texts:
Before I begin I know that what I am asking will deform the M.O but for what I am doing this for that is okay if it is only around the atoms and bonds.

My question is in JMOL is there anyway to display the isosurface of the molecular orbital and have it leave a gap around the molecule. I am going to a conference soon and need to print a model of a cyclic molecule. I would like to be able to "mount" the MO to the molecule using tiny magnets at certain points so I may dislodge the two phases and show the structure of the molecule. Yes using two different models (one with MOs and one without) is possible but not preferred.

I have explored isosurface command and different syntax and have not been able to find anything that may be of help.


texts:
Sorry if this is not the place for asking this question, but I'm going to do a real life project and don't know where else to ask.

I'm going to prepare and sell snow cones next summer. For making snow cones, I was told by ice cone makers that ice should come from carbonated water.

As in my country is quite difficult to find a proper ice factory that could produce ice with clean water, I'm planning to make my own ice for snow cones.

I was thinking to buy bottles of carbonated water, pour them in many plastic bags and freeze those bags in my refrigirator. In that way I could get carbonated ice.

My question is:

  Do you think that pouring carbonated water in plastic bags for producing ice would be a good idea? Or could I get adverse effects like water loosing sodium ?


texts: I'm trying to make an optical dissolved oxygen sensor. I need help finding an appropriate oxygen sensitive dye

texts:
I have been trying to make a dissolved oxygen sensor, the basics are described on this page.

I have a good understanding of the electronics behind this measurement, but I cannot find a suitable oxygen sensitive dye to use. I have read quite a bit about room temperature phosphorescence, and thought that erythrosin b might but a suitable candidate, it has an excitation wavelength of 525 nm, and radiates in near-IR. After more reading, I found that it needs to be in a sol-gel or similiar substrate. All of the reading I've done seems to require some sort of substrate and this isn't what commercial dissolved oxygen sensors are using. They appear as just a thin, hard disc. Additionally, I don't have any equipment or experience with sol-gels.

I'm looking for any information on what chemical and process commercial systems are using. Or, a simple way to get erythrosin b to work. My tests with it so far have not shown any phosphorescence at all.

Thanks for your time.


texts: How to predict the products of a organic chemical reaction

texts: Given a set of reactants, what aspects should I consider when predicting possible products?


texts: Potassium vs sodium bicarbonate in fire fighting

texts:
Why is it that potassium bicarbonate reduces flashback as opposed to sodium bicarbonate when fighting fires?

From what I understand, high heating of bicarbonate salts decomposes them into carbon dioxide, which helps suffocate the fire, and the corresponding metal hydroxide. Could it be potassium hydroxide that is interacting differently with the fire versus sodium hydroxide that causes this issue?


texts:
In the following pyrolysis reaction, we have to find how many $\ce{CO2}$ is formed.

According to me it should be 5 as there are five carboxylic acid.

But the answer is 4, how?


texts: Iodobenzene reaction with copper(I) ion?

texts: Does it reduce it to benzene like $\ce{LiAlH4}$ does? Any source for this reaction?


texts: I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)


texts:
At first I thought that the reason is what I was taught, the absence of vacant d-orbitals but then I did some research. Most of the answers stated what I initially thought but one particular answer told that it's a common misconception (d-orbital theory). According to it, there can be two possible reasons-

Not much electronegativity difference between O and F.
The atomic size of Oxygen is not sufficient for it to hold 6 atoms.

So which one is likely to be more appropriate, the d-orbital theory or the electronegativity and atomic size theory?


texts:
To calculate the dissolved oxygen in water at saturation pressure at 25 °C, we do:

$$
D_\ce{O2} = K_\mathrm{H} \times M \times p_\mathrm{g}
$$

$$
D_\ce{O2}~[\pu{g/L}]= 1.26\times10^{-3}~[\pu{mol/L/atm}] \times 32~[\pu{g/mol}] \times 0.21~[\pu{atm}]
$$

I used $\pu{1.26E-3 mol/L/atm}$ for the Henry's constant for $\ce{O2}$ in water at 25C which is from Warneck and Williams (2012), which was in turn taken from Battino (1981). This returns a dissolved oxygen of $\pu{8.47 mg/L}$.

Benson (1980) reports dissolved oxygen for "a body of pure water is in thermodynamic equilibrium with an atmosphere of standard composition saturated with water vapor at a total pressure $P$" as 8.26 mg/L which is a difference of 2.5 %. The Benson paper suggests an error of around 0.02 %. Why is there a difference in these two methods? Is it due to different assumptions being made? Or perhaps rounding errors in how data is presented?


texts: How strong are molecular bonds in layman's terms?

texts:
Suppose you had a single sheet of graphite the size of an A4 page. What would it feel like to handle it?

Would your fingers instantly tear through it as you tried to grasp it?

Could you punch your finger through on purpose?

Could you tear it like a sheet of paper?

Could you fold it into a paper aeroplane without breaking it?


texts:
I want to remove a layer of 2 mm thick carbon black on a copper bowl on the outside from hanging over wood and coal fire.
I have tried different solvents, but the carbon seems to be very resistive.

Which formula solves carbon black without solving copper? The bowl is made from pure copper. It will melt at roughly 1000 degree Celsius and has a high heat capacity.


texts: For solid-liquid mixtures, cooling crystallization process can be used to separate the solute substances from each other. Assume that we have two salts that have very close solubility in a certain solvent which we are going to use. First, we dissolve the salts in the solvent while heating. After a point, we let the mixture cool down and observe the crystallization. My question is, how can we do this experiment accurately if they have really close crystallization point that they would nearly crystallize at the same time?


texts: How is it that the equilibrium constant does not depend on the mechanism?

texts:
For a reaction of the form

$$\ce{aA + bB <=> cC + dD}$$

the equilibrium constant is

$$K_c=\frac{[\ce{C}]^c[\ce{D}]^d}{[\ce{A}]^a[\ce{B}]^b}$$

regardless of the mechanism of the reaction. Why is this the case?

I've seen derivations that use a reaction in one elementary step to demonstrate this, but this obviously doesn't work in general. The sample reaction used was $\ce{N2O4 <=> 2NO2}$.


texts: Stereochemical outcomes in opening of vinyl epoxides

texts:
Explain the outcomes of the following reactions. In each case the major product is shown.

Firstly, I don't understand why the chloride always attacks on the right hand side of the epoxide. Also, regarding the stereochemistry for (ii), I assume the chlorine can open the epoxide as it is antiperiplanar to the left hand side of the epoxide?


texts: Why is buffer capacity at a maximum when the ratio of its components is 1?

texts:
A buffer consists of a weak acid and its salt or weak base and its salt.

When the ratio of weak acid and its salt in a buffer (or the ration of weak base and its salt) is equal to 1, we say that the buffer capacity is maximum. How does this tell us that buffer capacity is maximum?


texts: How do we know a reaction is in equilibrium?

texts:
In teaching secondary science equilibrium, how can we actually show there is a backwards reaction occurring during equilibrium rather than no reaction. A lot of equilibrium experiments involve external changes such as temperature or change in pressure. This to me shows that a reaction can occur backwards, i.e reversible but it doesn't show that there is a forward and backwards reaction occurring at the same time at equilibrium.  What's a simple science experiment or everyday life experience that equilibrium can explain where the idea that an reaction just stops taking place doesn't?

Every video just claims that there is a forward AND backwards reaction but doesn't really explain why and is also something I've taken for granted

Thanks


texts: How many stereoisomers are possible for hepta-1,6-diene?

texts:
I am asked to identify the number of stereoisomers that are possible for hepta-1,6-diene $(\ce{H2C=CHCH2CH2CH2CH=CH2})$.

I drew the bond-line structure as follows, and I think that there can be cis and trans isomers, but my answer is wrong. The correct answer states that since neither of the double bonds exhibit stereoisomerism, this compound does not have any stereoisomers.

Originally, I thought that single bonds can be considered too. But I think I my error is that by looking at the single bonds, we are considering the constitutional isomers of this compound, rather than the stereoisomers (which are determined by the 'fixed' double bonds). Since double bonds lack the free rotation that single bonds have, for any compound that may exhibit stereoisomerism, we can only consider the double bonds. Also, are we considering only one double bond at a time?

Is this reasoning correct? Can someone clarify and expound more on this please?


texts:
Which of the following planar structures would be aromatic?

Could someone help me determining the aromaticity of the compounds?

My Attempt:

(i) Not an aromatic compound since it only has 4 pi electrons that does not satisfy Hückel's (4n+2) rule.

(ii) Not aromatic because it only has 4 pi electrons, however I'm not sure if the oxygen contributes a p-orbital, but it shouldn't matter since 5 pi electrons still does not satisfy Hückel's rule.

(iii) I'm very confused because I'm not sure if the ketones are considered "part of the ring" therefore do they also contribute p orbitals? However if we ignore the ketones, then I believe the Nitrogens contribute 2 e- since they are sp2 hybridized? Therefore the 2 N atoms and 2 C atoms contribute a total of 4-not aromatic either?


texts: What is the standard way of reporting/interpreting measurement uncertainty in scientific publications?

texts:
As an undergraduate student I was often told in lab classes to report every single measured or calculated quantity with its associated uncertainty in lab classes, in the form $(10.1 \pm 0.1 )~\mathrm{g}$ for instance, where 0.1 is the standard deviation or estimated uncertainty. I'm starting to find, however, that this practice is seldom followed in scientific publications.

When reporting uncertainty in a scientific publication, is it good practice to report every measurement in the form $(300.1 \pm 0.1 )~\mathrm{K}$ ? I sometimes see this done in the body of scientific papers, but usually never in tables/lists of data. This worries me because, in my understanding, all measurements have an uncertainty associated with them, so I find these data hard to interpret unambiguously.

Is it usually assumed that numbers written without an explicit uncertainty are accurate to the last expressed digit? (i.e. that $10.5~\mathrm{g}$ implies $(10.5 \pm 0.1)~\mathrm{g}$ ?) sometimes this seems to be the case, but doesn't this negate the difference between $ \pm 0.1$ and $\pm 0.5$ for instance? Is this difference usually considered unimportant?

As a side question: Regardless of the usual practice in academic writing, do you consider that demanding every single number to be reported with an associated uncertainty is a good idea if teaching a lab class?


texts: why does Zn become oxidised in the first place in operation of voltaic cell?

texts: I am so confused that during the operation of a voltaic cell, why does $\ce{Zn}$ gets oxidized? In anode side, there is a zinc metal in $\ce{ZnSO4}$ solution, but why does the $\ce{Zn}$ lost 2 electrons?


texts:
Are methyl n-propyl ether and methyl iso-propyl ether metamers?
It says so here.

So the difference must be in number of carbon atoms or the distribution?

Definition(http://dictionary.reference.com/browse/metamerism)


texts:
Do all reducing sugars show mutarotation?
I studied that for a sugar to be reducing it must possess a free aldehydo or keto group. Also, for a mutarotation interconversion between α- and β-forms of compound are required.
If there is a free aldehydo group or keto group in the compound must it show mutarotation?
Note: I am a high school student so please try to explain in a simpler manner.


texts: Why are copper salts less soluble than zinc salts?

texts:
Compounds with cations having pseudo-inert gas electron configurations have more covalent character than those that don't, therefore they should be less soluble.

Here are some solubility products:

$$
\begin{array}{lcc}
\hline
\text{Anions}    & \ce{Cu^{2+}}                 & \ce{Zn^{2+}} \\
\hline
\text{Arsenate}  & \color{red}{ \pu{7.95e-36} } & \color{red}{ \pu{2.8e-28} } \\
\text{Hydroxide} & \color{red}{ \pu{4.8e-20} }  & \color{red}{ \pu{3e-17} } \\
\text{Sulfide}   & \color{red}{ \pu{8e-37} }    & \color{red}{ \pu{2e-25} } \\
\text{Phosphate} & \color{red}{ \pu{1.4e-37} }  & \color{red}{ \pu{9e-33} } \\
\hline
\end{array}
$$

Zinc ($\ce{Zn^{2+}}$) has a pseudo-inert gas configuration ($\ce{[Ar] 3d^{10}}$), and its salts are more soluble than those of copper ($\ce{Cu^{2+}}$), which does not ($\ce{[Ar] 3d^{9}}$). Why?


texts: Is it possible to determine if a substance can dissolve in water just by looking at its chemical structure? For example, how am I supposed to know if $\ce{NaHCO3}$ and $\ce{Na2CO3}$ can dissolve in water or not? Or should I just memorize all of it?


texts: Does 1,3-butadiene in bromine/water do addition twice?

texts:
Considering 1,3-butadiene (below) added to bromine water (considering it as $\ce{Br2(aq)}$):

I've seen online that the products are 1,2-dibromobutene and 1,4

but what I don't understand is why wouldn't the other double bond undergo substitution again? They're on a carbon chain like normal so shouldn't they react with the bromine water too? Is something stopping it?


texts:
For the following question

Which molecules react to form a dative/coordinate bond?
A. $\ce{CH4}$ and $\ce{NH3}$
B. $\ce{C2H2}$ and $\ce{Cl2}$
C. $\ce{NH3}$ and $\ce{HF}$
D. $\ce{Cl2}$ and $\ce{HF}$

the answer scheme says C is correct, but I do not see how two already complete molecules can form coordinate bonds. $\ce{NH3}$ has a lone pair of electrons, $\ce{HF}$ having none. How can a coordinate bond between this lone pair and $\ce{HF}$ happen? I am confused.
The others are also equally confusing.


texts: Biodegradation time for biodegradable shopping bags?

texts: How long does it take for the plastic/polythene shopping bags marked biodegradable to biodegrade?


texts: Why are there free electrons in a metal?

texts:
Recently, we covered metallic bonding in chemistry, and frankly, I understood little.

I understand that:

Metals bond to each other via metallic bonding
Electricity can flow via free or delocalized electrons

But, I do not understand why the metal atoms turn into ions and delocalize the electrons, why don't the metal atoms stay as atoms?


texts:
The mark scheme says carbon dioxide is produced from carbonate + acid. I know hydrogen can't be produced because both the reactions are endothermic.
But where did the acid come from? Can someone give me an example of Solid B and D which produces a mixture and when added together it gives carbon dioxide


texts: What is the degradation mechanism of pyrrole?

texts:
A vial of pyrrole (that was occasionally exposed to air) changed its color while degrading from pale yellow to dark orange.

What is the mechanism of pyrrole degradation? What are the resulting products?


texts:
I want to do electroplating with diamond grit and make profiling, grinding and cutting disks. (see the attached photos)

I want to know the process to make the machine or the company whom is selling machinery to do it.

UPDATE :
My question is not about how to shape metal like this, I know how to do it.
My question is that, how can I electroplate diamond grit on the surface of these profiling wheels?


texts: In compounds with lone pairs or with charge it is easy to predict acidity of compounds but how to describe acidic nature of  such ($\ce{FeBr3}$, $\ce{AlCl3}$) transition element compounds ?


texts: We always hear about the different arrangements of molecules that lead to the formation of polymorphs, my question here is why would a polymorph form in the first place? The material was given enough time to solidify in  a proper arrangement, why did it choose to solidify in a form that isn't the most stable?


texts: What's the difference between RHF and UHF?

texts: I am doing a course on electronic structure methods and am somewhat puzzled by the content (I have a physics background). From what I understand Hartree-Fock is a method where you only use the Slater determinant for the ground state of occupied spin orbitals. Then configuration interaction (CI) is an extension of this where you include unoccupied spin orbitals for your Slater determinants. But if Hartree-Fock considers the ground state energy, then how can you have unrestricted Hartree-Fock?


texts: What if kinetic energy of ejected electron = 0

texts:
When hf ≥ work function, Then the electron still comes out. So, if I say kinetic energy of ejected electron = 0, it should still come out. Right ?
Then, how does the electron even move out or gets ejected if its $v=0$?


texts: How do I predict the solubility of a compound in a mixture of water and an organic co-solvent?

texts:
I'm trying to predict the solubility of long alcohols (e.g. 1-octanol, 1-decanol or 1-dodecanol) in a mixture of water and an organic co-solvent such as DMSO, acetonitrile or ethyl acetate.

For example, decanol in water with 25% DMSO or saturated with ethyl acetate (8.3%). I of course know the solubility of alcohols in water, but not in organic solvents or in mixtures.

I found a server to predict the solubility of any compound in any solvent, but I'm not sure how accurate it is and it only does predictions for pure solvents, not mixtures: http://showme.physics.drexel.edu/onsc/models/multisolvent.php

Any input on this would be greatly appreciated!


texts:
I'm a total layman in chemistry and am working on an interactive sculpture project and therefore am researching into fluids that have certain properties - long story short:
we are thinking on having a transparent sculpture where a fluid is flowing through it, a fluid that reacts visually on the heat of peoples hands on their touch - so if people touch the sculpture, the fluid changes colour or even emits light in a fluorescent way.
Sorry, I am conscious this may sound super vague and really naive - I'm just trying to reach out to check out possibilities and may come up with interesting insights.
Is there any known way of achieving such an effect? Where could I continue looking after? Any help or pointer towards a certain direction is highly appreciated. Thanks!


texts: Why can't pure water conduct electricity since it can be reduced at cathode and oxidised at anode?

texts: We all know that pure water can't conduct electricity. But during electrolysis, if add a small amount of $\ce{HCl}$ acid inside, water could be decomposed to hydrogen gas and oxygen gas, as it is reduced at the cathode and oxidised at the anode. So why can't pure water just conduct electricity by electrolysis?


texts: Can an organic compound have an ionic bond?

texts: Is there any organic compound that has another type of bond other than the covalent bond?


texts: If A reacts with B (aq), does that mean it is soluble in it?

texts:
For example, ethanol is soluble in water, but doesn't react with it. On the other hand, H2SO4 is said to be soluble because it dissociates (reacts) in water.

Would ethanol be soluble in HCl (aq)? It won't react with the HCl, but it can form hydrogen bonds with the water, right?

How about ethylamine or ethyl methanoate? Would they be soluble in HCl (aq)? They react with the HCl, so I guess they will be. Is this correct?


texts: How can I choose the right symmetry in CAS calculation using MOLCAS?

texts: With $C_{2\mathrm{v}}$ symmetry and a closed shell configuration, how can I choose the occupation for each irreducible representation in the input file?


texts: Why does ammonia causes unsymmetric cleavage of diborane, but carbon monoxide causes symmetric cleavage?

texts:
Diborane reacts with Lewis bases to form adducts.

I did some research on my own, and found that ammonia breaks it unsymmetrically but $\ce{CO}$ and $\ce{PF3}$ break it symmetrically. I cannot find the reason.


texts:
From this topic on MOs of butadiene vs ethene, it is clear that when two ethene molecules are combined to extend the conjugate chain, the HOMO is raised in energy and the LUMO is lowered in energy. This implies that the resultant compound is more reactive towards nucleophiles(Lower LUMO more easily matched in energy with HOMO of Nu), and also towards electrophiles (Higher HOMO more easily matched in energy with LUMO of E).
In "Why chemical reactions happens" by Keeler and Wothers, "The conjugative effect" is mentioned as something that decreases reactivity (see p. 163-165):
"The delocalization of a lone pair from X into the carbonyl π system decreases the reactivity of the carbonyl towards nucleophiles by raising the energy of the π LUMO" .
The second argument seems to contradict my original argument, so what am I missing?

Perhaps extending conjugate system by pi bonds, empty p-orbitals or filled single orbital (LP) etc. have different effects on the reactivity?

I think an extensive answer explaining the effects of conjugation on reactivity(towards nucleophiles and electrophiles), perhaps also touching on the common statement that "presence of conjugation stabilizes a compound", would be very helpful for the site.

EDIT: Seeing as my original question is very broad, i would appreciate if someone could simply explain the apparant contradiction between the previous post and the Keeler&Wothers quote.


texts: Is the iodide and persulfate reaction bimolecular?

texts:
Given the following reaction in an aqueous state:
$$ \mathrm{2I^- + S_2O_8^{-2}\rightarrow  I_2 + 2SO_4^{2-}}$$
Is it bimolecular o trimolecular? Because two molecules of iodide react with one molecule of persulfate, so I would say trimolecular.
Furthermore, I know it is a second order reaction because of the Iodide Clock experiment I performed, so would that mean that the reaction is complex and not an elementary reaction?


texts: How does iodine react with amylose and amylopectin, and can iodine colorimetry be used to determine the ratio between the two starches?

texts:
Based on some of the methods of studying starches in rice I looked at, I found that there are two general distinctions:

ones that focus on the ratio between amylose and amylopectin
ones that focus just on amylose, measuring percentage content

The former included methods such as electrophoresis, amperometric, potentiometric and spectrophotometric procedures. The latter used procedures primarily based on colorimetry using iodine.
Due to technical constraints, I think that colorimetry will be a realistic option for my task.
However, I am unsure about the differences in measurement for the two types:

given that iodine creates different colors with amylose and amylopectin, can this be used to calculate the ratio?
if the sample contains more than just amylose and amylopectin (such as rice flour, rather than starch), can the iodine colorimetry procedure still be used?

Example of a procedure that uses iodine colorimetry:
[C. M. Sowbhagya; K. R. Bhattacharya (1971). A Simplified Colorimetric Method for Determination of Amylose Content in Rice. , 23(2), 53–56. doi:10.1002/star.19710230206]
Example of a procedure using electrophoresis:
[José Manuel Herrero-Martínez; Peter J. Schoenmakers; Wim Th. Kok (2004). Determination of the amylose–amylopectin ratio of starches by iodine-affinity capillary electrophoresis. , 1053(1-2), 227–234. doi:10.1016/j.chroma.2004.06.048 ]
*I have done as much research as I can on this, but I am not fully familiar with the field. Please forgive any misunderstandings.


texts: First point of difference rule 1,6-dimethylcyclohex-1-ene

texts: According to the first point of difference rule, second one should be correct right?


texts:
I know the specific heat depends (slightly) on the conditions present. For example, methane's specific heat is 2.5 at 400 K, but 4.5 at higher temperatures.
How might specific heat depend on pressure, though. -- if we are under super low pressure (say 6 mbar rather than earth's typical 1014 mbar), how would specific heat change. I am expecting it to differ along with $PV = nRT$, but not sure.

Also, $\Delta H = mc\Delta T$ -- would I need to plug $\Delta PV/nR$ in for $\Delta T$?


texts: What would be the state of water in interstellar space or vaccum?

texts:
Consider the interstellar space: Far from radiations, heat, etc. You can imagine conditions equal to vacuum. At these conditions, what will be the state of water; Ice, liquid, vapours, or something else?

What I know is that in lab conditions in a vacuum flask if we do the same experiment with water:
First it starts to boil, as the pressure in vacuum is almost zero. As it takes no time for the water to reach pressure equal to surrounding pressure, vapour pressure is formed easily. Water starts to boil without any rise in temperature.
Second, since energy is spent in boiling all the kinetic energy is used up and the water molecules start to condense forming ice.

The question now is: What are the differences between lab conditions and interstellar space? Shouldn't the results be all the same?


texts: "Adjust pH of the solution to 5.0±0.1 with acetic acid (by potentiometry)"

texts:
In a procedure description I'm translating, there's this sentence (I here quote it literally, word for word, as it is in Russian):

  Adjust the pH of the solution to 5.0±0.1 with acetic acid (by potentiometry).

The meaning of "(by potentiometry)" is that the personnel should use a potentiometric pH meter diring the adjustment process.

However, I'm not sure what the custom is of indicating this in English.

Maybe "(control using potentiometry")? Or maybe one should add the word "potentiometrically":

  Adjust pH of the solution potentiometrically to 5.0±0.1 with acetic acid.

There must be some commonly used turn of phrase for this.


texts: What is the correct definition for the activation Gibbs energy?

texts:
i found several definitions of the activation energy in electrochemistry, but i dont know why they are different. For example in Atkins "Physical Chemistry" the activation gibbs energy is defined as:

$\Delta^‡G_c=\Delta^‡G_c(0)+\alpha F\Delta\phi$

and he assumed that $\Delta\phi$ is equal to $E^{eq}$ when no current flows through the battery.

In the Book "Electrochemical Methods" of Bard and Faulkner another definition ist used:
$\Delta G_c^‡=\Delta G_{0c}^‡+\alpha F(E-E^{0'})$

$E^{0'}$ is the formal potential.

I have also found a possible explanation in the Book "Electrochemical Dictionary"
, but I do not quite understand. The following sentence is in the book:

"If a reference electrode is used the Galvani potential difference can be replaced by $(E-E^{0'})$, i.e., with the difference of the electrode potential related to a reference electrode and the formal potential"
. But Why we need the reference to the formal potential?

I would be glad if someone can explain me why the used different definitions?


texts: Antiaromaticity can be explained by Hückel method?

texts:
Pentalene is one of the most famous antiaromatic molecules. But I obtained its energy of $\pi$ system as $8\alpha+10.46\beta$ by Hückel method (with a bit complicated but straightforward calculation). This value is lower than that of localized form $8(\alpha+\beta)$. So Hückel method looks to be not able to explain antiaromaticity. Are there any misunderstandings? It seems that many of antiaromatic molecules are predicted lower than their all-ethylene counterparts.

(I don't think radicality is a key for antiaromaticity, and I'd like to know a general, quantum mechanical explanation about antiaromatic molecules if it exists.)


texts: I just did a titration experiment at school, our teacher told us multiple times to add the solution of known concentration into the solution of unknown concentration. I am wondering if we can do it the other way, if not, why?


texts: Is there any method to synthesize salicylaldehyde from salicylic acid?

texts:
I know salicyclic acid can be produced from salicaldehyde by treatment with $\ce{KMnO4}$.

Is there any way to reverse this, i.e- produce salicaldehyde from salicyclic acid?


texts: What is the liquid which has the most hydrogen atoms per volume?

texts:
What is the liquid which has the most hydrogen atoms per volume at STP ?
Is there anything better than water?
This answer does not answer this question because none of the compounds listed in it are liquids at STP, which contain more hydrogen per volume than water.


texts: I have a confusion related to the structure of $\ce{N2O3}.$ I was taught 1 is the correct one, but I believe 2 is better since it has no formal charge on it. Why is 1 correct and 2 wrong?


texts:
Is it possible to put a substance with low volatility into a highly volatile solvent, thus make the original substance also vaporize quickly?

If not, are there anyway to increase it's volatility?


texts: Calcium chloride as a drying agent for solutions

texts:
I'm aware of the reaction Calcium chloride has with water vapour and how it can therefore be used as a good and inexpensive drying agent but could that be applicable for solutions?
For example if there is an Ethanol, water mixture which you want to dehydrate could you add Calcium chloride so it forms a complex with the water molecules and then destill the solution to obtain dehydrated ethanol?


texts:
I do not understand why the 3rd canonical form of propenal has the oxygen atom donating an electon.

Oxygen in electronagetive so instead of taking electrons why is it giving?

Maybe this why it is most unstable but how is it even formed ??


texts: I am about to do a hydrogenation lab, and a, struggling with how to prepare my Raney Nickel so it does not spontaneously ignite during my lab. Most websites say to just submerge it in water– is this correct?


texts: Why is NaBr only a reducing agent? Can you tell if something is a reducing/oxidizing/both agent?

texts:
I came across a question today that read "Which of the following can only act as a reducing agent?" The answer was $\ce{NaBr}$, and I knew this from a previous question I had seen before. Is there any way to determine these properties without rote memorization?

(If it helps to use as an example, the other answer choices were $\ce{I2,\;BrCl,\;HIO4}$)


texts: etymology of phosphatidates and phosphatidic acid

texts:
A phosphatidic acid is an ester of a glycerol, two fatty acids and a phosphoric acid.
Who coined this term, and is the word's "phat" part related to english "fat"?


texts: how do carriers actually stabilize nitroglycerine i.e. Dynamite? Do they disrupt the shockwave or free radical chain?

texts: To reiterate-does it prevent a shockwave from propagating, or does it disrupt the light, heat or free radical chain necessary for Detonation?? On a related side-question, does the Blasting Cap then work by breaking up the individual "cells" or by providing free radicals to initiate the explosion?


texts:
Which two substances react spontaneously?
(A) $\ce{Ag}$ and $\ce{Cu}$
(B) $\ce{Ag+}$ and $\ce{Cu}$
(C) $\ce{Ag}$ and $\ce{Cu^2+}$
(D) $\ce{Ag+}$ and $\ce{Cu^2+}$
$\tiny{\text{Taken from 2012 Chem Olympiad}}$

The given answer is B, yet I am unclear as to why. I believe it has something to do with reduction potentials/redox or the gibbs free energy. Can someone please explain?


texts: Generating neat orbitals/surfaces from molden/wfn-files

texts:
I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's Kohn-Sham-orbitals.

But when it comes that I have to use other programs than Gaussian - such as Turbomole, ORCA or Molcas - I am confronted with molden- or wfn-files that GaussView cannot handle.

Avogadro 1.1.1 (Lib 1.1.1, OB 2.3.2, Qt 4.8.5)

I quite like Avogadro because it can produce as fancy pictures as GaussView but especially for molden files at least on my computer it seems to fail hard. As you can see the orbital is reproduced perfectly from the file but Avogadro somehow cannot manage to show all atoms.

I hope that I'm not the only one around who can't manage this to work properly.

Thanks to Geoff's comments I learned that wfn-files can be imported through the Extensions $\rightarrow$ QTAIM menu which allows AIM analysis.

gmolden 4.x or 5.x

I have absolutely no idea which version this is.

What seems to be easier to open molden-files with molden? I guess that's something to try out. But for me molden stops being an alternative since I am unable to arrange my molecules in space as much as I want. Also molden produces only those stacked-layer orbitals that are not really up to date. Molden can produce pretty good orbitals after one gets how it works. Thank you hokru!

I am admittedly not a big fan of it and didn't try to get more out of it. I was always searching for better alternatives. I'm still no big fan but as those things that I want are implemented and I just have been unable to click the right buttons molden is getting an appropriate way to visualize those orbitals.

Gabedit 2.4.8

Now Gabedit is fancy ... there are a lot of input- and output-files that are supported - luckily molden files are part of it.

At least I can create orbitals somehow acceptable for me and arrange my molecule in space as much as I want it. There is also the povray-output stuff but I was not very successful with this approach, yet.

Now what stops me from using Gabedit at a regular basis. It is that there is everytime this point-and-click-adventurish menu -> orbitals -> selection -> again orbital selection -> quality settings -> isovalue settings -> wait and look. The settings were wrong? That's bad ... do the most things again and choose better values. Is there a simple way to compare orbitals fast? Not really, because the orbital slide show is a little bit tricky, too.

Did I say something about wfn-files? I think they are not supported.

Jmol 14.2.4_2014.08.03

Jmol is another program that can open molden files and I am again unable to create nice orbital images with this program. Even rising the so called "resolution" up to a reasonable degree only produces hexagonal-shaped orbitals.

Wfn-files? Who needs this? I guess no one except me.

Multiwfn 3.3.7

Now there is this free fancy little program from china. A big 400 pages manual/tutorial-pdf comes with it. With it one can quickly have a look on orbitals with a possibility to quickly change isovalues. It lacks unfortunately my favored free arrangement in space plus there are no proper lighting settings ... and the orbitals and structures are not really that beautiful.

But(!) it can read molden files and even wfn-files. It is also able to convert them to cube files that I afterwards can read in with GaussView to create what I want. It can also create those cube files for nearly all other surfaces that it can calculate. I like it much for this simple ability.

Conclusion

Well ... as I can use Multiwfn to convert the files that GaussView cannot read in by itself, there is always this curious feeling that there has to be a simpler alternative to all this. A program that can produce nice images without all the lackings and misbehaviours.

How do you do this stuff for visualisation of molden-/wfn-files to produce nice images of your orbitals and molecular surfaces?


texts: How does heat energy interact between two bodies of different heat capacities in order to attain thermal equilibrium?

texts:
Suppose there are two objects $A$ & $B$ of same mass; the former has specific heat capacity $C_A$ and the later has $C_B$ such that $C_A\gt C_B.$ Let $A$ be at temperature $T$ while $B$ be at $T+\Delta T.$ So, in order to attain thermal equilibrium, they have to attain the same temperature $T+ \frac{\Delta T}{2}.$ That means there would be a change of $\frac{\Delta T}{2}$ in both bodies. For that, $A$ must gain heat energy $Q_A= m\;C_A\cdot \frac{\Delta T}{2}$ while $B$ has to loss heat energy $Q_B=m\;C_B\cdot \frac{\Delta T}{2}.$ Now, $Q_A-Q_B\gt 0$ since $C_A\gt C_B.$

Then in order to attain the equilibrium temperature, $A$ has to get $Q_A$ energy which it receives partly from $B$ viz. $Q_B$ but where does the additional heat energy $Q_A-Q_B$ come from? It can't come from $B$ as that would deviate it from achieving the thermal temperature; $B$ can lose only $Q_B$ in order to attain $T+\frac{\Delta T}{2}.$ But where does $A$ get the extra energy $Q_A- Q_B$ from?

I'm confused as I thought so-far that when two bodies achieve thermal equilibrium, they do it by exchanging heat energy between themselves - the cooler body receives heat energy fro the hotter body till the equilibrium is reached.

But here, it seems that $A$ in order to achieve thermal equilibrium, needs energy $Q_A$ which cannot be provided by $B$ since the energy $Q_B$ it releases  is less than $Q_A.$ Where would then the extra energy $Q_A-Q_B$ come from?

Let's say, somehow $A$ gained that energy from the surroundings; however what would happen if they were isolated from the surroundings?

I don't know where I'm mistaking. Is it true that the hotter body itself provide the required energy to the cooler body to attain thermal equilibrium?

Please help.


texts: What typically happens to H2 molecules released into atmosphere (with no spark source)?

texts:
I'm wondering what happens when $\ce{H2}$ leaks from say a transmission pipe in an unenclosed area. No immediate source of ignition, I know it rises more quickly than helium (x2 I believe) and dissipates in concentration quickly but does it react with gases in atmosphere to form methane or other compounds?

Short of ignition and burning causing more $\ce{H2}$ to dissociate what can happen, especially in upper atmosphere with more UV and so on. Methane has reaction in the upper atmosphere giving it a half life of ~7 years for example.

  The covalent radius of a neutral hydrogen atom is 0.0371 nm, smaller
  than that of any other element. Because small atoms can come very
  close to each other, they tend to form strong covalent bonds. As a
  result, the bond dissociation enthalpy for the $\ce{H-H}$ bond is relatively
  large (435 kJ/mol). $\ce{H2}$ therefore tends to be unreactive at room
  temperature. In the presence of a spark, however, a fraction of the $\ce{H2}$ molecules dissociate to form hydrogen atoms that are highly reactive. Source: chemed.chem.purdue.edu


texts: Why doesn't water play a role in reactions in aqueous reactions?

texts:
$$\ce{Ba(NO3)2(aq) + Na2CO3(aq)}$$

In the above reaction both the substances are in water, however water plays no role in the reaction. Why is it that although water is present in the reaction, it does not play a reactant role? To clarify, why isn't the above written as:

$$\ce{Ba(NO3)2(aq) + Na2CO3(aq) + H2O}$$

Why does water act as a bystander and not a reactant?


texts: Why is thionyl chloride preferred for preparing alkyl chlorides from alcohols?

texts: Why is thionyl chloride ($\ce{SOCl2}$) preferred for preparing alkyl chlorides from alcohols, as opposed to say $\ce{PCl5}$ or $\ce{PCl3}$ ?


texts: What is the IUPAC name of fullerene like molecules?

texts: I wonder what the IUPAC names of fullerene-like molecules, I mean all those hydrocarbons with 3-D structure. Do we have another name of these compounds or are they classified as aromatic?


texts:
With reference to the paper McCasland, G. E. Pinacolic Rearrangements of Epimeric Aminocyclanols. J. Am. Chem. Soc. 1951, 73 (5), 2293–2295 DOI: 10.1021/ja01149a110. (ResearchGate link). It states that

  cis-2-Aminocyclohexanol on treatment with nitrous acid undergoes a pinacol rearrangement, yielding both cyclohexanone and cyclopentylmethanal as products.

However, it goes on to state that the trans epimer would specifically yield the latter as the major product. Can someone explain this (preferably via mechanism)?


texts: What is the difference between ∆G and ∆G°?

texts:
In Brady's Molecular Nature of Matter, I read that $\Delta_\mathrm{r} G^{\circ}$ is $\Delta_\mathrm{r} G$ at $25~^\circ\mathrm{C}$. But later, it gives a value for $\Delta_\mathrm{r} G^\circ$ at another temperature.

What is the meaning of $\Delta_\mathrm{r} G^\circ$?  Specifically:

Does it only refer to $25~^\circ\mathrm{C}$?
Does the $\Delta_\mathrm{r} G^\circ = \Delta_\mathrm{r} H^\circ - T \Delta_\mathrm{r} S^\circ$ equation only refer to $T=298~\mathrm{K}$?
If at $25~^\circ\mathrm{C}$, a system that has reached equilibrium ($\Delta_\mathrm{r} G=0$), and thus

$Q=K$
$\Delta_\mathrm{r} G^\circ=0$
$\Delta_\mathrm{r} G^\circ=0=-RT\ln K$
$RT\ln K=0$
$\ln K=0$
$K=1$

But doesn't $K$ vary from reaction to reaction? It shouldn't always equal 1, should it?


texts: I've heard the term cathode ray pretty much every year in school since they introduced chemistry, and I know that it's a stream(?) of electrons. I'm just having troubles relating it to the real world. I think lightning would be a prime example, but I'm not sure; looking for confirmation.


texts: A contradiction, probably from confusion

texts:
All things in nature tells us that high entropy is easier to happen.
But then why does it takes energy to break bonds, in order to achieve high entropy.

Any thing in gaseous state has higher potential energy than it is in solid state. But that creates less stability.


texts: Internal Cannizzaro reaction of phenylglyoxal

texts:
Phenylglyoxal $(\ce{PhCOCHO})$ can undergo both internal Cannizzaro reaction and between two molecules.

The internal Cannizzaro reaction is like this:

Which reaction will be preferred? Internal Cannizzaro or Cannizzaro reaction between two molecules?


texts: Why do batteries specifically vent *hydrogen* in the event of abuse?

texts:
When a battery is subject to overcharging or overdischarging (including attempts to recharge a primary cell), it may vent hydrogen.  It seems that every type of electrochemical battery I've read about or used specifically emits hydrogen under these circumstances.

Why is hydrogen emitted in all cases, and not some other gas or chemical? What role does hydrogen play in electrochemical batteries that other chemicals can't?


texts: Major Product of Alkene in Bromine Water

texts:
At school, we are taught that in bromine water, the following equilibrium is present:
$$\ce{Br2 + H2O \rightleftharpoons BrOH + HBr}$$
Therefore, when you add an alkene to bromine water, you don't get bromination, but rather the $\ce{BrOH}$ reacts instead and you get the following reaction (lets say for ethene for example):
$$\ce{C2H4 + BrOH -> C2H5BrO}$$
However I have looked at a few organic textbooks such as Clayden and they don't mention anything about $\ce{BrOH}$ forming in bromine water and then adding across the double bond. It says that the product of the above reaction will be $\ce{C2H4Br2}$.

In reality, both reactions probably both occur to some extent (also, for the first reaction, wouldn't you expect some of the $\ce{HBr}$ to add across the double bond as well?), but which one is the most prominent, or in other words, what is the major product?


texts: Measuring or calculating the pH of 4M NaOH? I prepared the solution in Milli Q water

texts: I prepared $4\ \mathrm{M}$ solution of $\ce{NaOH}$, and the glass electrode I use cannot measure it the $\mathrm{pH}$ correctly. What are the other options do I have to exactly know the solution's $\mathrm{pH}$?


texts: Why is the 2-bond (Sn-H) coupling constant larger than the 3-bond Sn-H coupling constant for tetraethyltin?

texts:
I was looking at the NMR spectrum of tetraethyltin [$\ce{Sn(CH2CH3)4}$], and found that the $\ce{Sn-H}$ coupling constant between $\ce{Sn}$ and $\ce{CH2}$ is larger than that between $\ce{Sn}$ and $\ce{CH3}$.
$\hspace{4.1cm}$

$$\begin{array} {|r|r|}\hline {}^2J({}^{119}\ce{Sn-H}) & {}^3J({}^{119}\ce{Sn-H}) \\ \hline \pu{49.2 Hz} & \pu{68.6Hz} \\ \hline  \end{array}$$
This trend is confirmed by literature values[1].
However, I am confused as to why this is happening. The magnitude of the coupling constant is determined by the Fermi contact mechanism, so surely the coupling constant over two bonds should be larger than the coupling constant over 3 bonds? The ethyl groups also should have free rotation, so any type of angle effects should be cancelled out on average.
So why is ${}^2J$ smaller than ${}^3J$ here?

Reference:

G. Barbieri, F. Taddei, "117Sn, 119Sn–proton long-range coupling constants in the 1H nuclear magnetic resonance spectra of alkylhalogenostannanes", J. Chem. Soc., Perkin Trans. 2, 1972, 10, 1327


texts: Is it possible to create a ketone using ozonolysis, when you have an alkene with no alkyl groups?

texts: Can Butan-2-one ($\ce{CH3-CH2-CO-CH3}$) be created from Butene ($\ce{C4H8}$) using ozonolysis?


texts: Does this activation of carbonyls usually involve a SN1 or a SN2?

texts:
The process I have seen in class to activate a carbonyl function is acetalisation.

One of the steps involved is the following :

So I was wondering, is that a $\ce{S_{N}1}$ or a $\ce{S_{N}2}$ ?

(PS : drawing molecules with paint is awful, anyone knows a good free molecules drawer ?)


texts: How to decide acidic or basic nature of oxides

texts: How can we theoretically decide the acidic or basic nature of an oxide? What are the reasons/ factors which make an oxide acidic, basic, amphoteric or netural?


texts: Using TBAI (tetra-butylammonium iodide) as a catalyst. Ideas on the mechanism or the driving force?

texts:
for my etherification of an alcoxide with alkylbromide I used TBAI as a catalyst. The catalyst transfers the alkylbromide into an alkyliodide which is more reactive.

I was wondering, what is the driving force for the Iodide to bond to the carbonchain instead of the bromide? Is there a mechanism to explain that?


texts:
I'm trying to generate a testing set of different chromatograms to check peak detection (whether peak boundaries are detected correctly) and smoothing algorithms. Currently I'm figuring out which features of chromatograms I should vary for my tests. Hopefully someone could help fill my blanks. So far I'm thinking of all combinations of all bullet points:

Peak shapes: Gaussian, ...?
Sharp & wide peaks
Different levels of skewness
Baseline drifts: any types? Should it also resemble Guassian peak?
2 peaks next to each other:

Peak resolution e.g. from .2 to 1. Allows to test valleys & round peaks.
Different peak heights. Together with different levels of resolution allows to test valleys, shoulders, rider peaks.

Tailing and fronting: are there some known distributions that resemble them?

As for smoothing:

High frequency noise: uniform distribution?

So far this is what I've got for each resolution that I choose: chromatogram-shapes.pdf. Want to add baseline drift next, but haven't decided which distribution(s) it should resemble.


texts:
The Perkin reaction gives an α,β-unsaturated aromatic acid by the aldol condensation of an aromatic aldehyde and an acid anhydride, in the presence of an alkali salt of the acid. Here is an a diagram showing what the reaction does

The anion of the salt acts as a base for abstracting the β-hydrogen in the acid anhydride. Later it attacks the carbonyl carbon of an intermediate but however leaves in the same step. Since the base is not ultimately involved in the product, is there any kinetic or thermodynamic reason as to why the salt of the acid of the acid anhydride is preferred over any other base?


texts: Problem with understanding the transformation of Hessian in primitive internal coordinates to Hessian in delocalized internals

texts:
I am currently working out the theory of Hessians in different coordinate systems. Using the Wilson B matrix $\mathbf{B}=B_{ij}=\frac{\partial q_i}{\partial x_j}$, where $q_i$ denotes the $i$th primitive internal coordinate and $x_j$ is the $j$th Cartesian coordinate I can form a $n\times n$ matrix $\mathbf{G}=\mathbf{BB}^\top$. After diagonalizing $\mathbf{G}$ I obtain a matrix $\mathbf{U}$ as the set of nonredundant eigenvectors of $\mathbf{G}$ with eigenvalues $\lambda > 0$. $\mathbf{U}$ spans the nonredundant subspace of the space of primitive internals $\mathbf{q}$. I can use $\mathbf{U}$ to transform the diagonal $n\times n$ Hessian $\mathbf{H}^{\text{prim}}$ in the space of primtive internal coordinates to the space of delocalized internal coordinates using:

$\mathbf{H}^{\text{DLC}}=\mathbf{U}^\top\mathbf{H}^{\text{prim}}\mathbf{U}$.

Can somebody explain this non-linear transformation in a physical and/or mathematical sense? I don't get why I have to use $\mathbf{U}$ two times (apart from deriving the right dimensionality of $\mathbf{H}^{\text{DLC}}$).


texts: What is the difference between tempering and hardening metals and their end products?

texts: I think I've heard hardening is when you dunk red-hot metal into cold water, and tempering is when you take that hardened metal, heat it slightly, and then let it cool slowly. However what is the difference between their end products?


texts: Physical meaning of (negative) pressure in molecular dynamics simulations

texts:
Lately I have been simulating a system in an NPT-ensemble where $N$ is constant and $P$ and $T$ are coupled to a Berendsen barostat/thermostat. The system is cubic and periodic in all directions.

I am trying to fathom how the pressure affects my system, why it fluctuates so much and how negative pressure should be interpreted in systems such as the one described above.

I have some knowledge of classical MD, and it is my understanding that (in general three dimensional system), the total pressure of the system is computed with the virial equation

\begin{equation}
P=Nk_{b}TV^{-1}+\frac{1}{3}\bigg<\sum_{i=1}^{N}r_{i}\cdot F_{i}\bigg>V^{-1}\tag{1}
\end{equation}
where $N$ is the number of particles, $T$ is temperature and $k_{b}$ is the Boltzmann constant.

By looking at equation 1, it is not fully clear to me what negative pressure would imply, so I looked how the equation is derived.

The derivation starts from the Clausius virial function

\begin{equation}
W(r_{1},...,r_{n})=\sum_{i}^{N}r_{i}\cdot F_{i}^{TOT} \tag{2}
\end{equation}

where $F_{i}^{TOT}$ is the total force acting on particle $i$.

This can be averaged over the whole MD trajectory, and integrated to obtain

\begin{equation}
\big<W\big> = -\lim_{t\rightarrow 0}\frac{1}{t}\int^{t}_{0}d\tau\sum_{i=1}^{N}m_{i}|r'(\tau)|^{2} \tag{3}
\end{equation}

from which, by using equipartition of energy, one can obtain

\begin{equation}
\big<W\big>=-3Nk_{b}T \tag{4}
\end{equation}

where 3 is the dimensionality, $N$ is the number of particles, $T$ is temperature and $k_{b}$ is the Boltzmann constant.

The force exerted by the container walls can be taken in to account by 'splitting' the $F_{i}^{TOT}$ term in to internal and external part, and then
evaluate $\big<W^{EXT.}\big>$ using:

\begin{equation}
\big<W^{EXT.}\big> = 3L³(-P) = -3PV\tag{5}
\end{equation}

Where $L$ is the length of the cubic box (so that $L_{x}~=~L_{y}~=~L_{z}~=~L$)

Now, since $\big<W\big> = -3Nk_{b}T$, one can rewrite it as:

\begin{equation}
\bigg<\sum_{i=1}^{N}r_{i}\cdot F_{i}\bigg> - 3PV = -3Nk_{b}T\tag{6}
\end{equation}

and get the original virial equation (1).

My questions are:

Is this correct? Mathematics (unfortunately) is not yet my strong suit, and I know that my reasoning (even with great help from different MD-related tutorials and sites) is prone to errors.
Could you explain the negative pressures in MD simulation simply by arguing that the force exerted by the container walls is negative?
If so, can one just argue that because the force is negative, the volume of the container must be increasing?

Thank you for your time.


texts: How many π-electrons are there in 2-methylene-2H-pyran?

texts:
I thought that the structure will be aromatic and stabilised because one of the lone pairs being delocalised with the help of conjugated double bond system but still only 3 π-bonds will be present at a time and 2 lone pairs, so the answer should be 8.

But the book says the answer is 10. Please explain.


texts: How quickly does sulfur hexafluoride mix with the atmosphere?

texts:
A common science demonstration is to float a "boat" on sulfur hexafluoride.
How long would the sulfur hexafluoride stay in the container (in the experiment linked above) if the container were to be left uncovered and undisturbed at room temperature?

Also, I'm wondering what would happen if you scaled the experiment up to the size of a lake, ignoring the time it would take to fill said lake and the impossibility of obtaining that much sulfur hexafluoride.  Let's also assume that there is no wind to blow it away. Could you have a large permanent pool of sulfur hexafluoride or would it eventually dissipate and mix with the atmosphere?

Would this change if a different dense (non-reactive) gas were used, like xenon?


texts: Why do self-replicating molecules dissociate?

texts:
I am new to chemistry (have only done a GCSE) so I apologize for my lack of knowledge. But I am confused about why self-replicating molecules dissociate.

It is my understanding that a self-complimentary molecule can gather the parts needed through bonding to create another copy of itself on its recognition surface. Once the new molecule is constructed I am unsure why it would then depart from the original one during this dissociation phase. Why would all of these bonds suddenly break apart? What exact mechanisms are involved in this process?


texts: Enthalpy of formation at other temperatures

texts: I was told each compound has an enthalpy of formation of 0 at the standard temperature if it is in it's lowest energy modification. But what if we change the temperature? It would make sense to me that we would also need to have a non-zero enthalpy of formation then, like for Hydrogen at 400K. Is that the case? Many exercises I had to calculate $ \Delta H_r$ in had no enthalpies of formation given for $H_2$, even if all compounds were at 400K.


texts:
Kevlar is an aramid fiber that is used in ballistics protection vests. From the structure (structure shown from Wikipedia article), you can see why it would work to dissipate the energy from a bullet since there is an extensive network of interactions between the linear chains. The wearer ends up bruised from the force, but unpunctured and avoids serious injury from handguns bullets.

More modern ballistics protection devices use ceramic plates (along with Kevlar) to give greater stab resistance and protection from higher velocity rifle rounds. My question is, what ceramics do they use? Do they have a "flexible" ceramic that will deform to absorb the energy and not break? Or do the plates work by breaking to absorb the energy and, thus, have to be replaced after each event?


texts: How to calculate the hybridization of ethane with H=½[V+M-C+A]?

texts:
I wanted to calculate the hybridization of this molecule $\ce{CH3-CH3}$. I noticed a shortcut formula given in my class notes for calculating the hybridization. It was

$$H=\frac{1}{2}×[V+M-C+A].$$

With

$H$: Hybridization
$V$: Number of valence electrons of central atom.
$M$: Number of monovalent atoms (i.e hydrogen or halogen) around central atom.
$C$: Cationic Charge.
$A$: Anionic Charge.

When I tried to calculate the hybridisation of $\ce{CH3-CH3}$ by using above formula, where for any one of the carbon atom $V=4$, $M=3$, $C=0$, $A=0$ then $H=\frac{7}{2}$. But as we all know hybridization of every carbon in ethane is $\ce{sp^3}$, i.e. $H$ should be $4$. I know other methods of calculating $H$ like $H= \text{no. of sigma bonds} + \text{no.of lone pairs}$, which gives me the right answer, but why does the above formula give something different? And also for any molecule if using that formula gives fractional answer then what does that mean?


texts: Why is Ka of weak acid increasing while being diluted?

texts:
I am calculating $K_\mathrm{a}$ and percent dissociation of acetic acid being diluted to $\pu{1.00 \times 10^{-1} M}$, $\pu{1.00 \times 10^{-2} M}$, and $\pu{1.00 \times 10^{-4} M}$.
The $\mathrm{pH}$ goes up as the weak acid is diluted, which is to be expected.
The % dissociation is inversely related to the initial concentration of acetic acid.
However, I fail to understand why the $K_\mathrm{a}$ value increases (slightly) as the solution gets more dilute. Isn't $K_\mathrm{a}$ supposed to be a constant (acid dissociation constant) therefore stay constant as long as the temperature stays constant? Isn't according to Le Chatelier's principle, $K_\mathrm{a}$ is a function of temperature?


texts: To Debunk the 9/11 conspiracy, what is the science behind melting of the towers architecture?

texts: I am wondering what the chemical validity is of jet fuel actually melting the steel beams that held up the twin towers during the September attacks.


texts: What is the product of a reaction between an acyl chloride and a secondary alcohol?

texts:
For the following two reactants, I want to predict the major product.

I would have thought the second reactant $\ce{CH3CH(OH)CH3}$ splits into $\ce{CH3CHCH+}$ and $\ce{OH-}$ , and the $\ce{OH-}$ would replace the $\ce{Cl-}$ in the first reactant $\ce{Phenyl-COCl}$, giving B.  My main reason for thinking this would occur is that I always see e.g. water form $\ce{H+ and OH-}$.

However, the answer is C. The $\ce{CH3CH(OH)CH3}$ gives up only its  $\ce{H+}$, and the rest of it joins $\ce{Phenyl-COCl}$ to form C.

How do I predict which atom(s) will leave/join? And for this particular question, how do I know the bond in the 2nd reactant cleaves at O-H not at C-OH?


texts: can you separate inorganic ions with chromatography?

texts:
For example,  if you run a solution of sodium and potassium chloride through a colum?
I am just wondering if i can get pure potassium chloride from a mixture of sodium and potassium chloride.


texts: Simulating enzymatic change rates of Carbonic anhydrase

texts:
I'm trying to simulate effects of carbonic anhydrase on cellular pH as caused by changes in bicarbonate. I assume a bicarbonate homeostatic mechanisms which replenishes intracellular concentrations from

$$\ce{CO2 + H2O <=> H+ + HCO3- }$$

One paper I’ve found states the assumptions and rates, but doesn’t parameterize the differential (difference) relation between the substrates and products. The paper merely states that given the time scales I’m considering, it’s ok to assume $p(\ce{CO2})$ is constant, since carbon dioxide’s diffusion is fast in aqueous media. Secondly, the article states that

  The equilibrium constant of the reaction was $10^{-6.35}\ \mathrm{M}$ and the rate constant for $\ce{CO2}$ hydration was $10^6\ \mathrm{s^{-1}}$.

How do should I think of this reaction, and more importantly how do I simulate it?


texts:
Consider the following reactions:
$$\begin{align}\ce{C + O2&->CO2}\tag{1}\\[1em]
\ce{2C + O2&->2CO}\tag{2}\\[1em]
\ce{2CO + O2&->2CO2}\tag{3}\\[1.5em]
[(2)+(3)]/2 &= (1)\end{align}$$

Since $G$ is a state function, why aren't the straight lines corresponding to these reactions in the Ellingham diagram concurrent?
I have checked the graph from other sites but found none to be concurrent.
Is there some kind of error in data or extrapolation of the graphs or any other specific reason for this?


texts:
How many moles of water are released on gentle heating of 1 mole of $\ce{Al2Cl6•12H2O}$?

Since the heating is gentle, the water molecules that are not present in inner orbital complex of compound and not directly attached to aluminium will be evolved, but the structure of $\ce{Al2Cl6}$ is a bridged tetrahedron. Then again, water is a better ligand than chlorine, so overall I cannot decide what the structure of the compound should be.


texts:
What are the products P and Q?

This was a question in my test series, but I don't have any experience with bridge head compound regarding the cis and trans transformation. I need help understanding this process.


texts: How to do complexometry titration of calcium oxalate?

texts:
My titration of  calcium oxalate with NaEDTA doesn't work. I need to calculate the ion calcium within my sample. My essay is to test anticalculi activity.

Why do I say I have problem? Because the colour keeps turning back to its initial colour (pink) more than twelve times. It's never ending and the titration end point is so premature.

In my preparation, I added HCl 0.5 M to my calcium oxalate so it dissolves. Calcium oxalate has very low solubility.

First, I used EBT indicator and ammonia buffer. When i add the ammonia the solution became foggy and there's a precipitation within the sample.
So I used substitution titration with Mg-EDTA (EBT indicator) = Still happens
Then change the indicator to hydroxynaftol blue and calcon = Still happens (I don't use buffer with this indicator, only NaOH, but when I add NaOH it's became foggy again)


texts:
Normally, chlorine doesn't form hydrogen bonds because despite its electronegativity, the size of the atom is such that its electron density is too low to form hydrogen bonds.

However, chlorine forms hydrogen bonds in chloral hydrate (2,2,2-trichloroethane-1,1-diol). What could be the possible reason for this?


texts:
I have chemical analyses of groundwater samples (I got the analyses from a previous study) and I want to work with it in my master thesis.

In these analyses, phosphate concentration is mentioned in micrograms/liter  and it seems phosphate was analysed by means of IC-ICP-MS.

My question is: When measuring phosphate concentration (orthophosphate) either using IC-ICP-MS or any other method as HACH Method 8114, do we measure the three species $\ce{PO4^{-3},HPO4^{-2}}$, and $\ce{H2PO4^{-1}}$ together and report the result as phosphate or we measure just $\ce{PO4^{-3}}$?


texts: Why does sodium sulfate initially harden instead of dissolving?

texts:
I was recently drying a product by passing it through a bed of sodium sulfate in a fritted glass Buchner funnel. Once I had finished up working my reaction, in an ill-advised attempt to clean up, I decided to wash the salt out with water before proceeding with acetone. Upon adding water, the salt starting foaming, and became hard as a rock and adhered to the fritted glass. I decided to leave it sitting in the water, and after a while it did finally turn gel-like and was able to be washed out.

My question is, why in the presence of so much water, why did the salt remain as the hydrated salt instead of dissolving, and why did it take so long to dissolve after it formed the large crystal? Also any idea what the bubbling was?


texts: What's the difference between ΔG° and ΔG°'?

texts:
In biochemistry contexts, one often sees $\Delta G^{\circ\prime}$ ("delta G naught prime"), rather than the normal standard free energy change $\Delta G^{\circ}$ ("delta G naught").

What's the difference between the two quantities?
Is there a formal definition of the two terms?


texts: How can the concentration of a solid be constant during a reaction?

texts:
The molar concentration is given by the ratio between density and molar mass. I understand the proof.
But how does this remain true during a reaction?

For example consider the reaction,

$$\ce{4Al(s) + 3O2 (g) -> 2Al2O3(s)}$$

If the amount of Al and O2 moles are equal, according to stoichiometry Al ought to be the reactant to end first. But, being a solid, Al’s concentration must be constant.
How can this be? What is wrong in my reasoning?

**Please note that I mistakenly assumed that the amount of Al and O2 are equal, without stating it, leading to the confusion that Al ends first at all times, I have edited the question appropriately


texts: Chemical Equilibrium - Le Chatelier's principle

texts:
If the concentration of reactants is increased such that one is a limiting agent, wouldn't the concentration of products also increase (because excess of a reactant will get carried to the other(product) side  of the equation considering that the limiting agent is in aqueous medium?

e.g.
  (Consider 1 mole of each reactant)
   $$\ce{H2O + NH3 <=> NH4+ + OH-}$$

Now, let us take another scenario in which  there are two moles of NH3 and 1 mole of H20. Then concentration of one reactant has increased (from the previous scenario). Wouldn't the concentration of the products also increase because one mole of NH3 does not react and gets carried to the products' side of the equation?

I am confused with how  Le Chatelier's principle is applied in the 2nd scenario. Why does the equilibrium shift to the right if the concentration of the reactants and products increase (if my assumption is right)

If my assumption is wrong (concentration of product increases to balance excess reactant), my concern is such an equation is not balanced. I am unable to reconcile how the Le Chatelier's principle is applied in the 2nd scenario.

(Based on the answers below, I would like to restate my question)
I understand that

$$\ce{2H2O <=> H3O+ + OH-}$$

Now if I add HCl, I have

$$\ce{H2O + HCl <=> H3O+ + Cl-}$$

The way I interpret this is : the concentration of reactants  is 1 + 1 = 2 moles and the concentration of products is also  1 + 1 = 2 moles. Since the concentration on both sides of the equation is same, why do we say equilibrium shifts left. What am I missing?


texts: What makes the odor of flatulence fade away?

texts:
If an individual expelled their intestinal gas in an enclosed space, that smell would seemingly fade away. Why is this so? I would think of 3 possible explanations:

The gases dilute in the air. If that space were tightly enclosed and sufficiently small, that smell would persist.
The odorous gases decompose upon contact with air or by exposure to light.
The odor does not fade away but the sense of smell adapts to the constant concentration. If another individual sampled that specimen later, they would experience the original intensity.


texts: Synthesize coumarin from 4-allyl-2-methoxyphenol (eugenol)

texts:
I'm trying to figure out how to get the following reaction: (coumarin from eugenol)

My immediate thoughts are

$\ce{OH}$ and $\ce{OCH3}$are bad leaving groups.
Could I just add $\ce{HI}$ to the $\ce{C10H12O2}$ to convert the methoxy ($\ce{OCH3}$) group to an $\ce{OH}$group? Then, I could add $\ce{Zn}$ to remove the $\ce{OH}$groups?
Or, is there a way to make the methoxy ($\ce{OCH3}$) group into methanol, which would be a better leaving group?
Once the methoxy and hydroxy groups are removed, I'm left with the benzene ring and the attached butene. I would need to add the $\ce{CO2}$ to form the second benzene ring, but I'm not sure how this would be done.
I might be thinking about this all the wrong way. I was thinking that I need to remove the methoxy and hydroxy groups since they're on a benzene ring, and my product's benzene ring doesn't have these groups. Maybe I don't need to get rid of the methoxy and hydroxy groups at all. Maybe I just need to shift the bonds around?


texts: Why does H₂Se have a bigger Ka2 than H₂Te

texts: Why does $\ce{H2Se}$ have a bigger $K_\text{a2}$ than both $\ce{H2S}$ and $\ce{H2Te}$?


texts: Electronegativity of zinc vs copper in galvanic cell

texts:
I am reading up on how galvanic cell works and I realised that the flow of electrons is from Zn to Cu. But Zn is more electronegative compared to Cu according to periodic table trends

I read it somewhere that when comparing transition metals, it may be different, but it was not  further elaborated. Can someone explain this to me how Cu is more electronegative than Zn?


texts: How to calculate current density in an Electrolysis Process?

texts:
I have an anode & cathode, both of $100 \times \pu{100\\mm}$ size. The process requires $\pu{450\\A/m2}$ current density. How do I reverse calculate this? Do I use the total surface area of both Cathode and Anode or just Anode?
Please help.

Thanks


texts: How much ozone is produced by ionization of air and how turn ozone into oxygen

texts:
I want to make a plasma speaker. I'm worried about the amount of ozone being produced by the ionization of the air and it possibly not being a safe amount. Even if it doesn't produce a dangerous amount, I don't like the smell of ozone. I'd like this all to be continuous. I am very unfamiliar with the chemistry here but I have read that UV light, around 250nm, can cause $\ce{O_3 \to O_2 + O}$ and also $\ce{O_2 \to 2O}$

But also without any help it seems that $\ce{2O \to O_2}$ and also $\ce{O + O_2 \to O_3}$. So it seems that if I shined UV light of the right frequency on the spark I'd make a lot of $\ce{O}$ and perhaps that would cause more $\ce{O_2}$ than $\ce{O_3}$ but I'm not really sure.

I was also thinking that it might oxidize some sort of metal filter really well and I could just keep replacing those but I wasn't sure. I could also heat the filter slightly to speed up the reaction if necessary.

Even if the UV light idea doesn't work out very well I still want a way to do this. Is the amount of ozone produced by a continuous electrical current though air harmful? Is there a way of getting rid of the ozone to make some odorless non-harmful chemical?


texts: How does NMO reform Osmium tetroxide after reaction with an alkene?

texts:
After Osmium tetroxide adds to a double bond and is then hydrolysed the following species is formed:

Because Osmium tetroxide is toxic, NMO is used to transform the above back to Osmium tetroxide. NMO is:

What is the mechanism for this?


texts: Why are bicarbonates of alkaline earth metals stable only in aqueous solution?

texts:
Numerous internet sources (1, 2, 3, etc.) state this fact, including a  Wiley publication "Alkaline Earth Metals: Inorganic Chemistry - William S. Rees Jr" (DOI: 10.1002/0470862106.ia005) on page 9:

  The bicarbonates of group 2 elements are stable only in solution.

Why is it so? Why do solid alkaline earth metal bicarbonates decompose/are unstable?

In other words, (thanks Zhe!), group 1 bicarbonates are stable. Group 2 bicarbonates are not. They decompose into the group 2 carbonate, water, and carbon dioxide. What is the principle difference between group 1 and group 2 bicarbonates that leads to a thermodynamic preference for the carbonate in one case and the bicarbonate in the other? Also, why is the preference only shown in the solid state, but not in the aqueous state?

I am not asking about thermal stability. I am just asking that what's the problem if we take these bicarbonates in solid state at room temperature and leave them there. Why would they decompose?


texts: Howcome orbitals become 'core-like' when electrons are removed?

texts:
It seems to me that f-orbitals for lanthanide metals are treated as 'core-like' when a certain number of electrons have been removed.

Or, as Radiochemistry puts it,

  The 4f binding energy is so great that the remaining 4f-electrons are regarded as "core-like". [Italic and emphasis added]

How is this justified exactly?

Effort

I am aware that

each electron will be harder to remove as Culonic attraction increases with positive ionic charge,

and probably

lathanide contraction is a part of the explanation.

You have to check out some of these other threads:

Why don't we see these lanthanide species?
What is meant by 'electrons of like/unlike rotation'?
What's up with this quarter / three-quarter rule?

Original topic: Predominance of III oxidation state for lanthanides


texts: How to explain two NMR spectra of the (allegedly) same compound with slightly different shifts?

texts:
For my synthetic lab work I synthesised a Horner-Wadsworth-Emmons phosphonate; for the sake of the question let’s assume it to be the one presented in the image below.

When first synthesising it, I of course recorded NMR data. I performed a Horner-Wadsworth-Emmons reaction using a tiny bit of the phosphonate and kept the rest in the fridge.

One month later I retried the HWE and got very bad yields, so I decided to record another NMR spectra. The two spectra themselves look identical and the signals (those that aren’t multiplets) also show the same coupling constants. However, when referencing the spectrum to the chloroform signal ($7.26~\mathrm{ppm}$), all signals are shifted by the constant value of $\approx 0.07~\mathrm{ppm}$.

I decided to check the old literature spectrum from 1986, but it was unhelpful: It only reported multiplets such that both of my spectra comfortably fall well within the multiplets’ limits.

Considering that the two spectra look identical and that the difference between two signals corresponding to the same hydrogens is identical as are the coupling constants, I want to assume that both spectra show an identical compound. However, the $0.07~\mathrm{ppm}$ shift for everything save chloroform still irritates me.

Both spectra were recorded at $500~\mathrm{MHz}$. The parameters of the earlier one state a temperature of $25~\mathrm{^\circ C}$, the later one was apparantly measured at $25.1~\mathrm{^\circ C}$. However, I don’t think that that could explain the shift.

What could explain this shift difference?

(My first thoughts were some changes to the compound that only affect the phosphorus atom, but aside from deoxygenation being chemically unlikely shouldn’t it also cause random chemical shift differences including slightly different coupling constants? In fact, shouldn’t any chemical modification cause the shifts to change in a seemingly random fashion depending on the proximity of hydrogen in question and entity modified?)

After checking because I was asked in the comments: The later spectrum (the one that has higher shift values) has broadened peaks. That includes the chloroform peak.


texts: Hosoya Z Index and Correlation with Boiling Point

texts:
I have recently read about the Z topological index found by Hosoya. The papers/sources The Z index is the sum of the coefficients of the matching polynomials (no. of ways to choose an independent edge from the set of edges in the graph - if we let each carbon atom be a vertex and each bond between a pair of carbon atoms is an edge.). The paper states that in particular for alkanes or saturated hydrocarbons, there is a correlation found between the Z index (which measures the extent of branching - in what way??) and the boiling point (bp) of these alkanes.

I know that the bp of alkanes increases with its size (due to strong force of attractions). However, I am confused about how the Z index measures the extent of branching, and any underlying reasons that the Z index will correlate with the bp and other physiochemical properties.

The papers I have read so far fail to enlighten me on these questions above. Please help.
Thank you.

  Some ideas I have so far:
  Since Z index measures branching (or at least correlates to branching since more compacted graph will have a smaller sum of matching coefficient?), and branching correlates to the bp of alkanes (due to less surface area sometimes if you have more branching), perhaps thats why the Z index correlates to bp...

Refer to Why do branched chain compounds have lower boiling points than the corresponding straight chain isomers?


texts: Calculate the percent composition of a sodium carbonate/sodium bicarbonate mixture

texts:
In a lab, we titrated a solid mixture of sodium carbonate and sodium bicarbonate with $\pu{0.1 M}\ \ce{ HCl}$. We are asked to calculate the percent composition by mass of sodium carbonate and sodium bicarbonate.
Data:

Unknown mass used: $\pu{0.107 g}$
Volume of $\ce{HCl}$ used: $\pu{16.6 mL}$

Here was my approach:
1) I determined the moles of carbonate by doing the following:
$$(\pu{16.6 mL} \ \ce{HCl}) \times \frac{\pu{1L}}{\pu{1000 mL}} \times  \frac{\pu{0.1 mol}\ \ce{HCl}}{\pu{1 L}\ \ce{HCl}} \times  \frac{\pu{1 mol}\ \text{carbonate}}{\pu{1 mol}\ \ce{HCl}} = \pu{0.00166 mol}\ \text{of carbonate}$$
2) I calculated the molar mass of sodium carbonate and sodium bicarbonate:
MM of sodium carbonate $= \pu{105.99 g/mol}$
MM of sodium bicarbonate $= \pu{84.01 g/mol}$
3) This is the part I'm unsure about. I said that
$$\frac{x}{\pu{105.99 g/mol}} + \frac{(0.107 - x)}{\pu{84.01 g/mol}} = \pu{0.00166 mol}\ \text{of carbonate}$$
Doing this math, I determined that the compound was 52% sodium carbonate and 48% sodium bicarbonate but I'm unsure if this is correct.
The instructor seemed to want us to solve it in terms of H+ using the following ratios:

$\pu{1 mol}$ of carbonate: $\pu{2 mol}$ of $\ce{H+}$

$\pu{1 mol}$ of bicarbonate: $\pu{1 mol}$ of $\ce{H+}$

but I'm not sure how you would use this information to answer the question. Any help would be greatly appreciated!


texts: How to determine the volume of water necessary to produce a solution with 4.9 g/l sulfuric acid?

texts:
The molar mass of sulfuric acid is $M(\ce{H2SO4}) = \pu{98.1 g/mol}$.
  We have $\pu{100 mL}$ of a $0.1$ molar solution of sulfuric acid. What volume $V$ in  $\mathrm{mL}$ of water, $\ce{H2O}$, do we have to add in order to obtain a solution that has $\pu{4.9 g/L}$ sulfuric acid?

I've done the following:

\begin{align}
M(\ce{H2SO4}) &= \pu{98.1 g/mol}\\
M(\ce{H2O})   &= \pu{18.0 g/mol}\\
\text{mass concentration of }  H_2SO_4 &= \pu{98.1 g/L}\\
c(\ce{H2SO4}) &= \pu{1 mol/L}\\
c_{\mathrm{contr}} \times V_{\mathrm{contr}} &=
c_{\mathrm{dil}}\times V_{\mathrm{dil}}\\
\Longrightarrow V_{\mathrm{dil}} &=
\frac{c_{\mathrm{conctr}}\times V_{\mathrm{conctr}}}{c_{\mathrm{dil}}}
\end{align}

The molarity of the diluted water I can't calculate with elementary formulas. So it leaves me with 2 unknowns.

I've tried using so many formulas to no avail.

What formula am I not thinking of? Or what variable am I missing?


texts: Experimental bond lengths and binding energies of diatomic molecules

texts:
Is it possible to find the experimental values of the bond length and the binding energy of the diatomic molecules $\text H_2$, $\text{Be}_2$, and $\text{Ar}_2$ in one source?

I found a lot of chemistry handbooks and databases, but non of the provided both, the bond length and the binding energy for all three molecules.

I guess the experienced chemists know some good sources?


texts: Non-mathematical explanation for why the 3d orbital generally has higher energy than the 3p orbital

texts: Why does the angular momentum of orbitals(l) affect the orbital's energy? Please provide a qualitative answer.


texts: Why is the cyclic voltammetry of my ferrocene compound not showing a standard shape?

texts:
I am trying to set-up a new cyclic voltammetry measurement station in my lab but the results are very poor. I am using the following parameters:

working electrode: platinum wire, 0.25mm diameter
counter electrode: platinum wire, 0.25mm diameter
reference electrode: none
solvent: acetonitrile
electrolyte: ferrocenecarboxaldehyde
support electrolyte: tetrabutylammonium hexafluorophosphate
scan rate: ~600mV/s

Platinum wires each have a submerged length of about 2mm to 5mm and are separated by about 2cm. I was previously using tetrabutylammonium iodide, but that is probably not a good support because the iodide ions will become iodine and forming a blocking layer on my electrode?

I also tried using graphite rods as the electrodes but obtained similar poor-looking CV shapes.

What should I change to obtain the standard CV shape of an outer-sphere redox species?


texts: The equilibrium constant of a reaction only involving pure solid or liquid

texts:
How to calculate the equilibrium constant of a reaction only involving pure solid or liquid.
For example reaction
$$\ce{S(s) + Hg(l) -> HgS(s)}$$
or
$$\ce{S(s) + Mg(s) -> MgS(s)}$$


texts: why does a pot of boiling water quiet down after it reaches boiling point but is still roiling?

texts: I've noticed that when water boils, it makes a lot of noise. After the water reaches boiling point, even though the water is still ""rolling", the water quiets down. What is all the noise about and why does it go away?


texts: What nomenclature do names like fumarate and malate derive from?

texts:
When reviewing the citric acid cycle, I find names like glutarate and succinate to be helpful in thinking about the structure of the molecules because I was taught about the sequential dicarboxylic acid naming scheme: oxalic (2 carbon), malonic (3C), succinic (4C), glutaric (5C) etc.
But I often struggle with fumarate and malate because I have not learned the numbering or nomenclature system that these names are derived from. Can someone point me in the right direction so that I can learn the background behind these names?
Knowing that will be helpful to my recall of the molecular structure. Then I can stop memorizing and start understanding.


texts: Risks of burning melamine formaldehyde adhesives

texts:
Background- I make biochar for gardening, and small scale carbon capture and storage. Most of my feedstock is clean, unpainted, untreated, end of life timber, but there is a small proportion of engineered particle board- MDF, chipboard, plywood and composite blocks containing, I believe, melamine formaldehyde binding resin. No halogens from PVC, no metals from CCA treated timber or old lead paint.  I want to establish what pollutants may be produced- I would in a worst case scenario be burning less than 50kg of the suspect material per hour.

All the charring happens in TLUDs- Top Lit Up Draft burners where all the pyrolysis gases are ducted through the hottest zone of the burn- round about 800-900C. I'm currently working to improve residence times and temperature gradients- carbon particulates are a known issue.

Does any of the above sound like it'll produce anything nasty from the carbon, hydrogen, oxygen and nitrogen going into the mix? PAHs? Anything else above and beyond nitrogen oxides and carbon particulates from clean wood?

To put it another way, do I err in favour of creating a pollution factory, or in favour of condemning a potential feedstock to be a disposal nuisance?

Thanks for any replies- I'd like to lay this to rest.


texts: Anomalous electronic configuration of platinum

texts:
Why is the electronic configuration of platinum
$$\mathrm{[Xe] 4f^{14} 5d^9 6s^1}$$

and not $\mathrm{[Xe] 4f^{14} 5d^{10} 6s^0}$ or
$\mathrm{[Xe] 4f^{14} 5d^8 6s^2}$?


texts: Which effect does adding hydrogen chloride have when determining the concentration of sodium hypochlorite in bleach via titration have?

texts:
Many of you might be familiar with this and I do understand this completely, however I do have a question.

If you are familiar with this, then this is the equation and this is the question for it.

$$\ce{ClO^{-} ~(aq) + 2I^{-} ~(aq) + H2O ~(l) -> Cl- ~(aq) + I2 ~(aq) + 2 {}^{-}OH ~ (aq)}$$

So for the equation above I understand everything except that in the titration process my instructions say to add $\ce{HCl}$ into the solution, I do not understand how adding $\ce{HCl}$ will have any impact.

I will provide an accurate reference later.


texts: Does presence of alkyl groups on alpha carbon increase yield of alkane in Kolbe's Decarboxylation?

texts:
We know that, during the synthesis of alkanes by Kolbe's Decarboxylation reaction,
the reaction proceeds via a free radical $\ce{R.}$ at the anode.

So, an alkyl group, say methyl, when substituted at the alpha carbon will increase the yield of alkane since the radical is stabilized by hyperconjugation. But my book states that the presence of alkyl group on alpha carbon decreases the yield of alkane. Why is it so?


texts: I want to remove Alkalinity from tap water by using an acid. The starting point is about 370pm alkalinity, and I am wondering to reduce this to about 50ppm, could I use a weak acid like citric acid? Or do I need to use a strong acid, such as HCl?


texts: I read from a source that 2-iodopropane undergoes iodoform reaction. What reaction mechanism is undergone here, and why does this happen?


texts:
I am trying to isolate certain pieces of information within a dsn6 file. Specifically, I want to find the electron density around two atoms within a protein. I want to then run a python code to determine if there is positive electron density between the two of them. In order to do so, I believe I need to convert the dsn6 file, which is stored in a very compressed format, into a format I can understand.

I have searched around found ways to view dsn6 files (such as through PyMOL or COOT in CCP4) as a model. However, I do not know a way to view this decompressed file as text. I have tried, but have been completely unsuccessful in trying to figure out how these programs decompress/read the files.

This is what a piece of a dsn6 file currently looks like:

˘>˝‰‡>™†≠>I14>)B=*À¢<™ÅK=i§=‰≤Ñ=ê8ºO∑ææÑ¸ΩﬁZ
Ω2…=wÇ=œjÖ=ÿm=◊6=â(:ÿ◊ôΩl≥æ=sËΩ,vzºËm
>dg>ÄàG>>hº&>è,>SªÂ=

I hope that the decompressed dsn6 file will look similar to what a pdb file looks like. For example,

ATOM    228  OG1 THR A  58       7.843  45.672  59.760  1.00 15.56   O
ATOM    229  CG2 THR A  58       6.672  44.132  61.223  1.00 14.90   C
ATOM    230  N   PRO A  59       9.292  42.373  62.754  1.00 13.16   N
ATOM    231  CA  PRO A  59       9.409  40.982  63.160  1.00 13.07   C

I asked this question in Stack Overflow, but thought that it might be better suited here. Thank you for the help!


texts: Is there a geometrically intuitive explanation of the equivalence of the numbers of irreducible representations and symmetry classes?

texts:
In group theory, as used in chemistry, we’re familiar with the idea that the number of irreducible representations of a symmetry group equals the number of classes of symmetry operations, e.g. three in the case of the $C_\mathrm{3v}$ group describing the molecular structure of the ammonia molecule.
There are proofs of this fact, ranging from the properties of the Great  Orthogonality Theorem and discussions of the dimensionality of the vector space of characters e.g. as given in R. Mirman’s Group Theory: An Intuitive Approach, through to more mathematical proofs relying on the application of Brauer's permutation lemma to Galois automorphism on conjugacy classes, as shown in
https://groupprops.subwiki.org/wiki/Number_of_irreducible_representations_equals_number_of_conjugacy_classes.
But given the physical nature of molecular structure and the geometric properties of the molecular orbitals corresponding to the symmetry group’s irreps, is there no geometrically intuitive explanation of exactly why the number of irreps and classes are the same?


texts:
Here is the issue of blood gases partial pressure.
On medical reports is common to see partial pressure of gas on blood, usually oxygen, but there is no gas in equilibrium with blood, so it is confusing. What they mean with partial pressure of a gas on blood is, according to this answer:

the partial pressure which would prevail in a gas phase in equilibrium
with the liquid [blood] at the same temperature.

I suppose they use a partially filled vessel with blood and a manometer or something like that, but I would like to know the way they measure it.
Question
How do they measure $p(\mathrm{O}_2)$?


texts:
Considering pyridazine and pyrazine molecules, I am asked to say if I can distinguish one from the other in a sample.

I supposed that is possible because pyrazine belongs to D2h and so it has the inversion center. Thus, in IR spectroscopy I can appreciate the antisymmetric stretching while in Raman I can identify the total-symmetric ones.

Then I am asked to say if this spectroscopic technique allows me to predict quantitive results. and how?

This question floored me because I have never done spectroscopic experience!


texts: Assigning E–Z configuration for alkenes with cyclic substituent groups

texts:
I was taught that according to CIP rules, we must check the priority order for the substituents. But how can we do the same for molecules with cyclic groups as substituents?
How do we compare the substituents for the following molecule?

How to determine E–Z configuration for such molecules?


texts: Hi I am new to laser pump-probe spectroscopy and want to understand the concepts better. At the moment I am struggling to understand the following: When one takes absorption measurements with lasers in a pump-probe manner, the spectra that are collected need to be normalized. What does the Normalization mean and how does one do it? Also, why are relative changes important as opposed to absolute changes (in absorption) because I think they should give the same information?


texts: When you have brackets such as $\ce{Zn(NO3)2}$, if there is a coefficient around the formula such as $\ce{2Zn(NO3)2}$, how would you read this? Would there be 2 zinc atoms, 4 nitrogen and 12 oxygen atoms if I am multiplying that out correctly?


texts: Color fading in contact with air over period of time

texts:
I am a product designer and I am wondering if there is a pigment or ink that is able to fade over time by staying in contact with air? I am designing a label that  should change color after approximately 6 months, in order to detect that the product is expired. What type of support is needed? I found these type of examples:

http://pubs.acs.org/subscribe/archive/ci/31/i02/html/02haas.html

Thank you!


texts:
I'm trying to compute bond orders in a molecule, let's consider S2 as an example. I'm not entirely sure what's the right way to do that, but I assume NBO (Natural Bond Orbital) should give me what I need. For calculations I'm using MOLPRO. I've tried to launch it with UCCSD(T)-F12 as follows:

 symmetry, nosym
 geometry = {
 S1
 S2, S1, bond
 }
 bond = 3.60529338 BOHR
 basis = cc-pVTZ-F12
 set, spin = 0

 hf
 uccsd(t)-f12a, scale_trip = 1
 nbo, keep_wbi = 1

It seemed to work and gave me the following output:

  - - - - - - - - - - - - - - - - - - - - - - - -
        NBO  OCCUPATION       LABEL     CENTERS
  - - - - - - - - - - - - - - - - - - - - - - - -
         1    2.000000         CR       1
         2    1.999827         CR       1
         3    1.999918         CR       1
         4    1.999989         CR       1
         5    1.999848         CR       1
         6    2.000000         CR       2
         7    1.999827         CR       2
         8    1.999918         CR       2
         9    1.999989         CR       2
        10    1.999848         CR       2
        11    1.999151         LP       1
        12    1.989845         LP       1
        13    1.999151         LP       2
        14    1.989845         LP       2
        15    2.000000         BD       1    2
        16    2.000000         BD       1    2

CR seems to stand for core, LP - lone pair, BD - bonding. From this I can conclude the bond order is 2, since we have two bonding orbitals with 2 electrons on each. However, the spin state was set to 0 here, whereas it's supposed to be 2 (2 unpaired electrons). When I tried to set spin to 2, the same calculation failed:

No suitable structure found!
 ? Error
 ? The problem occurs in nbo_transform

Can anyone suggest what is wrong here? Are there any other ways to compute bond order?

The full outputs: spin=0; spin=2


texts:
Since Neil Bartlett's 1962 discovery that xenon was capable of forming chemical compounds, a large number of xenon compounds have been discovered and described. Almost all known xenon compounds contain the electronegative atoms fluorine or oxygen. The oxidation state of xenon in its compounds is generally +2, +4, +6, or +8.

Xenon is known to form three fluorides: $\ce{XeF_{$n$}} \;(n = 2, 4, 6)$ where the oxidation states of xenon are +2, +4, and +6. $\ce{XeF8}$ is not known to exist even though the oxidation state would be +8. Why is this so? Could it possibly be due to the fact that 8 fluorine atoms can't fit around a xenon atom?

Xenon is known to form three oxides: $\ce{XeO_{$n$}} \;(n = 2, 3, 4)$ where the oxidation states of xenon is +4, +6, and +8. $\ce{XeO2}$ was not known until 2011. Why did it take so long to be discovered? Moreover, the lowest oxide of xenon $\ce{XeO}$ is not known though the oxidation state of xenon would be +2. Why?


texts:
When a hydrate decomposes it loses water molecules in steps.
Does each step have a chemical equation?

If so is the following equations for decomposition of cupric sulfate hydrate correct?
$$
\begin{align}
\ce{CuSO4 * 5 H2O &→ CuSO4 * 4 H2O + H2O}\\
\ce{CuSO4 * 4 H2O &→ CuSO4 * 3 H2O + H2O}\\
\ce{CuSO4 * 3 H2O &→ CuSO4 * 2 H2O + H2O}\\
\ce{CuSO4 * 2 H2O &→ CuSO4 * H2O + H2O}\\
\ce{CuSO4 * H2O &→ CuSO4 + H2O}
\end{align}
$$


texts: Proton removal during benzyne formation in substituted haloarenes

texts:
I encountered the following question in an organic chemistry paper -

The reaction follows benzyne mechanism. My answer was B.
However, the answer given in the test solutions was D. The mechanism given was as follows:

My question: The tert-butoxide being a bulky base is more likely to abstract the least hindered hydrogen, which is clearly present at the para-position to $\ce{-OCH3}$. Then the benzyne triple bond would form between the meta and para carbons, following which product (B) would be obtained. However, the given mechanism involves abstraction of the hydrogen from the ortho-position, which has two large groups on either side, and hence shouldn't occur.
Is my reasoning right? Are there any other factors affecting the reaction that decides which hydrogen will be removed?
I am also open to the possibility of the test solution's mechanism being wrong.


texts: In the textbook,it is said that bomb calorimeter measures the constant volume heat ,while the cup calorimeter measure Constant pressure Heat.I was wondering, why cup calorimeter is considered constant pressure,even though it also does not allow a gas to expand (it has a fixed volume).So if not then that means cup calorimeter allows some air to get in so that pressure is constant ?(I.e the system is not closed )?


texts: Calculating internal energy change of a reaction

texts:
We are asked to find the relation between $\Delta H$ and $\Delta U$, and also, the sign of the internal energy change of reaction:
$$\ce{CO(g) +\dfrac{1}{2}O2(g)   ->  CO2(g)}$$
This was part (3) of a question, and this one explicitly mentioned: "reaction happens in an isolated container". The other parts had "closed container".
Approach: For ideal gases, we know that $U=nCvT$. So, we have:
$U_{rectants}:(1*5R/2*T) +(1/2*5R/2*T)=\dfrac{15}{4}RT$
$U_{products}:(1*3R*T)=3RT$.
Thus $\Delta U=U_{products}-U_{rectants}=\dfrac{3}{4}RT>0.$
However, the answer given is $\Delta U$ is $0$.
And the answer also claims that $\Delta H$<$\Delta U$ , which is expected from the relationship $\Delta H$=$\Delta U$+$RT\Delta n$ is not true.
Now I do not know exactly how do we account for "isolated system" in the formula for internal energy.
What exactly does isolated system refer to in this context? And how exactly is it affecting the internal energy?
A possible approach might have to do with the FLOT. I (guess) that isolated system means that there is no heat exchange with the surroundings, so the expression reduces to $dU+P_{ext}dV=0$. Does "isolated system" somehow also imply that $P_{ext}dV=0$?


texts: Difference in major product of sulphonation of phenols

texts:
When phenol is sulphonated by fuming sulfuric acid at a lower temperature, the ortho product is the major whereas at higher temperature the para product is formed as the major.

Why does this happen, because looking at the reaction mechanism, it appears to me that para should always be the major.

Is it the kinetic control vs thermodynamic control effect?? If yes, then why is para thermodynamically more stable and ortho kinetically faster??


texts: Outermost electronic configuration of f block elements

texts:
Why is it $(n-2)\mathrm{f}^{1-14}(n-1)\mathrm{d}^{0-1}n\mathrm{s}^2$.

The only exception I thought to this formula was Thorium $\ce{5f^{0} 6d^{2} 7s^{2}}$.

So I feel it should be $(n-2)\mathrm{f}^{1-14}(n-1)\mathrm{d}^{0-2}n\mathrm{s}^2$.


texts: What is the proper way to prepare a solution from hydrate?

texts:
I am following a protocol that requires me to prepare $10~ \mathrm{mL}$ $\mathrm{1~M}~ \ce{Ca(NO3)2}$. However, there is only $\ce{Ca(NO3)2*4H2O}$ in the lab.

Originally I thought that all I have to do to figure how much $\ce{Ca(NO3)2}$ to weigh is

and then just add  $10~ \mathrm{mL}$  water. However, that might dilute the solution and make the concentration less than $\mathrm{1~M}$ as there is already water in the hydrate.

So then I found a protocol and made new calculations as followed:

How can I verify that I got $\mathrm{1~M}$ $\ce{Ca(NO3)2}$ as opposed to $\mathrm{1~M}$ $\ce{Ca(NO3)2*4H2O}$?

Which protocol is correct?


texts: Computing optimized 3D structures in python that take solvent into account

texts:
I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:
 (1) Adding hydrogens: AllChem.AddHs
 (2) Compute 3D coordinates: AllChem.EmbedMolecule
 (3) Clean-up with force field: AllChem.MMFFOptimizeMolecule

--But I would like to take into account different solvents so that the 3D structure more closely resembles in vitro activity. For example, an in vitro screen where small molecules are diluted in (1) DMSO or (2) ethanol or (3) water.
--I know that Psi4 can estimate properties in different solvents. But I have been unable to find a python library that generates an actual 3D structure that's optimized for solvents (e.g. a solvent-specific force field that would be applied after the 3D coordinates have been computed as in the RDKit example above).
--Any help/suggestions on how to do this (preferably using python) would be much appreciated.


texts: Troubleshoot anion exchange column (Fe, Cr, Co separation)?

texts:
I ran an anion exchange column to separatate Fe, Cr, Co from solution of concentrated HCl.  The column was Dowex 1x8, 200-400 mesh, diameter < 0.5 cm, lenth 7 cm.  A gradient of acid concentrations was used to elute: 12 M (1 mL), 9 M (3 mL), 4 M (3 mL), and water.  The metals were all radioactive isotopes (Cr-51, Co-60, and Fe-59) and Fe (III), Cr(III), Co(II) oxidation states.  I used an NaI(Tl) detector to determine when each of the metal ions eluted.

I intended the Cr to immediately elute as it forms only neutral or cationic species in HCl, then the Co to elute around 9-4M, and the Fe to elute when water was used.

The Cr and Fe did what I expected, but the Co eluted with the Fe (with the water instead of at 9-4M HCl), and the two peaks completely overlapped.

Does anyone know why this behavior might have been observed?  Could I do any better with a cation column instead?