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Building a solid-liquid interface
I am trying to build a solid-liquid interface to be simulate using molecular dynamics. Since, I would be using ab initio molecular dynamics (cpmd or cp2k), I need the minimum cell dimensions. Please suggest some ways to fix the cell dimensions.
The issues that I am concerned about are given in for example in the science paper (http://science.sciencemag.org/content/303/5658/658.full). It is said that there should be a minimum size of the system (specially in the direction perpendicular to the slab) to attain trustworthy results. I am not able to find how and why? For example, if I take 3-10 layers of atoms for making the surface how to determine which one would yield the trustworthy results?

First, when it comes to periodic boundary conditions, you should make sure that your system does not interact with itself through the boundaries.
A way to check it is to see if the electron density is low in vacuum (in case your system has some void separating surfaces).
Energies should also be checked to be converged with respect to cutoff energies, $k$ point selection, etc..
This means that you have attained the "maximum performance" you could; e.g. a well-converged result means that improving parameters do not significantly changes results.
Furthermore, convergence with respect to slab thickness is also important: as you increase slab thickness, the properties of the inner layer should approach the properties of the bulk.
How fast this happens depends on your system.
A good reference for all this is this one.


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R,S Configuration of asymmetric carbon atom when group priority 3 and 4 are not on wedge bond?
I am not blessed with the gift of spatial awareness. I understand how to determine the configuration when a group with priority 4 is on the hashed wedge or when the group with priority 4 is on the bold wedge and priority 3 is on the hashed wedge. However are there any rules I can follow for situations as shown in the image? The numbers show the priority.

A piece of chewing gum and four matchsticks can be a decent replacement for insufficient spatial awareness. Also, welcome to Chem.SE.

To do this, Put the lowest priority group as far away from you as possible.
In the 1 example, if I look at 4 from between 1 and 2 it would be farthest away from me. And i will see that the 3 group is on top, 2 on my left and 1 on my right.
And now if i move from highest priority group to lowest (1-2-3) it would be in clockwise sense. So the configuration is R.
2nd and 3rd example has S and R configuration respectively.

Highest priority to lowest is 1-2-3.

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What were the original methods for determining atomic weights?
I am reading "History of Chemistry" by William Brock and I am confused about the original methods (early 1800s) used to determine molecular weights and hence determine the correct formulae for pure substances. Now I may have the order or link between ideas wrong - which is why I am looking for clarification here. All of what I write below is "as I currently (mis-)understand".
Lavoisier is credited as introducing /emphasising the importance of accurate measurement when conducting chemical investigation.
In order to write chemical equations that capture the correct formulae of products and reactants in an irreversible reaction that runs to completion, some method of measuring the "quantities" reacting and produced is required.
By measuring masses before and after reaction in a closed system we can demonstrate conservation of mass in a chemical reaction but not much else.
The (a?) key to determining correct chemical formulae for compounds is some way of determining the "quantity" of reactants and products rather than mass. We can't use mass as the direct measure of "quantity" (was this ever tried?) because of the differing atomic/molecular weights of reactants and products (simplistically, comparing two samples of different pure materials of equal mass/weight the material comprised of "heavier atoms or molecules" will contain fewer atoms or molecule than the other (*)). The only means in the early 19th C available to determine "quantities" was gas volumes.
Now a bit of cart-before-horse here. Using modern notation and terminology
The reaction of hydrogen with chlorine
$$\ce{H2 (g) + Cl2 (g) -> 2 HCl (g)}$$
Which I can interpret by Avogadro's law: 1 volume (mole) of  hydrogen reacts (violently) with 1 volume (mole) of Chlorine to form 2 volume (mole) of hydrogen chloride gas.
Now where I have a problem (discernable to me) is this:
How do we ensure or know before we conduct the experiment that we have the correct volume (number of moles) of each gas so that there is no unreacted "reactant"?
For example mixing 4 volumes of hydrogen with 1 volume of chlorine would give
$$\ce{H2 (g) + Cl2 (g) + 3H2 (g) -> 2 HCl (g) + 3 H2 (g)}$$
4 volumes of hydrogen plus 1 volume of chlorine (5 volumes of reactant) produces 2 volumes of hydrogen chloride plus 3 volumes of hydrogen (5 volumes of "reactant"). Conclusion: hydrogen and chlorine react in the ration 4 : 1 ???
Separately, I assume the analysis and interpretation of volumes to determine the reaction is trickier for gaseous reactions that establish some kind of equilibrium such as hydrogen and nitrogen forming ammonia, the position of equilibrium (in a closed system) depending on the pressure and temperature?
Another follow up - a very basic question. Is it correct to say that once the atomic / molecular weights are established we can then work out correct empirical formulae for compounds but not molecular formulae.
(*) This idea of course depends upon the idea that different types of atoms have different "weights" but isn't that Avogadro?

You can (and should!) use the \ce{...} environment to format chemical equations and formulae; see here for a basic intro and here for a complete documentation.

I did think there  is mechanism to format chemical equations. However, I'm a mathematician (of sorts) and I only know Latex - so it was my first port of call to write something that was reasonably formatted. Thank you for the note about the \ce{...}. In what ways is it more appropriate than Latex for this task? Thanks.

mhchem is no more than a package for LaTeX. However the implementation of LaTeX on webpages (MathJax) can vary slightly from actual LaTeX (see here). As for why it is more appropriate this post has some more details and links.

OK. I have had quick scan. A Latex package - phew, not a whole load of new stuff to learn. In basic terms, the mhchem package eases the formatting of chemical formulae and equations rather than "highjacking" other Latex formatting tools ????

This seems to be really broad. Overall there are numerous ideas all rolled into this just starting off with "how were the elements identified?" Answering this would take a book.

@MaxW. Yes, re-reading my question it does read as broad. I will try and break it down into simpler "have I understood this bit?" questions - but I am still hankering after a "narrative" and "time lines" that link together the key concepts.

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Will electric field make organic matters (e.g. glucose) ionize in water?
After reviewing this post, I have a new question regarding ionization and dissolution.
If applying a strong electric field (DC or AC) in a water solution, will the electric field ionize the organic matters that are not ionizable? For example, an electric field makes $\ce{CH3COOH}$ ionize more? Or makes glucose ionized in water instead of forming hydrogen bonding with the water molecular? Thanks.

Stems from a question originally posted by OP in a comment on this answer.

The short answer to your question is no, particularly for your example of glucose. Part of the key to your question is the statement: "[...] will the electric field ionize the organic matters that are not ionizable?".  If they are not ionizable, then they are not ionizable :)
You could electrolyze glucose to polyhydric alcohols as in this patent. But in this case you are not ionizing glucose, but creating an entirely different compound (which is still not strongly ionic).
There are compounds that can be electrolyzed to ionic compounds, but that is really a very different process than what you are asking about.  You wouldn't have ionization of the compound, you would be electrochemically converting a non-ionic compound into an ionic compound. See for example, this abstract1 in which the authors electrolyze ethanol to acetic acid, which would then ionize in the aqueous solution to some degree.
But, as in your example of gucose, the ethanol itself would not be ionized. You would simply be producing, via electrochemical reaction, an entirely different, ionic compound.
1) Journal of the Electrochemical Society, "Electrolytic Oxidation of Ethyl Alcohol to Acetic Acid", 1947, volume 92, issue 1, 335-342

Thanks. How about compounds that partially ionizes in water, such CH3COOH? Will an electrical field alter the dynamic equilibrium into another balance?

No, it's an interesting idea, but an electrical field will not change the degree of ionization of a partially ionized compound. Though the ions may be locally attracted to one pole or the other, that has no effect on the degree of ionization (the dynamic equilibrium between the charged and uncharged species). I hope that helps.

Even under an extremely strong electromagnetic pulse? Just like tesla coil that can ionize air, can a strong pulse ionize compound in liquid phase?

Dissolved ions in aqueous solution can carry current, just like the ions formed in  air when the potential of a tesla coil or a spark plug becomes great enough to ionize the air and allow a current to flow. You could certainly blast an aqueous solution with a potential high enough to ionize the water and most anything else in there. But when we're talking about the dissociation of a weak acid for example, the net effect is not going to be an increase of dissociation. Let me continue in the next comment...

What we're really talking about is the ability of water to solvate the ionic species in solution, and that is not affected by the presence of a magnetic field. In my example of blasting the solution with a high potential, that will just lead to a bunch of new chemical species from the electrolysis reactions. You might even destroy some of your organic acid, forming some other species altogether, but through it all, not counting transient temperature changes and such, the net degree of dissociation of the organic acid will remain the same.

Thanks. So as I understand, the EM field won't change the ionization or dissociation balance, but only create new chemicals that may ionize by electrolysis. So in the example of Tesla Coil, the air (e.g. oxygen) becomes O2- that is considered as a new chemical. Am I correct? Will the EM field speed up the rate of dissociation/dissolution? For example, it takes 10 mins to get saturated in water under standard condition, then it takes only 30 seconds?

Yes to everything, almost ;). The EM field would only speed up the rate of dissociation/dissolution due to heating of the solution, and most ionic compounds are more soluble at higher temperatures. There are exceptions though. Calcium hydroxide, for example, is soluble to 1.89 g/L at 0C, but only 0.66 g/L at 100C. In this case, any heating from an EM field-induced reactions to form new compounds would result in lower solubility and slower dissolution of a compound like calcium hydroxide. That's an odd one though, and it sounds to me like you've basically got this figured out; nice job.

EM field heats the solution is due to speeding up the molecular inner energy. Is that possible the EM field only effect the electron of a certain compound to make the electron more easily to become a free electron, without heating the entire solution?

Again, to summarize, if there is an electric potential like a Tesla coil within your solution, the potential may ionize anything in the solution where the potential is great enough to do so. The resulting current will heat the solution. The solubility of the solutes, and the dissociation constant of any ions, will have some dependence, positive or negative, on the temperature of the solution. You will not see any difference in the degree of dissociation of a particular ionic compound (i.e. CH3COOH) at any given temperature due to the magnetic field.

What physical unit (volt or v/m?) should I look at to determine if the EM potential is great enough to ionize compounds in the solution? Should it be correlated to the chemical bond that would be ionized?


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What kind of stereoisomerism do cisplatin and transplatin exhibit?
Cisplatin and transplatin are obviously isomers, more precisely stereoisomers. Now, they aren't chiral, so they cannot be enantiomers. They cannot be diastereomers either since they don't have two stereocenters. They don't belong to cis/trans stereomers either since they are a subgroup of diastereomers and again require two stereocenters. So - what the heck?

Yes they do belong to cis/trans isomers, simply because they are called cis and trans, if not for other reason. True, this is a quite different kind of cis/trans from that known in organic chemistry. Whatever.

The definition of diastereomer does not include "requires two stereocentres" anywhere. It is simply

Diastereoisomers (or diastereomers) are stereoisomers not related as mirror images. (IUPAC Gold Book)

Therefore cis- and trans-$\ce{[PtCl2(NH3)2]}$ are diastereomers.
(E)- and (Z)-alkenes are also diastereomers of each other. Your "cis/trans stereomer" is in fact simply a subset of diastereomerism.


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"NBO diagrams" versus MO diagrams
Molecular orbital diagrams are well known by chemists.
According to Wikipedia (emphasis mine),

A molecular orbital diagram, or MO diagram, is a qualitative descriptive tool explaining chemical bonding in molecules in terms of molecular orbital theory in general and the linear combination of atomic orbitals (LCAO) molecular orbital method in particular.

An example is given below.

(Image by CCoil (talk) - own work, CC BY-SA 3.0, Link)
By the use of computational chemistry methodologies we can (1.) produce a molecular wavefunction of a diatomic molecule as a linear combination of basis functions (assume they are centred on each nuclei).
This would already satisfy the definition above and generate a suitable MO diagram.
On the other hand, there are special methodologies for obtaining the starting orbitals centred on atoms:

We could express molecular orbitals as a linear combination of optimised atomic orbitals of each atom, which would imply an extra calculation for each element in a molecule.
A change of basis for the MOs, from the basis set to the atomic orbitals, does the rest.
The natural bonding orbitals (NBOs) method allows one to produce natural atomic orbitals as well, which could also be used as initial orbitals centred on the atoms.

So my question is:
Are the three approaches above really arbitrary?
What makes one option better than the other?

NBO is a tool to analyse the wave function. With method 1, you obtain the canonical orbitals which are delocalised. You can take a wave function like this and by unitary transformation obtain localised bond orbitals, which is what the Natural Bond Orbital theory does. See this related question. I have not come across a method which would use them as a basis set. The NBO are also expressed as linear combinations of the basis set.

I am specifically asking about expressing the same MOs in a different basis (in the mathematical sense), i.e. 1. standard basis set, 2. true atomic orbitals or 3. natural atomic orbitals (NAOs).
When it comes to producing MO diagrams, could any of those options (or maybe something else) be regarded as "better" in some sense?
For instance, I feel true atomic orbitals (2.) could be less dependent on basis sets, as opposed to the first method.

MO diagrams are qualitative representations of what we interpret as bonding, simplifications so that we can fathom the complicated, as such the simplest approach would be fine. Canonical MO give nice results. NBO transforms atomic orbitals into hybrid orbitals, probably not even close to atomic orbitals; so this approach will probably not get you where you want to go.

A molecular orbital diagram is a schematic representation of how we interpret bonding in certain species. It is as much an accurate representation for a specific bonding situation as a Lewis structure for the the molecular geometry.
When we construct a molecular orbital diagram, usually we resort to shapes of hydrogen like orbitals. We most of the times do not even use mathematical descriptions, accurate energy levels, without changing the descriptive value much. Oftentimes we completely omit core orbitals and don't draw nodal planes/spheres for orbitals with $n=2$.
Such diagrams, however, provide qualitatively good descriptions of what otherwise is almost impossible to fathom. They even provide a solid starting point for quantum chemical calculations.
As such, the choice of atomic orbitals does not matter at all; a picture will never contain enough detail to work out the subtle differences of these choices.

By the use of computational chemistry methodologies we can (1.) produce a molecular wavefunction of a diatomic molecule as a linear combination of basis functions (assume they are centred on each nuclei). This would already satisfy the definition above and generate a suitable MO diagram.

Most basis sets indeed contain basis functions which are centred at the respective nucleus and they resemble atomic orbitals (they don't have to). Through a linear combination of such functions we can obtain suitable molecular orbitals within the respective approximations. The wave function is then obtained as a set of orthogonal molecular orbitals. This in principle is the essence of molecular orbital calculations, which is in turn essentially the same as calculations on the Hartree-Fock level of theory. We know that this level of theory doesn't contain nearly enough precision to accurately describe the most simple compounds because of the neglecting most of the correlation energy. Yet, it is impossible to represent the result of such a calculation as a diagram.

We could express molecular orbitals as a linear combination of optimised atomic orbitals of each atom, which would imply an extra calculation for each element in a molecule. A change of basis for the MOs, from the basis set to the atomic orbitals, does the rest.

Yes you can do that, but apart from adding significant computational cost, this would not really increase the accuracy of the calculation. First and foremost you need to account for a larger portion of the correlation energy, for example with density functional approximations, post-HF methods like perturbations theory MPn, coupled cluster, or configuration interaction. Instead of optimising the basis set for each atom in the molecule, it is much more effective adding more functions to the basis set until you reach the complete basis set limit. There are several types of basis set libraries in use now, which have been designed to effectively handle such calculations. I think it was John Pople who laid out the advantages of this system. And while his basis sets have significant shortcomings, they are still used today.
In any case, what you will not get is a better or more descriptive MO diagram.

The natural bonding orbitals (NBOs) method allows one to produce natural atomic orbitals as well, which could also be used as initial orbitals centred on the atoms.

Indeed natural bond orbital theory uses natural atomic orbitals (and other types), however, these are representations of the atomic orbital within the molecular environment.
The theory itself is a localisation technique of canonical orbitals that are already expressed in the chosen basis set. As a result we get a bonding picture which closely resembles a Lewis structure. While they are different from the actual basis set they still have the same functions and would still lead to the same solution.
It is best to treat MO diagrams as what they are: qualitative tools to describe bonding.


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Formal nomenclature for fulvene
I am a little bit confused trying to name the compound fulvene:

I'm not sure whether its name is 5-methylene-1,3-cyclopentadiene or                        3-methylene-1,4-cyclopentadiene.

Fulvene consists of a cyclopentadiene ring and a $\ce{{}=CH2}$ substituent group. According to the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book), the prefix ‘methylene’ is no longer recommended to designate the $\ce{{}=CH2}$ group. The preferred prefix is ‘methylidene’; thus, the systematic name of fulvene without locants is methylidenecyclopentadiene.
Concerning the numbering of locants, the current IUPAC recommendations read as follows.

P-14.4 NUMBERING
When several structural features appear in cyclic and acyclic compounds, low locants are assigned to them in the following decreasing order of seniority:
(…)
(e) saturation/unsaturation:
  (i) low locants are given to hydro/dehydro prefixes (…) and ‘ene’ and ‘yne’ endings;
  (ii) low locants are given first to multiple bonds as a set and then to double bonds (…);
(f) detachable alphabetized prefixes, all considered together in a series of increasing numerical order;
(…)

Therefore, low locants are given first to the double bonds in the ring according to (e) and then to the prefix ‘methylidene’ according to (f). Thus, the correct systematic name is 5-methylidenecyclopenta-1,3-diene rather than 3-methylidenecyclopenta-1,4-diene since the locant set ‘1,3’ for the double bonds is lower than ‘1,4’.

Note that according to IUPAC nomenclature since 1993, locants are placed immediately before that part of the name to which they relate (e.g. cyclopenta-1,3-diene rather than 1,3-cyclopentadiene).

@hBy2Py - Retracted close vote. Note: This is something that gets sorted out in a Google search in one click of the button - the first hit is Wikipedia, the third is PubChem, the fourth is ChemSpider (the second is the Wikipedia entry for Fulvenes). If we're going to be a proxy for an internet search engine, we probably ought to discuss it in Meta.

@ToddMinehardt You make a good point, but I feel all of the various nomenclature answers here add something that often is missing in resources like those resources you turned up in Google: explanation. Answerers here (Loong, often) typically go to considerable effort to explain why a given name fits the compound of the question. Much more valuable to the OPs and to future readers.

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Fluoride concentration in LiF and CdF2 solutions
Trying to learn how to use $\ce{K_{\mathrm{sp}}}$ values and not understanding. See question below:

Two saturated aqueous solutions are prepared at $\pu{25^\circ C}$
Solution1 is made by dissolving cadmium fluoride ($\ce{CdF2}$, $\ce{K_{sp}} = \pu{6.44E−3}$) in $\pu{100.0 mL}$ of water until excess solid is present.
Solution 2 is prepared by dissolving lithium fluoride ($\ce{LiF}$, $\ce{K_{sp}} = \pu{1.84E−3}$) in $\pu{200.0 mL}$ of water until excess solid is present.
Which solution has a higher fluoride ion concentration?"

I used the $\ce{K_{sp}}$ given for $\ce{CdF2}$ to get $s = 0.11720$, so $\ce{[F]} = 2s = \pu{0.2344 M}$, is that right? I guess I'm not sure what to do after that to get find the concentration in $\pu{100 mL}$.  Wouldn't it be $\pu{2.344 M}$?  I am told this answer is incorrect.

Please edit the question to show how you got to statement "... CdF2 to get s = 0.11720". Ksp is for molarity which is per liter.

I got CdF2 s = 0.11720 using the below formulae:
Ksp = [Cd^2+][F^1-]^2, therefore:
6.44 x 10^-3 = (s)(2s)^2 = 4s^3, solve for s, s = 0.11720, therefore:
F M = 2s = 0.2344 M

The problem as stated is not asking you which solution has the higher amount of fluoride but which one has the higher concentration of fluoride, i.e. the higher molarity (as this is usually the concentration unit more often used by chemists).
You need to calculate the fluoride concentration for the $\ce{LiF}$ solution in the same way you did for the $\ce{CdF2}$ solution. My answer comes to 0.04290 M.
Thus, the $\ce{CdF2}$ solution has a fluoride concentration of 0.2344 M while the $\ce{LiF}$ solution has a fluoride concentration of 0.04290 M. Therefore, the answer to the problem is: the $\ce{CdF2}$ has a higher fluoride ion concentration.

okay, so is the volume of liquid just a red herring?

@MikeW Please read my answer again. I did not say that CdF2 is 0.04290 M and that it has a Fluoride for 0.2344 M.

@Mike Yes, it is a red herring. If the problem were asking you to calculate which solution has the higher amount of fluoride then the volume would be necessary and you would calculate the number of moles from moles=V in L x M

Deleted 3 of my earlier comments. Your numbers are right. Your comment "MikeW Please read my answer again. I did not say that CdF2 is 0.04290 M and that it has a Fluoride for 0.2344 M." should have be to me...

Ugh. enough nonsense from me...

For $\ce{CdF2}$, $\mathrm{K_{sp} = 6.44\ x\ 10^{−3}}$

Let $x$ = molarity of $\ce{CdF2}$
$\ce{[Cd^{2+}]}$ = $x$
  $\ce{[F^-]}$ = $2x$
$\mathrm{K_{sp} = 6.44\ x\ 10^{−3} = \ce{[Cd^{2+}][F^-]^2} = (x)(2x)^2 = 4x^3 }$
  $x = 0.117$
$\ce{[Cd^{2+}]}$ = $x = 0.117$
  $\ce{[F^-]}$ = $2x = 0.234$

Lithium fluoride ($\ce{LiF}$), $\mathrm{K_{sp} = 1.84\ x\ 10^{−3}}$

Let $x$ = molarity of $\ce{LiF}$
$\ce{[Li^+]}$ = $x$
  $\ce{[F^-]}$ = $x$
$\mathrm{K_{sp} = 1.84\ x\ 10^{−3} = \ce{[Li^+][F^-]} = (x)(x) = x^2 }$
  $x = 4.29\times 10^{-2}$

Thus the $\ce{CdF2}$ solution has a higher fluoride ion concentration.


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Syntax and Typography of Atomic Orbitals
For mhchem (i.e. the \ce command you use here), I want to improve the support for atomic orbitals. (Reason: I see it quite often used here.) But only a few things about orbitals are mentioned in IUPAC documents. Many more seem to be "unwritten law".
As I am not a chemist I need your help.
1
The Green Book p. 32 defines the letters s, p, d, f, g, h, i, k ... (omitting j). They have to be typeset upright.
Question a: How far does this "alphabet" reasonably go? (Wikipedia goes up to i).
2
On the same Greek Book page, electron configurations are explained, e.g. $\mathrm{(1s)^2 (2s)^2 (2p)^1}$.
Many other sources write it without parenthesis: $\mathrm{[Kr]\mskip2mu4d^{10}\mskip2mu5s^1\mskip2mu5p^3\mskip2mu5d^4}$
Question a: What values can the left-side number take? (At Wikipedia, I see 1 to 7.) Can it be 2-digit?
Question b: What values can the right-side exponent take? (At Wikipedia, I see 1 to 10.)
3
I think I did not come across the configuration with one-electron orbitals (in Greek). $\mathrm{(1\sigma)^2 (2\sigma)^2 (3\sigma)^2 (1\pi)^1}$. (The Greek letters should be upright, but that's a drawback of MathJax.)
Would this be useful? Or not needed?
4
The examples introduce another notation, "electronic states"  $\mathrm{\cdot\cdot\cdot (2a_1)^2 (1b_2)^2 (3a_1)^2}$
a: What values could the letter take? b: The left-side number? c: The subscripts? d: The right-side exponent?
5
From Wikipedia, I learned that there are notations IUPAC does not mention: $\mathrm{p_x}$, $\mathrm{p_y}$ and $\mathrm{p_z}$. (All subscripts should be upright, because they are labels, no variables.)
But it does not end there. Here and here I saw:
$\mathrm{d_{xy}, d_{xz}, d_{yx}, d_{x^2{-}y^2}, d_{z^2}}$
This was confirmed by this book.
There are alternative styles
here ($\mathrm{{p_x}^1}$).
and
here ($\mathrm{p_{x1}}$).
a: I guess the $\mathrm{d_{z^2}}$ notation (with index z-square) is correct?
Oh, I just found this book that also includes $\mathrm{4f_{x(x^2{-}3y^2)}}$ and $\mathrm{4f_{y(3x^2{-}y^2)}}$.
b: Are there other indexes possible than x, y, z?
c: Can it be just squares? Or are other index-superscripts possible?
d: What about the 3 in the last examples? Could this also be any other numer?
(You see, I just look at the typography of things and don't know their meaning.)
e: Could there be any other forms of indexes?
f: Typographically, what does this dash stand for? Is it a hyphen or a "transition between a higher energy state and a lower energy state"?
6
Finally, there is orbital hybridization, which will lead to notations like $\mathrm{sp, 2sp, sp^2, 2sp^3, s^{0.5}p^3, s{-}s, sp^3{-}sp^3}$.
a: Can the superscript be any other value than 2 and 3? Can the "base" be any other thing than s, p and sp?
b: Is $\mathrm{2sp^3}$, is it $\mathrm{2s}$ and $\mathrm{p^3}$ or is sp one ... thing with a 2 before and a 3 in superscript.
c: Is it a hyphen or a "transition between a higher energy state and a lower energy state"?

Wow, tempted to flag as too broad.

Question 1 remember there are also the corresponding term symbols https://en.wikipedia.org/wiki/Term_symbol

@Mithoron Yes, it got rather long. However, I assume that there is a high correlation between the answers (e.g. "left-side number can be ..., everywhere") and a comprehensive answer would be less than 10 lines.

Question 1. The Green Book p. 32 defines the letters s, p, d, f, g, h, i, k ... (omitting j). They have to be typeset upright.
How far does this "alphabet" reasonably go? (Wikipedia goes up to i).

Section 2.6.3 of that version of the Green Book shows the term symbols (Wikipedia) which are capital letters S,P,D,F,G,H,I,K,... and used to indicate the electronic configuration of the valence electrons and for excited states.
The lower case letters are used for the azimuthal quantum number (ℓ) which is one of the four quantum numbers for an electron in an atom. You can typeset $99.9~\%$ of chemistry of even more using only the letters s, p, d and f, corresponding to the left-hand main group elements, the right-hand main group elements, the transition metals and the lanthanides/actinides, respectively. Everything above f is and will be for quite some time not relevant to chemistry outside a very small circle that would know how to deal with stuff.

Question 2. On the same Greek Book page, electron configurations are explained, e.g. $\mathrm{(1s)^2 (2s)^2 (2p)^1}$.
Many other sources write it without parenthesis: $\mathrm{[Kr]\mskip2mu4d^{10}\mskip2mu5s^1\mskip2mu5p^3\mskip2mu5d^4}$
Question a: What values can the left-side number take? (At Wikipedia, I see 1 to 7.) Can it be 2-digit?
Question b: What values can the right-side exponent take? (At Wikipedia, I see 1 to 10.)

This has two sub-questions.

By a similar reasoning as presented in the answer to 1, I think 8 will be the limit until the not-so-close future. But there is nothing intrinsically preventing it from becoming two-digit at some distant point.
The superscript can take values of up to $4l+2$, where $l$ can be considered ‘computer science counting’ of the letter sequence s, p, d, …; so for s $l = 0$ and thus $4l+2=2$; likewise for p ($l=2$) the value is maximum $4l+2=6$ etc. Note that $4l+2$ is actually $2(2l+1)$: each subshell gives up to $2l+1$ orientation possibilities that each can be populated with two electrons.

Question 3. I think I did not come across the configuration with one-electron orbitals (in Greek). $\mathrm{(1\sigma)^2 (2\sigma)^2 (3\sigma)^2 (1\pi)^1}$. (The Greek letters should be upright, but that's a drawback of MathJax.)
Would this be useful? Or not needed?

Yes, this is useful, especially for discussing molecular orbitals. The Greek letters you want to be aware of are σ, π and δ. Maybe a fourth will be added soon corresponding to f orbitals (υ?) but I don’t see that coming anytime soon.

Question 4. The examples introduce another notation, "electronic states"  $\mathrm{\cdot\cdot\cdot (2a_1)^2 (1b_2)^2 (3a_1)^2}$
a: What values could the letter take? b: The left-side number? c: The subscripts? d: The right-side exponent?

I’m going to answer that as one.
This notation uses irreducible representations to define orbitals. The bit between the initial number and the superscript can be any of the symbols that appear in Little Bobby Tables (courtesy of Orthocresol). They each represent a type of orbital with a certain symmetry.
Orbitals of the same irreducible representation (i.e. the same centre) are numbered from lowest to highest energy — so in principle the sky is the limit. Practically, however, you will be hard-pressed finding three-digit examples.
The exponent can at maximum be $2n$, where $n$ is the number in the first column of the respective character table (the E column). This number corresponds to a certain symmetry’s degeneracy (i.e. so many orbitals of the same energy) and each orbital can be populated by two electrons.

Question 5. From Wikipedia, I learned that there are notations IUPAC does not mention: $\mathrm{p_x}$, $\mathrm{p_y}$ and $\mathrm{p_z}$. (All subscripts should be upright, because they are labels, no variables.)
But it does not end there. Here and here I saw:
  $\mathrm{d_{xy}, d_{xz}, d_{yx}, d_{x^2{-}y^2}, d_{z^2}}$
  This was confirmed by this book. There are alternative styles
  here ($\mathrm{{p_x}^1}$).
  and
  here ($\mathrm{p_{x1}}$).
a: I guess the $\mathrm{d_{z^2}}$ notation (with index z-square) is correct?
Oh, I just found this book that also includes $\mathrm{4f_{x(x^2{-}3y^2)}}$ and $\mathrm{4f_{y(3x^2{-}y^2)}}$.
b: Are there other indexes possible than x, y, z?
c: Can it be just squares? Or are other index-superscripts possible?
d: What about the 3 in the last examples? Could this also be any other numer?
e: Could there be any other forms of indexes?
f: Typographically, what does this dash stand for? Is it a hyphen or a "transition between a higher energy state and a lower energy state"?

(Somebody please add and correct this.)
It was my assumption that the axis directions should be italicised but I don’t know. To discuss this, please go to the break-out discussion for this question.
p orbitals will always have $x$, $y$ or $z$. d orbitals will have one of the five you noted ($\mathrm{d}_{z^2}$ is correct — as I said, I am not sure on the upright versus italic question but I would have assumed italics). The f orbitals themselves can be labelled by various different polynomials in $x$, $y$, $z$, and $r$. See these two web pages: 1, 2. In general the subscript is just a polynomial.
Which symbols and exponents can appear here is fixed already by the results of the hydrogen-like orbitals — again, for most of chemistry d orbitals are sufficient and you can cover $99.9~\%$ by including f orbitals.
The ‘dash’ is a mathematical minus-sign operator. Yes, it truly is $x^2$ minus $y^2$.

Question 6. Finally, there is orbital hybridization, which will lead to notations like $\mathrm{sp, 2sp, sp^2, 2sp^3, s^{0.5}p^3, s{-}s, sp^3{-}sp^3}$.
a: Can the superscript be any other value than 2 and 3? Can the "base" be any other thing than s, p and sp?
b: Is $\mathrm{2sp^3}$, is it $\mathrm{2s}$ and $\mathrm{p^3}$ or is sp one ... thing with a 2 before and a 3 in superscript.
c: Is it a hyphen or a "transition between a higher energy state and a lower energy state"?

Sub questions.

Yes. You have $0.5$ as a superscript in your own examples. But, as posts by Martin and Ron somewhere point out, in $\mathrm{sp}^x$ the superscript $x$ can, in principle, be any number.
$\mathrm{2\,sp^3}$ is $\mathrm{\{2\}\{sp^3\}}$ — and there could potentially be another superscript making it $\mathrm{(2sp^3)^2}$.
I don’t know what that hyphen is supposed to be.

More question than a comment: do we use italics at all? I see sometimes s,p... italicized, and frankly, I use it often, too, because I found texts more readable when orbital notations pop up.

@Greg The orbital designation letters should be in upright type as they are not variables. So that bit at least is clear.

Great! I went through it step by step. At question 4, I am stuck. These tables surpass my brain capacity. Starting with the fact that everything is captical letters, there. Is it the left-most column you are referring to? So, the middle part could be anything like $\mathrm{e_1, d_{4h}, a_2''}$?

@mhchem Sort the answers by "active", and ignore the last two posts on "direct product tables" and "tables of descent in symmetry" - those are different things. Apart from those two posts, it can be anything in the left-most column, except for the header row. So, $D_\mathrm{4h}$ does not count, but $\mathrm{e_1}$ and $\mathrm{a_2''}$ are both possible. If you are referring to orbitals, then the capital letters will become small letters. The capital letters in the tables are referring to irreducible representations, which are sets of matrices describing the behaviour of the orbitals.

For question 1: if you take the orbital letters up to i you'll be able to handle ~100% of chemistry -- computational heavy-element chemistry needs to go higher than a lot of chemistry because they need to add on higher-level functions to allow molecular orbitals to be more finely shaped.

Re: $\sigma, \pi, \delta$ the next one is $\phi$, see here, and it is here ;)  Re: the denotations of $\mathrm{p}_{x/y/z}$ depend on the choice of the coordinate system, it could be different. Re: hybrids. $\mathrm{sp}^n$ is an abbreviation for another abbreviation $\mathrm{s}^{\frac{1}{n+1}}p^{\frac{n}{n+1}}$  which denotes a linear combination, etc. pp.. Theoretical there can be other types of hybrids based on s, p, d, f, g, ...

@Martin-マーチン It’s CW; feel free to edit ;)


text:
How does rubber toughening work?
I’m doing a research project which involves rubber toughening - the particular example I'm looking at is the toughening of SAN polymer (styrene-acrylonitrile) with polybutadiene to make ABS. What I'm looking for is a description of why the process makes the material tougher, whereas everything I can find online seems to be research about the effects of different factors on the toughness. If anyone could provide a source that would be great.

I think you need to be much more specific about what kind of "rubber."

Hello and welcome to Chemistry.SE! At this point I recommend taking the short [tour] of the site. As stated in another comment, you will need to be more specific about what you are really looking for in order to get a useful answer.

I think this Wikipedia article answers your question quite directly:

"This important property [rubber toughening] is entirely due to the
  small rubbery domains that aid in arresting crack propagation, thereby
  increasing toughness/energy needed to break the material."

The same article gives an example using the materials sited in your post:

"Well-known rubber toughened polymers include high impact polystyrene
  (HIPS), rubber-toughened nylon, and acrylonitrile butadiene styrene
  (ABS). In HIPS, polybutadiene domains are dispersed in a polystyrene
  matrix; in rubber-toughened nylon, typically cis-polyisoprene is
  dispersed in a Nylon matrix; in ABS, polybutadiene domains are again
  used, but for both polystyrene and acrylonitrile."


text:
Can 1 gram hyaluronic acid really hold 6L of water?
According to this study (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970829/), they make an (uncited) claim about hyaluronic acid: "One of its most important properties is that it can attach and hold large amounts of moisture; approximately 6L of water in just lg ."
Now, the MW of HA is $776.651$ g/mol, so there are about $\pu{0.00128865979}$ moles of HA in a gram. And about $\pu{7.757732e20}$ molecules.
Using google, 6L of water has $\pu{2.007e26}$ molecules.
So this is essentially telling me that roughly 1 million water molecules are able to hydrogen bond with 1 molecule of HA...
Firstly, is this fact true? And if so, how is this possible??

I agree, that claim is a stretch. My guess is there was a units error, and they meant to say that you can hold $6~\mathrm L$ of water in $1~\mathbf{kg}$ of HA.

Bear in mind that hyaluronic acid is a polymer, and one molecule may have up to ~25k monomers, so your 1 million water molecules figure may not be that far off. (of course, its MW is 776 Da/unit, so the polymer may be 5 million Da, which changes your calculation) I'm not sure what "attach and hold" is supposed to mean, but perusing the literature, people seem to be making hyaluronic acid hydrogels at 1–2 wt. %. Not sure how low you can go and still have something that appears gel-ish.

Note that the abstract at the original journal site here has not the typo which you copied,  ‘1g’ → ‘lg’.

Various figures can be found “on the internet”. E.g. ‘Hyaluronic Hydro Gel Has 1000 Times Water Holding Capacity Perfect for Hair to Heel’ (commercial link intentionally omitted).
Gel liquid phase absorption ability measure seems to be a ‘swelling capacity’ (ratio).
For hyaluronic acid (HA), it can be increased by additional crosslinking. In one paper from 1992, usual swelling ratio was found to be in the order of magnitude 1 to 10, the maximum figure was 120 (for crosslinking ratio much higher than 2.1; 25–30 for the ratio 2.1).[1]
In another paper, another guys are using biphasic nanoparticles (some composite of crosslinked and non-crosslinked HA), they state they have achieved for two different particle types ‘… swelling ratio 1270, 1000 %, respectively’[2] (note the percent sign). Which is, in both cases, approximately, not 1000× capacity, but rather 10× capacity, I'd say.
However, there are polymers with the claimed property – superabsorbents:[3]

3.27 superabsorbent polymer
Polymer that can absorb and retain extremely large amounts of a liquid relative to its own mass.
Note 1: The liquid absorbed can be water or an organic liquid.
  Note 2: The swelling ratio of a superabsorbent polymer can reach the order of 1000:1.
  Note 3: Superabsorbent polymers for water are frequently polyelectrolytes.

References:

Shah, Chirag B., and Stanley M. Barnett. "Swelling behavior of hyaluronic acid gels." Journal of applied polymer science 45.2 (1992): 293-298.
Chun, Cheolbyong, et al. "Effect of molecular weight of hyaluronic acid (HA) on viscoelasticity and particle texturing feel of HA dermal biphasic fillers." Biomaterials research 20.1 (2016): 24.
Compendium of Polymer Terminology and Nomenclature (IUPAC Recommendations 2008)

Attach and Hold - a bit of a misnomer; it forms a 3 D Lattice matrix containing water; given its inherent viscosity and inherent elasticity, it can be compressed and upon release of pressure spring back to its original dimensions thus the visco-elastic/shock absorbing properties advantages medically (knees) and cosmetically (skin fulfillment/youthful appearance etc).


text:
How to formally calculate the surface density of layered materials such as graphene?
Typically density is defined in units of mass per volume. In the case of graphene it is mass per area, i.e. surface density. What would be the correct way to calculate the surface density (mass per unit area) of graphene, for example?
Would it be correct to multiply the density of graphite by the van der Waals gap of graphite?

Let's fix the terminology and go from there. Density is grams per cubic centimeter. Surface area is centimeters squared per gram. Now what do you want?

@MaxW what is the "density" of graphene in grams per centimeter squared?

$\dfrac{1}{\text{Surface Area}} = \dfrac{\text{grams}}{\text{cm}^2} $

@MaxW ok so now how to actually calculate this "surface area" given carbon-carbon bond length etc.?

I'm still not sure what you are trying to do... // I think you're looking for  what the unit cell is in an infinite plane of graphene.

The C-C length in graphene is l = 0.142nm and the area of a hexagon can be calculated with the formula:
$ A = \frac{3\sqrt{3}}{2} l^2 =  0.0523nm^2$
In each hexagon, there are 2 full carbon atoms(1/3*6) so the surface density of one single layer is:
$ S_d = \frac{2*massCarbon}{A}  =  \frac{2*1.994 × 10^{-26}Kg}{0.0523× 10^{-18}m^2} = 76.26 × 10^{-8} Kg/m^2 = 7.63× 10^{-8} g/cm^2$
If you are considering 2, 3, etc. layers than the surface density it's twice, three times etc. the surface density of the single layer.
Additional note: The distance between layers is h = 0.335 nm and therefore its density can be calculated as:
$ d = \frac{S_d}{h}  =  \frac{7.63 × 10^{-8} g/cm^2 }{0.335× 10^{-7}cm} = 2.28 g/cm^3  $
This is very close to the experimental value I have found online says that the density of graphene is $2.267 g/cm^3$

Which is the value for graphite as well...


text:
How do I publish a formula?
I've been manipulating certain chemical properties and I've come up with a new formula that doesn't seem to already have been discovered. How would I go about publishing my findings?

Put it in a journal?

Look here, maybe it could help you https://www.researchgate.net/post/How_to_publish_a_scientific_paper


text:
Confusion in the order of precedence: alkyl side-chain vs. dimethyl at different positions
I've read that prefixes like 'tert-butyl, 'sec-butyl' and have been discarded while 'iso-propyl' is still retained by IUPAC. So I wrote another name according to the general rules. Is it correct? If not please correct me.

(The structure in question is framed)

EDIT: When I typed the name here it gave a slightly different structure so I tried putting 5-(1-methylpropyl) first, as in 5-(1-methylpropyl)-2,7-dimethylnonane, which gave the correct structure.

So, my question now is, since both substituents have same alphabetical order, why do we write 5-(1-methylpropyl) first?

I think your naming is completely right.

@Mockingbird no, it was slightly incorrect, please see my edited question.

I think it's just an convention..

Your starting point is correct. According to the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book), the name 5-(sec-butyl)-2,7-dimethylnonane is no longer recommended. (The prefix ‘sec-butyl’ was still contained in the 1993 recommendations.)
The names that are proposed in the question, 2,7-dimethyl-5-(1-methylpropyl)nonane and 5-(1-methylpropyl)-2,7-dimethylnonane, are unambiguous and describe the same structure. There may be many different ways to draw the structure of such branched alkanes. If you enter these names into the Open Parser for Systematic IUPAC nomenclature (OPSIN), which is mentioned in the question, the results are as follows:

2,7-dimethyl-5-(1-methylpropyl)nonane

5-(1-methylpropyl)-2,7-dimethylnonane
The structures may look different at first glance, but they actually describe the same compound. In this respect, there is no difference between 2,7-dimethyl-5-(1-methylpropyl)nonane and 5-(1-methylpropyl)-2,7-dimethylnonane. However, the name 5-(1-methylpropyl)-2,7-dimethylnonane is not in accordance with IUPAC nomenclature since ‘methyl’ is earlier alphabetically than ‘methylpropyl’. Therefore, the name 2,7-dimethyl-5-(1-methylpropyl)nonane is a correct IUPAC name.
Anyway, the preferred IUPAC name (PIN) according to current recommendations is 5-(butan-2-yl)-2,7-dimethylnonane.


text:
Boiling Point trend
Why does group 13 and 14 show reverse the trend of boiling point? In other groups, boiling point increases down the group but here it decreases.

http://chemistry.stackexchange.com/questions/33815/trend-in-the-melting-point-down-the-group

http://chemistry.stackexchange.com/questions/35716/why-there-is-an-exception-in-melting-and-boiling-point-in-p-block


text:
What materials for a boiler, if any, do not require a deaerator?
I'm imagining a portable boiler/turbine unit that burns wood and creates steam for a turbine, generating electricity.
I was planning on using freshwater from a river or lake. (A simple filter will remove particulate matter and minerals.)
But then I came across something called a Deaerator.
Basically, the deaerator removes oxygen and carbon dioxide from the water. Those substances often dissolve in the water and, in a boiler, can cause metal corrosion.
So I'd like to choose a material that doesn't require this, if possible. Titanium? Bronze? Carbon-carbon? Iron-Nickle like they use in jet engines?
Edit: For the curious, this question arose from studying old steam trains. Pretty sure they did not de-aerate the feedwater there and just let boiler lifetime suffer. I'm wondering if some modern "miracle" material, maybe carbon composites, can eliminate the need for de-aeration.

Hmm... fresh water from a river or a lake will contain particles and all sorts of minerals.

@MaxW Yes but a simple charcoal filter will take care of those. Once the water is turned to steam then condensed back to water, all particulate mater and heavy minerals will be filtered out anyway. It's the dissolved gasses that remain.

There are many more common alloys in the Inconel , Hastelloy , and Incoloy families. And some odd balls like MP35N, 5o:5o Cr- Ni, Vitallium , and others. Titanum won't take the heat. For all of these materials; if you need to ask the price ,you can't afford them.


text:
IUPAC numbering of carbon atoms in a chain
A chemistry handout for nomenclature of org. compounds I've been reading states a particular rule for every functional group viz.
If there is a choice in numbering not previously covered, the parent chain is numbered to give the substituents the lowest number at the first point of difference.
Can anyone explain what it means?

Consider a n-hexane compound
$\ce{CH3-CH2-CH2-CHCl-CH2-CH3}$
The Cl is different than the H of n-hexane.
Going left to right the Cl is on the 4th carbon. Going right to left it is on the 3rd carbon. So you should use the right to left numbering in this case.


text:
Redox Mg+Copper(II)
If I put solid magnesium in a solution of Copper(II) sulfate, what reaction occurs that causes the bubbles?
Looking at the Potential tables the only reaction that theoretically occurs is the reduction of copper and oxidation of magnesium...so why there are bubbles?
https://www.youtube.com/watch?v=LkUX5vhLjJ0

Copper (II) sulfate hydrolyzes in water and makes the solution slightly acidic.  Then the magnesium is reacting with the weak acid, displacing hydrogen, as well as displacing the copper.
Magnesium displaces hydrogen only slowly with pure water, partly because the magnesium hydroxide product is only sparingly soluble.  Just a little acid, even from an ammonium salt or (as here) hydrolysis of a transition metal salt, is enough to dissolve the hydroxide and launch the hydrogen displacement.

Is the hydrolysis reaction you refer: Cu(2+) + H2O --> Cu(OH)+ + H(+)?


text:
Products of decarboxylation of sodium carboxylate
My textbook says that the decarboxylation of sodium acetate with sodalime produces methane. But if we replace sodalime with barium oxide, pure methane is produced.
What is the difference between pure methane and the methane produced in the first case?

maybe percentage of other products is less with barium

if that were the case, it would have said that the yield of methane is more.

The first reaction is:
$$\ce{CH3COONa + NaOH -> Na2CO3 + CH4}$$
According to Encyclopedia of Inorganic Chemistry vol. 2:

The obtained methane in this process is not pure and may contain as
much as 8 % hydrogen and 10% other hydrocarbons such as the chloride
(to remove  acetylene) and concentrated sulfuric acid (to remove
ethylene and moisture). The purified  methane still contains hydrogen,
which may be removed as water by boiling at 110 °C the  excess oxygen
is absorbed concentrated sulfuric acid.

The second reaction doesn't make much sense to me with $\ce{BaO}$. If this reaction is happening in an aqueous medium, then $\ce{BaO}$ would probably have reacted to form $\ce{Ba(OH)2}$*. So I think you could justify representing the second reaction as:
$$\ce{CH3COONa + Ba(OH)2 -> CH4 + NaCO3 + BaCO3}$$
This is also how the aforementioned book represents the reaction, stating:

Heating sodium acetate with barium hydroxide, instead of sodium hydroxide forms nearly pure methane:
Sodium Acetate + Barium Hydroxide $\rightarrow$ Methane + Sodium Carbonate + Barium Carbonate
$$\ce{CH3COONa + Ba(OH)2 -> 2CH4 + NaCO3 + BaCO3}$$

So I guess the increased purity, in this case, is just due to the different amount of other products produced during the reaction.

BTW, the first paragraph you quote seems really horribly written, to the point of incomprehensibility. The last sentence isn't even grammatical (there seems to be something missing after "110 °C" and/or after "absorbed") and the first one isn't much better. I suspect there was an editing mistake of some kind, and that the paragraph is indeed missing some text.

Seems that way. The quote is from page 390. There seems to be other errors on the page as well, but nothing so severe that I wouldn't trust the main idea behind the text, which is that the latter reaction produces a better yield of methane.

Actually, I found a copy of the book on archive.org (not sure if it's legal or not, hence I'm not linking to it), and the whole book seems to be full of similarly broken English. :( If that's the textbook the OP is using, I feel sorry for them.

I'm using a different book-OP Tandon.


text:
Does mercury have an NFPA 704 classification?
I've searched on a lot of websites if elemental mercury (Hg) has an NFPA classification but I can't find any.
Does mercury have an NFPA classification?

every commercial chemical shipped has to have a MSDS somewhere and that MSDS will have the NFPA information. http://www2.durhamtech.edu/faculty/safety/Safety%20Data%20Sheets%20(SDS)/Chemistry/Mercury%20Hg%207439-97-6%20SDS.pdf // also http://images.mysafetylabels.com/img/lg/L/Mercury-NFPA-Chemical-Label-LB-1592-080.gif

See also this (unanswered) question.

According to Sigma-Aldrich
Some symbols:

GHS06: Acute toxicity (oral, dermal, inhalation), categories 1,2,3
GHS08: Respiratory sensitization, category 1; Germ cell mutagenicity, categories 1A,1B,2; Carcinogenicity, categories 1A,1B,2; Reproductive toxicity, categories 1A,1B,2; Specific Target Organ Toxicity – Single exposure, categories 1,2; Specific Target Organ Toxicity – Repeated exposure, categories 1,2; Aspiration Hazard, category 1
GHS09: Hazardous to the aquatic environment; Acute hazard, category1; Chronic hazard, categories 1,2

And according to ScienceLab:

Health: 3
Fire: 0
Reactivity: 0

I believe the ScienceLab information is the 'NFPA 704 classification'.
EDIT****
An email exchange between NIST and myself asking for clarifiation:
My Email (Pre-filled form on the website, I don't have the original):
Something along the lines of "Hello, I see NIST and a few other manufactures
of have different NFPA classifications (I provided links to the SDS's),
could you explain the difference between your ratings and theirs?"

Their response:
Good afternoon,
Our NFPA rating Health = 2 Fire = 0 Reactivity = 0 matches other manufacturers.
You can check Aldrich website for 99.99 Mercury
http://www.sigmaaldrich.com/catalog/product/sigald/215457?lang=en&region=US

Thank you,
Office of Reference Materials

Other manufacturers (Note, plural) apparently now equals 1 example

But see the link in my comment to the OP. Both NIST and NIOSH have values that disagree with the ScienceLab value, and Sigma-Aldrich gives a value of 4 on one of their MSDS's and a value of 2 on one of their SDS's. Is there a good reason to believe any of these, or the ScienceLab value you give, above another?

@airhuff Yes, I saw. I actually just sent an email to NIST with the links asking if they could explain their rationale on their rating vs. the others, I'll update my answer and comment there if they respond with anything relevant. I figure they're probably the most unbiased and knowledgable on the matter.

Awesome idea. I hope you get a response and look forward to seeing a good reason for this disparity. Thx for your response to my comment.

@airhuff They responded, but their response doesn't help at all, and the tone makes me think that they think I'm stupid for asking such a question. The email in full is in the answer above.

Well, nice try. I didn't read that they were condescending, just incompetent in their answer. No explanation of why the disagreement in the links you sent? Pretty weak effort on their part.

@airhuff Yeah, I'm probably just indignant. Oh well. Either way OP, don't eat the Mercury.

according the Federal Final Rule of hazard Communication Mercury has a NFPA rating of 0 because it does not burn.

NFPA has four ratings for everything...

Yeah according to Wikipedia NFPA has 4 ratings : Health, Stability, Flammability, and special

my apologies, there are 4 ratings (flammability, health, reactivity, and special notice) there is no special notice so it rates as follows: health hazard: 3, fire hazard: 0, and reactivity hazard: 0. Mercury was given these ratings because as you may be aware it is a stable metal, does not burn, and is a serious health risk if in contact with or if ingested.

Thank for the information but MaxW answer show that Mg have a level 4 for the health risks. Don't know why but all the informations aren't the same


text:
Does vinegar react with tap water?
In an effort to prevent mold in my humidifier, I added a little white vinegar to the tap water in the tank. This creates a white bloom that floats in the water. It is odourless and, despite its appearance, is not slimy. It feels more like paper pulp. After a while it adheres to the sides of the tank as a transparent sort of gel. Is this a known phenomenon? What is the white stuff?

Did you try mixing vinegar with fresh tap water? // So it isn't a reaction with the tap water itself.

Acidic acid (vinegar) does not react with water, and it is not soluble in water. The gel and white bloom may come from a reaction the acidic acid with minerals such as calcium that may be present in the dehumidifier. the gel could also come from the breakdown of the chitin cell wall of the fungi. If the white bloom appeared within a minute or two of the addition of acidic acid it was most likely a reaction with minerals or other compounds.

Acetic (not "acidic") acid is most certainly soluble in water. In fact, a 5% aqueous solution of acetic acid is called vinegar!


text:
CV redox peaks and Gamry Potentiometer
I'm using Gamry Potentiometer for taking CV measurements for finding the appropriate voltage values for oxidation/reduction peaks and Echem Analyst for analyzing. CV measurements has performed on liquid electrolyte in order to find if working electrode accept Li ions. My question is about interpreting the results.
How can I interpret if potential difference equal or below 1V has no oxidation or reduction peak (or has only one of them) while potential sweep between -2V to 2V bring good results but if I change it to 1 to -3 no reduction peak again. Moreover, going to negative values has a bad consequences such broke the working electrode. What does it mean going to negative values?
That was my first question, my second question is: Is it possible perform Chronoamperometry measurements (in other word, simulate) by using existing CV measurements via Echem analyst script editor?

Welcome to chemistry.SE! If you have any questions about the policies of our community, please visit the help center.


text:
Expressing solubility in binary solvents with non-additive volumes
I have experimentally obtained data that shows the molarity of a saturated solution   in mixed solvents, with different proportions of solvents.
The issue here is that the two solvents (water/ethanol) have non-additive volumes, and expressing the solubility as $\mathrm{mol}$ $\mathrm{L^{-1}}$ thus seems a bit odd, especially when comparing solubilities between different solvent ratios. Would mole fraction be a better alternative? If so, why? And is it possible to convert from the "old" amount-per-volume answer to the new, better one?
Also, I include a graphical representation of my results, with solvent composition on the x-axis and solubility on the y-axis. Would it be appropriate to use mole fraction (or whatever other unit is better suited) on both axes: the mole fraction of solvents on the x-axis and that of the solute in the mixed solvent on the y-axis?

Not sure where you're trying to go with this. Using molar concentrations works for some calculations and mole fraction works best for others. Neither works well for all calculations.

@MaxW Could you give some examples of situations where each of the units would work best for expressing solubility in binary solvents?

I'll start the list for you. For mixing sulfuric acid with water molarity works best. For density of a binary mixtures of two miscible liquids mole fraction works best // Sorry, I'm confused. I am not driving this question you are. What are you trying to prove? What don't you understand?

For solvent mixtures, especially in mixture or solubility design of experiments,  I work in mass for the solvents.  It's unaffected by temperature,  more accurate (very advantageous if small values are being used) and should get around your problem. You can quote your initial results as %w/w


text:
Why should fire extinguishers containing carbon dioxide not be used on magnesium fires?
As the title states, why should $\ce{CO2}$ fire extinguishers containing carbon dioxide not be used on fires with magnesium metal?
I understand that $\ce{CO2}$ extinguishers work by displacing oxygen, a crucial component of a fire. Does this somehow not work when magnesium is involved, or is there another reason?

The reaction of magnesium metal (Mg) with carbon dioxide is extremely exothermic (heat evolving). In other words, carbon dioxide makes magnesium metal burn.
$$\ce{2Mg(s) + CO2(g) -> 2MgO(s) + C(s)}$$

It's not just carbon dioxide.  Just about any gas that contains oxygen enables magnesium to continue to burn because magnesium is strongly reducing enough to pull oxygen out of the gas molecules, displacing the other element.  The reaction with carbon dioxide given by MaxW is typical.  Water (vapor) also contains oxygen and thus water also fails to extinguish burning magnesium; in fact water vapor would lead to displacing hydrogen and creating an explosion risk.  Burning magnesium also keeps going in nitrogen, forming a nitride.
It's not just magnesium, either.  Other active metals such as calcium have similar properties.  Special fire extinguishers, labeled Class D and containing dry powders that displace oxygen without generating other combustion reactions, are to be used to put metal fires out.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
How does the composition of a mixed solvent affect solubility?
I am trying to find out how varying the proportion of each solvent in a binary (water/ethanol) solvent solution affects the solubility of an organic acid. I know the solubilities of the acid in each solution. Is it as simple as a linear relationship between solvent composition, or is there something else going on?
This question deals with the same topic, and the conclusion there is that it is immensely difficult to predict solubility in mixed-solvent systems. My question is different for two reasons - I only want a qualitative answer, and I know the solubilities for the compound in both pure solvents.

In general, solubility is determined by the intermolecular interaction between a solvent and a solute. Electrostatic forces, hydrogen bonding, electron-pair donor/electron-pair acceptor interactions and solvophobic interactions are examples. The sum of the interaction forces can be related to the polarity of the molecule.
The dissolution of a substance requires that the interaction energy of the solute molecules and the interaction energy of the solvent molecules be overcome. In other words, for the solvation of A in a solvent B, we expect a stronger interaction A-B than A-A or B-B. Considering this, you will have the trend of solubility of polar and non-polar solutes in solvents: the old "like dissolves like" rule.
Now, if you have a solvent mixture, the interaction between unlike solvent molecules is important and leads to deviations from the ideal behaviour from Raoult's law, for example the water/alcohol mixture. Solvent mixtures can exhibit different physical properties compared with their pure components. Coming back to intermolecular forces, it has been found that the ratio of the solvent in the solvent shell of solvation can be different from that in the bulk solution, leading to a preferential solvation. This is caused by the variation of free energy of solvation of the solute in different solvents.
The acid-base equilibria is affected by a change in the 1) acidity or basicity of the solvent, 2) the relative permittivity of the solvent, $\epsilon_{r}$, and 3) its ability to solvate the species in the equilibria. There exists some formulas that relates the equilibrium constant and the relative permittivity (Born, Onsager, etc). In the case of the acetic acid, for example, the relative permittivity will have a strong influence in the solvation of the anionic and cationic species of the equilibria
$$\text{CH}_{3}\text{CO}_{2}\text{H}\rightleftarrows\text{CH}_{3}\text{CO}_{2}^{-}+\text{H}^{+}$$
since the two charges attract each other. The good solvation of the ions in a high relative permittivity solvent shift to the right the ionization. Consider that for water ($\epsilon_{r}\approx80$) and ethanol ($\epsilon_{r}\approx33$) the miscibility is similar, but also have distinct pKa's. Therefore, taking into account only the electrical interaction, between solute and solvent, is a poor approximation. The other problem is that it is practically impossible to find solvents that differ only in their relative permittivities and not in their acidity or basicity.
So, for instance, data on solubility in mixed solvents may be very difficult to obtain, but qualitatively the whole thing works in the form of intermolecular interactions.

The conclusions here are essentially the same is in the question that you linked; even a qualitative answer is not at all straight forward, and a simple interpolation of solvent concentration given the known solubilities of a compound in two different solvents may well give you vastly wrong solubilities in the mixed solvent.
Also, it looks to me as if you have the necessary reagents and information to do a quick, qualitative test this theory.  Try measuring the solubilities of a couple compounds over a range of mixtures of water / ethanol and see how that compares to values predicted by interpolation.


text:
Spatial form of an atom and type of chemical bond
As we know, the first excited states of Hydrogen atoms is $2p$.
The wave functions in cartesian basis we can represent as
$$
p_x          = \frac{1}{\sqrt{2}} \left( Y_{1, +1} + Y_{1, -1}\right)  =\sqrt{\frac{3}{16\pi}} \frac{x}{r}          \\
p_y          = \frac{i}{\sqrt{2}} \left( Y_{1, +1} - Y_{1, -1}\right)  = \sqrt{\frac{3}{16\pi}} \frac{y}{r}          \\
p_z          = Y_{1,0}                                                 = \sqrt{\frac{3}{4\pi}} \frac{z}{r}
$$
which is visulize in forms of dumbells:

My question as follows:

An H-atom in an excited state has the same shape?
How does an atom determines the axis along which to orient? Assuming that the directions equiprobable, the shape should be spherical. Or I'm wrong?
Type of chemical bond ($\sigma$, $\pi$, ...) is determined by the form of the type of atomic orbital ($s$, $p$, $d$, ..., or by their hybrides), but how it is possible if an atom is spherical yet?

(1) The first excited state could also be considered to be that with the electron in the 2s orbital. (2) In the absence of an external field (electric/magnetic) there is no preferred orientation of an atom. The Stark and Zeeman effects show the effect of external fields. (3) You are effectively asking someone to explain all about chemical bonding which is far too big a subject for here, but is explained in numerous texts as is the theory of the H atom.


text:
FeCl3 to [FeCl4]-
A 0.1 M solution of iron(III) chloride in $\ce{POCl3}$ is red and turns yellow on dilution. Titration of red $\ce{FeCl3/POCl3}$ solution with colourless $\ce{[Et4N]+Cl^{-}/POCl3}$ solution causes the colour to change from red to yellow with a sharp end-point at a 1:1 molecular ratio of $\ce{FeCl3:[Et4N]+Cl^{-}}$
Determine the equilibria.
From the molar equivalences it seems straightforward viz:
$$\ce{Fe2Cl6 + 2POCl3 -> 2[FeCl4]- + 2[POCl2]+
}$$
This equilibrium shifting to the right on dilution, giving the yellow $\ce{FeCl4-}$,
followed by:-
$$\ce{[FeCl4]- + [POCl2]+ + [Et4N]+Cl- -> [Et4N]+ + [FeCl4]- + POCl3}$$
but there could be another option:
$$\ce{Fe2Cl6 + 4POCl3 -> [FeCl2(POCl3)4]+ + [FeCl4]-}$$
again, shifting to the right on dilution, followed by:-
$$\ce{[FeCl2(POCl3)4]+ + 2[Et4N]+Cl- \rightleftharpoons 2[Et4N]+ + [FeCl4]- + 4POCl3}$$
any thoughts, anybody?

Does $\ce{Fe2Cl6}$ exist?!?

@MaxW ferric chloride dimerises in vapor phase-Wikipedia


text:
Constraints on the polar angle (θ) in the particle in a sphere problem
For constraint in $\phi$,  $\psi(\phi+2\pi$)= $\psi(\phi$) seems logical as after 2$\pi$ rotation we go back to the same point, therefore functions should be same. But how does it hold for $\theta$ as rotation of $\pi$ gives diametrically opposite point on the sphere, why should then   $\psi(\theta+\pi$) be equal to $\psi(\theta$)?

Isn't it the same? If you add $2\pi$ to $\theta$, the value of the function is the same. Usually, this value goes from $-\pi$ to $\pi$, but the invariant still holds.

but we are adding $\pi$ to theta

Are you sure about that?

$\theta$ ranges from $0$ to $\pi$, as far as I know. It's complicated by the fact that chemists usually use $\theta$ and $\phi$ a different way from the physicists, but I think OP is referring to $\theta$ as the angle made with the $z$-axis.

If $\theta$ is the polar angle measured as it were down from the north pole it ranges from $0..\pi$ and $\phi$ the azimuthal angle, (longitude round the equator) from $0..2\pi$.

There is no a priori restriction between the values of $\psi(\theta)$ and $\psi(\theta + \pi)$. Solutions of the particle-on-a-sphere problem are labeled by two indices $l$ and $m$, and solutions with even/odd $l$ satisfy $\psi(\theta) = \pm \psi(\theta + \pi)$

First of all, as orthocresol and porphyrin said, we should keep in mind that $\phi$ and $\theta$ must span different sets, and there are different conventions on them:

Any spherical coordinate triplet (r, θ, φ) specifies a single point of three-dimensional space. On the other hand, every point has infinitely many equivalent spherical coordinates.
[...]
If it is necessary to define a unique set of spherical coordinates for each point, one must restrict their ranges. A common choice is:
$r$ ≥ 0
0° ≤ $\theta$ ≤ 180° ($\pi$ rad)
0° ≤ $\phi$ < 360° ($2 \pi$ rad)

(Source)
In other words (using the convention above), you must have both $\psi(r, \theta, \phi) = \psi(r, \theta, \phi + 2 \pi)$ and $\psi(r, \theta, \phi) = \psi(r, \theta + 2 \pi, \phi)$ for spherical periodicity.
This is the basic symmetry on a sphere.
But the assignment $(r, \theta, \phi) \rightarrow (x, y, z)$ becomes "ambiguous" (not injective) if the function is defined as an application from $[0, \infty) \times [0, 2 \pi] \times [0, 2 \pi)$ to $\mathbb{R}^3$ and hence not invertible.
You can easily see this if you imagine mapping the surface of earth by having a very long rope with its ends fixed at both poles (half diameter, 180°) and an airplane carrying the middle of this rope around the globe (full diameter, 360° movement).
That being said, the mapping $(r, \theta, \phi) \rightarrow (x, y, z)$ must be taken from $[0, \infty) \times [0, \pi] \times [0, 2 \pi)$ to $\mathbb{R}^3$.
But that does not mean that $\psi(r, \theta, \phi) = \psi(r, \theta + \pi, \phi)$, and as higgsss observed, $\psi(r, \theta + \pi, \phi)$ is not necessarily equal to $\psi(r, \theta, \phi)$.
But higgsss also observed that, for some problems, some solutions might have symmetries allowing $\psi(r, \theta, \phi) = \pm \psi(r, \theta + \pi, \phi)$.
Solutions for the hydrogen atom are good examples of this: for the minus sign, p atomic orbitals, and, for the plus sign, d atomic orbitals.
You can see other orbital symmetries by looking at them here.

You have it backwards. $\varphi\to\varphi+2\pi$ takes you to the same point on the sphere, so the value of $\psi$ must be the same. $\theta\to\theta+\pi$ takes you to a different point.

You're right, I edited and corrected the mistake. Thanks!

That's good, but now your answer is unrelated to the question, since the latter was about $\theta+\pi$.

I think it is still related to the question, since it addresses the fact that $\psi(\theta + \pi)$ is not necessarily equal to $\psi(\theta)$, as was asked, but I will rephrase it to make it more explicit.

I also further improved the answer. I hope it looks good now.

Yeah, now that's spot on.


text:
Help me identify this glassware!
I'm a freshly graduated physics and math teacher moved into a small school from the late 1920s.  The equipment here is old and confusing, at the very least.  I have found many things which I have never seen before.  I would like some help identifying what I have and what I can do with them, if anything.
(Click the images to view them at full size.)

1. A load of copper pots.  For boiling something perhaps?

2. Some sort of wash bottle?  Why is the cork on there?

3. I managed to make out "unitized wash bottle" on the back.  This serves the same function as the last one, I presume.

4. It reminds me of a graduated cylinder until the frosted top and the "arms" that poke out the sides.  What is this for?

5. This reminds me of halogen bulbs.  Again, I have no idea what this is for.

6. I've taken to calling this "trumpet" glass pipe.  What is it used for?

7. This large bulb has confused me since day one.  I feel like it needs some sort of current passed through the ends.  It reminds me of a cathode ray tube in a way.  I'm completely lost on this one.

8. Here.  Have a free safety poster!  Not as good as old Carol, though.

Nice haul! (2) the cork is on there to act as a grip so your hand won't slip; and (5) looks like a condenser to me.

I added answers for each piece that I could identify so that other could comment piece by piece.

@MaxW: It seems to me that, given that you seem to know what all the items are, you should combine all of your multiple partial answers into a single one that answers the OP's entire question. It's not like there's any point in people voting to determine which of your completely orthogonal answers is the best.

@MaxW I highly suggest you merge your answers. It makes it very unpleasant to read them right now because they're scattered and out of order. Also, it's kinda playing games with rep.

I am surprised that so many people are recommending the answers be merged, and not  that the question be split.

Well this is fun! Just looking at this reminds me of a story by my organic chem professor about how they would design a glassware installation in russia, put it together and then actually meld the glass together. The ones with the frosted connections where too expensive.

Close voters: Why? There are over 2k views and clearly the OP's query has been satisfied by @MaxW's answers and other helpful comments: I certainly learned a thing or two from this post. The "too broad" closure vote is, in my opinion, not warranted as these items are clearly defined laboratory ware.

@ToddMinehardt http://meta.chemistry.stackexchange.com/questions/3590/arguably-too-broad-popular-question

Amoco R& D had a glass shop that kept 2 people busy making glassware, mostly custom. designs. So there is no limit to the designs you may find.

#4 is a collection vessel of some sort.
The ground glass fitting would have connected to some other ground glass fitting. A set of the ears would be on the connecting piece of glassware also. Then springs would hold the two pieces together.

Could you tell me why on earth you posted separate answer for each one?

@Mithoron - So that the comment about each different piece would stay together. I wasn't sure if anyone would have something more to add to the different pieces of apparatus or not. #3 I pretty sure about, but I've never seen that before. #4 I don't know if this would have some special use. #7 I'm fairly sure is a Crookes tube, but I don't know why the middle electrode is there.

@Mithoron and as a bonus, MaxW gets upvotes more times ;)

@Ruslan Not necessarily more times. One big answer could be more upvoted then all small ones together.

You do realise that if someone decides to up vote all of your answers here,  the votes will get reversed because of the serial voting script?

I think you should combine your answers. Accepting an answer that corresponds to just one piece of glassware doesn't really make that much sense, because the answer is really all 8

This answer is wrong. #4 is part of a gas washing bottle

#1 is copper pot to make steam
The steam would come out of the metal neck on the side.

Do you know why a copper cylinder fits inside the hole in the top to seal it?  Why not any other kind of stopper?  It's just odd.

It would be heavy to resist the pressure of the steam. // The screw lids would hold themselves of course.

Nope, that is probably because you could hang a container with material in there that would automagicly be kept at 100 deg C.

If you only wanted to seal it a screw top should be provided for, but probably all of them are lost by careless students...

No, I'm sure about the heavy weight "cap." With just the weighted cap you can easily remove if from a hot pot to refill the water. A screw top would really be harder to use.

#8 is a poster from Michigan Technological University in Houghton, Michigan
MTU started as Michigan Mining School because of all of the underground copper mines in the area.
Got my slide rule from what was then the mining school and a "toot bag." (The only engineers the locals knew about were train engineers.) Used the slide rule from high school through college and a year of grad school. Then I broke down and bought a TI scientific calculator with 8 digits (!!) of precision.

I've actually seen these in use (or at least most of them). I can't say that their use was exactly correct, but essentially (What I saw) it's a set  to mix liquids by boiling then re-condensing them.
The two wash bottles are just that. Wash bottles, the first has cork so  you don't drop it. The second, I think, allows you to control flow of the liquid by placing your finger over that air vent.
#4 is where the finished product goes. I'ts just a collection point nothing else.
#5 is a condensing tube, you run a cool substance (probably water) and in the outer chamber and then gas turns back to a liquid.
# 6 is Like the pipe under your sink. As long as there's no pressure it allows liquid to flow without letting gasses flow.
#7 is a Crooks tube. It is used to generate X-Rays. It doesn't have anything to do with the rest of the set. I have only seen one used once. It was used to demonstrate that you could "bend" X-Rays with a magnetic field.
#8 is a poster, to remind us that,even in history, the people making the safety posters didn't always choose their slogans wisely.
So what's missing is a bunch of tubing, but you basically end up with mad scientist looking way to mix liquids, or probably to condense a gas created in the copper pot.
For example, (totally guessing here) based on the history of the school,

Place rocks in copper pots
Use #2 and #3 to put a corrosive liquid onto the rocks.
Use #6 to collect gasses from chemical reaction of materials in rocks + corrosive liquid. The rock/liquid mixture probably has to be heated.
Use #5 to condense liquids to collect in #4.
Play with X-Ray tubes while you wait, and make fun of old timey poster?

#4 is part of a gas washing bottle

#2 is a simple distillation apparatus.
The cork is there to prevent too much condensation in the top part of the bulb. aka. to speed up the process.

#4 collector, but not an ordinary one
My problem with this one is that it has a male connector. There is a reason that male connectors are always on top of the female ones (no pun intended): it keeps liquids inside the apparatus. Do one the other way around and it leaks like crazy.
So this one is intended to be mounted upside down, but the elaborate foot also suggest a life in this orientation. Maybe it is used for gas collection like in the splitting of water in o2 and h2. Fill this thing with water, put a valve on it and place it upside down on your apparatus. Open valve, collect gas, close valve and put it aside.?

#4 is part of a gas washing bottle

#5 is a reflux condenser.
The metal fittings would have hoses for water going in at top and out at the bottom. The top of the picture with the straight glass tube would fit into a rubber stopper which would go into neck of vessel which was holding the liquid to be boiled (the pot). So the condenser cools the vapor from the boiling liquid turning it back to liquid which drips back into the pot.

What is the purpose of boiling a liquid and immediately condensing it back into the same container?  And at the bottom of the picture (the "top" of the tube where it flares out), the tube is open.  So, something is meant to escape this vessel out the top, no?

You're "cooking" some sort of reaction. Typical in organic chemistry. So I add two solids to react to benzene. Boil benzene to add energy to make reaction go, and keep it boiling while reaction occurs. Maybe a couple of hours.  Without the condenser the flask of benzene solution would boil dry.

It can be used in two scenario's: reflux and destillation. Take a look at this diagram.

reflux: "cooking" a mixuture for a prolonged period of time at the boiling point of the lowest one. This condenser makes sure that the compound with the lowest bp is condensed again and returned to the mixture.

distillation: separating a mixture. Same as above, but now you the condenser is after the watershed, so you will be able to collect it in a separate collector.

@RickyA - Nice catch!! You're right. It could be used as a distillation condenser as well. The large opening in the bottom of the picture could accept a stopper with a piece of glass tubing through it.

#6 is a thistle tube.
The loop would be a seal.
Let's say you wanted a low pressure stream of hydrogen gas. You put thistle tub and and glass tube through a stopper. The stopper goes into a container with Zn metal. You pour HCl solution through the thistle tube and hydrogen gas comes out of the other glass tube through the stopper. A bit of the HCl solution would stay in the loop sealing off that exit so the gas wouldn't escape there.

I was was inclined to say air lock too, but the amount of liquid is so small here that it would not really be effective so I think it might be something else.

@RickyA - I just made up the H2 gas experiment, don't know if that would really work. I'm sure it is for a seal. You're right to question that it is a "pressure seal."

#7 is a Crookes x-ray tube of some sort.
Similar picture of a Crookes tube at Wikipedia.

It looks like something to make lightning through a gaseous mixture.

@RickyA - No, I'm sure that it is an x-ray tube. The middle electrode is an anode and it is slanted to direct x-rays out of spherical part of the glass bulb. I don't know why there are two anodes though.

xrays don't  bend its a cathode ray tube generating an electron beam

#3 look like a wash bottle too.
Seem to be missing rubber stopper with glass tube that would go to bottom of the round bottom flask.
I assume black bulb on side can be pumped to inject air into the flask.
The top of the tube would be bent and have a rubber tube connecting to another piece of glass tubing drawn to a tip. The rubber connector is so that if the glass tip is bumped on something then it won't break the glass tube.

#2 does look like a wash bottle.
The cork would be for thermal insulation (to use with hot wash solution) and/or for better grip.
Looks like a bulb on side to pump to force liquid out.
The tube which is coming out of the top should extend all the way to the bottom of the round bottomed flask.
The top of the tube is bent and has a rubber tube connecting to another piece of glass tubing drawn to a tip. The rubber connector is so that if the glass tip is bumped on something then it won't break the glass tube.


text:
Is oxytocin's mirror image still oxytocin?
If you were to take the mirror image of oxytocin, does it remain the same or does it change? Say I want a tattoo of it on the left side of my chest, going from the widest part of oxytocin to the smallest part, but it won't fit the way it is depicted below.

Would it still be correct or does something need to be changed? I can just get it on the opposite side but I'd like to know the chemistry of this.

Hello and welcome to Chemistry.SE! I suggest you take the short [tour] to better familiarize yourself with this site.  This is an interesting and valid question. Many molecules, including oxytocin, have conformations such that their mirror image is not quite the same thing as the non-mirrored image. I don't know if that information alone helps you or not.  Basically if you have an image of the molecule, the tattoo should look the same if you hold the image next to it, or if you laid it over the tattoo everything should match up identically. But not if you flip it over 180 degrees. Good luck!

Oxytocin is composed of $\alpha$-amino acids, which with the exception of one (glycine), are all chiral. A chiral molecule's mirror image is called its enatiomer, and has identical chemical properties except in the presence of other chiral molecules, i.e. in the body. This means enantiomer of oxytocin does not have the same biochemical activity as oxytocin, so you were wise to question whether or not this would be the same molecule. In addition to flipping the molecule, you need to change the wedges to dashes and dashes to wedges for it to still be the same molecule:

Where did you find the mirror image?

It's not the mirror image, it is the same molecule viewed from the other side. I drew it myself.

Both are oxytocin. One is the front of the molecule, and the other is the back.


text:
how to calculate mols Ag from AgNO3 solution
Sorry for the very basic question but its been a very long time since I've taken chemistry and I'm having difficulty solving this problem.
If I titrate something with 1 molar AgNO3, adding 50 ml of AgNO3 solution... How would I calculate how many mols of Ag that equates to?
What I have so far is that 1 M means that there is 0.05 mol of AgNO3 in that 50 ml sample (M = mols/L). So then how many mols of Ag are there in 0.05 mol of AgNO3? Is there just 0.05 mols of Ag in AGNO3 or do I need to somehow take into consideration the proportion of the rest of the elements?
Thank you!!!

If I titrate something with 1 molar AgNO3, adding 50 ml of AgNO3 solution... How would I calculate how many mols of Ag that equates to?

A 1 molar solution of $\ce{AgNO3}$ is 1 mole per liter. 50 ml is 0.050 liters
$ 1 \dfrac{\text{mole }\ce{AgNO3}}{\text{liter}}\times0.050\text{ liters} = 0.050 \text{ moles }\ce{AgNO3}$

So then how many mols of Ag are there in 0.05 mol of AgNO3? Is there just 0.05 mols of Ag in AGNO3 or do I need to somehow take into consideration the proportion of the rest of the elements?

$0.050 \text{ moles }\ce{AgNO3}$ is correct since there is only one atom of silver per "molecule" of $\ce{AgNO3}$. There would also only be 0.050 moles of N atoms, but 0.150 moles of O atoms in 0.050 moles of $\ce{AgNO3}$.

Titrate with known concentration of $\ce{KCl}$ and find the how much $\ce{KCl}$ is required:
p ml.X mol $\ce{KCl}$ = q ml Y mol $\ce{Ag}$ is used there for Y mol of Ag = (p ml $\ce{KCl}$ x X molar $\ce{KCl}$ )/ (q ml $\ce{AgNO3}$ used).


text:
HDAC inhibitor and how it works on a cellular level
I have been working on a research project on the synthesis of a histone deacetylase inhibitor compound. I just realized that I am still a bit fuzzy on the how it works on a cellular level.
So, how does a histone deacetylase inhibitor work on a cellular level?

Do you have a more specific question? The best I can give you is the mode of action that is generally seen across most biological mechanisms:
An HDAC inhibitor would cause inhibition by binding to HDAC, thus causing a conformational change that disallows the protein from being able to transfer  acetyl-groups to a histone-residue (cysteine I believe?).
Usually, if a protein is something that is abundant in cells, an inhibitors/activators work directly through bonding to the target to cause conformational changes. There is probably also another inhibitor that can bind directly to the HDAC-gene to cease its expression (but I don't see this being beneficial in a growing cell - but maybe in mature cells).


text:
Stoichiometric reaction of hydrochloric acid, potassium nitrate, and copper
I have the following reaction involving these elements:

$\ce{HCl}$ (hydrochloric acid)
$\ce{KNO3}$ (potassium nitrate, a nitrate salt)
$\ce{Cu}$ (copper)

The reaction should produce nitrogen dioxide ($\ce{NO2}$).
The chemical equation should look like this:
$$
\ce{HCl + KNO3 + Cu -> NO2}
$$
But I'm clearly missing something. Can anybody help me equalize and complete this equation?

What kind of reaction is this? Are you putting acid into solution? I assume you don't know the other products and that is what you are looking for?

I don't really know what is the reaction type. No I'm not putting acid into solution, I'm producing nitric acid using a  nitrate salt, copper and hydrochloric acid, I don't know the products yeah that's it

Looks right to me. It is strongly encouraged on Chemistry.SE to answer your own question in a formal answer rather than an edit. This will help others to find the right answer if they have a similar question. You could also possibly earn the Self-Lerner badge! Just show any work that you did to get the right equation. Also you should use the proper formatting, which you can read more about here. It's really not that difficult. I will also edit your question so you have another example.

Thank you sir for helping me with the formatting ! I didn't know that I can answer my own question, I'll try this

My apologizes, I found the answer. The full equation is :
$$\ce{Cu + 4KNO3 + 4HCl -> Cu(NO3)2 + 2NO2 + 4KCl + 2H2O}$$
(I'll detail this later)

Why not CuCl2 and KNO3, more likely because chloride is a better complexant than nitrate. Write out the ionic equation.

What happens if all the nitrate is reacted? balance the equation then. The equation is bogus.

Copper reacts in more concentrated nitric acid to give NO2 and possibly some NO depending on concentration.  What happens in the above scenario depends on the concentrations of H+, equal at first to Cl-, Cl-, and NO3-; K+ balances the charge. If the amount of hydrochloric acid is enough, the process makes a mild aqua regia. Such solutions use the complexing ability of chloride to facilitate oxidation by nitrate. [with also the possible formation of Cl2]
In nitric acid:  Cu + 2NO3- + 4H+ = Cu++ + 2NO2 + 2H2O
With sufficient chloride ion: Cu + 2NO3- +4H+ + Cl- = CuCl+ + 2NO2 + 2H2O
An ultraviolet-visible spectrum should define what is going on. [Possibly just observing the solution would be sufficient.]


text:
Using electronegativity and atomic size to compare acidity of cysteine with serine
In proteins, the alcohol group of serine is generally more difficult to deprotonate than the thiol group of cysteine.
Serine and cysteine respectively:

In the literature, the explanation given is that the sulfur atom is larger than the oxygen atom, and therefore the resultant negative charge is stabilised over a larger surface.
But I am confused. Oxygen is a more electronegative atom than sulfur and therefore can more stably carry a negative charge. How are these two assertions compatible?

oxygen can carry negative charge more easily because it is more electronegative, and
sulfur can carry negative charge more easily because it is larger?

Clearly, they cannot both be true and in the case of these two amino acids, the size of the sulfur prevails over the electronegativity of the oxygen. Why is that? Why in some circumstances is it the other way around?

Related: Hydrogen halide acidity

Thanks for that link. Actually I think it completely answers my question.

Related: Why is cysteine more acidic than serine?

You are correct that Oxygen is more electronegative than Sulfur.  However, the relative size of the atoms affects more than their ability to carry charge.  In this case, the larger radius of the Sulfur atom actually causes the H-S bond in Cysteine to be longer than the H-O bond in Serine.  The longer bond is weaker and, thus, more easy to break, making Cysteine easier to deprotenate.