$$\Delta S = n C \ln{(T_\mathrm f/T_\mathrm i)}$$

where $C$ is the heat capacity and $T_\mathrm f$ and $T_\mathrm i$ are the final and initial temperatures of the liquids, respectively. However, I am unsure of what the final equilibrium temperature of the mixture comes to.


texts: Is bicyclo[1.1.0]butane chiral? I think it isn't, but if one of the hydrogen atoms bound to the tertiary or secondary carbon atoms is replaced with e.g. chlorine, the formed compound will be chiral, right?


texts: Can non-deuterated solvents be used for 13C-NMR (and in fact other nuclei)?

texts: Basically, my question is can you used a non-deuterated solvent for 13C NMR? I'm thinking that there might be some problems with locking?


texts: What criteria have to be met to term a carboxylic acid a 'fatty acid'?

texts:
So we were doing the chapter Biomolecules in class the other day, and my teacher told us that every carboxylic acid that consists of an aliphatic chain and a total carbon atom count that's four or more, is a fatty acid.

Now owing to my teacher's (rather annoying) habit of grossly over-simplifying things, I decided to look up 'fatty acids' in my trusty Oxford Science Dictionary (printed in 2003). According to it,

  Chain length ranges from one hydrogen atom (in methanoic acid) to nearly 30 carbon atoms.

But a quick Wikipedia search, gives me this:

  Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms, from 4 to 28.

So now I'm completely lost. Fine, chuck what my teacher said, but the other two sources seem to contradict each other. So I'd really appreciate it, if someone can help me get the following straight (I'd prefer a reliable source, if you're citing anything):

Q1: What is the minimum number of carbons in a carboxylic acid as a whole (includes the carboxyl group)? So is methanoic acid or butanoic acid that's the smallest fatty acid?

Q2: Is there an 'upper limit' on the total carbon atom count for fatty acids? As in; can I synthesize, say, an 80 carbon aliphatic carboxylic acid and still correctly call it a fatty acid?

Q3: Is there any other criterion that's necessary to classify something as a fatty acid that hasn't been mentioned by my teacher or the other sources? If so, what is it?


texts: How does the catalyst in a polyester resin or epoxy work?

texts:
I would like to understand how the polyester resin or epoxy catalyst works and to what degree it must be mixed with the base material in order to be effective.

Typical product instructions advise to thoroughly mix the catalyst for a specified period of time.

How thorough does this really have to be in order to have the material cure properly? Is the mixing done just to initiate a thermosetting behavior and does that just continue to propagate heat to the rest of the material to complete the curing of the entire mass? If this is the case, wouldn't the base material cure if it were heated sufficiently without the presence of a catalyst?

Or is something else happening when the catalyst begins the cure? And how does mixing effect the quality of the cure?


texts: How do I evaluate the PV term when calculating a change in enthalpy?

texts:
As we know enthalpy is defined by the equation $H = E+PV$.

Now to calculate this $PV$ factor for $\Delta H$, Sometime we take $P \Delta V$ and sometime $P_2V_2-P_1V_1$. Why are there so many different approaches?

I am also confused whether $P$ is external pressure or internal pressure.


texts: Suppose we have a non-dipolar molecule such as carbon dioxide. If carbon dioxide is ionized by some means in the gas-phase, will it develop a dipole moment? I am asking with reference to microwave spectroscopy, because the selection rule requires the presence of a permanent dipole moment. In the interstellar space,  $HCO_2^+$ has been detected and it does have a microwave spectrum, because it does have a dipole moment. However, carbon dioxide's dipole moment is zero, so its ordinary microwave spectrum does not exist. There are very weak lines due to its quadrupole.


texts: I am trying to synthesize 1-(2-amino-4-chlorophenyl)ethan-1-one from benzene. The answer I came up with is that the benzene must undergo nitration first, then halogenation, then hydration for $\ce{NO2}$ to be $\ce{NH2}$, then acylation. But from the readings I've made acylation cannot happen with $\ce{NH2}$. Is there another way to synthesize this to benzene?


texts: Why does sp hybridised orbital have more directional character than p orbital?

texts: It states so in my textbook. But since s orbital is non directional, shouldn't sp hybridized orbital be less directional in character than p orbital?


texts: Turns in beta-alpha-beta loops (protein motifs)

texts: In the context of protein secondary structure, do the loops between strand and helix in a beta-alpha-beta motif form into the conformation known as a beta turn?


texts: Why do unboiled eggs last longer than boiled eggs?

texts: Just like the title says, I watched this video https://youtu.be/CHMY4G9gTPA and then became intrigued.


texts: Why should all the acid be used up when making zinc sulphate crystals?

texts: So to make zinc sulphate crystals you add granulated zinc to heated sulphuric acid. However, you have to make sure all the acid is used up and you know so when the zinc stops reacting and producing bubbles "hydrogen". You then filter out the solution and set it on a water bath to crystallise it. The question is : if all the acid is not used up in the reaction, what will happen when I start to evaporate the solution of zinc sulphate?


texts: Does 2,2-dimethylpropan-1-ol give a positive Lucas test?

texts:
I learnt that the Lucas test involves the formation of a carbocation and it gives a positive test based on the stability of the carbocation formed, and hence primary alcohols do not show turbidity (condition for positive test).

Now consider 2,2-dimethylpropan-1-ol. It is a primary alcohol and I was taught that it will not give a positive Lucas test. But my doubt is, why won't a methyl shift take place making it stable and hence give a positive result?


texts:
Why are Pd and Pt completely soluble in Cu, but Ag only partly in Cu when forming a substitutional solid solution? If we look at the Hume-Rothery rules, they all are within the 15% atomic radius factor with respect to Cu and all have the same crystal structure:

+----+---------------+-----------------+-------------------+---------+
|    | Atomic Radius | Crystal Struct. | Electronegativity | Valence |
+----+---------------+-----------------+-------------------+---------+
| Cu | 0.1278        | FCC             | 1.9               | +2      |
| Pd | 0.1376        | FCC             | 2.2               | +2      |
| Pt | 0.1387        | FCC             | 2.2               | +2      |
| Ag | 0.1445        | FCC             | 1.9               | +1      |
+----+---------------+-----------------+-------------------+---------+

The last two rules are:

The solvent and solute should have similar electronegativity. Intermetallics tend to form when the difference is large.
Other factors being equal, a metal will have more of a tendency to dissolve another metal of higher valency than of a lower valency.

Then Pd and Pt have an electronegativity difference of 0.3 while Ag has 0.
Pd and Pt have same valency while Ag has one less.

I would have expected that Ag would form a complete solid solution while Pd and Pt would only partly form a solid solution with Cu because difference of 0.3 in EN is quite large, because the valence difference between Ag and Cu is only 1 electron and because of the words: 'Other factors being equal,' it sounds like the other rules are more important.

To sum up, my thought process was:

Pd, Pt and Ag meet rule 1 and 2. Pd and Pt don't meet rule 3, so only form partly solid solutions. Then Ag meets rule 3 and rule 4 is less important and yet it is still close, so Ag will completely dissolve in Cu.

Why is this thought process wrong? If a difference in EN of 0.3 isn't big, what is then the border? Like 15% is the border for rule 1?


texts:
The atomic mass (ma) is the mass of 1 atom of an element.
Elements have isotopes.
Therefore, there must be an atomic mass (ma) associated with each isotope of an element.
How do we know the atomic masses of the isotopes of an element?
https://www.ciaaw.org/atomic-masses.htm

The link above shows atomic mass (ma) data.
How was this data generated?

Also, I have come across the atomic mass constant (mu). It has a value of 1.6605402(10) x 10^-27.
How do I obtain this value? i.e. How was this number derived?
Thank you.


texts: Why is methyl group more electron-donating than tert-butyl group?

texts: As title says, why is methyl group more electron-donating than tert-butyl group? The context behind this is stabilization of conjugate base. (http://www.khanacademy.org/science/organic-chemistry/organic-structures/acid-base-review/v/stabilization-of-conjugate-base-iii look at 10:51)


texts: Why does the 3rd electron shell start filling up with scandium?

texts:
The electron configuration of calcium is 2, 8, 8, 2, where up to that point each shell, asides from the first shell counts up to 8 - why then does scandium have an electron configuration of 2, 8, 9, 2?

What causes the 3rd shell to start filling up, rather than the fourth?


texts:
Recently concerned with health effects by common chemicals existent in food I've been rather busy reading article after article; and just an interesting one came around:

  Acrylamide (or acrylic amide) is a chemical compound with the chemical formula $\ce{C3H5NO}$. Wikipedia

  Some evidence suggests exposure to large doses can cause damage to the male reproductive glands. Acrylamide is considered a potential occupational carcinogen by U.S. government agencies. Still wikipedia

  A series of case-control studies have investigated the relationship between dietary intake of acrylamide and the risk of developing cancers of the oral cavity, pharynx, esophagus, larynx, large bowel, kidney, breast, and ovary. These studies generally found no excess of tumors associated with acrylamide intake. Cancer.gov

Well, though the references are generally controversial, you can conclude that though nothing is proven by the studies, take care:

FDA: States that acrylamide is a carcinogen of animals, is a human concern, but "should I worry when eating high-temperature fried or roasted food?" "NO."

Food standards agency: Lab proves acrylamide a carcinogen, but real life didn't give up many victims, though this isn't a new issue.

Along with researches done by FAO and WHO, still the carcinogenic concerns aren't very serious.

As a chemist, what reasons would you have provided that acrylamide is carcinogenic or not? Should I really worry about it when I eat french fries?


texts: Aromaticity of 1,1'-bi(cycloprop-2-en-1-ylidene) and 1,4-dioxine

texts:
Are these Anti aromatic/aromatic or non aromatic?

1.

Here, if we were to consider the resonating structure(s) with charge separation

One ring is aromatic and other is anti aromatic, and secondly there is not continuous delocalization of pi electrons between those rings {if we don't include no resonating structures with no formal charges, as their contribution would not be equalish to normal form} what category would this go in?

2.

Like before, there can be no continuous electron delocalization like stated in previous example , only other ones the diff forms of

If we consider it to have enough delocalization, it would have 4n electrons and hence antiaromatic {although all the orbitals wont be mixed as 3 on each side twice with oxygen's lone pair being common between all of them}

As we can see in pyrene, if we consider central double bond to be non participating, huckle rule works, is there a better (and just by observation by eye) method that we could use for multi ring systems? what is the basic condition for aromaticity besides planar,cyclic,sp2 {nitrogen and oxygen in general change their hybridisation as to make it aromatic with their lone pair(s)}


texts: Why is phosphoric acid preferentially used for dehydrating alcohols during synthesis of alkenes?

texts: I have also seen concentrated sulphuric acid being used, but what makes phosphoric acid preferable to sulfuric acid?


texts: A titration mixture having pottasium oxalate and pottasium hydrogen oxalate!

texts:
I came across this question, this is how it goes-

A solution is prepared by dissolving a solid mixture of $\ce{K2C2O4}$ and $\ce{KHC2O4}$. A $\pu{10 ml}$ portion of this solution required $\pu{10 ml, 0.05 M \ce{KOH}}$ solution for titration reaction. In a seperate analysis $\pu{10 ml}$ of the same stock solution required $\pu{10 ml, 0.06 M}$ acidified $\ce{KMnO4}$ solution for titration.

I  have  to  find the ratio of $\ce{K2C2O4}$ to $\ce{KHC2O4}$ in the initial reaction mixture.

I know that(I think), 1 mole of $\ce{KHC2O4}$ would require 1 mole of of $\ce{KOH}$ for neutralization. While $\ce{K2C2O4}$ would not react with $\ce{KOH}$ (please correct me if I am wrong).

Also, $\pu{31.8 g}$ of $\ce{KMnO4}$ would oxidise $\pu{63.5 g}$ of $\ce{K2C2O4}$. But when I don't know how (differently) it shall oxidise $\ce{KHC2O4}$.


texts: How does adding acids (H+ ions) to limited soluble salts help it further dissolve?

texts:
For example, adding $\ce{HCl}$ to the very insoluble $\ce{CaF2}$ will help it further dissolve. How?

I believe the concept deals with equilibrium and Le Chatelier's Principle:

$$ \ce{ CaF2 <=> Ca^2+ + 2F^-} $$

Does adding $\ce{H+}$ react with the $\ce{F-}$, which shifts the equilibrium to the right-hand side and therefore further dissolve the salt?


texts: Why do reusable heat packs have a limited time frame before the reaction becomes irreversible?

texts:
I have two "rechargeable" heat packs which from my understanding operate on the phase change
$$ CH_3COONa_{(aq)} \rightleftharpoons CH_3COONa_{(s)} + \Delta H.$$
Triggering the crystallization releases heat, and leaving them in boiling water returns it to its supersaturated form. The packs say if they are left in solid form for more than two months, they may not be able to return to aqueous form. I left one solid for many months, and sure enough, I couldn't quite redissolve the crystals. It gets 90% dissolved, but the remaining crystals just trigger the forward reaction as the pack re-cools, even after multiple attempts. What mechanism prevents this?


texts: How to measure and transfer sticky solids

texts: What is the best way to measure and transfer a sticky compound in the lab, in particular for air/moisture sensitive reactions? I have a really sticky solid Wittig salt which I'm going to use in a Wittig reaction.


texts:
Why do azimuthal quantum numbers have a value lesser than Principal Quantum number.
example-
if n=1
it will have subshell "s" as 0


texts: How do you calculate the concentrations of multiple reactants in a certain point in time?

texts: For $\ce{A + B -> C + D}$, given that $v = k [\ce{A}] [\ce{B}]$. I know the derivation for $\ce{A->B + C}$ , being $\ln[\ce{A}]=\ln[\ce{A}]_0−νkt$, but I'd like to know how you can, given a point in time, calculate the concentrations of A and B in the first equation, given the initial concentrations.


texts: Photochemical ligand substitution of metal carbonyls - role of water cooled lamp-jacket?

texts: Why, in the photochemical substitution of a ligand in a carbonyl complex, is a water-cooled lamp jacket required to separate the solution and the mercury vapour lamp? It's shown in Figure 22.16 of Atkins' Inorganic Chemistry.


texts: How the Azimuthal quantum number describes 3d shape of the orbital?

texts: I read yesterday that Azimuthal Quantum number describes the shape of orbital....


texts: Why isn't 4s1 electron of Chromium the last electron?

texts:
I know that to aid the symmetry of singly occupied orbitals one electron jumps from 4s orbital to 3d orbital thus giving Chromium the configuration 3d5 4s1.

But my question is, when we're evaluating the quantum numbers of the last electron, shouldn't we definitively use the farthest electron from the nucleus? Irrespective of which electron is assorted last. Because it's not like a Chromium atom is created by sequentially inserting electrons one after the other voluntarily.

In a perfectly stable Chromium atom, which has the configuration Ar(18) 3d5 4s1, the last or ultimate electron in terms of energy level, orbital and radius, should be the 4s1 electron. Why is it that most references I found tell me to consider the 3d5 electron?


texts: Rate of electrophilic bromination of toluene and ethylbenzene

texts:
My book says that electrophilic bromination of toluene (methylbenzene) is faster than that of ethylbenzene. How is that possible?

I am doubting it because ethyl is a better $+\ce{I}$ group than methyl, so ethyl would increase the electron density in the benzene ring more than methyl. As a result, bromine, which is an electrophile, should react with ethylbenzene faster than methylbenzene.

So, why is the bromination of methylbenzene faster than ethylbenzene and please give the reaction mechanism, if possible?


texts: Why is an S-S bond stronger than an O-O bond?

texts:
I'm wondering why exactly the single bond between two sulfur atoms is stronger than that of two oxygen atoms. According to this page, an $\ce{O-O}$ bond has an enthalpy of $142~\mathrm{kJ~mol^{-1}}$, and a $\ce{S-S}$ bond in $\ce{S8}$ an enthalpy of $226~\mathrm{kJ~mol^{-1}}$. This one reports the $\ce{S-S}$ bond enthalpy to be $268~\mathrm{kJ~mol^{-1}}$, but I'm not sure which molecule they mean, or how they measured it. Anyway, it's still higher than that of $\ce{O-O}$.

Searching the Net, the only justification I could find was something similar to concepts they apply in VSEPR, like in this Yahoo Answers thread with such remarkable grammar. Quoting the answer, which might have borrowed some stuff from a high school textbook,

  due to small size the lone pair of electrons on oxygen atoms repel the bond pair of O-O bond to a greater extent than the lone pair of electrons on the sulfur atoms in S-S bond....as a result S-S bond (bond energy=213 kj/mole)is much more stronger than O-O(bond energy = 138 kj/mole) bond $\ldots$

Other variations of the same argument can be seen here, but it doesn't make sense, since one couldn't apply the same argument to $\ce{O=O}$ and $\ce{S=S}$. The first reference documents the $\ce{S=S}$ and $\ce{O=O}$ bond enthalpies to be $425$ and $494~\mathrm{kJ~mol^{-1}}$, respectively.

It's a bit shaky, and I'm looking for a solid explanation using MO or VB, or anything else that actually works. So, why is an $\bf\ce{S-S}$ single bond stronger than $\bf\ce{O-O}$, despite $\bf\ce{O=O}$ being obviously stronger than $\bf\ce{S=S}$?


texts: Reaction of hydrazine and hydroxylamines with carboxylic acids

texts:
Carboxylic acids and their derivatives on reaction with hydroxylamine $\ce{NH2OH}$ and hydrazine $\ce{N2H4}$ give hydroxamic acids and acid hydrazides, respectively, through acyl nucleophilic subsitution.

Why don't they give the same reaction as aldehydes and ketones (i.e. removal of $\ce{H2O}$) giving formation of oximes as the acids also have oxo ($\ce{=O}$) group?


texts: Stability of carbocations with -M groups in beta position

texts:
First part
The original question was to arrange the following compounds in the order of their rate of dehydration with conc. $\ce{H2SO4}$:-

(A) $\ce{CH3-CH(OH)-CH2-CH=O}$
(B) $\ce{CH3-CH(OH)-CH2-C(=O)-CH3}$
(C) $\ce{CH3-CH(OH)-CH2-C#N}$
(D) $\ce{CH3-CH(OH)-CH2-NO2}$

In each of the cases, a carbocation will be formed (+ve charge on the $2$nd carbon via E1 mechanism). Since all the groups(not talking about $\ce{-OH}$, because that’s the leaving group) are electron-withdrawing, the weaker the electron-withdrawing group, the higher the rate.
So, the order according to me should be B > A > C > D. But the answer given is the exact opposite.
"Edit- My teacher who gave me this question now told me that my answer is correct when the reaction takes place in acidic medium and reverses in basic medium."
Second part
Here is a similar question,

Arrange the following compounds in the order of their rate of dehydration with conc. $\ce{H2SO4}$:-
(A) $\ce{CH3-CH2-CH(OH)-NO2}$
(B) $\ce{CH3-CH(NO2)-CH2-OH}$
(C) $\ce{NO2-CH2-CH2-CH2-OH}$

Here, the answer given is C > B > A which I agree with because the further the $\ce{-OH}$ group is from the nitro group, the more stable will be the carbocation. But I feel it contradicts the first question.
Is my answer for the first question correct? If not, what is the correct reasoning?


texts: How's the IUPAC name of basketane determined?

texts:
A book of mine mentions a certain molecule, basketane, and provides its corresponding structure:

Now, I appreciate the book went on to mention this particular compound (I didn't know that organic molecules could be shaped like...well...a basket, so I find this interesting) but the problem is, that it didn't mention basketane's IUPAC nomenclature, much less how to go about naming it.

A quick internet search reveals the following IUPAC name for basketane:

  Pentacyclo[$4.4.0$.$\mathrm{0^{2,5}}$.$\mathrm{0^{3,8}}$.$\mathrm{0^{4,7}}$]decane

But I'm still having trouble finding out how people even arrived at this name. Heck, I don't even know if the above mentioned name is even correct. I consulted all my Org. Chem books, and predictably, there was no mention of how to even begin naming basketane. I'm still in high school, so this particular kind of nomenclature is still alien to me (I haven't dealt with any super-scripts or carbons assigned the locant: zero yet).

Would anyone be able to:

1) Validate that name I've come across

2) Explain (citing a decent reference will do as well) how I ought to go about even naming this thing.

EDIT- @DHMO has been kind enough to point out two possible duplicates in the comment section below; but I'd still beg to differ.


texts: Can we use liquid hydrogen to power a conventional engine?

texts:
Hydrogen has the best fuel efficiency, so if we were to use it in our engines wouldn't their efficiency increase as well.

The engines would require changes and all but would it be plausible to have that?


texts: If glucose can react with phenyl hydrazine to form osazone why can't it react with 2,4-DNP to give positive test?

texts:
If glucose can react with form phenyl hydrazine to form osazone why
  can't it react with 2,4-DNP?

Yes I know about cyclic form of glucose and its equilibrium with straight chain and all …

I read this, this and this Stack Exchange one too Does glucose react with Brady's reagent?

Still, didn't get an answer to my question. So requesting for clarification …


texts:
I have read that buckyballs are excellent electron acceptors, C60 in particular can accept up to 6 electrons.

However I do not understand why they have this ability and how they can accept a large number of electrons. I would appreciate if anyone could elaborate on this topic.


texts: How do I perform a partial optimisation in GAMESS?

texts:
Sometimes it is necessary to perform a partial optimisation of a molecule, i.e. keeping certain variables constant. One example might be to pre-optimise a transition state, taking advantage of not having to compute the force constants in the initial set-up.

For example, let's consider the transition state of the Diels-Alder Reaction of ethene and butadiene, where we want to freeze the distance between the two molecules.

How can I achieve this in the software suite GAMESS?


texts:
$\mathrm{Z= 32}$

$\mathrm{1s^2\ 2s^2p^6\ 3s^2p^6d^{10}\ 4s^2p^2}$

According to me it belongs the $\mathrm{IV\ B}$ group since it has the $\mathrm{d}$ completed, but it belongs to $\mathrm{IV\ A}$. But we know that in the $\mathrm{A}$ group only the $\mathrm{s}$ and $\mathrm{p}$ elements belong. Why does this happen?


texts: Using covalent or ionic radius when calculating dipole moment

texts:
When the ionic character of a bond is above 50% should I use ionic radius instead of covalent one when calculating the dipole moment?

The formula I have for dipole moment is $\mu = \text{(% ionic character)} \cdot e \cdot d$, where $e$ is the elementary charge and $d$ the sum of the two radii.


texts: Isolation of citric acid from lemon juice

texts:
I'm trying to extract citric acid from squeezed lemons.
After studying the subject, I found the following document on next URL.

http://www.staff.amu.edu.pl/~psorg/serp.pdf

Especially pages 68 - 69 are very interesting.

Does anybody know the reason for adding hydrochloric acid and sodium hydroxide on the end of page 68?

This looks very useless to me, since in this case the alkaline and acid neutralize each other.

Thanks in advance!


texts:
I was under the impression that chemistry almost exclusively involves valence electrons because there isn't enough energy to strip off electrons located closer to the nucleus.

If that is true, and elements in the same period have similar properties because they have the same number of valence electrons, then why is $\ce{SiO2}$ a solid and $\ce{CO2}$ a gas? Surely a difference in mass by a factor of 2.5 can't be that big a deal.

Is it because of a van der Waals force difference, because silicon has extra electrons which result in compounds being formed from it being more symmetrical than those formed from carbon?


texts: Hydrogen bonds: 1 donor with 2 acceptors at the same time possible (or vice versa)?

texts:
Can 1 donor (eg N-H) facilitate 2 H-bonds with 2 different acceptors (eg 2x O) at the same time (assuming that both are within range and angle constraint)? i.e. building an "h-bond triangle"?

Is it possible the other way round: 2 donors and 1 acceptor at the same time?


texts: A "function of proportionality" in a rate law

texts: I am currently studying rate laws and the determination of the order of a reaction. So first-order reactions remind me of linear functions $f(x)=kx$ while second-order reactions remind me of quadratic functions like $g(x)=cx^2$ in high-school algebra. Since we are dealing with reactants here, the input of the functions would be the concentrations of our substrates $[\ce{S_1}]$ and $[\ce{S_2}]$. I am wondering if there are any fancier functions that arise in "real-life" chemistry?


texts: When diagonalising the overlap matrix, what happens if the square root of the diagonal matrix does not exist?

texts:
I was looking at the code required for a simple RHF computation when I came across the section for the diagonalisation of the Fock Matrix.

Based on what I know, the diagonal matrix $\mathbf{s}$ is evaluated as

$$\mathbf{s} = \mathbf{U}^\dagger\mathbf{S}\mathbf{U},$$
where $\mathbf{S}$ is the overlap matrix.

The matrix $\mathbf{X}$ is then evaluated as

$$\mathbf{X} = \mathbf{U}\mathbf{s}^{-1/2}\mathbf{U}^\dagger$$

and the diagonalised Fock operator $\mathbf{F'}$ as

$$\mathbf{F'} = \mathbf{X}^\dagger\mathbf{F}\mathbf{X}.$$

But what happens if the matrix $\mathbf{s}$ has terms that are negative? What happens then? Do we simply take the magnitude and carry on?

Thanks!


texts: For second part of the question I'm wondering if the peaks on the right denote the chemisorbed layer, while the peaks on the left denote the physisorbed layers. Since chemisorption results in a stronger covalent bond, the energy to remove adsorbates than the physisorbed layers


texts: Why is tetramethylsilane (TMS) used as an internal standard in NMR spectroscopy?

texts: I understand that TMS has a large proton number, giving a strong peak in the NMR spectrum. But apart from that is there any other reason why just TMS is used and not any other molecule?


texts: Molecular orbitals symmetry - states notation

texts:
I'm reading some papers and I'm repeatedly seeing the following notation of system states:

Could you, please, explain to me the meaning of it?

E.g. the state $B^2 \Sigma_u^+$ - I'm aware, that $\Sigma$ is used as a substitute for $A$ in both $C_{\infty h}$ and $D_{\infty h}$. I'm also aware, that $u$ stands for "ungerade", i.e. it tells us, that the state is anti-symmetric with respect to the inversion.

But what does the $B^2$ before $\Sigma$ stand for? And what does $\Sigma^+$ mean?

I'm aware of the Mulliken notation, but it doesn't seem to contain these symbols.


texts: Calculation of Gibbs free energy of a chemical reaction

texts:
So, I'm trying to derive the equation: $$\Delta G = \Delta G^o + RT \ln Q\tag{1}$$
And trying to follow the steps detailed on this website here. I am having trouble deriving equation 7, which tries to sum chemical potentials. Previously, it derives the change in chemical potential, $\Delta \mu _i$ when the reaction is poised away from equilibrium, and for the reaction $A + B \rightarrow C + D$, four equations, each for $A, B, C$ and $D$ respectively.
$$\Delta \mu _A = \mu_A' -\mu_A = RT \ln([A']/[A])\tag{2}$$
Where $[A']$ is the activity away from equilibrium. Afterwards, it proceeds by:
$$\Sigma\Delta\mu_i = RT \ln\left(\frac{[C'][D'][A][B]}{[C][D][A'][B']}\right)\tag{3}$$
My confusion is regarding the arrangement of the activities in the $\ln()$ function. I assumed that:
$$\Sigma\Delta\mu_i = \Delta\mu_A + \Delta\mu_B + \Delta\mu_C + \Delta\mu_D = RT \ln\left(\frac{[A'][B'][C'][D']}{[A][B][C][D]}\right)\tag{4}$$
It says that we assume the concentration of the products increases by convention, but I don't get it. Even if the concentration of the reactants decrease and the products increase, the change in sign will be due to the $\ln()$ function. If you flip the activities of the reactants around, it doesn't give the net change in Gibb's free energy anymore.
If anyone can help explain this, I will be very grateful.
P.S. Sorry if the question seemed low effort, but the context is mostly given in the website, and I can't find an explanation anywhere :(


texts:
We've started learning about NMR in my ochem class and my instructor told us that in Hydrogen NMR an alcohol can have a fairly wide range of possible values - usually from about 2 to 5.  He said that because of this the actual ppm value is not very diagnostic - but the fact that alcohols tend to have a thicker peak is.

He told us not to really worry about why/how there is such a range or why the reading tends to be thicker, but now I'm curious.

I speculate that there can be such a wide range of possible values because Oxygen is fairly electronegative, and depending on its environment it will exhibit different levels of shielding/deshielding.  I have no idea about why it tends to be a thicker peak.

So I guess I have two questions:

Is my speculation as to the range of possible values correct?
Why is the peak generally thicker with alcohols than with other functional groups?


texts: Shifting of groups in carbocation rearrangement

texts: Phenyl has greater migratory power. However, why did methyl migrate in step 2 of the reaction?


texts:
Why does the standard 10gm/15ml lactulose solution turn dark when exposed to heat above 30 degrees Celsius?

This is probably a simple question. It is funny that the warnings/important information on the drug label of lactulose state that this effect is harmless, but then go on to warn not to use if it becomes too dark. How do I know if it is "too dark"? This is obviously very subjective and simply want to know why it becomes dark or "too dark" so it is scientifically understood why it is safe (or unsafe) to use when it is dark.


texts:
I'm not sure if I understand the reasoning behind this particular question.

The sigma and pi bonds of $\ce{C=C}$ have a combined bond dissociation energy of 632 kJ/mol. Using this information, predict whether the following reaction is exothermic or endothermic.

$\ce{C2H4 + H2O -> CH3CH2OH}$

My attempt:

The bonds being broken are the $\ce{C=C}$ pi bond and the $\ce{H-OH}$ bond. I realize there are two bonds being formed, but I am unable to correctly identify the second one. One is $\ce{CH_3CH_2-OH}$. I think the other should be $\ce{CH_2-H}$. The textbook says this bond is $\ce{CH_2H-R}$. I think R is referring to the side group, which varies (and in this case, is $\ce{CH_2-OH}$?), but the enthalpy value for breaking the $\ce{CH_2H-R}$ is listed as 410 kJ in the solutions. According to the table in my book, the value for a $\ce{CH_3CH_2-H}$ is 410 kJ/mol. I do not understand how these two bonds are equivalent. Can someone please explain this?


texts: Why is the conductivity of non-metals not equal to zero?

texts: My chemistry book says that delocalized electrons are the reason for electrical conductivity in a metal. However it says that nonmetals like sulfur, phosphorus and silicon have "low" conductivity. How can they conduct electricity if they have no delocalized electrons? Silicon has a giant macromolecular structure while sulfur and phosphorus have simple molecular structure. What causes them to conduct even for a little bit?


texts: Rotation around CC bond in 1,2-dioxetane: transition states and local minimum structures

texts:
TLDR:

What: Potential energy surface associated with rotation around CC bond in the ring-opened version of 1,2-dioxetane.

How: State average(4)-CASSCF(12,10)/VTZP constrained geometry optimizations keeping OCC'O' and one HCC'O' dihedral angle fixed. Active space is bonding and antibonding CC', OO', CO, and C'O' orbitals in the closed ring structure, plus the two nonbonding orbitals on the oxygens perpendicular to the plane of the ring.

Question: How explain the profiles in Figure 2.

I want to look at the transition states associated with the OCC'O' dihedral torsion in the biradical structure of 1,2-dioxetane (after ring opening). This is similar to the exercises in basic organic chemistry courses, where we look at the anti and gauche conformations of isomers. In Figure 1 you can see one biradical structure with an OCC'O' dihedral of about 70 degrees.

Figure 1. 70 degree dihedral OCC'O' angle minimum structure.

I decided to "map" the PES associated with CC rotation, by doing constrained geometry optimisations. I kept the OCC'O' and one HCC'O' dihedral simultaneously fixed at 10 degree intervals from 0 to 180 degrees, and optimizing the other internal coordinates. I did this with the state-average (4 lowest singlets) complete active space self-consistent field (CASSCF) method, using the atomic natural orbital type basis sets with polarisation at the triple zeta level (ANO-RCC-VTZP), using the Molcas suite. The energies of the singlet states can bee seen in Figure 2.

Figure 2. Mapping the $S_0$, $S_1$, $_2$, and $S_3$ potential energy surfaces, obtained as described above.

Qualitatively, the PES's mainly match what I expected, but with one major change: instead of a transition state close to 120 degrees, I see a minimum.

I am trying to understand why this is what I obtained, but I cannot really explain it. The change is so major, that any errors with my constrained optimization is likely not the cause, I reckon.

Figure 3 shows the C-C bond distance at the various optimized geometries. Here, the main features are present: minimum at 60 degrees and maximum state at 120. This makes sense as in a minimum the structure is more stable, which means shorter bond lengths. However, there is some weird behavior at the 90 degree data point, which probably is due to the same effect as the energy minima around 100 degrees.

Figure 3. C-C bond lengths in Å at the various optimized geometries.

So, my question, can anyone explain the anomalies presented in Figures 2 and 3?

Updates and answers to questions:

Yes, I changed the OCC'O' and noe of the HCCH dihedral angle simultaneously. I only chose one HCCH dihedral as I thought that was enough to keep the structure rigid during the geometry optimization.

The active space is the bonding and antibonding $\sigma$ orbitals of the closed ring structure (CC', OO', CO, and C'O'), plus the two nonbonding p orbitals on the oxygens (perpendicular to the plane of the ring).

I did not use symmetry to speed up the calculations.

For each dihedral angle used, I also measured the CC bond distance. I plotted this as an overlay on the energy profile, to see how the CC bond changed relative to the energy change.

As requested by Brian, the energies of all calculated states are included in the question.


texts: What does this property of transition metals mean?

texts:
what does it mean:

"Transition metals either have incompletely filled d subshells or readily give rise to cations that have incompletely filled d subshells.

I don't understand the portion starting from " or readily give rise to..."


texts: Why polar aprotic solvents don't surround negatively charged nucleophiles?

texts: Protic solvents can form a tight shell around a nucleophile. But what's stopping any polar solvent from doing so? Shouldn't a polar solvent surround negatively charged $\ce{F-}$ with its partially positive side?


texts: What will happen if I put this chemical into my water tank?

texts:
There is an 8000 liter water tank on top of my house which provides water for the house.

Bacteria, fungi, algae, etc often start developing in the tank, giving unpleasant smells, etc.

This chemical seems to be chlorine based. According to the bottle, the composition is:

  Sodium hypochlorite 5% max.

  Sodium hydroxide 1% max.

  Amine oxide 1% max.

I'm thinking of maybe putting 50 ml into the tank about once a week.

Nobody is drinking or cooking with the water. It's used for stuff like laundry, showers, washing dishes, etc.

I know it seems like a strange idea, but I live in the countryside in a developing country and it's not easy to find stuff here.

The water is ground water that we pump up there with our own pump.

What's gonna happen? Should I decrease or increase the amount? Or drop the idea entirely? (And maybe do something else?)

It's very hot here, maybe 40 celsius in the shade. This tank is in the baking sunlight.


texts: Why does phenol not undergo Friedel-Crafts alkylation and acylation reactions, whereas anisole does?

texts:
Friedel–Crafts reaction of phenol

The answer to the question at the above link states that : "Like aniline, phenol too reacts to a very less extent during Friedal-Crafts reaction.
The reason being that the oxygen atom of phenol has lone pair of electrons which coordinate with Lewis acid."

But isn't the case with anisole, the same? However, my textbook states that anisole does undergo Friedel-Crafts acylation and alkylation.


texts:
Why secondary alkyl groups are more prone to shifting than primary? I attach example from Grossman book [p. 20]:

When $\ce{R} = \ce{CH2CH2Ph}$, the coordinated $\ce{Al}$ simply transfers a $\ce{Me}$ group to the carbocation $\ce{C}$ (σ bond nucleophile). The $\ce{O}$ atom then coordinates another equivalent of $\ce{AlMe3}$ before the product is obtained upon workup.

When $\ce{R} = \text{cyclohexyl}$, the $\ce{R}$ group migrates (1,2-alkyl shift) to give a new carbocation. (2° Alkyl groups are more prone to migrate than 1° alkyl groups.) After $\ce{Me}$ transfer to the new carbocation and coordination of another equivalent of $\ce{AlMe3}$, workup gives the product.

This is quoted from "The Art of Writing Reasonable Organic Reaction Mechanisms", Second Edition by Robert B. Grossman, DOI: 10.1007/b97257.


texts: Do companies recover carbon dioxide and water from the purification step of cryogenic air separation, and how?

texts:
In the 3rd step of cryogenic air separation, filtered air is purified to remove water, $\ce{CO2},$ and hydrocarbons from the $\ce{N2}$-$\ce{O2}$-$\ce{Ar}$ stream. Im interested in knowing what happens with that $\ce{CO2}$ and water. Can both resources be recovered in a useful form? Can the $\ce{CO2}$ be purified? Are Praxair or others currently doing this?

Context: Im doing research on a theoretical industrial process which uses pure $\ce{CO2},$ water, and $\ce{N2}.$ I want to know if all these inputs can be obtained from a standard air separation facility (of course $\ce{N2}$ can). Im particularly interested in $\ce{CO2}$ recovery.

Please note I'm not interested in buying gases. I'm working on a publication about a theoretical system to produce protein from air and solar power. In your answer it would be helpful to provide links to papers or websites which give descriptions of the recovery process (energy costs etc).


texts: internal alkyne stability to strong alkali

texts:
Internal alkynes are relatively electron rich and are not usually prone to attack by strong (nucleophilic) bases such as hydroxide or alkoxide.
However, this isn't always the case.  A very nice overview of the most common reactions of alkynes says:

The sp-hybrid carbon atoms of the triple-bond render alkynes more electrophilic than similarly substituted alkenes. As a result, alkynes sometimes undergo addition reactions initiated by bonding to a nucleophile. This mode of reaction, illustrated below, is generally not displayed by alkenes, unless the double-bond is activated by electronegative substituents, e.g. $\ce{F2C=CF2}$, or by conjugation with an electron withdrawing group.
$\ce{HC≡CH   +   KOC2H5    —>[in C2H5OH at 150 ºC]   H2C=CH-OC2H5}$

I'm interested in more information about this and similar reactions, particular for internal (not acetylenic) alkynes.
Unfortunately, the linked page doesn't provide a reference for this reaction, and searching in Google Scholar for "internal alkyne" "potassium hydroxide" doesn't provide useful results.
Thus my questions are:

Does hydroxide ever react similarly with internal alkynes, at any temperature?  If so, under what conditions?
How long does the ethoxide reaction indicated above (at 150 °C) take?  Days?  Hours?  Minutes?  Would it be significantly different for an internal alkyne rather than acetylene?
In the case of a hydroxide reaction, would the ultimate product be a ketone (a.k.a. base catalyzed hydration)?


texts:
Can we make Gold in a Lab? Is it possible to make changes in metals that will create Gold? and How?
I have tried to search something related to this but didn't get any good results.
Thanks in Advance


texts: I have just been looking at      https://en.wikipedia.org/wiki/List_of_oxidation_states_of_the_elements and found that boron has a -5 oxidation state. I would like to know which boron compounds form this oxidation state.


texts: SbF5 forms a trigonal bipyramidal shape. There are polar bonds present and I assumed that it is non polar because of it's molecular geometry. However, The molecule itself is not entirely symmetrical (unless I'm thinking of symmetry incorrectly). If I'm not incorrect, can an asymmetrical molecule be non polar?


texts:
I wonder if there is a way to measure the chemical potential of a substance in a two-component mixture and also to account for its dependence on the number of moles. Explaining it further, suppose there is a mixture of a light component (like methane, C1) and a heavier one (like C20). Given temperature and pressure, one could add some amount of the light component to the mixture and that would rise the chemical potential of that first component. Thermodynamics tell us that the chemical potential can be expressed by

$$d \mu_i = - \bar S_i dT + \bar V_i dP + \sum_{m=1}^{n} \left(\frac{\partial \mu_m}{\partial N_i}\right)_{T,P,N_j[i]} d N_m $$

Being pressure and temperature constant, the increase in the chemical potential by adding some amount of light component depends entirely on the summation of $({\partial \mu_m}/{\partial N_i})_{T,P,N_j[i]}$. That is precisely the point: how could I measure or calculate that derivative or, alternatively, variations in the chemical potential by adding mass to the mixture?

Of course, one could use a cubic equation of state or the like and calculate fugacity and chemical potential etc. But I am interested in the more fundamental aspects of thermodynamics. One of them is that, given P-V-T data and specific heats, in addition to the composition, one is supposedly able to calculate all the thermodynamic properties of a mixture or of a component.

Now, the practical side of this question is this: if there is a two-phase mixture of C1 and C20, under ordinary T and P, the vapour phase is almost pure C1, but the liquid phase is a mixture of both. For given P and T, composition can be measured somehow. Given an increase in pressure, say $\Delta P$, with coexisting phases, there must be an increase in the concentration of C1 in the mixture, $\Delta x_1$ (or $\Delta N_1$, if the number of moles is to be used instead of concentration). The change in composition can obviously be calculated by equating the chemical potential of C1 in the vapour and in the liquid phases. While calculating the change in chemical potential in the vapour phase is quite easy because it is pure C1 and
$d \mu_1 = \bar V_1 dP$,
the chemical potential in the liquid phase depends on the above mentioned derivative:

$$d \mu_1 = \bar V_1 dP + \sum_{m=1}^2  \left(\frac{\partial \mu_m}{\partial N_1}\right)_{T,P,N_2} d N_m $$

Finally, by "measuring" chemical potential I mean any way of obtaining it from other variables that can be measured by ordinary instruments in a lab. And, just to mention, I have used the notation of Modell and Reid, "Thermodynamics and its applications".


texts: Which chemical should I use to wash soot precipitate from cast iron?

texts:
The soot deposition is quite strong (almost like graphite) and my iron object has a complicated shape with many grooves.
Which chemical would dissolve the carbon without oxidizing the iron?


texts: How can I rapidly liberate CO2 from dolomitie and siderite in the presence of organic carbon without oxidizing organic carbon to CO2?

texts:
I have an analytical apparatus that measures the total carbonate in solid materials by acidification of the material under a stream of $\ce{CO2}$-free air, followed by quantitative coulometric titration of the liberated $\ce{CO2}$.  The coulometer has a detection limit of about a microgram of $\ce{CO2}$, and so long as the material can be finely ground and homogenized we will typically use a sample size of 2 mg.  The sample is acidified with 5 mL of 2 M $\ce{HClO4}$ and heated to $\mathrm{80^oC}$ while sparging with the $\ce{CO2}$-free air stream.

For materials like $\ce{Na2CO3}$ or $\ce{CaCO3}$, the carbonates are thoroughly liberated as $\ce{CO2}$ and analyzed with full recovery within 5 minutes.  For materials containing significant amounts of dolomitic limestone ($\ce{CaMg(CO3)2}$) or siderite ($\ce{Fe(CO3)3}$), the analysis times can approach one hour or more. This is problematic not just because of the reduced sample throughput, but also because the detection limit of the coulometer increases with the length of analysis due to the time-integrated noise at the detector.

Although the issue described above has been a problem with this analysis for decades, it had always been given low priority until now.  Over the years we have tried different non-oxidizing acids (nothing volatile like halo-acids, as they would be titrated as $\ce{CO2}$), propietary commercial catalysts, and organic wetting agents.  The configuration described above has given the best results (lowest time to complete recovery of carbonate), even though in worst-case scenarios (i.e. low total carbonate, predominantly present as dolomite or siderite) the results are essentially useless and all we can do is report high detection limits.

I suspect that we probably can’t come up with a better acid than perchloric: it’s a very strong acid, it is not oxidizing under the conditions of this analysis, it’s non-volatile and perchlorate is stable and it doesn’t tend to form precipitates that might occlude portions of the sample, etc.

My thoughts are that there should be some reagent that would displace then complex the $\ce{Fe}$ and $\ce{Mg}$ in siderite and dolomite, respectively. We do not want to oxidize any organic carbon that might be present, however (at least not all the way to $\ce{CO2}$).

So, how can I alter this analysis so that the carbonates of dolomite and siderite are more rapidly liberated as $\ce{CO2}$, without oxidizing any organic carbon that might be present, and without introducing acidic gases to the coulometric detector?


texts: What bond exists in "red oxygen", and can something similar happen with hydrogen?

texts:
"Red oxygen" is the nickname for O$_8$. It only exists at extremely high pressures.

What kind of bond does it have? Can hydrogen theoretically have something similar at very high pressures too?


texts: Nickel plating with nickel acetate, nickel chloride, sulfur, saccharin and coumarin

texts:
I am a hobbyist trying to learn/apply a nickel electroplating process that I can safely do at my shop.  My substrate is a machinable non-stainless steel with unknown carbon content, and I'm looking to do a close variation of the "Watts Bright nickel" formula.  I have a 99.9% pure nickel anode, nickel acetate, nickel chloride, boric acid, sulfur powder, saccharin and coumadin powders.

The formula calls for nickel sulfate; is it possible to simply add the powdered Sulfur to the solution, or do I have to use a different process to synthesize the nickel sulfate? If so,  can I do so with the materials that I have?
Also, the Watts formula does not include the saccharin or coumarin, but I know that these chemical additives will increase the odds of a smooth mirror like finish.

Also, is there a recommended quantity range, or at least a starting point, for these two chemicals for this application? Any insights here from an experienced chemist/electroplater would be greatly appreciated.


texts: Retro Diels–Alder reaction in synthesis of corallopyronin A

texts:
I was looking at the synthesis of corallopyronin A in the following paper by Rentsch and Kalesse: Angew. Chem. Int. Ed. 2012, 51 (45), 11381–11384.
There is one reaction which is described as

oxidation and a retro Diels–Alder reaction generated pyrone

I understand that the DMP oxidises the secondary alcohol to a ketone, and at the end there is an intramolecular esterification to produce the lactone, but I don't quite understand how the retro Diels–Alder reaction works. Could someone explain the reaction steps?


texts: Conversion of molecular structure into Fischer projection for compounds having more than two chiral carbons

texts:
Question

What is the Fischer projection of the given compound's enantiomer?

Answer

My attempt
I tried to solve this by first converting it into the Fischer projection of the given compound and then taking its mirror image since that would provide the Fischer projection of the enantiomer
This is what I got as the Fischer projection of the given molecule.

Why is this wrong?
How do you find the Fischer projection for a compound having more than two chiral centers?


texts: Electrolysis of water: Which equations to use? (IB Chem)

texts:
There is a list of standard electrode potentials at 298 K from the p. 23 of IB Data Booklet 2016. Which of the following equations (forward/backward reactions), from the two possible ones involving the discharge of hydrogen gas and the other two with oxygen gas discharge, should I use for the oxidation and reduction of water in electrolytic cells?

$$
\begin{array}{cc}
\hline
\ce{\text{Oxidized species} <=> \text{Reduced species}} & E^⦵(\pu{V}) \\
\hline
  \begin{align}
    \ce{H2O(l) + e- &<=> 0.5 H2(g) + OH-(aq)} \\
    \ce{H+(aq) + e- &<=> 0.5 H2(g)} \\
    \ce{0.5 O2(g) + H2O(l) + 2 e- &<=> 2 OH-(aq)} \\
    \ce{0.5 O2(g) + 2 H+(aq) + 2 e- &<=> H2O(l)}
  \end{align}
&
  \begin{array}{r}
   -0.83 \\
    0.00 \\
   +0.40 \\
   +1.23
  \end{array}
\\
\hline
\end{array}
$$

(Unless the use of any of these equations cannot be generalized — for a concise explanation of why this is so and what to do then I would be equally grateful.)


texts:
The lewis structure of trinitramide has four major resonance structures, whereby the lone pairs of the central nitrogen can resonate with the nitro groups.

This seems to indicate that each of the nitrogen atoms would be sp2 hybridized, and the entire molecule would be planar. In fact, the Wikipedia ball-and-stick image for trinitramide seems to indicate it so.

However, based on quantum mechanical calculations, trinitramide is in fact non-planar. Why is this so? What drives its non-planarity?


texts: Decarboxylation of cyclohex-1-ene-1,2-dicarboxylic acid by electrolysis method

texts:
What is the major product when cyclohex-1-ene-1,2-dicarboxylic acid is electrolysed?

My try:

I got 2 cases but I am unable to decide which product is major, and need help here.


texts:
Is it a standard practice to name functional group by the greek alphabet of the carbon it is attached to?

Recently read a question in which the order of translation (protein synthesis) was asked and there were a couple of options with the $\ce{NH2}$ was labelled as $\ce{\alpha-NH2}$ and $\ce{COOH}$ as $\ce{\alpha-COOH}$.

I read wiki, it says H atoms are labeled in that way but are functional groups too labeled in the same way?


texts: A formula for the refractive index of a gas dependent on temperature and pressure

texts:
I am in search for a formula that gives me the refractive index of a gas at a given temperature and pressure. Does such a formula exist? Ideally the solution should have this form:

$n_g(t, p) = \ldots$,

where $n_g$ is the refractive index of the gas $g$, $t$ is the temperature and $p$ is the pressure.


texts: Behavior of NaCl in water with electrodes

texts:
If I had some NaCl dissolved in water, it is conductive, so if I were to put two electrodes in the container (powered), what is causing the flow of electrons?
Do the NaCl ionic bonds break and the ionic atoms collect at the oppositely charged electrode (how I'd assume electroplating works) with all of the atoms themselves moving to carry current, or are electrons loose in a "sea" like a metallic bond, with some of the atoms being pulled along with the flow?


texts: why is BTD(benzothiadiazole) electron acceptor?

texts:
I heard that electron donor is π-electron rich compound, and electron acceptor is π-electron deficient compound in donor-acceptor polymers.
https://www.sciencedirect.com/science/article/pii/S0927024819301795
according to this paper, thiadiazolo[3,4-c]pyridine which replaced a carbon atom at the 5-position of benzothiadiazole with nitrogen, is electron acceptor, saying that pyridine is electron-withdrawing group.
but I thought that pyridine is aromatic compound, so pyridine may be electron-donating group. (donor-acceptor concept in my question is about polymer, not Lewis acid-base or semiconductor doping)
how can we determine that moiety of polymer is donor or acceptor? I don't understand exact criterion.


texts:
I have a mixture of metal oxides in powder form. Mainly Iron oxide, silicon dioxide, and calcium oxide. I know for certain calcium oxide is in the mixture, but my handheld XRF is not detecting it.

I am analyzing my sample through a very thin plastic wrap, polypropylene.

I have even taken a sample of pure lime, and my handheld XRF is not detecting any calcium. Just a bunch of others such as $\ce{Si, Al, P}$ and so on.

How might this be?

Is the plastic having an adverse effect?

My XRF is in 'general metals' mode; does it need calibrating to detect the $\ce{Ca}$?


texts: Has anyone actually prepared Zn(HCO3)2 absent the presence of pressurized aqueous CO2?

texts:
Under normal conditions, I am not certain, as per Atomistry on $\ce{ZnCO3}$, the following quote:

  The hemihydrate, $\ce{2ZnCO3.H2O}$, was obtained by precipitating the solution of a zinc salt with ammonium bicarbonate and digesting the gelatinous precipitate in excess of the precipitant till it became crystalline.

where I would have expected zinc bicarbonate, and further:

  The basic zinc carbonate, $\ce{5ZnO.2CO2.4H2O}$, can be prepared by the direct hydrolysis of the normal carbonate, or by boiling a solution of zinc, zinc hydroxide, or zinc carbonate in an excess of aqueous carbonic acid.

And finally, a reference to a presumably formed zinc bicarbonate, and at times, citing the employment of pressure:

  Basic zinc carbonates can be converted into the normal carbonate by contact with water charged with carbon dioxide under pressure. The normal carbonate is itself somewhat soluble in water containing carbon dioxide - presumably forming the bicarbonate.

The last quote is unclear, in my opinion, as to whether under normal experimental conditions, should one expect the creation of a stable $\ce{Zn(HCO3)2}$?


texts: Why is the reactivity of primary alkyl halides with nucleophiles (SN2 mechanism) greater than secondary and tertiary alkyl halides?

texts:
For the reaction between alkyl halide and a nucleophile, following the SN2 mechanism, the reactivity of alkyl halides is in the order: primary halide > secondary halide > tertiary halide.

If you consider the reactivity of alcohols with halogen acids to form alkyl halides, the reactivity of alcohols is in the order: tertiary alcohol > secondary alcohol > primary alcohol.

Why is there a difference in order of reactivity in both the cases?


texts: If electrolysis splits water, why does only either hydrogen or oxygen (but not both) bubble up on one pole?

texts:
If electrolysis splits water, then that means that $\ce{H2O}$ is split into $\ce{H}$ and $\ce{OH}$ or $\ce{O}$.

How come that if a water molecule is split at e.g. the negative pole (anode), only the $\ce{O}$ bubbles up. What happens to the $\ce{H}$ and/or $\ce{OH}$? Do they react with the pole and stay there?


texts: pKa of phenols using UV-Vis spectroscopy

texts:
I have done an experiment where I dissolved four different substituted phenols in acidic, basic, and buffer solutions, and recorded the UV-Vis spectra for each. I'm supposed to pick a wavelength where the absorbances for the protonated, normal and dissociated forms are very different. I then use these equations given to me to calculate the $\mathrm{p}K_\mathrm{a}$ of that phenol:

$$x = \frac{A_\text{buffer} - A_\text{acid}}{A_\text{base} - A_\text{acid}}\tag{1}$$

where $x$ is the mole fraction; $A$ is the absorbance in corresponding medium, and

$$\mathrm{p}K_\mathrm{a} = \mathrm{pH} - \log\left(\frac{1-x}{x}\right)\tag{2}$$

I've calculated the $\mathrm{p}K_\mathrm{a}$ values of each phenol, but none of them are close to literature values. I'm not sure what I've done wrong. Can anyone help explain these equations and any ways I could have messed up?


texts: What is first protonated aldehyde or lactone?

texts:
In a six membered lactone with carbaldehyde in beta position, which oxygen gets protonated first? the lactone or the aldehyde?
(Using concentrated HCl)


texts: What is the mechanism by which phosphorus pentoxide ($\ce{P4O10}$) and a carboxylic acid form an anhydride? I can't find it anywhere online. Does $\ce{COOH}$ attack twice (I'm assuming it's the nucleophile) because there ends up being two carbonyls in the product? What leaves?


texts: What does this lambda–sigma notation mean?

texts:
I am currently reading the CRC Handbook of Phosphorus-31 Nuclear Magnetic Resonance Data by John C. Tebby (CRC Press, 1991) and on several figures (ex. pages 9 to 14) there is a caption that reads along these lines

  $\ce{^{31}P}$ NMR chemical shifts of three coordinate (λ3 σ3) phosphorus compounds. (Tables B to E.)

What does the (λ3 σ3) signify? I've not seen that notation before, and it is on the captions of some of the charts I need.


texts: I am looking for any substance that would be unstable or dangerous when it is cooler or not on heat, and is stable when it is being boiled

texts: I am a first responder and one of our protocols when entering any unknown lab environment is to turn off any burners. Most of the time, we try to not disturb the environment as much as possible so a colleague of mine and myself were curious as to any substance that would actually be more dangerous after turning off said burner. Thank you.


texts: I'm attempting to write the balanced equation of the combination of lithium metal and fluorine gas. I understand that this will produce an ionic solid because it is a reaction of a metal and a nonmetal. However, I'm confused with the fluoride ion having a charge of -1 and fluorine only occurring as a diatomic molecule ($\ce{F2}$). Is $\ce{F2}$ two fluoride ions or just one?


texts: Atomic mass number and mass number in atomic symbol

texts:
In chemistry classes or even many different branches of chemistry textbooks, I am told that the atomic symbol

$$\Large ^A_Z\ce{X}$$

includes the following notations:

$A$ – "atomic mass" or "mass number";
$Z$ – "atomic number".

But, because I want to make myself to remember easily, I would prefer to call $A$ "Atomic mass number" instead of simply "mass number". I think many say that I am making a big deal and unnecessary things. But as a non-native learner, if I can confirm that using the term "atomic mass number", it would make me easier to remember the term.


texts: Reacting calcium with warm water and magnesium oxide with carbon dioxide, what are the products?

texts:
So I have several descriptions of reactions and I have to give the net ionic equation. Are these just the equations or are they the proper net ionic ones?

Solid calcium is added to warm water.
$$\ce{Ca_{(s)} + 2 H_{2}O_{(l)} -> Ca^{2+}_{(aq)} + 2 OH_{(aq)}^- + H2_{(g)}}$$

Powdered magnesium oxide is added to a container of carbon dioxide gas.
$$\ce{MgO_{(s)} + CO2_{(g)} -> MgCO3_{(s)}}$$

Did I do those right, or am I on the wrong track?


texts: Comparing bond lengths of a molecule using valence bond theory?

texts:
My textbook says that all the bonds of $\ce{SF4} $ are not equal while in the case of $\ce{XeF_2}$, $ \ce{BF4-} $ or $\ce{SiF4} $ all the bonds are equal. No reason is stated for this observation.

So is there a general way or formula to check if all the bond lengths are equal or not for a given molecule?


texts:
Do catalysts themselves need an input of energy to work?

My book says "catalysts do not per se require an energy source". What does it mean by per se? If they don't use energy how do they activate?


texts: Why is the sneaky method of smothering a grease fire more effective?

texts:
In this demonstration, a grease fire is temporarily extinguished if you put the cover on the pan, but reignites as soon as you take the cover off.  However, if you slowly slide the cover across the pan, then the fire stays extinguished.

Why does sliding the cover on make such a big difference?


texts: Finding structure of a compound given its reactions

texts:
Question:

  An organic compound A (molecular formula $\ce{C6H12O}$) does not change the colour of acidic dichromate solution. Compound A on treatment with $\ce{H2SO4}$ produces alkene which on oxidative ozonolysis gives a molecule $\ce{C6H10O3}$ which gives positive iodoform test. Find out structure of A.

So I know about ozonolysis, but I do not know when acidic dichromate solution changes colour. From the question an alkene is produced so I guess it may be an alcohol, but if someone an explain about it and iodoform test, then I will be able to give another try on this problem.


texts: When a gas is dissolved in water does the state of gas changes ? We write it as aqueous but what is the state that exists ? does it has the properties of gases when it is dilluted ?


texts:
When a drop of ink or watercolour paint is placed on wet paper, rather than uniformly diffusing in all directions it forms tendrils which rapidly expand out from the spot.
Why is this and what is the chemistry or physics occuring?
This video may further show the type of thing I am referring to
https://motionarray.com/stock-video/black-silver-tendrils-pack-216423
It appears that the pigment solvent forms discrete channels outwards through the water. I wondered if this might be a surface tension interaction or something else.


texts: Assigning locants when both unsaturation and substituents are present in a hydrocarbon

texts:
For the following compound:

I understand that the longest chain is of five carbon atoms. However, I am having trouble assigning the locants here.

Going bottom to top we get the locant set as: 223.
Going top to bottom we get the locant set as: 244.

Obviously, there are no functional groups in this compound so the first point of difference rule should govern the numbering of locants. Hence, according to me, bottom-to-top locant assignment is correct here.

Unfortunately, ChemSketch uses top-to-bottom assignment :(

  What rule am I missing here?

I figure out the unsaturation is being given preference here, but I do not know any rule regarding it.

PS:
My IUPAC name: 2-bromo-2-methylpent-3-ene.
ChemSketch's name: 4-bromo-4-methylpent-2-ene