texts: How to Calculate Transition Dipole Moment from Two Known Wavefunctions

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I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment which was previously answered here:

How to calculate molecular dipole moment from a known wavefunction?

The information I have is the molecular orbital coefficients of alpha and beta from states 1 and 2 and the multipole matrix.
In considering just one Cartesian direction X, calculating the dipole moment along X would be something like

$$\mathbf{P_a} = \mathbf{C_a} \cdot \mathbf{C_a^T}$$
$$\mathbf{P_b} = \mathbf{C_b} \cdot \mathbf{C_b^T}$$
$$\mathbf{P} = \mathbf{P_a} + \mathbf{P_b}$$
$$\mathbf{\mu_{matrix}} = \mathbf{P} \cdot \mathbf{\text{multipoleMatrixX}}$$
$$\mu_{electronic} = trace(\mathbf{\mu_{matrix}})$$

$$\mu_{nuclear} = \sum_{\text{all atoms}}(Z_{nucleus} * \overrightarrow{r_x})$$

$$\mu_{X} = - \mu_{electronic} + \mu_{nuclear}$$

where $\mathbf{C_a}$ and $\mathbf{C_b}$ are the occupied alpha and beta molecular orbital coefficients, $\mathbf{P_a}$ and $\mathbf{P_b}$ are the alpha and beta density, $\mathbf{P}$ is the total density, and $\mathbf{\text{multipoleMatrixX}}$ is the multipole matrix for the X direction.

I might think that to calculate the transition dipole moment I might just change the densities to the transition densities doing something like I have show below. The transition denisty is based on page 10 of the article here:

$$\mathbf{S_a} = \mathbf{C_{a1}} \cdot \mathbf{C_{a2}^T}$$
$$\mathbf{S_b} = \mathbf{C_{b1}} \cdot \mathbf{C_{b2}^T}$$
$$\mathbf{P_a} = \mathbf{C_{a1}} \cdot \mathbf{C_{a2}^T} \cdot \mathbf{S_a^{-1}}$$
$$\mathbf{P_b} = \mathbf{C_{b1}} \cdot \mathbf{C_{b2}^T} \cdot \mathbf{S_b^{-1}}$$
$$\mathbf{P} = \mathbf{P_a} + \mathbf{P_b}$$
$$\mathbf{\mu_{matrix}} = \mathbf{P} \cdot \mathbf{\text{multipoleMatrixX}}$$
$$\mu_{electronic} = trace(\mathbf{\mu_{matrix}})$$
$$\mu_{nuclear} = \sum_{\text{all atoms}}(Z_{nucleus} * \overrightarrow{r_x})$$

$$\mu_{X,TDM} = - \mu_{electronic} + \mu_{nuclear}$$

where $\mathbf{C_{a1}}$ and $\mathbf{C_{a2}}$ are the occupied alpha molecular orbital coefficients from state 1 and 2, $\mathbf{C_{b1}}$ and $\mathbf{C_{b2}}$ are the occupied beta molecular orbital coefficients from state 1 and 2, $\mathbf{S_a}$ and $\mathbf{S_b}$ are the alpha and beta overlap matricies, $\mathbf{S_a^{-1}}$ and $\mathbf{S_b^{-1}}$ are the inverse of the overlap matrices.

I am unsure how to calculating the TDM since it is in disagreement with known calculated TDM values; some of these transitions should have a TDM of zero due to symmetry considerations. I have been unable to find any discussion on calculating the TDM from two wavefunctions, and most discussions I have seen are in the context of some perturbation on the ground state (i. e. TD or CI). I would be grateful if anyone could provide some suggestions or references to look at.


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I have noticed that, when a structure with bars (such as a gate or a grate) develops rust, this sometimes happens differently across the bars. In particular, it seems that the bars are alternatively clean and covered in rust.
The photos below (taken by me) illustrate this effect (I have highlighted the rusted bars with red arrows). In both cases, from inspection, all bars appeared to be made from the same material and covered in the same kind of protective paint (the rusted parts were exposed to the elements).
My theory is that perhaps the rusting process activates some sort of "circuit" between bars, such that one bar protects the next one from rusting.
Is this possible?


texts: Reactivity of thioesters with respect to nucleophilic attack

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Why are thioesters relatively reactive with regard to nucleophilic attack? Prof says to wait until pchem 3 when we learn about orbital symmetry. He also said that sulfur’s d-orbitals (?!) don't have the correct symmetry to participate in resonance with the carbonyl carbon.

Wait. I thought that sulfur didn’t utilize its d-orbitals. Was it previously taught that sulfur’s lone pairs were in d-orbitals? Why would sulfur even need d-orbitals when in a thioester? Can't we just explain this based on the poor overlap between carbon's 2p and sulfur's hypothetical 3p orbitals?


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A couple of weeks ago we did a lab where we had a bunch of standard solutions of alcohol, dichromate, and sulfuric acid. We also had one unknown concentration.

We heated them so they would all react, and the initial orange dichromate turned slightly green (the ion $\ce{Cr^{3+}}$ formed). Then we placed each reacted soln in a calorimeter which can emit light of certain frequencies. I believe we chose 635, which should have emitted orange light through the solution. the absorbance/transmittence were calculated for each standard soln until we had a line of best fit. Then the absorbance of the unknown concentration was given, so we used to line to match it to it's concentration (of alcohol).

I'm confused as to why we had to use the color orange in our emission and why a reaction was even needed in the first place.


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My book (NCERT India) says that the electrode potential of metals is decided by the following factors:

Enthalpy of atomisation
Ionisation enthalpy
Hydration enthalpy

It says that the first two require energy while the latter releases energy. That's all good and I can follow till there. But then it provided this table of thermochemical data for 3d series metals (Table 8.4 page 218):

It says that the electrode potential for $\ce{Cu^2+/Cu^1+}$ is positive because the hydration enthalpy does not balance the enthalpy of atomisation and the ionisation enthalpy - which requires energy. By the same logic, simply summing up 1 & 2 (sum of the first and second ionisation enthalpies) & 3 would give a positive value. How is it feasible for any of the there elements to have a negative electrode potential?


texts: Why does Ammonium sulfate cause proteins to precipitate?

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I'm trying to understand an observed reaction from a chem practical:

You have a solution of ammonium sulfate, which you add to a bovine serum albumin solution. The proteins precipitate, and the solution becomes cloudy. w/v % of $\ce{(NH4)2SO4}$ at this point is 57%.

When you add water (in a ratio of 2 parts water: 1 part serum solution)to the mix, the process reverses, and the solution becomes clear again.

This can be explained by the ammonium sulfate solution 'stealing' water from the proteins, which causes them to precipitate, and then the process reversing once more water is added. (Right?)

Question: Does the ammonium sulfate 'steal' the water because it wants to reach equilibrium, or because it's supersaturated, or what?


texts: sp2 hybridisation of alkyl radicals causing formation of racemic mixture

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What I know about $\ce{^{.}CR3}$ radical is that it has both $\ce{sp^2}$ and  $\ce{sp^3}$ character but the $\ce{sp^2}$ character dominates and so the radical is $\ce{sp^2}$ in nature.
So, suppose we have the above situation. In this, a radical is formed  at  the carbon of the 6 membered ring at which one $\ce{-CH3}$ is attached since the bromination is selective, but will it form enantiomers? That is, can the $\ce{^{.}Br}$ radical attack from both sides?
In this question, the answer given is (c), but I think that enantiomers can not form, as the electron of the radical would be present only on one side of the radical carbon, and so cannot migrate to other side.


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This is really basic knowledge, but I am a little confused. I understand that if you put a tablespoon of water and a tablespoon of olive oil in the same container the water descends at the bottom of the container due to its density. In other words, since we put the same volume, water weighs more and thus it will move below the olive oil.

My question is why is the volume irrelevant with this experiment? Had we put a much bigger volume of olive oil in the container and just a small amount of water, shouldn't the water move above oil, since its smaller amount weighs less?

Any help would be appreciated.


texts: Why does the Rosenmund reduction stop at the aldehyde stage?

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In the Rosenmund reduction, an acyl chloride can be reduced to an aldehyde by hydrogenation over a palladium catalyst poisoned with barium sulfate.

Why isn't the aldehyde product further reduced to an alcohol?


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Will the nuclear testing done during the past decades or if a nuclear war happened in the present day, affect the accuracy of carbon dating in the future? (Hypothetically, we haven't developed a better dating method)

I mean you could just adjust the dating to the amount of Carbon-14 if there will be a sudden change, but will the fossils found in around and near the blast sites be dated differently from the unaffected areas?

I'm sorry not really good in science, I don't know if this should be in Physics STEX and I might be wrong in my understandings. Thanks in advance!


texts: What fraction of the vapour in electronic cigarettes is water?

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Not a chemist but looking for an answer I can understand.

Electronic cigarettes use propylene glycol and/or vegetable glycerin as a base liquid. This is heated and vaporized at a low temperature (my e-cig is 7 watt). When exhaled the VG/PG absorbs water from the air producing the visible vapour cloud.

Assuming standard temperature ($\pu{20^\circ C}$) and humidity ($\pu{50\%}$), what ratio (or percentage) of the visible cloud is water?

It's not that I can't find an answer to this, just can't find an answer I believe. Most based on rumor and warm fuzzy feelings of what people want to believe.


texts: Variation of current with time in gel electrophoresis

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During gel electrophoresis, if the voltage of the power supply is kept constant, how would the current in the circuit change over time?

I was wondering whether the electrical resistance of the gel would change over time. There will be migration of ions present in the buffer and it will resist the change in pH. But how does the electrical resistance of the gel change? Can someone explain?


texts: What is the most rare element in periodic table? I have a lot of confusion about this.


texts: Which is a stronger nucleophile in aprotic solvent: water or hydrogen sulfide?

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Which one is the stronger nucleophile in aprotic solvent: $\ce{H2O}$ or $\ce{H2S}?$

According to my notes, nucleophilicity order is directly proportional to basicity order in an aprotic medium, and is inversely proportional to basicity order in protic medium.

And $\ce{H2O}$ is a stronger base than $\ce{H2S},$ so it should be the strong nucleophile, but the answer is given as $\ce{H2S}$ is the stronger nucleophile. What is the reason for that? Am I missing something?


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A chemistry test I did was an IGCSE test. One of the questions was

  Is Hydrogen Chloride ionic or covalent?

Now, on a sheet I have been given, it states the hydrogen ion is $\ce{H+}$. So, it forms a positive ion, like metals. I'm fine with that. I know that hydrogen is strange and I also know that the (I)GCSE chemistry curriculum simplifies/lies a lot. The bonding in Hydrogen Chloride is covalent. Now, since a 'Hydrogen ion' is just a proton, I wanted to know whether in reality it actually exists or not.


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The Royal Institution seems to claim that they still possess some of Faraday's original gold colloids: "These liquids are some of the first examples of metallic gold colloids, made by Michael Faraday over 150 years ago."

However, in a publication in Gold Bulletin (D. Thompson, Gold Bull. 2007, 40(4), 267-269.), the following is stated: "Faraday's original gold colloids were very stable and at least one example survived until the second World War, when it was accidentally destroyed by enemy action [...]."

Do Faraday's gold colloidal solutions still exist?


texts: Could you use All-Purpose Flour as a model rocket fuel?

texts: I'm building a model rocket, and I'm trying to find a good fuel. I've done a lot of research and I know about r-candy and the aluminum-ammonium fuel, but I was wondering, before I made any of these, if I could use All-Purpose Flour instead. From what I've seen, it is highly combustible, and I think it would do a good job. However, it appears to burn slower than r-candy. Would it still burn fast enough to get a rocket launched? I also noticed that it doesn't pack easily, and I'm looking to make a solid rocket motor. Could I use water to pack it into the motor tube, then leave it to dry for a few days? Or could I pack it some other way?


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I was once told on this site that it was incorrect form to use units that specify the chemical being referred to in dimensional analysis. For example:

$$150.~\mathrm{g}~~\ce{KNO3} \cdot \frac{1~\mathrm{mol}~~\ce{KNO3}}{101.103~\mathrm{g}~~\ce{KNO3}} \cdot{} \frac{1~\mathrm{mol}~~\ce{C7H4O}}{6~\mathrm{mol}~~\ce{KNO3}} \cdot \frac{104.106~\mathrm{g}~~\ce{C7H4O}}{1~\mathrm{mol}~~\ce{C7H4O}}=25.7~\mathrm{g}~~\ce{C7H4O}$$

This is the way I learned it, and I feel that this clears up confusion that might otherwise arise when from performing such a calculation.

My overall question is: is it acceptable to do dimensional analysis as I presented it? If not, please explain why it is not correct to do it this way and show me what I should be doing instead.


texts: Any way to see "cubic-active" vibrational modes in molecules?

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For molecular complexes with a moderate amount of symmetry there are usually vibrational modes that are neither infrared nor Raman active. Sometimes these modes transform as some cubic polynomial in x,y,z. For example the $B_{1u}$ irrep in the $D_{4h}$ group which transforms as $xyz$.

My question is: it possible to measure these kinds of vibrations using some sort of non-linear optics? For example, measuring the absorption of three photons instead of just one like in infrared spectroscopy/reflectivity. In the case of $B_{1u}$ above, this would translate to 3 photons polarized with x,y,z respectively and whose total wavenumber matches a $B_{1u}$ vibration. Or perhaps a more complicated multi-photon version of Raman spectroscopy could do this?


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I'm no expert in chemistry, but I know that corrosion can cause great problems in systems. I'm working on a prototype, and trying to figure out if corrosion will cause issues.

The setup
Imagine the following system. Two aluminium rods make contact with thin aluminium plates (3 mm thickness). Each aluminium plate is connected to the battery with copper wires:

The surface of contact between the aluminium rods and plates is subject to moist and dust infiltration (see figure above). Also the connections from the copper wires to the aluminium plates are in that "dirty zone".
When contact is made, a DC current of 10 Amp flows:

The contact surface between aluminium rods and plates is about 3 to 4 cm^2. The contact force is about 2 to 3 kg. Contact is not made in a very smooth way. Some gliding or even scratching can occur.

Possible issues
I'm afraid corrosion will appear on the contact surface between the aluminium rods and plates. I'm also worried about the copper to aluminium connections.

Possible solutions

Perhaps I should replace all aluminium in the system by copper. Copper is a more "noble" metal compared to aluminium. But copper lacks the same protective natural oxide coating like aluminium has.
Perhaps I should insert a "sacrificial metal" somewhere in the system. But I have no idea where to put it in this specific case.
Perhaps I have to put some sort of coating on the metallic parts. But I have no idea what coating would be best, and if it can withstand scratching and gliding when the rods make contact to the plates - in a rough way.
Perhaps I have to switch from DC to AC current. This would be a last-resort option. For reasons I won't explain here (because it would lead us too far off-subject), this solution would cause an economical issue.


texts: How to differentiate between iron and sodium flames?

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According to my textbook, when a flame test of an iron salt is performed, it produces an orange, mostly yellow flame. Sodium salts also produce a yellow flame.
As the colours of these two flames are too similar, how do I differentiate an iron flame from a sodium flame?


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I was looking for a good table of ionic radii for an experiment on the van't-hoff factor when I stumbled upon R. D. Shannon, Acta Cryst. 1976, A32, 751.

In table 1, it lists 1 of the ions of carbon with as so:

  C +4 1S 2 III .06 -.08

The bold numbers are of concern here. The first number, 0.06 Å is what the paper refers to as the crystal radius, while the second number, -0.08 Å, is referred to as the effective ionic radius. I was also unable to find any good distinction between the two in the paper, except that the radius of $\ce{O^2+}$ for the crystal radius is 1.40 Å, while the effective ionic radius for $\ce{O^2+}$ is 1.26 Å.

I also doubt that this is a typo since it agrees with this statement made later in the paper:

  crystal radii differ from traditional radii only by a constant factor of 0.14 [ Å].


texts: Why does ozone have an electrostatic potential map similar to that of SO2?

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This is the electrostatic potential for ozone.

This is the electrostatic potential for sulfur dioxide.

(Click to enlarge)

They look almost exactly the same except one is all oxygen atoms and the other has sulfur in the center instead of oxygen.

Why does ozone have an MEP (molecular electrostatic potential) similar to that of SO2?


texts: Nickel(II) acetylacetonate crystals coming out blue

texts: An experiment in my class has us synthesising the acetylacetonate complex from hydrated nickel chloride being added to a solution of ammonia, acetylacetone and water. The products came out pale blue, yet according to every source I can find, the crystals should be green. Just wondering what the structure would be to accomodate the colour.


texts: Is it correct to term boron trifluoride a "catalyst" in electrophilic aromatic substitution?

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In Friedel Craft Alkylation of aromatic compounds using $\ce{BF3}$ :

$\ce{BF3}$ acts as  a lewis acid

It is used as a catalyst

Amount of $\ce{BF3}$ used in the reaction is almost equal to that of amount of benzene used.

$\ce{BF3}$ acts as a nucleophile.

I am sure about options $1$ and $3$ being correct and $4$ th being incorrect but I am hesitant about option $2$.
Catalyst is a substance that lowers the activation energy and enhances the rate of the reaction, in the end remaining unconsumed.
Now, what Lewis Acids do is that they make halogens stronger electrophiles by forming  complexes with them. Taking this further we can say that yes they serve as "catalysts" in the reaction because otherwise the reaction would have been lot slower.
However, the given answer is $1,3$. Is my reasoning correct and the answer wrong? Is it functioning as a catalyst in the reaction?


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The lunar highlands are made mostly of anorthosite (90% anorthite, the rest oxides of magnesium, iron, a little titanium, and traces of others), and pretty pure anorthite ($\ce{CaAl2Si2O8}$) is common. No minerals that are more than about half silica are known. The use of typical batch reactions to purify chemicals is (mostly) not practical on the Moon, as there is no water*, no halogens, and no carbon, nitrogen, or hydrogen.

Human habitats are going to need clear glass, the more the better. If the Moon was being settled, a way to make clear glass locally would be a priority. There are of course many things to be considered about the proper use of glass, but that is a separate issue. This question is about an advanced colony, not the first few habitats. You can assume the infrastructure for an involved process is available.

Could anorthite be processed into decent clear glass? How much impurity could it have? How can I look into the properties it might have and things to consider about the process?

Below is a table from the Lunar Sourcebook, Ch. 5 pg 129, showing
percentages of pure anorthite in various minerals mixed in igneous rocks
from the highlands:

*Actually there is a lot of frozen water and other volatiles at the poles, but getting it in quantity is a big challenge, and it isn't found anywhere else.


texts: Why does the displacement reaction of zinc in copper(II) sulfate solution result in dark metallic copper?

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It is commonly known that when zinc metal is placed in a solution of copper(II) sulfate, a displacement reaction occurs, and elemental copper is deposited onto the decomposing zinc metal. A practical demonstration of this shows the zinc turning black from the deposited copper.

My question is, why is the deposited copper black? I thought metallic copper was red. Moreover, the dark color can be seen instantaneously, meaning the color cannot result from copper oxidizing.

I recently read a paper that claimed the copper is deposited in the form of plasmonic nanoparticles, and said nanoparticles display excellent solar absorption (and low thermal emittance, in fact). Any ideas?


texts: I am an A-level student going into university and I am looking for a source of organic synthesis problems and answers that is freely available on the internet. The difficulty level I am looking for is something like first year undergraduate level. Any links would be greatly appreciated.


texts: Why doesn't ionization energy decrease from O to F or F to Ne?

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I know that in general, the first ionization energy increases across a period due to increasing nuclear charge, reasonably constant shielding & decreasing atomic radius.
From N to O, however, the I.E anomalously decreases. The reason usually given is that the spin pair repulsion between the 2px2 electrons in oxygen outweigh the effect of the increased nuclear charge.
However, the additional electrons in F & Ne are also spin-paired. Why doesn't the extra spin pair repulsion outweigh the extra nuclear charge in this case? http://www.chemguide.co.uk/atoms/properties/ies.html#top says

Between nitrogen and oxygen, the pairing up is a new factor, and the
repulsion outweighs the effect of the extra proton. But between oxygen
and fluorine the pairing up isn't a new factor, and the only
difference in this case is the extra proton. So relative to oxygen,
the ionisation energy of fluorine is greater. And, similarly, the
ionisation energy of neon is greater still.

But I don't understand how being a new factor or not makes any difference on its effect. It's not like the atom adapts to the new factor in O, reducing its effect its effect in F & Ne


texts: Finding pH of a buffer solution on addition of hydrogen iodide to it

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Question:

  A buffer with $\mathrm{pH} = 4.88$ was prepared by dissolving $\pu{0.10 mol}$ of benzoic acid ($K_\mathrm{a} = \pu{6.3E-5}$) and $\pu{0.50 mol}$ of sodium benzoate in sufficient pure water to form $\pu{1.00 L}$ solution. To a $\pu{70.0  mL}$ aliquot of this solution was added $\pu{2.00 mL}$ of $\pu{2.00 M}$ $\ce{HI}$ solution. What was the $\mathrm{pH}$ of the new $\pu{72.0 mL}$ solution?

My solution:

Using the Henderson–Hasselbalch equation

$$4.88 = -\log(6.3 \cdot 10^{-5}) + \log \left( \frac{0.10-x}{x} \right),$$

$$x = \pu{0.0173 mol}$$

Amount of conjugate base in $\pu{70.0 mL}$ is

$$0.0173 \times 70/1000 = \pu{1.211e-3 mol}$$

Amount of $\ce{HI}$ added is $\pu{4e-3 mol}$.

I'm stuck here having more $\ce{H+}$ than my base.


texts: Does (chloromethoxy)ethane react in a bimolecular or monomolecular mechanism?

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It is known that (chloromethoxy)ethane forms stable carbonium ions based on Nobel prize Chemist George Olah research Olah's method. This would indicate that (chloromethoxy)ethane reacts through $\mathrm{S_N1}$ mechanism. However, $\mathrm{S_N2}$ mechanism is also very feasible for highly electrophile carbon.

  Which one of the mechanisms is dominant?

Organic chemistry books in this case are not very clear. For example Clayden speaks about Olah's method and neighbouring group participation (pp. 419, 970 1st ed) but also gives relative rate for $\mathrm{S_N2}$ mechanism (pp. 425 1st ed)


texts: Is dissolution of H2S in water exothermic?

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While doing certain laboratory tests for qualitative identification of cations, I found that on passing $\ce{H2S}$ in the solution, the temperature of the solution increased considerably. When the temperature decreased due to addition of $\ce{NH4Cl}$, the solution again attained room temperature in passing $\ce{H2S}$.

This rouses the question: is the dissolution of $\ce{H2S}$ in water exothermic? Or does it react with other components of solution to make an exothermic reaction?

The Wikipedia article stated only this:

  Hydrogen sulphide is slightly soluble in water and acts as a weak acid (pKa = 6.9 in 0.01–0.1 mol/litre solutions at 18 °C), giving the hydrosulfide ion $\ce{HS^−}$. Hydrogen sulphide and its solutions are colourless.

The full experiment can be found here.


texts: How to calculate the amount of substance of barium sulfate that is precipitated?

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Determine the amount (in mol) of barium sulfate that will be precipitated when $200.0~\mathrm{cm^3}$ of $0.450~\mathrm{mol\,dm^{–3}}$ barium nitrate solution is added to an excess of sodium sulfate solution, given that the equation for the reaction is:
  $$\ce{Ba(NO3)2 (aq) + Na2SO4 (aq) -> BaSO4 (s) + 2NaNO3 (aq)}$$

I have just tried doing it and I got an answer of $0.09~\mathrm{mol}$, but I am not sure if this is correct, because I have only just been introduced to $\mathrm{dm^{-3}}$ so didn't really know what I was doing. I converted $200~\mathrm{cm^3}$ to $0.2~\mathrm{dm^3}$ (is this right?), and then multiplied this value by the concentration, $0.450~\mathrm{mol\,dm^{-3}}$, and this gave me $0.09~\mathrm{mol}$. Since the stoichiometric ratio between $\ce{BaNO3}$ and $\ce{BaSO4}$ is 1:1, I just suspected that the amount of substance of $\ce{BaSO4}$ would also be $0.09~\mathrm{mol}$.

If anyone could tell me if I have done this correctly, it would be greatly appreciated.


texts: condensation of tellurium on inside of ampoule?

texts: After heating an ampoule of tellurium around its melting point in a furnace for about a day, I've noticed drops of the element on the upper inside surface of the ampoule, as if it condensed there. I've also noticed similar behavior with other intermetallic compounds. Is it common for something like tellurium to condense and resolidify in drops when an ampoule of it is heated (like water as shown here)?


texts: IUPAC name for 1,2,3-trichlorocyclopropane?

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What is the IUPAC name for the two isomers of 1,2,3-trichlorocyclopropane? Similarly what is the name for isomers of 1,2,3,4-tetrachlorocyclobutane, 1,2,3,4,5-pentachlorocyclopentane, etc?

1,2,3-trichlorocyclopropane has two isomers, one of them with all the chlorine atoms facing in one direction and the other with one chlorine facing the opposite direction of the other two. In CIP rule, if two substituents on an atom differ only in their absolute configuration, R takes priority over S. However I have difficulty applying the rule here: two of the substituents are exactly the same. Nevertheless the two molecules are clearly distinct.

In practice the problem could be circumvented by using trans- and cis- prefix. But it does not address the key problem and fails on longer chains --- 1,2,3,4-tetrachlorocyclobutane has 4 possible arrangements, though not necessarily all of them have the problem.

Here are the isomers of cyclobutane and their mirror images. I use + and - to denote a chlorine atom above or below the plane. The number in the parenthesis is the number of distinct molecules.

+ + | - -    (1)
+ + | - -

+ - | - +    (1)
+ + | + +

+ - | - +    (1)
+ - | - +

+ - | - +    (1)
- + | + -


texts: Is there a way to generate SMILES from ChemDraw files?

texts:
I have a set of ChemDraw .cdx files, and I would like to extract smiles strings from it.
Can Open Babel do that or maybe the rdkit in Python? Any other suggestions?


texts: What is the reason behind the 2% increase in silver metal composition just after melting the raw silver alloy (55% silver)?

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I determined the silver composition from an alloy obtained from a jeweler to be 55% and wanted to extract silver out of it. However, upon melting around 5 kgs of alloy, the silver composition went up to 57%. I noticed similar increase for another 2 times (different alloys of silver, i.e. different samples)

Could it be something related to oxidation/reduction of silver or any metal resulting in the increase in composition while in the furnace?

What are some of the analytical tests out there I could use to accurately determine the elemental composition and the compounds present in the original alloy vs the one just after melting it?


texts: Does this cycle of reactions appear in nature?

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Does anyone know a real-world example of a cycle exactly like this:

or in other words, this:

$$\begin{array}{ccc}
\ce{A + C1 -> C2}\\
\ce{X + C2 -> C3}\\
\ce{C3 -> B + C4}\\
\ce{C4 -> Y + C1}\\
\end{array} $$

where the reaction $\ce{A -> B}$ is exergonic (i.e., involves a decrease in free energy) while $\ce{X -> Y}$ is endergonic (i.e., involves a free energy increase)?

The idea is that the above cycle, presumably catalyzed so that all the reactions go fairly fast under normal conditions, 'couples' the exergonic reaction to the endergonic reaction, thus driving the endergonic one.

I would love an example from biochemistry.


texts: Relativistic effect: d-electrons in metallorganic complexes

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With higher period the d-electrons of the metal are less strong bonded and therefore oxidative addition is easier for $\ce{Ir(I)}$ than for $\ce{Rh(I)}$ and much easier than for $\ce{Co(I)}$.

For metal carbonyl hydrides, electrons with higher period are more stronger bound to the nucleus, so $\mathrm{p}K_\mathrm{a}$ increases in this order: $\ce{HCrCp(CO)3 < HMoCp(CO)3 < HWCp(CO)3}$
This explanation sounds logical!

I also wrote that for $\ce{CO}$-complexes because of the higher effective atomic number for higher period atoms (higher ionization energy) the $\pi$-backbonding is weak and therefore less stable as e.g. for $\ce{Cr(3d)}$.
This explanation sounds logical as well!

But is the written tendency of the oxidative addition not a contradiction to the other tendencies?


texts: Steric factors greater than 1 or less than 0?

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From my understanding, the steric factor accounts for the relative orientation required by reactants in order to react in collision theory. This implies that steric factors should probably always be below 1 and above 0, since the relative orientation logically should always be a limiting factor, but below 0 or equal to 0 would mean that the reaction cannot take place.

However, my textbook, as a thinking point, asked if there could be a case where the steric factor is more than 1. Specifically, the example it gave was the harpoon mechanism between potassium and the iodine molecule.

My question is, can the steric factor be above 1 or less than 0, and how does that apply to the harpoon mechanism?


texts: How to calculate the radius of gyration (Rg) and the molar mass from light scattering data (Rθ and θ/degree)?

texts:
I have a homework problem that I don’t have a solution for, so I would like understand how to solve it and to know if my suggested way of solving it is on the right track. The problem is as following:

  A polysaccharide was analyzed by light scattering at several angles ($\theta$), and the following data were at hand:

  the system constant $K = 2 \times 10^{-8}$,
  the concentration is $2.5~\mathrm{mg/mL}$,
  the effective wavelength $\lambda = 400~\mathrm{nm}$,
  the second virial coefficient is assumed to be $0$ (meaning that no correction is needed for the concentration dependence).

  Calculate the molar mass and the radius of gyration for the polysaccharide.

We are also given the following information, where I think $R_\theta$ is the measured Rayleigh ratio, and $\theta$ is the scattering angle in degrees:

  \begin{array}{rr}
R_{\theta}& \theta\\\hline
5 & 60\\
4 & 90\\
3.33&120
\end{array}

From the lectures I was given the following equation to find the molar mass and $R_\mathrm{g}$:

$$
\frac{K \times C}{R_\theta}
  = \frac{1}{M} \left( 1 + \frac{16\pi^2}{3\lambda} R_\mathrm{g} \times
     \sin \left(\frac{\theta}{2}\right)^2 \right)
$$

I am unsure if the way I think is correct — and I don’t really understand all the steps. But here is what I think I have to do, or at least how to starts:

extrapolate to zero concentration to account for large molecules (polysaccharide) and non-ideal solution. To do so I think I have to plot $\frac{K \times C}{R_\theta}$ against $\sin\left(\frac{\theta}{2}\right)^2$.
From this the plot I get the linear equation $y = ax + b$ which I can use to:

Find molar mass because: $y - \text{intercept} = \frac{1}{M}$
Find $R_\mathrm{g}$ because: $\frac{\text{slope}}{y - \text{intercept}} = R_\mathrm{g}$

I read somewhere that I should make some sort of a second graph from the first one, in order to remove the $\frac{1}{M}$ part of the equation, and thus, I can somehow calculate $R_\mathrm{g}$, but I don't understand this.

My Questions:

Am I generally on the right track here?
What units do I get the molecular mass in from the above equation? Is it KDa?
I think I get $R_\mathrm{g}$ value in nm?


texts: Why do the amino groups in EDTA deprotonate first, in contrast to amino acids?

texts:
We know that in amino acids, carboxylic acid groups deprotonate first than the amine groups. For example, in alanine, $\mathrm{p}K_\mathrm{a,\ce{COOH}} = 2.34$, $\mathrm{p}K_\mathrm{a,\ce{NH3+}} = 9.69$ according to this page.

But according to the structures of EDTA as searched from Google, and from this extract from p.325 of Analytical Chemistry, 8e by Christian, et al.:

  At sufficiently low pH, the nitrogens can also be protonated and this diprotonated EDTA can be considered a hexaprotic acid. However, this occurs at a very low pH and EDTA is almost never used under such conditions.

the hydrogens of these amino groups seem to be deprotonated first before those of the four carboxylic acid groups. Why is this so?


texts: Gibbs free energy in standard state vs. equilibrium

texts:
I have a problem with the definition of the standard Gibbs energy and its connection to the equilibrium constants.

I think, that I've basically understood what the different equation mean but there is one thing, I'm unable to understand:

On the one hand:

One may describe a chemical reaction with $\Delta G=\Delta G^\circ + RT\ln{Q}$. In equilibrium $\Delta G = 0$ and the equation reads $\Delta G^\circ = -RT \ln{K}$.

On the other hand:

The definition of standard state is very clear: pressure = 1 bar and all reactants and products must have activity = 1.

If I consider these two aspects separately, everything seems to be fine. But these two concepts have to be valid at the same time, what leads to $\Delta G^\circ = 0$ (always), since $K=1$ (all activities are per definition = 1).

Therefore, $\Delta G^\circ$ would be always zero. I know that this isn't true, but I don't understand why.

Can anyone explain this to me?

Thanks!


texts: How is the configuration of an ester enolate double bond assigned according to CIP?

texts:
Two principal modern methods for enantioselective aldol reactions — the Evans aldol and the Masamune aldol — use a carboxylic-acid derived enolate rather than a ketone enolate as e.g. in the Paterson aldol reaction. For ‘traditional’ ketone enolates, a rule of thumb dictates that (E) enolates give anti-products and (Z) enolates give syn-products, typically rationalised by the Zimmermann-Traxler transition state model. Assigning (E) or (Z) to the enolate of an ethyl ketone poses no problems, as oxygen always has a higher Cahn-Ingold-Prelog priority than carbon, so it is all about the orientation of the enolate oxygen and the methyl group (see figure 1).

An Evans aldol reaction, the enolate of which is also shown in figure 1, can be analysed similarly. Oxygen has a higher priority than nitrogen, so the same basic rules apply.

A Masamune aldol reaction, however, has two oxygens attached to the enolate carbon, formally making it an O,O-ketene acetal. The CIP rules would dictate to follow the connectivities atom by atom. The Masamune auxilliary, like any ester, has a carbon attached to the oxygen. The enolate anion may be strongly attached to a certain atom (e.g. when using a boron- or titanium(IV)-mediated aldol reaction) but also may not be, or the attachment may be ambiguous (e.g. a potassium salt used for enolating in the presence of $\ce{LiCl}$).

Figure 1: The enolates in a Paterson-, Evans- and Masamune-aldol reaction and their double bond configurations where known.

To establish whether the double bond geometry is (E) or (Z), must I know if and which atom is attached to said oxygen? What if two different possibly attaching atoms (e.g. potassium and lithium) would give two different geometries? Is it possible to ignore said attachment altogether and just define the enolate oxygen as a free monoanion?

And do the CIP rules differ from common usage?


texts: Why are acid catalysed reactions of carbonyl compounds reversible?

texts:
I am currently studying aldehydes and ketones and their reactions. I've noticed that acid catalysed reactions are represented with reversible arrows, while base catalysed reactions are shown with regular arrows. Why is this so? Is this because the addition of the nucleophilic base stabilises the electrophilic carbon? Or is there some other reason?

Update: Sorry, "all" would not be appropriate here. In my text-book, it is mentioned only once. Nucleophilic substitution by weak nucleophiles is carried out in a weakly acidic medium, while a basic medium is used for strong nucleophiles. The corresponding mechanism use the convention I've spoken about. I can't see the use of reversible arrows elsewhere. I wanted to know why is the nucleophilic addition reversible (as per my book) in a weakly acidic medium.

My text book (not a standard one): Nootan ISC Chemistry XII

The pictures of the reactions (I'm not able to rotate them for some reason)


texts: Determining chirality after considering conformational interconversion in a cyclohexane

texts:
Basically I want to know what does the question mean when it says "taking into consideration conformational interconversions."

I assume it means, when I draw the mirror image of the given compound, the mirror image can be same as the compound itself (the case with option (a) and option (c) ) or it (the mirror image) can be same as confomer of the compound (the case for option (a) and option (b) ), for the compound to be achiral.

Note: option (a) shows both the features because option (a) is same as it's confomer and it is same as it's mirror image as well.

Is my assumption correct?


texts: What is the difference between exponential factor and orientation factor in case of Arrhenius equation?

texts:
As per the book (Nivaldo J. Tro)

The Frequency Factor: The number of approaches to the activation barrier per unit time.

The Exponential factor: Number between 0 and 1 that represents the fraction of molecules that have enough energy to make it over the activation barrier on a given approach. The exponential factor is the fraction of approaches that are actually successful and result in the product.

Collision Frequency: It is the number of collisions that occurs per unit time.

Orientation Factor: Usually between 0 and 1, which represents the fraction of collisions with an orientation that allows the reaction to occur

I am unable to distinguish the between the exponential factor and orientation factor. Aren't they saying the same thing? How do they differ from each other?

Another doubt is what does the number of approaches mean? i.e. number of approaches taken by a single reactant per sec, or all reactant per sec.


texts: Why is the definition of the mole as it is?

texts:
I have asked my teacher, as she was introducing the concept of mole to us, why that number was chosen, instead of more convenient one. She told me that it came from the definition of the mole, that is the number of atoms in 12g of Carbon 12. When I asked why that definition was chosen, she answered me that my question wasn't really a question, and I understood from her stare that asking why? twice in a row was not appreciated.

However, I certainly hope that this definition wasn't chosen randomly and that there is a reason for it being it.

I gave it some thought and I came to believe that it may be for convenience after all. There are 12 nucleons in a carbon atom and if we say that the electrons mass can be neglected, then we get that a mole is the number of nucleon it takes to get one gram of them. However, can we really neglect the mass of electrons, when the atoms get bigger? And if so, why do the element's mass per mole do very rarely end up being integers?

This makes me think there may be another reason, or some things I do not understand. And if there are no reason, then I guess I might just as well be doing religious studies..!


texts: How to find pH by mixing two solutions of different concentrations?

texts:
A mixture is made by combining 110 mL of 0.15 M $\ce{HCl}$ and 215 mL of 0.055 M $\ce{HI}$.  What is the pH of the solution?

$$\ce{HCl -> H+ + Cl-}$$
$$\ce{HI -> H+ + I-}$$
According to what I thought, the molarity of $\ce{H+}$ is the same as $\ce{HCl}$, because it is a strong acid and the mole ratio.  So, I added the molarity of both acids: $\pu{0.15M} + \pu{0.055M} = \pu{0.205M}$ for $\ce{H+}$ in solution.

$$\mathrm{pH} = -\log[\ce{H+}]$$
$$\mathrm{pH} = -\log[0.205]$$
$$\mathrm{pH} = 0.689$$


texts: Why substitution and elimination reactions are favored respectively at lower and higher temperature?

texts:
I read about the competition between nucleophilic substitution and nucleophilic elimination depending on temperature here. Though the webpage clearly says higher temperature favors elimination while lower temperature favors substitution, the explanation on the webpage is unclear.

Need a clear explanation regarding the phenomenon.


texts: How can aqueous KOH give alcohol by SN2 of alkyl halide?

texts: I ask this because SN2 requires a strong nucleophile, and I have read $\ce{OH-}$ isn't a strong nucleophile in a polar protic solvent like water. So, how can $\ce{OH-}$ replace, say $\ce{I-}$ from $\ce{CH3I}$ (methyl iodide)?


texts:
For example in dinitrogen pentoxide, $\ce{N2O5}$, covalent as well as coordinate bonds (type of covalent bonds) are present, but it appears that it contains only covalent bond.

What is a proper method to find out which type of bonds are present in a molecule?


texts: Is there a relationship between London dispersion forces and hydrophobic interactions?

texts: Looking at examples of these two molecular interactions makes me wonder what the differences or similarities are exactly.


texts: What does the IUPAC definition of the emf of a galvanic cell mean?

texts:
IUPAC's Gold Book defines the emf of a galvanic cell in the following way:

The limiting value of E(cell) for zero current flowing through the cell, all local charge transfer and chemical equilibria being established, was formerly called emf (electromotive force). The name electromotive force and the symbol emf are no longer recommended, since a potential difference is not a force.

Check: https://goldbook.iupac.org/E01934.html

I understand that zero current is required to find the emf since passing a current through the cell decreases its voltage. Moreover, we want to find the emf of the cell at some specific composition of the electrolytes, also ensuring a reversible reaction is taking place.

But what does it mean by "all local charge transfer and chemical equilibria being established"? Isn't the emf of the cell ZERO when the cell reaction attains equilibrium? What "equilibrium" does it refer to? And what does "local charge transfer" mean?


texts: What is a prosthetic group of protein? What are prosthetic groups?

texts: I have found this term while I studying the topic of ETS in respiration in plants.


texts: Is there a formula or way to determine whether an acid is a strong one or a weak one without conducting experiments in real?

texts:
I know the common strong and weak acids but if a mineral acid like $\ce{H3BO3}$ springs up, I can't actually tell whether it is strong or weak.
Also can I justify in chemical terms why $\ce{H2SO4}$ is a strong acid but $\ce{H2SO3}$ a weak one?
Why is $\ce{HNO3}$ a strong acid whereas $\ce{HNO2}$ a weak one ?

http://catalog.flatworldknowledge.com/bookhub/2273?e=ball-ch12_s04

The above link shares a list of strong and weak acids but fails to state why one acid is weak while the other strong.


texts: Why is the boiling point of alkyl iodide is more than alkyl fluoride?

texts: As far as I know, more the polar character of the organic compound, more will be the energy required to break the bond and thus more boiling temperature. Here in this case, $\ce{R-F}$ is more polar in nature than $\ce{R-I}$. Then, how $\ce{R-I}$ has more boiling point than $\ce{R-F}$?


texts: Trends in pi backbonding for main group elements across a period

texts:
Recently, I have been re-reading some undergraduate notes and found that there's a period trend in pi backbonding of main group elements (i.e. no transition metals involved) but no explanation were given other than it correlates with the increase in number of nonbonding pairs (lone pairs?):

$\pi$ backbonding strength: Si>P>S>Cl.

While it is well known that the lewis acidity of boron halides are explained by the strength of $\pi$ backbonding which decreases down the group, the same kind of explanation cannot be used for period trends like those above (especially B-P, B-S and B-Si are almost unheard of to check that) as across a period,orbitals in the same principal quantum number will be involved mainly in bonding, thus we should not expect a large difference in the size of the orbitals across a period and hence their extent of overlap due to spatial overlap alone.

In Chemwiki usdavis an explanation of the periodic trend for the same ligand but different metals were provided as an increase in the energy gap of the d, $\pi^*$ orbitals. However since we are not talking about d orbitals here, that is not very relevant

I suspect that since periodic trends have orbital energies in general decreases across the period, that it might be down to the increase in energy gap of the overlapping orbitals in the $\pi$ bonding between a given electron deficient atom and the donor atom of the type listed above. However this explanation has a problem  in that the role of nonbonding pairs are not accounted for in the trend. I then suspect it might be due to an increase in repulsion of the nonbonding pairs, but a repulsion argument seemed to be too simple to explain since the oribtals involve in the same period should have roughly the same size

  What is the mechanism or underlying explanation of $\pi$ backbonding periodic trends in main group chemistry?


texts: Proving 1 = 2 by POAC( Principle of Atom Conservation )

texts:
I have been told that applying POAC in any equation means conserving the number of moles of an element in both reactant and product .
For example :
$$\ce{H2 + O2 -> H2O}$$
Here when we apply POAC on oxygen we write :

Equation 1 :

No. Of Atoms(or moles) of "O" in reactant =  No. Of Atoms(or moles ) of "O" in product

Equation 2: (obtained from equation 1)

2(moles of $\ce{O2}$) = 1(moles of $\ce{H2O}$)

Where equation 2 gives us the necessary data required in solving questions of stoichiometric calculations .
I understand how equation 2 comes from equation 1 but I don't understand why equation 1 is correct even when the chemical equation is unbalanced ?

As I think equation 1 can be applied only when the chemical equation is balanced .
As here :

No. Of Atoms of "O" in reactant =2

No of Atoms of "O" in product = 1

Thus by equation 1 we can say that  $1=2$ .

And my book says POAC can be applied even when equation is not balanced . So here equation is not balanced and when I apply POAC I get $1=2$ . So what's is wrong with my reasoning?


texts: How to determine the number of stereoisomers of a di-substituted allene, exhibiting both axial and central chirality?

texts:
What are the diastereomers and enantiomeric pairs of the compound below where A are chiral groups (central chirality)? There should be 3 diastereomers and 3 enantiomeric pairs (last page).

I previously asked a question about tetra-substituted allenes.


texts: Explain how to filter Ca and Ba ions separately out of solution using insoluble compounds

texts: I had a question on a test that said to use insoluble compounds to make precipitates to filter out Ca and Ba from solution separately, but I couldn't find anything that will react with one and not the other??


texts: Which atoms in indole possess the greatest amount of electron density?

texts:
Presumably the amine acts as an electron donor, but that would suggest extra electron density of the adjacent carbons, making them more shield, which isn't seen in the results in the image below.

Specifically I'm wondering what causes the carbon with a chemical shift of 111 ppm to be less deshielded than the carbon with 123 ppm, as they look like they should be similar electronically, and I can't work out a resonance form that gives different results. Any help with this, and a more general rule set for chemical shift in aromatic compounds, would be much appreciated.


texts:
A slightly deranged curiosity: if we had a 3D printer able to “print” anything starting from “cartridges” of pure chemical elements, how many of the 118+ possible cartridges (or of the 98ish for non-artificial elements) would we actually need to print most - or all - foodstuff?

(OK, one could have phrased the same question in a more mundane way, I agree.)


texts: What is the correct name for this lab technique in crystallization?

texts:
Take a glass rod and rub vigorously the wall of the flask, the substance will crystallize out of the solution.

Take a fire polished stirring rod and etch (scratch) the glass of your beaker. The small pieces of glass that are etched off of the beaker serve as nuclei for crystal formation

But reaching back to my halcyon years of organic synthesis and crystallization, recalling vivid memories of scratching the sides of Erlenmeyer flasks with a glass rod to induce crystallization

It's a common lab technique. But does it have a name?


texts: Stereochemistry of hydrogenation with Raney nickel

texts:
If I react the following with Raney nickel and $\ce{H2}$,

$\hspace{65 mm}$

then I am getting a meso compound, as the $\ce{H-}$ anion will have anti addition, right? One $\ce{H}$ will attack on right $\ce{C}$ from bottom and the other on the left $\ce{C}$ from the top. That makes it a meso. But in the book it says, there is racemization. How?


texts: Experimental Validation of Schrodinger's Electron Cloud theory

texts:
I am currently doing a report for school on the electron cloud atomic structure theory. One of the major points on my report is the experiments performed by the scientists (Schrodinger and Heisenberg) to validate their hypothesis.

I cannot find any evidence of any experiments performed by them to validate their claim. Did they perform any experiments or was their theory purely based on mathematics? (There seems to be a lot of that surrounding this topic)

Thanks in advance, Sam.


texts: Abnormal termination of GAMESS in frequencies calculation

texts:
I want to optimize geometry and to analyse frequencies for transition metals ($\ce{Cu}$, $\ce{Mn}$, etc.) compounds using GAMESS. I use Avogadro for preparing input files and I have a problem: one of my calculations terminates abnormally with the following message in the output file.

  NO FORCE FIELD, SCF DOES NOT CONVERGE AT VIB0 POINT
  EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Thu Mar 26

What is the actual problem and how can I overcome it?


texts: I need to find the Ka of a weak acid in titration with a strong base

texts:
I have been working on this lab forever and have not been able to get a $K_\text{a}$ anywhere close to the accepted value. I’m sure I’m missing something really simple.

We titrated $\ce{CH3COOH}$ with $\ce{NaOH}$.

I used $10.00\ \mathrm{mL}$ of $\ce{CH3COOH}$. Volume of $\ce{NaOH}$ at the equivalence point was $10.14\ \mathrm{mL}$, and the concentration of $\ce{NaOH}$ was $0.1530\ \mathrm{mol \cdot L^{-1}}$.

First I found the concentration of $\ce{CH_3COOH}$ by using $c_\text{a} \cdot V_\text{a} = c_\text{b} \cdot V_\text{b}$, so $c_\text{a} \cdot 10.00\ \mathrm{mL} = 0.1530\ \mathrm{mol \cdot L^{-1}} \cdot 10.14\ \mathrm{mL}$
$c_\text{a} = 0.1551\ \mathrm{mol \cdot L^{-1}}$

Then I used the equation: $\ce{CH3COOH + H2O <=> H3O+ + CH3COO-}$
and the pH (at the midpoint of $5.07\ \mathrm{mL}\ \ce{NaOH}$) which was $4.87$

$$K_\text{a}= \frac{[\ce{H3O+}] [\ce{CH3COO-}]}{[\ce{CH3COOH}]
[\ce{H3O+}]}=[\ce{CH3COO-}]= 10^{-4.87}= 1.36 \times 10^5
$$
$$
K_\text{a}= \frac{(1.36 \times 10^5)^2}{ 0.1551} = 1.19 \times 10^{-9}
$$
Any help on what I am doing wrong would be greatly appreciated!


texts:
I have a doubt regarding the polymerisation of ethene, in the case of polymerisation, we basically are arranging the molecules in a systematic order and thus decreasing its entropy so shouldn't we be providing a low temperature in order to keep the process spontaneous...
Whereas, in reality the conditions for the reaction are high temperature and pressure?
Please help...


texts: I am unable to write the iupac name of the following compound


texts: Generating PDB file from electron density without force field minimization

texts:
Is there a step-by-step tutorial on how to generate a PDB file from an electron density file (*.ccp4)?

For my current project, I am trying to take some statistics of some PDB files. However, I do not think that the empirical energy function (MM) implemented in x-plorer could accurately reproduce experimental or QM data. As a result, I would like to use x-plorer to generate the raw PDB file myself (without minimization), but since I have never done this before, I was wondering if somebody could provide me some guidance on how this could be done.


texts: Converting phenol to para-nitrophenol via nitrosophenol

texts:
Our class 12 text book says that if we treat phenol with mixture of concentrated $\ce HNO_3$ and $\ce H_2SO_4$, instead of nitration, the ring is oxidized to quinone.

So, the book proposes that we should treat phenol with $\ce NaNO_2$ and $\ce HCl$ to yield 4-nitrosophenol, and oxidize it to nitrophenol.

However, I could not find this method in any other standard organic chemistry textbook (eg. the book by Clausen, or by Solomons and Fryhle).

Is there any book where this particular reaction is illustrated in details?


texts:
Recently, I happened to find a problem that involved the synthesis of anthracene from bromobenzene in the presence of tert-butyl lithium, using THF as the solvent, and at room temperature.  I am wondering the mechanism for this transformation.

Taking into account that THF degrades in tert-butyl lithium this is the one that I thought of,

It starts with aryne formation.  Benzyne reacts with ethene in a [2+2] cycloaddition.  This undergoes cycloreversion.  The resulting product reacts with another mole of benzyne to create the dihydro-derivative.  This reacts with another equivalent of tert-butyl lithium to form anthracene.

I have a question regarding this.  I do not think a cycloreversion could occur at room temperature (wiki gives a temperature of 180 degrees and states that the conrotary opening is unfavored).  Is this the case or not?  Am I missing another possible mechanism here?


texts: Looking at this structure, I would say this molecule has five chiral carbons. However, its IUPAC name (3R,4R,5S,6R)-3-amino-6-(hydroxymethyl)oxane-2,4,5-triol suggests that there are only four. Which is it?


texts:
$\ce{[Ni(CN)4]^2-}$ is a low spin , inner orbital complex having $\mathrm{dsp^2}$ hybridisation. According to Crystal Field Theory, $\ce{CN^-}$ is a strong field ligand that causes pairing of electrons i.e electrons occupy the orbitals of the lower $t_{2g}$ level completely before they occupy the higher $e_{g}$ level. If I am not wrong, Hund's rule of maximum multiplicity is followed while filling the orbitals of $t_{2g}$ or $e_{g}$.

$\ce{Ni^2+}$ has a configuration of $[Ar]3d^8$. If we write down the electronic configuration of $\ce{Ni^2+}$ in this complex, 6 of the d-electrons would occupy the $t_{2g}$ level and the remaining 2 would occupy then $e_{g}$ level.

If we search for diagrams of electronic configuration of $\ce{[Ni(CN)4]^2-}$, many of them show the last 2 occupying the same orbital in $e_{g}$ which seems to contradict Hund's rule in my view. But I am pretty sure that the the diagrams on the Internet are correct according to experimental data of magnetic moments and other features.

My question is whether strong field ligands can pair up electrons within orbitals of $t_{2g}$ and $e_{g}$ like in this case where the 2 $e_{g}$ electrons are paired up within one orbital instead of letting them occupy two separate ones. Or is there some other factor at play?


texts: How do scientists study liquid tungsten?

texts:
Inspired by this What If article: https://what-if.xkcd.com/50/

In the above article, Randall Munroe mentions that liquid tungsten is difficult to study because of its extremely high melting point. Because of this property, containers for the tungsten tend to melt before the metal itself. This might be a fairly elementary question, but given this difficulty, what methods do modern chemists use to study it, or other materials with extreme melting points?


texts:
There are two nickel complexes: one is octahedral and the other square planar. One complex is diamagnetic, the other is paramagnetic. Both are high-spin.

Now, $\ce{Ni^2+}$ that is octahedral should be paramagnetic, as should $\ce{Ni^2+}$ that is square planar. Actually any high-spin complex should be paramagnetic. Is it possible that the octahedral $\ce{Ni^2+}$ is paramagnetic, and square planar $\ce{Ni^2+}$ diamagnetic (achieved by not filling the last orbital even tho that goes against high-spin concept)?


texts: Do magnetic fields generated from ion flow through a membrane channel have any physiological relevance?

texts: Membrane pores and transporters see millions of ions flow through them per second. This creates a current and therefore a magnetic field. Do cells have any use for these fields (like maybe drawing charged receptors together?) or is it physiologically irrelevant?


texts: What is the oxidation state of all the atoms in this compound, W(CH3CN)3(CO)3?

texts:
$\ce{W(CH3CN)3(CO)3}$

I'm thinking:
$\ce{CO}$ is neutral so $\ce{O}$ is -2 and $\ce{C}$ +2

$\ce{CN}$ is negative one so $\ce{C}$ is +2 and $\ce{N}$ -3

$\ce{CH3}$ is positive one so $\ce{H}$ is +1 and $\ce{C}$ is -2

$\ce{W}$ is neutral so $\ce{W}$=0

is this right?


texts: How to apply oxidation numbers in the reaction to form hydrogen peroxide from a superoxide?

texts:
In the following reaction:
$$\ce{2O2- (aq) + 2H+ (aq) <=> H2O2 (aq) + O2(g)}$$

I see where some oxygen atoms have lost electrons, but I do not see what has gained electrons.
On the reactant side, the superoxide has a $-1$ charge per oxygen atom. On the product side, half the oxygen atoms now have a $0$ charge, so they lost an electron each (right?). For it to be a true redox reaction, does not a species/atom have to gain electron(s)?


texts: Mechanism for condensation reactions of amino acids

texts:
It is well known that peptides are synthesized by a so called "condensation" reaction between an amine and a carboxylic acid group to form the final amide moiety (because it releases water). In its general form, it resembles the picture below.

However, what is the actual chemical mechanism behind this reaction? My thoughts are that the amine can deprotonate the carboxylic acid and form a carboxylate - which is a very bad electrophile - so how would it form the amide from nucleophilic attack? I am aware that in the body, it is possible that this reaction is mediated by biochemical catalysts but I am still not sure of the overall mechanism. If this reaction does indeed involve biochemical catalysts, is it possible to complete the synthesis without them?


texts: Why exactly does atomic radius increase down a group?

texts:
I realize this should be a fairly basic question, but I'm still not quite satisfied with what I've been told from numerous sources. The general explanation seems to state that as we go down a group, there are more electron shells present to contribute to a "shielding" phenomenon, where inner electrons cancel out part of the inward force from the nucleus with a repulsive force. Thus with more energy levels present and more shielding, valence electrons begin to reside further and further away from the nucleus.

But at the same time, textbooks make a big deal about the concept of effective nuclear charge, which states that the "effective" force a given valence electron feels is a function of the net charge of the nucleus and non-valence electrons combined—the effective nuclear charge. I find this contradictory, since as we go down a group, the effective nuclear charge remains constant (equal numbers of protons and non-valence electrons are added). So what am I missing here? Why does shielding matter? Is the force on a single valence electron a function of the net nuclear charge or do we have to look at it from a more piecewise level, considering how other electrons are in between it and the nucleus and how it interacts with those individual electrons?


texts:
Why $\ce{K_4[Fe(CN)_6]}$ give blue ppt with $\ce{Fe^{3+}}$.

I know that potassium ferrocyanide is used for the qualitative analysis of ferric salts. It forms a Prussian blue ppt of $\ce{Fe_4[Fe(CN)_6]_3}$. However I couldn't justify the blue colour of Prussian blue.

Edit. In my view the colour may be due to charge transfer between ligand and central atom. However I have no reason to accept it.


texts:
As we all know that,

  Any poison is nothing but a chemical compound.

And as discussed in the question: Chemicals-do-have-an-expiry-date!

So, my question is: Is poison still poisonous after its 'expiration date'? and Is every poison always as poisonous as just after it was synthesised  ?

please feel free to update with the suitable tag(s).


texts:
Hello,
I will list the questions directly, if you want to know details please read below.
As in the figure, we have water+baking soda in a plastic cup, there are 2 versions in figure that affects LED's brightness and current that flows in circuit.

In 1st version of figure, LED is bright and more current flows
(measured 9.76 mA with multimeter)
In 2nd version of figure, LED is
dull and less current flows (measured 0.22 mA with multimeter)

So my question is, why changing aluminium's place from negative to positive affects current flow of circuit? is it related with aluminium's chemical properties?
Details that explain how i got to this question:
My main aim was to make a home made diode by following instructions in this wonderful site, i did one and it worked.To understand the working mechanism better, i decided to setup things as in the figure upper and faced with this question that looks like main working logic of this home-made diode.In site there was an explanation but i couldn't understand it.


texts:
Question:

Classify each of the following ions according to whether they react with water to give a neutral, acidic, or basic
solution:

As a general rule:

Strong acid + Strong base $\rightarrow$ Neutral solution
Strong acid + weak base $\rightarrow$ acidic solution
Weak acid + Strong base $\rightarrow$ Basic solution

According to my solutions manual.

a) $\ce{F-}$ is the conjugate base of a weak acid, therefore  the solution is basic.
b) $\ce{Br-}$ is the anion of strong acid, therefore the solution is neutral.
c) $\ce{NH4+}$ is the conjugate acid of a weak base, therefore the solution is acidic
d) $\ce{[K(H2O)6]+}$ is the conjugate base of a weak acid, therefore the soltuion is basic.
e) $\ce{SO3^2-}$ is the conjugate base of a weak acid, therefore the solution is basic
f) $\ce{[Cr(H2O)6]^3+}$ is an acidic solution, therefore the solution is acidic.

However, all these answers imply that water is acting as a strong base. How is this possible when water pH is $\sim 7$?


texts: Amines react with ketones whereas amides do not. Can anyone please explain why?


texts:
I want to ask a question about the C=C streching modes of Salicylamide.

I was presented with the following spectra and asked to comment on the bonds causing the peaks.

I identified the molecule from this and its NMR spectra to be salicylamide.

Here is my understanding of the IR spectra (solid state, ATR).

  $3391.66 cm ^{-1}$ is the asymmetric stretch of the $\ce{N-H}$ in the amide.
  $3184.80 cm^{-1}$ is the symmetric stretch of the $\ce{N-H}$ in the amide.

From previous understanding, I was aware that the asymmetric stretch requires more energy, and hence a higher wavenumber than the symmetric stretch.

  $2736.27 cm^{-1}$ is most possibly the $\ce{O-H}$ peak of the phenol. I attributed this to a few reasons, possibly due to hydrogen bonding or due to the dissociation of the $\ce{O-H}$ bond, which is driven to the right hand side of the equilibrium by the presence of the EWG amide group.
  $1672.98 cm^{-1}$ is due to the $\ce{C=O}$ stretch of the amide.
  $1628.09$ and $1589.49 cm^{-1}$ are due to $\ce{C=C}$ aromatic stretches.

I tried to find information to help me describe the $\ce{C=C}$ stretches (i.e. what orientation, any dipole arrows) but I failed to find any information to support my argument.

I recall in ferrocene and acetalferrocene, the ring breathing effect is observed, whereby ferrocene has fewer IR peaks than acetalferrocene due to a lack of a net dipole moment being non-zero, and I wondered whether there was a similar vibrational mode to apply for these two $\ce{C=C}$ peaks, but I was not sure.

What are the directions of the C=C stretches in the molecule of salicylamide in the range $1580 - 1630 cm^{-1}$?


texts: In my experience, most foods smell like they taste. Fragrant soaps, however, taste quite awful in comparison to their fragrances. How can some things smell and taste identical while others are so vastly different? I have a feeling this may have something to do with the vapor pressures of the molecules that make up the "thing," but I cannot find anything to confirm my hypothesis exactly.


texts:
re.:

What is the efficiency of UV lamp in ozone generation (Ozone g vs. energy consumed )

I read a lot of papers from the Internet on using UV lamp for generating ozone but none discussed the efficiency of such process.

How much energy (kWh) gets consumed by UV lamp to generate 1g of ozone ?

I read  Ozone Formation from UV Light
https://www.oxidationtech.com/ozone/ozone-production.html#answer2

and related web links
and all I get as pros and cons is:

"
Ozone production from UV light for commercial applications
Advantages of UV Ozone Generator

Simple Construction – only a UV lamp with ballast and a fan

Low cost – due to simple construction

Lower nitric oxide production

Disadvantages of UV Ozone Generator

Low ozone output – g/hr

Low ozone concentration – less than 1% by weight

Bulbs and ballasts will need to be replaced

"

Let me know your opinion


texts: Calculating the partition function based on molar heat capacity

texts:
Given the molar heat capacity of a partition function as a function of temperature, how would one determine the partition function?

Say the molar heat capacity = $\alpha T^2$


texts:
The cupric salt of a monobasic acid contains $3$ molecules of water of hydration per atom of $\ce{Cu}$. $\pu{1 g}$ of hydrated salt yielding on strong heating $\pu{0.3306 g}$ of $\ce{CuO}$. What is the equivalent weight of anhydrous acid?

My approach:
Let the formula of the acid be $\ce{HE}$ (where $\ce{E}$ is some element). So, the formula of the salt is $\ce{CuE2*3H2O}$

Don't know how to proceed from here. Any help would be appreciated.


texts: How to calculate the volume or mass of carbon dioxide gas absorbed by a calcium hydroxide solution?

texts:
Carbon dioxide reacts with calcium hydroxide as shown by the equation:
  $$\ce{Ca(OH)2 (aq) + CO2 (g) -> CaCO3 (s) + H2O (l)}$$
  A solution containing $\pu{0.1 mol}$ of calcium hydroxide reacts with
  excess carbon dioxide at $\pu{298 K}$ and $\pu{100 kPa}$. Which statement about the reaction is correct?
  (a) It consumes $\pu{4.4 L}$ of carbon dioxide gas
  (b) It produces $\pu{24.5 L}$ of liquid water
  (c) It consumes $\pu{0.5 mol}$ of carbon dioxide
  (d) It produces $\pu{10.0 g}$ of solid calcium carbonate

I have assumed that if there are $\pu{0.1 mol}$ of calcium hydroxide would there also be $\pu{0.1 mol}$ of carbon dioxide (since they both have a stoichiometric coefficient of 1?), please correct me if I am wrong.

Under this assumption, I have calculated the volume of carbon dioxide gas using the equation:
$$n=\frac{V}{V_\mathrm{m}},$$
where $n = \pu{0.1 mol}$ and $V_\mathrm{m} = \pu{24.79 L/mol}$, as this is the volume  one mole of particles will be contained in at a temperature of $\pu{298 K}$ and a pressure of $\pu{100 kPa}$.

Solving for $V$, I got:
$$
  V(\ce{CO2}) = n \cdot V_\mathrm{m}
  = \pu{0.1 mol} \cdot \pu{24.79 L//mol}
  = \pu{2.5 L} \text{(1 dp)}$$

However, from the statements above, $\pu{2.5 L}$ of carbon dioxide gas is not an option. I am not sure whether I have calculated the volume wrong or if I am supposed to use another approach for this question.


texts: If I have $0.01~\mathrm{M}$ $\ce{HBr}$ in $0.09~\mathrm{M}$ $\ce{KBr}$, why would the presence of $\ce{Br-}$ ions from the $\ce{KBr}$ not reduce the dissociation of $\ce{HBr}$ based on Le Chatelier's principle? Or would it?


texts: Why should animal fats not be used for cooking?

texts: Why we are advised not to use animal fats for cooking oils? I know that vegetable oil contain long unsaturated carbon chains and animals contain saturated carbon chains. What’s the difference if we use this?


texts: I understand that electroplating involves using an anode (copper in this case) and an electrolytic solution containing Cu(II) ions with some sulfuric acid. Why exactly does the anode need to be copper if you want to plate something with copper; couldn't something like a graphite electrode be used instead, as the $\ce{Cu^2+}$ ions can be provided by the solution?


texts: What are the conditions for liquid metal to be corrosive to another, different solid metal?

texts:
I've had already been aware of the fact that metallic aluminum can be degraded by coming in contact with mercury, but also came across another question more recently here explains a similar reaction with liquid gallium.

So my question is more general regarding corrosive action of any liquid metal on other metals.

What are the more general conditions for a liquid metal to be corrosive to another, different solid metal?

Perhaps the word corrosive is not the most suitable choice. Corrosion refers to a chemical reaction. If I understand it right what's happening, at least in the case of $\ce{Ga}$ and $\ce{Hg}$ on $\ce{Al}$, is a weakening of the grain boundaries by displacement and amalgamation.

Another interesting thought occurred to me. Liquid sodium is often used as a coolant in nuclear power plants. It's pumped through metal pipe (material unknown). So here is a good example of a combination that doesn't lead to corrosion. Are there examples other than I've mentioned that lead to corrosion? So what makes the difference?


texts: Diazo transfer to 1,3-dicarbonyl with tosyl azide

texts: What is the mechanism for the above reaction?


texts: What happens if water is treated to AC power supply of 12 kV and 14 kHz?

texts: Generally water splits to oxygen and hydrogen at $\pu{1.23 V}$. What happens if we treat water at several $\pu{kV}$ with frequency range of $\pu{10 kHz}$ to $\pu{15 kHz}$ AC supply.


texts: Why do cations have higher ionization energies than neutral atoms?

texts:
I know that metals have low ionization energies and non-metals have high ionization energies, but once a metal/non-metal becomes a cation, why does the cation itself have a ionization energy higher than the original neutral atom?

What is the scientific reason behind this increase in ionization energy?


texts: What effect does hydrogen bonding have on H NMR spectra?

texts:
My thinking is that an increase in electron density caused by hydrogen bonding should cause the chemical shift of participating atoms to be moved downfield. Am I right or wrong?

Can someone provide an example showing this phenomenon?


texts: Is there any way of representing a dative/coordinate covalent bond?

texts:
I was wondering if there was any way of representing a dative/coordinate covalent bond on a chemical diagram.

A single bond can easily be represented as a single line, a double bond as a double line and a triple bond as a triple line.

Take the below structure of ethene, a compound with single and double non-coordinate covalent bonds: each bond is easily represented by a single and double line.

However, the ammonium ion does have a coordinate bond between the lone pair of electrons on the nitrogen and the H+ ion from whichever compound donated it (e.g. hydrochloric acid). Despite this, I am unable to see how a coordinate bond could be represented, as, to me, it just looks like 4 non-dative covalent bonds.

Is there any way of representing a coordinate/dative covalent bond on diagrams like these?


texts: Why is benzoic acid a stronger acid than 3-aminobenzoic acid? Obviously at meta position, only negative inductive effect will operate. But, how does that make it a weaker acid than benzoic acid?


texts:
I was learning about autoionization in science and my science teacher wrote $\ce{H3O+}$ as $\ce{H+}$ — now, my intuition would lead me to assume that:

$$\ce{H3O+} = \ce{H+}$$

But, $\ce{H+}$ is just an atom with a positive charge because its lack of electrons, while $\ce{H3O+}$ is the product of $\ce{H2O}$ nabbing that $\ce{H+}$, right?

So, is saying that $\ce{H3O+} = \ce{H+}$ just for the purpose of simplicity in the sense that we are assuming that in the solution (aqueous, is the context I am dealing with), the positive hydrogen atom (is it more specifically called an ion?) will bond with a water molecule?

P.S. I know that you would call $\ce{OH-}$ hydroxide, and $\ce{H3O+}$ hydronium, so  what would you call $\ce{H+}$ (if it even has a name)?


texts:
Order of hydrogen bond strength:
$\ce{O-H...N}$ > $\ce{O-H...O}$ > $\ce{N-H...N}$ > $\ce{N-H...O}$. Why is that so?

According to me $\ce{O-H...O}$ should have the maximum strength while $\ce{N-H...N}$ should have the weakest hydrogen bonds based on the fact that oxygen is more electronegative than nitrogen. It would develop a higher $\delta^-$ charge and the hydrogen attached to it will have a higher $\delta^+$ charge which would make the hydrogen bonding stronger.
I can't reason out the order given in my textbook. After observing it, all I can guess is that oxygen being highly electronegative leads to higher $\delta^+$ charge on hydrogen while nitrogen being less electronegative easily shares its electron cloud with hydrogen, making the hydrogen bond stronger.
I am not sure about this reason as according to this it is more stable for hydrogen to make a hydrogen bond with a less electronegative element and possibly even an electropositive element, (unless and until the hydrogen is attached to a highly electronegative element), which does not occur in normal circumstances.
It would be great if anybody could help me figure out the reason for the above trend.


texts: Collective term for acid/base; hydronium/hydroxide

texts:
When writing about acids and bases it would seem very natural for me to abstract the set of both acids and bases and have a single noun for them, instead of cumbersomly listing them both each time. Compare anions and cations, where one can simply say 'ions' if one means both kinds.

Is there a established collective term? If not, what is the elegant way to speak about them?

About the same thing applies to hydronium/hydroxide. Is there a collective term? What about 'water ions'?


texts: Prediction of solubility (from chemical structure) at different pHs

texts:
I would like to know What is the best method for predicting the water solubility (and in other solvents) of a compound given its molecular structure at different pHs. What I know now is based on the seminal paper from Eisenberg et al.;

Eisenberg, D. & McLachlan, A. D. Solvation energy in protein folding and binding. Nature 319, 199–203 (1986).

where partition coefficient can be estimated depending on each atom type and its exposed surface to the solvent (SASA). This seems to work well for many substances, but I have the problem that I need to know the solubility dependence of some substances against pH, and I the only thing I found now as Chemaxon tools, but their results are not very accurate. It seems that the best option might be quantum mechanical calculations and tools such as COSMO-RS. At the moment we can not pay its license.

So in summary, I wonder what approaches do you suggest for calculating solubility of small chemical compounds depending on pH. Any method/software/server would be fine for us.


texts:
I am doing a school project on antioxidants and I would like to find out what makes a good antioxidant. I know examples of antioxidants such as Vitamin A, C and E but I was wondering what commonality exists between them in terms of chemical structure and bonding.

I am a novice in chemistry so a simple but informative answer would be appreciated (little to know nomenclature).


texts:
I can smell a urine like odour from some coffees. I don't seem to be alone in this as there are multiple reports on the internet of people having the same experience.

I have read from a few posts that results of the Maillard reaction create ketoamines that could be causing it.

What's the science behind this?

References:

Reddit
Yahoo Answers


texts: The color of the most sulfides of p- and d-block elements

texts: My teacher said that many of the sulfides of d-block and p-block are black. Why?


texts: Cation falling off electrode after electrolysis

texts:
I'm trying to find the electrochemical equivalent for zinc in an experiment.
I am carrying out electrolysis of zinc sulfate solution.
According to Faraday's law, m=zq.
I made a 0.1 M solution and kept time for electrolysis constant (1 min).
To get a value for z I plotted the mass over the charge (I*t). The current was varied. I'm getting a linear trend (mass deposited increases with increase in current) but a huge discrepancy of 100%.
Also in the experiment, after the electrolysis I noticed that the zinc separated and got suspended in the solution when I disconnected the electrode to measure the new mass. This could have affected results.
Any reasons for this? I might be able to redo the experiment if someone knows how I can solve this or get better results.
The metal ions should undergo reduction at the cathode. Maybe that's not happening?

P.s I also did it for copper sulfate and it was worse. Almost no copper stayed on the electrode after electrolysis
Also I used graphite electrodes for this. Before this, for another experiment I electroplated zinc with copper and all of it deposited. Maybe get better results with zinc/copper electrodes for this experiment instead of graphite?

Regards,
Haseeb


texts: Oxidising power of oxides of 15th group elements

texts:
In case of oxides of 15th group elements in form of $\ce{M2O3}$ ($\ce{M}$ is the 15th group element), does oxidising power of oxides increase or decrease down the group?
I tried to check by comparing the standard reduction potential (SRP) values or other related issues but didn't find any reliable sources.


texts: Molecular weight of NiMnGaFe compund problem

texts:
I have a big problems calculating molar/molecular etc masses, because in my case I have a monocrystal, co I cannot imagine it as a molecule and my compound is made of Ni-Mn-Ga-Fe. I know the mass and the atomic and the mass percents and I need to get molecular weight.

In the atomic percents I have: 50% of Nickel, 25% of Manganese, 17,5% of Gallium and 7,5% of Iron. So the ratio (of number of atoms) is 2:1:0,7:0,3 and I can find the atomic masses of all these elements but what is going to be the molecular mass?

I am sorry for probably trivial question (I am really dumb in this area unfortunately and I was searching on the internet for answers but every time the structure of molecule was known and this is a crystal)


texts:
I have a question that applies to material science and chemistry, I have no idea how to answer it (my chem is weak) so I thought I would ask it...

I'm trying to make an SLA/DLP type 3D printer that uses DLP light to cure resins in UV spectrum...

I'm good to go mechanically and electronically... But I'm at the point now where I need to decide what build plate material to use... I need to resin to adhere well to the build plate for the printer to work properly... I've been doing research, but havent found much... Most people use aluminum or other metal plates, but I know there is a better material out there, I just haven't found it yet...

I found the MSDS stats on a certain resin, and thought if I figure out what the resin is made of, I can figure out what materials it will want to stick to given it's chemical properties... So here it is

Isobornyl acrylate (15-30%)

Acrylic monomer (15-30%)

Urethane acrylate (10-30%)

Acrylic monomer (5-10%)

Epoxy acrylate (5-10%)

Acrylate oligomer (2-5%)

Photoinitiator (<1%)

http://www.sculpteo.com/media/imagecontent/DOC-06119-Objet-VeroClear-RGD810-US.pdf

Do you have any ideas of what this would naturally want to stick to?


texts: Does potassium aluminum sulfate have any effect on sexual performance/sperm counts or anything relating to the functionality of the sexual organs?

texts: I recently read about potassium aluminum sulfate that it has astringent property and has the ability to constrict body tissues and restrict blood flow. Since, for penis, the erection happens with the flow of the blood being directed to penis' blood vessels, does this effect of potassium aluminum sulfate cause an erection problem or any other effect on male/female sex organ?


texts:
I was teaching the $S_N1$ mechanism to a friend. He asked a question a subtle question I can't shake off. Take a tertiary alkyl halide and aqueous sodium hydroxide. The first step is the formation of the carbocation. My friend asked how did the alkyl halide just do that all of a sudden. What about the presence of the $\ce{NaOH}$ made this compound do this if it doesn't even interact with it ( in the first step)? I first thought maybe it was just that the first step is something that is a feasible process, and that the alkyl halide would do (to an appreciable extent) that even without the $\ce{NaOH}$, but I am not sure.

Is my idea correct?


texts:
When you see a fire burning, you have wood (fuel) interacting with oxygen which (through a chemical reaction) gives off heat - and light.

But the light appears to emit at some point well-away from the actual fuel - i.e. the flames appear to rise inches (or more) above the actual fuel source where (I assume) the actual combustion/reaction is taking place.

I assume this obviously has something to do with the fact that heat rises - and there is oxygen up there, but there is no fuel up there.

I might conclude that the light is artifact of the elevated temperature of the oxygen, alone up there - but this wouldn't explain the fact that different elements burn different colors - i.e. color is related to the fuel.

So it would appear that the only logical explanations would be either:

a. Fuel becomes "detached" from it's (solid) fuel-source, rises with the heat and emits light after rising.

b. Light is emanated near the fuel-oxygen reaction but appears higher due to some sort of bending it it's travel path due to high heating of nearby air - like how light squiggles over a hot BBQ grill.

There is also the fact that in a very hot "coal" fire the light does emit from the fuel - but in a "roaring" fire the flames appear higher. (Is this because a "roaring" file has higher heat - which correlates to the difference in flame color?) Why would these flames appear "above" the fuel?

Okay - I hope I've illustrated my line of questioning sufficiently. So how does it work?


texts: How to calculate mole ratio of two volatile compounds in distillation?

texts:
I have two volatile compounds (such as ethyl acetate and ethyl propionate). I am going to separate these compounds by simple and fractional distillation.

How do I calculate mole ratios of the two compounds and determine the boiling point temperatures of the first drop based on the liquid and vapor phase diagram?


texts: Does the nitrogen atom move with in the molecule in an ammonia maser, or does the molecule flip?

texts:
This intriguing answer to Can reactions produce microwave or radio wave radiation? says (in part):

An ammonia maser qualifies as an inorganic RF-emitting reaction. As the nitrogen changes position in the $\ce{NH3}$ molecule, ~24 GHz radiation is emitted.
Similarly, organic methanol, $\ce{CH3OH}$ makes a maser found in nature, emitting at ~36.2 GHz and also at ~6.7 GHz

The first link is to The Ammonia Maser in Feynman's Lectures on Physics and it includes a picture of a triangular pyramid with the nitrogen pointing "up" in one case and "down" in the other as an illustration of the transition.
But how does it get there? Does it "tunnel through" the nitrogen triangle, or does the whole molecule flip around? Can we even ask that question? Could we, if for example we labeled the corners with $\ce{{}^{1}H}$ $\ce{{}^{2}H}$ and $\ce{{}^{3}H}$ as a gedankenexperiment to make the two distinguishable?


texts: Acetic Acid % in vinegar? Given average molarity of acetic acid

texts:
Question:

  The stockroom claims the percent acetic acid in vinegar to be $2.0\%$. The density of vinegar is $\pu{1.106 g {mL}-1}$. Using average molarity given ($\pu{0.2844M}$) calculate the mass percent acetic acid in vinegar for comparison to the stockroom claim.

Not sure how to approach the problem but this is what I've done:

$$\frac{\pu{0.2844 mol}}{\pu{1L}} \times (\pu{60.05g {mol}-1})\times \left(\frac{\pu{1L}}{\pu{1000mL}}\right) = \pu{ 0.01707822 g {mL}-1}$$

if you have $\pu{1000mL}$, you'll have $\pu{0.001106 g}\text{ Acetic Acid} \div \pu{0.0000170782 g}\text{ Vinegar}$ so that will give $\%$ of acetic acid? I could use some clarification in solving this


texts:
The Dumas method is the easiest approach to measure the molarity of Gases. However, this method assumes that all the vapor (i.e. from a vessel) is condensed in, for example, an ice bath.

What are the errors from the Dumas method? I believe that Henri-Victor Regnault stated this error but I cannot find any good explanation.


texts: How to prevent Tin ions from precipitating as Tin(II,IV) Hydroxides

texts:
Alright, so Tin ions in most of it's salts have the propensity to form Tin(II,IV) Hydroxides and then precipitating out of aqueous solutions. What can I throw in the solutions to prevent this? Using Tin Fluoroborate doesn't precipitate Hydroxides, but I don't have access Fluoroborates. I really don't want very acidic solutions, either, for safety purposes.

Is there any complexes out there that does the job?


texts: Organic polyether with carboxyl moiety reacting with aldehyde, following reaction with sulfuric acid

texts:
I want to react the following molecule with conc. sulfuric acid in the presence of methanol at room temperature:

If I am right, this would make a methyl ester to be formed on the carboxyl.

The aim afterwards is to let it react with vanillin (in the presence of left over sulfuric acid) at 90°C, so it will give a coloured derivative.

Below is the structure of vanillin. As you can see, this has an aldehyde group and a hydroxy group.

Is it possible to let an aldehyde and ester react at higher temperatures?


texts: Increasing concentration of acetylcholine via SPE

texts:
I am trying to increase the final yield of acetylcholine (ACh) in my biofluid samples. I need to get the yield high enough for high confidence annotation of ACh (currently all I can really say is that I've got something that matches the ACh expected mz).

My first samples were prepared using C18 solid phase extraction using a water liquid phase and methanol to elute. Based on my understanding of C18 SPE, I assume I've lost a lot of ACh at this step, because I assume the positively-charged ACh would have been washed away during the wash step.

Now that I have a polar analyte to target, I need to prepare more samples with a higher ACh concentration. I should be able to increase the concentration by using an SPE protocol more amiable for ACh extraction, but I can't find a protocol like this in the literature. How does one design a targeted SPE protocol? Can I assume any HILIC procedure that targets charged molecules will be appropriate here, or is there more to consider?

My problem is made more complicated because I need the final, concentrated version of my extract to be compatible with my downstream bioassay (i.e. no carry over from acid, no strong solvent that can't be removed)


texts: Gaussian: Warning - assumption of classical behavior for rotation may cause significant error

texts:
I am playing around with a prostaglandin molecule (23 heavy atoms) in Gaussian09. My goal is to calculate the vertical ionization potential and electron affinity for the molecule. I already managed to converge the geometry of a neutral molecule (with the invaluable help of @Wildcat and Greg at this forum) using Opt=Tight and Integral(Grid=Ultrafine) as well as Opt(Maxcycle=1000) and SCF(Maxcycle=1000). In the log file I got the long-awaited line "Stationary point found" :) However there are also two warning messages there that make me worry a bit:

1. Warning -- assumption of classical behavior for rotation may cause significant error

2. Warning -- explicit consideration of  37 degrees of freedom as vibrations may cause significant error

Now, the zero-point energy that I am interested in has been reported as:

  SCF Done:  E(RB3LYP) =  -1004.62842050     A.U. after   14 cycles

However, right below the warning messages I found something like:

  Zero-point correction=                           0.442805
  (Hartree/Particle)

  Sum of electronic and zero-point Energies=          -1004.185615

Now, my specific questions are:

Should I worry too much about these warnings if my resultant Ionization Potentials (IP) and Electron Affinities (EA) look reasonable?
Should I do my IP and EA calculations taking the Zero-point correction (see above) into account and use the value of -1004.185615 as my "true" zero-point energy?
What can I do to eliminate the warning messages mentioned above? I read something about a keyword "freq=HinderedRotor" that could be used in such a case.

I am eager to know how to interpret this whole mess and how to proceed. Thank you for any help you may offer!


texts: Is the current situation possible for recreaction in a lab?

texts:
I want to convert cellulose to another form (crystalline => amorphous). Cellulose requires a temperature of 320 °C and pressure of 25 MPa to become amorphous in water.(Is the pressure achievable in the lab?)

Is this doable in the lab and how should I begin on reproducing that situation (which tools would I need) ?

I'm guessing that a bunsen burner would produce high enough temperatures (but I'm not quite sure about the pressure)

EDIT to my question, following up the advice of bobthechemist...

Crystalline substance to amorphous - Other ways?
You can convert crystalline cellulose to the amorphous, more reactive form by heating it to a temperature of around 320°C under a pressure of 25MPa.

But are there other, less extreme ways, to achieve that amorphous form of the compound?
So because I can't achieve these high temperatures, how can I achieve it in another way?


texts: Please explain how to derive the magnetism  of polyatomic molecules? If we derive it using an addition of an oxygen atom to molecular oxygen ($\ce{O2}$) it will come to be paramagnetic like $\ce{O3}$?


texts: What is an intuitive explanation for Electron Configurations

texts:
I'm sort of self studying Chemistry. I'm now getting stuck wrapping my head around a concept (and I realize it was the same concept I had difficulty grasping years ago) and that is Electron Configurations.

I know that perhaps due to the nature of chemistry it is non-intuitive. However, I want an explanation that is more than "This is a bunch of numbers and letters that follow a pattern. Live with it" - which seems to just be the explanations I'm getting when I went to school.

So, my question is, what are Electron Configurations, and how would you explain them intuitively?


texts: What would be the effect of the addition of an inert gas to a reaction at equilibrium?

texts: Why does a dissociation reaction shift to the right with the addition of an inert gas?


texts: How to reconcile conflict between assumed oxidation state and the most stable multiplicity from electronic structure calculations?

texts:
Consider either of the small, neutral molecules containing two Zn atoms below. If I were to determine the oxidation state of Zn from this molecule, I would formally assume each Zn to be Zn(I) in order to balance the overall charge (if I give 2- for each O, 3+ for the Al, and 1+ for the H). I also assume that each Zn(I) has 1 unpaired electron as a result of this oxidation state. With this, I would assume that the molecule may have a triplet ground-state (putting aside the possibility of any broken-symmetry behavior for now).

The left and right images are the result of density functional theory geometry optimizations where I set the multiplicity to be 1 and 3, respectively. I find the (closed-shell) singlet structure is lower in energy than the triplet by 28.7 kcal/mol, in contrast with the prior discussion.

How can I reconcile these two conflicting notions? If I were to study reactions involving this molecule, do I assume the structure is a triplet because that's what the 1+ oxidation state on the Zn atoms would likely yield? Alternatively, do I assume that the structure is a singlet because that is what I calculated, even if that does not seem to agree with the oxidation state assumption?

If the appropriate approach is the former, then perhaps the oxidation states of each atom is not what one would formally assign. If the appropriate approach is the latter, then perhaps since Zn does not tend to be in the 1+ oxidation state, there is some unusual change in the electron configuration to stabilize this structure.

Computational details: this is computed using the M06-L functional, I have checked the stability of the wavefunctions, there is minimal spin contamination, both structures are local minima, and the trend holds true for other model chemistries.

Singlet state:   Triplet state:


texts: Why is NH3 a nucleophile in NH3+CH3 -> H3NCH3

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In the image below:

$\ce{NH3}$  has no charge as it has a full octet.

$\ce{CH3}$ needs 2 more electrons to form a full octet, so has a positive charge.

Why does $\ce{N}$ of the $\ce{NH3}$ want to bond with the $\ce{C}$, even though $\ce{N}$ already has a full octet and neutral charge, and bonding would make it have a negative charge?

Is it because $\ce{N}$ is more electronegative than $\ce{C}$ ?


texts: metallic bonding in transition metal sulfides

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I searched on the internet but failed to find a clear solution for this question:

Regarding transition metal sulfides like NiS or FeS, is there metallic bonding within their crystal structure?

If yes, how does it influence the macroscopic properties of the crystal and the possible reactions of the ions? Does the S atom affect the construction of the energy band and how do we calculate the certain effect?

If no, then how do we explain the low reflect rate, metallic luster and (semi-)conductivity?

My thoughts: there is metallic bonding in the crystals.

The polarization effect is most apparent in compounds of transitive metal which represents the covalent bonding in this type of compound. In other words, it signifies the extent to which the electrons are localized between the S atom and the metal atom. However, the formation of metallic bond needs the elections to be localized between metallic atoms. The paradox means that either the metallic bond can stabilize the S atoms, or the S atoms are involved in the formation of energy band, or the S atoms can form a special structure that stabilizes themselves.
Due to the structure of NiS crystal, this compound may have a layered structure. Hence, its fragility may be explained by a layered metallic bonding structure in the crystal.


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In discussing how best to deuterate chloroform, it occurred to me that we could use sodium metal to reduce hydrogen into hydrogen gas. If this could actually happen, this would be a great thing - we wouldn't have much if any residual hydrogen in the liquid phase of the system after treatment.

Is this possible? I had a possible mechanism in mind.

The problems I foresee are:

1) Won't reduction of chlorine to chlorine gas be a competitive, side reaction? From this page (http://en.wikipedia.org/wiki/Standard_electrode_potential_(data_page)) I see that the reduction potential for chloride ion to to chlorine gas is -1.36 V (unfavorable) and reduction of hydride ion to hydrogen gas is a +2.23 V (favorable). Am I interpreting and applying the data correctly?

2) What happens to the $\ce{CCl_3}$ radicals after hydrogen is reduced? Is dimerization going to occur to a large extent?

3) How then do we introduce deuterium and effectively incorporate it with $\ce{CCl_3}$ radicals?