texts: How to search substructures with explicit hydrogen in RDKit?

texts:
For a substructure search I would like to search for structures containing unfused benzyl.
The idea was to explicitly add hydrogen. But apparently this does not give the expected results.

So, I assume either my understanding or expectations are wrong or I'm using RDKit not properly.
I just learnt (Substructure search with RDKit) that I better use SMARTS expressions with Chem.MolToSmarts() where I get the expected results.

However, if I have much more complex search structures, how can I get from the SMILES to the SMARTS? Do I have always to figure out the SMARTS code myself? Is there maybe a way just drawing a molecule and add explicit hydrogen and search with this somehow? I guess it should be pretty clear (at least to a human) what I want to find (or not find) with structure 2. Are there maybe any tools or code which can assist here?

Code:

from rdkit import Chem

smiles_strings = '''CC1=CC=CC=C1
CC1=C([H])C([H])=C([H])C([H])=C1[H]
C1(C2=CC=CC=C2)=CC=CC=C1
C12=C(CC3=CC=CC=C3C2)C=CC=C1
C12=CC=CC=C1C=C3C(C=CC=C3)=C2
C12=C(C(C(C=C3)=CC=C4)=C4C=C2)C3=CC=C1
'''
smiles_list = smiles_strings.splitlines()

def search_structure(pattern):
    found = []
    for idx,smiles in enumerate(smiles_list):
        m = Chem.MolFromSmiles(smiles)
        if m.HasSubstructMatch(pattern):
            found.append(idx+1)
    print("Structures found: {}".format(found))

smiles_1  = smiles_list[0]
pattern_1 = Chem.MolFromSmiles(smiles_1)
smiles_2a  = smiles_list[1]
pattern_2a = Chem.MolFromSmiles(smiles_2a)
smiles_2b  = Chem.MolToSmiles(pattern_2a)
pattern_2b = Chem.MolFromSmiles(smiles_2b)
smiles_2c = smiles_2b
pattern_2c = Chem.MolFromSmarts(smiles_2c)
smarts_3 = '[cR1]1[cR1][cR1][cR1][cR1][cR1]1-[c,C]'
pattern_3 = Chem.MolFromSmarts(smarts_3)

print("\nSMILES 1 : {}\n# my expectation: [1, 2, 3, 4, 5, 6]".format(smiles_1))
search_structure(pattern_1)
print("\nSMILES 2a: {}\n# my expectation: [1, 2, 3]".format(smiles_2a))
search_structure(pattern_2a)
print("\nSMILES 2b: {} (Mol from SMILES)\n# my expectation: [1, 2, 3]".format(smiles_2b))
search_structure(pattern_2b)
print("\nSMILES 2c: {} (Mol from SMARTS)\n# my expectation: [1, 2, 3]".format(smiles_2c))
search_structure(pattern_2c)
print("\nSMARTS 3 : {}\n# my expectation: [1, 2, 3]".format(smarts_3))
search_structure(pattern_3)

Result:

SMILES 1 : CC1=CC=CC=C1
# my expectation: [1, 2, 3, 4, 5, 6]
Structures found: [1, 2, 3, 4]

SMILES 2a: CC1=C([H])C([H])=C([H])C([H])=C1[H]
# my expectation: [1, 2, 3]
Structures found: [1, 2, 3, 4]

SMILES 2b: Cc1ccccc1 (Mol from SMILES)
# my expectation: [1, 2, 3]
Structures found: [1, 2, 3, 4]

SMILES 2c: Cc1ccccc1 (Mol from SMARTS)
# my expectation: [1, 2, 3]
Structures found: [1, 2, 4]

SMARTS 3 : [cR1]1[cR1][cR1][cR1][cR1][cR1]1-[c,C]
# my expectation: [1, 2, 3]
Structures found: [1, 2, 3]


texts: Why are silyl chlorides more readily hydrolysed than alkyl chlorides?

texts:
I know that the $\ce{Si-Cl}$ bond has a slightly higher energy, but silyl chlorides are much more readily hydrolyzed compared to alkyl chlorides. I do not fully understand why that is. My thoughts so far are:

There is a better match in energy between the orbitals of the $\ce{Si-Cl}$ bond and water.
Reactions proceed when there is a favorable interaction between HOMO and LUMO.
In this case, the HOMO is the lone pair on the water molecule. The LUMO of a $\ce{Si-Cl}$ bond is closer to it in energy compared to a $\ce{C-Cl}$ bond.

Is this the right argument to take?


texts:
While studying about band theory of semiconductors, I observed that when the electrons were excited from the valence band to the conduction band, they left behind holes in the valence band. From my existing knowledge, I believe that the valence electrons alone occupy the valence band which tells me the valence band is negative. For the holes to exist, the valence band has to be neutral. So, why is the valence band neutral?

If my reason for the valence band to be negative was wrong, I would like to know the reason.


texts:
When water approaches both of them, no reaction is seen in the first compound, but the second compound react readily with water.

In my notes, it is written that CH3 causes steric effect and also +I effect which decreases the positive charge on the adjacent (sp2-hybridised) carbon. Hence, the first compound doesn't react with water.

But in CF3, I know it causes lots of -I, which increases the positive charge on the adjacent carbon, but won't it also cause steric effect too? The lone pair on Fluorine and approaching oxygen of H2O shall hinder each other? (But it does react.)


texts: Can chiral atoms have same substituents but with different orientations?

texts:
So consider this molecule. We have to determine whether nitrogen atom is chiral or not.

MY IDEAS:
Now going by all I have read, for chiral atoms only criteria is substituents to be different. Here two substituents are same but as we can see orientations of the substituents is different.
So aren't the two substituents technically different because after all they aren't going to react the same way to plane polarized light?

I tried to break it into possibilities:

Now in first case I think we could rotate around one of the sigma bonds attached to nitrogen and form a conformation with a plane of symmetry.
So is in this case nitrogen not a chiral atom?

Now in the second case I do think we can't prove the two substituents to be same, no matter how much we rotate. So chiral?

CONCLUSION: I am a beginner in this topic and not really confident about my thought process

Can we really use conformers of molecules to support their symmetry because after all conformers are ever changing, not stuck in one orientation?

Also what's the logic behind checking the plane and centre of symmetry of molecules? How does that relate to rotation of PPL light?

->If two substituents of a sp3 hybridized atom are identical, we say not optically active.
 But both being identical will rotate PPL light in same direction, so a net rotation will be produced.
->So isn't it optically active?


texts: In 1-chloroprop-1-ene(E), if we add HBr, where will the proton add to, C1 or C2? I am asking this because I can't decide whether mesomeric as well as negative inductive effect of Cl will dominate or hyperconjugation of methyl group at C2 carbon, which in turn will decide the position of the formed carbocation.


texts: Is the pressure in an HPLC system the same throughout?

texts:
I'm not sure if I'm articulating myself well enough, but here's my problem: I have a current HPLC system, where we typically have backpressure readouts of around 15 MPa. We are looking to get a new HPLC, and the rep said its DAD detector has a maximum pressure of 6 MPa. My questions are:

Is the pressure at the pump outlet the same as the pressure at the column inlet and outlet?
What pressure is actually being shown on the system readout when looking at the pump? (I'm assuming just the pressure at the pump outlet)
Is the pressure at the detector usually significantly less than at the pump outlet?
Assuming everything transfers from one system to our new one, and we end up with the same types of backpressures, will I have issues with this new detector?


texts: Effective chemical for protecting hide glue from microbial attack

texts:
One problem with hide glue is that it can be attacked and degraded by bacteria and fungi.

To protect hide glue from this kind of deterioration I am interested in identifying an effective anti-microbial. Toxicity against beetle larvae would be a plus. Note that hide glue is typically prepared at 140F and so the chemical must be stable at that temperature. Also, any kind of volatility is out of the question because it needs to last for a long time (100 years).

The main chemical I am considering right now is triclosan, but would be interested in any other ideas.


texts: What the difference between Gibbs free energy of activation and activation energy


texts: Change in internal energy for isothermal process

texts:
A gas expands isothermally against a constant external pressure of $1\ \mathrm{atm}$ from a volume of $10\ \mathrm{dm^3}$ to a volume of $20\ \mathrm{dm^3}$. It absorbs $800\ \mathrm J$ of thermal energy from its surrounding.
The change in internal energy is:

I came across this question and my doubt is, for isothermal process, $\Delta U=0$ ( change in internal energy) for ideal gas is zero right? Then how can we calculate $\Delta U=0$ here, assuming the gas to be ideal?
Is the error with the question or am I missing something?


texts: Are there more endothermic or exothermic reactions?

texts:
I'm wondering whether there are more endothermic or exothermic reactions.

Of course the amount of mass will stay the same, but I thought that not every exothermic reaction has an endothermic counter-reaction. Is this stream of thought correct and does that mean that there are more exothermic reactions than endothermic reactions?
In other words, does every reaction have a reverse reaction?


texts: What is the structure of 2-methylimidazolate?

texts:
Looking for the structure of 2-methylimidazolate, I find conflicting results:

this page on sodium 2-methylimidazolate gives:

this other page on cadmium 2-methylimidazolate gives another anion, namely a carboxylate derivative of 2-methylimidazole:

Which is it? Where in IUPAC nomenclature rules can I get the definitive answer?


texts: Can Gas diffuse according to its partial pressure, not according to its concentration in gas mixture?

texts:
by Raoult's law,

Partial pressure  =  total pressure  X  concentration(mole fraction)

In gas exchanging situation of 2 gas mixtures which are different in total pressure from each other(like higher temperature?) and include gas A of same concentration, each gas A in 2 mixtures will be the same in its concentration but different in partial pressure. Then, gas A will diffuse from high partial pressure to low partial pressure even though this diffusion is from low concentration to high concentration. Is this right??

Sorry for any misconceptions.


texts:
I am slightly confused about the concept of a salt bridge/porous disk. I understand that these are necessary in a galvanic cell since there is a charge buildup and the salt bridge and porous disks allow ions to flow in order to neutralize this charge and allow for the electricity to continue flowing.
What I am confused about is what ions are flowing. As an example I'm going to talk about a zinc-copper galvanic cell in which the zinc is oxidized at the anode and the copper is reduced at the cathode. What ions flow through the porous disk? Is it some of the $\ce{Zn^{2+}}$ ions and the anion from the copper solution, or is it separate ions? Is this the same in a salt bridge or is the salt used in the bridge the one that moves?
For example, if a salt bridge is made with $\ce{KCl},$ does the $\ce{K+}$ go to the cathode and the $\ce{Cl-}$ go to the anode or do the $\ce{Zn^{2+}}$ ions move through the salt bridge?
In other words, what ions flow through a salt bridge? Is it the ions from the separate solutions in the two half cells or the ions inside the salt bridge? What about a porous disk that has no ions inside of it?


texts:
I strongly feel that the answer should be option (1) as the ester functional group has a greater preference over the double bond and hence it should get a lower locant.
But the source of the question says that the answer is option (2). My question is why the double bond gets a lower locant than ester in this case?
As far as I know the lowest set out locants rule is applicable for substituents but when the comparison is between functional groups the preference order plays a greater role. Please let me know if I am wrong.


texts: We often see electronic states are named like nπ* or ππ* states. What is the reason behind this kind of naming ?


texts: What is the difference between these notations and terms?

texts:
I can't tell if they're being used interchangeably or if there's some nuanced difference betweem them. Here they are:
$E^∘$
$E_0$
$E_h$
$E^⦵$
If I understand correctly, electrode potential is the same as reduction potential. Redox potential can be both reduction potential and oxidation potential.
EDIT 1:
The context is electrochemistry. andselisk in the comments asked if it was $E^⦵$ or $E^∘$. When I had the superscripted $0$, I actually meant $∘$, as andselisk wrote. I hadn't seen that the sites had used this, and not a zero. andselisk also included this other symbol (⦵) I hadn't seen until now, but I'm now wondering about it too, as I've seen it is used in some equations relating to the topic of electrode/reduction potentials.
EDIT 2:
Here are some links that show why I'm confused:
This Wikipedia article #1 notates reduction potential as $E_0$, whereas this Wikipedia article #2 notates standard electrode potential as $E^∘$. Now, as said, I believe that
reduction potential = electrode potential
Perhaps the first article is referring to the unknown absolute reduction/electrode potential, and the second article is referring to standard reduction/electrode potential.
EDIT 3:
Perhaps there actually is a difference between reduction potential and electrode potential. Maybe they both describe the exact same phenomenon, but in different contexts. Here's the nuance I propose:
A species can only be said to have an electrode potential when this species exists as an electrode. Its electrode potential is the same as its reduction potential, but it is being viewed in the context of an electrode. One could still refer to the electrode potential as a reduction potential.
However, if one's is talking about the reduction potential of a species when it isn't an electrode, it is simply a reduction potential.
If it is an electrode: can use both reduction potential and electrode potential.
If it isn't an electrode: can only use reduction potential.


texts:
I am trying to compare the performance of few Quantum Chemistry property prediction ML models. I was looking at the following table from DOI:
10.1039/c7sc02664a

The problem is that it does not contain any units. A preprint (https://arxiv.org/pdf/1909.00259.pdf, Table 4) suggests that the energy units are Hartree. Among energy properties, HOMO, LUMO, and gap have reasonable values for Hartree unit. However, values reported for U0, U, H, and G look absurd. As a comparison, look at MAE for mean value of each property:

These are in [eV] units (1 Ha = 27.212 eV). In other words, for instance MPNN models MAE for U property is 55.78 [eV] vs 8.25 [eV] for the mean baseline. This does not make sense at all. [k cal/mol] sounds more reasonable but then why half the energies in one unit the other half in other unit, and then why there are no units in a paper published by Royal Society of Chemistry. Seems like I'm missing something. Thanks!


texts: In search of a safe and inexpensive solvent that can dissolve depolymerized polypropylene waste plastic

texts: I work at a place where we depolymerize post consumer waste polypropylene waste plastic through a thermal catalytic conversion process. During process shutdown we have to clear up the vessels which becomes a really difficult job as the depolyermized material which we call wax hardens without heat and have to hammered and scraped out which takes a lot of time. Therefore to make this cleaning process easy I am looking for a chemical clean up technique. Is there a reasonable and economical solvent that can dissolve/soften this wax?


texts: Solute mole fraction for hydrated magnesium sulfate dissolved in water

texts:
Problem: 70 grams of pure, hydrated $\ce{MgSO_4}$ is dissolved in 90
  grams of $\ce{H_2O}$. If the mole fraction of the solute is 0.039,
  find the molecular formula of the solute.

My flawed attempt at a solution:

Let the solute be $\ce{MgSO_4.xH_2O}$. In $70~\mathrm{g}$ of solute, the amount of solute is $$\frac{70}{120+18x}~\mathrm{mol}.$$

Likewise, in $\pu{90 g}$ of solvent, we have $$\frac{90}{18} = 5~\mathrm{mol}.$$

Plugging these values into the formula for mole fraction and equating it to 0.039, I thought I would get the value of $x$ as 7. Instead, I seem to be getting approximately 12.

Could somebody please help me solve this question? In general, when we have a hydrated solute in an aqueous solution, do we include the water of crystallisation in the total mass of available water while calculating the number of moles of water?


texts: Electronic configuration of chromium(II)

texts:
Which is the electron configuration for $\ce{Cr^2+}$

  (A) $\mathrm{[Ar]4s^23d^4}$
  (B) $\mathrm{[Ar]4s^23d^2}$
  (C) $\mathrm{[Ar]4s^03d^4}$
  (D) $\mathrm{[Ar]4s^43d^2}$

I referred to the periodic table and got the orbital notation for $\ce{Cr}$ as $$\mathrm{[Ar]4s^23d^4}\tag1$$
So $\ce{Cr^2+}$ would be $\mathrm{[Ar]4s^23d^2}$, or (B). But the teacher counted that wrong and said it was actually (C).

  Question: Shouldn't the answer be (B)? Why does $\ce{Cr}$ lose the $\mathrm{s}$ shell first?


texts:
I have recently been reading a paper, in which given dihedral angles of alanine dipeptide molecule $\psi$ and $\phi$, the conformation is catagorized as either $\beta$-1, $\beta$-2, or $\alpha$. I was trying to see if it is possible to extend the same idea to QM9 molecules and cluster them into different groups based on their properties? The properties provided for the QM9 dataset include:

Norm of the dipole moment ($\mu$)
Norm of static polarizability ($\alpha$)
Energy of the electrons in the highest occupied molecular orbital
(HOMO energy), lowest unoccupied molecular orbital (LUMO energy),
and their difference (Gap)
Zero point vibration energy (zpve)
Atomization energy (U)
Electronic spatial extent (R2)

The answer that I'm looking for is for instance something in the lines of: "based on the $\delta$ values, molecules can be divided into to two groups of $\gamma$-1 and $\gamma$-2". In other words does any of these properties inherently divide the dataset into k groups?


texts: Reaction of 1,3-dimethyl-2,5-dintrobenzene with NaOMe/MeOH

texts:
I have looked through articles and closest I feel is in this question there will be a nucleophilic aromatic substitution. Now, a lot of questions are available where there is a halogen and OMe group substitutes the halogen.
My take on this is maybe due to SIR effect (steric inhibition of resonance) The NO2 group present in between the two methyl groups would be substituted by OMe? Will this be the approach?


texts: Why don't metals form covalent bonds in bulk metal?

texts: I really don't understand why metals form metallic bonds. I mean, it makes no sense. It would make much more sense for them to form covalent bonds with themselves and have a 'pseudo-full' outer shell. How does freeing off electrons make them any more stable?


texts: Which d orbitals can form sigma, pi, delta bonds?

texts:
If two $\mathrm d_{xy}$ orbitals approach each other on $x=y,$ $z=0$, would a σ bond be formed? I would think so.

Can $\mathrm d_{z^2}$ form π bond with another $\mathrm d_{z^2}?$ (As all others can on $x$ or $y$ or $z$ as internuclear axis?) I am not sure but overlapping similar to p could be observed.

I would assume all except $\mathrm d_{z^2} - \mathrm d_{z^2}$ form δ bond. (both of same type like $\mathrm d_{xy}$ with $\mathrm d_{xy}.)$

What are the faults in my logic?


texts:
I remember that one of my old organic chemistry profs referred to mercury as being a "fancy proton". I think it was in the context of oxymercuration reduction.

What might have been his rationale for offering this comparison?


texts: Software for determining symmetry elements and point group of drawn molecules

texts:
The title represents my overall question. I would like to have a software that able to draw molecules (especially coordination complexes) and determine the symmetry elements and point group of the molecules. I have a PC with Windows 10 system and an iPad Pro.
Thank you.


texts: How to calculate the yield for an incomplete reaction?

texts:
I had a doubt in part b) of the following question.

a) When 0.527 g of platinum is heated in fluorine, 0.732 g of a dark red volatile solid forms. What is the empirical formula of this product?

b) Suppose fluorine was a limiting reagent, such that 0.155 g of platinum remains after all the fluorine has been consumed. Calculate the percent yield of this reaction. How many grams of product would be produced?

I've given part a) also because it was told that we should use data from a).

This is my attempt:

The answer for b) is given as 70.6% and 0.517 g, but I am unable to find where I am wrong. Is my logic correct? (I've double checked that my calculations at least are correct.)


texts: What are the magnetic quantum numbers for specific d orbitals?

texts:
I mean I know they’re $\ce{d_{-2}}$, $\ce{d_{-1}}$, $\ce{d_{0}}$, $\ce{d_{1}}$, $\ce{d_{2}}$ but how do these numbers relate to each one of $\ce{d}$ orbitals $\ce{d_{z_2}}$, $\ce{d_{xz}}$, $\ce{d_{yz}}$, $\ce{d_{xy}}$, $\ce{d_{x_2 - y_2}}$)?
I couldn't find a definitive answer anywhere.


texts: How is "F2/sig(F2)" the data quality in SXRD?

texts:
When I recieve a dataset from single crystal X-ray diffraction, I can determine the quality from a graph in which F2/sig(F2) is displayed in dependence of the frame.
But I forgot the basics... I have found that the $R_{int}$ value is calculated as such:
$$R_{int}=\frac{\Sigma|F^2-F_{mean}^2|}{\Sigma|F^2|}$$
Reference: http://www.canadiancrystallography.ca/cccw/files/CIF-file%20and%20validation.pdf
But what exactly is F2/sig(F2) now?


texts:
In reduction of carboxylic acid with $\ce{LiAlH_4}$ the first step is deprotonation.

But in the mechanism of reduction of amide with $\ce{LiAlH_4}$ (here), the first step is addition of hydride on carbonyl group. Why doesn't the hydride ion abstract a proton from $\ce{-NH2}$? Since acid base reactions are faster than nucleophilic addition.


texts: What is the Solubility of Common Noble Gases in Concentrated Phosphoric Acid, 85% w/v?

texts:
By Henry’s Law, the concentration of a dissolving gas in a liquid is proportional to the partial pressure of that gas in contact with the liquid, mathematically,
$ p = k_\mathrm{H} c$,
where $p$ is the partial pressure of the dissolving gas, $c$ is the concentration of the dissolving gas in the liquid (solution), and $k_\mathrm{H}$ is a constant (Henry’s constant?) which depends on temperature.

What is the value of $k_\mathrm{H}$ for common noble gases (in particular, xenon) in concentrated phosphoric acid, at, say $298~\mathrm{K}$? Can the solubility at other temperatures be calculated using an extrapolation formula?


texts: Can electrolyzing ice cause an explosion?

texts: I know electrolyzing water separates it into hydrogen and oxygen.  However, I am curious, if ice is electrolyzed, could it explode?  My thought process is that oxygen and hydrogen bubbles would build up in the ice, and continued electrolysis would ignite the gasses (forming water again).  However, since it is contained within the ice, it could ignite explosively.  Is this what would indeed happen?  One way to try this might be using a tazer or bug zapper on ice.  I believe this could be dangerous, and appropriate precautions would need to be taken.


texts: octahedral interstitial sites located entirely within a full hexagonal HCP unit cell at a height of $c/4$ up from the bottom of the unit cell

texts:
I have been trying to visualize and find the number of them for a while, through the image attached.
I can't tell whether the c/4 part includes the octahedral site or not...how should I go about approaching this problem?


texts: When does a pinacol undergo dehydration or rearrangement?

texts:
What happens when the above pinacol is treated with -
(a) conc. sulphuric acid
(b) dil. sulphuric acid

I'm confused between pinacol rearrangement and dehydration (E1 or E2?), as both possibilities exist. I think the concentration of the reagent might have a role to play, but I'm not sure. Please help.

P.S. It'd be great if you could quote data and sources with your answer.


texts:
Which would produce the largest change in the $\ce{H2O}$ level when added to water in a $\pu{25 mL}$ graduated cylinder?
(A) $\pu{10.0 g}$ of $\ce{Hg}$ $(d = \pu{13.6 g/mL})$
(B) $\pu{7.42 g}$ of $\ce{Al}$ $(d = \pu{2.70 g/mL})$
(C) $\pu{5.09 g}$ of iron pyrite $(d = \pu{4.9 g/mL})$
(D) $\pu{2.68 g}$ of oak $(d = \pu{0.72 g/mL})$

I approached this question by dividing the mass by density to find the volume change. Thus, I got the answer (D), but the answer is (B).
Can anyone please explain this?


texts:
How can I theoretically predict the time needed to photolyze n moles of $\ce{AgF}$? (with UV) (this is not a homework question)

The photolysis of $\ce{AgF}$ requires UV light - but I don't know which wavelength the UV must be at for the optimal photolysis. Then if the wavelength is known I can calculate the energy of one UV photon of a specific wavelength. After that I can calculate the required amounts of photons required for the reaction

I was thinking of this method:

First I need to find out which wavelength the UV must be at for the optimal photolysis of $\ce{AgF}$ (How?)
Then I need to calculate the amount of energy required for the photolysis of AgF : on wolframalpha I entered this equation: $\ce{2AgF -> 2Ag + F2}$ and it gave me a $\Delta{}H=409.2\:\mathrm{kJ/mol}$

And somehow I must be able to then figure out which lamp I could use and how long I should use it.


texts: Number of water molecules to contribute one molecule to every milliliter on earth

texts:
How many millilitres of water would it take so that, when they are thoroughly dispersed around the world, it would yield an average of one molecule of the original sample of water in each millilitre of water in the world?  For the sake of argument, assume that the H and O atoms do not dissociate, and the water molecules remain intact.

I calculated it once and got something around 40 ml, but I forgot how I made that calculation.


texts:
I was sorting out some old boxes in one of the rooms in my house, when I found a small container with about 10 grams of this blue crystalline powder. I assume that it contains some form of copper due to the colour, but the label's all ripped and I can't see the name of it.

So what compound is it?

It appears to glow in the image, but this is just the reflection from the camera flash and it doesn't look like this in real life.


texts:
I was trying to name the following compound and I thought that if both the aldehyde group carbons should be included in the parent chain or I should go with the longest chain . I saw the solution for this and got two answers as I) 3-(Formylmethyl)hexanal and 2) 3-Propylpentanedial.
Can someone please help me in naming it correctly??


texts: Designing a mathematics course for 1st year chemistry students

texts:
Background:
I am a mathematician with very little knowledge in chemistry (I do know some
physics). I will probably teach a course "mathematics for (1st year) chemistry
students" in the future (1st semester 3h + 1h exercises per week, 2nd semester
2+1h). This will be the only (mandatory) mathematics course in the chemistry Bachelor curriculum (and even the subsequent Master curriculum, as far as I know). The students should have high school mathematics background, such as onedimensional derivates and integration (at least of polynomials), but probably no complex numbers. I will have a lot of freedom in the selection and presentation of topics.
Questions:

Which topics are commonly covered in a "mathematics for chemistry
students" courses?
Closely related: Which textbook are most commonly used?

In more detail:

Can I safely assume that mathematical proofs and even rigorous definitions can/should mostly be skipped?

How black-boxy is Quantum physics used in the typical chemistry curriculum?
Even the most basic Quantum physics will need, as minimum, some linear algebra (Hermitian, normal and unitary operators, exponention of operators, etc.) as well as Fourier transformation and a little bit of differential equations. Should these topics be coverd, or is it enough to say "one can show that in an H atom, orbitals look like this", and just talk a bit about complex valued functions in R^3?
Do you ever do calculations with spins? (Mostly spin 1/2, I would assume? That might be a motivation to show some calculations with complex 2x2 Matrices?)

Which computer mathematics software are most commonly used in a chemistry curriculum? (Mathematica? Maple?) I assume it would make sense to do some calculations and exercises using such software?

Update answering some comments:

I am in Austria (sorry, do not know how to add an according tag), but I would be interested in how these things are handled in other countries as well.
This course has been held before at our department (not by me), but I would like to get "unbiased" input from people from chemistry, and therefore did not list the traditional topics / lecture plan.
Of course I will speak to people in the Chemistry department, but I would be happy to get some ideas here first (I do not know the Chemistry department people, and it could be that a randomly selected person who happens to be willing to indulge me has some unorthodox views).


texts: How can a conductivity meter be used to determine the equivalence point?

texts:
I know how a conductivity meter works. Power is supplied to electrodes and these electrodes change charge. The ions in the solution will be attracted to the oppositely charged electrode. The charge they carry at the electrodes is measured.

The equivalence point may be located graphically by plotting the change
in conductance as a function of the volume of titrant added.

I'm not sure this is an accurate enough answer. Is there something I'm leaving out or that could improve the answer?


texts: Does the "extent of reaction" have a physical meaning?

texts:
I am going to argue that it really doesn't have a useful or "comprehensible" physical meaning.

Lets say we have the following reaction:
$$3A\rightarrow2B$$

Chemists define the extent of reaction as:

$$\xi=\frac{n_{A_f}-n_{A_i}}{v_A}$$
where $n_{A_f}$ is the moles of $A$ once the reaction reaches equilibrium, $n_{A_i}$ is the moles of $A$ before the reaction began, and $v_A$ is stoichiometric coefficient of A for this reaction.

The numerator makes physical sense, it is simply how many moles of A are consumed over the course of reaction. The denominator makes sense because it states the amount of molecules needed to be consumed to generate the product.

But once you put the numerator over the denominator, it starts to lose any physical meaning to me and simply becomes a useful mathematical conversion factor. If there is an exact physical meaning here, what is it?

P.S. It has the units of moles which is weird because it doesn't equal the change in moles for this reaction or the amount of moles consumed and produced on either side.


texts: Can negative adsorption be considered equal to sorption?

texts: In my book it was written sorption is basically when the substance gets uniformly distributed into the bulk of the solid but at the same time its concentration is higher at the surface then in the bulk. for negative adsorption a same type of defination was there so is there any difference between them?


texts: How to get ionic radii for coordination number 12?

texts:
I am studying $\ce{ABX3}$ perovskites, and I would like to calculate Goldschmidt tolerance factors for them. The $\ce{A}$ sites in these materials have a coordination number $12$.

The Shannon's paper (R. D. Shannon, Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta. Cryst. A 32, 751 (1976)) provides values for ionic radii for the coordination number $12$ only for a few elements, but doesn't do it for most other elements.

Are there any sources, where I can get ionic radii for $\text{C.N.} = 12$ for all elements?


texts: Claisen rearrangement in substituted ring

texts:
This is an example of Claisen rearrangement, property of allyl vinyl/phenyl ethers.

I believe that the allylic migration should take place to the position ortho to both $\ce{-CH3}$ and $-\ce{OR}$ because:

There's more electron density there due to the presence of electron donating group $\ce{-CH3}$

and I read this in March under Claissen rearrangement:

  Since the Claisen rearrangement doen't involve ions, it shouldn't greatly depend on the presence or absence of substituent groups on the ring. This is the case. Electron donating groups increase the rate and electron withdrawing groups decrease it, but the effect is small.

So I expect the product to be 2-[(2E)-but-2-en-1-yl]-3-methylphenol:

However my teacher made us write the product to be 2-[(2Z)-but-2-en-1-yl]-5-methylphenol:

His rationalisation was that the carbanion like species attacking the allyl group is more stable at the place away from methyl group.

But my question is that if this reaction is single step, followed by tautomerism why should it even depend on the carbanion like species which isn't even formed.


texts: Is FA 18:2 undifferentiated the same as linoleic acid?

texts: On wiki, linoleic acid has the code number FA 18:2 cis,cis-9,12. But then what exactly is FA 18:2 undifferentiated?


texts: How To Calculate "İntermolecular Energy" as QM and MM?

texts:
In this article: http://ambermd.org/antechamber/gaff.pdf, in Table-7, authors have calculated "intermolecular energy" of a molecule set. I wonder how can I calculate this energy by using gaussian09 and amber-17? Is there any tutorial ? or what is the way for this? I need to calculate this energy to prove my "new force field parameters are correct" but I really don't know this.
Thank you.


texts: What other analysis suitable for water as general? Right now, I have turbidity, pH, Total Soluble Solid and color.


texts: What is the molecular mechanism of ammonia's toxicity?

texts: How does it damage proteins/lipids/DNA? There seems to be surprisingly little literature on its toxicity.


texts: I can find in literature what the density is for untreated viscose, but not for viscose that is bleached. Does this change the density? And what is the density for bleached viscose?


texts: Comparing the zero point vibrational energies of DCl and HCl

texts:
(a) Compare the zero point energy (i.e. $E_0)$ in joules for $\ce{H^{35}Cl}$ and $\ce{D^{35}Cl}$ (assuming both are anharmonic oscillators).
(b) Explain the effect this will this have on their chemistry (you may wish to use a diagram to help here).

I have calculated a value for the vibrational frequency and have a value of the anharmonicity constant for $\ce{H^{35}Cl}$ (but not the anharmonicity constant for $\ce{D^{35}Cl}).$ I am unsure on how to proceed with these as all I know is an equation linking vibrational energy to the vibrational frequency and anharmonicity constant. I would be so grateful for any insight into this.


texts:
To understand the behavior of solubility, it is helpful to look at the chemicals that misbehave, and apply the rules, and look for underlying explanations and common threads. Generally speaking, the solubility of some chemicals is lower at higher temperature.

The problem is, the explanation(s) for this is that entropy is negative for some chemicals, and solvation is difficult, and sometimes- the hydrated phases change (which is more like a chemical reaction, where the resultant chemical precipitates). So, I would like to identify the chemicals which misbehave and identify the explanation(s) or the excuse(s).

Here are a couple of links to other questions on this SE about this phenomenon:

Why do some solid chemicals dissolve better in colder water? and Why does sodium sulfate have an unusual solubility-temperature curve?.

What are some chemicals that dissolve better in cold water than hot water?


texts: Surface passivation is done to deal with "dangling bonds" (for example, $\mathrm{SiO_2}$ layer on top of a $\mathrm{Si}$ layer). But isn't the new surface will have dangling bonds on its own at the new formed surface?


texts: To what degree an N99 active coal filter can protect against products of burning paraffin oil?

texts:
I sometimes do firedance and a part of it is waving a stick with burning endings made of Kevlar soaked in paraffin oil. I started to be a bit concerned about how healthy is it to inhale lot of paraffin oil fumes.
I was wondering if I can protect somehow against it and my idea is to wear a mask with N99 active coal filter. The vendor claims that it blocks dust of size 0,1 mm and more. What noxious products of burning paraffin oil can it block? Which of them it can't?


texts: Preparation of alkyl halide from alcohols

texts:
$\ce{R-OH + HBr -> R-Br + H2O}$

An $\ce{R+}$ carbocation is formed during this reaction.

If $\ce{R}$ is any alkyl group instead of methyl or ethyl, can the beta hydrogen to the hydroxy group be removed to form a double bond, similar to a dehydration??


texts: So, I remember in high school chemistry when my teacher combined hydrogen peroxide with potassium iodide and it exploded into a yellowish foam. He said it was an exothermic reaction so it's really hot. I was just wondering exactly how hot is it? Is there a way to calculate the heat from the amount of chemicals used?


texts: Detecting a gas molecule moving through a small pinhole

texts:
Suppose I have the four DNA base chemicals - thymine, adenine, cytosine, and guanine. Imagine I turn each of them into a gas, make a "cartridge" of the gas for each chemical, and then have a "pinhole" that is opened or closed by a semiconductor. When the pinhole is open, the gas will, of course, expand through the pinhole and exit the cartridge. The system must emit only one molecule at a time.

If I send a command to the semiconductor to open the pinhole, what kind of sensor can I use to detect a molecule passing through? If necessary, you can modify the base chemicals as long as it would not interfere with their chemical properties in any way other than to improve detection of those molecules, if that makes sense.

The cheaper and more compact the system, the better, of course. I was thinking about the way an inkjet printer works, with a piezoelectric crystal vibrating the ink into droplets, but even the smallest droplets (a picoliter or so) are still bigger than a single molecule, so that doesn't work. Other possible methods I've thought of include a MALDI like system, a system where a weak laser is set up with a light detector; when a molecule passes through, the beam is interrupted, using a scanning tunneling microscope (STM; no idea how that would work), or a system using fluorophores.


texts: Why the bond strength of HCl is more than HBr?

texts: Most people say that it is because the 3p orbital of chlorine when overlapping with the s orbital of hydrogen covers more area than when 4p orbital of bromine overlaps with the s orbital of hydrogen which makes bond between H and Cl more stronger than the bond between H and Br. But how can we say that the area of overlapping is more for 3p and s orbital compared to overlapping of 4p and s orbital?


texts: Why do PBr3 and PCl3 have larger bond angles than PH3?

texts:
According to the Colby Chemistry Database, the bond angle of $\ce{PBr3}$ and $\ce{PCl3}$ are around $101$ degrees, but the bond angle of $\ce{PH3}$ is $92$ degrees. (Source: PCl3 PBr3 PH3)

There was a previous question on Stack Exchange about the bond angle difference in $\ce{PF3}$ and $\ce{PH3}$ here: PF3 and PH3, but the accepted answer mentions back bonding as a factor to increase the bond angle in $\ce{PF3}$. I was skeptical about this answer, because in $\ce{PCl3}$ and $\ce{PBr3}$, there should be less back bonding than in $\ce{PF3}$ because bromine and chlorine are both much larger than fluorine and there will be worse orbital overlap between the halogen. Less back bonding should make the bond angle of $\ce{PCl3}$ and $\ce{PBr3}$ smaller than that of $\ce{PF3}$, if back bonding were the major factor here? In reality, that is not the case. Why not?


texts:
Sorry for coming in here with little chemistry knowledge and a pretty inane question, but my googling skills have completely failed to cut through the enormous combined output of the baking brigade and all the lovely people making lovely things with this stuff.  Unsurprisingly not one of whom has paused to mention what's actually happening on a chemical level.

For the uninitiated, salt dough is made by mixing half a part table salt with one part wheat flour, and one half to one part water, though recipes vary greatly. This is then moulded into the desired shape and baked in an oven at anywhere between 60 and 180 °C, resulting in a hard and surprisingly tough (to me anyway) finished article which is often used as a decoration on Christmas trees. But what is actually happening?

I can guess at something involving the re crystallization of the sodium chloride, but wheat flour, whilst being so incredibly common, is to me a completely incomprehensible mix of proteins, starches and all manner of other stuff. All of which involves chemistry way over my head.

I would greatly appreciate an explanation of what's going on in this hardening process.


texts: Find ratio of quantities of water and of argon in airtight container

texts:
I am working on my EJU exam past papers (2013) and got stuck at this question. Knowledge of high school or first year university chemistry is assumed. I honestly do not know where I should start.

  When argon and water were placed in an airtight container with a
  constant volume and the gas mixture was kept at 373 K, the pressure of
  the gas mixture became P1 with a portion of water remained as liquid.
  When the whole was heated to 403 K, all the water was vaporized and
  the pressure became P2. From (1) to (6) below choose the correct
  formula representing the ratio, water/argon, of the quantities (in
  mol) of water and of argon in the container. Assume that the vapor
  pressure of water at 373 K is Pv, that argon is an ideal gas not
  dissolving in water, and that the volume of water before heating to
  403 K can be neglected.

Please note that answer key provided is (1). I tried to think that we could form an equation from total moles of gases equate to the sum of total moles of water and argon at 403 K since all are vaporized. Then use the ideal gas law to find the total amount of gases at 403 K. However, I cannot connect these pieces and information given at 373 K together. Could anyone give me a solution to this question or at least a hint so I can continue working on it?


texts:
I need some acid-washed sand to smooth out boiling in diethyl ether synthesis. I aready have pre-washed sand for general filtration purposes, but it is not labeled as acid-washed.

Unfortunately, I have not found any reliable lab manual for acid washing of sand.

I found one reference instructing to wash 30 g of sand twice with 0.05 M sulfuric acid, then four times with distilled water.

However, other references instructing to use only hydrochloric acid and de-ionized water, but have not specified how much or the concentration.

Yet another reference says that sulfuric, hydrochloric or phosphoric acid can be used interchangeably.

I don't know how seriously should I take the acid washing step (for the ether synthesis from ethanol and sulfuric acid) and how to check whether it is properly washed (pH measurement?).

I know one can just purchase acid-washed sand, but I have excess of good quality sand and the professional acid-washed one is overly expensive.


texts: What is the meaning of 'anion water' in coordination chemistry?

texts:
In Mechanisms of Inorganic Reactions by Fred Basolo and Ralph G. Pearson, a passage discusses the history of coordination chemistry. Ammoniates had been assumed to be analogous to hydrates. They assess the comparision as,

  This analogy is essentially correct for in hydrates, except for interstitial and anion water, the water is coordinated to the central metal ion. [emphasis added]

What is the meaning of anion water, as used in this context?


texts: Is NaCl the only precipitate when you add HCl to concentrated NaCl

texts:
When aqueous HCl is added to a saturated salt water solution, is NaCl the only precipitate or does some HCl crystalize as well?

Sources online say that NaCl crystallizes but they don't say what happens to the HCl

https://bouman.chem.georgetown.edu/S02/lect8/lect8.htm
http://www.csun.edu/~ml727939/coursework/695/common%20ion%20effect/recrystallization%20of%20NaCl%20solution%20with%20HCl.htm


texts: Why do resorcinol and iodine react to give 2-iodobenzen-1,3-diol?

texts:
I am supposed to perform the above shown reaction in the lab soon, but I don't really understand the mechanism behind it. I got told by my lab assistant that the mechanism is an electrophilic aromatic substitution in which resorcinol (benzin-1,3-diol) acts as the electrophile and iodine as nucleophile. I imagine the resorcinol also electron-poor because of the -I effect caused by the electronegative Hydroxide substitutes. But isn't the +M Effect stronger? Then why should resorcinol act electrophilic?
Why is Iodine nucleophilic when there is no Lewis-acid present?
And last but not least: why is the Product 2-iodo-1,3-diol and not 4-iodobenzen-1,3-diol?


texts: How to find the possible valence states of elements in the lower end of the d block and the f block?

texts:
For silver, why don't the electrons in the 4d orbital move to the 5p orbital?

Is it possible for any elements to move their electrons between $n$d and $(n+1)$p orbitals?

When the f orbital is completely filled with 14 electrons, should we take it in consideration to find the valence states?

When Z=58, can you show me the electronic configuration and how do we form the valence state(s)?


texts: Does the decay of Carbon-14 effect health in biological systems?

texts:
Please note that this is not fundamentally a Biology question. It relates to the properties of molecules containing Carbon and Nitrogen.
Carbon atoms are everywhere in living systems from sugars to proteins etc.
Carbon-14 is present in living systems in a certain percentage compared to Carbon-12.
This Carbon-14 is decaying to Nitrogen-14 even when the system is alive.
Does this effect the health and functioning of the living system at all ?
I mean take a glucose molecule $\ce{C6H12O6}$, suddenly one of the Carbon atoms randomly decays to a Nitrogen atom. Does this molecule continue to function as a glucose molecule ? This question extends to every molecule in the body that contains Carbon atoms.


texts: Can a change in internal energy always be expressed as the product of the constant volume heat capacity and the change in temperature?

texts:
It makes sense to me conceptually that $dU=C_VdT$ but is that always the case because I have seen that result derived thus:
$$dU=U(V,T)=(\frac{\partial U}{\partial T})_VdT+(\frac{\partial U}{\partial V})_TdV$$

(Not the typical expression for internal energy $dU=TdS-pdV$

But for a perfect gas $(\frac{\partial U}{\partial V})_T=0$ so for a perfect gas internal energy is only a function of $T$: $U=U(T)$. Thus, it follows that;

$$dU=(\frac{\partial U}{\partial T})_VdT=C_VdT$$

However, is this only true for a perfect gas? I ask this because, the knowledge of this equality is required to show that entropy is a state function and I was wondering whether the proof that uses the above argument is only valid for a perfect gas or whether it's valid more generally?

I will show you the proof now:

$$dU=dq-pdV=C_VdT$$
$$dq=C_VdT+pdV$$
$$\frac{dq}{T}=\frac{C_V}{T}dT+\frac{nR}VdV$$ (using pV=nRT)

Then if you differentiate appropriately you can show it's an exact differential. However, is this only valid for a perfect gas?


texts:
Why is the acoustic absorption coefficient of hexane in air less than air? A 120 kHz pulse train exhibits a larger amplitude after traveling in a hexane/air mix than in pure air.

My hypothesis is that the hexane molecule has fewer degree of freedom than that of $\ce{N2/O2}$. Is this plausible?


texts:
What is the difference between:
atomic mass
relative atomic weight
relative isotopic weight
standard atomic weight
atomic weight
relative atomic mass
I am told by Wikipedia that:
relative atomic weight = atomic weight
and a the start of the article it says:
For a single given sample, the relative atomic mass of a given element is the weighted arithmetic mean of the masses of the individual atoms (including their isotopes)
so standard atomic weight = relative atomic weight
But at https://en.wikipedia.org/wiki/Relative_atomic_mass#Standard_atomic_weight#Definition it says:
It is a synonym for atomic weight, though it is not to be confused with relative isotopic mass. Relative atomic mass is also frequently used as a synonym for standard atomic weight and these quantities may have overlapping values if the relative atomic mass used is that for an element from Earth under defined conditions. However, relative atomic mass (atomic weight) is still technically distinct from standard atomic weight because of its application only to the atoms obtained from a single sample; \textbf{it is also not restricted to terrestrial samples, whereas standard atomic weight averages multiple samples but only from terrestrial sources}
I am told here that:
The standard atomic weight (Ar, standard) of a chemical element is the weighted arithmetic mean of the relative atomic masses (Ar) of all isotopes of that element weighted by each isotope's abundance on Earth.
But in this video I am told this is the definition of relative atomic mass.
Here I am told:
Atomic mass (ma) is the mass of an atom. A single atom has a set number of protons and neutrons, so the mass is unequivocal (won't change) and is the sum of the number of protons and neutrons in the atom.
Atomic weight is a weighted average of the mass of all the atoms of an element, based on the abundance of isotopes. The atomic weight can change because it depends on our understanding of how much of each isotope of an element exists.
In other words:
Atomic weight = standard atomic weight
Also, which of these definitions is used to convert grams of a substance into moles


texts: How can nitrogen be both inert and bond with everything in periodic table?

texts:
Aren't below statements from this link contradicting each other?

Nitrogen bonds to almost all the elements in the periodic table    except the first three noble gases, helium, neon, and argon

Nitrogen gas is mostly used as an inert atmosphere whenever the    oxygen in the air would pose a fire, explosion, or oxidising problems

How can one element be both inert and bond with everything at the same time? Aren't inertness and bonding mutually exclusive?


texts: How can I get rid of 700 million tons of chlorine gas?

texts:
I am conducting a thought experiment in which 40 million tons of hydrogen are supplied through saltwater electrolysis each year, creating 700 million tons of chlorine gas (Cl2) and 800 million tons of sodium hydroxide. (Lye)

I think I can get rid of a good chunk of the sodium hydroxide by mixing it with nitric acid and creating sodium nitrate for use as substitute for ammonium nitrate fertilizer, but I am not sure on how to get rid of the chlorine gas.


texts:
Hello,

Normally, it seems like enantiomers have inverted R/S configuration at every chiral centre. However, in the pair below which are clearly enantiomers (note the methyl and benzyl groups are going in and out of page) as mirror image of one is superimposable on the other, the configuration of the carbon in the main cycle attached to the nitrogen seem to have the same stereoconfiguration in both structures.

I suspect this has to do with the "prochiral" / meso nature of the molecule without the extra groups on the nitrogen, but have never heard of such exceptions.


texts: It is easier to iron cotton clothes when slightly wet, why?

texts: As the title says, why is it easier to iron cotton clothes when slightly damp ? Has this got something to do with the hydrogen bonding in cotton ?


texts: What exactly is the significance of molar mass in chemistry? Why not just mass?


texts: Keeping one component concentration constant and varying another in a solution

texts:
This is a simple question but it has been so long since I have done any chemistry. Basically I would like to keep the concentration of A constant and the concentration of B variable and vice versa.

Assuming we want to make a 50 ml solution with constant concentration of A and variable concentration of B.From my knowledge I would use C1V1=C2V2 in order to dilute A to its fixed concentration lets say from 4% to 3%. But how do i go about keeping it constant and B concentration variable for a final 50 ml solution.

EDIT:
Ok. So lets say A had an initial concentration of 4%. I want a constant A concentration of 3% in a volume of 50 ml. So I calculate my starting volume according to C1V1=C2V2 and get V1 to be (3*50)/4 and a starting volume of 37.5 ml. My remaining volume is 50-37.5 and get 12.5 ml. I want to make 5 solutions with 50 ml end volume. I put 12,5 ml of A in each flask giving me a constant A concentration of 3%. How do i finish up my 50 ml with different B concentrations?

2nd EDIT:
Apologies, this is my first time using this site and was told to edit my question and add my comment. I didn't put values as I believed it was clear enough but I guess not.

@ y chung that is what I have carried out in order to create the solutions, so I'm guessing I did it correctly then.

@ bon thanks for the comment. I will tell you exactly what Im trying to accomplish. I have two solutions one is A with a concentration of 9% and one is B with a concentration of 7%. I want to create 5 solutions each 50 ml with a constant 5% concentration of A and varying concentration of B from 1-5 %.

What I have done is as follows:
I reduced my A concentration to the required 5% by C1V1=C2V2 for a 50 ml solution getting 28 ml. I put 28 ml in each volumetric flask of 50 ml capacity.

I then calculated how much volume of B with the 7% concentration I would need to get it to say the 15 concentration based on my remaining volume of 22 (50-28). For the 1 % concentration this yielded a volume of B at 7% of 3.14 ml. I added that to my flask contain the 28 ml of A and made up the solution to 50ml.

The question is, is this correct? from what I gathered from y chung ,it is.
Thanks


texts: What's the difference between polyurethane finish and polyurethane plastic?

texts:
The plastic version is made by mixing two liquid chemicals (MDI & polyol) which react immediately and become a solid. Polyurethane finish is applied as a liquid and dries, no mixing involved.

Or are they not related at all?

Prompted by Veritasium YouTube video.


texts: What are the products of a reaction between copper sulfate and sodium bicarbonate?

texts:
I have been trying for a while to determine what products are produced when copper sulfate reacts with sodium bicarbonate at room temperature and standard pressure. However, while I was looking, I found conflicting information concerning what products are formed. Some sources claim that the products are copper hydroxide and sodium sulfate, while other sources state that the products are copper carbonate and sodium sulfate.

I believe the reaction is:

$$\ce{CuSO4 + 2NaHCO3 -> CuCO3 + CO2 + H2O + Na2SO4}$$

Is this correct?


texts: How can I determine the pH of a solution when I add more analyte after the equivalence point?

texts:
In titrating 25 mL of a 0.2 M weak acid, HA, with 0.5 M of a strong base, say NaOH, the equivalence point is reached after 10 mL of base is added. I can calculate the pH by first setting up an ICE table to calculate the moles of A- remaining at the equivalence point, and then setting up an additional ICE table for the hydrolysis of A- to calculate the moles of OH- at the equivalence point. From that, I can determine the pOH and thus the pH.

My question is this: what would be the effect of adding more weak acid? Would I need to set up an ICE table with non-zero initial values for HA, OH-, and A-? If that's the case, then how do I determine the pH?


texts: There are many different DFT method available, is this simply because individuals find a better DFT method to suit specific types of molecules?


texts: Why do thiols have such a propensity for bonding with mercury?

texts:
Historically, thiols $\ce{-SH}$ were known as "mercapto-" due to their strong propensity to bond with mercury.  Certain drugs still carry this designation, though mercaptopurine has an $\ce{=S}$ group instead of a thiol.

What makes the thiol group bond so strongly with mercury in particular? Why don't alcohols make such a strong bond with $\ce{Hg}$?

If it's known, was there any historical reason why it was important to be able to "capture" mercury?


texts: Comparing two oxidizing agents using electron configuration

texts:
Which oxidizing agent from the pair $\ce{K_2IrCl_6/K_2PtCl_6}$ is stronger? Explain your answer using their electron configurations.

We write the electron configurations for $\ce{Ir/Ir^{4+}}$ and $\ce{Pt/Pt^{+4}}$:

$$\begin{align}
\ce{Ir:\ [Xe] 4f^{14}\ 5d^{7}\ 6s^2 \ &\implies \ Ir^{4+}:\ [Xe] 4f^{14}\ 5d^{5}}\\
\\
\ce{Pt:\ [Xe] 4f^{14}\ 5d^{8}\ 6s^2 \ &\implies \ Pt^{4+}:\ [Xe] 4f^{14}\ 5d^{6}}
\end{align}$$

From those, we notice that $\ce{Ir^{4+}}$ has all 5d orbitals half-filled, whereas $\ce{Pt^{4+}}$ has 4 half-filled 5d orbitals and one filled entirely (which is a less stable configuration);
so it's much easier for $\ce{Pt^{4+}}$ to get reduced than it is for $\ce{Ir^{4+}}$.

Therefore, the strongest oxidizing agent is $\ce{K_2PtCl_6}$. What's wrong with my solution?


texts: Self aldol condensation of butanal under basic conditions

texts:
The reaction is such:

I've counted the number of carbons on each side: LHS=4, RHS=8
My working is such:


texts:
So I was studying for an exam I have thursday when I came across a question regarding half-life. I had previously thought that the definition of a half-life is the time it takes for the amount of material to half in its decay process. However, this question had a y-axis of Disintegration Rate, and used the same process.

They gave an answer of 8 days for the half life of this radioactive element(so they treated it as normal)

So my question is, what exactly does the half in half life represent? A halving of rate or an actual halving of decay of the nuclei?


texts: Absorbtion of light by a coordination compound

texts:
A $\ce{[M(H2O)6]^2+}$ complex typically absorbs at around $600\ \mathrm{nm}$. It is allowed to form a new complex $\ce{[M(NH3)6]^2+}$ that should have absorbtion at?

The absorbtion is because of transition of $\mathrm{e_2g}$ electron to $\mathrm{t_{2g}}$ and vice versa which depend on crystal field stabilization energy as:
$$\Delta = \frac{hc}{\lambda=600\ \mathrm{nm}}\approx2.0\ \mathrm{eV}$$

But I don't know how to convert it in terms of $\Delta_\text o$ so that I can know the actual configuration.

In $\ce{H2O}$ there will be no pairing of electrons as it is weak and reverse with $\ce{NH3}$.

This looks useful but isn't without the metal configuration:
$$\frac{\Delta_{\text o,\ce{H2O}}}{\Delta_{\text o,\ce{NH3}}}=\frac{\lambda_{\ce{NH3}}}{\lambda_{\ce{H2O}}}$$


texts: Maximum Pressure of Covalently Bonded Material

texts: At high enough pressure, atomic material no longer exists, for example under the conditions of a neutron star.  Is there a different maximal pressure above which covalent bonds no longer exist?


texts: How is the formula of mean activity coefficient derived?

texts:
The mean activity coefficient is defiend as follows:
$$\gamma_\pm = (\gamma_+\gamma_-)^{1/2}.\tag{1}$$
If Debye-Hückel equation
$$-\log\gamma_i = 0.5z_i^2\mu^{1/2}\tag{2}$$
is used, then the mean activity coefficient has the form
$$-\log\gamma_\pm = 0.5|z_+z_-|\mu^{1/2},\label{eqn:3}\tag{3}$$
where $\mu$ is the ionic strength, $z_i$ is the charge of species $i,$ $\gamma_i$ is the activity coefficient.
But I'm confused about the equation \eqref{eqn:3}. It can be found as equation \eqref{eqn:3-38} in Snoeyink and Jenkins' Water Chemistry [1]:

[…] developed for ionic strengths of less than approximately $\pu{5E-3}$ and can be stated as
$$-\log\gamma_i = 0.5Z_i^2\mu^{1/2}.\tag{3-34}$$
Because anions cannot be added to a solution without an equivalent number of cations (and vice versa). it is impossible to determine experimentally the activity coefficient of a single ion. Therefore, Eqs. 3-34, 3-35, and 3-36 cannot be verified directly. However, it is possible to define, and measure experimentally, a mean activity coefficient, $\gamma_\pm,$ as,
$$\gamma_\pm = (\gamma_+\gamma_-)^{1/2}.\tag{3-37}$$
The Debye-Hückel and Güntelberg relationships can be extended to the mean activity coefficient thus:
$$-\log\gamma_\pm = 0.5|Z_+Z_-|\mu^{1/2},\label{eqn:3-38}\tag{3-38}$$

Below is my derivation process:
$$
\begin{align}
-\log\gamma_+ &= 0.5z_+^2\mu^{1/2};\tag{4.1}\\
-\log\gamma_- &= 0.5z_-^2\mu^{1/2},\tag{4.2}
\end{align}
$$
so
$$
\begin{align}
-\log\gamma_\pm &= -\log[10^{-0.5z_+^2\mu^{1/2}}\times 10^{-0.5z_-^2\mu^{1/2}}]^{1/2} \tag{5.1}\\
  & = -\log[10^{-0.5\mu^{1/2}(z_+^2+z_-^2)}]^{1/2} \tag{5.2}\\
  & = 0.25\mu^{1/2}(z_+^2+z_-^2). \tag{5.3}
\end{align}
$$
This result is different from $0.5|z_+z_-|\mu^{1/2}.$ Can someone tell me which step is wrong in my process?
Reference

Snoeyink, V. L.; Jenkins, D. Water Chemistry; Wiley: New York, 1980. ISBN 978-0-471-05196-1.


texts: Choosing polar aprotic solvents for substitution reaction

texts:
It is known that common polar aprotic solvents include acetone and DMSO. Since they do not have hydrogen bonded to highly electronegative atom, they cannot only form dipole-dipole interaction with nucleophile, instead of hydrogen bond & ion-dipole interaction.

Moreover, the electrons in 2 R-CH3 groups in acetone / DMSO are repelled by electrons of the nucleophile, hence increasing the distance of dipole-dipole interactions, further decreasing the solvating effect.

My question is: from (2), is it better to use reagents that have more bulky R groups linking to the partial positive atom like pentan-3-one & diethylsulphoxide instead? I know this will decrease the polarity of solvent, but won't these better decrease the dipole-dipole interaction hence further increasing the nucleophilicity?


texts: How many coordinates should be used for the potential energy surface of a non-rotating linear molecule? (3N-6) or (3N-5)?

texts:
Take, for example, $\ce{CO2}$.  It is pretty clear that in the absence of rotation, the energy of this system depends only on the two bond lengths and the bond angle.

So if I wanted to build a potential energy surface for this molecule that was valid near and far from equilibrium, it should depend on these coordinates.  But how do I rectify this with the fact that $\ce{CO2}$ has four vibrational modes? As we learn in undergraduate chemistry, it has two stretches and two degenerate bends.

If I build a Hamiltonian in the three valence coordinates, could it possibly describe the ground state energy correctly?  That is, would it contain the zero-point energy for all four modes?  Would it be able to find the right low-lying excited states of the bending mode(s)?

EDIT:
Wildcat has brought up the point of symmetry and point groups below, and perhaps that can help get to the heart of my question.  When we say that $\ce{CO2}$ is a linear molecule, that means that the lowest energy configuration has a bond angle of $\pi$.  But in no way do I want to restrict the symmetry of the molecule.  I want to work with a potential surface that is valid for symmetric and asymmetric geometries.

But here is where I get confused.  Let's say I did restrict it to be linear.  I would then have a two-dimensional potential, a function of the two bond lengths.  Of the seven normal modes, I only keep two: the symmetric stretch and anti-symmetric stretch.  The ground state energy would be the sum of the zero-point energy of these two modes.   So therefore the number of modes is equal to the number of coordinates I used to write my Hamiltonian.

If I further constrict the symmetry, and impose the $D_{\infty h}$ point group, then the potential is now a function of one parameter.  I will now only have one vibrational mode, the symmetric stretch, and the ground state energy is the zero-point energy of this mode.  So, again, the number of modes is equal to the number of coordinates I use to write my Hamiltonian.

But what if the symmetry were not restricted in any way?  I can write the potential as a function three internal coordinates, be they bond lengths and angle, othogonormal rectilinear coordinates, jacobi coordinates, etc.  This potential, and the Hamiltonian I construct with it, should find the same modes described above, as well as the bending modes.  But will it find both bending modes?  I don't see why it should.  Based on the two reduced-dimensional examples above, I would expect the number of modes to equal the number of coordinates.  I would expect therefore, not to find the right ground-state energy, etc.

Specifically, I am concerned about the accuracy of dynamical simulations performed using this three-dimensional potential.

Likewise, what about a tetratomic liner molecule like $\ce{C2H2}$? I would use three bond lengths, two bond angles, and one dihedral angle, for a total of 6 coordinates - but it has 7 vibrational modes.  Would I model the dynamics properly?


texts: Bonding and coordination of oxygen in a Ga2O3 crystal structure

texts:
I'm trying to find the crystal structure of gallium oxide ($\ce{Ga2O3}$). However, I find the images of the crystal structure in the peer-reviewed journals problematic.

First, I hop to the wikipedia article of Gallium oxide and find this image:

There was no labeling of the color, but I think Cyan is Gallium, and Red is Oxygen. The trouble is Ga typically has 3+ and Oxygen has 2- valence. Yet in this image we see Ga have 4 and 6 bonds! How is this possible?

The source is from a paper:  J. Åhman, G. Svensson and J. Albertsson: A Reinvestigation of β-Gallium Oxide. In: Acta Cryst. (1996). C52, 1336-1338. (The image was made by a wiki admin on chemistry structure, who made many structures for wikipedia.)

So I check out the article and it has this figure:

That's basically unreadable, so I go to Acta Crystallographica Section C and it has an interactive 3D chem model viewer and a model for Gallium Oxide:

Again I see Gallium with 6 bonds and oxygens with 3 bond! Is this correct? please tell me how?

In Galazka's β-Ga2O3 for wide-bandgap electronics and optoelectronics,I find this description:

  Crystal structure of $\ce{β-Ga2O3}$

  $\ce{β-Ga2O3}$ crystallizes in the base-centred monoclinic system in the
  space group C2/m. The unit cell (figure 1) contains 20 atoms
  consisting of crystallographically inequivalent $\ce{Ga^3+}$ and $\ce{O^2−}$ atoms. In this low symmetry structure Ga atoms are coordinated tetrahedrally and
  octahedrally (Ga1 and Ga2, respectively), while O atoms are
  coordinated three and fourfold (O1/O2 and O3, respectively). O1 shares
  two bonds with Ga2 and one bond with Ga1, O2 shares three bonds with
  Ga2 and one bond with Ga1, while O3 shares two bonds with Ga1 and one
  bond with Ga2. The lattice parameters of $\ce{β-Ga2O3}$ are listed in table
  1. There are two easy cleavage planes: the (100) plane formed by O3 atoms and (001) plane formed by O1 atoms.

and this figure:

Can someone please explain the crystal structure of $\ce{Ga2O3}$, beta-gallium oxide?


texts: what voltage is needed to reduce Silver (I) Oxide in alkaline medium against an inert electrode

texts:
consider the following electrochemical cell:

silver (I) oxide is anode, platinum electrode is cathode, 6M KOH is
electrolyte

what voltage is needed to be supplied to the cell OR what voltage is generated by this electrolytic cell, with the reaction being:

$\ce{2 Ag2O -> 4 Ag + O2}$

where half reactions are:

$\ce{2 Ag2O + 2H2O + 4e- -> 4Ag + 4OH-}$

$\ce{4OH- -> 2 H2O + 4e- + O2}$

Is the reverse reaction spontaneous in alkaline electrolyte with inert electrode like platinum:

$\ce{4 Ag + 4OH- -> 2 Ag2O + 2 H2O + 4e-}$

$\ce{O2 + 2H2O + 4e- -> 4OH-}$

(the platinum electrode is for oxygen reduction reaction and oxygen evolution reaction)

I am a computer science engineer trying to learn chemistry, excuse me if my equations are not precise


texts: Why does the standard enthalpy of formation diverge so far from the standard Gibbs free energy of formation for some substances?

texts:
If you look at a Table of Thermodynamic Values for chemical substances, most substances have very close values for their standard enthalpy of formation ($\Delta H_{\mathrm{f}}^\circ$) and their standard Gibbs free energy of formation ($\Delta G_{\mathrm{f}}^\circ$). This makes intuitive sense because differences in enthalpy, which in chemical reactions is mostly just a signifier of internal energy because so little work is done by reactions, under normal circumstances correlates with the change in free energy of that system. When heat is lost through a reaction, that system has both less internal energy but also less free energy because the production of heat and then exporting of heat to the surroundings requires the 'use' of free energy.

My question: why do some substances have widely diverging values for $\Delta H_{\mathrm{f}}^\circ$ and ($\Delta G_{\mathrm{f}}^\circ$)? It appears that some substances containing nitrogen have the widest divergence for standard conditions of 25 °C and 1 bar, whereas most substances have a $\Delta H_{\mathrm{f}}^\circ$ and ($\Delta G_{\mathrm{f}}^\circ$) differing by no more than 30%. For example, $H_\mathrm{f}(\ce{AgNO3}) = −124.39$ kJ/mol and $G_\mathrm{f}(\ce{AgNO3}) = -33.41$ kJ/mol, and $H_\mathrm{f}(\ce{N2O4}) = 9.16$ kJ/mol and $G_\mathrm{f}(\ce{N2O4}) = 97.89$ kJ/mol.

A mathematical explanation would be helpful, but I'm most interested understanding this conceptually and why these nitrogen-containing compounds exhibit these properties. Are these properties more common among other substances at extremely high or low temperatures and pressures?


texts: Smoky lights at events - Piped in or a chemistry reaction of some kind?

texts:
Was at Dreamhack MTL this weekend and realised that in the whole venue there seems to be just a little bit of smoke in the spotlights and other light sources.

You also see that kind of smoke in shows and conventions. So I was wondering is that smoke something that gets piped in for that volumic effect on the lights, or is it just something that tends to happen when you shove 3000+ human beings in an enclosed space?

And if so, what is happening here, on a chemistry level, to cause that smoke?


texts:
I'm looking for an explanation of the bonding in the phosphate (PO43−) ion:

(Image courtesy of Wikipedia)

Phosphorus (15P) - being the fifteenth element - has fifteen electrons, five valence electrons and the following electron configuration:

1s2
2s2 2p6
3s2 3p3

This being so, by what means does it form its bonds? Naively, one might expect it to form 3 single covalent bonds and be happy. But it doesn't, it forms five bonds, presumably using each of its five electrons. My first question is - why would it do this? It seems to me that this would result in the Phosphorus atom having ten electrons in its outer shell (four from the double bond with the oxygen and two each from the single bonds with the other three oxygens).

Apart from the oxygen with a double-bond, we have three oxygens forming single bonds. Does this not leave them one electron short?

Finally, why are the oxygens shown as carrying a negative charge?


texts: Why don't proteins form branched polymers?

texts:
My reference book (Princeton Review for SAT Chemistry Subject Test) mentions that:

Proteins and carbohydrates are both polymers; however, only
carbohydrates commonly form branched polymers. Glycogen and cellulose
are both carbohydrate polymers made up of glucose monomers; glycogen
is a highly branched polymer while cellulose is primarily
straight-chained.

But I don't get why proteins cannot form branched polymers. Proteins have both an amino group and a carboxylic acid group, and I understand that the two groups join together with the elimination of a water molecule during polymerization.
Branched polymers are formed when a hydrogen atom (or any other substituent) is replaced by another monomer unit, and I don't see why this can't take place in the case of proteins. Could someone please explain?


texts: High chemical resistance, high thermal conductivity?

texts:
I'm redesigning a microfluidic circuit to include a heating element. I'm running into problems because the ETFE tubing I'm using is too thermally resistant for me to get any energy into the fluid within. My options are to either 1) replace the ETFE tubing with a polymer with similar chemical and surface properties but a higher thermal conductivity, or 2) replace just the beginning of the circuit tubing with a similarly chemically resistant, but possibly rigid, material that can transfer a lot of heat to the fluid, which would then be insulated by the ETFE on its way to its destination.

Thoughts?

Thanks!

[Edit]: Also, affordability is a slight factor. This question is industrial in nature so a certain operating budget can be assumed - but exotics are going to be hard to get.

I like the diamond comment though; I wish I could pull that off.


texts: The effect of HCL concentration on the Solubility of Hydroxyapatite

texts: Recently I conducted an experiment to investigate the effect of HCL concentration on the solubility of hydroxyapatite [Ca5(PO4)3(OH)]. This was done by taking a sample of the solution after hydroxyapatite was left to dissolve in HCL, and conducting an EDTA titration using this solution to find how many calcium ions were present. I have already established that hydroxyapatite is more soluble in solutions of HCL at higher concentrations (lower pH). However, I was wondering what the exact scientific theory behind this reaction was.


texts: Safe and responsible disposal of aluminum chloride?

texts: This answer affirms that reacting aluminum with HCl is a (seemingly convenient) way to produce hydrogen for use in other experiments, but the byproduct, AlCl3, is rather nasty. What's the best way to dispose of it? My naive guess is that reaction with baking soda would produce carbon dioxide and aluminum hydroxide, which would be fairly harmless. Is this correct?


texts: Would standing next to a pool of mercury do you any harm?

texts:
I was watching this clip from the 2017 film The Mummy in which the characters stand next to a pool of mercury which was being used as part of an elaborate prison.

Several comments under this video imagine that standing next to a pool of mercury would be very dangerous, but I can't see any reason to think that a significant amount of vapour would be coming from the pool so it seems like the mercury just being there in liquid form would be quite harmless. But maybe I shouldn't go robbing any graves any time soon.

The automatic warning dialogue told me the question appears quite subjective. So, let's say you're standing next to the pool for no more than ten minutes and we'll define harm as requiring medical intervention or (if chronic) as having a demonstrable, long-term health effect, such as erethism. I have no idea how large the pool is in the video, but for the purposes of the question, we'll say it's a circular pool of 10 metres in diameter.


texts: Is water a better nucleophile than bromide?

texts:
I am a student of biochemistry. My organic chemistry professor was giving a lecture and he talked about halohydrin formation reactions. At one point, he said that "water attacks instead of bromide because water is a better nucleophile than bromide". He repeated that five times or so.

A classmate argued that, because water is the solvent in the reaction and is in greater proportion, it will attack faster. But that still doesn't mean water is a better nucleophile, right? Bromide itself has a negative net charge, while water has no net charge, only 2 free electrons.

The question is, was my professor wrong or is there something I'm missing? Thank you very much.


texts: Custom-defined functionals in Gaussian 09

texts:
As stated before I want to try out custom-defined functionals. Besides the question about B3LYP itself, there is another related question.

Short excerpt:

  $$\text{XC-Functional}=a E_x^\text{local}+(1-a)E_x^\text{HF}+b E_x^\text{non-local}+c E_c^\text{non-local}+(1-c) E_c^\text{local}$$

  The Gaussian documentation for DFT inputs specifies how one could change the amounts of each "sub-functional" by using the IOp-Statements through:

  IOp(3/76=mmmmmnnnnn) IOp(3/77=mmmmmnnnnn) IOp(3/78=mmmmmnnnnn)

  Where mmmmm and nnnnn will get divided by 10000 and 3/76=$P_1P_2$, 3/77=$P_3P_4$ and 3/88=$P_5P_6$. Those $P_{1,..,6}$ values are part of the following equation, which is a modified version of the equation above.

  $$\text{XC-Functional}=P_2 E_X^\text{HF} + P_1 \left(P_4 E_X^\text{Slater} + P_3\Delta E_x^\text{non-local}\right) + P_6 E_C^\text{local} + P_5 \Delta E_C^\text{non-local}$$

Now Gaussian's description site about DFT tells that one simply has to choose one exchange and one correlation functional, i.e. B and LYP. But then B would be used for $E_x^\text{non-local}$ and LYP probably for $E_c^\text{non-local}$.

Does that mean, that the $E_c^\text{local}$-part

cannot be defined,
is always the VWN functional as in B3LYP, or
is also the chosen correlation functional?


texts: Converting cyclic compounds to linear compounds (possible ?)

texts:
Can one convert from cyclic convert to linear compound?
Like

$Cyclohexane$ $+$ $?=Hexane$

Even in High Temp and Pressure?

I know it is very tough since we are going from a stable compound to a relatively more unstable compound.But still...???

And can we also convert $Benzene$ to some $Unsaturated Compounds$ ?

And if possible can anyone please tell the reaction mechanism of it?

Thanks


texts:
In many places I have come across the following derivation
Work done in isothermal expansion

By first law of thermodynamics

$\mathrm dU=Q+W$

As $\mathrm dU=nC_V\,\mathrm dT$, and in isothermal process $\mathrm dT = 0$

$\therefore\mathrm dU=0$
$W=-Q$
i.e heat absorbed is completely converted into work

The second step doesn't make any sense at all. As far as my understanding $\mathrm dU=nC_V\,\mathrm dT$ is true only when volume is constant, but it's clearly mentioned expansion in the statement.
So how to justify the use of $\mathrm dU=nC_V\,\mathrm dT$  expression even when volume is not constant?
Please consider the fact that I'm a school student so please answer in a simple manner.


texts: What is that process called in which we add water molecules to an ion to form a complex?

texts: An example would be $\ce{[Fe(H2O)6]^2+}$ in which it has 6 water molecules associated with it. What is the process of adding these water molecules called?


texts:
We need to calculate the heat produced by a set of $\mathrm{N_R}$ reactions in our reactor model.

\begin{align}
\mathrm{Q_r = \sum_{j=1}^{Nr} Rr_j*\Delta H_{R,j}}
\end{align}

$\mathrm{Rr_j}$ is the reaction rate of reaction $\mathrm{j}$, in $\mathrm{\frac{kmol}{kg_{cat} s}}$

$\mathrm{\Delta H_{R,j}}$, in  $\mathrm{\frac{kJ}{kmol}}$, is constant and calculated as:

\begin{align}
\mathrm{\Delta H_{R,j} = \sum_{i=1}^{Nc}\nu_{i,j}*\Delta h_{i,j}^f}
\end{align}

Now consider these:
\begin{align}
\mathrm{R1:}\ \ce{H2 + 1/2O2 \rightarrow H_2O}
\end{align}
\begin{align}
\mathrm{R2:}\ \ce{2H2 + O2 \rightarrow 2H_2O}
\end{align}

They are undoubtedly the same reaction, but the R2 gives a  $\mathrm{\Delta H_R}$ that is twice the $\mathrm{\Delta H_R}$ in R1. It is naturally so, but greatly affects my energy balance.

How do I know which is the "correct" way to write the reaction?

Does it mean that the reaction rate should be specific to R1 or R2?


texts: After opening, when is a can of Diet Coke most acidic? (Based on a true story)

texts:
Situation: Clogged toilet, no plunger.

Goal: Trying to use the acidity from a can of Diet Coke as toilet drain cleaner.
Question: How can I maximize the acidity of a Diet Coke?

Question 1: Should I heat up the Coke (using a microwave)?

Is an acidic solution more acidic when it is hot or cold?

Question 2: Would heating the Coke make the Coke less soluble to Carbon Dioxide (which is acidic)?

Is a solution more soluble to gases when it is hot or cold?

Question 3: What is the loss of carbon dioxide (acidity) during the time taken to microwave the soda?


texts: What hinders SN2 more: geminal alkyl group or alkyl group on the aromatic ring?

texts:
Which among these two (1-chloro-1-phenyl-ethane and 2-(chloromethyl)-1,3-dimethylbenzene) is more reactive towards SN2?

I strongly believe that it should be Y because of lesser hindrance on the electrophilic carbon.
However, the answer key of my exercise book states that X > Y. What's the reason behind that?


texts: How to get 3D molecular structures for 270 compounds?

texts:
I need to calculate 10 properties for 270 molecules using Gaussian 09. Could you please suggest me what is the best and shortest way to have the structure of 270 molecules (in the format .com or .xyz)?

Is there any website which collected all the molecular structures?


texts: Raman or FTIR spectroscopy to identify metals?

texts:
Metals are opaque, so doesn't most of the light reflect? And does the IR source even cause vibrations in the metal?
Same goes for Raman spectroscopy, is it useful for use of metal identification?
Is it better to use EDS to identify unknown metals?


texts: Why does bubbling carbon dioxide through calcium hydroxide result in a precipitate?

texts:
Why does the addition of carbon dioxide to calcium hydroxide create the precipitate calcium carbonate? What happens chemically for such a molecule to form? How exactly do their interactions come into play?

Now CaOH isn’t terribly soluble in water but the parts that do dissolve, disassociate into their respective OH- and Ca2+ ions. So when we bubble CO2 through the CaOH solution the calcium ion is attracted to the partial negative charge on the oxygen atoms of carbon dioxide. So that forms CaCO2 so my question is where does the other oxygen of calcium carbonate come from? Is it snatched from a hydroxide ion?

Calcium carbonate also has a resonant structure, I don’t know what that is exactly but it’s like electrons are being shared uniformly throughout a given structure so that means carbons original double bonds get disbanded too I guess? If anybody can explain what happens here as well, it would be great.

Here are my drawings, they may be simplified but it’s all I know:


texts: How to find the equilibrium constant under non-standard conditions?

texts:
Given the following thermodynamic data at $\pu{298 K}:$
$$
\begin{array}{lrrr}
\hline
\text{Compound} & \Delta_\mathrm{f}H^\circ/\pu{kJ mol^-1} & S^\circ/\pu{J K^-1 mol^-1} & C_p^\circ/\pu{J K^-1 mol^-1}\\
\hline
\ce{HI(g)} & 26.5 & 206.6 & 29.2 \\
\ce{I2(g)} & 62.4 & 260.7 & 36.9 \\
\ce{H2(g)} & 0.0 & 130.7 & 28.8 \\
\hline
\end{array}
$$
determine the equilibrium constant $K$ for the following reaction at $\pu{475 K}$ and $\pu{1 bar}:$
$$\ce{I2(g) + H2(g) <=> 2 HI(g)}$$
NB: Do not assume that the enthalpy and entropy of reaction are independent of temperature. What assumption(s) do you need to make?

At first I thought I could work out the enthalpy change using Kirchhoff’s law of thermochemistry
$$\Delta H(T_2) = \Delta H(T_1) + \int_{T_1}^{T_2}\Delta C_p\,\mathrm dT$$
and then find the entropy change of reaction similarly. Then apply
$$\Delta G = \Delta H - T\,\Delta S$$
and use the equation relating $\Delta G$ and $K,$ but I know that is only for the Gibbs free energy change under standard conditions. The question tells me to assume the enthalpy and entropy depend on temperature, so I’m not sure what my approach should be for this.


texts: Atmospheric carbon removal: asphalt from CO2?

texts: In reading a text about $\ce{CO2}$ recycling and sequestration of various kinds, I came to think about storing atmospheric $\ce{CO2}$ as asphalt. Given cheap energy as in the case of Iceland, and improved atmospheric carbon capture technologies, could this be feasible? Is there a name for the reverse cracking process?


texts:
$$\ce{2SO2(g) + O2(g) <=> 2SO3(g)}$$
  The equilibrium constant for the reaction above is $0.13$ at $\pu{830^\circ C}$.
  In one experiment $\pu{2.00 mol}$ of $\ce{SO2}$ and $\pu{2.00 mol}$ of $\ce{O2}$ were initially present in a flask until it reaches dynamic equilibrium. What must the total pressure of equilibrium be in order to have an 80.0% yield of $\ce{SO3}$?

How do I approach this type of problem?  Is it correct to assume that the total pressure of the equilibrium would be the pressure from the both sides of the equation (pressure of $\ce{SO2}$ + pressure of $\ce{O2}$ + pressure of $\ce{SO3}$)? And how do I find these different pressures?

I am thinking of using the method: $K_\mathrm{p}=0.3=\Large\frac{p^2_\ce{SO3}}{p^2_\ce{SO2}\times p_\ce{O2}}$

Hence, to find the respective pressure of the gasses, I attempted the RICE table, (Reaction, initial mol, change in mol, equilibrium point). How can I proceed further ?


texts: Covalent vs Ionic bond in Silicon dioxide

texts: I was wondering why silicon dioxide tends to be a covalent bond instead of an ionic bond. Based on lewis structures, the octet rule seems to work for silicon dioxide so shouldn't it also be an ionic bond?


texts: skeletal structure of dimethylamine? HN(CH3)2

texts:
I don't understand how to draw this skeleton.
 I know there is a NH2 in an amine structure, but this only has NH?
and dimethyl means there a 2 identical single side chains right? but where on the skeletal structure are they?
I'm totally stuck as to how the skeletal structure is supposed to look.


texts: How do I determine the mass percent of Barium nitrate and Sodium acetate in an original unknown solution

texts:
I am given $20 \mathrm {mL}$ of the unknown mixture of Barium Nitrate and Sodium Acetate dissolved in water. I am given the total mass of the two solids before they were put into the mixture.
I am given $0.200 \mathrm{M}$ of $\ce{NaOH}$, $0.200 \mathrm{M}$ of $\ce{Na2SO4}$, $0.200 \mathrm{M}$ of $\ce{NaCl}$ and ethanol to separate a precipitate.
I am learning about selective precipitation.


texts: How can I clean solid sulfur and its oxides from test tube?

texts:
I was experimenting with sulfur few years ago. The test tube I used for that purpose has still sulfur stuck onto it. I was searching for a way to dissolve it.

I found an idea to try warm acetone. Sounded like cheap solution, but doesn't work - or it will take ages to dissolve.

I'm not a chemist, so I don't have any strange chemicals at home.


texts:
I just learned what chain reactions are, but I can't seem to wrap my head around them because it seems utterly useless and doesn't accomplish anything. At least that's how I understood it because the textbook doesn't have any real world applications for it.
So what I am asking is do chain reactions serve any purpose. If so, it would be great if you could support your answer with a real world example or application.


texts: Compare ONO bond angle in nitrogen oxides

texts:
Which has maximum $\ce{ONO}$ angle?

  $\ce{NO3-}$
  $\ce{NO2+}$
  $\ce{NO2-}$
  $\ce{NO2}$

According to me $\ce{NO2+}$ should have the maximum angle because the structure is linear but in answer it is given $\ce{NO3-}$. We can consider the lone pair in $\ce{NO2+}$ but still also by VSEPR theory I don't think it is possible to decrease angle from 180 to less than 120.


texts: Why do electrons not flow through the electrolyte?

texts:
Why do the electrons not flow through the electrolyte instead of the external circuit in a electrolytic cell connected to an external circuit? I mean, if an electrolyte is a conductor why would the electrons take the way through the external circuit rather than through the electrolyte to the other electrode of an opposite charge?

Like:


texts: The way I was told is that a saturated solution contains the maximum amount of solute and a supersaturated solution contains more solute than a solution can hold at a particular temperature. But I was also told that if you add more solute than it can hold, that it will not dissolve and will settle at the bottom as a solid. So how is that supersaturated? Since it didn't dissolve, isn't it still just saturated? It was also mentioned that a supersaturated solution needs to be cooled, but if the temperature dropped, wouldn't the solute just come out of solution and settle at the bottom (like sugar and cold coffee) and remain saturated?


texts: So if you put a mint mentos in a cup of soda it will explode everywhere. The mint in the mentos makes the soda have a chemical reaction which will then make the soda explode right? Well what would happen if we put a mento in different types of soda would that make a difference in how much chemical reation there will be? I already put mentos in cream soda and it made a small explosion. So I wondering if the different sodas had different effects on  how big the explosions are.


texts: Liquid to gas phase exothermic hydrolysis reaction examples

texts:
I am working as a petroleum engineer and most of our crude oils are heavy oils (very dense). In reservoir, I want to start an exothermic liquid to gas phase hydrolysis reaction.

I am planning to inject my feed into reservoir from wells and the feed will make the reaction with reservoir brine (There is too much water in the reservoir with oil). With this reaction, I am planning to achieve the followings:

With heat, the viscosity of the crude will decrease and production will increase.
Liquid phase feed is easy to inject and gas phase product (especially $\ce{CO2}$) may be an additional force to increase production, which is called as gas flooding.

I found some reactions like the hydrolysis of $\ce{CaO}$. But here, the feed is in solid phase. The product in this reaction is an alkaline and it may enhance oil recovery by changing the wettability or reducing the interfacial tension between oil and water.

I wonder if there are any other reactions like that.


texts: Electrolysis of auric chloride solvent with different metals in anode and cathode

texts:
Question:

  Write down possible reaction in anode and cathode for electrolysis of $\ce{AuCl3}$ with solid $\ce{Au}$ electrode in anode and solid $\ce{Ag}$ electrode in cathode.

As far, I could write the anode reaction. In the anode, there are 3 competitors ($\ce{Au}$ electrode/$\ce{Cl-}$/$\ce{H2O}$), so the final reaction would be

$$\ce{2Cl- -> Cl2 + 2e-}$$

But I couldn't figure the cathode reaction because there are 3 competitors in cathode ($\ce{Ag}$ electrode/$\ce{Au3+}$/$\ce{H2O}$) that I have no idea what I need to do with the $\ce{Ag}$ here.

Some sources said $\ce{Ag}$  is an inert metal. How the reaction for cathode would be?


texts:
If 2.30 mol of sodium reacts with 1.95 mol of water, how many moles of sodium hydroxide are produced?

Would it be 2.3 mol NaOH?


texts: How to test acid-base reactions under pressure?

texts:
I am trying to test chemical reactions, more specifically reactions between an acid and a base, at different levels of pressure.

I would like to know if there is some kind of equipment I can get that has adjustable pressure, and will let me get the reactants into the vessel without changing the pressure significantly.

I am looking for something that I just get at home, so not too big, and hopefully not too expensive. It doesn't need to be super high-tech, as I'm not going for a high level of accuracy, and I'm not going to be testing extremely low or high pressures.

Does anyone know of any equipment that will create significantly different levels of pressure, even if it is very expensive?


texts: How to run electrochemical tests on Microorganism (bacteria in a medium)?

texts:
I am trying to run some electrochemical tests(e.g.CV (Cyclic Voltammetry) & EIS (electrical impedance spectroscopy)) using half cell configuration on micro-organisms (e.g.bacteria). The bacteria are cultured in a medium (liquid). The half cell configuration is working, counter, and a reference (AgCl) electrodes.

Usually, it is easy to clip a metal or any thin solid material. However, I don't know how to deal with a solution. Since the beaker will be filled with electrolyte, I am afraid it mixes with bacteria solution causing it to be removed from the electrode. I am avoiding add another material like tape or something as it might alter the measurement.
I am looking for a way to attach the Micro-organism to the working electrode.


texts: What are the differences between the HMQC and HSQC experiments?

texts:
This afternoon, I was having some trouble with an HSQC (Heteronuclear Single Quantum Coherence Spectroscopy) spectrum I was trying to acquire, and the spectroscopist recommended I try HMQC (Heteronuclear Multiple Quantum Coherence) spectra, as they are more robust. I did so and got a very nice spectrum in about half the time an equivalent HSQC would have taken, and didn't have to phase it, to boot.

So, what is the downside? Why doesn't everyone use HMQC spectra instead of HSQC? I know they are rather different on a quantum-mechanical level, but as an end-user what, if any, is the difference in the data the two techniques give me, what are the advantages and disadvantages of each, and in what situations might I prefer one over the other?


texts: how to mathematically predict reaction results

texts:
I've been trying to computationally achieve the following (I have no lab, I'm 14 years old, and I want to make a Minecraft mod to teach real Chemistry):

I want to mathematically predict the range of temperature and pressure (if the reaction is between gases) or temperature and concentration (if the reaction is in a solution) in which a given chemical reaction can happen, and the rate at which it happens, with the variation of those two arguments.

EDIT 1:

Regarding the first part of @sixtytrees answer I suppose I must calculate $K$.

I assume $\Delta G$ would be:

$$\begin{align}\Delta G &= \Delta G_\mathrm f^°{_\text{methanol}} - \Delta G_\mathrm f^°{_\text{carbon monoxide}} - 2 \Delta G_\mathrm f^°{_\text{hydrogen}}\\[6pt]
&= -162.5 - 137.3 - 0\\[6pt]
&= -299.8\ \mathrm{\frac{kJ}{mol}}\end{align}$$

Now to solve for $K$:
(I believe $R$ must be $0.0083144598\ \mathrm{\frac{kJ}{mol\ K}}$, because $\Delta G$ is in $\mathrm{\frac{kJ}{mol}}$
Also, I think we have to take $25\ \mathrm{^\circ C}$ as the temperature which is $298\ \mathrm K$)

$$\begin{align}\ln K &= \frac{\Delta G}{-RT}\\[6pt]
&= \frac{-299.8}{-0.0083144598 \cdot 298}\\[6pt]
&= \frac{-299.8}{-2.4777090204}\\[6pt]
&= 120.99887336713996006405304847878\\[6pt]
K &= \mathrm e^{120.99887336713996006405304847878}\end{align}$$

And now I realize I must have made some mistake because this number will be too big.
☹

EDIT 2:

I just woke up and I noticed I miscalculated $\Delta G$, because I added them together when I should be subtracting. Let's see how it goes now.

$$\begin{align}\Delta G &= \Delta G_\mathrm f^°{_\text{methanol}} - \Delta G_\mathrm f^°{_\text{carbon monoxide}} - 2 \Delta G_\mathrm f^°{_\text{hydrogen}}\\[6pt]
&= -162.5 - (-137.3 - 0)\\[6pt]
&= -25.2\ \mathrm{\frac{kJ}{mol}}\end{align}$$

Now $K$ will be:

$$\begin{align}\ln K &= \frac{\Delta G}{-RT}\\[6pt]
&= \frac{-25.2}{-0.0083144598 \cdot 298}\\[6pt]
&= \frac{-25.2}{-2.4777090204}\\[6pt]
&= 10.170685820053125395644218884808\\[6pt]
K &= \mathrm e^{10.170685820053125395644218884808}\\[6pt]
&= 26126\end{align}$$

Still not as small as 10 that @sixtytrees predicted.

$$26126 = \frac{[\ce{CH3OH}]^1}{[\ce{H}]^2[\ce{CO}]^1}$$

What now?

EDIT 3:

I've been thinking, and decided Chemical Equilibrium is not something I need to bother with, because as the reaction progresses, it is assumed that the final products are drained out as they are formed, and additional pressure is added to account for the reduction of total molarity. This way I don't need to distinguish between reversible reactions, irreversible reactions, and virtually irreversible reactions (when there are trace amounts of the reactants in the final products).

This only works if the reactants are gases, I don't know how to sustain the rate of the reaction if I take away the products from a solution.

The original question remains, now that equilibrium is irrelevant, is it possible to predict the temperature and pressure/concentration range of the reactants in which the reaction can occur?

I downloaded Orca, by the way. No idea how to use it.

EDIT 4:

Ok, so let´s say this is all happening in a sealed container with 1L of volume, so

$\begin{align}
26126 &= \frac{[CH_3OH]}{2^2 \cdot 1^1}\\
[CH_3OH] &= 26126 \cdot 4 = 104,504
\end{align}$

What does this mean? It can't mean I end up with more than one hundred moles in 1 liter. It makes no sense, I don't have enough reactants to get so much product. So, I am clearly doing it all wrong, can someone explain it to me?


texts: Why is the radius of Europium so unusually high and out of the general trend ? Moreover, at different sources I am getting different values of radii. In some (e.g., Wikipedia) the radii are following the regular trend and in some Europium has been shown to be bigger. (Source : NCERT Class 12 Chemistry Part-1)


texts: Why are calcination and roasting processes carried out at a temperature just below the ore's fusion temperature?

texts:
I had read about the two important methods used for the concentration of an ore - Roasting and Calcination. I have a doubt regarding why both the methods are carried out at temperatures not above the ore's melting point.
After some research, I have been able to conclude that one of the reasons is the formation of complicated slag (i.e., difficult to remove from the ore) that tends to form if the ore is molten.
Could someone please explain what exactly happens so that a complicated slag is formed? Also, are there more reasons behind keeping the temperature below the ore's fusion temperature (any specific reasons pertaining to roasting and calcination individually)?


texts: When is it necessary to consider size consistency?

texts: For what kinds of reactions is it essential to account for size consistency? To my understanding for dissociation reactions $(\ce{AB -> A + B})$ it is important to consider. However, is it also necessary to consider for isodesmic reactions? How about for other addition or insertion reactions?