text:
How to know the formula of different compounds?
For example, if I didn't know the compound tin chloride, and I was asked to write out its formula, how would I know how to? Because it seems unreasonable to know the formula of every compound in existence. Many thanks for the help!

You should have a look on possible and common oxidation states of tin and chlorine and then you should be able to figure out the formula of tin chloride.

But if you didn't know what tin o r chlorine was how would you determine  what to write if you had no books or data or anything to refer to?

@Joel That's a pointless question. If you wouldn't know what "addition" or "subtraction" mean you couldn't answer questions like "1+2=?" or "3-5=?" ... you simply have to learn certain things to answer questions.

It wasn't a question it's a comment supporting the validity of the question which according to you is a pointless question . Someone at some stage would of had to have worked it out somehow. By learning.

No question is pointless, some are less interesting than others depending on who's reading it.

I do not agree that this question should be closed. The answer could reasonably be short, as @PH13 subtly mentions it. Lacking research != Too many possible answers/too long answers.

No one knows every formula, however there are rules and algorithms to find such formulas.

In my experience if someone says something like tin chloride they are usually insinuating you know the most common oxidation state that metal is found in when complexed with the chloride atoms. This is a bad practice of them if they haven't explained further but I digress... In this example with the metal center of the complex being tin, the most common oxidation state is +2. This means the formula in its neutral state would be $\ce{Sn^{+2}}$ with 2 chlorides with a (-1) charge making the molecule neutral at $\ce{Sn(II)Cl2}$.
Different effects cause  common oxidation states for specific elements. These are outlined further with Mendeleev's Periodic Law. It breaks down into how shielded the nucleus is by electrons, and how big the radius of the atom is.
A further explanation of tin's common oxidation state calls upon knowledge of the inert pair effect, where elements to the right of the second and third row transition metals such as: In, Tl, Sn, Pb, Sb, Bi form compounds that are less reactive than one would think where the oxidation state is 2 less than the expected group. This is caused by the $\mathrm{ns^2}$ electrons being relatively inert. The cause of that nonreactive state is because of two reasons specifically:

Larger-than-normal effective
nuclear charges in these elements.
Lower bond energies in their compounds.

A good book to use referencing this subject further is Descriptive Inorganic, Coordination, and Solid-State Chemistry by Glen E. Rodgers. This is the book I own and used for when I studied periodic trends, and inorganic chemistry as an undergraduate. It's a great book for this subject, among others.
Also there are commonplace names that are used as somewhat of a slang for certain compounds used in research frequently. These can be learned through experience, or you can just google common names... All formal names are dictated by the rules set forth by the IUPAC. Learning those rules would be good idea. Also keep in mind that in some research projects you will encounter molecules that have informal nicknames too.

Actually, the rules for naming compounds have been converging on the notion that you should be able to construct the compound from the name. How you do this is simply research and practice. There are sites for inorganic and organic naming conventions. Regarding your example, I immediately knew you were talking about an inorganic salt of tin, and I further knew than tin tends to be in the $+2$ state, resulting in the formula $\ce{SnCl2}$. But I also know lots of other possible formulas simply based upon the linked rules. You may not know everything, but you can know a lot simply by learning some basic rules.
Also, @Ryan Lee's answer points out that "tin chloride" is potentially ambiguous, and modern convention has been changing in a direction to make this more clear. The preferred name for this compound is tin(II) chloride, which emphasizes the the fact the the oxidation state of tin is $+2$. Most naming conventions have been formalized so that they encode a way to completely reconstruct the molecule. Nonetheless, tradition exists, so we often still call that solvent acetone rather than propan-2-one, the latter being much more structurally descriptive (i.e. ketone functional group substituted at the 2nd carbon of propane).

The other answers here have already given good responses to how you would find the answer to the specific example you gave. I want to focus on the question and this particular quote:

...it seems unreasonable to know the formula of every compound in
  existence.

You're absolutely right. In principle, we're supposed to have formal naming systems (thanks trb456 for the first two links) that describe exactly which molecular formula you're dealing with. Unfortunately, chemical naming conventions are a bit of a mess, with multiple names for every molecule. So what's a chemist to do?
The answer is that instead of learning the formula for every molecule in existence, you learn to extrapolate and make some pretty good guesses off of what you know. For instance, let's say someone's talking about lead chloride. Well, I don't know what the formula for that is! It could be any number of chlorines!
Luckily, I do recall that $\ce{PbO}$ is often used in microscopes. And since oxygen can only take on a 2- charge, that means that lead has to be +2, so the formula is $\ce{PbO2}$!
Oh wait, but I also remember something in my textbook about a $\ce{PbO2}$ compound. That means that there's two possible forms of lead chloride, $\ce{PbCl2}$ and $\ce{PbCl4}$. And now I've narrowed it down to two possible formula, which the Wikipedia disambiguation page helpfully shows us are the only two.
As to which one is specifically being talked about (and you'll have to believe me on this), I would be inclined to believe that it's the lead(II) variant simply because you see lead(II) so much more often than you see lead(IV).
Another trick you can use is to look at common naming conventions and try to guess why they were named that way. While common names are a lot more unpredictable than the official IUPAC rules, there are some common themes that still get involved.
To take a simple example, the following molecules are named acetylene, and acetate, respectively.

Notice a trend: these are all two-carbon molecules with some functional group coming off the end. In that vein, I can guess that acetonitrile will be a two-carbon molecule with some sort of nitrogen group coming off the end...and I'd be correct!

Ultimately, it's silly and somewhat pointless to try to memorize the official name, common name, and molecular formulas of every single compound you'll ever use. Instead, there are two sets of tricks you can use:

Nature follows a pattern. Look at compounds you already know and try to figure out what rules compounds you haven't seen should follow
Humans didn't pick names for no reasons. Look at the names and see if there's a common pattern.

It's not easy, but if you work hard at it for a year or two, you should have enough knowledge to piece together information about most of the compounds you'll hear about.


text:
If a chemical formula for a mineral contains a comma, are there limits on the amounts of each element?
I have a chemical formula for the mineral actinolite which is: $$\rm{Ca}_2({Mg,Fe})_5{Si}_8{O}_{22}({OH})_2$$
The formula contains a "," which I understand means that the magnesium and the iron can have different combinations (up to 5 total).
The question is, if magnesium is the dominant atom, is it possible for the amount of magnesium to be less than iron and still be actinolite, or must magnesium always have the greatest amount?

Actinolite is a mineral that is part of a so-called solid-solution series, which means that you get different but related minerals depending on the amounts of (in this case) iron and magnesium that are present. The magnesium-rich end member is tremolite; the iron-rich end member is ferro-actinolite; and what lies between is actinolite.
According to Wikipedia's article on actinolite, the formula is more precisely:
$$\rm Ca_{2}(Mg_{4.5-2.5}Fe^{2+}_{0.5-2.5})Si_{8}O_{22}(OH)_{2}$$
So, for your question:

is it possible for the amount of magnesium to be less than iron and still be actinolite, or must magnesium always have the greatest amount?

the answer is no: at best, Mg and Fe can be present in equal amounts for the mineral to still be called actinolite, but note that in that particular case you are on the "border" between actinolite and ferro-actinolite, so perhaps what you choose to call it is up to you. And as mentioned above, if magnesium is dominant, the mineral is tremolite.
In the case where iron is the dominant atom, the mineral is called ferro-actinolite with the formula:
$$\rm Ca_{2}(Mg_{2.5-0.0}Fe^{2+}_{2.5-5.0})Si_{8}O_{22}(OH)_{2}$$

That answers the specific issue with actinolite, but does not address the more general notational issue. If you have chemical formula that is not more precisely specified, is there any difference between ...$\ce{(Mg,Fe)5}$... and ...$\ce{(Fe,Mg)5}$...? - that is, does the order of elements in the parenthesis tell you anything about the relative amounts of the element in the compound? (The formula given for ferro-actinolite indicates "no", but it would be nice to have it explicit.)

The order of the elements does not tell you anything about the relative amounts of each, as you correctly indicate. The more specific ranges on stoichiometric ratios - indicated above by subscripts and typically seen for minerals in solid-solution series - gives the more specific description.

If the order of the elements does not tell you anything about the relative composition, then are they listed by increasing atomic number?

Honestly, I don't know - there are enough historical artifacts in re: naming and conventions that it could be the case. There is a reference on Wikipedia that states that in one database (mindat.org), the dominant cation goes first in the parentheses. BUT the International Mineralogical Society is the IUPAC equivalent for minerals since 1959, and if you look at their 2015 master list of mineral names, you'll see the formulae for the 3 minerals here with Mg first and Fe second.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
What are actually the differences between Sidgwick & Powell theory and Nyholm & Gillespie Theory?
The famous VSEPR theory was proposed by first Sidgwick & Powell. It was modified then by Nyholm & Gillespie.
I was reading Inorganic Chemistry by J.D.Lee where he discusses very briefly the theory of Sidgwick & Powell; I couldn't somewhat conceive the language. So, I googled it but to my misfortune I could nowhere get more info other than this:

The idea of a correlation between molecular geometry and number of valence electrons (both shared and unshared) was originally proposed in 1939 by Ryutaro Tsuchida in Japan, and was _independently presented in a Bakerian Lecture in 1940 by Nevil Sidgwick and Herbert Powell of the University of Oxford. In 1957, Ronald Gillespie and Ronald Sydney Nyholm of University College London refined this concept into a more detailed theory, capable of choosing between various alternative geometries [1]

Everyone would give the historical info that Sidgwick & Powell was the first to introduce the theory which was later modified to the present VSEPR theory. I don't want that!
Can anyone please help me to bring me forward the original Sidgwick-Powell theory? Also the million-euro question: What are the differences between the two theories? In another way to say: What were the modifications that Mr. Nyholm & Gillespie brought forward that "improved the original" theory?
[1]https://en.wikipedia.org/wiki/VSEPR_theory#History

Perhaps you should read the original papers: N.V. Sidgwick and H.M. Powell, "Stereochemical types and valency groups", Proceedings of the Royal Society of London Vol 176, No. 965, pp 153-180 (1940), and R.J. Gillespie and R.S. Nyholm, "Inorganic Stereochemistry", Quarterly Reviews, Chemical Society 11 (4) 339-380 (1957).
To quote out of Gillespie's paper:

Sidgwick and Powell assumed that lone pairs of electrons and bonding pairs were of equal importance and that they arranged themselves symmetrically so as to minimise the repulsions between them. The ligand(or crystal)- field theory is concerned with the influence of the non-bonding electrons upon the arrangement of the ligands which are assumed to be negative ions or dipoles surrounding a central metal atom. Recently the influence of covalent binding has also been considered. These various theories are in fact closely related and an attempt has been made in this Review to integrate them. It appears that the simple theory of electron-pair repulsions receives considerable justification from quantum-mechanics and when refined to take into account differences between the repulsions between lone pairs and bonding pairs of electrons provides a very satisfactory theory of the stereochemistry of inorganic molecules.

That should get you going...

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Generating neat orbitals/surfaces from molden/wfn-files
I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's Kohn-Sham-orbitals.
But when it comes that I have to use other programs than Gaussian - such as Turbomole, ORCA or Molcas - I am confronted with molden- or wfn-files that GaussView cannot handle.

Avogadro 1.1.1 (Lib 1.1.1, OB 2.3.2, Qt 4.8.5)
I quite like Avogadro because it can produce as fancy pictures as GaussView but especially for molden files at least on my computer it seems to fail hard. As you can see the orbital is reproduced perfectly from the file but Avogadro somehow cannot manage to show all atoms.

I hope that I'm not the only one around who can't manage this to work properly.
Thanks to Geoff's comments I learned that wfn-files can be imported through the Extensions $\rightarrow$ QTAIM menu which allows AIM analysis.

gmolden 4.x or 5.x
I have absolutely no idea which version this is.
What seems to be easier to open molden-files with molden? I guess that's something to try out. But for me molden stops being an alternative since I am unable to arrange my molecules in space as much as I want. Also molden produces only those stacked-layer orbitals that are not really up to date. Molden can produce pretty good orbitals after one gets how it works. Thank you hokru!

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

Gabedit 2.4.8
Now Gabedit is fancy ... there are a lot of input- and output-files that are supported - luckily molden files are part of it.

At least I can create orbitals somehow acceptable for me and arrange my molecule in space as much as I want it. There is also the povray-output stuff but I was not very successful with this approach, yet.
Now what stops me from using Gabedit at a regular basis. It is that there is everytime this point-and-click-adventurish menu -> orbitals -> selection -> again orbital selection -> quality settings -> isovalue settings -> wait and look. The settings were wrong? That's bad ... do the most things again and choose better values. Is there a simple way to compare orbitals fast? Not really, because the orbital slide show is a little bit tricky, too.
Did I say something about wfn-files? I think they are not supported.

Jmol 14.2.4_2014.08.03
Jmol is another program that can open molden files and I am again unable to create nice orbital images with this program. Even rising the so called "resolution" up to a reasonable degree only produces hexagonal-shaped orbitals.

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

Multiwfn 3.3.7
Now there is this free fancy little program from china. A big 400 pages manual/tutorial-pdf comes with it. With it one can quickly have a look on orbitals with a possibility to quickly change isovalues. It lacks unfortunately my favored free arrangement in space plus there are no proper lighting settings ... and the orbitals and structures are not really that beautiful.

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

Conclusion
Well ... as I can use Multiwfn to convert the files that GaussView cannot read in by itself, there is always this curious feeling that there has to be a simpler alternative to all this. A program that can produce nice images without all the lackings and misbehaviours.
How do you do this stuff for visualisation of molden-/wfn-files to produce nice images of your orbitals and molecular surfaces?

VMD is my go-to: http://www.ks.uiuc.edu/Research/vmd/. As with anything, it takes some getting used to, but the wealth of options and pretty high level of configurability make it the king of visualizers in my book.

Do you know a good tutorial on VMD?

Not offhand, unfortunately. I have had in mind for some time now to write one up for the ORCA user's wiki, but haven't yet gotten around to it.

Often different quantum chemical programs require different analysing tools. Unfortunately there is no universal standard (program), that can do it all. If there were, someone would come along and just invent something new.

I personally prefer ChemCraft for producing publication ready images. It is a commercially distributed program. It mainly supports any Gaussian and GAMESS file formats (and Firefly by extension). It can visualize quite a few more formats now. What I especially like about the program is that it can read the files generated by the NBO programs. It makes visualisation of all kinds of localised and canonical orbitals much simpler.
There are some more features of the program I really got attached to, like symmetrizing molecules or building molecules from scratch. It has the big advantage of writing the symmetry adapted data group for GAMESS for custom basis sets, which I have not been able to find anywhere else. But this is certainly not the target of this post.
 Unfortunately it is not able to read molden or wfn[1] files.
The program comes with a large number of visualisation schemes, which can easily be modified to produce a personalised style. Below is a small demonstration.

Most of the times I would use one of the above, depending on whom I have to impress. Often it is far more beneficial to have monochrome images, like the ones below.

A quite recent addition came with styles that allow you to generate simple 2D like structure. It is still possible to overlay these structures with orbital plots. (Unfortunately the transparency is hard-coded and cannot be set explicitly.)

The caveat is obviously, that it cannot read molden or wfn[1] files, not even Turbomole output.
A feature that I am still missing is the batch production of orbital pictures. You still always have to save them by hand, which can be incredibly tedious for large molecules (and large active spaces). (But I have written a feature request for that.)
Support for the program is quite good and the available help files are even helpful. Most of the features can be understood intuitively, however, as always, it takes time to get used to working with it.
Another caveat is, that the windows version outperforms its little linux brother by a lot. If you already run windows somewhere, that is probably fine for you. If you run linux almost everywhere, then you have to deal with some missing features (or recently it can be ported via wine, making it slow though).

I do use molden (Xwindow) quite a lot for intermediate visualisation, since it is one of the fastest interfaces available. It is very robust and has low graphics; you can easily use it whit a rather slow internet connection. It is free for private and non-commercial usage. Since my first days as a computational chemist involved the use of 56k-modem for checkup routines, this was one of the only go to programs. It will always be the first program I install on a work-dedicated computer. One simply does not forget his or her oldest friend.
A very big plus is the very well structured and written postscript files produced by molden. Some of the purists might even like it. Here are a few converted samples, but you can download the source here (via tinyupload.com).

Such files can become extremely handy, when preparing posters (especially when using LaTeX). I have on occasion seen molecular plots generated by molden in publications; I am even guilty of that. However, nowadays I believe there are more elegant methods.

Visualising Turbomole output has been, is and will probably always be a painful experience. For some of the deeper features you should probably be an expert in gnuplot, too. For the basics of structure and orbitals, the current recommendation is to use TmoleX, the GUI to turbomole. If it is done by the same people who designed define, then it's will be quite painfully to use. When I was a heavy user of turbomole, this did not exist, so I should probably shut up.
Judging from the current (version 7.0) manual the workflow I used is still somewhat recommended. It is to let the native modules create the binary *.plt files, which are gOpenMol input. Unfortunately, what was once a very aspiring program is nowadays not developed any more. You can still obtain an unsupported copy. The source code is available, but the current license state of the program is somewhat unclear. Since VMD (see Brians post) and TmoleX do now support gOpenMol files, the necessity of learning a deprecated program is probably not useful any more. One of the prime features of this program however was that it has a tcl interface and hence was fully scriptable - apparently something that VMD now also has.
It is well capable of producing nice orbital pictures, you might have seen them on this page already. (I tweaked the Gaussian output a bit, since I do not have Turbomole available.)

Although it supports quite a few file formats, molden input and wfn[1] is unsupported.

[1] Let's come to the last part: wfn files. However you produce them, they are probably not up to date. The main (and probably only) purpose for those files is the analysis with AIMPAC -  a program that is no longer developed. They have one very big disadvantage: they cannot deal with functions higher than of f type. If you are using a triple zeta basis set, you probably have those functions. Another disadvantage is, that they don not include information about possible effective core potentials.
For the purpose of analysing the electron density with the quantum theory of atoms in molecules (QTAIM) the much superior version wfn extended (*.wfnx or *.wfx) should be used. I am currently only aware of Gaussian to create such files correctly. The main program which uses these files is AIMAll. It is also a commercially available program. You can learn more about these files on the specification page there.
The only valuable point of creating molecular orbitals with this program is, if you want to overlay it with the bond paths instead of just sticks. Just like in this example:

Apart from this usage, the process is very tiring and needs many steps to be completely performed. Working the program non-local is very, very slow. And to be perfectly honest, what is the purpose of the above other than impressing a few organic chemists?
Another negative aspect of the program is the very high demand of memory and storage, especially for large molecules.
In conclusion: If you are not doing QTAIM analysis you should probably refrain from *.wfx files for visualisation purposes. For every QC program there usually comes a workable interface/visualisation program. With any program there is the activation barrier of learning how to do things to overcome. In any case, I suggest having a few ready to work with, you never know where you go and you might have to learn a new program any time.
I think the biggest loss of any visualisation tool is the neglect of writing good tutorials or even a basic documentation.

what is the ChemCraft visualization scheme where the orbitals are transparent (the first one)?

@gannex I created my own styles and this one uses the wireframe option for contour surfaces. I can't check now, because I'm only on mobile, but you should find it in the customisation section, if I remember correctly.

The WFN format is actually the POLYATOM format from even before the advent of (QT)AIM.  Hence, it is/was useful elsewhere.  Having written a few QTAIM frameworks, I can say it doesn’t require much more memory than the storage of the wave function itself.  It is computationally expensive to do integration, because the atomic basins have to be delimited (e.g. shooting rays out and deciding whether the emanating ray still belongs to the atom in question).

Also, AIMAll is just one (excellent) QTAIM analysis package. I am not sure if it is the “main” one—critic2 is free/open-source and is applicable to gas-phase and solids.  (The solid state community seems to have a lot of affection for QTAIM given their focus on the observable electron density.)

for completeness, gmolden can actually produce high quality pictures like these:

You need to click the button in the top right in density mode to get the opengl rendering. It is also fully rotatable.
While i really like molden for its quick response opening structure files, usability is not its strength. Also it is slow to generate the orbitals.

Another program is Molekel, which uses openbabel (i think) to read various file formats. It works fine with molden-type files.
Much faster than molden to make the orbitals and more flexible (color, resolution, bounding box). I never tested wfn files.

VMD is my current go-to for molecular visualization.  As with any software, it takes some getting used to, but the wealth of options, what seems to be a robust feature set, and generally flexible configurability make it the king of visualizers in my book.
I've only ever tried it with ORCA output, and I've only been able to make it work with "gOpenMol binary" files as generated by the orca_plot utility (ORCA's Molden files appear not to be completely read), but I'm quite satisfied with the results.  The steps I typically follow are:

Run the ORCA computation to get the .xyz and .gbw files
Run orca_plot basename.gbw -i to generate the gOpenMol .plt binary file of the desired function (atomic/molecular orbital, electron/spin density, etc.)
Run VMD and load the .xyz and .plt files

File > New Molecule to reach the 'open' dialog
Browse... to the desired .xyz file; Determine file type should automatically detect the XYZ format
Load to pull the geometry into VMD
Change 'Load files for' to New Molecule
Browse...' to the desired '.plt' file;Determine file type` should automatically detect the 'gOpenmol plt'
Load to pull the binary information into VMD
Close the 'open' dialog

Change the molecule display mode

Click Graphics > Representations
Under 'Selected Molecule' choose the .xyz file
Under 'Drawing Method' choose the desired method (I usually use 'licorice')
Run up the Sphere Resolution and Bond Resolution, and tweak the Bond Radius as desired

Apply the desired formatting to the isosurface(s)

Again in the Graphical Representations dialog (don't have to close after setting the geometry drawing method), select the .plt from the Selected Molecule dropdown
If plotting a quantity with negative regions (orbital wavefunctions, possibly spin density, etc.), click 'Create Rep' once, to get a second 'representation'.
Change 'Coloring Method' to ColorID, and the number in the dropdown that appears to whatever color desired for one phase (positive or negative)
I usually set Material:Transparent (so as to see the molecule under the isosurface) ... Drawing Method:Isosurface ... Draw:Solid Surface ... Show:Isosurface ... Step:1 ... Size:1
Set the Isovalue appropriately for the signedness, positive or negative, by typing the number into the box and pressing Enter; I usually start at a magnitude of 0.02
Repeat the above for the opposite-signed portion of the plot, if required.

A quick example is below -- the SOMO of gas-phase monoaquo-Cu(II):

The three keyboard shortcuts I use the most are those that change the mouse behavior: R to rotate, S to scale (zoom), and T to translate.
VMD can apparently export to a number of 3-D file formats, as well as PostScript vector graphics.  The direct bitmap export is fine if you don't need to zoom in, but pixelates pretty badly if you do.  The PostScript is pretty blocky in gswin64, but might do better in, e.g., Inkscape.  I don't have IS installed at the moment, so I can't tell if a better renderer does a better job of things.
One further nifty feature of VMD is that it can render in stereo.  Even if you don't have 3-D glasses, you can still look at things Magic Eye style by clicking Display > Stereo > SideBySide. (Turn Display > Stereo Eye Swap on if you need to cross your eyes to see it, instead of looking into the distance.)
You would probably have to fiddle around with the different file types generable by each software package to find the best one to interface with VMD.  I don't have a copy of either Molcas or Turbomole to test them out, unfortunately.  VMD does support Gaussian CUBE files, so worst-case you can dump a (possibly huge) grid and plot it that way.

Does it come with any capability to run a script for batch generating of orbitals?

I don't know how that works, but NCIPlot uses scripts for VMD ... so I would guess that scripting is possible

@Martin-マーチン Scripting is definitely possible; I think it's Python-based..?

Scripting in VMD uses TCL

I use VMD with .cube files generated by Molden. For high-quality images I increase the resolution in Molden quite a bit (100-200, default is 61), and possibly the box size. Then in VMD I choose Render > Internal Tachyon or, if I feel adventurous, POV-Ray, and then tweak the scene (sometimes using "media" for the orbital, instead of isosurface)

I use Avogadro obviously.
In Avogadro v1.1.x you can not only use wfn files, but perform QTAIM analysis. Open it under the QTAIM menu.
Send me the Molden file if you can't read all the atoms, that's a weird bug. It works on any Molden file I've tried.

Unfortunately it works for no one here. :/ Maybe wrong drivers or something like that? It's Win7 x64 Ult ... and I have to change my text ... it's version 1.1.1/Lib 1.1.1/OpenBabel 2.3.2/Qt 4.8.5

Are you using primarily ORCA, @PH13? ORCA's Molden files are peculiarly structured, and don't play nicely with a lot of programs that they ought to.

E.g. the file for uracil was made through Turbomole's TM2MOLDEN

It is possible to use Multiwfn to convert molden files into fchk files that could then be read by GaussView.
The way that satisfied me enough is not the most efficient, I guess, but as it is scriptable, it is acceptable easy and gives nice images.
The way to go: QC program > molden file > Multiwfn > cube file > UCSF Chimera.

Generate your molden file
Use Multiwfn to create the MO cubes:
200 Other functions (Part2)
3 Generate cube file for multiple orbital wavefunctions
29,30
3 High quality grid
1 Output the grid data of these orbitals as separate cube files

This will give you orb000029.cub to orb000030.cub to work with.
Generate a python session file with Chimera by opening an xyz file of your molecule, orienting it as you want it and File > Save Session As.
Write a program to generate something like the following input, which can be fed into Chimera.
open session.py
preset apply pub 2; color byelement
copy file geometry.jpeg supersample 4 dpi 100 width 1450 height 1068
open orb000030.cub
preset apply pub 2; color byelement
volume #1 level -0.04 color 0,.5,.6 level 0.04 color .9,.7,.1 step 1
copy file orb000030.jpeg supersample 4 dpi 100 width 2175 height 1602
close #1
…
stop

This input would be called with chimera input.cmd which at this point only shows the geometry of the molecule because it was saved in the session file. My script then saves an image of this geometry and afterwards opens all cube files to produce nice images of them.


text:
Attachment of disulfide (protected) thiolated oligonucleotide on gold surface
What will happen if I incubate a clean gold surface in un-deprotected
($\ce{oligo-C6-S-SH}$) thiolated oligonucleotide solution instead of deprotected ($\ce{oligo-C6-SH}$) solution. I have read clean gold surface can cleave disulfide bond.

I don't have references at the ready, but I would expect the disulfide would cleave and you'd end up with oligo-$\ce{C6}$-S-Au on your surface

How stable are those hydrodisulfides?  Wouldn't they be prone to disproportionation to things like oligo-S-S-oligo, oligo-S-S-S-oligo, and oligo-SH?

What actually happens in sulfur-gold bonding is not very well known. There have been many proposals and studies done, well-summarized here. There is some evidence, including computational studies, that suggest that dissociation into two thiolates is energetically favourable. Bridging across protruding bits of gold (we often draw gold surfaces as straight lines, but they're seldom that flat) may also be involved. This case, where you only have a chain on one of the two sulfurs, may be less interesting and I haven't found many studies of terminal disulfides so the exact process might be different.
To answer the practical question, Can I stick a disulfide-functionalized molecule onto gold?, yes you can, and they will stick very well.


text:
Why is the resonance concept not required in molecular orbital theory?
In valence bond theory, resonance plays a pivoting role; why isn't such concept needed in MO theory? Why is it told that "MO theory provides a global, delocalized perspective on chemical bonding"?
(This is a follow up to What is actually the difference between valence bond theory and molecular orbital theory?)

Because MO is closer to reality.
Resonance is a convenient fiction used to simplify the visualization of some molecules, and rationalize their actions in the frame work of Lewis structures. But every resonance structure you have ever seen in your life is a lie.
Well, this is not exactly true. It's more precise to say that resonance structures are like blind men trying to describe an elephant: they each give a partial snapshot of truth while being wholly inadequate to describing it all. The "true" structure is a weighted average of all the resonance structures based on how stable they would be if they were the actual molecule.
MO cuts to the chase and attempts to directly describe the molecule in terms of its molecular orbitals: another convenient fiction, mind, but one that is closer to the truth. The reason you don't need "resonance" MO structures is because molecular orbitals are inherently a probabilistic construct: they already take into account the uncertainty in the electrons' positions.

"The reason you don't need "resonance" MO structures is because molecular orbitals are inherently a probabilistic construct: they already take into account the uncertainty in the electrons' positions."- what do you mean by that, sir? Atomic orbitals are themselves  wavefunctions; they are also probabilistic construct & resonance is the superposition of wavefunctions of different electron arrangements for same nuclear frame; it is also a probabilistic construct! What do you actually want to point out among them saying "probabilistic construct"??

Let me make myself plainer. An atomic orbital is probabilistic, but only takes into account the possibilities of an electron being in one atom space. In pure valence bond theory, either the wave function for the electron is over in one atom, or the other. The issue is that the electrons are in fact delocalized. In VBing, the resonance structures are what show this delocalization. However, in MO theory, the delocalization is inherent in the construction of the molecular orbitals: the wave functions are already distributed across all the atoms a given electron interacts with.

In MO theory, the molecule is described by Molecular Orbitals that are approximately calculated from atomic orbitals; I believe the process is referred to as constructing "Linear combinations of Atomic Orbitals" (LCAO).
My understanding is that you use "weighting coefficients" to say how much a particular atomic orbital contributes to a given Molecular Orbital.You also always get out as many MO's as AO's you put in.
Take for example, Benzene. If you start adding up the atomic orbitals it would be understandable to assign each atomic orbital equal weight in the calculation. So in the end you get 6 equivalent MO's.
I would like to hear someone else's perspective on this, but I'm guessing that you sort of "infer" a structure similar to that obtained from resonance because of this equivalency.


text:
How do flavonoids absorb UV radiation?
I know that energy is absorbed due to chromophores which enable electron transition which uses up energy. But I am a bit unsure about what happens after the absorption and where this absorbed energy went.
I am not very sure if the energy is dissipated since it would contradict with the law that energy can't be destroyed. If the energy is lost as heat, then it is a bit contradictory again according to the equation $E= hc/\lambda$.
The wavelength would be big for infra-red and thus, the energy lost must be less than the absorbed energy from UV.
So how exactly are these flavonoids shielding UV radiation? And also, if these flavonoids are in the excited state, it makes me feel that they might be quite reactive and may form free radicals.

The energy adsorbed may be re-emitted as another photon (the phenomenon known as fluorescence) or dissipated into thermal energy or used up in a chemical reaction (a subject of photo-chemistry)

"The wavelength would be big for infra-red and thus, the energy lost must be less than the absorbed energy from UV." Who said you could only emit a single photon? Why can't we absorb a photon of say, 4eV (about 300nm) and emit 20 photons of 0.2eV (about 6.2 micron)?

So how exactly are these flavonoids shielding UV radiation?

Due to the structure of the flavonoids, there are many transitions to absorb the UV radiation. Also, there are many transitions to release the energy. Most of the time, it is released in 2 steps (2 photons) which equal the energy of the photon that exited the molecule.
Fluorescence emits a photon that is close to the same energy as the first photon. For quercetin, the excitation is at 440 nm and the emission is at 540 nm.

My guess is that they absorb UV because they have conjugated pi bonds in their structure (i.e. $\ce{= - = - =}$ structures).  A system of three of these in a row might form a box of the right length to absorb at around 250 nm (since that is what hexatriene absorbs at), which is ultraviolet.
check out Wikipedia.

This could be improved with the inclusion of references.


text:
Trying to Understand Entropy
I'm currently looking at Principles of Chemistry by Atkins, and I have a few questions involving entropy. These questions probably arise from my poor understanding of reversible/irreversible processes.

Why are reversible processes called reversible? Is it necessarily true that reversible processes can be reverted spontaneously, or is this a common misconception that people have?
So my chemistry textbook gives the definition of entropy as
$$\Delta S = \frac{q_{rev}}{T}$$
where $q_{rev}$ is heat transferred reversibly. However, I get lost at how entropy could increase during a reversible process.
Why is the reversibility condition necessary for the definition of entropy?

Just me with a trivial comment again, but I'll say that entropy is more correctly defined with infinitesimals: $\mathrm{d}S = \mathrm{d}q_{\text{rev}}/T$. The equation in OP's question is obtained via integration of this, and is therefore only valid if the process is isothermal, i.e. the temperature of the system is constant throughout the process.

They're called "reversible" because the processes can run backwards without additional input of energy. There aren't really any truly reversible processes in the universe, though (some come very close, but the construct of "reversible" is an ideal, not a reality).
Entropy of a system can increase just fine during a reversible process: expanding a gas "slowly enough" is reversible ("slowly enough" means in an infinite number of infinitesimal steps), but the entropy of the gas increases as it expands as it has more microstates to go into. The entropy that remains constant in a reversible process is that of the system plus the surroundings (in other words, the universe).
The process does not need to be reversible to have entropy. However, we measure entropy based on the heat of the reversible process because entropy is a state function (it depends on the beginning and end points of your process, nothing more) while heat is a path function (it depends on the path you take to get there).

Regarding item 2, if the process is adiabatic and reversible, the entropy of the system does not change.  If the process is isothermal and reverisble, the entropy of the system increases.

Second law of thermodynamics tells that:

Energy tends to disperse from being localized if it is not hindered from doing so.

Why does a hot cup of tea become cool? Because the higher vibrational energy of the hot mug & tea was localized only to the tea-mug system. When it is brought in the surroundings, the localized energy disperses to the surroundings. This is what second law of thermodynamics says about.
Let me give you another example of energy dispersal approach to entropy.
Suppose there is a gas enclosed by a stop-cock in of the bulbs of a two-bulb container. When you open the stop-cock, the gas expands & covers the two bulbs. Why did it happen so? It happened because as you open the stop-cock(removed the hinderance), the localized energy of the gas molecules spread over the whole volume to disperse its energy over a larger volume.
Change in entropy measures how much energy has been dispersed at a specific temperature. Entropy is a state property & how it changes doesn't matter at all. However it is far easy to take the course of the change as a reversible process.
Entropy of the universe(system + surroundings) always increases or doesn't change but never decreases.
For example, take a hot body at temperature $T$. Now, bring in another body which is at a temperature $T - dT$. Since, the difference is infinitesimal, the process of transfer of heat can be considered as reversible. Let $dQ$ heat energy be transferred from the hotter body to the colder body. Decrease in entropy of the hotter body after the heat transfer is $\dfrac{-dQ}{T}$ & increase in entropy of the colder body is $\dfrac{dQ}{T - dT}$. By simple inequality, we can show that $$\dfrac{dQ}{T - dT} > \dfrac{dQ}{T} \implies -\dfrac{dQ}{T - dT} < -\dfrac{dQ}{T} \implies \dfrac{dQ}{T - dT} - \dfrac{dQ}{T} > 0 \implies dS > 0$$.
In classical thermodynamics, there is no definition of entropy actually; what is concerned here is actually the change of entropy.
However, in statistical Mechanics, entropy can be defined as the number of microstates the system has at a particular state.
What is a microstate?  each particle in a system collides & now & then they redistribute the energy among themselves without changing the total energy of the system. Microstate is one of the arrangements of the particle's energy for a particular state. It describes how each molecule is distributed at various energy levels at a certain instant. ( As you are reading Atkins, you can get the taste of this approach soon; he has described it beautifully.) It is not that the particles are at various microstates at a single time; it rather describes at a certain instant how the particles are distributed among various energy levels(Total energy is always same; it is just redistributed now & then due to the random collisions of the particles.)
More the microstates for a given state(temperature, pressure, internal energy of the system), more is the entropy at that state. Why? Because here the total energy has more ways to get dispersed to a certain microstate. Suppose, you have two systems $A$ & $B$ having the same energy $U$. However, $A$ has more microstates than $B$. So, the energy $U$ in $A$ owing to its having larger number of microstates has more ways to redistribute among the particles at a certain instant than in case of $B$. So, the energy $U$  disperses more in $A$( as it has more ways to distribute its internal energy) than in $B$ where the energy $U$ disperses lesser (since it has lesser number of ways to redistribute its energy) & hence its energy is localized. Thus entropy of $A$ is more in $A$ than in $B$ as in the former, energy isn't localized & disperses to more microstates than in $B$ .

@thkim1011: Has it helped you somehow? Have you read my answer? Please comment.

uhh.. I guess it was informative. But most of my misunderstanding was in question 2. I didn't consider the fact that the surrounding lost entropy which results in no change in the entropy of the universe. Thanks for the response though. I appreciate it.

@thkim1011: Do follow this site for the understanding of second law of thermodynamics & entropy.

If you'd like to get a better understanding of entropy and the second law of thermodynamics so that you have what you need to solve homework problems, see the following link:
https://www.physicsforums.com/insights/understanding-entropy-2nd-law-thermodynamics/

I generally don't like the Physics Forum means of question & answering  contrary to  the SE. However, the link you have offered is really greatly intuitive . Lucidly written  about how Clausius comprehended the concept of entropy; the page is excellent. An awesome job, sir(hope that you have written).  However, for understanding , I do follow Frank Lambert's approach of energy dispersal which is highly conceivable unlike the term disorder. +1 for providing the link, sir.

However, sir, if you don't mind, can you please at least write the gist, what your link provides, in the answer because in case your link gets broken, then also the future users may have a view to your excellent intuitive work ? It is better to provide the info a link supplies in the answer as sometimes the link may not work:)

Glad you liked it and hope it will help with your understanding and with your ability to do your homework problems.  The reason I wrote the Physics Forums Insight article is so that I wouldn't have to always paste it into answers to Physics Forums thread questions.  That's why I don't want to give the gist again here.  It is one of the most accessed Insight articles to date, and is sure to survive over time.

It needs to get survive! This is one of the best articles I have ever read on classical thermodynamics. Most texts do not at all clarify the things. I got the intuition first from Frank Lambert's energy-dispersal approach; that was greatly intuitive . Now after reading your article, I wish I could get that earlier!! Really an amazing page:)

You're making me blush.  How would you summarize the gist of the article?


text:
How to show/represent an ionic bond visually?
How to represent/ show an ionic bond visually?
For example in NaCl

Some examples are as follows,
$$
\ce{[Na]+ [Cl]-} \, , \\
\ce{[Mg]^2+ 2[Cl]-} \, , \\
\ce{3[Mg]^2+ 2[N]^3-} \, .
$$
Hopefully you get the idea, so a general rule is:
$$
\text{#ions}[\text{element symbol}]^{\text{magnitude of cation charge}} \text{#ions}[\text{element symbol}]^{\text{magnitude of anion charge}} \, .
$$

I appreciate your answer but my concern is how to represent in 3D model. Let's say Sodium acetate,the ionic bond between Na+ and O- .You may refer jmol for 3D models.

Concerning the depiction of ionic bonds,  the Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008) read as follows:

Structures that are known to be ionic should be depicted as such. They should be drawn with atoms bearing explicit positive and negative charges, and there should be a space (rather than a bond) between those atoms.

I think you should expand the quote to include some points from the next section "GR-7.2 Positioning of components" as well, namely: 1) that there are two ways to position components and 2) what is the recommended way of drawing salts with more than two components.

I appreciate your answer but my concern is how to represent in 3D model. Let's say Sodium acetate,the ionic bond between Na+ and O- .You may refer jmol for 3D models.


text:
Why can oxygen have a coordination number of 3 in a complex between silver and SiO2?
I am running an MD simulation of silver with $\ce{SiO2}$. Initially, my silver atom is neutral and oxygen has a coordination of 2 with silicon having a coordination of 4. After the deposition of silver atoms, I find that the coordination of silver atoms ranges up to 12 and oxygen has coordination of 3 where a bond is formed with silver. Since $\ce{Ag-Si}$ bonds are not present, silicon's coordination number does not change.
I want to understand why oxygen is able to have a coordination number of 3 as with 2 bonds with silicon, the valency is already satisfied. I know silver forms a fcc-lattice where the coordination number is 12 but I want to get a more in depth detail of this change of coordination number. The basic physics behind it.

Welcome to Chemistry.SE. This is an interesting question. I have edited the question title to better get to the heart of what you want to know, which is why/how these coordination numbers are possible. If you have any questions about how our site works, please consider taking the [tour] and visiting our [help].

Just because it exist in an MD, it doesn't necessary mean it is real. From your description is not clear what calculation method you used, what kind of geometries you are talking about  and what you consider coordination. You may want to share more details on these. The "coordination"  of 12 neighbors in metallic silver is rather irrelevant to the question what is the coordination number of silver ions in complexes.

Hi Greg, I have a fixed charged potential where the charges on the atoms remain fixed.  As the silica lattice is amorphous and is to be kept neutral, I have qSi = 1.89 and qO = 0.945 and I simulate a deposition event of uncharged silver atoms on the lattice. The silver is having a coordination from 1-12 depending upon the site it is present on the lattice. I want to understand what leads to this variation and also the oxygen coordination of 3.

Dunno why you have problem with this, you know coordination number but act as if know nothing about coordination complexes?

High coordination numbers are really not uncommon in solid-state compounds. For example, consider the structure of $\ce{Li2O}$, an anti-fluorite structure. In fluorite proper, calcium ions form a cubic closest packing structure and the fluoride ions occupy the tetrahedral voids. In $\ce{Li2O}$, it is reversed: the oxide ions form a cubic closest packing and lithium occupies the tetrahedral voids. That gives each lithium a coordination number of 4 and by maths and symmetry oxygen must have a coordination number of 8.
Tricoordinated oxide anions are also well-known in solid-state structures. The prime example would be the rutile structure of $\ce{TiO2}$ with hexacoordinated titanium and tricoordinated oxide ions.
In your specific case, the silver cations are acting as Lewis acids while the oxide anions (which have to lone pairs not directed towards neighbouring silicium atoms) can act as Lewis bases. A coordination number of three points to a somewhat covalent (and not so ionic) structure — which makes sense considering significant fragments of $\ce{SiO2}$ are still there.


text:
Is there any reaction between amines and AgNO3?
I found a question in a book about the reaction between $\ce{AgNO3}$ and aromatic/aliphatic amines, but I couldn't find any information about
it. What should be the expected reaction mechanism and products formed in this reaction?

Hint: It is easier to find what happens with $\ce{Ag+}$ and $\ce{NH3}$.

I don't think this is the intended reaction but it might be of interest.

@bon makes an interesting point. Ag(I) is a pretty good oxidant.

I found this reaction between amines and silver nitrate:

I think this is the reaction I was looking for

Note: aromatic amines behave differently (obviously)

Any link to valid references?

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


text:
How can I convert the number of particles per liter to gram per liter
How can I convert the number of particles per liter to gram per liter? I know the size of these particle and so, I calculated the volume and then by the density I calculate the mass. After that I don't know what to do

Do you know which substance this is or only how many particles per liter are in your solution?

I am not sure about the substances. Because I am still investigating that. They are about 8e8 particles per ml

$$x \frac{particles}{L} \times \frac {1 mol}{6.023 \times 10^{23}particles}\times \frac{MW gm}{mol}$$

I would go with the Avogadro constant -> calculate how many moles per liter there are in your mixture and then, using the molecular mass, you can calculate the concetration in g/L. That is if you know your compound.

Thanks, but I am not certain what these particles are!! So it is hard to assume molecular mass


text:
How do I visualize an atom?
I have searched and searched, oh how I have searched.
I am looking for a 3-dimensional visualization of a whole atom, one that that includes all the orbital geometry. A proper "layered" view of the orbitals.
What I am not looking for:

Individual orbital geometry.
A "picture" of an atom (i.e. what looks like television static to me).
Little spherical balls.
Dot-and-cross diagrams.

I think I understand that this cannot be expressed in just one picture alone, so I look forward to discovering software, or a collection of pictures, that could help express this. Maybe something similar to an exploded view, for atoms?
Please. The universe is weird and I want to see.

Comments are not for extended discussion; this conversation has been moved to chat.

I have searched and searched, oh how I have searched.

Do you know what I always tell my mom when she asks me to find something in the Internet she was not able to find herself? I ask her: "Are you sure that the thing you are looking for even exists?"

I am looking for a 3 dimensional visualization of a whole (moderately
  complex, hydrogen is just a ball) atom that includes 3 dimensional
  orbital geometry.

Hydrogen atom is not "just a ball".
There is no orbitals. In short, except for one-electron systems (such as the hydrogen atom) orbital description is just an approximate model of the reality.
Usually when one asks to visualize a physical object, he/she wants to visualize its physical "boundaries" with respect to some medium. The notion of such "boundary" simply looses its meaning in the microscopic world: atoms do not have "boundaries" like macroscopic objects do.

Please. The universe is weird and I want to see.

Sorry, but you can not do this: you can not visualize some things in the Universe, you can not even imagine them. Our visualization & imagination abilities (unlike an atom) has some boundaries, because they are based ultimately on our senses which in turn has their boundaries.
As Paul Dirac said on that matter:

[…] the main object of physical science is not the provision of
  pictures, but is the formulation of laws governing phenomena and the
  application of these laws to the discovery of new phenomena. If a
  picture exists, so much the better; but whether a picture exists or
  not is a matter of only secondary importance. In the case of atomic
  phenomena no picture can be expected to exist in the usual sense of
  the word 'picture', by which is meant a model functioning essentially
  on classical lines. One may, however, extend the meaning of the word
  'picture' to include any way of looking at the fundamental laws which
  makes their self-consistency obvious. With this extension, one may
  gradually acquire a picture of atomic phenomena by becoming familiar
  with the laws of the quantum theory.

If something, even the usual description of hydrogen atom is just an approximate model of the reality. It neglects the whole bunch of QED and QCD effects and even just relativistic dependence of particle energy on its momentum.

That final sentence of the quote is what really matters. This is a great question, specifically because it gives a crazy answer. The answer can never be, "here is a link". The real answer is, "Congratulations, your question indicates you're ready to learn quantum mechanics! Then you'll understand why you can't have your nice 3d picture. And, oh man, is it cool!"

@ericksonla, agree. There is nothing depressing out there. On the contrary, the Universe would be a boring place if could we visulaize/imagine everything in it. :D

Orbitals still exist in non-hydrogen-atom-type objects; it’s just that we cannot accurately calculate them.

@Jan not strictly true. We construct orbitals for multielectron atoms under the assumption that we can form multielectron wavefunctions from the antisymmetric product or 1 electron wavefunctions (orbitals).

I am looking for a 3 dimensional visualization of a whole (moderately complex, hydrogen is just a ball) atom that includes 3 dimensional orbital geometry.

3 dimensions is only enough to represent the probability density function of hydrogen.  Given that the origin is the location of the nucleus, each point in  3-dimensional space will have a corresponding probability density of the electron being at the point.
For helium, 6 dimensions would be needed to represent the probability density.  This is because for each pair of points at which the nucleus and first electron are located, every point in 3-dimensional space will be associated with a probability density for the second electron.  Understanding this, I would recommend the figures in 2-Particle density: Correlated motion of electrons as the next step in visualizing an atom beyond hydrogen.

As a matter of fact, despite the answer you accepted, these orbitals can be visualized.  The way this is done, is that an isosurface of the probability density can be plotted.  That is, a surface of constant probability around the nucleus can be visualized.
There weird thing is that there is not a unique way to visualize the orbitals on the molecule.  They way you choose to visualize the orbitals will depend on what kind of chemical insight you want to have.
I recommend software like Avogadro to visualize molecules.

This has already been stated in various forms in the question, comments and answers and doesn't actually answer the OP's question. If you have anything new to add to the answer then please edit it.

@bon I disagree.  No one has suggested plotting an isosurface which is the default way chemists choose to visualize orbitals.  Also no one has suggested software capable of visualizing the orbitals.  Also no one has mentioned that a given orbital representation is not unique.

@olliepower I would read this comment in the way bon suggested.

OP himself stated this doesn't interest him.

Orbitals are only mathematical functions that approximate the quantum state of an electron. Not only orbitals do not visually represent atoms, but orbitals do not have physical existence, they are only mathematical objects.
To really visualize atoms we have to use some topological definition of atom that uses electron density $\rho$, and then plot this density in 3D using some computational software.
A topological definition of atom is as a region of real space bounded by surfaces through which there is a zero flux in the gradient vector field of the electron density. Thus an interatomic surface satisfies the "zero-flux" boundary condition for every point $\mathbf{r}_s$ on the atomic surface
$$\nabla \rho(\mathbf{r}_s) \cdot \mathbf{n}(\mathbf{r}_s) = 0$$
and where $\mathbf{n}(\mathbf{r}_s)$ is the unit vector normal to the surface.
The shape of a free atom is well-represented by spherical symmetry, but atoms in molecules have very different shapes. Even the same kind of atom can have different shapes and volumes (and so different physical and chemical properties) in different molecules. Some examples for small molecules (you can check, for instance, as H atoms have different shape and volume on different molecules)

can you please share the source?

Already there are sufficient answers to your question .but I want to share my opinion too ;) .
Pre-note : Orbital does not means electron , what you can visualize  is just where it will likely to be found which is basically an orbital .
First of all you can't visualize an orbital because it has 3 independent variables (only In case of Hydrogen like atom . for other atoms having 2 or more electrons it is greater than 3 ) , to visualize it you need a 4-D vision , which is certainly not possible.
But you can visualize some of it's fraction , like 99% by using of shades. Where it is more likely to be found you can make it darker or where it is not likely be found leave it white

1s Orbital

2s Orbital
2p Orbital
There is another way but it does not look nice , the way is we enclose some consecutive volumes to describe the probability density for finding electron in respective volume (Something like layers ) (The right image is the Contour plot, the left one is the same as above ).

If you move on any line , you will find yourself on a area where probability density is same . These are called isosurfaces . These can be very fancy , nice to visualize . Here are some Iso Boundary Surfaces of some orbitals .
Caution : Any of these images does not show images of orbitals , these are only Boundary Surfaces . (In many books these pictures are referred to Images of orbital without any clarification which can be misleading )

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


text:
Chemical incompatibility between aluminum hydroxide [Al(OH)3] and carbomer polymer [-CH2-CH] N-COOH]
I am currently adsorbing proteins to an aluminum hydroxide gel.  By adding a carbomer (polymer of acrylic acid cross-linked with allyl sucrose), I achieve a somewhat synergistic formulation.  Shortly after adding the carbomer, a granular precipitate forms that adheres to glass.  Questions: 1) What is this precipitate?; 2) Will my adsorbed protein release from the aluminum hydroxide after carbomer addition?; 3) Is there possible long-term instability of this mixture?  Thank you!


text:
Chloroform-acid wash
If I wash chloroform (stabilized with amylene) with sulphuric acid in a separating funnel, where will the chloroform be found (top or bottom)? I think the chloroform will be at the bottom, because it is heavier than sulphuric acid.

Do you mean concentrated sulfuric acid or an aqueous dilution?

Usually, you shake chloroform with concentrated sulfuric acid, wash with water, dry over $\ce{CaCl2}$, and distill.
The density of chloroform is approximately $\rho = 1.48\ \mathrm{g\ cm^{-3}}$, whereas the density of concentrated sulfuric acid is approximately $\rho = 1.84\ \mathrm{g\ cm^{-3}}$.
Therefore, after you allow the layers to separate, the concentrated sulfuric acid is in the lower layer and the chloroform is in the upper layer.
After that, however, when you wash with water ($\rho = 1.00\ \mathrm{g\ cm^{-3}}$), the chloroform is in the lower layer and the water is in the upper layer.
If there is any doubt about the identity of a layer, add a drop of the layer in question to a small amount of water in a test tube. If the drop does not dissolve, the layer in question is the organic layer.
Caution: The mixture may become hot when the remaining sulfuric acid is removed with water, and chloroform boils at $61.2\ \mathrm{^\circ C}$.

Pure, concentrated sulfuric acid has a density of 1.84 grams per cubic centimeter.  Chloroform has a density of 1.489 grams per cubic centimeter.  Thus a chloroform phase will form on top of a pure sulfuric acid phase.
However, if you are using dilute sulfuric acid, the density will be closer to that of water (1 gram per cubic centimeter), and chloroform may form beneath an aqueous acid phase.
There is a concentration of water in sulfuric acid at which the density of the aqueous acid phase will be equal to that of the chloroform.  In that case, the layers will never separate (at least not vertically).


text:
Reaction between ruthenium and bleach
I have recently seen a video of ruthenium on youtube. It says that ruthenium is invulnerable to many acids, especially aqua regia, but it gets destroyed by a simple household chemical, bleach. The video did not give a proper explanation about why this happens, it only gave the reaction mechanism. What is the reason for this Achilles' heel of ruthenium?

What exactly are you asking? Are you looking for the thermodynamic reason why the reaction is favourable, the kinetic reason, or what?

If I had to guess, it has to do with the fact that ruthenium oxide is much more soluble in base than in acid.

Energetically favorable electronics?

This paper actually explain the reason for which ruthenium is vulnerable to bleach. Bleach actually contains $\ce{OCl^-}$ ions which acts as an oxidising  agent and thus oxidises ruthenium. But the research on this phenomenon was done by using sodium hypochlorite, $\ce{NaOCl}$ in presence of a caustic alkali.
The experiment was done in two-fold process. First only using $\ce{NaOH}$ and the second using both $\ce{NaOCl}$ and $\ce{NaOH}$. In the first attempt, there was nothing occuring. The solutions with  $\ce{NaOH}$ were stable for a considerable time, but after several weeks began to break down, giving a deposit of the black oxide. In the second process, when a little of hypochlorite was given, it gave a orange-red solution as you can see in the above video.

Some more attempts were made by repeating the experiments and found that concentrated alkali hypochlorite more or less dissolved any ruthenium present. From these experiments, the conclusions were made that ruthenium, is rather soluble in concentrated alkaline solutions of hypochlorites and this might help to distinguish ruthenium from other metals. The overall reaction of this process is(from the video):-
$$\ce{Ru + 3NaOCl + 2NaOH -> Na2RuO4 + 3NaCl + H2O}$$
$$\ce{Ru + 7NaOCl + 2NaOH -> 2NaRuO4 + 7NaCl + H2O}$$
$\ce{NaOCl -> 2NaCl + H2O}$ (ruthenate catalyzed)
$$\ce{Na2RuO4 + NaOCl + H2O-> RuO4 + NaCl + 2NaOH}$$

There are no tables, but people do fake them

You can't make tables in mathjax. People do find workarounds, but nothing actually officially tabular.


text:
Radical Computational Calculations
I am trying to calculate the total energies for a particular organic molecule that undergoes radical decomposition. I was able to calculate the neutral molecule with the exact results of a paper I found. My trouble is obtaining the correctly calculated energies for the radical molecules. I am new to computational chemistry and am looking for a bit of guidance on this.

The question is too broad. You did not mention neither the molecule in question, nor the level of theory. Anyway, reproducing someone's results is usually a tough task; in many cases it requires the use of exact same program. But since you was able to reproduce the results for the neutral molecule, then presumably you use exact same level of theory (and maybe even the same program). For radical the first thing to check is which formalism was used in the published work: restricted open-shell or unrestricted.

I am using qchem( Theory:M06-2X, BASIS: 6-31G(d,p)) The molecule I am working on is p-coumaryl alcohol. I know this is the level of theory  and basis set the author used.

The best way to make the discussion much more meaningful is: 1) to provide the reference to the published work you're aiming to reproduce; 2) to provide the details of your attempts to reproduce it (i.e. input files).

OK. So, that is DFT. Then if a different program was used in the published work, you shouldn't expect the exact identity of energies in the first place, since there are many "degrees of freedom" in DFT calculations... But then again you said that you reproduced the neutral molecule results exactly which is somewhat surprising. Could you check then which formalism was used for the radical specie: was it ROM06-2X or UM06-2X?

I do not see any mention of restricted or unrestricted in the paper. (dx.doi.org/10.1021/jp2122449 | J. Phys. Chem. B 2012, 116, 4760-4768)

True. Then, presumably, the default, i.e. unrestricted, formalism was used for radical species. That is fine, since it is the default option in (almost?) all programs; at least it is also default in Q-Chem (according to the manual). What I don't understand is that in the referenced paper Mo6-2x was not used;  ωB97X-D was used instead. How then you was able to reproduce the total energy for the neutral molecule using a different functional?

I skimmed through the paper (as well as the supporting materials), and I couldn't see any total energies out there, but only relative total energies. If you reproduced relative total energies for the neutral molecule, then how good the reproducibility was? You've said it was "exact", but what do you actually mean by this? Do you have exact same relative total energy in kcal/mol for neutral molecule? And what is the difference for radical then?

The total energies I'm comparing to came from a document my advisor forwarded on to me from the author. When I said exact I meant to a certain decimal place (that was reported in the forwarded document).

To which decimal place in particular? Usually, the absolute total energies (in Hartree) can be considered to be the same if they agree at least to 6th decimal place. I seriously doubt this is the case (since you use a different functional) but even if they agree so well, it is nothing but a coincidence.

@EdwardHD I suggest you [edit] the details you provided in the comments into the body of your question. Right now it is in the close queue. I would also like to encourage you to follow wildcats advise and provide as much context as you can. Only this way, we will be able to help you.

Disclaimer: this is a preliminary answer based on the current state of the discussion with OP; it might be the subject to major changes in the near future.
So.

OP (original poster) is trying to reproduce some relative energies previously computed at ωB97X-D/6-31+G(d,p) at a different M06-2X/6-31G(d,p) level of theory. OP has exact same results for closed-shell molecular species in question, the meaning of which is probably that the resulting M06-2X/6-31G(d,p) relative energies in kcal/mol or kJ/mol are exactly equal to the previously published ωB97X-D/6-31+G(d,p).
OP also mentioned that he has some troubles in reproducing the relative energies for open-shell species, by which he probably means that for open-shell species M06-2X/6-31G(d,p) spits out different numbers in kcal/mol or kJ/mol than ωB97X-D/6-31+G(d,p).

Before we have some numbers let me say few things which hold in generality.

The difference in few kJ/mol in relative energies computed using two different functionals is pretty normal (even at exact same geometry). One should not even expect exactly same relative energies with any two different functionals in the first place.
OP presumably run geometry optimization at M06-2X/6-31G(d,p) but did not mention how different are the equilibrium geometries obtained at this level from those at ωB97X-D/6-31+G(d,p) level published previously. In fact, this would be difficult to do, because I could not find the Cartesian coordinates of the species in question in the Supporting Information for the work published previously. But at least some quick visual comparison has to be done to make sure that equilibrium geometries are at least not totally different.
OP did not mention why M06-2X functional was chosen. Even if the ultimate goal is not just to reproduce the previously published work, it is mentioned there that:

ωB97X-D, a range-separated double-hybrid functional, has been shown to describe reaction energies accurately.45

But, first of all, ωB97X-D is not a double-hybrid functional. And secondly, the paper quoted there is fairly well-known benchmark of density functional methods done by Lars Goerigkab and Stefan Grimme, and in fact, Goerigkab and Grimme found M062X-D3 and not ωB97X-D to be "statistically the best of all hybrids". Note though that M062X-D3 differs from M062X: the former includes the empirical dispersion correction while the later does not.
With respect to the empirical dispersion correction, today it is usually recommended to include it in DFT calculations, since it is available at almost no (computational) cost but can substantially improve the results. Note also that dispersion correction is already included in case of ωB97X-D functional but has to be "manually" added for the case of M06-2X. In fact, the absence of it might explain some differences in equilibrium geometries and relative energies.


text:
Why is the original Pauling's theory of resonance that uses superposition of wavefunctions not used today?
I have recently studied superposition of states (also the famous Schrodinger's cat), measurement problem, decoherence & so on. I then read the resonance concept from Atkins' Physical Chemistry where it was written as:

It is the superposition of wavefunctions representing different electron distributions in the same nuclear framework. [...] A better description of a molecule of $\ce{HCl}$ is $\psi_\ce{HCl} = \psi_{\ce{H-Cl}} + \lambda\psi_{\ce{H^+} \ce{Cl^-}} $.

Thus this is the general wavefunction which is superposition of all the states. $\lambda$ is a numerical coefficient (can be found out by variation theorem) whose square predicts the probability of being in the ionic state when we inspect the molecule. Just like typical wavefunction-collapse after measurement! This is the original Pauli's theory of resonance. Unfortunately Atkins halts down here; after all it is physical chem-book! Nowhere have I found this approach to resonance; no organic chem book I possess: Morrison, Boyd; Solomons; R.K. Gupta ... They all say it is just the weighted average of all Lewis structures. No, it is not correct! As is said here:

This essay contains information that I have never found in any organic chemistry textbook. This can mean two things: the information is too difficult or you don't really need to know it. Maybe both are true .
[...]  When Linus Pauling developed resonance theory, he defined "resonance" as the superposition of wave functions. Unfortunately, this detail has been lost in the intervening decades, and modern chemists incorrectly treat "resonance" as the superposition of Lewis structures (resonance forms)
[...]Suppose you have a molecular AB that is a resonance hybrid:

  and you want to calculate the electron density on atom A.
The usual (wrong) prediction procedure. The usual procedure says, "combine what you see in each Lewis structure." In other words, combine the electron density (ED) on A in form IV with the electron density on A in form V:
$$ED_\text{wrong} \text{(hybrid)} = 1/2 [ED(IV) + ED(V)]$$
The much-ignored (correct) prediction procedure. You may recall that electron density (ED) is given by the square of the wave function (WF). If we want to know the electron density on A, we must look at the square of the wave function near A:
$$ED\text{(hybrid)} = WF\text{(hybrid)} ^2 \implies ED\text{(hybrid)} = ED_\text{wrong} \text{(hybrid)} + \boxed{WF(IV)WF(V)}$$
The final formula shows the discrepancy between the right answer, ED(hybrid), and the usual (wrong) answer, EDwrong. The correct formula includes WF(IV)WF(V). This term is called the "interaction density" or "overlap density," and is a product of two different wave functions. The interaction density affects the electron density everywhere in the molecule, and its appearance tells us that the electron density obtained by the "usual" procedure is wrong.
Electron density is just one of many properties that interest chemists, but all property predictions -- electron density, bond type, atom charge, dipole moment, geometry, energy, etc. -- have something in common with electron density prediction: the prediction procedure must start with WF(hybrid), and their answers always include interaction terms.

This is one of the great reasons why the modern concept of resonance is wrong; they don't take the "interaction term"!
So, why does only one book (which is not organic) contain the correct interpretation? Why do people follow the wrong version? Resonance is not at all the weighted average of Lewis structures; rather it is just a superposition of wavefunctions? So, why do most of the sources (people & book) advocate the wrong theory? Can anyone tell me which organic chem book still follows Pauling's original theory of resonance?
Added: In my quest to find the resources which still define Pauling's theory of resonance of wavefunctions, Feynman's Lectures, which I have just completed reading, is really worthy to be gold to be noted. Feynman completely describes the benzene molecule as the superposition of base states; it can be found in the CALTECH site.

If you look for the term "valence bond theory" you'll find more books that deal with the full/correct approach.  I have a colleague who's specialty is applying V.B. theory in computational organic chemistry, so there are certainly people who understand and use this approach.  However, there was a historical shift with the introduction of molecular orbitals theory where many people abandoned V.B. theory (M.O. calculations scale better for larger molecules).  Unfortunately, this means many chemists only have a vague/qualitative understanding of V.B. theory.

My two cents: when the concept of resonance is first introduced in general chem, or organic chemistry courses, describing it as a weighted average of resonance structures, is easier both for the instructors as well as for the students to gain a working intuition. Most curricula introduce quantum theory a little bit later.

If I recall correctly VB calculations scale extremely poorly, and not really used with anything bigger then a benzene molecule. In other words, VB may sound like a good idea but full VB treatment makes no practical sense.

why does only one book (which is not organic) contain the correct interpretation?

I bet that there are many books with correct descriptions of  it. Almost any computational chemistry book that makes mention to the subject.

Why do people follow the wrong version?

It depend of the individual. Many because ignorance. Others because they are lazy and prefer do not immerse in modern (¿1920-1930?) ideas of quantum mechanics. Others both of them.

Resonance is not at all the weighted average of Lewis structures; rather it is just a superposition of wavefunctions? So, why do most of the sources (people & book) advocate the wrong theory?

I am unsure about the exact meaning of sentence

It is the superposition of wavefunctions representing different electron distributions in the same nuclear framework.

In principle, any state (approximation to a solution of Schrödinger equation restricted to an antisymmetric subspace) is different to other state because the electron distributions are not the same.
Even more, eigenfunctions of the Hamiltonian operator are vectors that form a complete set. That implies that any state can be represented by a linear combination ("superposition") of eigenvectors (wavefunctions for example).
So "resonance" defined in such way is too vague. Arises so many question with this definition:  When a superposition implies resonance? The wavefunctions used for the combination, correspond to a stationary state? Is Atkins speaking about a particular kind of difference in electron distribution?
There is an awesome amount of literature about general chemistry, inorganic and organic chemistry with very serious mistakes, conceptual mistakes. Almost every book I've read in the subject. I do not believe that they are wrong because of simplification in post of clarity, because I can realize in which sense is good clarity about something that is completely wrong and not useful. Speaking about in-existent thing that contradicts quantum mechanics principles and at the same time do not allow make any prediction is not useful imho.

Can anyone tell me which organic chem book still follows Pauling's original theory of resonance?

Not me, sorry, I am not familiar with organic textbooks. I've seen some titles like "Theoretical and Computational Models for Organic Chemistry" that suggest a good theoretical background, but I can not assure it. I recommend you do not pay too much attention to resonance.

Ha! A nice answer; actually I was quite ignorant then; I had to learn that resonance is the weighted average of all the canonical structures. But in reality, as we all know (which, to me, was kind of revolutionary new idea then), resonance is the quantum superposition of wavefunctions describing different base states- this is greatly summed up in Feynman's Lectures & of course, in 'almost any computational chemistry book'. But really my main concern was the undergrad Organic texts which lack that description. Now, I'm pretty much more literate than the then me & I know quite many books ...

now which bear this more accurate definition of resonance. Though till now, I've not found any undergrad Organic text that deals with this definition- may be due to keeping the facts straight rather than rigorously analysing. I was a bit lazy not to delete this question but, well, it was destined for your answer ;)

Thanks. To my understanding those non rigorous ideas are useful to predict qualitatively with good probability of success. They allow to skip a rigorous treatment that can be very time consuming and sometimes technically  impossible to afford up to date. It is not bad to use them, but it is convenient to be aware of the inaccuracies of this ideas/models.

In my experience it is hard to find people that likes both approach, I suppose that this is the reason why there are not many good books in this sense (I do not know anyone). For the fast progress of chemistry the usage of both approach is a bless. :-) . But for "interdisciplinary" works, sometimes can be very difficult understand each other views, I certify that ;-).

But what are the implications of seeing it as a "superposition of resonance structures" rather than a "superposition of wavefunctions"? Other than the fact that it is inconsistent with the original theory and that it provides a wrong estimate of electron density, as illustrated in the question post above?

@TanYongBoon In practice this is not a problem if they are not taken too seriously. They are not taking into account when computing properties of molecules at equilibrium. However, they correspond to a model which is known to lack of good prediction power, and may lead to misunderstanding.

TL;DR:
It is a useful tool to use experimental values to skip math (and math that is tedious even without considering inter-molecular/environmental interactions like VDW and adsorption)

resonance concept from Atkins' Physical Chemistry where it was written as: It is the superposition of superposition of wavefunctions
$\psi_\ce{HCl} = \psi_{\ce{H-Cl}} + \lambda\psi_{\ce{H^+} \ce{Cl^-}} $.

That's a good interpretation, but a slightly incomplete one again. In here, if $\ce{HCl}$ is the hybrid form we want to study, it exists in a combination of:

a "perfect" covalent bond: $\ce{H-Cl}$ : where the electron cloud is uniformly distributed.
a "perfect" ionised form:   $\ce{H^+}$ separated from $\ce{Cl^-}$ sufficiently for their local electron wave functions to not interact (yes, yes, WFs are infinite - and this separation distance should be infinite too - hence the quotes around "perfect")
and a set of states where the electron cloud around the bond is shifted from ever-so-slightly to heavily polarised.

In effect, you're dealing with an integration problem over $N$ states where each state has a probability of $\lambda i\,\, (1 \Leftarrow i \Leftarrow N)$

incorrectly treat "resonance" as the superposition of Lewis structures (resonance forms)

Again, true, but this gives us three important advantages:

It allows us to represent most bonds/moieties as discrete extreme states. Think of the simplistic representation of the benzene ring and the electron jumping around the circle alternating between a polar $\ce{C^+ - C^-}$ bond and a $\ce{C=C}$ double bond.

Experimentally observed bond energies and polarisation constants give us a good relative approximation to allow us to represent the whole cohort of possible intermediate waveforms as a single:

$$\psi\textrm{(bond)} = \psi\textrm{(extreme-state 1)} + \lambda \psi\textrm{(extreme-state 2)} + \,\,\textrm{( more if the bond requires it)}$$

And given the number of molecules being observed, we can assume that some of molecules must be in these extreme states - and describe chemical reactions in familiar terms. (Bonus: With the tendency of the molecule to revert to a stable superimposition state, we can further explain why reactions that rely on said marginal states can fully use up the reactant)

A better, more concise explanation:
http://chemistry.stackexchange.com/a/38987/28144


text:
Discrepancies between smell and taste
In my experience, most foods smell like they taste. Fragrant soaps, however, taste quite awful in comparison to their fragrances. How can some things smell and taste identical while others are so vastly different? I have a feeling this may have something to do with the vapor pressures of the molecules that make up the "thing," but I cannot find anything to confirm my hypothesis exactly.

The food that you eat regularly is something that you are used to. You know exactly which smell combines with which taste ... but that does not imply that the chemicals you smell are the same that you taste.
If you had been eating your whole life long fragrant soap with apple smell, you would wonder about the taste of real apples as you wonder right now about the taste of apple soaps.
There are a lot of different substances that are responsible for the special taste of everything you eat. You can find more about flavor or aroma compounds on wikipedia.
In contrast to real fruits, fragrant soaps and other industrial products with a certain smell only contain those substances that are responsible for the characteristic smell of e.g. fruits (often only the main one or two aroma substances or even only synthetic aroma substances that smell similar to the natural products).
But as not all products that shall smell like certain thing also need to taste like those things you only smell the "apple" but you won't taste it.

You have about 400 smell receptors which only sense volatile compounds that can travel to the olfactory bulb. Taste (pure taste) on the other hand is limited to salt, sweet, bitter, sour, pungent, astringent, savory, fat, smokey and only a few more. Taste can tell between an apple and a pear alone, you need smell to sense the various ester compounds that give them distinct taste/smell. You can test all of this by eating while holding your nose$-$there will be a difference in tastes.
Soap is no exception. Soap is loaded with essential oils that smell great, but it also has sodium based organic salts namely sodium dodecyl sulfate and cocamide diethanolamine, and a few others. These compounds are basic and because of that are bitter. But the sodium salts are not volatile therefore you do not smell them but do taste them. That is why soap smell good and tastes bad.


text:
Could a magnet pull oxygen out of the air?
I read that the $\ce{O2}$ molecule is paramagnetic, so I'm wondering: could a strong magnet pull the $\ce{O2}$ to one part of a room – enough to cause breathing problems for the organisms in the room?
(I'm not a professional chemist, though I took some college chemistry.)

I'd expect there to be a slight increase in concentration of oxygen gas in the surroundings of a strong magnet, though I'd be really curious to see if anyone can provide some quantification.

Even MRIs, weak as they are, are powerful enough to cause vertigo. I don't think an organism in a magnetic field that powerful would be very happy.

Well before the magnetic field strengths required, other strange physics will start to manifest. http://www.physics.org/facts/frog-really.asp

Here's a video in case anyone wants clear visual proof that oxygen molecules are attracted to magnets. It also shows the lovely pale blue of liquid oxygen.

I'm pretty sure osmotic pressure will step in and fix the problem long before it gets unbreathable.

Its not quite what you asked, but it is a common lecture  demonstration that liquid oxygen in a suspended  test-tube is easily pulled to one side by a small magnet.  Liquid nitrogen, as expected is unaffected.

Not directly relevant, but maybe of interest?  Oxygenated  hemoglobin (Hb) is diamagnetic (as is CO-Hb), but deoxygenated Hb is magnetic. The electronic structure of oxygen is profoundly different when bound to Hb. (See here)

I'm a physicist, so apologies if the answer below is in a foreign language;  but this was too interesting of a problem to pass up.  I'm going to focus on a particular question:  If we have oxygen and nothing else in a box, how strong does the magnetic field need to be to concentrate the gas in a region?  The TL;DR is that thermal effects are going to make this idea basically impossible.
The force on a magnetic dipole $\vec{m}$ is $\vec{F} = \vec{\nabla}(\vec{m} \cdot \vec{B})$, where $\vec{B}$ is the magnetic field.  Let us assume that the dipole moment of the oxygen molecule is proportional to the magnetic field at that point:  $\vec{m} = \alpha \vec{B}$, where $\alpha$ is what we might call the "molecular magnetic susceptibility."  Then we have $\vec{F} = \vec{\nabla}(\alpha \vec{B} \cdot \vec{B})$.  But potential energy is given by $\vec{F} = - \vec{\nabla} U$;  which implies that an oxygen molecule moving in a magnetic field acts as though it has a potential energy $U(\vec{r}) = - \alpha B^2$.
Now, if we're talking about a sample of gas at a temperature $T$, then the density of the oxygen molecules in equilibrium will be proportional to the Boltzmann factor:
$$
\rho(\vec{r}) \propto \mathrm e^{-U(\vec{r})/kT} = \mathrm e^{-\alpha B^2/kT}
$$
In the limit where $kT \gg \alpha B^2$, this exponent will be close to zero, and the density will not vary significantly from point to point in the sample.  To get a significant difference in the density of oxygen from point to point, we have to have $\alpha B^2 \gtrsim kT$;  in other words, the magnetic potential energy must comparable to (or greater than) the thermal energy of the molecules, or otherwise random thermal motions will cause the oxygen to diffuse out of the region of higher magnetic field.
So how high does this have to be?  The $\alpha$ we have defined above is approximately related to the molar magnetic susceptibility by $\chi_\text{mol} \approx \mu_0 N_\mathrm A \alpha$; and so we have1
$$
\chi_\text{mol} B^2 \gtrsim \mu_0 RT
$$
and so we must have
$$
B \gtrsim \sqrt{\frac{\mu_0 R T}{\chi_\text{mol}}}.
$$
If you believe Wikipedia, the molar susceptibility of oxygen gas is $4.3 \times 10^{-8}\ \text{m}^3/\text{mol}$;  and plugging in the numbers, we get a requirement for a magnetic field of
$$
B \gtrsim \pu{258 T}.
$$
This is over five times stronger than the strongest continuous magnetic fields ever produced, and 25–100 times stronger than most MRI machines.  Even at $\pu{91 Kelvin}$ (just above the boiling point of oxygen), you would need a magnetic field of almost $\pu{150 T}$; still well out of range.

1 I'm making an assumption here that the gas is sufficiently diffuse that we can ignore the magnetic interactions between the molecules.  A better approximation could be found by using a magnetic analog of the Clausius-Mossotti relation;  and if the gas gets sufficiently dense, then all bets are off.

Interesting calculations but take a look at the patent in ToddMinehart's answer

The patent claims to yield a difference in density of 50% (30% vs 20% oxygen), which would correspond to a Boltzmann factor of 1.5, or $\chi_\text{mol} B^2/(\mu_0 RT) = \ln (1.5) \approx 0.4$.  That'll bring the necessary $B$ down to $\sqrt{0.4} \approx$ 63% of the threshold value above, which is still pretty high.  And as was pointed out in the comments of @ToddMinehart's answer, the patent office doesn't certify that the ideas will actually work with current technology...

Physics says yes. And at the US Patent Office, it certainly looks like the answer is yes, according to (at least) this US patent application. The abstract reads:

A process for separating O$_2$ from air, that includes the steps effecting an increase in pressure of an air stream, magnetically concentrating O$_2$ in one portion of the pressurized air stream, the one portion then being an oxygen rich stream, and there being another portion of the air stream being an oxygen lean stream, compressing the oxygen rich stream and removing water and carbon dioxide therefrom, to provide a resultant stream, and cryogenically separating said resultant stream into a concentrated oxygen stream and a waste stream.

I would say the yes is conditional in that you'd probably need a room that is sealed from communication with the atmosphere (otherwise equilibrium will be re-established with respect to oxygen pretty quickly), is vented to the outside in order to dispose of the oxygen, houses one heck of a strong magnet, and has a strongly-locked door to prevent the unfortunate organisms from leaving.

Once you have a room sealed from communication with the atmosphere and with a strongly-locked door, the unfortunate organisms will cause their own breathing problems eventually ;-)

The patent office don't check whether inventions actually work.

What if you just walk to where the magnet is? Unless it's a REALLY strong magnet that can pull the $O_2$ to a height that the organisms can't reach (in which case organisms like frogs might experience other side effects) chances are you could just stand next to the magnet. Of course your life span depends upon how quickly the $O_2$ is removed from the room and whether or not you can get help within that time limit.

Even if this works it is likely that the only way to achieve notable changes in concentration would involve a multi-step cascade involving thousands of steps (a little like the gas centrifuge process for concentrating specific isotopes of uranium using gas diffusion of UF6). Not, therefore, practical or cheap.

No, to separate oxygen from air you need extremely high gradients of field strength. in this paper http://link.springer.com/article/10.1007%2Fs11630-007-0079-1#page-1 they used about $\pu{0.4T}$ per $\pu{mm}$, but to cause breathing problems it is enough to get the $\ce{O2}$ concentration below 17%, so lets say $\pu{0.1T/mm}$ is needed. To sustain such gradients over a whole room (lets say 4 meters), the field strength on one side of the room needs to be around $\pu{400T}$, which is very likely to kill humans (dissolved ions begin to circle due to lorentz force instead of going where they should, moving around induces huge currents…), and has never been achieved in a continuous field. (from nationalmaglab.com:  …45-Tesla hybrid magnet, which offers scientists the strongest continuous magnetic field in the world…)

Doesn't mean its not possible. Just means that other much bigger effects occur. http://www.physics.org/facts/frog-really.asp

I totally forgot about that effect, so in addition to all the things mentioned above everyone in the room woulb be crushed against the wall…


text:
What chemicals could be used to repair rubber tires?
I have a beaten old R/C car that I am restoring for my son. It has some nice rubber tires on it, but they are kind of old and worn. The rubber itself is almost moldy and looks matte.
I could just fetch some wonderful product of a shelf somewhere that promises to restore the rubber, but I would like to really know what can be done for old rubber on a low level.
So, how can I treat my rubber, and which chemical process works best (if any)?


text:
What's with the 70% ethanol?
Is there a reason for all the bottles being 70% ethanol, or is it convention.

Could you be more specific? Where are you seeing the bottles?

I mean that they are not 50 percent or 90 percent, but 70 %.

Could you take a picture and post it to the question? Maybe provide a little more context, at the moment it is really hard to tell what you are asking.

Primarily it is used as an anti-microbial agent. There is lots of data out there showing that the efficacy of ethanol at killing bacteria peaks at the 70% mixture. As they are making tons of it (literally) for the microbiologists, it's easier to just scale production then set up a new production facility for chemists to use at an arbitrary concentration.