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Enamine formation mechanism. Can't there be alternatives?
I'm studying organic chemistry, more specifically the imines and enamines. I've read about the mechanism of formation of enamine from a generic ketone and a question popped up in my mind. The mechanism proposed by my book (and everywhere else) goes from the ketone, to the iminium ion when the water molecule goes out, and then to the enamine by the the breaking of the C=N double bond. Now, I've studied in the past the reactions of alcohols, and I remembered that a tertiary alchol can undergo by dehydration as an elimination reaction (E1 or E2), forming as a consequence a C=C bond. Now going back to the enamine formation where the water molecule is present, can't the water go out with the direct formation of the C=C bond forming the enamine by conseguence? Is the choice of the mechanism determinated by some kind of kinetics or spectroscopic study that confirm the presence of the iminium ion?

During enamine formation, “water does not go out” but rather hydroxide does. The hydroxide deprotonates the immonium cation to form water and the enamine. The immonium cation is isoelectronic with a ketone, and it is more readily deprotonated.


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Possibility of carbocation rearrangements in SNi reactions
According to several sources, the $S_{N}i$ reactions follow a mechanism allowing carbocation formation while others disagree. Precisely, for example, according to A Guidebook to Mechanism in Organic Chemistry - Peter Sykes, it states that

Whether the breaking of the C-O and the S-Cl bond occurs simultaneously, or whether the former occurs first, is still a matter of debate.

Thus, it's unknown if a carbocation formation occurs or not. Now my question is if carbocation formation occurs, wouldn't that imply hydride and methyl shifts are possible within the cation? However, in the case when the reaction is concerted, such rearrangements are not possible. Take the case of the following reaction for example,
$$\ce{3-Methylbutan-2-ol + SOCl2 \to 2-Chloro-3-methylbutane (Major)}$$
Is the above more likely or the following after carbocation rearrangements:
$$\ce{3-Methylbutan-2-ol + SOCl2 \to 2-Chloro-2-methylbutane (Major)}$$
Now shouldn't the latter imply the carbocation formation and the former reject it? Which reaction occurs in reality and why is it the reaction mechanism undetermined exactly?

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


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NIST SRMs: Determination of the Validity Period
The National Institute of Standards and Technology (NIST) produces Standard Reference Materials (SRMs) of basically anything. That also means that things like peanut butter are among those SRMs. SRMs come with a Certificate of Analysis (CoA) and have a validity period attached.
Given that NIST makes sure to know almost everything about their SRMs, how do they determine the validity period? Complex matrices can have difficult to estimate long-term influences on all the compounds in the sample. If they are running stability studies, when do they start those and for how long do they run?

Search Accelerated Stability Tests for Certified Reference Materials. Also read the poster on "Certification process for organic certified reference materials (CRM) using high-performance quantitative 1H-NMR (HP-qNMR®): special focus on stability studies." It is available on ResearchGate for free.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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HPTLC Densitogram - Not Showing Other Secondary Metabolites
I have run a HPTLC analysis of methanolic extract of Gymnema Sylvestre R.Br. plant in order to determine the concentration of active ingredient (Gymnemic acid using Gymnemagenin as standard). Sample run was outsourced to a third party. The densitogram of standard and sample are presented. Is it possible that other secondary metabolites do not appear as peak in the densitogram of the plant extract. In the result of the sample only the peak of the gymnemic acid appears while no other significant peak is witnessed indicating presence of other metabolites?.

For readers, read about the anti-sweetener Gymnemic acid


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Ionsiation enthalpy of Zinc Cadmium and Mercury
Why is ionisation enthalpy of Zinc, Cadmium and Hg in the increasing order, when ideally, all periodic groups have decreasing order of enthalpy downward?
An argument could be that F and D orbitals show less screening effect, but this is true for all the transition metal groups.
Another argument about fully filled shells being more stable also arises,... but even 3rd, 4th and 5th groups have fully filled S shells. When it comes to D orbitals, how does it being fully filled affect the ionisation enthalpy? It is not the valence shell afterall.


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At what temperature is bismuth the densest?
Both water and bismuth have denser liquids compared to solid forms, and we know water is the densest at the temperature of about 4°C.
Does the same thing apply to bismuth? Of course, I know the melting point of bismuth is about 271° C. So the temperature of interest should be around it I think.

The reasons that water has that density anomaly do not apply to bismuth. NIST has tabulated density values to peruse at your leisure.

So what's the reason for bismuth?

I guess I'm a bit confused - do you mean the liquid being denser than the solid, or that water is densest at about 4C?

Both. And in the case of bismuth it's densest at about 310C based on the paper in Nilay Ghosh's answer. While in the case of antimony there's no such an anomaly but its liquid form is also denser.

For water at 4C, see https://chemistry.stackexchange.com/questions/81756/why-is-density-of-water-maximum-at-4-degree-celsius/105390#105390. For the rest, you need to understand that thermal expansion coefficients of many (well, all really) materials are not a constant and can even change sign. Why? the shape of the potential well the atoms find themselves in.

If all materials have a non-constant thermal expansion coefficients then why do most materials have a denser solid?

Density change on a phase change does not correlate with thermal expansion coefficients of a specific phase. But, at a high level, atoms in liquids want to move around so need more elbow room. Note that Bi (and Si, Ge, Sb, ...) are not close packed crystals. Si goes from a 4-fold coordinated semiconducting diamond cubic solid to an 8-fold coordinated metallic liquid. That one is easy to see how it could happen.

The densities of Sb and Bi melts were investigated by an improved Archimedean method. The results show that the density of the Sb melt decreases linearly with increasing temperature, but the density of the Bi melt firstly increases and then decreases as the temperature increases. There is a maximum density value of $\pu{10.002 g/cm^3}$ at 310 ℃ ,about 39 ℃ above the melting point. The temperature dependence of the Sb melt is well fitted with the expression $\pu{ρ = 6.8590 - 5.8105 × 10^{-4} T}$ , and that of the Bi melt is fitted with $\ce{ρ
= 10.3312 - 1.18 ×10^{-3} T}$.

Source: Geng, Haoran & Sun, Chunjing & Wang, Rui & Qi, Xiaogang & Zhang, Ning. (2007). Temperature dependence of densities of Sb and Bi melts. Chinese Science Bulletin. 52. 2031-2034. DOI: 10.1007/s11434-007-0309-7
Also see:

Greenberg, Y. & Yahel, Eyal & Caspi, E. & Benmore, Chris & Beuneu, B. & Dariel, M.P. & Makov, Guy. (2009). Evidence for a temperature-driven structural transformation in liquid bismuth. EPL (Europhysics Letters). 86. 36004. DOI: 10.1209/0295-5075/86/36004.
Tournier, R.F. Multiple Glass Transitions in Bismuth and Tin beyond Melting Temperatures. Metals 2022, 12, 2085. DOI: 10.3390/met12122085

Why does this say the density of liquid bismuth is 10.067 g/cm$^3$ which is bigger than 10.002? Also, there is another article saying the number as 10.022.

@SnackExchange You should check latest papers which has improved measurement techniques. Density of bismuth around melting point is just above 9.9 g/cm3 which goes to maximum value of 10.002 g/cm3 at around 310 C (the ref.2 has a better graph). The Wikipedia article needs to have the values corrected.

When I plugged temperatures in the density formula of bismuth, I found the temperature should be about 280 K in order to have a density of about 10 g/cm$^3$. But when we put 583 K (310 C) the answer is about 9.6! How can it be explained?

@SnackExchange If you follow the paper, it says that in the range of m.p. and 310 C, the equation is $\mathrm{ρ = 9.44903+1.73×10^{−3} T}$ giving density value within 1.3% error. Above 310 C, the equation is $\mathrm{ρ =10.3312−1.18×10^{−3} T}$


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Please explain the order of Lewis acidic strength in trichlorides of boron group
The order of decreasing Lewis acid character as per online sources is as follows:
BCl3 > AlCl3 > GaCl3 > InCl3
Reason cited is: As we move down the group, the size of atom increases, and as a result, the tendency to attract electrons decreases. This leads to a decrease in Lewis acid nature down the group.
However, it is also known that BF3 is the weakest Lewis acid among the boron trihalides on account of back bonding effect (BI3 > BBr3 > BCl3 > BF3) as the energy gap between boron and fluorine (2p-2p) is less resulting in a stronger bond and the energy gap between boron and iodine (2p-5p) is the most, resulting in the weakest bond.
Why can't we apply the above explanation to BCl3, AlCl3, GaCl3, InCl3 as well, saying that Al and Cl should have the least energy gap (n=3 for both) and thus have the strongest bond and weakest Lewis acid character.
Please feel free to point out any fundamental mistakes in my assumptions and reasoning as I am still figuring things out and may have a limited/incorrect understanding of back bonding.

Related: https://chemistry.stackexchange.com/questions/135554/lewis-acidity-order-of-aluminum-halides/135643#135643, https://chemistry.stackexchange.com/questions/153768/towards-a-hard-lewis-base-like-water-which-is-the-stronger-lewis-acid-silicon-t, https://chemistry.stackexchange.com/questions/129558/why-is-phosphorus-trifluoride-the-strongest-lewis-acid-among-the-phosphorus-trih


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Organic solvents distillation for purification
I've realised that the majority of the solvent that we use in my lab are contaminated with grease (peaks at 1.26 and 0.86 ppm in $^1H$ NMR in $CDCl_3$), since they come in plastic containers (I guess that's the reason).
One solution would be to buy better grade solvents, but we have a large amount of these solvents in the plastic containers. I was thinking about distilling them to purify them and keeping them in glass bottles, but I thought of some issues that could appear.
Some organic solvent present stabilizers. For example, dichloromethane is often added amylene (like in my case), so I'm afraid of losing the stabilizer when distilling. Amylene has a boiling point of 38.5 ºC, so it should distill with the DCM. However, I was thinking of using the rotavap for practical reasons, but I think that maybe the amylene would not condense at the conditions used for the DCM. Also, I don't know if more stabilizers are added, since sometimes I get peaks that resemble BHT but I don't use any solvent that has BHT in it.
Could I use the rotavap for distilling the DCM or should I perform a simple distillation? Would the simple distillation work for keeping the stabilizer and preserving the DCM for long periods? Also, in the bottles of ethyl acetate and n-hexanes it doesn't say anything about stabilizers, is it alright to assume that they don't need any and I can distill them without problem?

If your solvents come from the producer in plastic bottles, the impurity is probably not grease. It is probably some impurity coming from the plastic itself. You can distill DCM in a Rotavap : the amylene will distill together with the dichloromethane. I have never heard that ethyl acetate and hexane contain stabilizers.

I'd argue that, if a supplier has used plastic bottles, they are not the most likely source of contamination. They will be designed to transport pure solvents. More likely, other lab practices are creating impurities. We used to use cheap PVC piping for inert gas transport (when doing air sensitive chemistry). The plasticisers (often alkyl phthalates) and preservatives in those pipes were a big source of contaminants.

Can you filter thru activated charcoal? Or thru a silica column?

Using the rotovap to distill the DCM proved useful, as it left a yellow oil as a residue. After that, the solvent was clean by NMR, only with some peaks that seem to be from amylene (the stabilizer present in DCM).
As far as I know, n-hexane and ethyl acetate don't need stabilizers. The ones we have in our lab are clean, although they also come in a plastic container.
I don't know if the contaminated DCM that we have is due to a bad batch, the plastic being dissolved or the actual quality of the DCM. It could be easily tested, but I haven't done it.

Purifying solvents can be difficult. I sort of solved it by encountering a local glassblower and devising a minimal holdup system with a Vigreux column. I used a dedicated distilling flask for each solvent. Collection was into a glass bottle saved from purchases of HPLC grade solvent. I tested by evaporating about 10 mL in a CLEAN [washed, Oven dried, pyrolyzed, at high T], Erlenmeyer flask and letting the last bit dry on a 4-bounce atr cell No detectable residue. This worked for methanol, methylene chloride, n-pentane, chloroform, cyclohexane, benzene, DMF and heptafloro-2-propanol[used to extract fluorinated oils]. Ethanol and iso-propanol were distilled from activated magnesium to remove water. The alcohols and DMF were checked by infrared or the nmr OH peak.
The removal of stabilizer is not a problem if purified solvents are used deliberately and not stockpiled.
A story about stabilizers: A colleague synthesized a rather large molecule with an ethyl group. He had an nmr with a weak quartet and came to us to corroborate his assessment. the chemical shift looked suspicious. It turned out that the deuterochloroform was stabilized with regular ethanol; we never heard back.


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To check if something is prefixed as a Pyro
How to figure out if something's a Pyro by looking at its formula?
The thing I know about Pyro compounds is that

Ortho acid + Ortho acid - $\ce{H2O ->}$ Pyro compound

I have no issues if I end up with the ortho acid I am quite familiar with. For example, everyone pretty knows what $\ce{H3PO4}$ is and thus if I am asked if $\ce{H4P2O7}$ is prefixed with a Pyro, I wouldn't have any trouble.
The problem comes when I deal with compounds of $\ce{As, Sb, Si}$ and I have to check if they are prefixed with a Pyro or not....
For example, take $\ce{As2O3}$. How do I know if that's a Pyro? Now take $\ce{H4As2O7}$. How do I know if that's a Pyro?
One way I think would be to check if their oxidation states comply to their occurrence states. But that is definitely not an ideal approach. So how do I go with this? Do I need to remember these ortho acids or can I go just remembering a few?
Please someone help me in this
PS: I have already checked this webpage but I couldn't find the solution to my problem in this- What do the prefixes meta, ortho, pyro mean in inorganic chemistry?

The rule of thumb is the compound has to be known long enough and widely enough to deserve the pyro- prefix before the prefix was stopped being used for such condensed anions. By other words, the prefix is used for historical reasons.

Oxides do not use pyro prefix in their names. // For acids/ anions of acids, there is not a simple general rule, you need to know historical circumstances. Memorizing those few where pyro- is used may be easier. And even then, it is not the preferred naming. // Absence of a simple rule, based on basic principles, is rather a rule than an exception in chemistry.

@Poutnik I didn't know this..... it's weird they still ask questions based on Pyro acids and yes my bad, an oxide is not prefixed with a Pyro

Pyro compounds contain $2$ central atoms (different from oxygen and hydrogen). Exemple : $\ce{H4As2O7}$ contain $2$ arsenic atoms. It can be considered as a pyro- acid.

okay, I did not see this either, thanks @Maurice


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Deriving the equation of motion for adiabatic approximation
In the textbook, Theories of Molecular Reaction Dyanmics by Flemming Y. Hansen and Niels E. Henriksen, there is a derivation of the equation of motion for the adiabatic approximation (pgs. 5-7). The author starts by showing that the wavefunction can be written as a product state by separating the slow and fast components (i.e. nuclear and electronic) as shown below,
$ \Psi(r,R, t) = \chi(R,t)\psi(r;R)$
where $\chi(R,t)$ is the nuclear component and $\psi(r;R) $ is the electronic component which depends parametrically on the nuclear position (R).
We take the following time-dependent Schrodinger equation, written as
$ i\hbar \frac{\partial \Psi(r,R,t)}{\partial t} = (\hat{T_{Nuc}} + \hat{H_{e}}) \Psi(r,R,t)$
and plug in the product state to get the following equation
$ i\hbar \frac{\partial \chi(R,t)}{\partial t} = [\hat{T_{Nuc}} + E_{i}(R) + \left< \psi \right|\hat{T_{Nuc}}\left| \psi \right>_0] \chi(R,t)$.
It is said that this term is equal to zero, leaving us with the equation of motion of the adiabatic approximation
$ i\hbar \frac{\partial \chi(R,t)}{\partial t} = [\hat{T_{Nuc}} + E_{i}(R) ] \chi(R,t)$.
Questions

How do we get the $\left< \psi \right|\hat{T_{Nuc}}\left| \psi \right>_0 $ term during the derivation? I am confused on how that arises.

What does this term mean? Is it just the coupling between the nuclear and electronic states?

The term is the diagonal element of the nuclear kinetic energy operator with respect to the adiabatic electronic state basis. The term is obtained when the equation is projected on the adiabatic electronic state $\langle \psi| $ and integrated over electronic coordinates,
$$
i\hbar \partial_t  \chi(R,t)\psi(r;R) =(\hat T_N+ \hat H_e) \chi(R,t)\psi(r;R) \stackrel{\langle \psi|_r}{\Rightarrow} \\
\int dr\psi^*(r;R)i\hbar \partial_t  \chi(R,t)\psi(r;R)=\int dr\psi^*(r;R)(\hat T_N+ \hat H_e) \chi(R,t)\psi(r;R)\\
\langle \psi|\psi\rangle_ri\hbar \partial_t \chi(R,t)  = \big (\langle\psi|\hat T_N|\psi\rangle_r + E(R) \big)\chi(R,t)\\
i\hbar \partial_t\chi(R,t)=\big(\langle\psi|\hat T_N|\psi\rangle_r + \hat T_N + E(R) \big)\chi(R,t)
$$
The expansion of $\hat T_N$ applied to the product of $\chi\psi$, according to the product rule, also leads to a mixed term with first order derivatives $ \sum_{Nuclei}\frac{\hbar ^2}{2M}\langle\psi| \hat P_N|\psi\rangle_r \cdot (\hat P_N \chi(R,t)) $, which I have already omitted since this first order term is exactly zero when using a purely real $\psi$. This is also mentioned in the textbook.
But it should be noted that this mixed first order term only vanishes for the diagonal elements of $\langle \psi |T_N|\psi\rangle$, i.e. when $\psi$ is the same adiabatic electronic state. In the general case, this term leads to nonadiabatic effects, where different adiabatic electronic states become coupled by the motion of the nuclei, inducing nonadiabatic transitions.
The nuclear kinetic energy term $\langle \psi| \hat T_N|\psi\rangle_r $ does not vanish when using a real $\psi$, but is typically small in comparison to $E(R)$, in particular around nuclear equilibrium coordinates. But in principle it is an additional energy term that could/should be included in the Hamiltonian for the nuclear wavefunction, and it is due to the coupling of electronic and nuclear motion.
The term can be calculated if $|\psi\rangle$ is known as function of $R$, but is typically very small due to the inverse dependency on nuclear masses and the rather slow change of $\psi$ with $R$. Sometimes it is included at zero-order I.e. the zero-order Taylor expansion term at some $R_0$ is added as correction to the potential energy $E(R)$, for that reason it is also known as diagonal Born-Oppenheimer correction term. But in most cases it is assumed to be negligible.


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Lifetime components in phosphorescence decay
I'm studying the phosphorescence decay of diacetyl in acetonitrile (it has a high quantum yield of intersystem crossing). The fluorimeter than I'm employing has microsecond resolution and, since the decay of the phosphorescence isn't too long, I have to measure the IRF (width of 1-2 $\mu$s) in order to perform a reconvolution fit. However, I get a biexponential fitting with a long time (like 20 $\mu$s) and a very short time (around 30 ns). Does that make sense? I thought that the short lifetime could be due to fluorescence, but I get it even in the decay of the righmost peak while using a long pass filter. Moreover, I don't know if it makes sense to have a lifetime with more resolution that the limit of the aparatus.
Does this make sense or has any meaning? Maybe is an artifact or I'm making some mistake with the measurements?
Edit: I'm using the Spectrofluorometer FS5 from Edimburgh Instruments, and employing its software (Fluoracle) to make to fittings. The light source is a flash lamp. By reconvolution/convolution I mean a fitting that takes into account the IRF (instrument response factor), as the lifetime of the decay approaches the duration of the IRF.
The fittings look like this:

Figure 1: monoexponential fitting

Figure 2: biexponential fitting

What is the fluorimeter’s light source? Is it a flash lamp? If so, maybe the short component of the output is an electrical artifact due to the flash lamp.

Please add more details about measuring instrument response function, what is meant by reconvolution? Add a figure that explains what you are doing.

If response function is 1-2 microseconds, you can't measure & quantify 30 ns decay with any reasonable amount of accuracy. So while one might exist, I don't think your data shows that. It must be instrumental as EdV points out. It's a fitting artifact of some kind, but with so little information available (as AChem and porphyrin point out) it's hard to give much of an answer. However, if it was real I would say it's due to nonradiative recombination which is density dependent - excitations kill each other off quickly until the remaining density is so low that they can decay at their own rate.

@uhoh, I added information to the post. I also think its an artifact, but I don't know how to get rid of it. I thought that and artifact of the lamp would be take into account with the IRF.

That fast exponential drop decreases by a factor of 100 in about 1.12 µs. Divide that by 4.61 (i.e. ln(100)) and that decay has a mean life of 0.24 µs. https://i.stack.imgur.com/6lAg5.png If I were you I would (try to?) get the data out somehow as a text file and analyze it with a separate program - I really don't like the fitting results it's giving you. You can consider sending the raw data to Edinburgh Instruments directly as well to see what they think.

Phosphorescent materials, such as “glow in the dark” paints and tape, are readily available. Perhaps make up a test specimen using such a material and see how it behaves in your fluorimeter. If the short lived component is always present, then the evidence for an artifact is stronger.

@uhoh, I just tried fitting in Origin with the Fit Convolution app. I followed the tutorial but I didn't get a good fitting, neither mono or biexponential.

Phosphorescence should be at a longer wavelength than any fluorescence so carefully using a filter or grating should remove any fluorescence. Also measuring at different wavelengths will change percent of any fluorescence still getting through a filter. Is there a tiny bit of scattered light being mixed in with the phorphorescence? (Some types of glass filters do fluoresce but usually you need to excite then directly).
How are you doing the convolution,  Marquardt type non-linear least squares iterative convolution is normal. What sort of chi-squared are you getting for the fit, what type of weighting is used? How does a 1 exponential vs 2 compare? What do the residuals look like and so on. Are you fitting to a background also? However, 30 ns is really too short to be confident that it actually exists if the irf is 1-2 microsecs.

I added some information to the post. I'm just doing the convolution with the software (Fluoracle) of the aparatus, so I have no clue about the type of convolution or the parameters. Would it be better to use Origin or another tool? Moreover, I'm not fitting to a background, I just followed the manual of the aparatus (it said I just needed the IRF and the decay).

Well, now we can see the data there is definitely a lot of a short lifetime there. Have you tried a cell filled with only solvent to check scattering or no cell/empty to check any electrical noise? If all is ok then there is a real short fluorescence / phosphorescence component.

Related to the comment immediately above, the OP could spike a little nitromethane into the solution, to quench both the fluorescence and phosphoresce and see what results. (I assume the solution is oxygen free, more or less.) Also, since a flash lamp is used, how good is the instrument at blocking direct excitation light or “after glow” from the Xe (?) flash lamp?

@porphyrin, I monitored a decay with only solvent (at the same wavelenghts and bandwidths than the sample) and I get some signal. Perferming a convolution fit with this signal and the IRF gives me a lifetime of around 50 ns. However, this signal is very weak (5 min of measurement to get a very weak signal vs 1 min to get the strong signal of the sample), so I don't know if that could be the lifetime that I'm seeing.

So it seems that you do have some scatter coming through which it would be best to totally eliminate if you can,  but further to Ed V's comment you could also purge with a heavy atom gas such as Xe or add say iodide ions to cause heavy atom quenching. The short decays will be unaffected if is scatter. All I can now suggest is that you look at, say, Ru trisbpy which has a long excited state lifetime, or some other well measured species to check how you instrument is working.


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Mobility of coordinate complex ions
Conductivity of ions depend on mobility of ions, but I doubt if a Coordinate complex formed can affect the mobility of that ion.
Let's say we have AgNO3 dissolved in Ammonia water. How can we compare mobility and Ion  Transport number of Ag+ in Water and in NH3-water, so that {Ag(NH3)2}+ complex is formed.
I think Mobility is decreased due to complex formation.

Consider the implicit coordination of $\ce{H2O}$ in both $\ce{Ag+}$ and $\ce{[Ag(NH3)2]+}$ as  $\ce{[Ag(H2O)n]+}$ and $\ce{[Ag(NH3)2(H2O){n-2}]+}$.


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What reaction products are formed if an unsaturated fat is reacted at 20 - 50 °C with H2O2 of 35 %?
My question is:
What reaction products are formed if an unsaturated fat is reacted at ca. 20 - 50 °C with aqueous hydrogen peroxide of ca. 35 %?
To find the answer, we can subdivide the question into the questions about the elementary reactions:
a) Which reaction products are formed in the oxidation step?
b) Which reaction products are formed in the further reaction steps?
I already know:

Blowing with compressed air at higher temperatures yields a hydroperoxy group in $\alpha$-position to the double bond.
Epoxidation with hydrogen peroxide or alkyl hydroperoxides can be improved by transition metal complexes.
Peroxycarboxylic acids (e.g. performic acid or peracetic acid formed in situ from the aqueous acid and aqueous hydrogen peroxide), which are more electrophilic, convert the double bonds to epoxides without metal catalysts.

But what about aqueous hydrogen peroxide alone?
We know hydrogen peroxide is a hydroperoxide and a weak acid. Does the hydrogen peroxide react according to ionic or radical mechanism under my reaction conditions?
Are the hydroperoxides formed, the epoxides, the monoalcohols, or the dialcohols?
The references contradict each other in these points or don't contain any information on the reaction conditions.


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Relationship of acids and bases with pH. (Proportional Relationship)
Can someone please clarify the relationship between acidic-basic strength and pH? I have come across conflicting information and am unsure about the correct understanding.
Some people including my chemistry teacher say that
$\text{Acidic Strength} ∝ \frac{1}{pH}
\\
\text{Basic Strength} ∝ pH$

According to my research, it's called proportional relationship.
Well, I'm asking whether this information is accurate or not. If not? show me the correct one.

Express the relations quantitatively and decide yourself. E.g. the simplified equation for weak acid is pH=0.5(pKa - log c), for weak base pH= 14 - 0.5(pKb - log c).

There is either a wrong terminology at play, or something lost in translation/definition.  pH is not how acidic/basic strength is quantified at all.

In pH p stands for "potenz" Which means taking negative logarithm of active mass of hydronium ion  $$ pH = -log(a) $$ where a is the active mass of hydronium ions.
As we know that the acidic strength increases with the increase of active mass of hydronium ions the negative logarithm of active mass i.e., pH should decrease with acidic strength.
Therefore,$$Acidic Strength ∝ 1/pH  And  Basic Strength ∝ pH$$

Chem+Math Expression formatting reference:
MathJax Basics / Chem+Math expressions/formulas/equations / Upright vs italic / Math SE Mathjax tutorial
// MathJax is preferred not to be used in CH SE Q titles.

Nothing written here is coherent or correct from the point of logic, formatting or facts, and does not address the main point (flaw) in OP's question at all.

The p for pH as $Potenz$ is nothing but a common myth.


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Seeking Online Resources and Textbook suggestions
I want to learn chemistry, and I want to know if there is an online resource that would provide me with a list of textbooks, telling me the order to read them to bring me from a complete beginner to a college level. I have looked to see if any colleges released their course syllabus so I could follow, but I was unable to find any that also listed the textbooks. I also looked to see if the government has set something in place for self-education, but I was still unable to find anything. If something like what I have described does not exist, and if you still remember what textbooks you read, could you please tell me? Thank you in advance.


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Can two resonance structures of a molecule have different cas numbers?
From this Wikipedia article :

Specifically, when a molecular structure is said to be represented by a resonance hybrid, it does not mean that electrons of the molecule are "resonating" or shifting back and forth between several sets of positions, each one represented by a Lewis structure. Rather, it means that the set of contributing structures represents an intermediate structure (a weighted average of the contributors), with a single, well-defined geometry and distribution of electrons. It is incorrect to regard resonance hybrids as rapidly interconverting isomers, even though the term "resonance" might evoke such an image.

Therefore, one should never treat two resonance structures of a molecule as distinct substances, right?
Well, here is an example of (what appear to be) two resonance structures of a molecule, which however have each a distinct cas number, different name, and are even sold separately (different catalogue number) by a single vendor:
https://www.combi-blocks.com/cgi-bin/find.cgi?HC-3087
273-13-2

https://www.combi-blocks.com/cgi-bin/find.cgi?JH-8440
22706-22-5

How can this be explained?
Is the attribution of distinct cas numbers to resonance structures of a molecule 'allowed' or 'correct', for some reason, despite the fact that they point to the exact same chemical entity? Or have they just got it wrong in this case?
Do you know of any other examples of resonance structures of a molecule being assigned distinct cas numbers?


text:
What's the current of an aromatic ring?
Aromatic molecules like benzene have a ring current, created by the movement of electrons around the ring. This is most visible during proton NMR, when the magnetic field of the ring current opposes that of the NMR superconductor.
What's the current though?  How fast are electrons moving around the ring at room temperature?

Well, they don't exactly "have" it.  Ring current can be induced in the ring by magnetic field, like in any loop of conductor. Afaik actual velocities of drift of electrons in electric currents are very small, negligible in comparison with overall speed of electrons.


text:
Why does the melting point of hexafluorosilicic acid differ that much in these two solution concentrations?
From the Wikipedia article for hexafluorosilicic acid:

Melting point:
ca. 19 °C (66 °F; 292 K) (60–70% solution)
$<$ −30 °C (−22 °F; 243 K) (35% solution)

What's the reason for this huge difference in melting point while the solution concentration differs by about 30%?

if you compare it to e.g. the phase diagram of water - sulfuric acid, it is not a huge difference at all.

Yeah, it's nothing special. One could say something like (H3O)2SiF6 is essentially a compound that melts, not a solid solution.


text:
Dipole Moment in P4O8 molecule

So from the structure, which seems to be quite symmetrical, according to me the dipole moment should be zero.

It's difficult to comment on dipole moments of such extended oxides as they are usually isolated in the crystal phase and will require QC calculations. However even on a basic observational basis, we can perhaps comment that not all the P-O bond lengths are same. Also, you called P4O8 "symmetric", but a cursory glance at a 3-D model will show that the two P=O vectors don't exactly cancel each other. So qualitatively we may suspect this to have a dipole moment. But proper bonding analysis and confirmation will require computation.

You may check the conformer here: https://pubchem.ncbi.nlm.nih.gov/compound/Tetraphosphorus-octoxide#section=3D-Conformer

Try this one link.springer.com  but paywalled.  sci-hub.se may be blocked in some countries.

@Poutnik Ok i will check it out..

@YusufHasan yes the 3d model shows the P=O aren't symmetric, yes I understood, that there is no such symmetry...Thank you!

Try to work out the point group, its possible it is C2v .

http://csj.cumhuriyet.edu.tr/tr/download/article-file/1055622 says P4O8 is C2V, but it's a computational study so I'd like to study the method more carefully before I believe it, on first glance the basis set doesn't look that big. (note I am a computationalist). https://pubs.aip.org/aip/jcp/article/5/8/626/209772/The-Molecular-Structure-of-P4O6-P4O8-P4O10-and is an experimental study from 1937 (!) which says they can't tell.

This is an example of the danger of reading too much into two-dimensional paper representations of three-dimensional molecules.
Imagine the two pendant oxygen atoms were not there and you had just $\ce{P4O6}$. The phosphorus atoms would then be equivalent. So to make  $\ce{P4O8}$, instead of putting the two additional oxygen atoms on top and bottom you might have put one on top and one on the right. Now the molecule looks (di)polar.
To resolve this paradox, you must use the third dimension properly. In the $\ce{P4O6}$ core each phosphorus atom is the vertex of a polyhedron whose edges lie along the $\ce{P–O–P}$ linkages. Thus four vertices and six edges, meaning a tetrahedron (not a square). With a tetrahedron the two additional oxygen atoms are not on opposite vertices because a tetrahedron does not have any such pair of vertices, so those bond polarities do not cancel and $\ce{P4O8}$ ends up having a nonzero dipole moment.


text:
Relative magnitude of the crystal field and spin-orbit coupling
In the EPR part of the book 'Physical methods in Inorganic Chemistry' by S. Drago i found that relative magnitudes of crystal field and spin-orbit coupling affect the g values.
I understand that the chemical environment of a metal complex partly removes the orbital degeneracy, but i don't find the way to imagine a sustaining effect which implies that if an electron has an orbital angular momentum this is manteined by coupling to the spin angular momentum. I have read that consequently a net orbital magnetic moment results, giving a g value different from the free electron.
I also can't imagine how when the crystal field increases the LS coupling is broken down completely.


text:
Density of unknown metal

An empty flask weighs $\pu{115.713 g}$. When filled water at $\pu{20 °C}$ it now weighs $\pu{365.263 g}$. The flask is then emptied and a $\pu{15.000 g}$ sample of unknown metal is added to it. It is then filled with water at $\pu{20 °C}$. The combined mass is $\pu{378.426 g}$. What is the density of the unknown metal? The density of water at $\pu{20 °C}$ is $\pu{0.9982 g/ml}$.

Here is my calculation:
Weight of the water: $\pu{249.552 g}$
The volume occupy by the water: $\pu{249.551 g}$ divide by $\pu{0.9982 g/mL}$ yield $V = \pu{250 mL}$.
Then, I don't know what to do I think I should divide the volume of the water by the mass of the unknown metal but I don't understand why I should to that.

For future reference: chemistry.se offers to use mhchem for the body of questions, answers, and comments.  Do not use it for the headers of questions, because it is not guaranteed every browser processes this equally well.  It equally provides the \pu{} command for numerical results, which keeps units typed upright; and the space between the figure and unit in input yields a non-breakable space in the output which mostly is fine (except for the description of angles, and percentage/permille sign in English typography).

\begin{array}{|l|l|l|l|}
\hline \text{Parameter} & \text{Symbol} & \text{Relation} & \text{Value} \\
\hline
\text{Flask mass} & m_0 & &\pu{115.713 g} \\
\text{Flask mass with water} & m_1 & & \pu{365.263 g} \\
\text{Water mass} & m_2 & m_2=m_1 - m_0& \pu{249.55 g} \\
\text{Water density} & \rho_\ce{H2O} & &\pu{0.9982 g cm-3} \\
\text{Flask volume} & V_0 & V_0 = \frac{m_2 }{ \rho_\ce{H2O}} &\pu{250.00 ml} \\
\text{Metal mass} & m_3 & & \pu{15.000 g} \\
\text{Mass of flask+metal+water} & m_4 & & \pu{378.426 g} \\
\text{Mass of water only} & m_5 & m_5 = m_4 - m_0 - m_3& \pu{247.713 g} \\
\text{Volume of water only} & V_1 & V_1 = \frac{m_5 }{ \rho_\ce{H2O}} & \pu{248.160 ml} \\
\text{Volume of metal} & V_2 & V_2 = V_0 - V_1 & \pu{1.840 ml} \\
\text{Density of metal} & \rho_\ce{m} & \rho_\ce{m} = \frac{m_3 }{ V_2} & \pu{8.151 g cm-3} \\
\hline
\end{array}


text:
What exactly is meant by standard state in thermodynamics?
I was told that the standard enthalpy of a reaction is the enthalpy change when the reaction occurs with all reactants and products being in there standard states and under standard conditions(1 bar pressure for gases and 1molar concentration for solutions),but when we say 1 bar pressure for gases,do we mean that the partial pressure of each of the gaseous reactants and products is 1 bar,or that the total pressure of the reactants and products combined is 1 bar?

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion may be removed.


text:
Why 2-methyl-1-propene's halohydrin formation does not involve steric effect?
This concerns Marc Loudon's Organic Chemistry 6th Edition's 5.2 page 187.
Consider 2-methyl-1-propene and its halohydrin formation mechanism. Usually, there will be formation of bromonium, where I assume there is no way that solvent stabilization will create carboncation.
$Q:$ Why does not hydronium attack C1 from opposite side of bromide of bromonium ion to open the ring? Consider swapping methyl group at C2 position by t-butyl group. I would expect significant steric hindrance from 2 t-butyl groups and this would force ring opening attack at C1 position as attacking happens at opposite side of bromide. If I remember correctly from Sunderberg's Advanced Organic Chemistry reading on bromonium cation, there is possibility of steric hindrance happening.

There is a steric effect, but it cuts both ways - bromine is large and its symmetric coordination to both C atoms would also cause greater clash between methyl groups. Essentially, this thing is like t-butyl cation stabilised by neighbouring Br.


text:
Some advice on inorganic textbook
I'd like to have some advice on Inorganic textbooks.
I've already consulted some books (Kettle, Drago, Keiter, Cotton) and they are all very useful, but now I'm searching for a textbook which focuses deeper on the relationships between electronic configurations, periodic properties and reactivity.
I'd like to have a guideline which explain why some elements are more inert than others or their affinities but based on the description for example of the shielding properties and kind of valence electrons.


text:
How does an organic acid change the structure of chrysotile asbestos?
This patent (https://patents.google.com/patent/US5041277A/en) describes how dilute acids such as lactic acid and acetic acid can change the fibrous structure of chrysotile asbestos with up to 98% efficiency. The inventor goes on to say how the end result is no more dangerous than sand, but I don't understand why. What is the new structure after it reacts with the acid?

Mmm, wording in this patent it pretty lame. Essentially, this is simple acid-base reaction, with stronger acid displacing weaker.


text:
Free alternatives to ChemDraw
My school doesn't offer me a ChemDraw license and I need to be able to draw quite complex chemical structures (e.g. porphyrins). This is why I am interested in some good free alternatives to ChemDraw. So far I have only been able to find programs that are a pain to use and it is very hard for me to draw anything more complex.


text:
Group theory and exact Eigenfunctions of Hamiltonian
I think I've understand why the real Eigenfunctions of Hamiltonian belong to a given irreducible representation and I've read that also MOs have to transform as irreducible representation due to the commutation properties of the individual hamiltonian and the point group operators.
My question is how the fact that real solutions have this symmetry is exploited in practice (no need complex discussions, only intuitive ones).
And mainly if and how the fact that we try to construct correct symmetry MOs is exploited in methods like CI.

Related: https://chemistry.stackexchange.com/questions/82656/what-constraints-are-imposed-on-a-wavefunction-by-the-symmetry-of-the-system/82660#82660


text:
Integration of Artificial Intelligence in Chemistry
How is Artificial Intelligence impacting the design and discovery of new compounds and medications?
Given the rapid advancements in artificial intelligence and machine learning methodologies over the past decade, how are these computational tools being integrated into the realm of chemistry, specifically in the design and discovery of novel compounds and medications?
Moreover, how do these AI-driven techniques compare in terms of efficiency, accuracy, and innovation to traditional human-driven research methods? And, what potential challenges or ethical considerations arise when relying heavily on AI for such pivotal and impactful scientific endeavors?

In context of pre-synthesis computational screening of potential drug candidates, AI starts to compete with quantum chemistry computations.

Seems a bit broad in scope. You may want to find a more specific question that will not require an essay to answer. Questions regarding ethics are not generally for this site but you may look for a more specific question. Potential challenges sounds a bit broad and fuzzy, do you have any particular examples in mind?

@Poutnik I'm curious, do you have an example or news article for that? I know that ML approaches have been used and developed for pre-screening purposes in the last millennia. I wonder where the AI came in. As far as I know, this has never extended (practically) to the realm of QC computations as it is too costly. Many semi-empiric and dft-substituting approaches have been developed to tackle the inefficiencies. So I'm really curious where this is heading. Given the verbosity though, this is better discussed in [chat].

@Martin  Hi Martin, I posted the follow up post in Periodic table chat But no special new info about AI in O. chemistry.

Can you narrow the question?  Perhaps cheminformatics applying e.g. PCA for decades to recognize the most important contributions to a function (see the primer by Sidou and Borges, for example) is less visible to you than protein folding (keyword alphafold) which equally appeared in the press not specialized on chemistry.  There is at least one journal dedicated to the field, Journal of Cheminformatics. With Craig Plot by Ertl, for example, data sets can be analyzed for common substituents.  Perhaps your company wants to commercialize a product in the same niche as your competitor, but to circumnavigate their patent, the structure of your active molecule has to be sufficiently structurally different on paper to merit a separate IP protection while the ADMET properties are still similar enough (or better) to justify the investment.
AI can help in the identification of plausible routes of synthesis.  Formalized retrosynthesis e.g. by Corey has been a field of application for long; digitized databases of known reactions and publications crawled by OCR ease to build/improve tools like the open source AiZynthFinder (Reymond group, University of Berne), ASKCOS at MIT, or closed source IBM RXN for Chemistry.  (Too many to name them here, Wikipedia compiled a list.)  It equally extends to virtual catalyst screening, too (e.g., Yang et al.).  Similar to AI in ChatGPT, it can become a very helpful guide / source of inspiration to follow a route you are less familiar with, because your working group tackles a synthesis of motif A preferentially / always by a special method developed locally.  The potential danger to students (and users/workflows in general) is relying too much on these tools.  For one, what happens if you change your current group for one which does not have a subscription to this infrastructure [anymore]?  What are quality and coverage of raw data the AI accessed, and their digestion / model building (else AI is perhaps not about artificial intelligence, but an artificial idiot)?
Note, Artificial Intelligence Applications in Chemistry is one recognized keyword on the landing page for journals by The American Chemical Society.*  As by today, there are 7741 publications by this publisher alone.  The search by this link can be narrowed further e.g. by the type of publication (article, review, perspective), or/and topic (based on your question, biological chemistry, medicinal chemistry, organic chemistry possibly the more interesting sections for you).  With artificial intelligence alone (link), there are 10066 (and counting).  And ACS is only one (of the larger) publishers relevant to chemistry.
* one of the analogues about chemometrics.
(1) Sidou, L. F.; Borges, E. M. Teaching Principal Component Analysis Using a Free and Open Source Software Program and Exercises Applying PCA to Real-World Examples. J. Chem. Educ. 2020, 97, 1666–1676. doi 10.1021/acs.jchemed.9b00924.
(2) Ertl, P. Craig Plot 2.0: An Interactive Navigation in the Substituent Bioisosteric Space. J. Cheminform 2020, 12, 8. doi 10.1186/s13321-020-0412-1.
(3) Yang, W.; Fidelis, T. T.; Sun, W.-H. Machine Learning in Catalysis, From Proposal to Practicing. ACS Omega 2020, 5, 83–88. doi 10.1021/acsomega.9b03673 / entry on pubchem.


text:
Do the paired electrons of subshells' degenerate orbitals contribute to the total exchange energy?
For instance, in d7, there are 5 electrons with the same spin, and 2 electron with the opposite spin, meaning that there are only 3 unpaired electrons. So, which of these would be correct?

(i) Total number of exchanges taking place = 3? (only unpaired electrons)
or
(ii) Sum of individual exchanges of the same spin electrons, so 10 + 2 = 12?
Or is it something else entirely?
Also, if the first one is correct, then how do we explain the stability of d10 over d5?
ALTERNATIVELY:
Does the pairing of electron reduce the exchange energy?


text:
Quantum chemistry and covalent bonding
How can the formation of a covalent bond be described from a quantum perspective, and what implications does it have for traditional chemical bonding theory?
Specifically, in the context of many-electron systems where electron correlation becomes significant, how do modern quantum chemical methodologies, such as Hartree-Fock theory and Density Functional Theory, contribute to our refined understanding of covalent interactions? Furthermore, how does this quantum perspective challenge, extend, or complement classical notions of bonding, as represented by Lewis structures, valence bond theory, and molecular orbital theory?

https://chemistry.stackexchange.com/questions/710/fundamental-forces-behind-covalent-bonding

What is a covalent bond outside of a quantum perspective? How do you explain electronic structure outside of a QM perspective? You can't.

If there is anything like traditional chemical bonding theory, it is likely wrong and obsolete. Lewis structures are rooted in quantum theory. Valence bond theory and molecular orbital theory are approaches to solving for the wave function. Hartree-Fock is basically just an implementation of MO Theory. I don't understand this question.

@Martin-マーチン Agree, not sure what is being asked. If I had votes I would vote to close for lack of focus

Quantum Chemistry and Covalent Bonding:
Quantum chemistry, a nexus between quantum mechanics and molecular science, furnishes an in-depth framework for comprehending and predicting the nuances of chemical bonding. By incorporating quantum principles, this domain offers a granular look into electron behaviors in atoms and molecules, surpassing the sometimes oversimplified interpretations of classical models.
Atomic and Molecular Orbitals:
Atoms are characterized by wave functions or atomic orbitals, which are mathematical representations of the probability density of an electron, indicating the likelihood of finding an electron at a given location. As two atoms approach each other, their atomic orbitals begin to overlap. This overlap can result in the formation of molecular orbitals — either bonding (when the overlap is constructive) or antibonding (when the overlap is destructive). It's crucial to note that this phenomenon isn't driven by "intent" but by the intrinsic properties and behaviors of electrons in the atomic orbitals.
Wave Function and Superposition:
At its core, quantum mechanics presents the notion of the wave function, which encapsulates the probabilistic nature of electron positions. Electrons in a bond don't reside in a fixed location; they exist in a state of superposition. This means they have a probability of being in multiple locations simultaneously. The Schrödinger equation provides a time-dependent wave function, representing the state of the system, encapsulating this electron behavior.
Electron Correlation and Many-Electron Systems:
A particularly challenging aspect in quantum chemistry is addressing electron correlation, especially in systems with multiple electrons. Electrons, being fermions, adhere to the Pauli exclusion principle and also repel each other due to their like charges. Capturing the behavior of one electron influenced by all others is a computational challenge. This is where methods like Hartree-Fock theory, which offers an approximation by treating electrons as moving independently in an average field created by others, and Density Functional Theory (DFT), which considers the electron density rather than the wave function, come into play.
Quantitative Approaches in Theoretical Chemistry:
Delving deeper into bonding characterizations, there are quantitative methodologies in theoretical chemistry. Atoms in Molecules (AIM) theory provides a method to study chemical systems using the electron density, allowing for the analysis of bond critical points and bond paths. Electron Localization Function (ELF) helps in visualizing areas where electrons are likely localized.Then, Natural Bond Orbitals (NBO) analysis provides insight into bonding and antibonding interactions, giving a clearer definition and quantification to the concept of covalent bonds.
Implications for Traditional Chemical Bonding Theory:
Quantum chemistry refines our understanding from traditional bonding theories. Lewis structures and valence bond theory provide intuitive visual models, but they don't capture the nuanced electron behaviors that quantum mechanics does. Molecular orbital theory, rooted in quantum principles, offers a more accurate depiction, especially for molecules exhibiting resonance or delocalized electrons.
In essence, while classical theories provide a foundational understanding, quantum chemistry and its myriad of methodologies grant us a more intricate, quantitative, and comprehensive insight into the fascinating world of molecular interactions and electron behaviors.

This answer now addresses the criticisms and integrates the suggested improvements.
I hope this provides a comprehensive dive into the topic!
For further information I recommend to read Ira.N.Levine "Quantum Chemistry".

"When two atoms come close together with the intent of forming a bond." QM does not ascribe electrons with "intent". They just are what they are.

I downvoted, for such a long answer its lacking quantitative content. This could be improved by mentioning quantitative approaches(AIM, ELF, ELI-D, NBO's, etc.) that exist in theoretical chemistry to characterize bonding and to give the conceptual idea of covalent bonds a clear definition.

I updated the answer, I always try to do my best....

This is informative, sure. I'm not sure it answers the question. But as I've stated above, I'm not even sure what the question is. | More to the topic though: I disagree that Lewis structures are traditional bonding theory. And given that VB and MO theory are congruent when used within the same framework, one cannot be more accurate then the other. I'm sure you mean the right thing, but it reads like there is resonance in MO theory.


text:
How to analyse emission spectra/absorbance spectra to show quenching
I have two samples with different chemical structures (but with the same core which is a fluorophore) and I need to prove that a structural change has resulted in the quenching of the fluorophore. Stern-volmer analysis would not be suitable as the molecular part which is believed to cause quenching is intramolecularly incorporated inside the molecule (not intermolecular). Sample A (without the quencher)'s max. emission intensity is much higher (sample A is almost two-fold higher), as compared to the Sample B (with the quencher).

(in case it's helpful, x and y has a difference of 1.04 nm.)
With the information above, can I conclude that the quenching is happening? Can I say, with the info above, that the absorbance baviours are similar but the emission behaviours are different?


text:
Pure MEA vs Aqueous MEA Solution for CO2 Scrubbing
I was wondering if using pure MEA (Monoethanolamine) or a MEA solution using water would be a better solution for scrubbing $\ce{CO_2}$.

Based on this image, I would think the key reaction would be able to occur with both pure MEA and an MEA solution. However, in this reaction, it takes 2 amines to react with one molecule of $\ce{CO_2}$. The other reaction involves water, so I don't think it would be able to take place with pure MEA. It seems to only use 1 amine to react with one molecule of $\ce{CO_2}$, so theoretically it would would increase the $\ce{CO_2}$:MEA ratio, but I don't know the magnitude of that reaction compared to the main one.
So, it seems that having an aqueous MEA solution might improve efficiency. But the issue with an aqueous solution is that when the MEA is heated to release the CO2, it is above the boiling point of water, so the water would have to be replenished. Therefore, I would like to use pure MEA.
Ultimately, my quesion is:
Is it reasonable to use MEA as a pure liquid rather than in an aqueous solution?

If pure MEA would work OK, it would be used. It's less polar solvent without water and, perhaps counter-intuitively, less basic, afaict.


text:
What is the major product on mono chlorination of 2-methypentane?
I understand that mono chlorination of 2-methylpentane are :

My Question is : How can you determine the major product from those results ?
The probability of monochlorination of :
Amount of 1-chloro-2-methylpentane: 6 (number of 1°hydrogens) × 1.0 (relative reactivity) = 6.0
Amount of 1-chloro-4-methylpentane: 3 (number of 1°hydrogens) × 1.0 (relative reactivity) = 3.0
Amount of 2-chloro-4-methylpentane: 2 (number of 2°hydrogens) × 3.8 (relative reactivity) = 7.6
Amount of 3-chloro-2-methylpentane: 2 (number of 2°hydrogens) × 3.8 (relative reactivity) = 7.6
Amount of 2-chloro-2-methylpentane: 1 (number of 3°hydrogens) × 5.0 (relative reactivity) = 5.0
From the calculation above, the major product will be 2-chloro-4-methylpentane and 3-chloro-2-methylpentane with the same yield. But we should choose one from the two. I am confused. Do you have any idea ?


text:
What's the reason of curvature in Tanabe-Sugano diagrams?
Analysing Tanabe-Sugano diagrams it's evident that some of the lines are pretty parallels to that of the ground field whilst others are inclinated or have some curvature.
I know what's the effect on the line width of the spectra, but I'd like to have an explanation on why we have so different behaviours.
The fact that in Orgel diagrams some lines are straight and others have curvature is related to this?

For readers:  Wikipedia: Tanabe-Sugano diagrams and Orgel diagram // See also Libretexts   here and here


text:
Is there any equation to predict the salting out concentration of a polymer?
I have to roughly calculate the salting out concentration of a polymer with respect to NaOH.
Is there any method to calculate?

There is a method, using  diagrams and/or empirical equations. It is universal, applicable to all  systems. It is not in favour, as it has unknown parameter values, particular for particular systems, that have to be gathered experimentally.


text:
How can I calculate the electrostatic energy between two fragments?
I have a 2-fragment molecular complex with partial charge transfer from fragment 1 to fragment 2. The binding energy is ~0.3 eV and I want to evaluate what fraction comes from electrostatic attraction. I have the wavefunction file and I was wondering if there is a way I can evaluate the electrostatic attraction between the two fragments on either Gaussian or Multiwfn.
I can think of a simple approach of performing some type of atomic charge assignment (eg using NAO) and calculating the Coulomb attraction by treating each atom as a point charge, but I was hoping to be able to account for distributed electron density in the calculation.

EDA NOCV comes to mind, but I'm too long out of the game to judge correctly. But look it up and judge for yourself.


text:
Bromate ion point group?
Would the bromate ion have C3v point group due to the trigonal pyramidal geometry? I see a C3 rotational axis and a vertical plane of symmetry. Am I missing anything in terms of the double bonds or are those the only symmetry operations in this molecule?

As its not planar it should be should be C3v, the double /single are just a representation of bonding.


text:
Identifying Key Chemical Series, Pharmacophores, and Scaffolds in a Large SDF Dataset
fellow computational chemists!
I have encountered a challenge that I'd like to discuss and seek advice on. Suppose I have a substantial dataset in SDF format containing thousands of molecules. My goal is to identify the major chemical series, pharmacophores, or scaffolds within this dataset. The primary motivation behind this task is to reduce a large dataset into a more manageable one that retains representative structures. This curated dataset will then serve as a reference for subsequent hit selection processes in my research.
The overarching objective is to ensure that my hit selection process captures sufficient chemical diversity from the larger dataset for subsequent in vitro testing. This is crucial for the success of my research, as it helps guarantee a broad exploration of chemical space and increases the likelihood of discovering novel compounds with desirable biological activity.
I would greatly appreciate any insights, suggestions, or experiences you might have to share regarding this process. Have you encountered similar challenges in your computational chemistry work? Are there specific tools or techniques you've found particularly useful in identifying key chemical features in large datasets? Your input will be invaluable in helping me streamline my research and improve the diversity and representativeness of my hit selection process.
Thank you in advance for your contributions to this discussion!

Probably a better fit at [mattermodeling.se].


text:
OOM Error Calculating ESP Charges with Psi4
I'm trying to create a script to generate partial charges for a given .dat file.
As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro file, which i wrote a script to convert to min.dat so I can use Psi4. Here is the script:
def gro_to_dat(input_file, output_file):
    with open(input_file, 'r') as gro, open(output_file, 'w') as dat:
        # Skip the title and total atoms lines in the .gro file
        gro.readline()
        num_atoms = int(gro.readline().strip())

        # Write the initial lines to the .dat file
        dat.write("molecule mol {\n")
        dat.write("   0 1\n")

        # Process each line in the .gro file
        for _ in range(num_atoms):
            line = gro.readline()
            atom_symbol = line[12:15].strip()[0]  # Extract the first character of atom name
            x, y, z = line[20:28].strip(), line[28:36].strip(), line[36:44].strip()
            dat.write(f"   {atom_symbol}   {x}   {y}   {z}\n")

        dat.write("}\n")

gro_to_dat("min.gro", "min.dat")

And it creates a .dat file, which looks like this:
molecule mol {
   0 1
   C   3.384   2.059   2.720
   C   3.419   2.209   2.725
   C   3.308   2.297   2.664
   H   3.465   2.000   2.761
   H   3.368   2.026   2.617
   H   3.294   2.038   2.777
   ...
}

Finally, my partial charge generation script:
import psi4

# Set Psi4 memory and number of threads
psi4.set_memory('8 GB')
psi4.set_num_threads(8)

# Read the min.dat file for molecular geometry
with open("min.dat", 'r') as f:
    lines = f.readlines()
    molecule_data = "".join(lines[1:-1])  # skip the first and last lines

# Create the molecule object using the data from the file
molecule = psi4.geometry(molecule_data)

# Set computation options
psi4.set_options({
    'basis': 'STO-3G',
    'scf_type': 'df',
    'e_convergence': 1e-6,
})

# Perform a single-point energy computation to obtain wavefunction
energy, wfn = psi4.energy("SCF", return_wfn=True, molecule=molecule)

# Compute the ESP charges
esp_charges = psi4.core.MoleculeESP.compute_esp_charges(wfn.molecule())

# Write the ESP charges to a file
with open("esp_charges.txt", 'w') as f:
    for charge in esp_charges:
        f.write(f"{charge}\n")

print("ESP charges written to esp_charges.txt")

I actually want to use 6-31G*, but even using STO-3G, the computation does not finish.
My output is very long, but it basically is this:
 ==> Geometry <==

    Molecular point group: c1
    Full point group: C1

    Geometry (in Angstrom), charge = 0, multiplicity = 1:

       Center              X                  Y                   Z               Mass
    ------------   -----------------  -----------------  -----------------  -----------------
         C            0.901238549949    -0.441467579029     0.193243059784    12.000000000000
         C            0.936238549949    -0.291467579029     0.198243059784    12.000000000000
         C            0.825238549949    -0.203467579029     0.137243059784    12.000000000000
         H            0.982238549949    -0.500467579029     0.234243059784     1.007825032230
                               ...
Running in c1 symmetry.

  Rotational constants: A =      0.00022  B =      0.00020  C =      0.00020 [cm^-1]
  Rotational constants: A =      6.53586  B =      6.11387  C =      6.09670 [MHz]
  Nuclear repulsion = 18130296.238725978881121

  Charge       = 0
  Multiplicity = 1
  Electrons    = 13000
  Nalpha       = 6500
  Nbeta        = 6500

  ==> Algorithm <==

  SCF Algorithm Type is DF.
  DIIS enabled.
  MOM disabled.
  Fractional occupation disabled.
  Guess Type is SAD.
  Energy threshold   = 1.00e-06
  Density threshold  = 1.00e-06
  Integral threshold = 1.00e-12

  ==> Primary Basis <==

  Basis Set: STO-3G
    Blend: STO-3G
    Number of shells: 8500
    Number of basis functions: 11500
    Number of Cartesian functions: 11500
    Spherical Harmonics?: true
    Max angular momentum: 1

Killed

I've tried increasing memory, and have already downgraded my basis set, but nothing seems to be working.

Suggestion: because the question is more about the setup of an eventually successful computation, move it to mattermodelling.  To increase visibility of your question on the sibling page, there is the specific tag psi4 (examples of previous questions).


text:
Vapour pressure and Raoults law
Suppose we take a binary ideal solution having components A and B ....  let's say that their mole fraction is 1/3 and 2/3 respectively (for simplicity)
Now ... We know that this solution will start evaporating untill a dynamic equilibrium is achieved ... And some molecules of A and some molecules of B from solution will break apart from solution and go into vapour phase .... Also the molecules breaking apart will be different for A and B(depending on which is more volatile)
Now **my **
In the expression of raoults law
what value we have to put in for  Xa(mole fraction of A) .... The initial one before dynamic equilibrium (1/3) or the final one after equilibrium is achieved (which will be different)
And if both the mole fractions are same then how come that is true??

The prior site search about the topic is the basic prerequisite for asking on most sites.


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Solubility of fluoroalkanes
I know haloalkanes generally aren't soluble in water due to their inability to form hydrogen bonds in water, despite being moderately polar. I was wondering why this is the case with fluoroalkanes too as fluorine is quiet capable of forming H bonds.
Someone suggested to me that fluorine atoms bonded to carbon atoms cannot form hydrogen bonds but this logic seems flawed. Take the case of chloral hydrate. If chlorine can do it, why not fluorine? Please correct me if I'm wrong.


text:
Why is the 'cis-1,3-dimethylcyclobutane' conformation of both methyl groups at the bottom more unstable than both at the top?
I'm having trouble understanding why both methyl groups on top of the ring is a more stable conformation than both at the bottom of the ring.
I found a reasoning that says the steric strain between two -CH3 groups are less when both groups are on top. (Figure (a))
Are the methyl groups closer to each other when they are both under the ring? Can this have something to do with the ring structure being a little 'twisted' or 'puckered' to minimize torsional strain?

The cyclobutane ring is ~35 degrees out of plane an conformationally flexible. Same principle apply as in 1.3-dimethylcyclohexane.


text:
How does one obtain K and stoichiometry from the Isothermal Calorimetry binding curve?
In Isothermal Calorimetry, I can appreciate that data is fitted to equations to obtain $K, \Delta H, \Delta G, \Delta S$ and stoichiometry, $n$.
However, I have seen from multiple sources that $K$ and $n$ can be obtained directly from the graph of enthalpy change against molar ratio of ligand added as such:

Obtained from wikipedia: https://en.wikipedia.org/wiki/Isothermal_titration_calorimetry
Where $n$ is the midpoint of the binding curve and $K_a$ is the slope (?) of the curve at what seems to be the midpoint.
But can also be seen here:https://www.youtube.com/watch?v=o_IpWcWKNXI&ab_channel=MalvernPanalytical (Just to show that the graph can be seen from multiple sources)
I can't figure out intuitively or mathematically why the $K$ and $n$ can be obtained directly from the graph as such. I have tried (taking $M_t = 1$ and $V_0 = 1$) substituting $Q = \frac{\Delta H}{2}$ into equation 7 from this document as well as differentiating equation 7 with respect to $X_t$. The results do not seem to agree with what the graphical method suggests.

Well, not directly, but with a bit of calculating...


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Temperature change when mixing different ratios of NaOH and H2SO4 solutions
Under the same conditions, mixing how many ml of 1M $\ce{KOH}$ solution and 0.5M $\ce{H2SO4}$ solutions to form a total volume of 100ml produces a rise in temperature?

If there is already the tag thermodynamics, the title thermodynamics question carries literally zero additional information, like a book title "The Adventure book" in the bookstore section "Adventure books". // The question itself as the English sentence is formulated in very confused way, words almost in a random order and it is  not trivial to guess wht is asked. // Note that questions looking like homework/test/exam/lab questions/tasks without written significant resolving attempts are explicitly off-topic on this site and will be closed.

Review the guide How to ask and Asking FAQs to prevent clarification requests, objections,  down-voting or closure.

What is the question  ? Is the "rise in temp" to be read as "rise of temperature" ?

@Maurice Or "What volumes...?".  It is not a question, it is a riddle or encrypted message.

What you've asked is a neutralisation reaction. Any amount of acid and base mixed together would cause a neutralisation reaction, and in general, neutralisation reactions are highly exothermic reactions:
$$\ce{H+ + OH- -> H2O}$$
The enthalpy change for this reaction is $\Delta_\mathrm{r} H = 57.62$ $  \mathrm{kJ/mol}$, which is pretty high. Also since both of your reactants are strong electrolytes, your heat of neutralisation is not pH dependent.
So, mixing any amount of the acid and the base to create a $100$ ml solution would cause a rise in temperature.

I don't think this answer totally covers the question. The molar enthalpy of generic acid-base reaction is useful but not fully explanatory.


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Electrodeposition using Ionic liquids
I haven't found to many research papers yet, but would it be possible to electroplate nickle-aluminide onto a niobium alloy using an ionic liquid? I know certain industries are already using this combination for rockets or thruster according to my research so far. I'm looking in to using something like 1-ethyl-3 methylimidazolum bis (trifluoromethyl-sofonyl)mide or [EMIM] [TG2N] as the ionic liquid in the electroplating to act as the solvent. With what I know so far, should this be a plausible process for electroplating a niobium alloy?

Please do not duplicate posts! Remove this question or https://chemistry.stackexchange.com/questions/176834/electrodeposition-using-an-ionic-liquid . If you wish to make a change, edit the question you've submitted.

Nickel-aluminum alloys can indeed be deposited from solutions of nickel chloride in an organic chloroaluminate salt. As one example, Ali and Nishikata [1] describe an electrodeposition process on platinum and mild steel. From this reference:

Electrodeposition of aluminum–nickel intermetallic compounds (particularly Ni3Al) has been carried out onto platinum and mild steel cathodes from a 2:1 (mole ratio) aluminum(III) chloride-N-(n-butyl)pyridinium chloride (BPC) molten bath saturated with nickel(II) chloride at room temperature. A single phase of Al–Ni alloy is difficult to obtain by controlled-potential and controlled-current methods; however, it can be obtained by pulse current plating. ...

For a broader eeview, consult Oriňáková et al.[2].
References

Ali, Muhammad & Nishikata, Atshushi & Tsuru, Tooru. (2001). "Electrodeposition of Al–Ni intermetallic compounds from aluminum chloride-N-(n-butyl)pyridinium chloride room temperature molten salt". Journal of Electroanalytical Chemistry. 513. 111-118. 10.1016/S0022-0728(01)00607-6.

Oriňáková, Renáta & Morovska Turonova, Andrea & Kladeková, Daniela & Gálová, Miriam & Smith, Roger. (2006). "Recent developments in the electrodeposition of nickel and some nickel-based alloys_. Journal of Applied Electrochemistry. 36. 957-972. 10.1007/s10800-006-9162-7.


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Why do grignard reagents add to carbonyls at the carbonyl carbon, and not deprotonate at the alpha carbon to form an enol?
I thought that since grignards are such strong bases that they would be immediately protonated by the alpha hydrogen since it is an acidic hydrogen. However, I keep seeing answers that are saying that they just add to the carbonyl. I understand that they are strong bases, and therefore make bad leaving groups (forming a stable tetrahedral compound) once they add to the carbonyl, but I don't understand why they would add rather than deprotonate.

https://chemistry.stackexchange.com/questions/134270/grignard-reagent-will-act-as-a-base-or-a-nucleophile https://chemistry.stackexchange.com/questions/113023/grignard-reagent-and-acidic-hydrogen


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Automatically extracting SMILES of sub-group of larger SMILES structure?
Is there any software tool that can automatically extract SMILES of fatty acid legs of phospholipids if the SMILES of the parent lipid is given? Or any tool that can do it in InChI ?
Any advice will be really appreciated.


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Apparent color of nickel(II)chloride and nickel(II)chloride hexahydrate
Why does anhydrous nickel chloride (NiCl2) appear yellow, even though chloride ions are considered weak field ligands, which should result in a smaller ligand field splitting energy and the absorption of longer-wavelength light, while nickel chloride hexahydrate (NiCl2·6H2O) appears green, despite the presence of water, a strong field ligand that should lead to a larger ligand field splitting energy and the absorption of shorter-wavelength light? Can someone clarify this apparent contradiction?
In this example, NiCl2 absorbs in the violet region of Vis-light (high energy) as a solid, so appears yellow, although chloride ions are weak field splitting ligands according to the spectroscopic series. NiCl2 hexahydrate appears green in solid form, so absorbs in the red region of Vis-light (low energy), although water is a comparatively strong field splitting ligand. Why?

Maybe the chloride ions are not acting as ligands in anhydrous nickel chloride, like in $\ce{NaCl}$


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Is *.xyz a standard file format in computational chemistry?

https://youtu.be/f6K8k0sH2TY

The above YouTube tutorial talks about a file format called XYZ.
Later, the tutor uses this format to compute the bond length and bond graph of a molecule.
Is *.xyz a standard file format in computational chemistry? Or did this tutor just make it up for the convenience of his computations?
If this is a standard format, then is he following the standard in his XYZ files?

The tutorial series elected the .xyz file format because this utility format is syntactically simple plain ASCII, without a patent limiting its use, and widely used.  By custom in this community, the Cartesian coordinates are (implicitly) set in Angstrom ($1 Å = \pu{10E-10 m} = \pu{0.1 nm} = \pu{100 pm}$) because it is a unit of length close to typical bond lengths (the $\ce{C=C}$ double bond in ethene fore example $\pu{134 pm}$, or $\pu{1.34 Å}$, ref).

the organization of information eases to extract/parse the information with a script or program you might want to write for yourself / one of the many structure viewers around

in comparison to other file formats to represent a molecular structure, its content is very basic.  Some information, for instance which atoms are connected with each other, or the relevant bond order (e.g., single, double, aromatic, triple) organized in blocks (see for example chemical table formats as in .mol and .sdf (an entry on Wikipedia)) are missing. No indicator if the structure consists of one, or multiple molecules, nor if there is a charge, either.

it is not the input file format to launch one of the more advanced computations in typical quantum chemical programs (MOPAC, Gaussian, GAMESS-UK/GAMESS-US, etc.).  In addition to the atoms' coordinates and the intended computation (and level of theory, keyword basis set), they expect an input explicit about spin multiplicity (singlet, doublet, triplett) and  overall charge of the structure submitted.
Departing from for example a .sdf file, there is help to prepare these input files.  If not already provided by the program itself, openbabel (most recent documentation here, specific to quantum chemistry formats here), input generators of Avogadro, or gabedit
are among the assistants available.

To best of my knowledge, there is no (ISO like) standard regarding the representation of the (x,y,z) coordinates as 3F10.5.  If you would like a consistent representation of your data, you always can request openbabel in lines of
obabel input.xyz -O output.xyz

(additional examples of application here) to «tidy up» .xyz files to stick to the F10.5 format for each column.


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Does electroplating with copper takes less time than electroplating with zinc?
is electroplating with copper quicker than electroplating with zinc -- assuming that in both scenerios the cathode is steel, the surface area, the current, the thickness are the same, and the electrolyte is either zinc sulfate or copper sulfate? Thank you in advance.

There is an old saying "It can be quick, good and cheap. But not all at the same time."  Seriously, it depends much more on used particular technology than on used metal. There are dozens or hundreds of possible surface preparations, electrolyte compositions, geometry of the cell, used current densities..... Some are faster or better than others. You would have to compare particular techniques. But if everything is the same, plating by Zn is slightly faster (Zn molar mass, density)// More seriously, do not use StackExchange as an alternative to search engines. Do your search before asking.


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Is -NR3+ really meta directing?
For electrophilic aromatic substitution, it is said that -NR3+ is meta directing, but since it only shows electron withdrawing inductive effect and inductive effect decreases with distance so it must para directing since at para position inductive effect will be minimum.So is -NR3+ meta or para directing?


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When relaxing the strong field interaction, the (t2g)^2 configuration splits into 4 states. What is the symbolic configuration of the Eg state?

When relaxing the infinitely strong field, the electrons start to feel one another's presence. They will, therefore, give rise to sets of states such as T1g, T2g... for the (t2g)^2 initial configuration. Given that Eg is a doubly degenerated state, which symbolic configurations (arrangements of electrons in dxy, dxz, dyz--> t2g) would fit this state?


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Why ordinary oil was not recommended in Millikan oil drop experiment?
Why was it recommended not to use ordinary oil in Millikan oil drop experiment? What were the properties of oil used by Millikan?

Ordinary oil may contain double bonds that may chemically react in the experiment.

What is "ordinary oil"? There is a huge variety of chemicals called "oils" with a very wide range of properties.

Converting my comment into answer:
Quoting from here:

Ordinary oil wasn’t used for the experiment as it would evaporate by the heat of the light and so could cause an error in the Millikens Oil Drop Experiment. So, the oil that is generally used in a vacuum apparatus which is of low vapour pressure was used.

What type of oil is used then? Please check: Which oil was used by Robert A. Millikan in his oil drop experiment?


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Determine potential and electric field distribution between electrodes
I want to analytically determine a simplified potential and electric field distribution around planar electrodes, and an 40nm square electrode in an 50nm insulating well.
I think that the Poisson-Boltzmann equation should be appropriate but I’m unsure about a few things:

how do I account for the presence of the stern layer?

how do I find the electric field distribution when the potential applied is high (e.g. 2V? Where the Debye Huckel approximation cannot be used)

Cheers,
Bryan


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Storage of air and temperature sensitive reagents
What's your method for storing air/moisture and temperature sensitive reagents? For example:

A solid. Should I just blow some argon, screw the lid, put parafilm and put it in the fridge? Can a dessicator with silica be put in the fridge?

A liquid. Do you trust the septa seal that come with some bottles? I guess that after a few punctures, air can get inside the bottle. Moreover, sometimes I get bottles of air sensitive reagents with no septa. What is your procedure with this? Use a rubber septa or schlenk flask, maybe?

In general, do you trust your methods or purify your reagent before using it? For example, for something like $\ce{BF3 * OEt2}$.

Thank you in advance.

I am not much of a synthetic chemist, but here are my 2 cents. Schlenk + argon line + septa is good for one day's work, not for storage. Other than that, methods vary. Some things may sit in a fridge, some in a glovebox, and some have to be purified or prepared each time before use.

For future reference: for the body of questions, answers, and comments, chemistry.se offers to use mhchem as a comfortable method to add chemical equations.

Your question can not be easily answered. The only valid reply must be: It really depends on the individual case and the reactivity as well as physical properties.

Is your compound easy to evaporate? If not, it is good practice to
flame dry a Schlenk flask and to flush the flask multiple times with argon.
In the best case, you have dried the argon prior with driderite for
example. When the substance is transfered to the flask either through
the sept or in argon counterflow, it can be put under high vacuum for elongated periods of time to remove residual water and oxygen and than again flushed with
argon. Best to to this multiple times. For some hygroscopic compounds, also additional heating might be necessary in combination with high vacuum to get it really dry.

If your compound can be easily evaporated, and has a boiling point significantly different from water, destillation in a previously dried apparatus might be an option. I would add activated molecular sieve (see below) to the sample and  collection vessel to keep the water isolated.

As it was pointed out already, septs are prone to puncture and more
often you use them, more leaky they will get.  For longer term
storage, I put para film around the sept. Personally I found, that
silicon septs are better seals, but not as chemically resistant in
comparison with rubber. I perform some reactions which destroy the sept after one single use, so keep this in mind that you have to replace them more or less often.

When you are using a chemical that is sealed by the manufacturer, use always a balloon with inert gas, ideally argon because it is heavier than air to repressurize. Always use a balloon that was flushed several times beforehand with inert gas, otherwise it will contain residual water and oxygen.

Melting and sealing glas valves gives you a very good seal, but you need special equipment (oxygen flame, inert atmosphere). In combination with overpressure this might even be dangerous. Also, you can not easyly remove your compound from such a container.

If your substance of choice is a liquid, you may want to put
activated, that means very dry molecular sieve to the flask, to keep
it dry for a longer period of time. The proper way of activating
molecular sieve is to heat it to 400 degrees Celsius under high
vacuum until the pressure stabilizes. But be aware that there are
substances that will deteriorate the molecular sieve. You can not use
it for hydrofluoric acid or a reaction which contains oxalylchloride because they will attack
the silicon. I have however used molecular sieve for drying TBAF. If
a substance is extremely wet, molecular sieve is also not the perfect
choice to dry it, a better way would to start with $\ce{Na2SO4}$ first and
than apply molecular sieve. I had to do this once for wet
acetonitrile that was delivered in a fresh, sealed bottle. Molecular sieve can be obviously also used in the fridge or the freezer but continued freeze cycles may limit the lifetime.

For storing water sensitive solids I would use an excicator. The best way probably would the use proper high vacuum grease and use Schlenk flasks that are put under vacuum and than placed in the excicator. Subsequently the excicator itself would be put under vacuum. For the drying agent I use anhydrous $\ce{CaCl2} that was heated to 250 °C under vacuum for a couple of hours.

Regarding temperature dependence of compound stability, one has to keep in mind, that if the flask and its internal atmosphere are cooled down in the freezer, this creates a negative pressure and might suck humidity into the flask. You could counteract this be cooling a flask to freezer temperature under protective atmosphere first. If I have a compound that is very prone to hydrolysis and is kept in a freezer I put it immediately to the Schlenk line before it warms up, so the moisture is evaporated before it can react.

For substances that need to be cooled and still kept dry, I would use a Schlenk flask under argon and put these in a plastic container either with silica gel or $\ce{CaCl2}$ to avoid condensation water upon warming up to room temperature.

There are substances that are so reactive, that they are delivered to
you in sealed glas valves. Example are TMSI or
N-(trimethylsilyl)dimethylamine. In these cases it is best to order
just quantities that can be readly consumed in a small timeframe,
because they will often attack most sealing materials (TMSI
especially). On the other hand, due to their reactivity some substances like this might be used to dry your reaction mixture very efficiently.

Other ways to dry liquids, especially solvents, are the usage of elemental sodium or destillation over benzophenon. Here it is always necessary to check the compatibility. For example one can not use sodium with DCM but with THF.

Useful info on drying solvents:
https://chem.libretexts.org/Ancillary_Materials/Demos_Techniques_and_Experiments/General_Lab_Techniques/Drying_Solvents
http://books.google.com/books?id=SYzm1tx2z3QC

When you are not sure if a sample contains water, it is always good
practice to do a quick proton NMR to check for a residual water peak.
This will obviously just work when the water is not reacting itself
with your compound or only very slowly. In this case you can test the
fresh compound and also deliberately add a little bit of water to see
how the spectrum changes to have a reference  chemical shift for hydrolysis
deterioation product. For many compounds, this works especially well
with heteroatoms like 31p. (Here you can give very easily give an estimate in percent for deterioation just by comparing the integrals.

A special case might be the drying of gases: As mentioned above one can use an indicator drying agent like driderite that changes it's color when it absorbed specific quantities of water. Alternatives would be the stream though concentrated sulfuric acid or through granulate of $\ce{NaOh}$, $\ce{CaCl2}$...

In some cases it is not sufficient to keep a compound or reaction dry but it is necessary to remove oxygen beforehand. For liquids and solvents I flushed solvents with argon. Helium might also work in some cases. Otherwise sodium benzophenone ketyl not only reacts with water but with oxygen and creates a blue color, when no oxygen, water or peroxides are present.

Thanks for the comprehensive answer. However, I have so quick doubts that I hope you could help me with.

If the reagent has to be stored under inert atmosphere, as is sensitive to oxygen and moisture, would you store it anyways in a vacuum desiccator or simply in a Schlenk flask under argon/nitrogen?

Does your institution pose a problem if you store reagents in recipients without a proper sticker with pictograms and information? Or you place the sticker (or a new one) on the new recipient?

Three thoughts:

As soon as you pierce the septum, it is perforated. Depending on what you aim to store in the bottle, the material of the septum and its age (not age, but what happened to the septum [light, temperature, time of exposure to chemicals so far including the lab dishwasher, etc]), you can't trust the thing as much as you did prior to this. It is noteworthy that lids and septa are available in different materials. The gradual move away from fluorinated materials (PFTE/Teflon) with new seals of different chemical resistance and mechanical properties (more prominently seen on seals on GCMS vials) is a story on its own.
You can degrade a chemical in a bottle closed by a septum, but the cause isn't the perforated septum in first place.  If the chemical is stored in the fridge to compete decomposition, and your first puncture (esp. across an already pierced septum) is the needle to draw the reagent solution instead of the one with gentle overpressure by the Schlenk line to add dry nitrogen (meh), or argon (better for its density, but more expensive), chances are increased that for pressure release you draw (humid) air back into the bottle.  Or you open the still cold container, and humidity condenses on the walls, this water starts to decompose your chemical.  The cross on Aldrich's SureSeal septa helps you (like a grid) to minimize the number of punctures, though.
What do you understand as storage?  If it is long term, infrequent draw, and your chemical is compatible to glass (there a multiple sorts of glass), than sealing it in a glass vial still is the most reliable option in different volumes, white glass/brown glass, under own atmosphere/under inert gas; just a matter of equipment and some training for dexterity.

As for the purification of chemicals, the typical goto in organic chemistry (though not only covering $\ce{C_xH_yO_z}$, but a fair amount of inorganics), is Perrin/Amareggo' Purification of Laboratory Chemicals.
The idea of putting a dessicator into a fridge is foreign to me: typically too heavy to support it on the grid, it occupies too much volume per volume of the sample of interest (don't forget the valve to evacuate the inner), it is too expensive if this falls to the floor and shatters (not only for the chemicals to store + the drying agent).

Fresh parafilm over septa each time your use it will help preserve the contenrs

To store air-sensitive and temperature-sensitive reagents:
Air-Sensitive Reagents:

Use air-tight containers.
Inert gas can help displace air.
Store in a cool, dry, dark place.

Temperature-Sensitive Reagents:

Follow recommended storage temperatures.

Use appropriate storage equipment.

Prevent temperature fluctuations.
Label containers clearly, monitor conditions, and handle with care, following safety guidelines.

Regarding the third bullet, mentioning BF3·OEt2, two answers.
1, As has been noted by at least one other, in the safe practice of preparative chemistry, especially involving anhydrous/air-sensitive reagents, there are no good, sufficient answers to overly general questions. Purification, handling, and storage of each reagent, product, solvent/solution, is an individual problem to be addressed.
2, With regard to the specific reagent mentioned as an example, BF3·OEt2 [CAS No. 109-63-7]—taking this not as a general example, but as a specific question of how that reagent should be handled, purified, stored:
Veronica Cornel addresses the BF3.Et2O reagent in her entry in the Encyclopedia of Reagents for Organic Synthesis (EROS), here: https://onlinelibrary.wiley.com/doi/10.1002/0471264180.or013.01
Cornel addresses the observation that advantitious air oxidizes (and so darkens) commercial preparations, making redistillation prior to use the standard course for careful work (because the if reagent titre varies with time since distillation, a portion used in chemistry that is not redistilled is being used without knowing actual concentration). She cites Zweifel and Brown's 1963 Organic Reactions chapter with regard to use of Ca(OH)2 for capturing impurities and addressing problematic bumping. [https://doi.org/10.1002/0471264180.or013.01]
She also generally addresses this reagent's precautions, and handling and storage, but in this regard we refer to our longer post here, that such reading is not sufficient to teach these things.

Feel free to flag questions or answers that seem to be a safety issue. The community can close questions they feel are off topic. The moderators can do so as well.


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Is polarizing power related to solubility, melting point of a compound?
It is stated in this websites that
"It is found that the greater the possibility of polarization, the lower is the melting point and heat of sublimation and the greater is the solubility in non-polar solvent"
Is it true for all circumstances? As the only application of polarizing power that I've known is to define the ionic or covalent character of a bond.

There is the general rule about rules in chemistry that all rules have their exceptions. Except those they do not, as this rules applies on itself too.
Most of the rules are partly relying on rough models, partly being empirical. As they frequently do not consider minor effects, or are not even aware of them, there usually have exceptions.
Raising of covalent character can lead to molecular structures with low melting/boiling points like hydrogen halogenides, or long range structures and high melting points like silicon carbide.


text:
For CVD diamond in a reaction chamber why does a lower temperature lead to a greater height value/thickness
I've learned that for CVD (chemical vapor deposition ) crystals in a reaction chamber, the greater the temperature the smaller the growth rate so the crystals have a smaller height. I know at lower temperatures the growth rate is faster and this is something to do with the balance between etching and growth rate but I'm not sure why this happens. Also, we have to compare the height at different times and why there is a fluctuation as you leave it in the reaction chamber up to an hour (3 min, 10 mins, 20 mins, 40 mins and 60 mins)
Also we have learned that at larger temperatures it is a slower reaction in the reaction chamber, however I am not sure why it is slower so why the grain size is larger.

Huh, homework about making of diamonds? Some people are more lucky ;)


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Specific temperature ranges of kinetic combustion mechanisms
Do kinetic combustion mechanisms typically operate within specific temperature ranges? I tested some mechanisms from the scientific literature, and apparently they were only working at temperatures greater than 1000 K. Is this common to happen or am I probably making an error in my tests?

related https://chemistry.stackexchange.com/questions/16664/what-is-the-lower-bound-to-the-temperature-at-which-a-fire-can-burn


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Self heating of Hydrogen
I have read that hydrogen can undergo self-heating, through a catalytic process, without the presence of oxygen or air. Is that true?
I understand that this is not "burning" or "ignition", since this occurs without oxygen, and I don't think this is due to decomposition or rearrangement, as happens to $\ce{NI3}$ or 1,2,3-trinitroxypropane (nitroglycerine), since there's just molecular hydrogen, $\ce{H2}$.
Could someone explain if that occurs, and if so, where does the heat (energy) come from?

In case of hydrogen, it is not possible without oxidant, that may not be oxygen. Unless you mean nuclear reactions, like catalytic CNO cycle in massive stars.

Jack, I've taken some liberties in editing your question to make it more meaningful, i.e., changing "ignition" to "heating". Please let me know if my understanding is correct.

Perhaps you're thinking of para-ortho conversion of hydrogen, which is certainly not combustion, but does release a bit of heat.
Nuclei (e.e., protons) in a hydrogen molecule can have parallel or anti-parallel spins, called spin isomers. Weitzel at al state, "Freshly liquefied hydrogen... consists of a 3-to-1 ortho-para mixture." When hydrogen is liquified, the para spin isomer is energetically preferred. Slowly, the protons reorient, releasing about 1.5 kJ/mol as heat -- which causes hydrogen to boil off, even though the container is insulated from outside heat sources.
Clearly, it's not desirable for rocket fuel, for example, to be lost due to that energy release. During production of liquid hydrogen, catalysts, such as $\ce{Cr2O3}$, $\ce{Fe2O3}$ and $\ce{Fe3O4}$, can speed up the transition, so that the work of the extra "cooling" is done during production, rather than in storage.


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Methanisation in the Haber Porcess
I've been reading up on the Haber process lately.
In one such industrial case of ammonia synthesis, hydrogen is created through steam reforming, which creates some carbon monoxide. As the reaction continues, there exists both carbon monoxide and carbon dioxide.
In the final reaction chamber before the actual synthesis chamber, the Carbon monoxide and carbon dioxide are removed through methanisation - so it the majority (due to equilibrium) turns into water and methane.
My question is: how is the water and methane specifically removed without disturbing the remaining hydrogen and nitrogen?


text:
VBT and MOT at the same time!
In the SNAr reaction, it is said that the electron withdrawing groups should be at the ortho or para position for the effective electron delocalization to take place, and we draw Kekule's structure to justify it.
But can we justify it on the basis of Molecular Orbital Theory?

Yes. VB and MOT are different developments of the same theory, in the limit they are identical. So yes, if it can be justified in VBT it can also be justified in MOT.  I leave the details to the reader.