texts: Boltzmann Distribution in Molecular Dynamics Simulation?

texts:
The Boltzmann distribution is often used to describe the population of energy states at different temperatures, i.e. something like

$$\dfrac{g_i}{g_j} = \mathrm{exp}\left(-(E_i-E_j)\times \frac{1}{k_B\cdot T}\right).$$

For two given states $i,j$ with energies $E_i,E_j$, we thus have the population given by $g_i$ and $g_j.$

So if I have some observable $\sigma$ calculated for each state $i$, the natural way to calculate the observable of the ensemble would be

$$ \sigma_\mathrm{ensemble} = \left(\sum_i g_i \times \sigma_i\right) / ~\sum_i g_i~.$$

So, if I calculate $n$ ground states, let's say by geometry optimization of several guess structures, I employ the above weighting scheme to calculate the observable for the ensemble.

But here is my problem: If I perform an MD simulation instead, then the states should already be automatically populated according to the Boltzmann population (e.g. higher energy states are less likely to be observed in the MD simulation). So the population of the MD simulation already converges to the Boltzmann population for increasing simulation times $t$

$$ \lim_{t\rightarrow\infty} \frac{g_i^{MD}}{g_j^{MD}} = \frac{g_i}{g_j} $$

Now I am confused, because that would basically mean that there is a continuous transition between e.g. two states that clearly have to be boltzmann averaged up to the "long MD simulation", that is automatically populated accordingly. Where in the latter case, I would accidentally apply the Boltzmann population weighting twice.

Are there any resources on this weird population dichotomy or am I just overlooking something?


texts: Why don't such ions form if half-filled or full-filled configurations are considered stable?

texts:
We all know atoms want to stabilize by having an octet or duplet configuration. But if you see nitrogen which has an electron configuration of $\ce{2p^3}$. It has half filled p orbital, so it is technically stable, isn't it? Then why don't elements like oxygen form a monovalent oxygen ion?

By similar logic, sodium has $\ce{3s^1}$ configuration which should also be stable because it has a half filed orbital. But sodium is reactive as we know.

Can you please point out the flaw in my argument?


texts:
(This is a question similar to this and this, but none of the answers to those two questions answer my question.)

I've seen many places explain the dipole moment of ozone from the formal charges of the O atoms. However, I don't quite feel comfortable with this explanation since I feel like formal charges are not actual charges; they're more like a bookkeeping convention.

From this question, it seems like we should take into account the lone pair on the central O when summing the dipole moments. Thus, shouldn't the central O be the negative end of the dipole (since it has the lone pair)? But why does this contradict the prediction made by formal charges?

In general, to find the overall polarity of a molecule, when is it appropriate to sum up all the dipole moments (including those from the lone pairs), and when should we use formal charge instead?


texts: How are the hydrogens attached to the nitrogen atom in the ammonium ion?

texts:
Naively attaching hydrogens to a nitrogen atom's electron orbitals results in a picture like this:

However, there are two problems with this drawing that I can see.

First, I have heard that the ammonium ion has a tetrahedral geometry so the hydrogens would have to be moved around and the orbitals would have to be stretched around or distorted for this picture to make sense.

Second, while I have drawn each of the hydrogens attaching to different external orbital I don't actually know which orbitals the hydrogens would attach to or why.

How are the hydrogens actually attached to the nitrogen atom in the ammonium ion?

I suppose one possibility might be to have the molecule be a hybrid of various $\ce{NH3 + H^+}$ configurations. I guess this could be tested by analyzing the charge distribution of ammonium and to see if the positive charge is more distributed around the outside or the inside.


texts: Technical name for the holes (missing electrons) in a p-type semi-conductor?

texts:
When a pure silicon crystal (giant lattice) is doped with boron atoms one of the four covalent bonds made between one boron atom and four surrounding silicon atoms is missing an electron as boron has three valence electrons. Is there a technical name for these holes (lack of electron in a covalent bond).

Is it acceptable to say that these holes are indirectly the charge carriers as they are allowing the movement of the electrons?

Furthermore, could you say that these holes are positively charged?(Hence the name p-type semi-conductor?).


texts: Confusion in thermodynamically and Kinetically controlled reaction

texts:
I am confused in following reaction:
$\ce{(CH3)2CH-CHO}$ when reacts with conc. $\ce{NaOH}$, will it undergo cannizaro reaction?
According to our professor,  It can undergo both Cannizzaro as well as aldol condensation reaction.
If we consider aldol condensation,  we get tertiary carbanion as intermediate,  which is unstable and can be formed in thermodynamically controlled reaction, but the aldol is kinetically controlled .
Therefore, it undergoes Cannizzaro reaction also which is a thermodynamically controlled reaction.
Now, I know a thermodynamically controlled reaction means getting product that is stable and kinetically controlled means getting product which forms fast.
I am not able to understand how the Cannizzaro reaction being thermodynamically controlled helps.


texts: Is liquid hydrogen rocket propeller pollution free?

texts:
If one searches for the different fuel types used in rockets, one can find that over the years, NASA and other space agencies have used both solid fuels and liquid fuels. I can see that more and more rockets are propelled by using a combination of Liquid Hydrogen (LH) - Liquid Oxygen (LOX). Then, I assumed that the reaction would be:
$$\ce{2H2(l) + O2(l) ->[heat] 2H_2O(v)}\tag{1}$$

By looking at this reaction, one can see that the product of this reaction is water (which most probably will be in a vapor state). Now, I have three questions:

Is this reaction correct?
If the product is water, does that mean that such a combustion reaction is pollution free?
I assume that I am wrong thinking that is pollution free. What would be the polluting agent in this situation and how bad is it, compared to let's say the burning of the same amount of Kerosene?

Thank you!


texts: Can Silicon be used as anode for Li-Ion batteries

texts: Can Si be used as anode. I assume you could store much more energy in Si since the atom is much larger than C, but then Si seems not to like to bond with itself. Can there be a solution?


texts: How do we find the angular, radial nodes and the quantum numbers when the radial probability distribution curve's equation is given?

texts:
I am having serious conceptual issues with the Schrödinger equations. Please note that I only have basic school level (11th grade) knowledge of these equations and we are expected to know very little about it. But we are given these type of questions so I guess I will be able to understand things within the boundary of this question.

$$\psi_r = k_1 * e^{-r/k_2} * (r^2 - 5k_3r + 6k_3^2)$$

Solving the equation we get $r = 3 k_3 , 2 k_3$

It is also given that $k_3 =1$ . So $r = 3, 2$

Now, since there are 2 nodes therefore, $n = 3$ . Does the equation $\psi_r$ represents only radial nodes or all nodes?
What is the azimuthal quantum number?
How many angular nodes are present?
What is the angular momentum of the given orbital?
Is this equation of an atom or an orbital?

This equation was given as an MCQ question and we were asked to find the quantum states of the given orbital on the basis of the equation. But I guess we must have conceptual insight too to answer the question so asked it here.


texts: Photochemical Bromination of Cyclohexenes

texts: I am still very confused with the bromination of alkenes. Can I ask help in finding the structure of the main product when each of these 3 are subjected to photochemical bromination? I know for a fact that the Br will replace an H atom, but I don't know what to do anymore if there's another functional group present at one/both ends of the alkenes.


texts: What makes teflon such a strong material?

texts:
I don't know much about polymers but recently teflon made me get addicted to study their properties and nature.

As far as I know, the teflon polymer contains fluorine which is one of the most reactive elements but in the polymer state it is totally stable and moreover, it is applied as a coating to kitchen-wares and many utensils which are exposed to very high temperatures.

How did a reactive element like fluorine got such an exciting stability?


texts: Can I use lipophilicity (partition coefficient) as a way to quantify solublity?

texts:
I am looking at investigating factors affecting the solubility of drugs using databases. So far, I am thinking of having my independent variables being the polar surface area, melting point, and size. My dependent variable would be lipophilicity. The reason why I am not directly measuring the solubility is that databases provide inconsistent solubility values.
Would quantifying solubility as lipophilicity be valid?


texts: Why don't ions form crystal lattices in water and other polar solvents?

texts:
Ionic compounds are in the form of crystal lattices, and when they are dissolved in a polar solvent, they are bonded with the corresponding cations/anions of the polar solvent. For example, $Na^+$ bonds with $OH^-$ and $Cl^-$ bonds with $H^+$ when NaOH is dissolved in $H_2O$.

The reason why $NaCl_{(aq)}$ conducts electricity is because $Na^+$ and $Cl^-$ do not form crystal lattices with $OH^-$  and $H^+$  respectively. But why don't they form crystal lattices?


texts:
We have to compare their acidic strength, and we know acidic strength is directly proportional to stability of the anion.
So the first compound is more acidic due to its being aromatic after deprotonation. The second most acidic is the fifth compound, because of $\mathrm{\% s}$ character of $\ce{C-H}$ bond. And the least acidic is sixth compound because its anion is antiaromatic.
But how would we compare the second, third and fourth compounds?

Source: MS Chouhan; Advanced Problems in Organic Chemistry 11th Edition; Chapter 1 General Organic Chemistry problem 27


texts:
I have a collection of old books (all 80+ years old), recently, I received a British Chemistry text from 1903 (intro page below) - this being the oldest book of my collection (112 years old at the time of writing this question):

One thing I notice is that there is a distinct smell that comes from the pages of older books. (the smell is not unpleasant) - it seems that the older the book, the more distinct the smell.

What is the chemistry behind the old pages in a book smell?


texts: Why won't my propane combust when I spark it?

texts:
I need to run an experiment and have some pretty basic questions. I'm trying to get combustion of propane in a controlled environment. I understand that that looks like this:

$$\ce{C3H8 + 5O2 -> 3CO2 + 4H2O}$$

Meaning I need 5 times more $\ce{O2}$ molecules than $\ce{C3H8}$. But, I want to do this based on the volumes of the gases at STP. Do I just go with 5 times the volume of $\ce{O2}$ to the volume of $\ce{C3H8}$? Do the gas laws require that I take into account the size of a molecule?

And seeing that $\ce{O2}$ comprises about $\pu{21\%}$ of the volume of air, I would need to multiply the volume of oxygen by roughly 5 to get the correct volume of air needed...yes?

That gets me a 25 to 1 ratio between air and propane by volume. So, I tried it, but I couldn't get it to burn.

Doing further research, I see something called the Limiting Oxygen Concentration, but I think either I don't understand it, or this isn't the problem.

I also found that the lower and upper limits of flammability for propane are $\pu{2.15\%}$ and $\pu{9.60\%}$ respectively. My concentration is roughly $\pu{4\%}$, so this shouldn't be the issue either.

The only other thing I can think of is that my spark isn't "good enough". Is there a minimum amount of heat required from my spark to ignite the mixture?

Anyone have any ideas as to what I am missing here? Any help would be much appreciated!


texts: (Computationally) finding similarity between two organic compounds

texts:
I have been struggling to find an acceptable answer for this question for my purposes.

There are many ways to find similarity between two organic compounds - some of which are particularly popular in chemoinformatics. The seemingly most popular way is to use fingerprints of molecules, which then somehow correlates to the structure/function of various parts of the molecule. This approach seems very good when you're looking for general similarity between molecules. It also has the added benefit of making it fast to compare huge amounts of molecules, as each molecule can be encoded separately (so it's generally speaking $O(n)$), rather than comparing every pair of molecules (which would be $O(n^2)$).

However, for some purposes, this fingerprinting approach is not very good. I need a function of two molecules with the following properties:

If $A$ and $B$ are two molecules, then $f(A, B) \in [0, \infty).$
$f(A, A) = 0$
$f(A,B) + f(B,C) \geq f(A,C)$

These are similar to the basic requirements for a metric space. (The big omission is that I don't necessarily need $f(A,B) = f(B,A),$ although this certainly couldn't hurt!)

The reason that I want such a function is because I'm designing a neural network that essentially outputs a molecule, and I want to have some sort of error on the output.

I have played around a bit with Python-RDKit, and its similarity module, but haven't really been able to form a good "error" function from the output.

I've also experimented a bit with an algorithm I created that looks for the largest identical connected subgraphs of two molecules, and essentially finds matches for each part of the query molecule. The final output is then how many different parts the molecule needs to be split into to find a match.

For instance, if the "true" molecule is ethylbenzene, while the query molecule is m-xylene, then the algorithm would find that the m-xylene needs to be broken into 3 parts for each part to find a perfect match: a benzyl group missing a hydrogen at the third carbon of the aromatic ring, the methyl group that was formerly attached at the third carbon, and the hydrogen that remains from the benzyl group.

However, this algorithm suffers from several problems:

If the query is a subset of the true answer, then the algorithm will always give the answer as 2 (one part is the subset, and the other part is the hydrogen that caps it - try seeing it with something like query - methane, true - acetic acid). This isn't that big of a concern, as you can simply run the algorithm twice - once comparing the query to the true molecule, and once in reverse. That way, if the two molecules are indeed far apart, it's not hard to see (the superset molecule may need to be broken into many pieces to be identical).
This algorithm is slow. Don't really see a way to speed it up. It searches for maps from subsets of the query molecule to the true molecule, then gradually builds up from there. It also can't pick maps randomly as being the best, then growing from there, as picking the wrong direction can easily make the "best" map drastically short. So it has to do all possible maps at the same time. Which is slow.

In short, this is a somewhat open-ended question that boils down to:

How can we put a (loose) metric on the set of organic molecules?


texts: Number of orbitals in full configuration interaction

texts: I am using one quantum chemistry package where I am supposed to assign a number of active orbitals I want to be included in the FCI (full configuration interaction) calculation. For example if I have  ${H_2}$ molecule (singlet) and I use $cc-pV6Z$ basis set of Dunning, what would be the maximum number of active orbitals in the FCI? Can somebody provide me insight into this problem?


texts:
I synthesised a dihydropyridine molecule today and recieved my NMR. I am wondering where the complex splitting for the 7 and 22 protons is coming from.
My spectrum:

1.26ppm, triplet, 6H
2.33ppm, singlet, 6H
4.16ppm, multiplet, 4H
5.20ppm, singlet, 1H
5.65ppm, singlet, 1H
5.94ppm, doublet of doublets, 1H
6.21ppm, doublet of triplets, 1H
7.21ppm, singlet, 1H

Here is the multiplet form 4.16ppm:

The molecule:

Thanks very much!


texts: How did scientists discover the concepts of anode and cathode without knowing about electrons?

texts:
Scientists researched electrons and came to know about electrons after the battery was developed as we can see in the JJ Thomson's model that he used the cathode and anode. My question is that that if the scientists have known already that there are positive and negative charge that they have made the battery they should have known about electrons.

I am confused in this. Research tells that electrons were first discovered by JJ Thomson and that there are negative charges in atoms. My question is that that, without knowing about electrons how were the ideas of cathode and anode developed.


texts: Why is no dynamical correlation recovered in the CASSCF method?

texts:
Configuration interaction is the only certain way to get a calculation to converge toward the exact solution of the many-body Schrödinger equation (within the approximations used for the framework of the method). In such calculations, the wave function is expanded in all possible electron configurations, and will therefore often take too long to be practical. For full CI, all dynamical correlation is recovered.

In truncated CI, part of the dynamical correlation is recovered. The wave function expansion is, for example, limited to include only single and double excitations (CISD).

In a CASSCF calculation, a subset of all orbitals is chosen, and the wave function is expanded in all possible electron configurations within this subset of orbitals. However, here it is said that no dynamical correlation is recovered. This is stated so often I suspect it is common knowledge for computational chemists, but I can provide references if someone want them.

It is my understanding that the CI method recovers dynamical correlation in allowing electrons to be moved into virtual orbitals (and hence "react" to the instantaneous coulombic repulsion from other electrons). In allowing for higher a number of excitations, a larger portion of the dynamical correlation is recovered (CISDT > CISD).

So, why is no dynamical correlation recovered in the CASSCF method? Imagine a good set of orbitals are chosen for the active space, such that no important configurations are left outside of the wave function expansion, surely dynamical correlation is described? What if we extend this to the generalized actice space (GAS) formulation. In developing GAS, the original authors aimed to remove the "deadwood" of configuration state functions; that is, exclude CSF's with near-zero coefficients. So now a larger active space can be used, and hence a larger number of excitations can be used. Why is not more dynamical correlation recovered?

If indeed CASSCF recovers no dynamical correlation, a CASSCF calculation should give the same energy as a HF calculation. Is this the case?


texts:
When a chemical reaction dissipate heat to the surrounding, the molecules that participate in the chemical reaction will have high kinetic energy and will transmit some of the kinetic energy to the surrounding and the remaining kinetic energy will increase their temperature.

When we say that heat is dissipated to the surrounding we are talking about "some of the kinetic energy" right? Also when we write that heat dissipated is equal to $\Delta H$, it is included the remaining kinetic energy?

Can somebody confirm whether my understanding is correct or clarify where I went wrong if it is not?

Sorry, but I am far from chemistry field.


texts: Identifying a Positive or Neutral Ligand Inside Coordination Sphere?

texts:
There are some coordination compounds like $\ce{Na2[Fe(CN)5NO]}$, where ligands like $\ce{NO}$ are used which exist as both $\ce{NO+}$ (nitrosonium ion) and $\ce{NO^.}$ (neutral nitrosyl). How to identify which ligand is being used in such complexes?

A similar question was also on Quora but none of the answers were satisfactory.

Please don't answer with respect to Raman/infrared using stretching frequencies etc. since all that is out of scope at the level I'm currently studying.


texts: Unexplained peak cluster in proton NMR trace?

texts:
I am working on a straight-forward NMR graph as part of my test prep. I have a pretty limited understanding of NMR, but I thoroughly read the chapter leading up to this practice question and am having difficulty explaining all of the peaks that I am seeing. Let me show the question and my understanding:

Here is the chemical and the trace that results.

My understanding of this problem is that there are four groups of equivalent hydrogens, and I numbered them 1-4. The 1st group has 3 equivalent hydrogens, with two adjacent non-equivalent hydrogens (group #2). Using the n+1 rule, the H group #1 should create 2+1=3 peaks in a cluster. Same goes for H group #4, since there are two adjacent hydrogens, so another 3 peaks. When considering H-group #2, the three hydrogens from H-group #1 should be 3+1=4 peaks. Same goes for H-group #3, which has the three hydrogens from H-group #4 so 3+1=4.

So, I am expecting to see 2 groups of 3 peaks and 2 groups of 4 peaks. I see the two groups of 4 peaks, but not the 2 groups of three peaks. Instead, I see 1 group of 6 peaks.

Am I supposed to believe that the 2 groups of 3 are just located so near it appears to be 6? Or am I missing something?

Thanks for any help!


texts: Calculate the Magnitude of Nonadiabatic Coupling

texts:
I'm in the great position to be able to calculate nonadiabatic couplings with TDDFT.

The result of such a calculation is a displacement for every atom in x, y and z.

  Atom         X              Y              Z
---------------------------------------------------
   1      -0.000000      -0.000000      -0.160841
  ...         ...            ...            ...
   N       0.000000      -0.000000       0.009654
---------------------------------------------------

How do I calculate the magnitude of that coupling?

(It would be great, if you'd be as tutorial-like as possible.)


texts: How to slow/prevent corrosion of a steel post

texts:
I have a steel post set in limestone, about 18-20 inches deep, with some concrete around it.

I just noticed that I have about 6 inches of water inside the post. The limestone had a small seam in it and I believe the water seeps through it.
I am concerned about long term corrosion.

I am about to cap the post, so I will have no access to it in the future.
What can I do to prevent/slow the corrosion?

A. Nothing. Do not worry about it.
 B. Fill the post with crushed limestone 12 inches above grade.
 C. Fill the post with concrete 12 inches above grade.
 D. Install a fitting in the post and dump some concentrated washing soda solution or powder once or twice per year to raise pH.
 E. Some type of cathodic protection.
 F. Other.

I am leaning toward B. This would be easy to accomplish and inexpensive, and limestone is supposed to raise pH level, which I think should slow corrosion.


texts: Could the aerobic respiration reaction occur outside the body to produce water? If it is possible how would it occur


texts: what surface would liquid wax adhere to best?

texts:
I want to make a very thin sheet of wax by pour hot wax over a surface and letting it cool. What surface would wax spread out on best? I.e. which one would give the best wettability?
Many thanks everyone

THanks guys - will let you know how this goes!


texts: I got this term while reading a portion of specific heat capacity in Ideal gas chapter. What does it mean? Does it mean internal energy?


texts: Bent's rule: electronegativity and s character

texts:
I'm very much confused about Bent's rule. What I perceive from it is that more electronegative element occupies a position which has less s character.

What I can infer from here is that s character is inversely proportional to electronegativity which is not true. Please do explain.


texts: Why won't water freeze if you put ice in it, despite ice being frozen?

texts: Just now I got some room temperature water and added some ice to cool it, and it just came to me, like the scientist I wish I was ... why doesn't frozen (freezing point) ice added to higher temperature liquid compound force the water molecules to solidify?


texts:
Can you figure out the reactant's reaction order (First-order, second-order, third-order, etc.) JUST by looking at a chemical reaction? What if you were given a multi-step reaction? A single step reaction?

For example, can you tell what order $\ce{2NO_2Cl}$ is just by looking at this equation: $$\ce{2NO_2Cl -> 2NO_2 + Cl_2}$$

Or this multistep equation?

$$\ce{NO_2Cl -> NO_2 + Cl}$$

$$\ce{Cl + NO_2Cl -> NO_2 + Cl_2}$$


texts:
What is the Theoretical Drying capacity of CaSO4 when used to dry solvents? e.g. How much water can 1 gm of CaSO4 remove?

Now since CaSO4 itself comes in several forms (anhydrous, hemihydrate, dihydrate) I am wondering which is the form best suited for water absorption?

If I assume that the drying transition is from CaSO4 (anhydr.) to CaSO4.2H2O (dihydrate) then I get a drying capacity of approx. 0.26 gm H2O per gm CaSO4 used.

Is this the right capacity? Or am I using an incorrect reaction?


texts:
I've been searching some things regarding the ability of sulfur to accomodate negative charge and reached the conclusion that it's due to its size and its ability to expand its valence shell.

I can't fully understand the expansion part though. It is mentioned in various sites and books that sulfur uses the 3d orbitals due to their similar energy level with 3p orbitals in order to achieve this "expansion". However, 4s are supposed to be filled first. I even came across this question: How does expansion of electron shells work? but the answer given didn't really helped me. So why do we consider the expansion to happen with 3d orbitals, while 4s is filled first?


texts: Determination of Urea and Hydrogen Peroxide in Cow Milk by ATR-FTIR(Attenuated total reflection-Fourier Transform Infrared Spectroscopy)

texts:
I am doing a research on cow milk adulteration. I am checking Urea and Hydrogen Peroxide content in milk by ATR-FTIR(Attenuated total reflection-Fourier Transform Infrared Spectroscopy). I am using $\ce{1M}$ Urea solution and $\ce{1M}$ Hydrogen peroxide solution. I am adding this to cow milk and testing through FTIR. But i am not getting good IR peaks of $\ce{H2O2}$.

Should i dilute the solutions? As we know, UV spectrophotometer gives better peaks at dilution. But in case of IR what should i do to get better peaks? what concentration of $\ce{H2O2}$ should i use?


texts: Are there plastic materials that turn into ceramics?

texts: Are there other materials that like clay, are plastic (as in they can be shaped by hand) but set to form a hard ceramic, especially ones harder than the fired clay?


texts: Mixtures readily oxidzing organic matter

texts: Are there other mixtures than piranha solution with similiar or better ability to completely and readily oxidize organic matter? Perhaps peracetic/performic acid?


texts: How long the block starting with element 121 will be?

texts:
I remember from my chemistry classes that (after the initial irregularities) a new block of elements starts every two periods. After the initial s-block and p-block following it shortly, we have d-block starting at period IV, and f-block starting at period VI.

Now that Element 118 has been discovered, we're about to open period VIII and we're two elements short of a new block.

What block will it be? How many groups, what name etc?


texts: Order of activating ability in electrophilic aromatic substitutions

texts:
From A Guidebook to mechanism in organic chemistry by P. Sykes [1, p. 155]:

The activating effect of $\ce{Y}$ on the nucleus is found to increase, i.e.
the overall rate of substitution increases, in the approximate order:
$$\ce{OCOR} < \ce{NHCOR} < \ce{OR} < \ce{OH} < \ce{NH2} < \ce{NR2}$$
$\ce{NR2}$ is more powerfully activating than $\ce{NH2}$ because of the electron-donating effect of the $\ce{R}$ groups.
It should not be forgotten, however, that in acid solution, e.g. in nitration, these two groups will be converted into $\ce{^\oplus NHR2}$ and $\ce{^\oplus NH3},$ respectively; the nucleus will then be deactivated and substitution will be predominantly m- (cf. $\ce{^\oplus NR3},$ p. 151).
The $\ce{OH}$ group is sufficiently activating to cause phenol to be brominated instantaneously to the 2,4,6-tribromo derivative (the p- and both o-positions all attacked) by bromine water at room temperature.
The groups $\ce{OCOR}$ and $\ce{NHCOR}$ are less powerfully activating than $\ce{OH}$ and $\ce{NH2},$ respectively, because of the reduction in electron-availability on $\ce{O}$ and $\ce{N}$ by delocalisation over the adjacent, electron-withdrawing carbonyl group:

Why is $\ce{OR}$ a less activating group than $\ce{OH},$ but $\ce{NR2}$ is a more activating group than $\ce{NH2}?$
One would expect that that alkyl groups increase the electron density via their inductive effect and thus make the group more activating towards electrophilic aromatic substitutions (EAS) reactions, both in the case of $\ce{OR}$ as well as $\ce{NR2}.$ However, $\ce{OH}$ is a better activating group despite such an effect. Why is this so? Why would the same effect not be applicable for $\ce{NH2}?$
Reference

Sykes, P. A Guidebook to Mechanism in Organic Chemistry, 6th ed.; Longman; Wiley: Harlow, Essex, England; New York: New York, NY, 1986. ISBN 978-0-582-44695-3.


texts:
In one of the lectures of my spectroscopy course, the professor claimed that there is a strong absorption band in the UV/Vis spectrum of bromine, associated with a singlet-state to triplet-state transition. He asked us to think about why this spin-forbidden transition occurs.

So far I haven't really come up with a satisfactory answer. Nevertheless, here are two of my ideas:

Broadly speaking, spin-forbidden does not necessarily mean that a transition is not observed, but rather that the intensity of the spectral line will be considerably diminished. Hence, a spin-forbidden transition could be observed in a spectrum.
An electronic transition is usually associated with a vibrational transition. Through the vibrational excitation the geometry of the molecule is changed such that the spin selection rules are "relaxed".

Am I on the right track with these ideas?


texts: What is the difference between an ionic and molecular activity model? (Example: Diopside-Hedenbergite)

texts:
Original question:

When looking at a Diopside-Hedenbergite solid solution, what is the difference between an ionic and molecular activity model? Why does the moleclar model yield higher values?

Post-Edit question:

The two activities calculated below seem to me like I'm just comparing some random values. What is the true activity of the Fe- or Mg-mineral?

So far I got:

Dipside and Hedenbergite are Pyroxenes. Pyroxenes have to metal sites (M1 and M2):

\begin{align}
M^1M^2[Si_2O_6]
\end{align}

The difference between Hedenbergite and Diopside is:

\begin{align}
Hedenbergit (Fe^{[M1]}Ca^{[M2]}[Si_2O_6]) \longleftrightarrow Diopside (Mg^{[M1]}Ca^{[M1]}[Si_2O_6])
\end{align}

The activity of an element is assumed to be equal to the concentration:

\begin{align}
a=\color{Red}{\gamma}x \\
a=x
\end{align}

In the next step one has to calculate the concentrations on the M1 site because it's the site where the ion exchange happens:

\begin{align}
x[Fe]=\frac{[Fe]}{[Fe]+[Mg]}
\end{align}

\begin{align}
x[Mg]=\frac{[Mg]}{[Fe]+[Mg]}
\end{align}

The molecular mixing model apparently compares the activity of the Fe- and Mg-mineral on the M1 site:

\begin{align}
a[Mg]=x[Mg]
\end{align}

\begin{align}
a[Fe]=\frac{1-x[Mg]}{x[Fe]}
\end{align}

Whereas the ionic mixing model compares the activities of all the cations of the minerals:

\begin{align}
a[Mg]=x[Mg]^{[M1]}x[Ca]^{[M2]}
\end{align}

\begin{align}
a[Fe]=x[Fe]^{[M1]}x[Ca]^{[M2]}
\end{align}

Why are there two activities? Shouldn't there be one true activity? What does the one activity mean and what does the other mean?


texts: Why do complex ions not emit light from de-excitations of electrons?

texts: I understand that complex ions are coloured due to d-orbital splitting which results in electrons being able to absorb wavelengths of visible light and become excited to the higher energy state meaning the transmitted light is coloured. However I don't see why the electron would not simply de-excite and emit the same wavelength of light that it absorbed which would result in no visible difference. Is there some reason why the same wavelength is not emitted or perhaps the electron does not de-excite at all?


texts: How obtain mass-weighted coordinates used to plot intrinsic reaction coordinates

texts:
I have obtained the energies from an IRC calculation. Usually these are plotted in papers vs the mass weighted coordinates; often something like this is labeled on the x axis: $Å \times \sqrt{\mbox{amu}}$.

How do I obtain these coordinates?

Possible solution

With some reading, I came up with a possible solution. Apparently the IRC step size (used in Molcas calculations) are in units of Bohr in normalized mass-weighted coordinates. So all I need to do is to do the following

Set the TS data point to 0
Multiply the step number (TS is "step 0") with the step size
Multiply the above with the Borh-to-Ångström conversion factor (0.529177249)
The direction to reactant should be negative
The direction to product should be positive


texts: How do i create a significantly correct world with large crystal formations in my novel?

texts:
I have uploaded an shorter and less broad Question which is largely the same but requires a different kind of answer. What i want to say is that i re-asked my question in a different way because i do not want to delete the answers i got  here so far and because the answered also would be incorrect in the context of my re-asked and re-written question
link: Which crystals can exist permanently (and do not break down) under normal earth like outside conditions?

Hi I am not really all that well versed in chemistry or molecules for that matter but I am trying to find a way to "create" a scientific and realistic (trough probably unlikely) world with large crystal formations on the surface. The reason I want this is because I want to create a species for my novel that has its culture based around the large crystal formations living on the planet.

Now to limit my question a bit I would like the answer to these two points:

What kind of crystal(s).
How do you think the process should work.
What limitations it creates.

The criteria are that:

The crystals must be permanent without breaking down in normal earth conditions/atmosphere.
Preferably no interference required by intelligent lifeforms.
There will be oxygen and carbon dioxide in the atmosphere.
They must be able to grow quite large. I’m thinking about large hexagonal crystal columns.

What are the tools?:

Well you can more or less use anything in nature, you can make suns explode if need be. But a more probable start would be selecting the chemical composition and what would be needed to form crystals from that point.

For instance if you need a long period of very high heat and then cooling down to “normal” temperatures you can make the system sun go red giant and heating the planet before becoming a white dwarf.


texts: Conversion of units for concentration: mol/l to ppm

texts:
The concentration of an aqueous solution of $\ce{Mg(SO4)2}$ is  $0.001\, \textrm{mol} \cdot \textrm{dm}^{-3}$.

Find out the concentration of solution and the concentation of $\ce{Mg^{2+}}$ ion in ppm.

How to do this? How to find moles in ppm?

If anyone could clearly describe, it would be great.


texts:
From Practical skills in Biology by Allan Jones et al.

  At high concentrations of certain ionic solutes, $\gamma$ (activity
  coefficient) may increase to become greater than unity.

My questions : If activity coefficient $\gamma$ $=$ $  {a}/{[C]} $ where $a$ is activity which signifies effective concentration and $[C]$ is concentration, how can $a$  be greater than $[C]$ ?


texts:
I learnt that Gibbs free energy is the maximum amount of non-expansion work.
But the phrase non expansion work confuses me. Work is defined as pressure times change in volume. If there is no expansion, how can work be done?


texts: When precessing nuclei absorb electromagnetic radiations, am I supposed to consider the wave nature or particle nature of light?

texts:
I decided to peek into the NMR section of my spectroscopy book, and I found out lots of interesting stuff. And along with the interesting stuff, I did come along some stuff that I didn't understand.

My book tells me this (not copied word-for-word):

  Under the presence of a magnetic field, the two spin states of the nuclei split up, and if a correct wavelength of light is incident upon the sample, the nuclei get excited to a higher state.

In the above scenario, I believe light behaves as particles, wherein a photon of light collides with a nuclei, and push it to higher spin states.

There's another thing my book says:

  Under the presence of a magnetic field, the nuclei begin to precess (wobble like  a spinning top). If an incoming electromagnetic radiation has the same frequency as the nuclear precession, resonance occurs and the light is absorbed.

In this case, light behaves as a wave. It's the oscillating electromagnetic fields that are resonating the nuclei, and causing them to absorb the energy.

Out of the two cases that I mentioned, which is the one that actually happens? Is it resonance or spin excitation?


texts: Does 99.8% acetic acid cause severe skin burns like formic acid?

texts:
I've so far handled only concentrated fuming nitric, sulfuric & hydrochloric acids from the inorganic side. Even during an accidental spill on the hand I did say only the $\ce{HNO3}$ affects the skin by turning it yellow and the top layer sometimes peels off.
But in the organic acid side I've had once experience in the past long long ago with formic acid and it was pretty nasty. A really pungent smell and if it gets on the hand then immediately the top layer of skin will peel off. Worse than there inorganic ones. Is 99.8% acetic acid this strong?
I'm about to prepare some homemade stop bath solution for Black and White film development. I'm going to prepare a 10% acetic acid solution. Just wanted to know though I will wear nitrile gloves, in case a few drops come on the skin how bad will it be? I can't seem to find any video or much info of it's effect on YouTube or anywhere either? Just want to take all precautions.


texts: Can we tell if a compound is explosive by just looking at its chemical structure?

texts: If I showed you a compound's chemical structure will you be able to tell if it can be used as an explosive or we can only know that by conducting chemical experiments?


texts: Change in concentration when acids are diluted

texts:
I came across this formula to calculate the resultant [H]+ concentration when two weak acids are mixed (Both acids of equal volumes are mixed together).

The only problem i have with this is that, we are completely ignoring the fact that the concentration of both the acids are going to be halved after they are mixed together since, the volume is doubling. Is there anything i'm missing? The only way, this could be correct is if the concentrations that are given to me in the question are those after the acids have been mixed.

EDIT: This is the question i was talking about

This is the solution i was given


texts: Why is the methyl chloride and sodium hydroxide reaction irreversible?

texts: Is the reaction of methyl chloride and sodium hydroxide (aq) irreversible simply due to the relative stability of sodium hydroxide and sodium chloride? Or is there more to it than that?


texts: Requirement of different reagents for bromination of different substituted benzene rings

texts:
Consider the bromination reactions of phenol and anisole. We know that the former can be brominated by aqueous bromine, while the latter requires the catalyst $\ce{FeBr3}$ instead.

Our teacher said that $\ce{-OH}$ is a stronger ring activator. So, polarization of bromine takes place easily and, hence, phenol doesn’t require a Lewis acid for bromination.

But, this related question had the conclusion that both anisole and phenol are practically equally activating. So, does aqueous bromine react with anisole too? If not, why is there a difference in the reagents? If yes, do we get 2,4,6-tribromomethoxybenzene?

We have a similar case with chlorobenzene also. Difference in electronegativity between $\ce{C-O}$ is more than that in $\ce{C-Cl}$. So, chlorine must be able to give one of its lone pairs and activate the ring more readily than oxygen. But even bromination of chlorobenze requires a Lewis acid. Why is this so?

PS: I checked this similar question on our site but a proper reason wasn’t stated to my question.


texts: Why is a singlet state called singlet and a triplet state called triplet?

texts:
I kind of get the idea of singlet and triplet states. But why are they called singlet and triplet (what is the single and what is the triple in these cases)?

I feel that I am missing something obvious!


texts: Why is carbon monoxide stable(compare with other flammable gas) in room temperature?

texts: I know carbon monoxide can burn with high temperature, but why doesn't it explode easily compared to other flammable or explosive gas?


texts: How can I get xyz coordinates of atoms of a unit cell structure from CIF format files?

texts:
I'm trying to run DFT or other 1st principle simulation of Pyrope ($\ce{Mg3Al2Si3O12)}$ and Grossular $\ce{(Ca3Al2[SiO4]3)}$ unit cell structure. So, I'm looking for unit cell xyz periodic box structure of Pyrope and Grossular.

I found some data from several places (here, here and here)

CIF format files from those databases do not give me proper atomic coordinates of unit cell. I downloaded CIF files for Pyrope from those databases, and converted with Open Babel, and even visualized with VEGA ZZ.

However, it displays only 4 atoms in the periodic box, while Pyrope or Grossular should have 20 atoms in the periodic box based on their formula (Pyrope ($\ce{Mg3Al2Si3O12)}$ and Grossular $\ce{(Ca3Al2[SiO4]3)}$).

This means either CIF of database is wrong, or I am. Or the software is unable to read CIF properly. I think I'm doing something wrong, but I'm not sure what is wrong with my CIF conversion.

If anyone knows how to retrieve the unitcell structure of crystals from CIF from those databases, please help me.


texts: Why is ammonia more basic than acetonitrile

texts:
Why is $\ce{NH_3}$ more basic than $\ce{CH3CN}$?

I tried to reason it out with the hybridization of nitrogen in both the molecules. In $\ce{NH_3}$ nitrogen is $\mathrm{sp^3}$ hybridized while in $\ce{CH3CN}$ nitrogen is $\mathrm{sp}$ hybridized. Hence it follows that nitrogen in $\ce{CH3CN}$ is more electronegative as compared to that in $\ce{NH_3}$, which makes $\ce{NH_3}$ more basic. Is this the main reason for $\ce{NH_3}$ to be more basic or is there any other reason?


texts: Prove that a 10-Degree Temperature Increase Doubles the Rate Constant (k), when the Activation Energy is Approximately 50 kJ/mol

texts:
I read that increasing the temperature by $10~^\circ\mathrm C$ will double the rate constant ($k$), when the activation energy for the reaction is relatively close to $50~\mathrm{kJ/mol}$.

However, no matter how hard I try to wrap my head around it (through graphical examples that require plotting the natural logarithm of $k$ vs the inverse of temperature), I just can't grasp this so called "rule of thumb".

As a result, I tried proving this statement through mathematical expressions:

(Note that the activation energy was evaluated for $50\,000$ because it needs to be expressed in $\mathrm{J/mol}$ to be used in Arrhenius' equation)

Prove that...

  A rise of temperature of $10\ \mathrm{^\circ C}$ will double the rate constant, when the activation energy for the reaction is approximately $50\ \mathrm{kJ/mol}$.

Proof starts here -----------------------------

For:  $\Delta T = T_2 - T_1$ ($T_2$ is the final temperature, and $T_1$ the initial temperature)

When: $\Delta T = 10 \rightarrow T_2 - T_1 = 10$

It follows that: The ratio between $k_2$ (at $T_2$) and $k_1$ (at $T_1$) will equal $2$, owing to the doubling of the rate constant ($k$):

$$
{k_2\over k_1} = 2
$$

Employing Arrhenius' equation:

$$
{k_2\over k_1} = {A\mathrm e^{\left({-E_\mathrm a\over RT_2}\right)}\over A\mathrm e^{\left({-E_\mathrm a\over RT_1}\right)}}
       = \mathrm e^{\left[{-E_\mathrm a\over R}\left({1\over T_2} – {1\over T_1}\right)\right]}
       = 2
$$

Or simply:

$$
{k_2\over k_1} = \exp{\!\left({-E_\mathrm a\over R} \cdot \Delta{1\over T} \right)} = 2
$$

So:

$$
\exp{\!\left({-E_\mathrm a\over R} \cdot \Delta{1\over T} \right)} = 2
$$

This might be the part where I messed up -------------------------

$\Delta{1\over T}$ can be set in terms of $\Delta T$:

$$
\Delta{1\over T} = \left({1\over T_2}-{1\over T_1}\right)
       = \left({T_1\over T_1T_2}-{T_2\over T_1T_2}\right)
       = \left({T_1-T_2\over T_1T_2}\right)
       = \left({-\Delta T\over T_1T_2}\right)
$$

Since Arrhenius' equation above holds true for $\Delta T = 10$ ...

And since $\Delta{1\over T}$ can be expressed as $-\Delta T \over T_1T_2$ ...

Then, the rate constant ($k$) will double when:

$$
\Delta{1\over T} = {-10\over T_1T_2}
$$

Substituting into Arrhenius' equation:

$$
\exp{\!\left({-E_\mathrm a\over R}\cdot{-10\over T_1T_2}\right)} = 2
$$

Simplifying:

$$
\begin{align}
\exp{\left({10E_\mathrm a\over RT_1T_2}\right)} &= 2 \\
{10E_\mathrm a\over RT_1T_2} &= \ln{2} \\
{1\over T_1 T_2} &= {R\cdot\ln{2}\over 10E_\mathrm a} \\
T_1 T_2 &= {10E_\mathrm a\over R\cdot\ln{2}}
\end{align}
$$

From $T_2 - T_1 = 10$ we can solve for $T_2$ as $T_2 = T_1 + 10$. Substituting above:

$$
\begin{align}
T_1 (T_1 + 10) &= {10E_\mathrm a\over R\cdot\ln{2}} \\
T_1^2 + 10T_1 - {10E_\mathrm a\over R\cdot\ln{2}} &= 0
\end{align}
$$

For $E_\mathrm a = 50\,000$:

$$
T_1^2 + 10T_1 - {500\,000\over R\cdot\ln{2}} = 0
$$

Solving the quadratic equation:

$$
\begin{align}
T_1 &= 290~\mathrm K \\
T_2 &= 300~\mathrm K \\
\Delta T &= 10~\mathrm K
\end{align}
$$

I don't think this proof is correct because substituting any value for activation energy ($E_\mathrm a$) onto the quadratic equation will produce different values for $T_1$, but that doesn't tell me anything.

What did I do wrong?
Can this be proved any other way?


texts:
I am currently taking a Biochemistry course and one of the topics on midterm covers various weak forces and its distance dependence. We covered:

charge-charge (ionic)
hydrogen bonds
van der waals
hydrophobic effect

I am not sure how to put them in order and how they interact with each other once distance comes into play.
If anyone can explain in details, it would be very helpful.
Thank you in advance.


texts: How to graph spherical harmonics in the Mac "Grapher" application?

texts:
I was wondering if it was possible to graph the spherical harmonics in the Mac grapher app. In their manual, there is a section that talks about graphing the spherical harmonics (page 54):

This is my attempt at graphing the spherical harmonic for l = 1 and m = 0:

There is clearly something wrong. My suspicion is that (for some reason) the application may be using a rectangular coordinate system, since this is the exact graph in rectangular coordinates. However, as you can see in the image, I am supposed to be in spherical coordinates. Any help would be greatly appreciated.


texts: Normally when you do electrolysis, you would use a glass container. Would it be wise to use a acrylic container? I have one spare but not sure if this would affect the electrolysis process. Is there any reaction between the acrylic container in the electrolysis process?


texts: Physical Interpretation of Gibbs Free Energy

texts: I know that $\Delta G = \Delta H - T\Delta S$ and that if $\Delta G$ less than $0$ a reaction will be spontaneous. What I am wondering is what is the actually physical interpretation of Gibbs free energy. I mean, if the Gibbs free energy of a particular reaction $20\ \mathrm{J\ mol^{-1}}$, what does that actually mean?


texts: Nanoscopy Nobel Prize - why are all the tools in the visible light range?

texts:
It seems like all the new advances in molecular imaging/microscopy are in the visible light range of the EM spectrum. An example would be the most recent Nobel Prize for Chemistry.

Is there some reason we are only looking for things in the visible part of the EM spectrum? I'd love to know why, and also what techniques look outside of this range?


texts: Is Dalton's Atomic Theory a theory or a postulate?

texts:
It is always mentioned that Dalton proposed an Atomic Theory. But when you read it, it consists of the following:

  The main points of Dalton’s atomic theory, an explanation of the structure of matter in terms of different combinations of very small particles, are given by the following postulates:

  All matter is composed of indivisible atoms. An atom is an extremely small particle of matter that retains its identity during chemical reactions.
  An element is a type of matter composed of only one kind of atom, each atom of a given kind having the same properties. Mass is one such property. Thus, the atoms of a given element have a characteristic mass.
  A compound is a type of matter composed of atoms of two or more elements chemically combined in fixed proportions. The relative numbers of any two kinds of atoms in a compound occur in simple ratios. Water, for example, a compound of the elements hydrogen and oxygen, consists of hydrogen and oxygen atoms in >the ratio of 2 to 1.
  A chemical reaction consists of the rearrangement of the atoms present in the reacting substances to give new chemical combinations present in the substances formed by the reaction. Atoms are not created, destroyed, or broken into smaller particles by any chemical reaction.

(From the book: General Chemistry by Ebbing and Gammon)

I'm sure many of you might be knowing that postulates and theories are quite different. Can someone explain me whether Dalton proposed a postulate or a theory?


texts: How are the toxic components in a mixture identified?

texts:
I was doing research on buckwheat sprouts (as to whether I should include them in my diet) and I came across a website that said eating too much can cause fagopyrism, which is caused by compounds called fagopyrins:

I was just wondering how they came to the conclusion that it was these compounds that were dangerous? If someone reports side effects, with the number of different chemical compounds in a plant, how would they narrow it down to that one?
Do they just toxicity test all of the possible compounds? Or do they look for certain functional groups and structures to narrow down their search? Ie is there a way you can predict from the structure that a compound could be potentially toxic?
Thanks!


texts:
When you melt a covalent network, you break intramolecular covalent bonds, is that not a chemical change?

Also, is ionisation a chemical or physical change?


texts: Calculating the UV/Vis spectrum of perylene

texts:
I recently started to do computational chemistry and am now trying to write some basic inputs for important calculations. One, which I guess is quite important to me would be to predict UV/Vis spectra of molecules. So I looked for a basic input file on the net, and although my tutor warned me about using DFT for absorption spectra (it's not a topic of the lecture and therefore he wasn't sure what to use either) the first few simple molecules, mostly long conjugated systems and a few azo-compounds gave really good solutions in comparison to literature values.

Now I wanted to predict a perylene in benzene as solvent as well and gave the structure optimization (HF/VDZ) six cycles, which took forever to calculate before I stopped it. Then I used the geometry at each of the six steps to predict the spectrum and compared the results. What surprises me is that the optimization, while becoming better, moves the first absorption peak at ~435 nm further from experiment. From its position and the direction, it seems to better describe the second peak (~410 nm) instead of the first one.

I am also only getting one peak only but for the other molecules, it had been pretty much the same as well, where one peak was quite big and the rest, although being at the right positions were too small to really see.

Now I know about the quantum mechanics and the theoretical backgrounds of UV/Vis spectroscopy but we never really discussed the effects in real spectra. I know from NMR that peaks can split and multiply in experiment, while your theoretical model only contains one signal.

Is there a reason, perhaps due to the big delocalized system why perhaps the bands shift or multiply in some way or why I am not able to see the first band? Or perhaps my calculation shows the first band and it's really far off?

All UV/Vis calculations were done with Orca using RI-BP86/SV(P) and COSMO for the solven.

Here is the experimental spectrum I am referring to:

Please note: Those are my very first calculations and I am still trying to understand when the simple approaches yield good results and when I need to switch to different approaches.


texts: Why does no antitoxin for botulinum type H exist yet?

texts: Antitoxins against the botulinum toxins type A–G produced by Clostridium botulinum are known. Why does none exist against the type H botulinum toxin yet?


texts: Why are reversible reactions spontaneous?

texts:
If a reversible chemical reaction is spontaneous in one direction, shouldn't it be non spontaneous $(ΔG > 0)$ in the other? In other words for the reaction:

$$\ce{A + B ⇌ C + D}$$

if

$$\ce{A + B -> C + D}$$

has $ΔG < 0$ and thus proceeds spontaneously, doesn't this imply that

$$\ce{C + D -> A + B}$$

would have $ΔG > 0$ and thus proceed non spontaneously?


texts:
Anode: $\ce{2 H2O_{(l)} -> O2 + 4 H+_{(aq)} + 4e^-}$

Cathode: $\ce{ 2 H2O_{(l)} + 2 e- -> H2_{(g)} + 2 OH-_{(aq)}}$

Can someone show me the steps for adding the two. For the overall reaction, it is $\ce{2 H2O_{(l)} -> 2 H2_{(g)} + O2_{(g)}}$


texts: Has anyone encountered the use of Omega to represent equilibrium?

texts: One of my lecturers last year (a pharmacologist by training) used the symbol $\Omega ^m$ as a shorthand for equilibrium. He implied it was common practice but I've never come across it elsewhere. I was wondering if anyone else has encountered it?


texts: Is there an easy way to remember charges on ions?

texts:
I have a chemistry test coming up and I might need to know the charge that goes with the different ions like $\ce{SO4}$ has $-2$, $\ce{NO2}$ is $-1$ and  $\ce{PO4}$ is $-3$.  Is there an easy way to remember this by looking at the periodic table or something like remembering that the second row elements are all going to be $\ce{something-O3}$  and the next row is all $\ce{something-O4}$ for the -ate endings (except $\ce{Cl}$ which is the odd man out). It will make writing out the different acid combos easier, if I can remember the charge difference that needs offsetting by the hydrogen.

I'm just trying to lay down some associative triggers for myself.


texts:
When we dip zinc metal in zinc sulfate solution, does zinc sulfate ionize into Zn and sulfate ions? Zinc ions come into the solution as Zn$^{+2}$ so why is the metal not completely dissociated?

Why is zinc sulfate used as an electrolytic solution?


texts: How to find all published Pharmacophore Structure of a Drug target?

texts:
Other than literature review how do you find the structures of Pharmacophore of a drug target? I am searching Pyruvate Dehydrogenase Kinase (PDK) inhibitors and I have reviewed lots of literature but I've only found few structures. I have tried searching google by "PDK inhibitors patent reviews" "PDK inhibitors general review" but I am not finding any concrete literature. There are 4 sub classes: PDK1, PDK2, PDK3 and PDK4.

I am looking for drug candidates which are potential Pharmacophore for this drug class.


texts: What are the applications of poly-crystalline GdFe₂?

texts: Poly-crystalline $\ce{GdFe2}$ is a ferromagnetic compound but where is it practically used for its magnetic properties?


texts: Output of the Sugar & Sulfuric Acid Reaction?

texts:
When a reaction of sugar and sulfuric acid occurs, some form of carbon is produced. Is this carbon bonded as graphite? If not, than what is it bonded as?

$\ce{C6H12O6 ->[H2SO4] 6C + 6 H2O }$


texts: Reactions of alkynes with sodium/ammonia vs sodium amide

texts:
What happens when alkynes react with sodium in ammonia ($\ce{Na/NH3}$), or when they react with sodium amide ($\ce{NaNH2}$)?

Are these two sets of conditions different?


texts: Is the enthalpy of a molecule determined by the energy of the electrons?

texts:
I understand that the strength of the bond of a molecule is determined by the potential and kinetic energy of the electrons. I also understand that a reaction where the bond strength of the products is stronger than the bond strength of the reactant releases energy (is exothermic).

My textbook states that in a reaction where NaOH dissolves in water, the energy of the solid NaOH is greater than the energy of the dissolved ions in water. Is the "energy" of the reactants and products determined by the bond strength?

Also, my textbook states that enthalpy is "the amount of energy, in the form of either kinetic or potential energy, a substance has." I'm a bit confused about enthalpy. My textbook enthalpy changes:

Are these enthalpy changes determined by the bond strength also? And is the enthalpy of a certain molecule also from the bond strength?


texts:
It is (mostly) used as an "oxidizer" in motors and engines, I understand that much. The oxygen "oxidizes" with other chemicals, while the nitrogen returns to the air.

But $\ce{N2O}$ also produces "euphoria" in human beings, works as a mild anesthetic, and causes people to laugh. Why does this happen?


texts: The effect of structure on the boiling points of organic molecules

texts:
Why do molecules like methoxyethane, ethoxyethane and so on have lower boiling points than isomeric alcohols?

I think it has something to do with the structure, but I don't exactly know what it is.


texts: Confusion about atomic/molecular orbital terminology

texts:
I have come across several different orbital terms: atomic orbitals, natural orbitals, split-localized orbitals, molecule-intrinsic orbitals, quasi-atomic orbitals.

I don't know what the difference between these are, or whether some of them describe the same thing. Could someone help clarify what these are?


texts: What is the best invisible ink for clothing?

texts:
I am interested in writing and revealing a message in invisible ink for theatrical purposes. I found a list of potential compounds here but I am having a hard time prioritizing which to experiment/rehearse with.

The message will be written on a lab coat and revealed in the dim lighting of a night-time bonfire so the ink must be dark enough to see easily. Because I will be writing on cloth, I will need an ink that will not run, so that when the message is revealed, it will be legible and not distorted.
Heat-activated inks are preferable because I will have the bonfire on hand for the reveal but there is the danger of revealing the writing too soon.
Chemically-activated inks are less desirable because of the less-theatrical reveal and because many of the revealing-solutions look like they will stain the coat making the message difficult to read but I will keep them as candidates because I have not tested my staining hypothesis and because of the added control they offer.
Blacklight-activated inks are not suitable.

I don't have enough lab coats to test all the compounds listed so my question(s) are:

Which of the inks listed are least likely to run when applied to cloth?
Of the remaining inks, which will appear darkest when revealed?
Of the remaining heat-activated inks, which are easiest/hardest to reveal, in terms of temperature/time required?


texts: Which has a higher priority while naming: Double or a triple bond?

texts:
Which has higher priority in IUPAC naming: A double or a triple bond? given that both are located at the terminal/equivalent positions in the molecule.

My chemistry textbook says a double bond has a higher priority than a triple bond but I'm skeptical over it.

If someone can provide some more authentic source citing this rule, I'll be highly grateful.

EDIT: Drawing the hydrocarbon linear


texts:
Functional groups like $\ce{OH}$, $\ce{NH2}$, attached to unsaturated compounds (chromophores) are called auxochromes. These groups tend to shift the absorption wavelength to the infrared region, which is called a bathochromic shift.

Why do these groups shift the light absorption wavelength?
Why exactly to the infrared region; that is, why is the absorption red-shifted or lowered in energy?


texts: If all molecules have basically the same KE at a given temperature, why do lighter isotopes evaporate more readily?

texts:
One of the proxies used for paleoclimate is the ratio of oxygen-18 to oxygen-16 in ice cores and in sedimentary rocks.  The idea is that water molecules with oxygen-18 generally evaporate less readily than oxygen-16, and condense more readily;  and this proclivity varies with temperature.  One can then use the deviations of oxygen-18 concentration from a standard ratio to say something about Earth's temperature in the distant past.
Why do light water molecules evaporate more readily?  It makes some intuitive sense that lighter molecules would evaporate more easily.  But how does this square with the equipartition theorem and the idea that all molecules have the same amount of kinetic energy at a given temperature?
It would seem to me that because the intermolecular forces between two water molecules are independent of their mass, it should take a certain amount of energy to remove a water molecule from its neighbors in the liquid phase and move it far away.  This energy requirement doesn't depend on the mass of the molecules, only on how the force on it varies with distance ($W = \int \vec{F} \cdot d\vec{r}$.)  So by this argument, molecules with the same amount of kinetic energy would have the same likelihood of evaporation.  And by the equipartition theorem, the translational kinetic energy of a water molecule is only dependent on the temperature, not on the mass of the molecule.
EDIT:  Just to pre-empt the "it's velocity that matters, not energy" argument:  I agree that lighter molecules would, on average, have a higher velocity.  But from classical physics, we know that applying a fixed force to a smaller mass leads to a larger change in velocity, while a larger mass gets a smaller change in velocity.  That would imply that the "escape velocity" required for a heavier molecule would be smaller; since it's heavier, its motion would not be affected as much by the force it feels from the other molecules. This would imply that while heavier molecules are moving more slowly on average, they also don't need to be moving as quickly to escape.  In other words, the velocity threshold for evaporation should be lower for heavier molecules.  These two effects (lower speeds and lower threshold for evaporation) should cancel each other out.
Where does my logic fail?


texts: Efficient, low overhead means to scrub acid gases without water loss?

texts:
This question is pretty much what it says on the tin: what would be an efficient (low pressure drop, reasonable energy consumption), low overhead (simple, lightweight) means to scrub acid gases from a feedstock stream without water loss (and ideally, with water capture)?

Say, the stream is primarily $\ce{CO2}$, a few percent nitrogen, 80kPa / 25°C; the $\ce{H2O}$ partial pressure is ~5 Pa (~20ppm); and there's a variety of acid gases in the dozens to hundreds of ppm range, and you'd like to scrub at least 90% of the $\ce{H2O}$ and acid gases, preferably more.  Obviously if you were to just, say, run it through a packed bed with water you're just going to humidify the gas stream in the process of scrubbing, because the vapour pressure of water is three orders of magnitude higher than the $\ce{H2O}$ partial pressure already in the stream.  Obviously if the gas stream were compressed to several hundred atm or more then you could do that, but such levels of compression would neither be efficient nor low overhead.  You could likewise freeze out $\ce{CO2}$ to increase the partial pressures of everything else, and even distill the remaining gases - but these are anything but efficient, low-overhead solutions.  I thought about the use of dilute sulfuric acid as the scrubbing medium to drop the vapour pressure, but the vapour pressure drop isn't nearly enough until high molarity, which would be relatively useless for scrubbing.

I'm sure there's a "right" solution for such a case, but I'm not sure what it is.  Adsorption into a solid chemical bed, with subsequent regeneration (and if so, what sort of chemical)?  Multistage, with say acid gas scrubbing first, then water scrubbing (and if so, what method for the latter to get down to under a few pascals partial pressure)?  Selective membranes - say, to exclude $\ce{CO2}$, with a partial vacuum drawn on the other side?  Some sort of ion pump?


texts: Why are 'sec-' and 'tert-' prefixes printed in italics?

texts: While reading about nomenclature of branched alkyl groups, I read that certain common names are also approved by IUPAC. Among those names, only few prefixes are italicised (namely sec- and tert-) and others like iso and neo are printed normally. These names are documented in the IUPAC blue book. What can be the reason for italicising sec- and tert- and leaving out the others?


texts: Making three membered ring using different reactants

texts: I am struggling with the above question. It will be the conjugate base of trichloromethane that is involved. The same is true of the carboxylate. However, I have no idea about the reaction mechanisms. Please help.


texts: Conversion of grams to milliliters using kg/m3 density

texts:
Convert 100 grams of a solution to milliliters with a density of $681.9\rm~\frac{kg}{m3}$. It also has a density of 5.69 pounds per gallon.

Are any or all of these correct?

$$\rm100~g \times \frac{1~mL}{681.9 \frac{g}{cm^3}} = 0.146649~mL\quad(\approx 0.15~mL)$$

$$\rm1,000~g \times \frac{1,000~mL}{681.9~\frac{g}{cm^3}} = 1,466.4906~mL\quad(\approx 1,500~mL)$$

$$\rm1~kg \times \frac{1~L}{681.9~\frac{kg}{m^3}} = 1.4664906~L (\approx1.5~L)$$

Or, can it be as simple as: 100 g x 681.9 = 68.190 mL? The unit kg/m3 is what's confusing me. I'm used to g/cm3 or g/mL for densities. Does 681.9 g/cm3 = 681.9 kg/m3, while scaled-up a thousand-fold? Can I consider using the same density with the math involved by substituting kg/m3 for g/cm3 in the equation, or do I have to utilize a conversion within the metric system?


texts:
Doing a grade 9 experiment comparing the alkalinity of antacid tablets.
Using bromothymol blue indicator.
Dissolved tablets in both tap water and distilled water and in all situations antacid came out  yellow in with bromothymol blue indicator ... so the antacid is an acid?
I was intending to have students compare brands by titrating with HCl and comparing the volume of HCl used, but have nowhere to go as the antacid is already an acid?
Can anyone explain what is wrong?


texts:
The internet is full of videos like this showing water bottles for drinking used to supercool water. These bottles, not unexpectedly, appear a bit finicky, since they have lots of edges to serve as nucleation sites for ice crystals. What container would work best for this sort of demonstration?

Is the most important quality just to eliminate edges or does the material have an important effect? It's important in lab to add boiling stones as nucleation sites when boiling water in glassware. Could I use this trait for freezing too? Is the important quality of the glass the high surface energy or the smoothness of the surface? Alternatively, it seems like something like PTFE coating with super low surface energy might be effective?


texts: Illustrating moles with sand grains, Are there more moles of SiO2 in a grain than moles of sand on the earth

texts:
I have been trying to understand the scale of atoms, thinking about sand grains as an example.
With approximately $7.5\times10^{18}$ grains of sand on the earth that is $1.25\times10^{-5}$ moles of sand grains. Source
I've found that a beach sand has approximate density $2.5\times10^{3}$ grams/litre or 2.5g/cm$^3$. Assuming a quartz grain of diameter 0.05cm, so volume of approx $5\times10^{-4}cm^3$ and mass of approx 0.001g. Source
With moelcular mass 60, then there are $2.2\times10^{-5}$ moles of $\ce{SiO2}$ per grain.
This surprised me. Are there really more moles of $\ce{SiO2}$ in a grain of sand than moles of sand on the Earth? And is there any verfication of this by a more serious study?


texts: Why can toluene be chlorinated at either the benzylic position or the ring depending on the conditions?

texts:
My book mentions a reaction for the preparation of benzaldehyde with toluene in which side chain chlorination of toluene gives (dichloromethyl)benzene, which upon hydrolysis gives benzaldehyde:

Why does the chlorination occur at the methyl group and not the aromatic ring in this case? Also, why chlorination with $\ce{FeCl3/Cl2}$ lead to 2-chlorotoluene (and 4-chlorotoluene), without any chlorination of the methyl substituent?


texts: What would this aromatic boron compound be called?


texts: Why is Diiron nonacarbonyl so exceptional?

texts:
My textbook(NCERT) says:

  With exception of $\ce{Fe2(CO)9}$, all other metal carbonyls are soluble in hydrocarbon solvents.

Weller, M.; Overton, T.; Rourke, J.; Armstrong, F. Inorganic Chemistry, 6th ed. states:

  The most striking exception among the common metal carbonyls is nonacarbonyl diiron(0), which has a very low vapour pressure and is insoluble in solvents with which it does not react.

Other metal carbonyls are well soluble in hydrocarbon solvents but not Diiron nonacarbonyl. Why? What makes Diiron nonacarbonyl so exceptional? Is it because it has low vapor pressure?

There are no explanations regarding the insolubility of diiron nonacarbonyl. Is there any experiment conducted to determine the reason for its insolubility or is it just mere observation?

Update

@Orthocresol has told me to draw comparison of diiron nonacarbonyl with $\ce{[Mn2(CO)10]}$ and $\ce{[Co2(CO)8]}$ because of their similar molecular weight. Based on this fact, I went on to research further on this topic and from various handbooks and research notes I delved upon, I have drawn the following solubility comparison table. [Note: Only binuclear metal carbonyls were considered of form $\ce{[M2(CO)_x]}$ because they have same structure and thus should have same physical properties].

\begin{array}{c|c}
\mathbf{Metal~carbonyl} & \mathbf{Solubility} \\\hline
\ce{Mn2(CO)10} & \mathrm{ether, other~organic~solvents}\\
\ce{Tc2(CO)10} & \mathrm{ether,acetone} \\
\ce{Fe2(CO)9} & \mathrm{Insoluble~in~benzene,ether,petrol.Only~soluble~in~THF}\\
\ce{Rh2(CO)8} & \mathrm{organic~solvents}\\
\ce{Ir2(CO)8} & \mathrm{Ether,CCl_4}\\
\ce{Co2(CO)8} & \mathrm{petrol,benzene,alcohol}\end{array}

Also, a table of comparison for the other two iron carbonyls for a reference.

\begin{array}{c|c}
\mathbf{Iron~carbonyl} & \mathbf{Solubility} \\\hline
\ce{Fe(CO)5} & \mathrm{soluble~in~all~organic~solvents~like~ether,petroleum.Insoluble~in~water}\\
\ce{Fe3(CO)12} & \mathrm{Insoluble~in~water. Soluble~in~non~polar~organic~solvents.
} \end{array}

We can observe that there is a drastic anomaly in case of solubility of diiron nonacarbonyl in both the tables. Any explanation to this?


texts: Which solvent is good for using SU-8 particle in Optical tweezers?

texts: I'm studying Optical tweezers. I've used Polystyrene for samples. Nowadays, I've got SU-8 pillar. I wanna use that for sample, but its density is heavier than water. I can't use that. So I wanna know some liquid for replacing water.


texts: Why 1-ethenyl-3-ethyl-5-ethynylbenzene has that name?

texts:
I would priorized these funtional groups based on two options (following the ciclohexane rules):

Molecular weight
Representing each pi bond as a alkane branch. e.g. Ethenil as a isopropil backbone.

But, none of these option works. Why this molecule has that name?


texts: Does any compound exist with multiple liquid phases?

texts:
I've seen some phase diagrams and I found really interesting, how many exotic solid phases of most elements exist on higher pressure and temperature.

But I've seen always only a single liquid phase and also only a single gaseous phase.

The second is understable, but the first not. I think, if there is an unconventional potential energy field between the molecules, maybe it is not impossible.

Does any chemical compounds with multiple liquid phases exist?

If not, why not?

Extension: Well, superfluid helium is one of them. Maybe I don't formulate enough well, but I think on a distinct phase border, like between ice-I and water. As I know, the superfluid helium is a mix of its superfluid and normal fluid phases.


texts: Hydrolysis of an amidine derivative under acidic conditions

texts:
I know that an imine can undergo acid hydrolysis to yield a corresponding amide:

https://chem.libretexts.org/@api/deki/files/13283/10.jpg?revision=1

But I am looking at a mechanism for acid hydrolysis of a drug where the doubly-bonded N remains, and instead a different R-group (NH3) is cast off.

  https://imgur.com/zH43bi4

Empirically, this the primary degradant produced after exposure to acid, so I know it's 'correct', but I don't understand why the general imine-to-amide mechanism is not occuring. Does it have something to do with the relative properties of the NH3 and NHSO2NH2 R groups?


texts:
I read online that C=O is more stronger than C=N and the reason behind this was, 'Since bond between C and O is more polar hence it will have a slightly higher ionic nature than C and N. As we know ionic bonds are stronger than covalent bond hence C=O bond is stronger.'
Then I tried to find the bond strenght between C-O and C-N by applying the same logic but the result turned out to be the opposite of what I had calculated. According to factual data C-N is stronger than C-O. Can anyone please explain me what's wrong in my reasoning and whether it's right or not.


texts: Why is magnesium ascorbate, which is a conjugate base of a weak acid, acidic?

texts:
Why are magnesium ascorbate and potassium acetate, which are salts of strong bases with weak acids, acidic?
I discovered with litmus paper that magnesium ascorbate is acidic and found out from https://foodb.ca/compounds/FDB015417 that potassium acetate should also be acidic.
How can this be? Shouldn’t conjugate bases of weak acids, ascorbate and acetate in this case, be basic and the strong dissociated spectator ions, $\ce{K+}$ and $\ce{Mg^2+}$, neutral?


texts:
I read about electrode potential today, the book says that:

  Metals more reactive than hydrogen will have negative electrode potential value and metals less reactive than hydrogen will have positive electrode potential.

I'm a bit confused by the sign of the voltage, can voltage have negative value? What does negative voltage mean?

Another question is why metals more reactive than H have negative electrode potential?


texts: Can ethylene glycol give victor mayer test?

texts:
I think there should be no problem for it to give red coloration in victor mayer test as a standard primary alcohol but a problem I encountered showed it otherwise.

Therefore, I would like to have a clear cut view of possibilities of what could happen, what actually happens and why?


texts: Are β-sheets formed from one or more polypeptides?

texts: I know that a β-strand forms bonds with another β-strands and so on and thus a β-sheet is formed, but are those strands from the same polypeptide? And does their distance matter? Do they have to be close or it is not necessary? Thanks in advance.


texts: Why are the calculated NMR values on the DFT & GIAO level of cyclopentane-1,3-dione so far off?

texts:
I'm trying to simulate the 13C NMR spectrum of cyclopentane-1,3-dione (PubChem CID: 77466; CAS 3859-41-4; ChemSpider ID: 69875; SDBS No: 15258; SMILES: C1CC(=O)CC1=O). There are three equivalence classes of carbons: The two directly attached to the oxygens (≈197 ppm, call this class 1), the one carbon between those two (≈105 ppm, call this class 2) and the "other two" (≈31.3 ppm, class 3).

I've been using Gaussian 16 via the guidance provided by Dean Tantillo's group at UC Davis, the chemical shift repository (CHESHIRE) in particular first performing molecular structure optimization at some level (e.g. B3LYP/6-31+G(d,p)) and then calculating shieldings (at mPW1PW91/6-311+G(2d,p) with solvent corrections, scrf=(solvent=chloroform, smd)). But I keep getting shielding values that are radically off.

In particular, regardless of the settings I arrive at isotropic shielding values for classes 1, 2, 3, of ≈-34,  ≈136, ≈144. Now of course observed chemical shifts and shieldings are often related by a linear scaling, per the Tantillo group's work (and others), which means that it's very odd that classes 2 & 3 here (the non-Oxygen-attached carbons) have nearly identical shielding values.

I am new to chemistry and DFT methods, so I worry I might be something wrong, but it might also be the case that this is just a "hard" molecule for DFT methods to get right. I wanted to know:

Are there any higher levels of theory that I should try / better methods for shielding calculation that would be worth assessing?
Is there any way of analyzing the output from Gaussian16 to get a hint that things might be going awry?
Is there something that just makes this a "hard" molecule to calculate? I get the impression that the contributions in liquid state from various rotamers, etc. is relatively minor as it seems quite rigid (although I have not quantified this).


texts: Reasonably complete infrared spectral database with data in CSV form?

texts:
I'm currently developing a neural network that analyses IR spectroscopy signatures. I've found a very complete data set at The Spectral Database of Organic Compounds, but data is only available as images, which are not ideal for training neural nets.

Does anyone know of a reasonably comprehensive open database of spectroscopy data that offers data in CSV/tabulated form?


texts: Fluorination of Carbonyl Compounds using Molybdenum Hexafluoride

texts:
What is the mechanism of halogenation of carbonyl compounds using molybdenum hexafluoride? How does it work?

Here's a reaction I came across:

Can we use it for all carbonyl compounds? Are there any limitations to the method?


texts:
What is the meaning of the word root "aceto"?

I believed that "aceto" meant a methyl attached to a carbonyl group. For example, as in acetamide. Then, why do we name $\ce{CH3C\bond{3}N}$ as acetonitrile, even though it does not have any carbonyl group?


texts: Which make HCO3- to show two pH values at two scenarios?

texts:
According to the below two titrations,

Image Reference
If we consider the reactions, at the first reaction (in first figure after adding 1.0), there is $\ce{HCO3-, NaCl,}$ and $\ce{H2O}$ at the first equivalence point. At the second one (after adding 1.0), there is $\ce{HCO3-,}$ and $\ce{H2O, Cl-}$ at the first equivalence point. $\ce{HCO3-}$ only affect to the $\mathrm{pH}$ of the medium. But,

According to the first figure, $\ce{HA- + H2O → H2A + OH-}$    it acts as a base
According to the second figure, $\ce{HA– + H2O → A2– + H3O+}$    it acts as a acid

I am doubtful on why do $\ce{HCO3-}$ perform as two types at these different situations? Do anything in the medium  manipulate $\ce{HCO3-}$ to work as a base or an acid? How to describe these two scenarios? Generally I can't see a theoretical method for describe it.
I searched this in so many resources, but I couldn't find a satisfied answer. So, I hope a theoretical answer, for this problem, not a mathematical description.


texts: Is toulene be a part of the systematic IUPAC name?

texts:
Consider the following compound:

The name engraved below it is what ACD ChemSketch generated for me. However, my book mentions that "3-chlorotoluene" is the iupac name for this compound.

This is another compound:

My book mentions "2,4,6-trichlorotoluene" is the IUPAC name, while the above is the name generated by ChemSketch.

Now, I am confused as to which name to agree with.

  Which name is correct?
  Which IUPAC rule says that toluene (and other related siblings like phenol) should be/should not be a part of the IUPAC name?

NOTE: I know that even common names can be considered as PINs, but in my post I am dealing with systematic IUPAC name only.


texts: Enthalpy of neutralization of strong acid and strong base differing from enthalpy of formation of water from ions

texts:
If the neutralization between strong acid and bases has enthalpy of neutralization of around $\pu{-57.1 kJ mol^-1}$, why is it that when I try to calculate the enthalpy of formation of water from $\ce{H+}$ and $\ce{OH-}$ ions I get approximately $\pu{-55.8 kJ mol^-1}$ using the reference values?

Why is there this difference in enthalpy if the reaction between say $\ce{NaOH}$ and $\ce{HCl}$ is only between $\ce{H+}$ and $\ce{OH-}$ ions, while $\ce{Na}$ and $\ce{Cl}$ remain dissociated?

Calculations: From the Wikipedia page, the standard enthalpies of formation are:

$$\begin{align}
\ce{H2(g) + 1/2 O2(g) &-> H2O(l)} &\quad \Delta_\mathrm{f,1}H &= \pu{-285.8 kJ mol-1}\tag{1}\\
\ce{1/2 H2(g) &-> H+(aq) + e-} &\quad \Delta_\mathrm{f,2}H &= 0 \tag{2}\\
\ce{1/2 H2(g) + 1/2 O2(g) + e- &-> OH-(aq)}&\quad \Delta_\mathrm{f,3}H &= \pu{-230 kJ mol-1} \tag{3}
\end{align}$$

Computing $\Delta_\mathrm{f,1}H - \Delta_\mathrm{f,2}H - \Delta_\mathrm{f,3}H$ gives us the reaction $\ce{H+ (aq) + OH- (aq) -> H2O (l)}$ with the associated enthalpy change $\Delta_\mathrm{f}H(\ce{H2O(l)}) = \pu{-55.8 kJ mol-1}.$


texts: Columnar crystallization of ice under small pieces of eroded granite

texts:
Walking through mountains in northern Portugal I noticed a curious formation of ice cristals whose explanation I was unable to give to my grand children (Photo 1). I searched in the internet but I couldn't find it.
On the soil, in the areas covered with raw sand, resultant of erosion of granit, the grains of sand were raised up by long ice cristals (photo 2). With the weihgt of the sand grains the "prismatic" cristals of ice curved (photo 3)
Why cristals elongate this way, raising the grains of sand? Why they do it as separate columns of ice?
I would be very glad to obtain an explanation
Thank you very much
PS I couldn´t send the images


texts: The IUPAC name of a multifunctional carboxylic acid compound

texts:
What is more preferred name when ester is present as junior functional group bis-carboxylic acid? (refer the image attached):

to count carbon of ester and consider two branches on it (one oxo and other like methoxy).
to consider whole ester group as branch.

(According to me answer by first method: 4-(formyloxy)-4-oxobutanoic acid and by second: 3-(formyloxycarbonyl)propanoic acid) please correct me if I'm wrong.


texts: We know that the lower the energy gap between bonding and antibonding orbital the easier it is to break the bond making it unstable. However, in a conjugated double bond, the overlapping of wavefunctions cause the energy gap between the bonding and antibonding orbital go down. Then why conjugated double bonded molecules are more stable??


texts: What drives a molecule/atom towards stability?

texts:
I'm very familiar with the concept that chemical reactions occur because the reactants a state of stability via the reaction. It's a very satisfying and fulfilling statement. But my question has always been - "How do the molecules know what to do? Do they have a certain amount of intelligence? Are they living?" I'm really sorry that the question isn't properly framed because this topic is just a mess inside my mind.

It's like the reactants already know what to do in order to attain stability.

The question arises because we are taught chemistry in a way relatable with moral values and actions humans perform under a given circumstance. So who is to be frowned upon - the way we are taught, or the lack of understanding within the students?

Thanks for going through the mess :)


texts: Multiple stir bars have lost their magnetism

texts: I'm attempting to produce sodium metal chemically. It is a proven process. It requires 15 hours of heating with continuous stirring. I've run the process 4 times now. Every time the stir bars get demagnetized and of course don't work anymore. I've replaced the stir bars with different sizes, types, and from different manufacturers. Regardless the stir bars inevitably quit working. The temperatures used are 120 C for two hours, and then 200 C for the remainder of the 15 hours. The process calls for quantities of Mg, NaOH, Menthol Crystals, and Mineral Oil. So, that's what the stir bar is stirring. The rate of spin is not high since the stir bar would be thrown to the side of the flask, so the rate is very carefully set. The rate, however, doesn't seem like it would be the issue here.  Does anyone have any information or suggestions. please.


texts: What do dashes mean in chemical formulas?

texts:
I'm working on summarizing some research for an essay; here's the main article.

The basic premise is making nanoparticles from gold and iron(III) oxide that have properties of both gold and iron.

The formula they give is $\ce{Fe2O3-Au}$. The procedure involves chemical reactions, so I'm assuming it is a new molecule or particle of some sort, but what does the dash mean in the formula? Does it relate to the type of bond or something?

Also, and this is probably bonus since the useful part of the question deals with dash notation, but from the procedure I've generated the partial equation:

$$\ce{Fe2O3 + H2O + Na3C6H5O7 + HAuCl4 → Fe2O3-Au} + \text{something}...$$

After the reaction, the samples are put through a centrifuge and some unknown supernate is then removed, leaving the $\ce{Fe2O3-Au}$. Do you have any guesses on what the supernate is composed of? I was thinking something along the lines of $\ce{HCl}$, but I'm not sure what would happen to the sodium or carbon.


texts: Mechanism for hydroxyethylation on nucleobases (e.g. Thymine)

texts:
I'm trying to figure out the following reaction mechanism

There's a reference paper by Yanagi and Akiyoshi(1959) showing the hydroxyethylation of imides resulting in the following

I have two questions :

(1) Why would the hydroxylethylation occur in the 1 position instead of the imide at the 3 position? I would imagine that this reaction occurs for the more acidic amine, but I have no idea why there doesn't seem to be any literature about that reaction.

(2) Why would this reaction produce a HydroxyEthyl and not a urethane, as shown here :

Any insights would be appreciated, thanks!

Yanagi and Akiyoshi : http://pubs.acs.org/doi/abs/10.1021/jo01090a601

Reaction in red (from a patent application): http://www.huntsman.com/performance_products/Media%20Library/a_MC348531CFA3EA9A2E040EBCD2B6B7B06/Products_MC348531D0B9FA9A2E040EBCD2B6B7B06/Carbonates_MC348531D1109A9A2E040EBCD2B6B7B06/files/jeffsol_alkylene_carbonates_synthesis_of_hydroxy_alkyl_urethanes.pdf


texts: Is anyone familiar with a piece of equipment that can be purchased like a small burette? I need to find a way to dispense a liquid at a constant rate, however, the amount of liquid that I need to dispense will probably be less than 5 mL. A syringe is good in that regard, but it requires that I am able to push down with a constant pressure (which I doubt I can do). I've heard that they make burettes that are smaller (i.e around 25mL). Does anyone know if they make them smaller or at least not 2 feet long. Thank you for any useful information.


texts:
I understand that polarity corresponds to an electronegativity difference and that the larger the electronegativity difference, the more polar the bond.

However, I have read that carbon dioxide is nonpolar. This doesn't make sense to me.

In carbonyl compounds, the carbonyl carbon is partially positive and thus carbonyls are polar. $\ce{CO2}$ is simply two such units bonded together, so wouldn't it be that you would have an even more positive carbon and two partially negative oxygens causing $\ce{CO2}$ to be overall polar?

On top of that, $\ce{CO2}$ dissolves to a much larger extent in water compared to $\ce{O2}$, despite both molecules supposedly being nonpolar.


texts: Correct stability order of resonance structures

texts: Question no 9 as far as I know none of the rules of relative order of stability apply to this( completion of octate,charge seperation etc.) So they all must be equally stable but the answer is (D)


texts:
I've recently gained an interest in the whole topic of lapping and the creation of flat surfaces.
Lapping is done in different ways, but the one I'm interested in is essentially just rubbing 2 surfaces together with an abrasive in the middle. The slurry is a liquid with the very tiny abrasive particles suspended in it (usually things like diamond, aluminium oxide, silicon carbide, etc..).
These particles can be different sizes of course, for example 1/4 micron or 9 microns. And they can make this slurry to these "tolerances".
A layman such as me looking at their cheap prices is lead to believe that maybe this isn't such a complicated manufacturing process. I don't know much about chemistry, but I am mighty curious about this.
How are these big batches of really tiny abrasive particles made to within such a small tolerance for cheap? Thank you!


texts: What is the reason for isotropy in amorphous solids?

texts:
In my book, it's been mentioned that crystalline solids are anisotropic whereas amorphous solids are isotropic in nature. The reason for these has been explained (with a diagram) as:

Crystalline solids are anisotropic in nature, that is, some of their physical properties like electrical resistance or refractive index show different values when measured along different directions in the same crystals. This arises from different arrangement of particles in different directions. Since the arrangement of particles is different along different directions, the value of the same physical property is found to be different along each direction.
Amorphous solids on the other hand are isotropic in nature. It is because there is no long range order in them and arrangement is irregular along all directions. Therefore, value of any physical property would be same along any direction.

My question is: similar arrangement of particles in different directions in crystalline solids gives rise to different physical properties. Then, how can disarrangement in amorphous solids in all directions give rise to same physical properties?
In other words, why do crystalline solids have properties (like electric conductivity, thermal conductivity, mechanical strength, and refractive index) different in different directions, and the amorphous solids have these properties same in all directions?


texts: Predicting pressure inside a container based on temperature

texts:
I'm a mathematician and computer scientist, and for this particular problem I would benefit from some chemical expertise.

Suppose I fill a container up with some liquid propane. I believe this is done under very cold conditions so that the propane remains liquid while the container is being filled. It is then sealed off. Suppose now the inside of the container changes temperature. I would like to calculate the pressure that would be exerted on the walls of the container at any given internal temperature $T$.

Intuitively, I would think that the pressure would be a function of temperature and some initial conditions (how full is the tank initially)? If I filled up the tank to 95% capacity with liquid propane, and then heated the tank, I would expect the resulting pressure on the walls of the container to be much higher than if I filled up the tank to only 1% capacity and did the same thing.

However, the only resources I've been able to find so far relate to the vapour pressure, which is a function of only temperature and this seems incomplete.

Can anybody point me in the right direction on how to approach this problem? Some factors that seem to complicate things are:

The containers always seem to contain some level of liquid (due to internal pressure?), the rest is gas. Does the liquid have an effect on the pressure exerted on the walls? Can I just ignore it?
If, rather than fill up the tank with liquid at very cold temperatures, the tank is just directly filled with gas, how does this change things? My guess is that given the initial pressure and temperature you can predict the pressure at a different temperature, but I think the fact that some of the gas becomes liquid at some point is tripping me up and I'm not sure how to approach the problem.


texts: Does sanding the oxide layer of a magnesium sample break bonds?

texts:
We all know that if we keep a piece of magnesium metal exposed in open air, an oxide layer forms on it. This layer prevents further oxidation of the bulk metal. If we then rub it with sand paper, the magnesium metal can react again because the oxide layer is removed. So my question is:

Does that mean abrasion with sandpaper can break the oxygen bonds with magnesium?


texts:
According to my chemistry teacher, sodium in ethanol can reduce ketones, aldehydes, acid halides, esters, cyanides, isocyanides, nitro compounds and acid anhydrides.

Now surfing over the web, I could only verify that it reduces, aldehydes, ketones and esters. Can someone please confirm whether Na in EtOH reduces other mentioned compounds also?


texts: Grignard reagent will act as a base or a nucleophile

texts:
R- from grignard reagent (RMgBr) and gilmann's reagent (R2CuLi) although being a strong base reduces the carbonyl group and does not act as a base.

Why can't it abstract the alpha hydrogen forming an enolate ion?


texts:
I don't understand why the stoichiometric coefficients of reactants and products are expotentialized in law of mass action.

So I checked on Wikipedia. And this popped out:

  In the 1879 paper[9] the assumption that reaction rate was proportional to the product of concentrations was justified microscopically in terms of collision theory, as had been developed for gas reactions. It was also proposed that the original theory of the equilibrium condition could be generalized to apply to any arbitrary chemical equilibrium.

How does collision theory explain this?


texts: Formal Charge in Coordinate covalent bonds

texts: I am in an honors chemistry course right now and I would like to know the formal charges of the atoms in CO, my confusion is that because the bond is partially coordinate covalent, are the bonded electrons still counted as #bonds/2 or should I count the number of electrons donated by each atom (making the formal charge 0 for both) Please help me understand and explain WHYnot just how. Thanks a lot.


texts:
So I had an exam today in which one of the questions was in what class (I-IV) of the Biopharmaceutical Classification System (BCS) the drug nifedipine falls in. Class I drugs are considered highly soluble and highly permeable, class II badly soluble and highly permeable, class III highly solube and badly permeable and class IV badly soluble and badly permeable.

  Solubility

  The aqueous solubility of a drug substance is considered as high according to the HHSFDA
  BCS criteria when:

  The ratio of the highest orally administered dose (in mg) to the solubility (mg/ml)
  is less than 250 ml
  This criterion is met over the pH range 1-7.5 at 37°C. [1]

  Permeability

  According to HHS-FDA a drug is considered a highly permeable, when more than 90%
  of the orally administered dose is absorbed in the small intestine.[1]

Obviously judging from literature it falls under BCS class II and you'd probably assume so if you look at the solubility (practically insoluble in water <1g/10000ml) and the permeability, which is good because it is absorbed well (>90%). [2] However the way the question was asked was interesting because of the information given. It explicitly said that a dose of 20 mg was the maximum dose and no exact solubility was given except that the solubility was "practically insoluble", meaning a solubility of < 1 g/ 10000 ml. Now whether the solubility is 1g /10001 ml or 1g/ 100002 ml, nobody knows... The extent of absorption given was 90% and thus high permeability was assumed. However when you calculate how much volume of water is needed to let this fully dissolve, you'd come with the answer 0,02 * 10000 = 200 ml water. This is smaller than 250 ml and thus one would be inclined to then assume the solubility is high according to the specifications stated above, which would lead you to think the drug falls under BCS class I. Of course in reality you'd have to take into account the exact solubility which probably isn't exactly 1 g/10000 ml and the exact volume of the gastrointestinal tract which probably isnt exactly 250 ml.

Now what am I supposed to believe in this situation? In this case the dose plays an important role in determining the BCS class and thus answering the question. Would you in this case have taken the rules for what they are and follow them like I did, taking into account dose and assuming the lowest solubility or would you have based it purely on the "practical insolubility in water" of the drug and conclude low solubility and thus BCS class II?
Maybe I'm thinking too hard about this, but I'm curious if anyone has something to say on this.
I personally think it would've been fair if the exact solubility (perhaps even a fictive solubility) of nifedipine and exact volume of GIT were given in this situation to make this question more clear.

Sources:

http://www.who.int/medicines/services/expertcommittees/pharmprep/QAS04_109Rev1_Waive_invivo_bioequiv.pdf
http://www.dissolutiontech.com/DTresour/200905Articles/DT200905_A01.pdf