texts: Can a s orbital overlap with any p orbital to form a sigma bond?

texts:
In internet resources, only $p_z$ orbitals are shown to overlap with $s$ orbitals to form sigma bond. But my teacher says that according to Valence Bond Theory, $s$ orbital overlaps with all three $p_x$, $p_y$ and $p_z$ orbitals to form sigma bonds. I am really confused about this. I heard that the concept changes when it comes to molecular orbital theory. Only similar orbitals (like $1s$-$1s$,$2p_x$-$2p_x$,$3p_y$-$3p_y$) form bonds but ($2s$-$2p_z$) do not.
Please clarify if there is any difference in concepts of overlapping between 'Molecular orbital theory' and 'Valence Bond Theory'.


texts: Springer Materials database molecule visualizer's 'crooked' straight-chain alkanes — science or art?

texts:
The Springer Materials database includes a molecule visualizer tool:

  Enhanced data visualization features display interactive crystal structures, data tables, and phase diagrams with export options for further analysis.

I noticed that some of the straight-chain alkanes $\ce{ C_nH_{2n+2} }$ appear to be clearly curved, other's look more like random displacements, while others nearly straight. I'm wondering if this is:

Just some random noise "as a helpful reminder" to the viewer that these are quantum systems with vibrations
"...helpful reminder" that long chain molecules bend and wiggle depending on temperature
Representation the static shape of the molecules
Something else?

Does octadecane really "look like" a human spine?

above: GIF is made from python-processed screenshots of n-octane through n-octadecane from Springer Materials molecule visualizer. Still are the last three in the series. Most have slight atomic displacements that appear at first to be random, but the last one available $\ce{ C_{18}H_{38} }$ suddenly looks like my spine when I've been slouching over StackExchange all day instead of getting work done. Why?


texts: Can acetaldehyde be condensed with methyl vinyl ketone to form 2-Cyclohexen-1-one as per the Robinson annulation

texts:
I have seen that cyclohexanone can react with methyl vinyl ketone to form a fused bicyclic cyclohexenone, I am wondering if the same reaction can be used to produce cyclohexenone the single ring product.
I have since seen that the process can be acid catalyzed in Tetrahedron Lett. 1971, 12 (52), 4995–4996, might there be any obstruction to the formation of the cyclohexenone product?


texts: Alcoholic potassium permanganate for oxidation

texts:
A question in my textbook:

  Though alkaline and acidic $\ce{KMnO4}$ are both oxidizing agents, in the manufacture of benzoic acid from toluene, we only use alcoholic $\ce{KMnO4}$ as an oxidant. Why?

I am not able to figure out the answer. But I think maybe the acidic and alkaline $\ce{KMnO4}$ are too strong and may oxidize the benzene ring. Or the benzoic acid may react with the alkaline medium. (Though I wonder why it wouldn't react with alcohol to give ester)

I also tried digging around the web but couldn't come up with anything satisfactory.


texts: Can you separate CO2 into carbon and oxygen using pyrolysis?

texts: I recently read about a pyrolysis process that separates methane into Carbon and Hydrogen. The basic technology/process is you have a vertical column of super-heated liquid metal and you inject methane into the bottom of the column. The methane breaks down into hydrogen and solid carbon. Are there any similar processes that separate CO2 into solid carbon and oxygen using liquid metals and/or salts etc.?


texts:
In chemistry class, we discussed how metallic bonding occurs when metals lose electrons and become cations while the lose electrons become delocalized electrons and bind the metal cations. These electrons are then free to flow around the metal cations. But could the metal be replaced with an ammonium cation instead? (Or any other polyatomic cation, but we only learn ammonium and I'm not aware of any others minus hydronium which doesn't exist out of a solution.) Would the electrons still be free? How would you make it? And how could you prevent the following from occurring?
$$\ce{2NH4+ + 2e- -> 2NH3 + H2}$$


texts: In what way trans alkenes are more symmetric than cis alkenes?

texts:
While providing the reason for the higher melting point of trans molecules, everyone says that trans molecules are more symmetric than cis molecules. An example can be found over here, where the OP states that:

trans-2-Butene has more symmetry than its cis isomer which results in better packing and hence higher melting point.

But to my (uneducated) eyes there doesn't seem any more symmetry (if any) in trans form than cis form of but-2-ene. I mean cis form is vertically and horizontally symmetric, whereas trans form is not.
Why do we call trans form more symmetric than cis form?


texts: Rate of reaction increases exponentially with concentration

texts:
In our chemistry practical we dropped 0.07g of Magnesium into various concentrations of an acid (sulfuric or hydrochloric - only one was used, not sure which), and measured the rate of reaction by the rate of the H2 produced (used a gas syringe). We then collected data at a suitable interval of the culmulative amount of H2 produced.
We drew the graph (with multiple concentrations - 0.25, 05, 0.75, 1, 2). Then we measured the steepest point (fastest rate) and took the gradient.
Plotting rate against concentrations (0.25, 05, 0.75, 1, 2), we came to the conclusion that rate varies exponentially with concentration.
But the rate law of a typical reaction is:

r = k * [A] * [B]

, which would mean doubling [B] would double the rate law, not have an exponential effect on the reaction. Why did we come to the conclusion that concentration has an exponential effect?

In our case the rate law, I would think, would be elementary, but we are not dealing with concentrations of both Mg and HCl, just HCl, as the Mg was solid - therefore no concentration of Mg in solution.

My question is: In a reaction between two liquids, is the rate of reaction linearly dependent on the concentration?
AND: What is the rate law of our reaction? - Why did we come to the conclusion we did?

Thanks for the help!! :)


texts: ChemSpider versus SciFinder for finding chemicals without CAS number

texts: Just trying out a couple of difficult options for identifying chemicals without CAS number information, and wondering whether Chemspider or SciFinder is a better tool for doing these searches. Do they search the same databases/repositories? Also, which has better features and is easier to use?


texts:
I know molar conductivity is conductivity of solutions by molarity,  but then I see on next page of my book it defines molar conductivity $\Lambda$ as follows:
$$\Lambda = \frac{\kappa a}{l},$$
where $\kappa$ is conductivity, $l$ is the distance between electrodes and $a$ is the area of cross section. Where does this formula come from?


texts:
Osmium(VIII) oxide or osmium tetroxide is a volatile chemical compound with the formula of $\ce{OsO4}$. It is highly toxic for supposedly irritating mucous membranes, but I'm not too sure if it is that or because it is a really strong oxidizer.
PubChem rates it as corrosive and highly toxic and according to Wikipedia, the toxic effects of $\ce{OsO4}$ are as follows:

$\ce{OsO4}$ is highly poisonous. In particular, inhalation at concentrations well below those at which a smell can be perceived can lead to pulmonary edema and subsequent death. Noticeable symptoms can take hours to appear after exposure.
$\ce{OsO4}$ will irreversibly stain the human cornea, which can lead to blindness. The permissible exposure limit for osmium(VIII) oxide (8 hour time-weighted average) is $\pu{2 µg/m3}$

How is $\ce{OsO4}$ toxic in nature? What makes it so?


texts: Preparation of standard Fe from FeSO4 • 7H2O

texts:
We were assigned to prepare a standard Fe for spectrophotometry determination of Fe. What we did is basically obtain a mass of FeSO4•7H2O, add a small a mount of distilled water before adding 18M of H2SO4 then dilute.

My question is what exactly is the purpose of H2SO4? I asked my prof about it and she said it was to prevent Fe2+ from oxidizing. I'm not really satisfied with that answer. Maybe because we did add hydoxylamine hydrochloride later to reduce the Fe3+ present so I don't see the need to do that addition aside from a different purpose. Can anyone provide the redox reaction of it if it really is a redox reaction happening? Thank you so much for any help much appreciated


texts: why do cone cells have broad responsivity spectra peaks?

texts:
My understanding of vision is that, although the cone cells in our eyes can detect three colors, there is enough overlap in the responsivity spectra (as shown here: https://en.wikipedia.org/wiki/Spectral_sensitivity) that we can see any wavelength in the visual range.

What is the physical reason for the broadness of the responsivity spectra peaks? Is it interactions with water molecules, interactions with the protein that the retinal molecule is attached to, or is it broad because many vibrational states of the retinal can be excited?


texts: What is the nucleophile in alkaline hydrolysis of a haloalkane?

texts: We know that haloalkanes are able to undergo $\mathrm{S_N1}$ or $\mathrm{S_N2}$ in alkaline hydrolysis, and the hydroxide ion is the nucleophile responsible for attack. But when we talk about hydrolysis, isn't it a reaction with water? Where does the hydroxide ion that attacks the haloalkane really come from; the water, or the alkaline catalyst?


texts: What are methods of identifying which amino acids are in a sample of protein?

texts: Are there any methods out there to identify which amino acids are in a sample of protein? Perhaps using NMR?


texts: Competitive 'Wittig' vs 'Peterson' C=C bond formation

texts:
If one considers the intermediate above, there are immediately two possibilities for subsequent reaction:

1. A Wittig-type olefination which would lead to a vinyl silane: This reaction happens to be unproductive as the vinyl silane can't do any further chemistry under the reaction conditions

2. A Peterson-type olefination: Which gives a vinyl phosphine (sp.), which may further be deprotonated to give another ylid (with concomitant formation of TMSOH) which will carry on to eventually give an allene.

My question is why is the Peterson faster than the Wittig. The immediate thing that springs to mind is the difference between acid and base catalysed Peterson reactions in which the base mediated version snaps shut before the C-C bond has a chance to rotate (i.e. kinetically very fast), but this isn't an explanation.

Potentially more promising is comparing the electronegativity/positivity of the elements, and noting that silicon is significantly more electropositive and hence a better electrophile however in the Peterson, the leaving group isn't such a driving force as the phosphine oxide from the Wittig.


texts: Is it possible to create a 4 inch by 4 inch channel through concrete using acid?

texts:
I'm trying to figure out a way to eat through concrete without damage pex tubing inside (its a radiant heated slab). Is there any way using some type of acid (hydrofluoric, muriatic ) to eat a 4 inch wide, 4 inch deep, and 71 foot long channel through the slab that could be tapped out with a blunt chisel? Pex tubing is resistant to most acids so it would not be damaged.

Also, this needs to be cost effective (under $1000).


texts:
After an injury or getting a scare it is typical to use medical products containing iodine. They typically leave a huge red spot on the skin.

Why are creams and solutions containing iodine used in the medicine?


texts: Crystallization of zinc sulfate monohydrate

texts:
I'm currently running an electrolysis experiment and I have a few questions regarding crystallization of zinc sulfate monohydrate $\ce{ZnSO4 * H2O}$.

I have prepared a saturated solution of zinc sulfate, will it crystallize as monohydrate, or only heptahydrate $\ce{ZnSO4 * 7 H2O}$ will?

And if so, what is the reason behind it? Does it has to do with the monohydrate and heptahydrate part?


texts:
In my course, I've come across H2 and Ni catalyst as a reducing agent for alkenes and LiAlH4/NaBH4 as a reducing agent for carbonyl groups. I know LiAlH4/NaBH4 can't reduce c=c as it is nucleophilic but can H2 and Ni reduce the carbonyl group? I've found uncertain and conflicting answers over the internet. My text book says it is possible and even gives the conditions for the reaction but past examination papers say otherwise.

question(compound Q):

answer:


texts: I have mostly come across examples of solids whose solubility increases in liquids with an increase in temperature. However, there seem to be exceptions to generalized rule this such as the solubility of $\ce{Ce2(SO4)3}$ in water. What makes this substance so special?


texts: Synthesis of 1-naphthaleneacetic acid: Methods

texts:
I am trying to synthesizing 1-naphthaleneacetic acid from naphthalene and monochloroacetic acid. I found some patents and papers, and I have tried to synthesis but the yield is low. I used iron powder and $\ce{KBr}$ as catalyst. Papers and some patents mentioned about the yield is 70% but I achieved only 35%. I tried different iron compounds such as $\ce{FeCl3, Fe2O3}$ with $\ce{KBr}$ but the maximum yield gained is 35%.
Could you please help me for this synthesis method for high yield?


texts: Small but modest displacements at negligible forces from DFT

texts:
When looking at a Gaussian log file today, I noticed the following information in the convergence criterion section after an analytical frequency calculation was performed:

         Item               Value     Threshold  Converged?
 Maximum Force            0.000001     0.000450     YES
 RMS     Force            0.000000     0.000300     YES
 Maximum Displacement     0.000190     0.001800     YES
 RMS     Displacement     0.000030     0.001200     YES

This struck me as odd. How could the forces be so low but the maximum displacement still be non-negligible? Does anyone have any hypothesis about why this phenomenon would occur? This makes me wonder if the convergence condition for the maximum displacement is unreasonably low if essentially no acting forces can result in a maximum displacement that's merely 1 order of magnitude lower than the default threshold. I believe the force units are Hartrees/Bohr and the distance units are angstroms.


texts: Calculate the potential of each electrode, $\ce{Mn(OH)2}/\ce{Mn}$ ox/red couple

texts:
So the exercise goes like this:

We consider the chemical battery(i have no idea what is its actual english name since i'm translating), $\ce{Mn_{(s)}/Mn(OH)_2//Cu^{2+}/Cu_{(s)}}$ Where $\ce{Mn}$ is submerged in a saturated solution of $\ce{Mn(OH)_{2}}$ of $\ce{pH}=9.86$

first is to calculate the constant of solubility $\ce{kS}$ and $S$
this i think i can do, since we have the concentration of $\ce{OH^-}$, and we have the relation $\ce{2S=[OH^-]}$ then we can get the $S$ then the $\ce{kS}$ which is equal to $\ce{kS=[OH^-]^2*[Mn^{2+}]}$ with $\ce{Mn^{2+}}=S$

Then comes the question that I couldn't do, it says to calculate the potential of each electrode, for the electrode with the Copper element i can do, but for the electrode with the $\ce{Mn(OH)2}/\ce{Mn}$ couple I'm confused.
We have the demi-reaction of Oxidation(Since the standard potential of the Copper couple is higher than the Manganese one):

$\ce{Mn +2OH^-\leftrightarrow Mn(OH)_2+2e^-}$

Now for the electrode potential:

$\ce{E=E^0+\frac{0.06}{2}log(\frac{1}{[OH^-]^2})}$

This is the one I'm not sure of at all.

Another question is to deduce the potential of the oxred couple $\ce{Mn^{2+}/Mn}$ from the previous data we have.
I think this one I have to equal the potentials of the couple $\ce{Mn(OH)_2/Mn}$ and $\ce{Mn^{2+}/Mn}$ since they coexist at the same electrode(I'm not sure of this either and I need confirmation)

Note: The potential standard of $\ce{Mn(OH)_2/Mn}$ is a given.

This isn't a homework, just me trying to understand the oxred batteries better and getting stuck.

Thanks for your help!


texts: Explanation of phase changing/solid and liquid water existing in the same container at same temp

texts: I was trying to explain to a friend the other day why when ice and water are in the same container, the water is 32 degrees Fahrenheit or 0 celcius, but not frozen, because the ambient temp is above freezing and the ice I'd going through a phase change. Can anybody explain or label this please?


texts:
Feldspars are mostly composed of three compounds:

KAlSi$_3$O$_8$
NaAlSi$_3$O$_8$
CaAl$_2$Si$_2$O$_8$

I notice they each have Aluminum. Feldspar is far more common than Bauxite (the only Aluminum ore commercially mined). As it stands now, Feldspar is used in glass-making, but I'm wondering if there's some chemical refining process that can extract the Aluminum somehow?---especially that third one, since it has two Al's.

Note: I'm not looking for an economical method. That's proly asking too much. I'm not worried about aluminum reserves, because bauxite is still very plentiful. I'm simply interested in a chemical method to extract Aluminum, or at least Alumina (Al$_2$O$_3$), from Feldspar, purely for reasons of chemical curiosity.

The only thing I've researched is the Bayer Process, but I have no idea if it can be applied or modified for Feldspar.


texts: Why NaBH4 does not reduce carboxylic acid while LiAlH4 does?

texts: My teacher told - "To reduce carboxylic acid  to alcohol, $\ce{LiAlH4}$ is used. But since $\ce{LiAlH4}$ is an expensive reagent, it is commercially reduced by forming an ester and then to alcohol". I asked that we can also use $\ce{NaBH4}$ as it also contains 4 hydrogen bonds. He said that $\ce{LiAlH4}$ is a strong reducing agent that $\ce{NaBH4}$. I was not satisfied by his answer. I want an answer in terms of a reaction mechanism.


texts:
I'm looking at a cycloaddition that produces a bicyclic intermediate, there are two different ways of doing the addition which can be described as endo/exo. However, all three bridges are the same length. How do I assign priorities and endo/exo here?
Here's a simplified example of this reaction. In my opinion on the dienophile the $\ce{NH2}$ has the higher priority, on the pyridazine I would suspect the $\ce{N-N}$ bridge to be higher in priority which means the left product would be endo, the right one exo. But I cannot find information that confirms this.


texts: chemical possibility in oil - 8th graders have questions for a project

texts:
I have a team of kids (8th graders) that are doing the First Lego League competition this year. As part of that they have to come up with a possible solution to a problem that relates to the human water cycle.  They need to contact experts and share their thoughts and get feedback of their solution.  We would greatly appreciate any feedback.  I've listed what the problem is they are trying to solve and their suggested solution below, and then some questions.

Problem:  Oil spills in water (caused by various things - accidents, hurricanes, etc)

Their proposed solution:  Create an environmentally safe chemical that can be put in the oil, that if there is a leak, as soon as the oil comes in contact with water, the chemical causes the oil to solidify thus sealing the leak or at least slowing it down.  The solidified oil would be buoyant so that it could be easily skimmed out of the water.  The solidified oil could also be reprocessed back into usable oil.

Questions the kids have:
    Does such a chemical currently exist that can do this?
    If so, why is it not being used - any downside to using it?
    If not, is it possible to invent such a chemical?  Now or in the future?
    What kind of components could be used to do create such a chemical?

We really appreciate any response you can give.
Thank you so much!


texts: Mechanism of dehydration of alcohols by iodine/triphenylphosphine

texts: This paper describes the dehydration of an alcohol to form an alkene. What is the mechanism of alcohol dehydration with iodine? Why can only iodine of all the halogens be used?


texts: How does solution which electrodes are immersed in effect electrode potential?

texts: When we make an electrochemical cell, we dip the electrodes in the salt solution. How exactly does the electrode potential change as we dip the electrodes in the salt solutions?  Would different salt solutions change the effect of the electrode potential?


texts:
What makes bonds break apart from heat?

I am wondering if anyone could explain the reasons why new bonds are formed in the absence of energy. I have found that they form in order to lower the overall energy, presumably because electrons move closer to the nuclei via bonds.

But in a reaction like $\ce{2 K (s) + 2 H2O (l) -> 2 K+ (aq) + 2 OH- (aq) + H2 (g)}$, I wonder what makes the bonds break? I just don't understand why $\ce{2 K}$ would suddenly split to form new bonds unless I'm missing some sort of energy being put into the system. Maybe potassium is able to attack $\ce{H2O}$ since it is a polar molecule?

But, I truly can't find a reaction mechanism that explains these phenomena.


texts:
I got tripped up by this question; I thought these were all enantiomers when in fact they were all meso compounds.

How can one prevent this from happening?

How does one rotate the Fischer projection, for example, in the first problem; I understand that one has to hold one group in place, but then what?


texts:
You have discovered a new strain of bacteria called Tankeromyces subtilis that has a special outer membrane that is capable of withstanding high levels of osmotic pressure. These bacteria can survive osmotic pressure as high $\pu{1.3 kJ L-1}$, but not higher. The $(iC)_\mathrm{total}$ value for the inside of these bacteria is $\pu{630 mM}$.
What is the lowest concentration of $\ce{NaCl}$ (in otherwise pure water) in which these bacteria can survive without bursting due to osmotic pressure?
$R = \pu{8.3153 J mol-1 K-1}$ and $T = \pu{296 K}$.

The answer is $\pu{0.10 M}$, but I have no idea how to drive at that answer. However, I do know that it involves this equation:
$$p = iCRT$$


texts: I know that stability of alkali metal hydrides decreases down the group,Hence the lowest member in the group easily breaks into its cation but does this easiness of breaking into cation has any relation with its reducing nature.I also wanted to know what is order of reducing character in alkali metal group?


texts: Deciding which α-Η gets abstracted in aldol condensation

texts:
Consider the base catalysed aldol condensation of methyl ethyl ketone. The first step involves the abstraction of a proton by the base. However I am having trouble deciding whether the proton will be abstracted from the $\ce{-CH2-{}}$ group or the $\ce{-CH3}$ group.

I think it should be from the latter as the $\ce{CH^-}$ ion so formed in the former experiences undesired $+I$ effect by the two groups neighbouring it; but I'm not sure.


texts: Does glycerin promote bacterial growth the same as water?

texts:
A sodium chloride + water solution draws the water out from bacteria through the process of osmosis.

Would a sodium chloride + glycerin solution have the same antibacterial effect?

If I understand correctly if the concentration of water is greater on the outside of a bacterial cell the water will go inside the bacteria allowing it to multiply or grow faster. Does glycerin have the same effect?


texts: Reactions of differents halohydrins with tert-butoxide

texts:
I have two compounds (1R,2S)-3,3-dimethyl-2-bromocyclohexanol and (1R,2R)-3,3-dimethyl-2-bromocyclohexanol, both of them are treated with $\ce{KO^tBu}$ (a strong but bulky base) to form two different isomers of $\ce{C8H14O}$ which is not an alcohol.

I though that (1R,2R)-3,3-dimethyl-2-bromocyclohexanol is going to form an epoxide due the configuration of the halogen and the hydroxyl (although I don't know if it is required an specific configuration) and (1R,2S)-3,3-dimethyl-2-bromocyclohexanol is going to have a E2 reaction due steric hindrance but that will end with an alcohol anyway.


texts: How do I write orders of magnitude in scientific notation when margin of error is involved?

texts:
My TA has me confused about how to use scientific notation when margin of error and orders of magnitude are involved.

The number I wrote: 3.78 ± 0.02 * 10^-3

My TA told me that this means: 3.78 ± 0.00002

I thought that this meant: 0.00378 ± 0.00002

Which one is correct? I've been looking online to find something that explains the proper notation when writing out margin of error with orders of magnitude but I haven't been able to find anything (I'm at a loss of what terms to search for). If what I wrote isn't the correct way to say 0.00378 ± 0.00002, then what is? Writing it as 3.78 * 10^-3 ± 0.02 or  3.78 * 10^-3 ± 0.02 * 10^-3 seems kind of foolish.


texts:
I'm researching cyanide for a biology project and noted that one of the largest sources of carbohydrates in the tropics is the cassava root -- which I previously researched as a food that contains a cyanogenic glycoside that is metabolized into hydrogen cyanide.

Most of the sources I reviewed claimed that, while boiling the cassava, the cyanogenic glycosides were broken down into components such hydrogen cyanide, which made the plant safer to consume. I have a limited understanding of chemistry and can't resolve why this is considered a safe way to cook the plant.

My research indicates that inhalation of hydrogen cyanide is significantly more toxic than the oral route, so why would this method be considered beneficial? Not sure why this is considered safer, unless the information I've found is not correct. Any help in putting this together would be appreciated. Thanks!


texts: At what composition is Maximum deviation from Raoult's law observed?

texts:
Raoult's law states that in an ideal binary solution of two volatile components, the partial vapour pressure of each component is proportional to its mole fraction in the solution.

A plot of total pressure to mole fraction of one of the components gives:

If A and B form a non-ideal solution with positive deviation, then the following graph is observed:

At what composition of the two components is the deviation (difference in total pressure) maximum?
My guess would be that maximum deviation is observed when mole fraction of both the components are equal.
My reasoning is that the deviation is observed because of the fact that interactions between A-A and B-B particles are not equal to the A-B particle interactions. When the quantity of both the components are equal, there is a maximum amount of A-B interactions. Hence, the deviation must be maximum.
Is this reasoning correct?


texts: How to calculate which ionic compound has the highest melting point?

texts:
Which of the following compounds has the highest melting point: $\ce{PCl5}$, $\ce{H2O}$, $\ce{NaCl}$, $\ce{SrCl2}$, $\ce{CaF2}$?

In general, ionic compounds will have higher boiling points than those of dipole-dipole interaction compounds.

So, the compound above that will have the highest melting point will certainly be an ionic compound, either $\ce{NaCl}$, $\ce{CaF2}$ or $\ce{SrCl2}$.

I thought that I should calculate the molar weight but that won't work, because the correct answer is $\ce{CaF2}$, and $\ce{SrCl2}$ has a greater molar weight.

Between ionic compounds, how can the one with the highest boiling point be predicted?


texts: What is the Italian ‘Acido Psammico’ (Psammic acid?)

texts:
I am reading an Italian detective novel — Lo stato delle anime by Giorgio Todde — in which someone is poisoned with ‘acido psammico’.

  Marini trova nello stomaco della vittima un ostia con all’interno dell’acido psammico (usato per conciare le pelli), l’acido ha ucciso la donna avvelenandola.

Which I think translates into English as:

  In the stomach of the victim Marini finds a communion wafer, inside of
  which is ‘psammic acid’ (used to tan hides): the acid had killed the
  woman by poisoning.

I have spent quite a time with dictionary and Google searches using the Italian, French (acide psammique) and English (psammitic acid comes up but is not defined) terms without success. The term ‘psammico’ seems to come up in a geological context, but infrequently and without clarifying things.

I should add that the novel is set in rural Sardinia in the 1890s and the implication is that shepherds would have access to it.

Does anyone know what the modern name and chemical composition of this is?

Addendum: Further Information

I am now reading further in the book (slowly, very slowly) and on p. 101 the protagonist (Marini) is in the capital city (Cagliari) and enters a chemist’s  (pharmacist’s) shop to ask for ‘acido psammico’. He receives the following reply:

  La sabbiolina mortale?

In which ‘sabbiolina’ (not in my dictionaries) appears to be a diminutive related to ‘sabbia’ — sand. (‘mortale’ = ‘deadly, fatal’, of course.)

Consistent with this, further down the page we have:

  La sabbia velenosa…

“The poisonous sand…”


texts:
I am trying to teach myself about Electron Ionization, and am very confused about the formation of the CH4+ Ion.

Do the dotted lines between the C and the H, and between the two Hydrogens indicate a resonance structure of sort? I have taken organic chemistry, but cannot wrap my head around this.


texts: How can we confirm the number of protons in an atom?

texts: The periodic table tells us that there are 6 protons in a carbon atom. Is there a way to verify this first-hand? Or are we just expected to believe it unquestioned?


texts: What elements and/or substances without water are liquid at room temperature?

texts:
I was thinking about liquids, and I started to wonder theses related questions:

1) Besides mercury, what elements are naturally liquid at room temperature?

2) What naturally found family of substances/mixtures that do not contain  $\ce{H2O}$ are naturally liquid at room temperature?


texts: How is Bent's rule consistent with LCAO MO theory?

texts:
Bent's Rule states that $s$ orbitals on a central atom participate contribute more to molecular orbitals directed towards more electropositive ligands. (For a longer explanation, see this question and answers: What is Bent's rule?). Lone pairs are considered to be the extreme limit of an electropositive "ligand".
Many sources claim that this Rule is consistent with LCAO MO theory representations of electron density. It seems, however, that this claim is easily disproved by considering the example of simple molecules of the type $\ce{AH2}$.
We can start with $\ce{H2O}$, whose LCAO MO diagram is well known:

Source: H2O-MO-Diagram.svg by Officer781 on Wikimedia Commons
The orbitals contributing to the O-H bonds are the lower two in energy. Ignoring orbital mixing for now, these are formed from linear combinations of the hydrogen $s$ orbitals with the oxygen $2s$ (giving $\mathrm{2a_1}$) and $2p_y$ orbitals (giving $\mathrm{1b_2}$). The lone pairs are a pure $p_x$ orbital ($\mathrm{1b_1}$) and a combination of $p_z$ with a small contribution from the hydrogen $s$ orbitals ($\mathrm{3a_1}$). Based on the contributing oxygen atomic orbitals, that gives 100% p lone pairs and $50\%$ $p$/$50\%$ $s$ for the bonds, the opposite of the result predicted by Bent's rule, which is that the lone pairs should have more $s$ character.
If we properly account for orbital mixing, there is no effect on the $\mathrm{1b_1}$ lone pair orbital, while the $\mathrm{3a_1}$ lone pair does in fact get more $s$ character, but this increased $s$ character is not expected to exceed $50\%$, since that would just mean a switch of label between the $\mathrm{2a_1}$ and $\mathrm{3a_1}$ orbitals. $50\%$ $s$ in the $\mathrm{3a_1}$ represents the maximum mixed case. That gives a final result of a maximum of $25\%$ $s$ in the lone pairs ($50\%$ in the $\mathrm{3a_1}$ and $0\%$ in $\mathrm{1b_2}$) and $25\%$ in the $\ce{O-H}$ bonds ($\mathrm{2a_1}$ and $\mathrm{1b_2}$), still contradicting Bent's Rule, which predicts that the lone pairs should have more $s$ than the bonds, not the same amount. [One a side note, we know that $\ce{H2O}$ does not represent the maximum mixing case, as $\ce{SH2}$ has a smaller bond angle consistent with even greater orbital mixing, but that's beside the point here.]
The paper by Clauss et. al.[1] reconciles this result by claiming that the 1b1 orbital is "always excluded from the Bent's rule competition for in-plane p-character", but I've never seen any formulation of Bent's Rule that indicates such an exception. If there is such a qualification to Bent's Rule, how do we know what lone pairs to include or exclude?
I conclude from this analysis that Bent's Rule is much like VSEPR - useful in some cases as a pedagogical tool, but ultimately inconsistent with LCAO MO theory. Or perhaps it's only consistent when applied to actual bonds rather than to bonds and lone pairs? I'm not concerned with why people still use it, but I am confused as to why so many people argue that it is consistent with LCAO MO theory. Am I missing something here?
References:

Clauss, A. D.; Nelsen, S. F.; Ayoub, M.; Moore, J. W.; Landis, C. R.; Weinhold, F. Rabbit-ears hybrids, VSEPR sterics, and other orbital anachronisms. Chem. Educ. Res. Pract. 2014, 15 (4), 417–434. DOI: 10.1039/C4RP00057A. Or as a free preprint


texts: Why does ionization violate the stable or lowest energy rule in atoms?

texts:
Electrons that fill orbitals always do so in such a way that the resulting structure has the lowest energy state possible, though there are anomalies like chromium and so on.

But ionization no matter which element tends to violate this rule. When electrons are ionized they are from the outermost (valence) shell. But this doesn't always produce the lowest energy state possible like the case with 3d and 4s.

To clarify, all I am asking is why in that specific case, is the electron taken out of the 4s orbital first instead of the 3d orbital, since the 3d orbital is a higher energy level?


texts: I read from a book that average kinetic energy is equal to $3kT/2$ where $k$ is Boltzmann's constant and $T$ is the kelvin temperature. I don't know how the formula was derived. Any help to gain insights into the derivation of this formula would be helpful.


texts: Why does electronegativity generally increase across a period?

texts:
I've been doing some research and the only answer I seem to be getting is that the increase of protons means electrons are more attracted to the atom.

I thought though it was because as you go across a period, an atom will slowly fill up its outer shell, and hence reduce its need to gain or hog electrons?? Or is this incorrect?


texts:
Preamble:
Now, I am aware that directly editing the inchikey is, generally speaking, a bad idea, but...

Can I just change the 2nd block of an inchikey to "UHFFFAOY" to get the correct main-layer-only version of the inchikey of that molecule?

example where this seems to be the case (from pubchem):
BSAIUMLZVGUGKX-BQYQJAHWSA-N = trans-2-nonenal
BSAIUMLZVGUGKX-FPLPWBNLSA-N = cis-2-nonenal
BSAIUMLZVGUGKX-UHFFFAOYSA-N = 2-nonenal

I have seen lots of other examples (100s if not 1000s) to support this hypothesis (both for cis/trans and for sterochemistry) and never a counter-example.


texts: How does lime prevent soda lime glass from dissolving in water?

texts: How does lime addition as an ingredient prevent soda lime glass from dissolving in water? Does it form calcium silicate in the process of melting?


texts:
In my textbook, under the topic "Asymmetric and Dissymmetric Compounds", the following statement is given:

  A molecule which does not possess plane of symmetry, centre of symmetry, and alternating axis of symmetry is called dissymmetric.

Why the definition didn't include the "axis of symmetry" as a condition for molecular dissymmetry?


texts: Is there a function to approximate atomic mass from the atomic number?

texts:
The product of $2Z$ generally approximates the value of $m_\mathrm{a}$ of atoms that comprise relatively few protons. Whereas, the product of $2.5Z$ generally approximates the value of $m_\mathrm{a}$ of atoms that comprise relatively many protons. The product of $((2+2.5)/2)Z$ generally approximates the value of $m_\mathrm{a}$ of atoms that comprise a moderate number of protons.

What function from the $Z$ values produces a value that maximally approximates the $m_\mathrm{a}$ that corresponds to $Z$?


texts: What is the first ionization energy of the hydride ion?

texts:
What is the first ionization energy for hydride?

Since there are two electrons in the s orbital, I suppose it should be more stable than hydrogen, despite the extra electric charge, so the ionization energy should be greater than the 13 eV needed to ionize hydrogen. However, I could not find any table with the energies for hydride.


texts: How is ascorbic acid oxidized into dehydroascorbic acid? What is the reduction reaction in this case? Where are the 2 hydrogen atoms going?


texts: Molecular orbital diagram of a complex including an oxido ligand

texts:
With highly oxidized metal centers, we expect that the hydroxido ligand's proton becomes acidic and will be lost to the surrounding media, creating an oxido ligand.

The oxo ligand is a $\pi$ basic ligand and we expect both $\sigma $ and $\pi$ donation into the metal center.

The metal's $\mathrm{t_{2g}}$ orbitals are lowered in energy by the presence of the oxido ligand's filled p orbital donating into the $\mathrm{t_{2g}}$. My question is regarding the symmetry of the ligand group orbitals. A p orbital does not have $\mathrm{t_{2g}}$ symmetry and as we know non-symmetry interactions are forbidden. Therefore I am struggling to understand the details of the oxido ligand.

My only explanation is that the complex's symmetry is reduced with the presence of an oxo ligand maybe from $O_\mathrm{h}$ to $C_4$ or similar. This would then change the symmetry of the $\mathrm{t_{2g}}$ orbitals on the metal center, but I really need some help explaining this!


texts:
I am doing some exam preparation and I came across this Question which I am finding challenging:

List from least polar to most polar, the following molecules:

Naphthalene, Phenol, 3-aminophenol and chlorobenzene.

I believe I know that Naphthalene is least polar as the benzene ring is very stable however, the confusion arises with chlorobenzene as the substituent Chlorine is very electronegative hence, it is strongly inductively electron-withdrawing thus is less polar than a simple benzene ring. So which is less polar, chlorobenzene or naphthalene?

Also which is most polar? 3-aminophenol or phenol? Phenol has a lone pair on oxygen in the oH group which can donate electrons to the ring, although with 3-aminophenol, both the NH2 and OH donate electrons, so wouldn't 3-aminophenol be more electron rich and hence more polar?

Please give the order of the molecules from least to most polar, explaining the order itself.

Thank you!


texts: Calculating heat of combustion in a bomb calorimeter

texts:
In a constant volume bomb calorimeter, we measure the change in temperature of the calorimeter and find out it's change in  internal energy. We then convert it to change in enthalpy.

To determine $\Delta H_c$ we write the balanced chemical equation to find $\Delta n_g$ and using the value of $\Delta U$ obtained from calorimeter, we apply $$\Delta H = \Delta U + \Delta n_g RT$$

The above equation is only valid for constant pressure and temperature. How can we apply this equation on calorimeter, where the temperature change is observed?


texts: Distribution of acid in Organic and Aqueous Phases

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The value for the distribution constant for an organic acid, HA, between chloroform and water is $10^2$.  The dissociation constant of the acid in water is $10^{-5}$, and it can be assumed that it does not dissociate or dimerize in the chloroform phase.  Increasing the pH of the aqueous phase from 4 to 9 has what effect on the fraction of HA extracted into the chloroform phase?

(a) The fraction is more than doubled.

(b) The fraction is increased but not doubled.

(c) The fraction is unaffected.

(d) The fraction is decreased but is not halved.

(e) The fraction is reduced to less than half.

The correct answer is (d).  I understand why the concentration of HA in chloroform should decrease, but I'm not sure I'm completely confident as to why it decreases to less than half.

As the acid in the organic phase is in equilibrium with the acid in the aqueous phase, obviously, increasing the pH past the pK$_a$ of the acid will drive it to completely dissociate, causing the HA in the organic layer to go into the aqueous layer.  How can I quantitatively know that this process will decrease the $\frac{[HA]_{CHCl_3}}{[HA]_{water}}$ to less than 50?

EDIT: So, I've taken your suggestion, but I seem to be getting stuck.

I'll use the notation HA$_{org}$ to denote the acid in the chloroform layer and HA$_{aq}$ to denote the acid in the water layer.

H$^+$ + A$^-$ $\rightleftharpoons$ HA$_{aq}$

HA$_{aq}$ $\rightleftharpoons$ HA$_{org}$

K$_a$ = $10^{-5}$ and the equilibrium constant for the bottom reaction is K$_D$.

We know that:

Our wanted ratio, D = $\frac {[HA]_{org total}}{[HA]_{aq total}}$ = $\frac {[HA]_{org}}{[HA]_{aq} + [A^-]} =  \frac {[HA]_{org}}{[HA]_{aq} + 10^{-5}[HA]_{aq}/[H^+]} = \frac{K_D [H^+]}{[H^+] + 10^{-5}}$

But, I don't know what K$_D$ is and it would also change with pH.


texts:
I know P is the pressure, but is it the outside pressure or inside pressure? I know that in equilibrium, it doesn't matter, but then in this problem I got confused:

193 mL of O2 was collected over water on a day when the atmospheric pressure was 762 mmHg. The temperature of the water was 23.0 o C. How many grams of oxygen were collected?

How would you do that?


texts: Is there a way to counteract the problems with weighing hot objects?

texts:
I am currently performing an experiment in which it would be greatly beneficial to be able to accurately measure the mass of a hot object without waiting for it to cool. The current plan is simply to place the hot object in a crucible with a lid and attempt to measure the mass quickly, before the crucible has time to heat up. The thought is that the convection currents around the object won't matter as much if they are contained within the crucible.

I will be testing this method in the next few days for accuracy and reproducibility, but would appreciate any other ideas to mitigate the problems with weighing hot objects, or insights on how this idea could be better.


texts: How to visualise the total electron density from a Gaussian 16 calculation?

texts:
I am trying to generate a 3D visualisation of the total electron density of a molecule. Using Gaussian 16, I have optimised this structure, with DFT, and formatted the resulting .chk file into a .fchk using the formchk utility. I have used the cubegen utility:

cubegen 0 fdensity=scf molecule.fchk molecule.cube -5 h <0.20_3d_cube.xyz

to generate a .cube file with 0.20 angstrom spacing about a cube of the molecule.

However, the resulting .cube file fails to visualise any total electron density in visualisation software. Gaussview 6 fails to create a surface, prompting an error:

  Surface build failed! Processing mesh, No data to plot. IsoValue may be out of range

VMD allows the visualisation of an isosurface, but visually nothing appears.


texts: Does anisole react with concentrated nitric or sulfuric acid

texts:
Can we add concentrated $\ce{H2SO4}$ and concentrated $\ce{HNO3}$ to anisole?

I heard that we can't add acids into phenol and aniline which make them blast.


texts:
I am into running some leaching experiments and wanted to study the effect of different parameters on my dissolution results. But I am confused with determining the parameters range. For example, I wanted to investigate the effect of temperature on my results. But I am not sure in which temperature range I should run my experiments. Should I test different temperatures (or other parameters as well) and see the change in the results and if by changing more in the level of that parameter, no change happened, so I can say for example that level is one of my upper of lower range?

The system I am going to study is: Oxidation of arsenic bearing sulfide (AsS) in aquatic leaching medium. I want to see the effect of different parameters; pH, Eh, temperature, oxidant agent on the As dissolution behavior. However, choosing the right range for each of these parameters are my main concern.

I am going to derive the equilibrium state for my mineral dissolution (so I can derive chemical stoichiometry) and then I should study the dissolution rate of my goal element (As).  I am going to study both synthesic (pure) ore and real ore from mine location, therefore I asked my question as a general one.


texts:
In my book the laboratory preparation of dinitrogen is as follows:

$$\ce{NH4Cl(aq) + NaNO2(aq) -> N2(g) + 2H2O(l) + NaCl(aq)}$$
Small amounts of $\ce{NO}$, $\ce{HNO3}$ are also formed in this reaction: these impurities can be removed by passing the gas through aqueous sulfuric acid containing potassium dichromate. $\ce{N2}$ is collected by downward displacement of water.

So my question is how does it actually happen that impurities can be removed by passing the gas through aqueous sulfuric acid containing potassium dichromate? What are the reactions involved? Any video in which the following process is being illustrated will be helpful to understand.
I have understood what does it mean when it is said that $\ce{N2}$ is collected by downward displacement of water.This video  https://www.youtube.com/watch?v=Ol-2JN01Cfo illustrates it nicely.


texts: How does the radial distribution function of Vanadium differ from that of Calcium and how does this affect the ionic electron configurations?

texts: When Vanadium is ionised it loses the 4s electron first, meaning that it's 3+ ion has a different electron configuration to Calcium despite it being isoelectronic. Can it be explained in terms of radial distribution functions? Maybe the maxima of the 3d and 4s become further apart as the effective nuclear charge increases?


texts:
Why can't carbon and nitrogen be detected in ICP-MS and ICP-OES techniques?

My book says this technique is efficient for detecting multiple elements, with exception of halogens and carbon. I found somewhere that ICP is an open system, therefore it doesn't allow carbon detection. But why is that exactly?


texts: Why CO is a stronger and more common ligand than N2?

texts: Both N2 and CO are considered sigma-donor and pi-acceptor. Their MO diagram is similar, so I wonder why CO binds generally more strongly and it is a more common ligand.


texts: Azimuthal Quantum Number and Magnetic Quantum Number

texts:
I know that azimuthal quantum numbers and magnetic quantum numbers are used to find the no. of and the orientation of subshells respectively, but why do they have to be called so?
I reckon that azimuth means the angle w.r.t North or something but have no idea so as to why magnetic quantum no. has to be called so, doesn’t  the spin of an electron determine its magnetic properties? So won’t the spin quantum number be a better choice to express the magnetic properties? How does the 3D orientation of orbitals have something to do with the term ‘magnetic quantum number’? Similarly for azimuthal quantum no. and it’s relation with the no. of subshells .


texts:
$U$ and $H$ are defined as
$$U=\sum E_{pot} +\sum E_{kin} ; dU=dq+dw $$
$$H=U+pV$$

However, it was stated in a lecture note that for a fixed molar number, $U$ and $H$ can be defined using any two properties, example: $U(Temperature,Volume)$ and $H(Temperature, Pressure)$.

However, I cant figure out why only two quantities are enough, even if we consider the above example.

Can somebody show how by using just these two quantities is enough to figure out $U$ and $H$? (Just proving for the above example would be fine)


texts: I want to know what is an equivalent and how is it different from equivalent mass. How to calculate and why is it used in chemistry for knowing concentration?


texts: Is it possible to name compounds with lone pairs on the double bonded species using the cis-trans nomenclature? For instance, can't you name $\ce{Ph-N=N-Ph}$ by the relative position of the nitrogen atoms' electron pairs?


texts: Hydrogen storage using activated carbons

texts: On Wikipedia, a possibility of using activated carbons to store hydrogen is reported. According to the Wikipedia page, this solution can be used to store around 5 wt% by cooling down the hydrogen to -196$\;^\circ$C at 1 bar. I am wondering if the storage system has to be kept always at this temperature?


texts: Charging Paint either negatively or positively to repel paint with the same charge

texts: Is it possible to give paint a negative or positive charge.  Once dry, if you tried to paint on the surface with the same charged paint, would it just run down and refuse to stick?


texts: Thermodynamic Derivation of Ideal Gas Law

texts:
The ideal gas law is perhaps the best-known equation of state, and admits both a derivation via the kinetic theory of gases and via statistical mechanics. But these are both microscopic theories, and the ideal gas law is a macroscopic equation.

Can the ideal gas law be derived from macroscopic thermodynamics alone, without recourse to microscopic theories? If so, how? If not, why not?

Assume now that $$U = \frac{3}{2}Nk_\text{B}T,$$ as is the case for a monatomic ideal gas.

Can we now derive the ideal gas law?

Perhaps something to consider regarding the second question. From thermodynamics, $$P = -\left(\frac{\partial U}{\partial V}\right)_{S,N} = -\frac{3}{2}Nk_\text{B}\left(\frac{\partial T}{\partial V}\right)_{S,N} \stackrel{?}{=} \frac{Nk_\text{B}T}{V} \quad \Longleftrightarrow \quad \left(\frac{\partial T}{\partial V}\right)_{S,N} \stackrel{?}{=} -\frac{2}{3}\frac{T}{V},$$ where $\stackrel{?}{=}$ is read "is to be shown equal to." This is an interesting identity, I suppose, but I'm not sure if or where I can proceed from here. As usual, any help is appreciated.


texts:
Below is a problem I got stuck at in a test .

The first compund in this chain was easy to figure out , it was something like this :
Then I had this intermediate compound for B.(I didn't add the bromide anion because this is where my confusion starts)
Now ,here it shouldn't be correct to do a hydride shift outside the ring as it would result in a much less stable carbocation . But if I proceed using that idea and solving further for part D and E , I am getting option (b) as my answer and the correct answer is option (d).
Although if I do a hydride shift there then that opens a way for a ring expansion and hence a correct answer (according to the answer key) .


texts:
I'm just blindly experimenting. I tried to dissolve some potassium permanganate in water before performing electrolysis.

I can't see much difference. How is $\ce{KMnO4}$ dissolved in water? How does it react during electrolysis?

I added salt and the electrolysis was so violent that the copper started to burn (probably reacting with something).


texts: Why is hydrated barium peroxide used in the preparation of hydrogen peroxide?

texts:
I read about the laboratory method of producing hydrogen peroxide. The chemical reaction in question is: $$\text{BaO}_2.8\text{H}_2\text{O} + \text{H}_2\text{SO}_4 \rightarrow \text{BaSO}_4+\text{H}_2\text{O}_2 + 8\text{H}_2\text{O}$$
I wanted to find out why the hydrated form of barium peroxide is used. Apparently, what made barium peroxide so attractive to use in this reaction was the fact that the product, barium sulphate, being insoluble, is easy to filter out after the reaction. However, the side effect is that it precipitates on the barium peroxide sample, preventing further reaction. Using the hydrated form of barium peroxide solves this problem as the salt molecule is "surrounded" by water molecules.
I don't understand exactly how this works. What does a hydrated $\text{BaO}_2$ molecule look like in space, and how does its geometry help avoid the problem of a precipitate forming on its surface?


texts: Why is the OO-H dissociation is unlikely for the Caro's Acid?

texts:
Let us consider the Caro's Acid: $\mathrm{H_2SO_5 \equiv SO_3H-OOH}$.
It is widely known that the hydrogen tied with the $\mathrm{-OO-}$ group is pretty much unlikely to dissociate:
$$ \text {Terminal dissociation: }\mathrm{SO_3H - OOH \rightleftharpoons H^+ + [SO_3-OOH]^-} \\
   \text{An unlikely step: }\mathrm{[SO_3-OOH]^- \rightleftharpoons H^+ +[SO_3-OO]^{2-}} $$
The first time I encountered that fact I was presented a pretty inconclusive piece of argumentation: it was stated that $ \mathrm{-OO-} $ group is way more electronegative than $ \mathrm{-O-} $, which somehow brings about an obstacle for the dissociation.

Unfortunately, it was a long time ago and I cannot remember the exact details. I stumbled upon this problem not so long ago. Having a better background in chemistry, I attempted to apply the Sanders' electronegativity balance theory, but the result was pretty inane in terms of our chemical reality: $\chi_{eq}(\mathrm{H_2SO_4}) \approx 2.89894; \chi_{eq}(\mathrm{H_2SO_5}) \approx 2.96803 $. In other words: $ \chi_{eq}(\mathrm{H_2SO_5}) > \chi_{eq}(\mathrm{H_2SO_4}) $.

What am I doing wrong? Is it possible to tweak my attempt to use Sanders' theory? Is there any other approach to this problem?


texts: What to do with (large) imaginary frequencies for constrained minimum structures?

texts:
I am performing DFT calculations using ORCA 4.0.1 on an enzyme active site model. The model contains 89 atoms including the substrate (see Animation 1), five of which are fixed in space (the spherical atoms in Animation 1). I am using dispersion-corrected B3LYP with 6-31g(d,p) basis set, with the "RIJCOSX" approximation, and with a CPCM model for the solvent (dielectric constant $\epsilon = 4)$. From what I have seen in the literature, this method is often applied to enzyme models with success, and this is the reason for using it. Once I start computing reaction paths, I plan to try different functionals and basis sets to see if this give drastically different results. My geometry optimization tolerances are

Energy change: 5e-6;
Max gradient: 2e-3;
MRS gradient: 5e-4;
Max displacement: 4e-3;
RMS displacement: 2e-3

The two gradient tolerances have been loosened slightly in order to converge the calculations. By using the default gradient tolerances, the calculations simply do not, I have found (especially the maximum gradient). Additionally, it has been absolutely necessary to compute a better guess for the initial Hessian for the optimization, done at the B3LYP/3-21G-rijcosx level.

The fixed atoms are kept fixed to maintain the orientation of the active site residues. Only atoms where the side chain or backbone has been truncated are kept fixed. Without fixing these atoms, the residues will most likely  deviate way too much from the crystal structure, and no longer represent the enzyme environment we try to simulate.

Now, due to the constrained atoms, I expected imaginary frequencies to occur. However, for one of my presumably converged structures, I have quite strong imaginary frequencies. The list of frequencies start as follows: -220.645934, -69.117105, -65.597557, -61.314719, -48.720497, -40.439949, -32.562415, -21.395791, -16.637113, 6.126145. The two strongest negative frequencies are mainly a sigma bond rotation of a methyl group (of which the carbon is fixed in space during the optimization).

It is difficult to find any good literature on what to do with and how to interpret such negative frequencies in constrained optimizations. Is it "safe" to disregard the frequencies that mainly involved fixed atoms? Should I converge my geometry tighter to come closer to the true minimum? That's not so easy, I find, as the molecule is quite flexible. It took me quite some time to come up with a method that converges, which involve computing a good guess for the initial Hessian used in the optimization (computed at the B3lYP/3-21G level). I hope the imaginary frequencies are artefacts of the constraints, and that I can safely disregard them. However, they seem to have quite higher frequencies than what other people report in the literature (many say that their imaginary frequencies are around 20 cm-1).

This has to be a common challenge for people doing electronic structure calculations on large and constrained systems, but very few address this issue specifically in their publications.

I did read through this question, but it addresses not quite the same issue that I face.

Animation 1. The active site model. A total of 89 atoms.

Animation 2. Imaginary mode with frequency -220.645934 cm$^{-1}$.

What I am trying right now

I have three jobs waiting in the queue right now:

I have made a small rotation of the methyl groups strongly involved in the strong imaginary mode
I have started another geometry optimization of the structure given above (exhibiting the imaginary frequencies), but by reading the computed Hessian (the "exact" one, from same level of theory as optimization)
I have restarted an identical optimization, but by computing the "exact" Hessian from the start, giving a much better guess of which direction to go in.

I can add here later what these attempts result in.


texts: Which it is the oxidation state of indium and phosphorus?

texts:
I would like to know what the oxidation state of indium and phosphorus in a structure type rock salt. It could be +1 and -1? Yes or not? and why?

Thanks


texts: How could alcohol be made into a powder?

texts:
In the news recently is 'Palcohol', powdered alcohol, that you add to water or existing liquids to make it alcohol. Presumably this would dissolve and break apart into alcohol and {some other compound}.

What could bond to ethyl alcohol in order to:
1) Create a solid, and
2) Not be disgusting as a side product?

Most things have some associated taste, $\ce{NaCl}$ is certainly out. If the 'other' components somehow combined to $\ce{H2O}$ or a gas like $\ce{O2}$ or $\ce{CO_2}$ that might remove any residual taste.

What would be in the list of available combinations with ethyl alcohol that are safe to consume, gaseous, or don't otherwise add weird tastes to the liquid?


texts: What are the parameters of protonation of a molecule?

texts:
Adding an acid replaces the $\ce{-MgBr+}$ with an $\ce{H+}$. Why does this happen? Is $\ce{H+}$ a better electrophile than $\ce{MgBr+}$?

Or, to put it another way, why doesn't $\ce{MgBr}$ stays attached to $\ce{O}$?


texts: Why is the standard enthalpy of formation of diamond not zero?

texts: Why doesn’t diamond have $\Delta H_\mathrm{f}^\circ=0$, when graphite does? Is it something to do with the definition – diamonds can’t really form at STP, even though it is naturally occurring?


texts: Dipole moment of water using the definition

texts:
In many Chemistry books, the dipole moment of molecules is calculated through algebraic formulas. However, another definition of the dipole moment is

$$\vec{\mu} = \sum_i q_i \, \vec{r}_i$$

So, how can we calculate the dipole moment of water, for example using this formula? Is there a difference in interpretation of dipole moment in Physics and Chemistry?

Here is the Definition.


texts: What are the cheapest basis sets able to model intermolecular dipole interactions inside a metal complex and give good relative energies, with DFT?

texts:
As a example, If I have a square planar complex of a cation with both a weakly polar ligand (X) and strongly polar ones, like ammonia and water I expect a bit of stabilization due to formation of a hydrogen bond between ammonia and water, if they are in adjacent positions:

   NH3
   │
X─ M² ─OH2
   │
   X

What would not happen if they were in opposite positions:

     X
     │
NH3─ M² ─OH2
     │
     X

I think it is a bit tricky to model that, as intermolecular interactions are long-range, and most small basis sets approximations start to break down in such ranges. I imagine it's necessary at least some diffuse and polarization functions to start seeing such interactions. So my guess is that one needs to start at least with 6-31+G(d) level or higher. But I'm not sure. If you need do do a large number of such calculations, would it be possible to go lower than that, and still get reliable results, at least in a relative way, say, finding the first structure has lower energy than the second, even if neither value matches experimental data very well?


texts: How can I prevent my spin-coated silica thin film from cracking when I heat it up?

texts:
I am spin-coating a porous silica solution on a glass microscope coverslip, and then heating the resulting thin film to $\pu{350 °C}$, in an attempt to create a thin film of porous silica sol gel. I am trying to replicate only the porous sol gel portion of the work of Yantasee et al.:
  Nanoengineered electrochemical sensor based on mesoporous silica thin-film functionalized with thiol-terminated monolayer

The problem I am encountering is that my heated sol gel is cracking and partially delaminating. This is unacceptable. Can anyone offer advice on how to prevent this cracking when heating to $\pu{350 °C}$?

Relevant Information

The recipe for the silica precursor solution is:
2.578 g quantity of Pluronic F-127 surfactant was dissolved in 3.430 g of deionized water and 8.846 g of ethyl alcohol. Then 0.108 g of concentrated $\ce{HNO3}$ was added into the mixture. Finally, a 5.0 g quantity of TEOS was added to the solution.
 The solution was sonicated for 8 hours and then spin-coated at 3000 rpm onto the surface of a 12 mm glass microscope cover slip.

 Film thickness: ~10 μm.

Possible Causes

 Perhaps I am using the wrong type of glass for the substrate, and the respective thermal expansions are causing cracking at the interface. If so, what relatively cheap glass could I use?

 Maybe I need to rigorously prepare the glass substrates by cleaning them with a solution of acid (or base) and solvent. Could an ill-prepared substrate contain contaminants acting as nucleation sites for crack formation when heated? If so, what best method is used by these groups to prepare their slides? I can't seemed to find a paper on sol gel thin films where they describe their substrate preparation.


texts: Why does neighbouring group participation increase the rate of reaction?

texts:
I don't see any reason why the transition state of an SN2 reaction that happens after an internal nucleophilic group attacks(which is known as NGP) would be more stable. In fact, the nucleophilic group that attacks is often a strong nucleophile that is quite reactive (more than the leaving group which is usually a weak base) which would only destabilise the transition state when the external nucleophile does attack.

My question is: Why is the internal attack and the external attack combined faster than simply the external attack since the rate of such reactions where neighboring groups are involved is greater than normal SN2 reactions?


texts: Standard reference for thermodynamic properties for octane

texts:
where can I find thermodynamics properties for octane at saturated Temp.$T_s$?
I need this properties or where can i find all ?

$$liquid-density=\rho_l=?$$
$$vapor-density=\rho_v=?$$
$$latent-heat-of-evaporation=h_fg=?$$
$$liquid-kinematic-viscosity=\mu_l=? $$
$$liquid-conductivity=k_l=?$$


texts: How does symmetry of half filled and fully filled orbitals lead to stability

texts: I googled a lot about why symmetry of half filled and fully filled orbitals decreases their energy but every time it is repeated that symmetry leads to stability. So the question is why symmetry leads to stability? What is the actual logic behind it?


texts: Qualitative Analysis of Different Cations

texts:
So, we were taught in lab how to identify a couple of cations and anions through elimination and confirmatory tests. I was wondering, however—how would this work if the test solution were made up of multiple ions?

For example, calcium and zinc would form a white precipitate, respectively, if you add $\ce{NaOH}$. In excess, zinc would dissolve; calcium would not. $\ce{Fe^3+}$ would form a red precipitate.

In a test solution with these three in it, I would assume that there would be red precipitate and white precipitate if you add $\ce{NaOH}$, is that right? And if you add in excess, only some of the white precipitate would dissolve … or something like that. How would you effectively go about the process of identifying the ions?


texts: What happens to a molecule while it is reacting?

texts:
I recently learned about the graph of activation energy that looks like this (source):

I was wondering, what actually happens to the reactants as time passes on the graph? If we were to look at the molecules when the graph was at its peak, what would we see? And lastly, can the reaction be stopped somewhere in between, say at the peak, or does it always have to stop either at one end as a reactant, or at the other as a product?


texts: Why does the Leidenfrost effect (seemingly) not apply to the case of molten NaCl when it is poured into water?

texts:
On pouring molten sodium chloride into water you can see that when molten $\ce{NaCl}$ (table salt, i.e. sodium chloride) is poured into water ($\ce{H2O}$), the Leidenfrost effect appears to be nonexistent, whereas it clearly manifests itself in instances where other molten salts such as sodium tetraborate (1) (borax) and sodium carbonate (2) are poured into water.

Why does the Leidenfrost effect in molten NaCl last much shorter than that of the other salts, appearing to be nonexistent?

Input from paracetamol:

  "The Leidenfrost effect (physical phenomenon) does show up. See the "cushion" of water vapour around the blob of molten salt in the video? Though short-lived, it's pretty apparent. Now why molten table salt would react with water faster than molten borax or soda (as implied in your post) is an interesting question."


texts: Aqua complex scarcity for transition metal ions of second and third row

texts:
I've read that for the second and third row of the transition metal ions, almost no [M(OH$_2$)$_6$]$^{2+}$ or [M(OH$_2$)$_6$]$^{3+}$ complexes are known, while they're very common for the first row.

My question is: why is that so? I think it has to do with the fact that elements in the second and third row in oxidation state +II and +III tend to be readily oxidized further, but does somebody have a deeper and clearer explanation?


texts: Structure of Niobium and Tantalum carbonyls

texts:
$\ce{V(CO)6}$ is well known to be an unusual 17 valence electron, paramagnetic octahedral complex.

Do the corresponding tantalum and niobium species form simple dimers or more complicated structures ?


texts: How do I get MarvinSketch to use the ACS style of drawing?

texts:
I have a Wikipedia account and the people there have a tendency for getting upset over chemical structures that I created using MarvinSketch not conforming to the ACS drawing style.

Is there any way to make MarvinSketch use the ACS drawing style?


texts: Obtaining calcium iodide from calcium and iodine

texts:
According to:

https://www.webelements.com/calcium/chemistry.html

Calcium reacts with iodine upon heating as follows:

$\text{Ca}_{\,(s)} + \text{I}_{2\,(g)} \to \text{CaI}_{2\,(s)}$

I am effectively attempting this by dropping elemental calcium and iodine into a flask and putting it under a Bunsen burner. I have a tube leading from the flask to a beaker of water to safely condense escaping iodine gas.

However, this reaction is not occurring at any appreciable rate. I am wondering if I should be using powdered calcium instead of these larger pebble-sized chunks or if a Bunsen burner is insufficient to breach the energy barrier. Are these measures or others sufficient to increase the rate of reaction?


texts: What is the major side product of the reaction between 2-bromo-2-methylpropane and hydroxide ion?

texts:
I know that one of the products will be 2-methylpropan-2-ol, arising via a $\mathrm{S_N1}$ reaction. But what else is formed?

Specifically, I am looking for a side product that is gaseous.


texts: Feasibility of Nucleophilic Substitutions

texts:
Can $\ce{NH3}$ substitute an alcohol? The OH group will depart as a weaker base - some O is more electronegative - so will be a better leaving group than amine.
And what about using ammonium ions - such as in an ammonium salt? They will donate an $\ce{H+}$ to protonate the alcohol and make it a good leaving group, then show substitution followed by deprotonation to form an amine?
How is the the feasibility decided in case of nucleophilic substitution reactions? Is there any rule of thumb to know what happens, and what doesn't?


texts: Efforts made to reduce the amount of CFC

texts:
Till now I have heard $\ce{CO2}$ is the main reason of global warming. I have studied the remedies to control $\ce{CO2}$ many times through books, awarness programs, etc.

But today I learned about Chlorofluorocarbon ($\ce{CFC}$). It have 38 million times more "Global Warming Potential" than $\ce{CO2}$    according to UN.

In my book they have mention the sources of $\ce{CFC}$ like aerosols, refrigerators, air-conditioners, foams in fire extinguisher, etc.

But it does not tell what effort we should make or scientist are doing in order to reduce harmful of $\ce{CFC}$.

I have heard that $\ce{CFC}$ is replaced by 1,1,2,2-Tetrachloroethane, nothing else.

So, I want to know what else we are trying to reduce harmful effect of  $\ce{CFC}$?


texts:
How do you measure dissolved oxygen reliably in a culture of cells? This page has info on one sensor: http://water.me.vccs.edu/concepts/domeasure.html

how would you know that this sensor is working - meaning that only dissolved oxygen triggers the electrical change in the sensor, and not other atoms? and how would you calibrate the sensor to translate changes in electric signal to the change in number of dissolved oxygen atoms?

also, how would one get pure dissolved oxygen in varying amounts as 'positive control' for the sensor?


texts: It is said that mobile phones using potassium battery can be charged within a few minutes. Was it an accidental discovery or the companies made a new design for faster charging?


texts: Shi Epoxidation Issues - Any help would be appreciated

texts:
As part of my PhD project, I'm currently looking into running a Shi Epoxidation reaction. The first step is to reproduce the current literature on this reaction by using trans-stilbene as my substrate. However, from the multitude of reaction conditions I have tried, none of them seem to work as described in the papers (very low to no conversion observed). I have tried the reaction conditions from the following papers:

"An Efficient Asymmetric Epoxidation Method for trans-Olefins Mediated by a Fructose-Derived Ketone" - the original Shi paper - using oxone as oxidant
"An Efficient Catalytic Asymmetric Epoxidation Method" - Shi - optimized conditions - using oxone as oxidant
"Asymmetric epoxidation using hydrogen peroxide ($\ce{H2O2}$) as primary oxidant" - Shi - using hydrogen peroxide as oxidant

The catalyst I have used in my reactions is the Shi Diketal Catalyst purchased from Sigma (https://www.sigmaaldrich.com/catalog/product/aldrich/520160?lang=en&region=CA). What I've tried so far:

testing different batches of oxone, including titrating it and running test reactions ($\ce{aldehyde -> COOH}$ oxidation) - > 90% conversion observed
trans-stilbene + m-CPBA -> oxidized product is quantitative
I've left reactions run for > $\pu{6-24 h}$ with low conversion observed (< 30%).
$\mathrm{^{13}C}$ and $\mathrm{^{1}H}$ NMR of the catalyst show that it's clean

I am slowly running out of things to try out. It's weird because it's a published and highly used reaction ... If you have any experience with this reaction I would really appreciate your help!


texts: Seeming discrepancy between pKa and corresponding Ka of methylamine

texts:
The first entry in PubChem for the $\mathrm pK_\mathrm a$ of methylamine is $10.657$ at $25\ \mathrm{^\circ C}$. My elementary understanding is that this would be found as the negative log of the $K_\mathrm a,$ but the $K_\mathrm a$ is given as $2.70\times10^{-11}$ for which the negative log is about $10.568$.

My guess was that the two are determined independently, but can anyone shed some light on the seeming discrepancy?


texts: Why don't hydride shifts occur with hydrohalogenation of 4-methyl-cyclohexene?

texts:
My book (see bottom) implies that hydrohalogenation of 4-methyl-cyclohexene follows this mechanism:

Why not undergo consecutive hydride shifts to furnish a tertiary carbocation?
I would guess that the second step, nucleophilic attack by bromine, is much faster and prevents this from happening. But when I try to confirm this by looking up some examples I see this one at masterorganicchemistry.com:

This implies the following very similar mechanism:

The carbocation in the example is a smaller ring, meaning it should be less stable and even more reactive (less able to perform hydride shifting.) But then again the charge is closer to the tertiary carbon and easier accessible.
Could someone explain what is happening?

Vollhardt, P.; Schore, N. Molecules: Structure and Function, 6th edition; W. H. Freeman: New York, 2014, p491 exercise 12-6:

Exercise 12-6
Predict the outcome of the addition of HBr to (a) 1-hexene; (b) trans-2-pentene; (c) 2-methyl-2-butene; (d) 4-methylcyclohexene. How many isomers can be formed in each case?


texts: Why do the reactions of Magnesium in steam and cold water differ?

texts:
"Magnesium has a very slight reaction with cold water, but burns in steam.

A very clean coil of magnesium dropped into cold water eventually gets covered in small bubbles of hydrogen which float it to the surface. Magnesium hydroxide is formed as a very thin layer on the magnesium and this tends to stop the reaction.

Magnesium burns in steam with its typical white flame to produce white magnesium oxide and hydrogen." - From Chemguide.

May I know why the reactions of Magnesium in steam and cold water differ?


texts: why maximum (w/w) percent concentration of commercial acids is same to their molar mass?

texts:
i want to know why maximum (w/w) percent concentration of commercial acids is same to their molar mass, for example for HCl the maxmim concentration is 37 and it's molar mass is 36.5 and maximum concentration of H2SO4 is 98%(w/w) and it's molar mass is 98.
thanks alot!


texts: Why doesn't hydrazine contain a double bond between two nitrogen atoms?

texts:
I know that the Lewis structure of hydrazine contains $\mathrm{sp^3}$ hybridized nitrogen atom but on analyzing it's structure I realized there are many bond pair and lone pair repulsions. Instead of a single bond between the N atoms they could also have a double bond and a dative bond with h atoms.

When I asked my professor about this he said that the formal charge imparts much more instability. I was not satisfied with the argument. So, can anyone please provide a rigorous explanation of why I am wrong?


texts: How to calculate the thickness of the double layer at an electrode

texts:
I need help calculating a double layer thickness. In this situation two insulated planar electrodes are placed in an electrolyte (in this case drinking water) and a voltage is applied to them of 10V across a 10mm gap (field strength 1V/mm) the field is quickly cancelled out by the electrical double layer, where the ions within the water have been attracted to the insulated surface of the electrode and block out the field.

The equations I have seen such as the Debye length equation don't seem to factor in an electrode potential, can anybody point me in the right direction or better yet show me an equation for calculating what the thickness would be? (apologies if I have missed something obvious)


texts:
What is the method to be followed to prepare $\ce{Sn(NO3)2}$?

I tried to prepare $\ce{Sn(NO3)2}$ from reaction below:

$$\ce{SnCl2 + 2HNO3-> Sn(NO3)2 + 2HCl}$$

But $\ce{SnCl2}$ is not soluble. We are getting a turbid solution.


texts: If acyl chlorides are reacted with aqueous ammonia, will carboxylic acids also be formed?

texts:
As part of my A-level chemistry course, I have been taught that an acyl chloride will react violently with water to produce a carboxylic acid and hydrochloric acid. I have also been taught that an acyl chloride will react with an aqueous solution of ammonia to produce an amide and ammonium chloride. My question is, would the acyl chloride also react with the water in the aqueous ammonia solution? If so, this could decrease the yield of the amide, because some of the acyl chloride will react to produce the carboxylic acid.

I would appreciate any additional relevant details about the reaction, such as answers to the following questions (assuming that the acyl chloride does react with the water):

Is there an easy method to separate the amide from the
carboxylic acid?
Would it be best to use a concentrated ammonia solution, so that
there is plenty of ammonia for the acyl chloride to react with
instead of reacting with the water?
Is the reaction with water negligible compared to the reaction with ammonia?

Thanks in advance!


texts: The temperature rise after neutralisation

texts:
The answer to this question is B, however, I don't quite understand.
If considering Q= mc delta T, the heat released is to some extent being influenced by the no. of moles. If using that line of thought, wouldn't we want C where it has also the same no. of moles?
If we really have to arrive at B, my other proposition would be that the increase in heat is dissipated in a larger volume, hence giving a temperature rise of 6 degrees C.
I am a bit confused by this question. Any comments would be very helpful. Thank you in advance


texts: Boys function for Gaussian integrals in ab-initio calculations

texts:
A few days ago I mentioned a problem with an Hartree-Fock program I am writing (HF using cartesian Pople's STO-3G basis set). I can reproduce overlap and kinetic integrals of some references for ($\ce{H2}$, $\ce{HeH+}$ and $\ce{H_2O}$). Things start to change (at the third/fourth decimal digits) in the nucleus-electron attraction integral. At the beginning I thought the error I get on the total energy was mainly caused by electron-electron repulsion integrals (as errors on nucleus-electron attraction seem minimal). But now I am quite convinced the problem comes from my calculation of the Boys function
$$
    F_n(x) = \int_0^1 t^{2n}e^{-xt^2}\, dt.
$$
A clue of this comes from the fact that for $\ce{H2}$ and $\ce{HeH+}$ everything works fine: in this case Boys function is only computed for $n = 0$.

In order to compute this function I used numerical integration routines of SciPy (Python library) or directly QUADPACK (I traduced my Python program into FORTRAN90). However, looking at the literature it seems that nobody compute Boys function via numerical integration. I tried to implement different versions (recursive, asymptotic values, ...) of Boys function but all of them eventually had problems (depending on the range of $x$ or on the value of $n$).

Since I am loosing too much time on this problem, which seems to be numerical, I was wondering if there is some standard implementation of Boys function that I can simply use in my code.

Do you know any Python or Fortran library containing a good (safe and efficient) implementation of Boys function? If not, there is a simple algorithm that works well in any range of $x$ and is not sensible to numerical errors?


texts:
I have read that vapor pressure is only affected by temperature, but all of the examples have been in a sealed vessel. I have also read that pressure does not affect vapor pressure. I am looking for clarification of if and how pressure affects vapor pressure in sealed and unsealed vessels.

Also I would be appreciative if someone could provide an in depth, intuitive explanation of vapor pressure and why it is unaffected by pressure.


texts: How does this ring expansion on a steroid system occur?

texts:
The correct answer is supposedly B, as shown by Gravestock et al.[1] In this reaction after ozonolysis of the C=C double bond, two ketones are formed. How is a rearrangement or expansion of the ring possible, since carbocations are not formed as intermediates?

Gravestock, M. B.; Johnson, W. S.; Mccarry, B. E.; Parry, R. J.; Ratcliffe, B. E. Acetylenic bond participation in biomimetic polyene cyclizations. Model studies directed toward the synthesis of 20-keto steroids. Synthesis of dl-progesterone and dl-Δ4-androstene-3,17-dione. J. Am. Chem. Soc. 1978, 100 (13), 4274–4282 DOI: 10.1021/ja00481a044.


texts:
My professor asked us the reason of the melting point of potash alum being so low, despite it being an ionic salt. He later went on to answer it by saying that melting point is a misnomer for the phenomenon that is happening here.

  What's happening here is that the alum is losing its water of hydration and is then dissolving in that water itself. So it is actually a dissolution point rather than melting point.

I couldn't find any sources for what he said. Though what he said makes logical sense, I would like to read a bit more about it. Can you please provide some sources confirming what my professor said?


texts:
This is the question:
$$\ce{Cl-CH2-CH2(Cl)2->[alc KOH][Δ]?}$$
Now, I got the answer right but I think that the reaction should go by the $\ce{E1}$ mechanism because of the high temperature/heat, however, my teacher says that the mechanism will be $\ce{E2}$.  I don't understand why it will be like that. Everyone seemed to agree, so I didn't have the guts to ask in class. Please tell me why it's $\ce{E2}$? And then, what's the use of high temperature/heat? It was there to make ionization easy, right?


texts: Why do big thermoplastics (like Polytetrafluoroethylene) behave like thermosets? I know for sure it has to do with the van der Waals force and the fact that the molecules are huge, but why? Why does a big molecule break down before the van der Waals forces break?


texts: Why IUPAC name this amine is written as 2-methylpropan-2-amine and not as 2,2-dimethylethanamine?

texts: Why IUPAC Nomenclature of following amine is written as 2-methylpropan-2-amine and not as as 2,2-dimethylethanamine?


texts: Why does activated carbon preferentially adsorb anions?

texts:
Brands like Brita and Pur (in the U.S.) have made a name for themselves for the ability of their product (essentially a large-pore filter with activated carbon/charcoal) to extract the added chlorine from tap water.  I visualize $\ce{C}^*$ as a vast network of channels in which ions are "trapped".  I had assumed that most cations and anions were trapped effectively, but it seems to favor chlorine and iodine.

According to Wikipedia:

  Activated carbon does not bind well to certain chemicals, including alcohols, glycols, strong acids and bases, metals and most inorganics, such as lithium, sodium, iron, lead, arsenic, fluorine, and boric acid.

Why would it not bind effectively to fluorine?  Is it an issue of atomic radius?  Does $\ce{F-}$, with a radius of 0.136 nm sneak by, while $\ce{I-}$ and $\ce{Cl-}$ at 0.181 and 0.216 nm, repectively, get caught up in the matrix?  Why do the cations get passed through?


texts: Does a chiral centre have to have 3 or 4 different groups attached?

texts:
I am seeing conflicting answers on the net

e.g.

  A carbon atom is chiral if it has four different items bonded to it at the same position. (Wiki)

compared to

  Stereocenter (chiral center): An atom with three or more different attachments (Chem.Ucla)

Why does one say 3 or more, and one say 4?

Also, there is a double bonded carbon atom here that is said to be a stereocentre, which I cannot understand.  Isn't the double bond counted as two of the "same" attachments (so not even satisfying the 3 different groups criteria). How is that still a chiral centre?


texts: In NaCl electrolysis, why does chlorine ion get oxidized but not oxygen ion?

texts:
In $\ce{NaCl}$ electrolysis, on the positive electrode (aka. on the electrode where oxidation happens), $\ce{Cl-}$ ions are oxidized to $\ce{Cl2}$. But why don't we see any $\ce{O^2-}$ (naturally present in water's $\ce{OH-}$ ions) oxidized to $\ce{O^2}$ at all?
My pre-existing knowledge, may or may not be correct, that led to this question:
[1] I am under the impression that chemical reaction is a messy business in the real-world with many reactions reversible, many intermediary steps happening and many small reactions happening in the sideways. So the real-world scenario is never as neat as one clean equation.
[2] I am aware of the concept of electronegativity, and I also have feelings that
$\ce{O^2-}$ and $\ce{Cl-}$ should require a similar amount of energy input to get them oxidized. So we should really expect both reactions to happen.
With my pre-existing knowledge laid out above, I find it remarkable that not a trace of $\ce{O^2-}$ is oxidized at all. This led me to guess that the $\ce{OH-}$ ion itself may have imparted some degree of protection to the $\ce{O^2-}$ inside of it?


texts: Entropy change in an adiabatic expansion

texts:
Question
  One mole of ideal gas initially at a pressure of 1 atmosphere and $T = 298\ \mathrm K$, is
  expanded into a volume 50 % larger adiabatically.

In this adiabatic process, no work is done on the surroundings and $\mathrm dQ=0$. And entropy is defined as $\mathrm dS=\frac{\mathrm dQ_\text{rev}}{\mathrm dT}$. However, there must be a change in entropy surely?

Is the definition $\mathrm dS=\frac{\mathrm dQ_\text{rev}}{\mathrm dT}$ only at a constant volume? Because I have also seen entropy defined as $\mathrm dS=\frac{C_V}{T}\,\mathrm dT+\frac{R}{V}\,\mathrm dV$ and there would be a change in both temperature and volume. However, how do I find what these changes are? Would it make a difference if the expansion was reversible or irreversible (the question didn't make it explicitly clear)


texts: Is it possible predict the oxidizing/reducing nature of a compound?

texts:
I have recently begun with Inorganic Chemistry and am finding it totally difficult to understand things (I am trying to minimize memorization and approach logically).

One of the things I am having problems with is understanding oxidizing and reducing agents.
Given a compound(and a few other necessary conditions in some cases), can I predict whether the compound will behave as a reducing or an oxidizing agent?
Well obviously if there is any such rule, there will be exceptions. But is there anything as such to reason out a few statements and take me partly towards the answer?

For example I have begun with Group 1 and the book says at some point that peroxides and superoxides of alkali metals act as strong oxidizing agents, group 1 hydrides are powerful reducing agents etc. Well I find it difficult to understand these statements and my book offers no explanation.


texts: Why can two carbon atoms not form more than triple bond with each other?

texts: Why two carbon atoms don't form more than triple bond with each other? Please tell me simply as I am a student of 10th class.


texts: Peroxide in acidic conditions being reacted with iron sulphate mechanism

texts:
For the proposed mechanism, I would like to think the $\ce{O-O}$ bond would be cleaved first, thus creating two radicals (an $\ce{OH}$ radical and the radical situated on the other Oxygen), then radical on the oxygen will go into the ring to form a double bond in which the alkene double bond will donate 1 electron towards that bond and 1 electron to the carbon on the end of the opened ring.
My mechanism would be incomplete as I cannot seem to figure out how this reaction occurs.
However, I have another suggestion in which there is an epoxide formation. Can anyone elaborate as to which one is correct or can give me some insight?


texts: Comparison of C-Cl bond length in CH3Cl and CF3Cl

texts:
How can one compare the $\ce{C-Cl}$ bond lengths in chloromethane ($\ce{CH3Cl}$) and chlorotrifluoromethane ($\ce{CF3Cl}$)?

Bent's rule is also consistent with Gillespie's VSEPR model, and may provide alternative rationalisation for effect of electronegativity. So it is restated as: 'more electronegative atom not only prefers to stay in the orbital having more $\mathrm{p}$ character but also can increase the $\mathrm{p}$ character in its attached orbital from the central atom depending on the circumstance.'
With increase in $\mathrm{p}$ character in an orbital, bond length will increase while with increase in $\mathrm{s}$ character in an orbital, bond length will decrease. For example, $d_\ce{(C-Cl)}$ in $\ce{CH3Cl}$ ($\pu{1.78 \unicode{xC5}}$) $\gt d_\ce{(C-Cl)}$ in $\ce{CF3Cl}$ ($\pu{1.75 \unicode{xC5}}$).

Source: Concise Inorganic Chemistry for JEE (by J.D. Lee and Sudarshan Guha)
I understand this alternative statement to Bent's rule.
Can anybody explain how have the $\ce{C-Cl}$ bond lengths been compared here? I don't get this. I understand that fluorine is more electronegative than hydrogen and might induce small positive charge on the carbon atom. Also, the $\ce{C-F}$ bond will have more $\mathrm{p}$ character than the $\ce{C-H}$ bond. How do I proceed further to reach the conclusion?


texts: Migration of R group in Hofmann rearrangement

texts:
In the mechanism of Hofmann rearrangement, one step involves migration of $R-$ group from carbon to nitrogen as shown: This reaction proceeds even if the migratory aptitude of the $R$ group is poor (like in the case of ethanamide). What motivates the migration of $R$ group and makes the reaction proceed?

P.S.: I think the reason cannot be the negative charge on oxygen since it already delocalized by resonance, which shifts the electron cloud partially towards nitrogen, which is in turn partially shifted towards Bromine due to its -I effect. Here's my depiction:


texts: Is there anything we lose by using Google Colab for DeepChem?

texts: DeepChem does not run on windows, so I am considering to try Google Colab. Is there any key feature I would be missing by using Google Colab remotely from Windows rather than the original DeepChem on Linux?


texts: Can the thermodynamic information of a compound be calculated or must it be found emperically?

texts: Do attributes such as heat of formation have to be found through experimentation or can they be calculated based on the attributes of the bonds and the atoms involved?


texts: Does boric acid catalyze esterifications with isopropanol?

texts:
I am going to synthetise isopropyl salicylate. From what I have read on phillysim.org (pdf) the formation of ethyl salicylate can be catalyzed by boric acid. I could use sulfuric acid but it would be much more convenient with boric acid.
Ethanol and isopropanol have some differences, so I am not sure if it works for both of them.

Has anyone tried this? Does it work? Would it be better to just use sulfuric acid?


texts: Why is salt needed when using vinegar to clean pennies?

texts:
Let's say you have a solution that is vinegar and it has salt (NaCl) dissolved in it. Then you place old dull pennies in it. Then you look at it 5 minutes later and the pennies are clean and looking like new again.

I understand acid can etch the copper compound but why is the salt necessary for this process and what exactly does it do?


texts: Formating a chemical equation - Physical states

texts: I study chemistry in an University and I have two professors that says opposing things. One says that the physical state must be subscribed (1 at the picture) and other that it must be written to the left side (2). Since both of them are posdocs and have way more experience in chemistry than me, I really don't know to whom I should list. i've tried to look for a recommendation in the IUPAC site, but I couldn't find anything about that. Someone could help me with a link from some organization (preferably an international one) that recommends about this topic?


texts: We know that quantum tunneling is the reason behind several natural phenomenon like alpha decay and thermonuclear fusion inside the stars. How can it influence chemical reactions by tunnelling a species through the activation energy? If so how does it influence the kinetics and fraction of molecules taking part in the reaction.


texts:
I went through a question about the EAN rule. At first, it was all clear to me, but now I'm just confused on how to decide which ligand will donate how many electrons. How do we decide which ligand is monodentate, bidentate, etc.?

This question came to my mind when I saw cyclopentadienyl complex in which cyclopentadiene donates 6 electrons to the metal atom. Does that mean all compounds try to donate all the pi electrons to the metal? No, am I right? Carbonyl group donates only 2 electrons though it has 2 pi bonds i.e. 4 pi electrons. How does carbon of carbonyl group donate an electron pair, considering it has only one electron left in it's octet? Again, for $\ce{CH2=CH2}$, how many electrons will it donate? The answer is two. Which electrons are donated? Obviously the pi bond since carbon has no free electrons.

In which case electrons are donated from pi bond, in which from lone pair, and in which from unpaired electrons?


texts: How do I separate graphite powder from light oil?

texts:
I have a sample of very fine graphite powder suspended in light oil. I've attempted to separate the two by placing the mix in a 2 micron filter sock. The oil will slowly drip through. If I apply pressure the graphite and oil will force their way through. No pressure, I believe the graphite will collect on the filter and eventually blind the filter preventing oil from coming through.

Any ideas on how I can separate and re-use both items?


texts: Does reaction of alkali and alkaine earth metals' reaction with water an acid-base reaction?

texts:
In my chemistry notes the teacher gave me the note that reaction of alkali, alkaline earh metals' reactivity with water, acids(e.g. H2S) increases down the group and bases(e.g.NH3) decreases down the group,

And also I have some doubts that

-alkali metals such as Li first react with water and produce oxides first and those oxides react with water and produce hydroxides as end product, is this true?

-and normally water has H2O molecules, (H3O+,OH- ions at small concentration). And when alkali metals react with water do they react with H2O molecule or H3O+ molecule?, If someone could give me a reaction mechanism of an alkali metal with water?

-do alkli, alkaline earth metals act as bases when reacting with water?

Any help would be most greatfull


texts: Collision that governs kinetic model of gas

texts:
From Atkins' Physical Chemistry 10th, it states that

The kinetic model is based on three assumptions:

The gas consists of molecules of mass $m$ in ceaseless random motion obeying the laws of classical mechanics.
The size of the molecules is negligible, in the sense that their diameters are much smaller than the average distance travelled between collisions.
The molecules interact only through brief elastic collisions.

I quite can't get the second assumption. The intermolecular distance between the molecules are greater than the diameter of the molecules, so we can neglect the volume. Given Boyle's law apply (as omitting size and volume of molecules is a property that ideal gas has), there will be many molecules collide with the walls and the molecules will hit another molecules after its collision with wall (right?), thus the pressure of the system should be low. How often the collision of what kind happens under what condition?
If the separation doesn't result any influence on each molecule (because third assumption said elastic collision, so any interaction (hydrogen bonding, van der Waals, so on) higher than the collision energy should be omitted), will the collision come purely from their collision with walls, not collision between each molecule?
Wikipedia states also the assumption that

The number of molecules is so large that statistical treatment can be applied.


texts: Is hybridization used in ab initio valence bond calculation?

texts:
Many general chemistry textbooks introduced the concept "hybridization" to construct a symmetry-adapted VB-type wavefunction. In the textbooks, usually the minimal basis is used and without optimizing all resonance forms.

My question is, in the ab initio valence bond calculation with extended basis set and optimizing many resonance forms,

(i) do people still use hybridization to construct the wavefuntion?

(ii) if the answer to question (i) is yes, does the result differ from the textbook description? For instance, the lone pair electron in the $\ce{H2O}$ molecule? (is there any unitary equivalent result like orbital localization in MO-based method?)

I asked the question (ii), since NBO analysis tends to give non-equivalent composition for lone pairs in $\ce{H2O}$, one sp, the other p. I am wondering what is the answer in ab initio valence bond method.


texts: Periodic trends: why is effect of protons greater than electrons?

texts: Why is it that adding protons has a greater effect than electron-electron repulsion on periodic trends like atomic radius and ionization energy (assuming # of shells constant)? It seems that if protons and electrons have the same charge and electrons are actually closer to the electrons in question (e.g. for ionization energy), that their effect would be the same?


texts: Ignoring initial H+ Concentration For Addition of Strong Base to a Buffer Solution

texts: When adding a strong base to a buffer solution, with a generic weak acid HA and generic weak conjugate base A-, is the initial amount of H+ ignored because it is so small? Specifically, at least in my text book, we only consider what happens to HA and A- when a strong base, say NaOH, is added.


texts: Free software to draw Newman projections

texts:
I need to draw Newman projection of a molecule. Particularly 1,2-dicloroethane rotamers, but have no idea if there is any program to do that kind of things.

Do you know about some program available for Linux?

I refer to this kind of sketch:


texts:
Every one knows that liquid oxygen is flammable, but why this tank labeled like this:

so is it really liquid oxygen is non flammable?


texts: Why No Change in Polarizability in Asymmetric Stretch?

texts:
In order for a molecule to be Raman active, there must be a change in the polarizability, meaning that there must be change in the size, shape or orientation of the electron cloud that surrounds the molecule. And this change said to occur in symmetric stretching, but not asymmetric stretching.
Please explain using plain english (without any rules or tables) why is that in asymmetric stretching like the following, there is no change in the size, shape or orientation of the electron cloud that surrounds the molecule? Specially considering each side independent has its own electron cloud.