text:
Given a CIF (crystallographic interchange format) file (and thus cartesian atomic coordinates), how can you find the bonds between atoms?
Applications like Vesta show bonds when viewing a CIF file; how could one algorithmically find all bond pairs?
Here is an example CIF file:
# generated using pymatgen
data_LiF
_symmetry_space_group_name_H-M   Fm-3m
_cell_length_a   4.08342738
_cell_length_b   4.08342738
_cell_length_c   4.08342738
_cell_angle_alpha   90.00000000
_cell_angle_beta   90.00000000
_cell_angle_gamma   90.00000000
_symmetry_Int_Tables_number   225
_chemical_formula_structural   LiF
_chemical_formula_sum   'Li4 F4'
_cell_volume   68.08861619
_cell_formula_units_Z   4
loop_
 _symmetry_equiv_pos_site_id
 _symmetry_equiv_pos_as_xyz
  1  'x, y, z'
  2  '-x, -y, -z'
  3  'z, y, -x'
  4  '-z, -y, x'
  5  '-x, y, -z'
  6  'x, -y, z'
  7  '-z, y, x'
  8  'z, -y, -x'
  9  'x, -y, -z'
  10  '-x, y, z'
  11  'z, -y, x'
  12  '-z, y, -x'
  13  '-x, -y, z'
  14  'x, y, -z'
  15  '-z, -y, -x'
  16  'z, y, x'
  17  'y, -z, -x'
  18  '-y, z, x'
  19  'y, x, -z'
  20  '-y, -x, z'
  21  'y, z, x'
  22  '-y, -z, -x'
  23  'y, -x, z'
  24  '-y, x, -z'
  25  '-y, z, -x'
  26  'y, -z, x'
  27  '-y, -x, -z'
  28  'y, x, z'
  29  '-y, -z, x'
  30  'y, z, -x'
  31  '-y, x, z'
  32  'y, -x, -z'
  33  '-z, x, -y'
  34  'z, -x, y'
  35  'x, z, -y'
  36  '-x, -z, y'
  37  'z, -x, -y'
  38  '-z, x, y'
  39  '-x, -z, -y'
  40  'x, z, y'
  41  'z, x, y'
  42  '-z, -x, -y'
  43  '-x, z, y'
  44  'x, -z, -y'
  45  '-z, -x, y'
  46  'z, x, -y'
  47  'x, -z, y'
  48  '-x, z, -y'
  49  'x+1/2, y+1/2, z'
  50  '-x+1/2, -y+1/2, -z'
  51  'z+1/2, y+1/2, -x'
  52  '-z+1/2, -y+1/2, x'
  53  '-x+1/2, y+1/2, -z'
  54  'x+1/2, -y+1/2, z'
  55  '-z+1/2, y+1/2, x'
  56  'z+1/2, -y+1/2, -x'
  57  'x+1/2, -y+1/2, -z'
  58  '-x+1/2, y+1/2, z'
  59  'z+1/2, -y+1/2, x'
  60  '-z+1/2, y+1/2, -x'
  61  '-x+1/2, -y+1/2, z'
  62  'x+1/2, y+1/2, -z'
  63  '-z+1/2, -y+1/2, -x'
  64  'z+1/2, y+1/2, x'
  65  'y+1/2, -z+1/2, -x'
  66  '-y+1/2, z+1/2, x'
  67  'y+1/2, x+1/2, -z'
  68  '-y+1/2, -x+1/2, z'
  69  'y+1/2, z+1/2, x'
  70  '-y+1/2, -z+1/2, -x'
  71  'y+1/2, -x+1/2, z'
  72  '-y+1/2, x+1/2, -z'
  73  '-y+1/2, z+1/2, -x'
  74  'y+1/2, -z+1/2, x'
  75  '-y+1/2, -x+1/2, -z'
  76  'y+1/2, x+1/2, z'
  77  '-y+1/2, -z+1/2, x'
  78  'y+1/2, z+1/2, -x'
  79  '-y+1/2, x+1/2, z'
  80  'y+1/2, -x+1/2, -z'
  81  '-z+1/2, x+1/2, -y'
  82  'z+1/2, -x+1/2, y'
  83  'x+1/2, z+1/2, -y'
  84  '-x+1/2, -z+1/2, y'
  85  'z+1/2, -x+1/2, -y'
  86  '-z+1/2, x+1/2, y'
  87  '-x+1/2, -z+1/2, -y'
  88  'x+1/2, z+1/2, y'
  89  'z+1/2, x+1/2, y'
  90  '-z+1/2, -x+1/2, -y'
  91  '-x+1/2, z+1/2, y'
  92  'x+1/2, -z+1/2, -y'
  93  '-z+1/2, -x+1/2, y'
  94  'z+1/2, x+1/2, -y'
  95  'x+1/2, -z+1/2, y'
  96  '-x+1/2, z+1/2, -y'
  97  'x+1/2, y, z+1/2'
  98  '-x+1/2, -y, -z+1/2'
  99  'z+1/2, y, -x+1/2'
  100  '-z+1/2, -y, x+1/2'
  101  '-x+1/2, y, -z+1/2'
  102  'x+1/2, -y, z+1/2'
  103  '-z+1/2, y, x+1/2'
  104  'z+1/2, -y, -x+1/2'
  105  'x+1/2, -y, -z+1/2'
  106  '-x+1/2, y, z+1/2'
  107  'z+1/2, -y, x+1/2'
  108  '-z+1/2, y, -x+1/2'
  109  '-x+1/2, -y, z+1/2'
  110  'x+1/2, y, -z+1/2'
  111  '-z+1/2, -y, -x+1/2'
  112  'z+1/2, y, x+1/2'
  113  'y+1/2, -z, -x+1/2'
  114  '-y+1/2, z, x+1/2'
  115  'y+1/2, x, -z+1/2'
  116  '-y+1/2, -x, z+1/2'
  117  'y+1/2, z, x+1/2'
  118  '-y+1/2, -z, -x+1/2'
  119  'y+1/2, -x, z+1/2'
  120  '-y+1/2, x, -z+1/2'
  121  '-y+1/2, z, -x+1/2'
  122  'y+1/2, -z, x+1/2'
  123  '-y+1/2, -x, -z+1/2'
  124  'y+1/2, x, z+1/2'
  125  '-y+1/2, -z, x+1/2'
  126  'y+1/2, z, -x+1/2'
  127  '-y+1/2, x, z+1/2'
  128  'y+1/2, -x, -z+1/2'
  129  '-z+1/2, x, -y+1/2'
  130  'z+1/2, -x, y+1/2'
  131  'x+1/2, z, -y+1/2'
  132  '-x+1/2, -z, y+1/2'
  133  'z+1/2, -x, -y+1/2'
  134  '-z+1/2, x, y+1/2'
  135  '-x+1/2, -z, -y+1/2'
  136  'x+1/2, z, y+1/2'
  137  'z+1/2, x, y+1/2'
  138  '-z+1/2, -x, -y+1/2'
  139  '-x+1/2, z, y+1/2'
  140  'x+1/2, -z, -y+1/2'
  141  '-z+1/2, -x, y+1/2'
  142  'z+1/2, x, -y+1/2'
  143  'x+1/2, -z, y+1/2'
  144  '-x+1/2, z, -y+1/2'
  145  'x, y+1/2, z+1/2'
  146  '-x, -y+1/2, -z+1/2'
  147  'z, y+1/2, -x+1/2'
  148  '-z, -y+1/2, x+1/2'
  149  '-x, y+1/2, -z+1/2'
  150  'x, -y+1/2, z+1/2'
  151  '-z, y+1/2, x+1/2'
  152  'z, -y+1/2, -x+1/2'
  153  'x, -y+1/2, -z+1/2'
  154  '-x, y+1/2, z+1/2'
  155  'z, -y+1/2, x+1/2'
  156  '-z, y+1/2, -x+1/2'
  157  '-x, -y+1/2, z+1/2'
  158  'x, y+1/2, -z+1/2'
  159  '-z, -y+1/2, -x+1/2'
  160  'z, y+1/2, x+1/2'
  161  'y, -z+1/2, -x+1/2'
  162  '-y, z+1/2, x+1/2'
  163  'y, x+1/2, -z+1/2'
  164  '-y, -x+1/2, z+1/2'
  165  'y, z+1/2, x+1/2'
  166  '-y, -z+1/2, -x+1/2'
  167  'y, -x+1/2, z+1/2'
  168  '-y, x+1/2, -z+1/2'
  169  '-y, z+1/2, -x+1/2'
  170  'y, -z+1/2, x+1/2'
  171  '-y, -x+1/2, -z+1/2'
  172  'y, x+1/2, z+1/2'
  173  '-y, -z+1/2, x+1/2'
  174  'y, z+1/2, -x+1/2'
  175  '-y, x+1/2, z+1/2'
  176  'y, -x+1/2, -z+1/2'
  177  '-z, x+1/2, -y+1/2'
  178  'z, -x+1/2, y+1/2'
  179  'x, z+1/2, -y+1/2'
  180  '-x, -z+1/2, y+1/2'
  181  'z, -x+1/2, -y+1/2'
  182  '-z, x+1/2, y+1/2'
  183  '-x, -z+1/2, -y+1/2'
  184  'x, z+1/2, y+1/2'
  185  'z, x+1/2, y+1/2'
  186  '-z, -x+1/2, -y+1/2'
  187  '-x, z+1/2, y+1/2'
  188  'x, -z+1/2, -y+1/2'
  189  '-z, -x+1/2, y+1/2'
  190  'z, x+1/2, -y+1/2'
  191  'x, -z+1/2, y+1/2'
  192  '-x, z+1/2, -y+1/2'
loop_
 _atom_site_type_symbol
 _atom_site_label
 _atom_site_symmetry_multiplicity
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
  Li  Li0  4  0.000000  0.000000  0.000000  1
  F  F1  4  0.000000  0.000000  0.500000  1

Pair atomic distances have been mentioned plenty. I can only recommend Pekka Pyykkö's tabulated data for covalent bonds. It's referenced by Geoff in his excellent answer to Newer ionic radii data than Shannon's 1976 compilation? This question is also quite similar (which I have answered with referencing PP): How should elements be colored? And how many bonds does an atom have?

Your question does not detail out what you mean by how is it done.  Indeed, your question may be answered twice:

determine the distances between atoms, pairwise compare the sum of van der Waals radii; if the distance is equal or less to a threshold (previously extracted from experiments, tabulated e.g., in the International Tables of X-ray crystallography); as in @Greg's answer. or

given a .cif file, I need to establish a file with a connection table and with information about bond orders.  In this case, cod-tools by the Crystallography Open Database, freely available (e.g., repackaged for Linux Debian and related distributions like Ubuntu (tracker for Debian)) contain a nice tool codcif2sdf running on the command line to convert a .cif into a .sdf file.
Note that some databases (e.g., CSD by CCDC) allow the download of their data not only as .cif, yet equally in formats like .mol2 (reference), .sdf, .pdb, or SMILES strings from their more advanced interfaces (in case of CSD, conquest, or their Python API (an example).

The content of your example .cif file was copied into file test.cif.  Because the data are not the result of a X-ray diffraction experiment with subsequent structure solution and structure refinement, one may pass some of the problems listed by checkcif, though PLAT113_ALERT_2_B should not be dropped.
The file was processed by codcif2sdf test.cif > test.sdf to yield a .sdf file.  Jmol, running with the automatic computation of bonds (cf. the GUI, Edit -> Preferences -> Bonds) will assign a bond, while the .sdf file lacks the connectivity table typically seen for organic molecules.
At the level of codcif2sdf, in comparison to performing such a transformation for data about an organic molecule like benzene, the example of $\ce{LiF}$ might indicate a lack of encoded data.  However, what do the struts drawn between the atoms represent?  In crystallography, they indicate that the distance between two atoms is less than the sum of their van der Waals radii.  As an example, see the drawing in this question on chemistry.se, and an answer tangentially relevant here:

In other fields, where you write one, or multiple dashes between two atoms, you state that there is non-zero electron density between the two atoms.  This then covalent bond, two atoms participate (in an analogy, share with each other).  This directed bond may be polarized, i.e. with one partner participating more in the electron density, than the other.  However, this contrasts to  $\ce{LiF}$ with a difference of electronegativity so large that one partner (here: $\ce{F}$) practically withdrew all electron density of this bond, where the other (here $\ce{Li}$) practically gave up all of its share by valence electrons.
As a result, $\ce{LiF}$ is not a covalent molecule, but an ionic salt. If you lower the level of description, and describe electrons as countable spheres, it consists of  which consists of $\ce{Li^+}$ and $\ce{F^-}$.  Their interactions in the sample resembles those of point charges.  Have a look at illustrations in my answer here for a comparison of e.g., $\ce{N#N}$, $\ce{NaCl}$, and $\ce{Cu}$.

I am definitely looking for an actual implementation that I can use. odcif2sdf does not seem to work though. It produces "ERROR, the maximum number of polymer atom repetitions 100 was hit for the atom O11 (1), to get around this limit, please increase --max-polymer-atoms, to say, --max-polymer-atoms=200 or decrease --max-polymer-span (e.g. --max-polymer-span=2)", only to then throw a "unknown option '--max-polymer-atoms=200'." error when I try to do that.

codcif2sdf (presumably) was written with the small molecule models on COD encoded in .cif in mind and in my experience, works reasonably well, especially for entries about organic molecules without positional/orientational disorder. The .mmcif format you use is different to the of .cif (wasn't mentioned in your question). A test file of Jmol however is processed by OpenBabel obabel -immcif 114D.mmcif -ocif -O test.cif and codcif2sdf test.cif > test.sdf with some success (552 atoms).

So far, I did not deal to rewrite .mmcif into other formats.  However, would be a service like https://mmcif.pdbj.org/converter/ a suitable converter for you?

himm... I am not using mmcif files (I know because they do not contain "."s in their headers). Also, my molecules do not have any where near that many atoms.

@maxbear123 One option may be to edit the original question and to add the problematic file's content in a code block (enclosed by three grave signs in the line to start, three grave signs in the line after to end this). Alternatively, to add in the OP a link which points to a reference outside chemistry.se (e.g., on zenodo, or pastebin).  Then, it is easier for the interested to attempt a conversion to yield, e.g. a .sdf file.

@maxbear123 For clarification, I edited the answer.  The .sdf is deposit on pastebin.com, with a minor edit of the time stamp.

You didn't ask about macromolecules, but I'll write about it anyway.
Macromolecular CIF files (mmCIF) also don't contain bonds.
This information is stored in separate dictionaries.
In particular, the PDB maintains Chemical Component Dictionary –
a huge CIF file which contains, among other things, a list of bonds for each residue and small molecule found in PDB entries.
Connectivity between monomers in a polymer can be inferred from the sequence information.
Other connections are listed explicitly in the struct_conn category.
It'd possible to just use distances between atoms pairs, but this is less reliable – atomic coordinates in macromolecules may not be precisely determined.

+1 for commenting on the component dictionary for mmCIF.

The most software find bonds in a structure from cartesian coordinates by finding atom pairs that are closer than a certain threshold distance (something shorter than the vdw radius of the given atoms). Generally, you can set this distance yourself if you need for some reason.

how could one algorithmically find all bond pairs

Here is a sketch of an algorithm that takes crystal symmetry into account:

Move all atoms into a single asymmetric unit
Apply all symmetry operators (including centering) to the asymmetric unit to generate the content of the unit cell
Duplicate the unit cell content to also create the units cell contents on the left, right, top, bottom, front, back of the unit cell.
For each atom in the asymmetric unit, find the neighbors within bonding distance, using a fixed-radius near neighbors algorithm and appropriate distance cutoff.
Filter the list of neighboring pairs to exclude duplicates and unrealistic geometries.

This sketch of an algorithm might be slow for large structures, and there might be simple optimizations, especially for spacegroups where the asymmetric unit is a rectangular prism along the cartesian axes.
Example

The CIF file for sodium chloride contains two atoms, one sodium (purple) on the origin and one chloride (green) in the center of the unit cell. The crystal is face-centered. To find the closest neighbors of the chloride, you have to generate all the sodium ions in or touching the unit cell, using the centering operation and various unit-cell vector translations. Then, you can find the six sodium ions that are closest neighbors of the chloride ion (above, below, left, right, in front and behind the chloride ion on the faces of the unit cell).
To find which chloride ions make up the (inner) coordination sphere of the sodium ion, you have to generate the symmetry mates of the chloride ion within the unit cell. Then, you have to translate the unit cell in multiple directions (and combinations of directions) to make sure you also find bonding partners outside of the unit cell you started with.

The VESTA program allows one to try different cutoff distances for the bonds it displays. Sometimes it has a distance by default (that works and produces plausible bonds). Other times it shows no bonds (and inputting any cuttoff distance produces clearly inplausible bond pairs). How does one pick an "appropriate distance cutoff"?

@maxbear123 Jmol (the program used in for illustration) equally has this option.  In the GUI, Edit -> Preferences -> Bonds allows you to switch off/on the automatic computation of bonds (if these are not stored in a connectivity table of the file read, like in a .sdf file (and contrasting to .cif/.xyz)).  It then allows you to adjust (independently of each other) a minimal bond bond distance (0 to 1 Angstrom), and a bond tolerance (sum of van der Waals radii of the atoms in question + x) equally with an x in range of 0 to 1 Angstrom.

@maxbear123 "Chemical bonds" make the most sense in covalent compounds, but you are most probably dealing with inorganic (ionic or metallic ) structures, right? In those materials connecting atoms is not much more than an illustration of close interactions, but you shouldn't take it literally.


text:
Can we split solid ionic compounds into their constituent ions when writing an ionic equation?
The equation for the reaction between magnesium and copper(II) oxide is:
$$\ce{Mg + CuO -> MgO + Cu}$$
Here, we can write the net ionic equation as:
$$\ce{Mg + Cu^{2+} -> Mg^{2+} + Cu}$$
The $\ce{CuO}$ here is a solid, so why can we still separate it into its constituent ions?
In a neutralization reaction, if the base is a solid then we cannot split it into its constituent ions (as far as I know). For example, the net ionic equation for the reaction between copper(II) oxide and sulfuric acid is:
$$\ce{CuO + 2H+ -> Cu^{2+} + H2O}$$
So why are the rules different in the two reactions? Why can we split the $\ce{CuO}$ into its constituent ions in one reaction but not the other?

You may find useful these links for text formatting (not to be applied to titles):
Notation basics ,  Formatting of math/chem expressions  and
upright vs italic

For solid phase reactions, using ionic form of equations is very unusual. It makes more sense if cations and anions move and react independently, like for dissolved or melted salts.  It is rather $\ce{2 CuO <=> 2 Cu + O2}$ and $\ce{2 Mg + O2 <=> 2 MgO}$. Additionally there is lot of covalent character of bonds in these oxides.

We may formally split in both cases, but it makes little sense.

@Glorfindel In my experience with mhchem, {} in ion charge is not necessary, as $\ce{Cu^2+}$  $\ce{Cu^2+}$  is displayed the same as $\ce{Cu^{2+}}$ $\ce{Cu^{2+}}$. Not sure, if there is preferred the way with or without {}.

P.S.: Checked with all renderers but not available MathML and displaying of both is the same. I do agree it would be different for general MathJax.

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text:
Would the Daniel cell work just as well if a solution of zinc ions wasn't used?
I know that, in a Daniell cell, the zinc anode is immersed in a solution of zinc ions. As I see it, though, these ions are irrelevant to the reaction taking place.
Would the cell work just as well if the zinc was immersed in a solution of sodium chloride instead?

Can I make orange juice, if I use apples instead of oranges ? It would still be juice, just not orange one. The Daniell cell is defined as the system $\ce{Zn(s)|ZnSO4(aq)||CuSO4(aq)|Cu(s)}$. Your proposed cell would be still a galvanic cell, just not the Daniell one.

Be aware that laconic, not elaborated questions are usually closed on the StackExchange network.  Aside of lack of expected explicit a priori effort, they are generally hard to work with, due possible question misinterpretation, needed clarification and  difficult estimation of the OP knowledge .  How do I ask a good question?.
Describe the question well, search, think, refer and summarize.  Well elaborated questions have higher probability to  receive acceptable answers.

Using a different ion solution might lead to a different undesirable reaction with the ions of that solution. We use solutions with similar ions to minimize interference

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text:
Planning regio selective protection of functional groups in glycochemisty
Lately I was trying to get a thorough understanding of some questions,
I have delved into many research resources such as Scifinder, Google Scholar, and Organic Chemistry Portal.
but I'm not satisfied with the set of tools available, it takes me way too much time to find an answer.
Can scientists here share with me their workflow, it seems to me there is a more efficient way to reach those answers and those reproducible experiments.
In glycochemistry using selective protection is not trivial due to steric effects and reactivity of the hydroxyl and in many cases protection of the saccharide requires multistep protection/deprotection of the hydroxyl. I would like to ask what approach you will take to selectively protect the hydroxyl in the scheme with benzoyl using small number of simple steps. How do you design the synthetic route and how do you find the appropriate process?

The primary alcohol likely will exhibit a greater reactivity towards benzyl chloride, thus react faster than/ahead of the secondary alcohols to yield a benzyl ether. Did you consult  the typical suspects (regarding examples) in the books by e.g., Kociensky, or the by Greene?

One equally could search (with permutation of the configuration of the stereogenic centers) complement the search in a bibliographic database (like SciFinder) by a search in reaction database (like Reaxys [by Elsevier], thanks to Beilstein; or Science of Synthesis [by Thieme], thanks to Houben-Weyl) if there are reports about similar-enough structures like the intended product.

I am not a specialist in glycochemistry. I think it will be possible to selectively protect the primary alcohol with something like a bulky silyl ether beyond that the selectivity looked difficult.

I think you might be able to protect C-4 and C-6 hydroxyl groups with an acetal/ketal (please search literature, as I'm not sure of conditions and I may well be wrong anyway) but I'd expect that establishing selectivity between C-2 and C-3 is going to be a lot harder. (I'm very much not a specialist either.)

C2 & C3 are also nicely set up to form an acetal/ketal, but that does not help in distinguishing between them.


text:
Tight-binding model in the presence of a metal atom
Consider a molecule such as a porphyrin ring. For many purposes, a simple tight-binding model in which only pi-electrons are included provide a very good description of the electronic levels, shape of the molecular orbitals, etc.
Now imagine there's a metal atom in the center of the ring. DFT analysis of the projected DOS show that, around the Fermi level, only the pz orbitals of the non-metal atoms and some of the d orbitals of the metal play a role (I am assumming the molecule is on the XY plane). This suggests also that it should be possible to construct a very simple model (similar to the one in which only pi-electrons are treated in hydrocarbons) with hopping between the pz and d orbitals (of course, many-body terms will be important in the d-shell, but focus now on the one-electron part and the coupling with the rest of atoms).  Are there standard tight-binding hamiltonians for such systems, with parametrizations for the pz-d hoppings, something akin to Huckel hamiltonians but for systems with metal atoms? And how to count then the number of "pi'' electrons that enter the calculation? (I was guessing by looking at the number occupations of lowdin orbitals in a previous DFT calculation)

As far as I am aware there are no universal parameters for p-d only calculations, but tight-binding models were widely used in solid-state physics to described oxides and other compounds.
A more chemically relevant method is DFTB, a tight-binding method that has extensive parametrization for a wide range of elements. DFTB has several implementation, including an efficient open-source version, DFTB+.
Another closely related tight-binding method is Grimme's xTB, which is also implemented in the DFTB+ package.


text:
Balancing a chemical reaction with oxidation numbers
We have been teached how to balance chemical reactions with oxidation numbers in school, but somehow I can't understand it.
This is the equation to balance
$$\ce{Cu(s) + NO3−(aq) + H+(aq) -> Cu^2+(aq) + NO2(g) + H2O(l)}$$
At first I looked at the oxidation numbers. The only oxidation numbers that change are $\ce{Cu}:\ 0\ \rightarrow \ 2+$ and $\ce{N}:\ 1-\rightarrow \ 4+$, both are oxidized.
Then I'm a bit lost. In a typical redox reaction I would create partial reactions for both oxidation and reduction, but nothing is reduced in this reaction. I made two partial reactions with $\ce{Cu}$ and $\ce{N}$ being oxidized, but I think that it's not how it should be done. I came to a very different result than my book.
Is there anyone who knows how I should balance this reaction? I'm a bit lost.

You may find useful these links for text formatting (not to be applied to titles):
Notation basics ,  Formatting of math/chem expressions  and
upright vs italic

Welcome to chemistry SE! Before asking, read available textbooks, google relevant keywords and study  search results. Check for duplicates or related Q/As by insertion the search term site:stackexchange.com. Search other valuable sites with the term site:libretexts.org or  site:hyperphysics.phy-astr.gsu.edu or site:en.wikipedia.org .
This prevents cases of asking for answers that have been already written in many ways on many places.
// Review also Chemistry SE: resources-for-learning-chemistry

I have tried to watch videos and learn from the book, but I still dont understand how this should be solved. @Poutnik

In the book it was $NO^{3-}$, not $NO_3^-$, is it an error? @Poutnik

Note that oxidation numbers, in opposite to charges, are used to be written by Latin numbers with oreceeding sign, i.e. +IV, not 4+.

There are 3 O atoms and only one negative charge, tbe book has it erroneous ( and you should notice it yourself ).

Element symbols are never italic, use the mhchem MathJax package \ce{} - see the links above. $\ce{NO3-}$as $\ce{NO3-}$

Generally, to paraphrase Robert Fulghum, all, what one needs to enumerate chemical equations, one has learnt in elementary school. Counting with small integer numbers and using the "magical formula" m.n=n.m.

For the record, that is not the proper reaction equation, there is a mix of NO2 and NO gases and the mechanics is under debate. Here is a citation from one of the latest articles: "Mechanistic Study of the Production of NOx Gases from the Reaction of Copper with Nitric Acid" Rebecca K. Carlson, Ping Yang*, Samuel M. Clegg, and Enrique R. Batista* Inorg. Chem. 2020, 59, 23, 16833–16842 doi.org/10.1021/acs.inorgchem.0c00607 –

What is the counterion (anion) for $\ce{Cu^2+}$?

The counter ions are $2$ $\ce{NO3^-}$ These ions are coming from the $4$ $\ce{HNO3}$ molecules implied in the final equation $$\ce{Cu + 2 NO3^- + 4 H+ ⟶ Cu^{2+} + 2 NO2 + 2 H2O}$$ Two ions $\ce{NO3-}$ ions are spectators at left. They are used at the right hand side to neutralize the $\ce{Cu^{2+}}$ ion.

The equation we need to balance is this:
Cu (s) + NO3− (aq) + H+ (aq) ⟶ Cu2+(aq) + NO2 (g) + H2O (l)
Using simple oxidation state rules
The oxidation states on the left hand side:

Cu is 0 - Elements are always 0
O in NO3 is -2 (per atom), adding to -6 for 3 atoms of O
Since the oxidation states of all the atoms in a molecule must add to the charge of the molecule, N is equal to:
-1 (charge of the molecule) - (-6) (charge of all the oxygen atoms). Hence, N is -1 - (-6) = +5
Finally, H+ is +1, since the oxidation numbers of all monoatomic ions as the charge of the ions

The oxidation states on the right hand side:

Cu is +2 (monoatomic ion)
O is -2 per atom, which adds to -4 for 2 atoms of O
N is +4, since the overall molecule is neutral
O (in H2O) is -2
H is +1 (H is +1 in all its compounds) for each atom, adding up to +2, which also accounts for the overall molecule charge of 0

Only the following oxidation states are changing:

Cu from 0 to +2
N from +5 to +4

Now we can split the equation into half-reactions:

Cu ⟶ Cu2+ + 2e-
NO3- + e- ⟶ NO2

Balancing the equations:

Cu ⟶ Cu2+ + 2e-
NO3- + e- + 2H+ ⟶ NO2 + H2O

Multiplying the equations:

Cu ⟶ Cu2+ + 2e-
2NO3- + 2e- + 4H+ ⟶ 2NO2 + 2H2O

Balancing the equations together:

Cu + 2NO3- + 2e- + 4H+ ⟶ Cu2+ + 2e- + 2NO2 + 2H2O
Cu + 2NO3- + 4H+ ⟶ Cu2+ + 2NO2 + 2H2O

Formally correct, but more complicated than necessery.  // Oxidized Cu changes ON by 2, reduced NO3- by 1, therefore Cu + 2 NO3- // Adding 4 H+ to maintain charge balance, together with H2O as product. Cu + 2 NO3-  + 4H+ -> Cu^2+ + 2 NO2 + 2 H2O.// Do O and H inventory as independent check. // You are done.

For the record, that is not the proper reaction equation, there is a mix  of NO2 and NO gases and the mechanics is under debate. Here is a citation from one of the latest articles: "Mechanistic Study of the Production of NOx Gases from the Reaction of Copper with Nitric Acid"
Rebecca K. Carlson, Ping Yang*, Samuel M. Clegg, and Enrique R. Batista*
Inorg. Chem. 2020, 59, 23, 16833–16842
https://doi.org/10.1021/acs.inorgchem.0c00607

@AJKOER Factually it is correct, but for educative approach toward the OP it is unnecessery confusing detail. The reaction is about the outcome, not mechanism. At beginner level, it can be considered correct for concentrated HNO3.

Agreed. Learning the language a bit will help in learning advanced principles. Much easier to balance  Cu + 4 HNO3  = Cu[NO3]2 +2NO2   +2 H2O when one knows what nitric acid and nitrate ion are. If the actual reaction is a consecutive series and one is concerned about mechanism each reaction deserves its own equation. [The abstract of the above link offers nothing]


text:
Can an electron be excited to a spin state with s ≠ 1/2?
I used to think that all nuclei have fixed intrinsic value of the nuclear spin quantum number, $I$. For example, $\ce{^1H}$ must have a nuclear spin of $\frac{1}{2}$, $\ce{^{14}N}$ must have a nuclear spin of 1 and so on.
Not until I study Mossbauer spectroscopy, in which the transition involved is the excitation from $I = \frac{1}{2}$ to $I = \frac{3}{2}$ of $\ce{^{57}Fe}$ nuclei. It is the $I$ that got changed, not the $m_I$ as in typical NMR!

Source: Wikipedia, Mossbauer Spectroscopy
How can the $I$ of a nuclear species be changed? It was just as weird as changing the mass of a particle, which is an intrinsic property. Any insight will be appreciated.
Since the spin of nuclei can be changed, is it also possible to change the spin, $s = \frac{1}{2}$ of an electron, if given high enough energy?

"is it also possible to change the spin, s = 1/2?" No. Just no.

Just a small note about formatting; please use $\ce{^57Fe}$ $\ce{^57Fe}$ instead of $^{57}$Fe $^{57}$Fe. The latter looks correct, but the alignment of superscripts might not be entirely correct (depending on e.g. fonts), and (more importantly) if you resize your window the Fe may be shifted to the next line (see example here). Using MathJax to typeset the entire nuclide symbol avoids this issue, and is probably a bit easier to keep track of mentally anyway.

@Thelearner An alternative, plain text notation is iron-57.

The major mistake is considering a nucleus like if it were an elementary particle.
Compare a nucleus spin configuration to spin electronic configuration of atoms. In both cases, there are multiple fermions (nucleons or electrons) that can have various total spín configuration.
There are multiple known isotopes with known excited high spin nuclear isomers.
My favourite isotopes of tantalum show that some isotopes have up to 7 isomers like tantalum-179, with spin 7/2, 9/2, 1/2, 21/2, 23/2, 25/2 and 37/2.
One of known meta-stable nuclear isomers is even naturally occuring and  observationally stable (due forbidden transition): tantalum-180m, even if the lower energy tantalum-180 is unstable and has the half-life about 8 hours, beta decaying to hafnium-180 (EC, 86%) or tungsten-180($\beta -$, 14%).
Military circles have been interested for some time in the metastable isomer hafnium-178m2 with the half-life 31 years. The supposed stimulated gamma emission would provide about 1/100 energy density, compared to nuclear fission, while bypassing nuclear weapon regulations, as seen in hafnium controversy.

Is there a story as to why tantalum is your favourite? :-)

@orthocresol No special story :-), I have just mentioned  $\ce{^{180\mathrm{m}}Ta}$ several times recently on CH SE, in various context. It is the only stable odd-odd nuclide after 14N, kinetically protected by its high spin configuration.

Tantalum-180m is also the only metastable nucleus known to occur in nature.

While the stable one is unstable. // See also hafnium controversy about hafnium-180m2.

oops. hafnium-178m2


text:
Comparing acidic strength of phthalic acid isomers
I'd like to compare the acidic strengths of phthalic, isophthalic and terephthalic acids. As I understand, phthalic acid is the most acidic due to steric inhibition of resonance (SIR), but as terephthalic acid has a negative mesomeric effect (−M) operating, it should be more acidic compared to isophthalic acid.
However, the data from Wikipedia suggests that isophthalic acid is more acidic:

Acid
Structure
$\mathrm{p}K_\mathrm{a1}$
$\mathrm{p}K_\mathrm{a2}$

Phthalic acid

$2.89$
$5.51$

Isophthalic acid

$\color{red}{3.46}$
$4.46$

Terephthalic acid

$\color{red}{3.51}$
$4.82$

Also, why is there such tiny difference in their acidic strengths?

even I believe that the acidity order should be phthalic acid > terephthalic acid > isophthalic acid for all the reasons you already mentioned.  I'm not sure about the reason for the discrepancy but I believe that the pKa values here are likely to be more accurate cause it is specified that they are measured at a constant temp 25 C. https://onlinelibrary.wiley.com/doi/pdf/10.1002/3527600418.mb8899isme0025

pka1 phthalic acid - 2.76      pKa1 terephthalic acid - 3.52    pKa isophthalic acid - 3.70

do anyone know some factors which effects acidic behavior but are not very frequently used in deciding acidic strength orders?

Pthalic acid tops the list of acidic strength among the three because of the famous ORTHO effect in organic chemistry according to which, irrespective of the nature of substituent on ortho position, ortho derivatives are the strongest acid.


text:
Sodium Chlorite Listed as Active Ingredient in Anti-Fungal/Anti-Bacterial Fish Medication
My hobby is Fish Keeping. About 6 months ago I picked up a medication called Maracyn Oxy. It's a non-antibiotic treatment for true fungal and some bacterial infections and it works like an absolute charm!
However, nobody in the hobby seems to know exactly how it works. The active ingredient is sodium chlorite.
Back of the bottle:

INSTRUCTIONS:  1/2 capful (1/2 tsp/2.4mL) per 10 gallons (38 liters) of water.
Repeat daily as needed for more than five days.
It is suggested to always increase tank aeration during treatment to ensure there is an adequate oxygen supply for infected fish.  Turn off UV Sterilizers during treatment.  Should fish exhibit signs of distress, neutralize the medication by using an aquarium dechlorinator (like FritzGuard), follow manufacturers directions for dosing.  Use of a hospital tank is recommended.  No water changes, pH or temperature adjustments necessary if readings are in ideal range.  Maintain normal filtration.

So I went down a rabbit hole. Below I've outlined my theory.

Chlorine Dioxide?
I don't think that sodium chlorite itself is what is actually what is killing the harmful microorganisms. Most of the articles I've found talk about it being used to create Chlorine Dioxide - especially in water treatment plants where it is used to kill bacteria and etc.
After a couple more Google searches I found this article that cites the following:

First, (equation 1), chlorine reacts with
water to form hypochlorous acid (HOCl) and
hydrochloric acid (HCl). These acids react
(equation 2) with sodium chlorite to form chlorine
dioxide, water, and sodium chloride (NaCl).

The reason I included the instructions on the back of the bottle is because of two statements that I believe help this theory:

"Turn off UV Sterilizers during treatment" - I've read several articles that state that UV light is effective in neutralizing CLO2.
"Should fish exhibit signs of distress, neutralize the medication by using an aquarium dechlorinator" - according to this article (from the same organization as the other) although sodium sulfite is most effective, sodium thiosulfate (a common ingredient in tap water conditioners) can neutralize concentrated solutions of sodium chlorite.

I'd love to learn:

Am I probably right about Chlorine Dioxide? If not, what is more likely?
If so would it be that it's chlorine + sodium chlorite that's actually in the bottle, and the chlorine dioxide gets created when added to the water?

If my tags are off I appreciate any help.

The chemistry of chlorine is complex, with many possible species of different oxidation states. The company selling the product has a safety data sheet (SDS) that states the ingredients as propriatary, but then classifies the product as chlorite solution for transport. Chlorite $\ce{ClO2-}$ (and
chlorous acid, $\ce{HClO2}$) have a +3 oxidation state, chlorine dioxide a +4 oxidation state, hypochlorite (active ingredient in bleach, $\ce{ClO-}$) a +1 oxidation state, and the chloride ion (in table salt) a -1 oxidation state.

Source: https://www.onlinechemistrytutor.net/oxidation-state-examples/
What it probably is not
Chlorite, as stated by the OP, can be used to synthesize chlorine dioxide gas by adding chlorine or hypochlorite. It is unlikely that there is chlorine or hypochlorite in the product.
Chlorite in an acidified form is used as desinfection agent to kill bacteria on chicken and cows during meat processing. In this application, chlorine dioxide is produced:
$$\ce{4 HClO2 -> 2 ClO2 + ClO3- + Cl- + 2H+ + H2O}$$
$$\ce{5 HClO2 -> 4ClO2 + Cl- + H+ + 2 H2O}$$
A strongly acidic solution (very low pH) would probably kill the fish, so that formulation is also unlikely.
What it might be
There is a product for cleaning contact lenses where chlorite is combined with sodium chloride and trace amounts of hydrogen peroxide.

Source: https://www.sciencedirect.com/topics/medicine-and-dentistry/sodium-chlorite
This is a possible formulation. A putative mechanism of action is discussed here: http://advancedeyecareresearch.co.uk/pdf/regard.pdf, but they don't say much about the chemistry. The key is to have a formulation that is stable until it comes in contact with the organisms you want to kill, and does not kill the fish, plants and snails.
Mechanism of action
Chlorite is toxic for vertebrates, bacteria, fungi, and other organisms. The claims that it has benefits as part of a "Miracle Mineral Solution" are false and dangerous; ingesting chlorite is life-threatening, damaging kidneys, intestines and the hemoglobin in our red blood cells.
Some micro-organisms have a dedicated chlorite dismutase enzyme that breaks down chlorite into chloride and dioxygen. Organisms that break down perchlorates have these enzymes; more recently, they were also find in ammonium-utilizing bacteria.
In the absence of chlorite dismutase (or when administering doses that are to high for efficient detoxification), the chlorite ions could have multiple damaging and deadly effects. In humans, the iron in hemoglobin is oxidized from the +2 to the +3 oxidation state (the hemoglobin is called methemoglobin), interfering with oxygen transport.
In a study on the toxic effect of chlorite on mammalian cells and on microorganisms, glutothione (an intracellular redox buffer) was readily oxidized by chlorite. The authors saw this as evidence that chlorite imposes oxidative stress on cells.
It would be very difficult to state the exact chemical reactions going on in the cell when exposed to chlorite. The chlorine chemistry is rich, and there are thousands of possible reaction partners in the cell. Fish "medication" is not controlled by government agencies, so there is no requirement for clinical studies that support efficacy and exclude harm to fish - if a manufacturer finds a formulation that sells, they are all set. There are also less requirements to disclose the formulation and data about the effects of the product on different organisms, and surely there is less research done compared to how drugs for human use are studied.
Questions

Am I probably right about Chlorine Dioxide? If not, what is more likely?

Chlorine dioxide probably forms when chlorite reacts with organic matter, and not in the bottle.

If so would it be that it's chlorine + sodium chlorite that's actually in the bottle, and the chlorine dioxide gets created when added to the water?

There already is water in the bottle. Dry sodium chlorite is explosive. There is no evidence for the presence of chlorine in the bottle. The combination would be dangerous.

[OP in comments] ... increase aeration ...

In humans, sodium chlorite poisoning oxidizes hemoglobin to methemoglobin, lowering oxygen supply to the organs. High aeration might counteract slight toxicity to fish (at the recommended dosage).

I am really surprised by your last source: CONTACT LENS MONTHLY. Obviously, I will re-consider my ACS citations. Also, where is the evidence for claiming an acidified chlorite reaction?

Just the opposite, I am excluding reactions that require low pH because that would kill the fish. @AJKOER

So exactly how is ClO2 created here? And why the aeration? Both of which, by the way, are points my answer addresses.

I have just finishing editing my answer as my claimed OH radical path now has a source. Namely this 2017 research work: "New insights into the decomposition mechanism of chlorine dioxide at alkaline pH"
where interestingly, this recent (2017) source cites this hydroxyl radical path as a possible avenue, to quote: "The generation of HO˙ could be one reason for cellulose degradation by ClO2 at alkaline pH..."

Thanks for your answer. I read that contact solution article and noticed in Table 1. MPS vs H2O2 it is mentioned that a pro of the MPS is its "selective antimicrobial action". Beneficial bacteria (that converts NH3 > NO2 > N03) is very important to an aquarium. Could the aforementioned "selective action" allow this solution to preserve the good bacteria? I've never experienced an ammonia or nitrite spike while dosing the medication, which means that beneficial bacteria is unaffected by this product.

Also, duh, there's water in the bottle. insert Patrick Stewart facepalm meme

Maracyn is a line of water additives to treat fungal diseases in aquarium fish, and the "oxy" product  is just one in the line without antibiotics, relying instead on the oxidizing activity of the reaction products of sodium chlorite. The solid Na chlorite is a fire hazard but not explosive afaik (hypochlorite is explosive).

@BuckThorn "Sources of ignition, such as smoking and open flames, are
prohibited where Sodium Chlorite is used, handled, or
stored in a manner that could create a potential fire or
explosion hazard." source, maybe it is not the chlorite itself but in combination with air or humidity.

Nitrifying bacteria might be less susceptible, http://users.unimi.it/biofilms/appl%20biotec%20amb_LM/metal%20detoxifcation%20(2)/maixner_chlorine%20dismutase_nitrospira.pdf

For completeness, from https://cameochemicals.noaa.gov/chemical/1479: "SODIUM CHLORITE is self-reactive. The trihydrate crystals of sodium chlorite explode on percussion. Sodium chlorite reacts with acids to form spontaneously explosive chlorine dioxide gas (ClO2). If heated above 347°F, the reaction yields enough heat to become self-sustaining, [Mellor 2 Supp. 1:573 1956]. Ammonia with chlorites produces ammonium chlorite, which is a shock-sensitive compound. "

@KarstenTheis Thank you for your additions to your answer. I'm mostly disappointed that nobody even gave ajkoer's answer the time of day. I haven't heard anything that's said the solution is not plausible. Therefore, I've given ajkoer the bounty, but you the accepted answer since you cite a commercially available product in a rational way. I don't think you're worried about the rep.

@MikeCiffone It is an intriguing question you posted, and has taught me a lot about aquarium chemistry while researching the topic.

@KarstenTheis I have found myself learning so much chemistry from being in the hobby! I believe that a reason many are unsuccessful keeping fish is the lack of understanding the chemistry going on in their system.

The actual path I suspect is from the interaction of hypochlorous acid with ferrous ions in the tap water forming the powerful hydroxyl radical that can further interact with the aqueous $\ce{NaClO2}$. This could result in the liberation of $\ce{.ClO2}$ as claimed (being an alternate path to the standard lab prep cited, only arguably appropriate here with tap water and aeration).
Note: the following cited chemistry is advanced noting radical formations (including the stable $\ce{.ClO2}$ free radical).
First, the so-called Fenton-type reaction based on $\ce{HOCl}$ (in place of $\ce{H2O2}$ as in standard Fenton chemistry):

$\ce{Fe++ + HOCl -> Fe+++ + .OHCl-}$

At pH > 5 (or in presence of chloride):

$\ce{.OHCl- -> .OH + Cl-}$ k = 6.1 x 10^9 (Source: Supplementary Material and click on Supplement File 1 to download)

Next, the liberation of the stable free radical $\ce{.ClO2}$ radical with  the help of the hydroxyl radical:

$\ce{.OH + ClO2- <-> OH- + .ClO2}$  (Source: "New insights into the decomposition mechanism of chlorine dioxide at alkaline pH")

where interestingly, this recent (2017) source cites this hydroxyl radical path as a possible avenue, to quote:

The generation of HO˙ could be one reason for cellulose degradation by ClO2 at alkaline pH, but possibly not the unique one, as it was not proved in this article, whether or not ClO2 is able to directly attach the OH functions of anhydrosugars at alkaline pH.

Further, to account for the statement: "It is suggested to always increase tank aeration during treatment to ensure there is an adequate oxygen supply for infected fish", this is likely the result of the following reaction involving so-called metal auto-oxidation forming the superoxide radical anion:

$\ce{Fe++ + O2 -> Fe+++ + .O2-}$ (Source: see, for example, this ACS article)

which is suspected further of interacting with $\ce{.ClO2}$ as follows:

$\ce{.ClO2 + .O2- -> ClO2- + O2}$  (Based on H2O2 as noted here)

reforming the chlorite, and thus even possibly cycling the disinfecting process, especially in the presence of sunlight and photosensitive Ferric chloride.
Supporting source: A Dutch study: Chlorine Dioxide as a Post-Disinfectant for Dutch Drinking Water, to quote:

In this paper, results are presented of experiments into the consumption and reaction kinetics of chlorine dioxide in a number of (drinking) waters in The Netherlands. It was found that chlorine dioxide consumption is related to the dissolved oxygen content (DOC) of the water and the reaction time.

I hope this, albeit, technical discussion helps with your understanding on what is likely occurring.

This is a very interesting answer. While a lot of this is over my head, I've read a bit about the things that I don't understand. I like that you accounted for the instructions to increase aeration. Hopefully Karsten can address that. A big problem with this theory, however, is that Aquarium tap water conditioners not only dechlorinate, but also remove metals. We add these solutions to tap water before adding it to a tank. So a hurdle to get over is where else the ferrous ions that interact with the hypochlorous acid would come from. Perhaps the bottle somehow? Would that be safe?

Decomposition of NaClO2 from CO2 presence may be a source of HClO2 and  HOCl. Action of light or any aeration formed superoxide can react with HOCl creating OH per the reaction: .O2- + HOCl = O2 + .OH + Cl-  (see https://ar.iiarjournals.org/content/33/9/3589 ) as if there was not enough chemistry already cited! But, in my opinion, all interesting and valuable info!

In a highly stocked tank without plants, CO2 from poop would be abundant. Most planted tanks are actually supplemented with CO2. So this is plausible. Also, I am curious about your thoughts on my comment on Karsten's answer regarding beneficial bacteria. Could this solution be selective?

Only selective in the sense that weak HOCl is not as problematic as strong hypochlorous acid (see comments here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1135139/). So, to the extent that aeration removes HOCl via superoxide creation, it could be helpful, in my opinion.

Spot on!
short answer, confirmation of your theory is all right here
Yes, Chlorine Dioxide ClO2 is being produced. Chlorite and Chlorine Dioxide are very similar. Chlorite is an ion and Chlorine Dioxide is that ion as a free radical (with an extra electron). As seen in the chart Karsten's answer gave, Chlorine Dioxide has an additional oxidative punch.
Both Chlorite and Chlorine Dioxide are well known and widely used throughout many industries. They are often preferred over other disinfectant compounds when health (such as food or water safety) is a concern. In your case, they are preferred over hypochlorite (bleach) or chlorine because they will not chlorinate like those compounds do, and only work via oxidation. As a bonus, molecular oxygen is left behind when ClO2 is fully reduced.
That's where you went a little off. No Chlorine gas is required to get Chlorine Dioxide from a chlorite solution. Putting Chlorine or a chlorinator like hypochlorite (HClO) into the bottle would defeat the gentle aim of the product: do no harm to fish. Correct me if I'm wrong, but didn't you already spend so much energy getting chlorine out of the tapwater when you filled the tank?
So, you noticed the oxidation of chlorite by chlorine to get chlorine dioxide but didn't find the more applicable method of simple acidification. Probably because you assumed the whole aquarium would have to lower in pH. No, everything is dynamic. You can have tiny pockets of acidity even in your alkaline tank. Pathogens often create acidity. They also join together and hide using biofilm. For both these reasons, chlorite is the right tool for the job.
Chlorite itself will oxidize, but not as strongly as the free radical Chlorine Dioxide.
What likely happens is the chlorite floats around until it encounters acute acidity at which point it can jump up an oxidation level to Chlorine Dioxide which will oxidize any pathogen around, bacteria, virus, or fungus. Pathogens generally require and make acidity. With enough ClO2 the product can even tackle protozoa and multi-cellular pathogens, even ones with glutathione defense. The ClO2 would have to deplete that defense first of course, but as Karsten indicated in his answer, that's not a problem. Chlorine Dioxide is particularly effective against biofilm.
here's a quote from wikipedia, "Chlorine dioxide is also superior to chlorine when operating above pH 7, in the presence of ammonia and amines, and for the control of biofilms in water..." Chlorine dioxide is considered a selective oxidant because it generally spares organic matter. This is why it is preferentially used in the water, food, and medical industries.
So what is the mechanism?
Eventually oxidation of amino acids, and likely cysteine in particular. In larger organisms ClO2 oxidizes GSH to GSSG and leaves it there, generally not oxidizing further. When ClO2 oxidizes, O2 (molecular oxygen) is left behind. O2 being key for most life, especially the kind considered non-pathogenic, like your fish, or the beneficial aerobic microbes in your tank.
Now you might think, "Well this sounds great, Chlorine Dioxide can kill anything!" and you'd be right. Well, technically. Which brings us to Karsten's otherwise excellent answer and its faint aroma of fear-monger or concern-troll.
Kill Everything!
Sodium Chlorite, the active ingredient (and the active ingredient of "MMS," which Karsten brought up), can indeed oxidize hemoglobin at high enough concentrations. Also, at those concentrations your fish would be long dead. In fact, if you and your fish drank Chlorite solution in increasing concentration/doses your fish would likely die long before your methemoglobin creation became life-threatening. What's the fish equivalent of 'Canary in a coal mine?' Why is that? Just like the canary, they're smaller than you. that's all.
But wait, this product is perfectly safe for the fish, isn't it? Yep.
let's talk concentration.
MaracynOxy contains 4-5% "chlorite solution" as per the SDS.
for comparison:
MMS (infamous "Master Mineral Solution" referenced above) is a 22.8% chlorite solution. (although in fairness it is dosed in drops, a drop being 0.025-0.05mL)
Aquamira water purifier tablets are 5-7% chlorite.
Closys mouthwash is 0.1% or (1000ppm) chlorite.
and here is an SDS for simply chlorite salt
at 5% concentration you have 0.12mg chlorite in 2.4mL dose
.43mL of MMS would be needed. that's 8-10 drops
or 120mL of Closys mouthwash
Karsten is keen to remind us how dangerous chlorite and chlorine dioxide is while supplying examples which contradict this. Chlorine Dioxide is so dangerous that it is preferentially used to disinfect meat in the food industry. He cites a study as evidence chlorite is so bad which concludes chlorite is less toxic than commonly used compounds in personal care products. He cites a very special enzyme unique to some bacteria (all aerobic, I assume) to deconstruct chlorite into harmless Chloride and molecular Oxygen. The implication being humans don't have that special dismutase. Quick question, when GSH (glutathione) reduces ClO2 what is left behind? any wild guesses?
Karsten neglected to remind us not to drink anhydrous ammonia, Hydrogen Peroxide, hand sanatizer, or isopropyl alcohol.
In the study Karsten cites concerning oxidative stress they demonstrate how chlorite depletes glutathione. The study also concludes chlorite has a lower toxicity to mammalian cells than benzalkonium chloride. Yes, chlorite is considered a less toxic oxidant than peroxides, sodium hypochlorite, or BZK. By the way, you are all absorbing BZK when you use many common eyedrops, eardrops, nasal sprays, hand sanitizers, antiseptic spray, wet-wipes, throat lozenges, mouthwash, disinfectant cleaners, and even spermicidal cream.
BZK is (relatively) safely used in all of these products applied on or in the body even though this study showed Chlorite to be less toxic.
BZK is genotoxic (it damages DNA), causes cellular damage, alteration in catalase activity, acetylcholinesterase activity, and lipid peroxidation 10.1016/j.etap.2016.04.016. But sure, BZK doesn't affect glutathione.
Chlorine dioxide is the preferred compound for treating cooking fats and oils.
Why? It does NOT cause lipid oxidation.
It is precisely the presence of glutathione and the mild way in which chlorite and chlorine dioxide oxide GSH which make it effective in killing smaller organisms while leaving bigger ones. A virus doesn't have glutathione. Chlorine dioxide will bust that cysteine or histidine on the virus structure and now the virus is in pieces. Similar things happen to fungus and bacteria and simple multi-celled organisms too. The bigger the organism, the more complex, and the more resources and tools it has to deal with oxidation. This is why the fungus dies but the fish don't. Now if you bought the 16 oz bottle and decided instead of reading the directions you would just dump the whole thing in you would probably get some floating fish.
that brings us to
a medical case of MMS
(chlorite solution) ingestion requiring a hospital visit (cited in Karsten's answer).
In the study they very scientifically tell us the child ingested 'a small amount.' Well, a 'small amount' of a substance dosed in drops isn't small at all. what are we talking, 10mL? 30mL? that's 2.8mg and 8.4mg of chlorite respectively and 66-200 times the usual adult starting dose of 3 drops. What substance that is generally safe at regular doses is ever taken at 66-200 times? Would that substance still be considered safe? A usual 'dose' of water is 8 oz, let's say 250mL. who here has taken 16.5L of water at one time? 50L? Anyone care to imagine what might happen if you did? If a child did so, would the parent take that child to the hospital? I would think so considering that's over 10% the LD50 for water. That child's life may very well be in danger. (LD50 of chlorite can be found in its SDS cited above. it's 284mg/kg in rats. rat to human dose conversion is generally 0.162x in mg/kg, so if the oral LD50 of chlorite for rats is 284mg/kg we get the HED (human equivalent dose) of 46mg/kg of chlorite which for a 60kg human would mean ingestion of 2.76g to achieve LD50. a 30kg 9-10yo child would be half that.)
The whole 16oz bottle of Maracyn Oxy would be 23.65mg of chlorite and if it didn't kill your fish, especially the smaller ones, it would very likely make them sick. By the way, the LC50 to minnows for Chlorine dioxide is 20ppm concentration over 96hrs.
With Chlorine Dioxide you see gentle vital use after gentle vital use, right up until mention of MMS and instantly the compound is transformed into the most caustic and destructive chemical known to man. Curious. And yet the very same outlets decrying Chlorine Dioxide as terribly toxic and dangerous are keen to promote NO, another free radical associated with wild health claims. Go figure!
Does Chlorine Dioxide have legitimate health claims?
I'm not making any here, but clearly many do make such claims, and it isn't all from kooks either. The compound is well researched but the health research is sparse, only beginning to pick up. It stands to reason organisms utilizing oxidative phosphorylation would benefit from readily accessible O2, hypoxia being a driver of disease. And that's in addition to any pathogen-killing (eg in blood) or biofilm dissolving (eg in bowels) action. As always, appropriate concentration and dose are vitally important.
Methylene Blue solves methemoglobin, if anyone is curious. Also happens to be another common active ingredient in aquarium treatment. And another unpatentable compound with seriously wild health claims (backed by research), which I wouldn't recommend you down entire bottles of or even mouthfuls.
and yes, UV would mess with the chlorite, UV is also redundant since the chlorite is doing the disinfection already.
boy this answer needs some more editing! meh.

to be fair, Karsten very likely would provide disclaimers and remind us not to drink those other compounds in the context of some other answer concerning them. It is important to know these things.


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Why 3 and not 6 in U = 3/2RT from the equation for the internal energy of an ideal gas?
Internal energy of an ideal monatomic gas is
$$U=\frac{3}{2}RT.\tag{1}$$
While I understand the derivation, I do not understand why we multiply by $3$ rather than by $6.$ According to Khan Academy video the force of gas molecules hitting one of the six faces of the wall is
$$pV=Nmv_x^2.\tag{2}$$
Why don't we multiply by $2$ after we multiply by $3$ to account for the pressure arising in the $y$ and $x$ directions as well to account for the force applied to all six faces of the theoretical box?

Probably the answer to Is Internal Energy = (3/2)nRT for a ideal monoatomic gas? could be more helpful since there is no boxes involved in derivation.

Pressure is force divided by area. If you count double the force (hitting two faces of the wall), surely you need to double the area as well?

Also, your expression is not right; it should read $pV = Nm\langle v\rangle ^2$. The angle brackets denote mean values (in general velocities are a distribution, e.g. Maxwell–Boltzmann), so there is no single velocity $v$ that you can use; but more importantly, $v$ is the magnitude of the 3D velocity vector ($v = |\mathbf{v}| = \sqrt{v_x^2 + v_y^2 + v_z^2}$), whereas $v_x$ is the $x$-component of the velocity. In general, you have that $\langle v^2 \rangle =  3\langle v_x^2 \rangle$, which is where the factor of 3 comes from.

Err, that first bit of my last comment is totally wrong, in fact. :-/ It should not have gotten three upvotes. Sorry. The correct formula is $pV = Nm\langle v_x^2 \rangle$, which is the same as the one in the question, except that you do need the angle brackets. The rest is correct.


text:
How to promote oxidation of copper(I) chloride to copper(II) chloride with oxygen in solution?
I recently discovered that copper(I) chloride in hydrochloric acid can react at about 80 °C with bubbled-in oxygen gas and oxidize into copper(II) chloride. I found almost no documentation on the web, but this is my suggested reaction:
$$\ce{4 CuCl + 4 HCl + O2 -> 2 H2O + 4 CuCl2}$$
However, the reaction is incredibly slow, taking at least several hours per mole. Does anyone know of any catalyst that may speed it up by a considerable amount? (by that I mean any amount). If not, is there a way to see what type of catalyst may work on this reaction?

This reaction is immediate if you replace $\ce{O2}$ by $\ce{H2O2}$

That is not an option, it has to be done with air or pure oxygen

Every useful relevant word omitted in the question formulation is paid later by several words posted by responders and the question poster during clarification. Provide sufficient relevant context/background in your question, otherwise receiving not applicable advices is your fault.


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Bonding in boron icosahedra
How do boron atoms make five bonds with other boron atoms even if the electron configuration of unbound boron atoms is [He]2s²2p¹, i.e. there is an insufficient number of outer electrons? Are the inner electrons ([He]) involved in binding?

$\ce{B12H12^2-}$, source: https://commons.wikimedia.org/wiki/File:Dodecaborate(12)-dianion-from-xtal-3D-bs-17.png

Even though you've completely rewritten the question, it's still cryptic. Boron-12 refers to an isotope $\ce{^{12}B},$ but I think you are asking about the $\ce{B12}$ icosahedra of either a standalone cluster, or a certain allotrope (which one?). Also, what "stable core" are you asking about? I suspect this could be a duplicate of https://chemistry.stackexchange.com/questions/32319, but I'm not sure I fully understand the question.

Be aware that laconic, not elaborated questions are usually closed on the StackExchange network.    How do I ask a good question?.
Describe the question well, search, think, refer and summarize.  Well elaborated questions have higher probability to  receive acceptable answers.
Lack of explicit, a priori effort may cause missing existing answers, question misinterpretation, needed clarification and  difficult estimation of the OP knowledge .

The short answer is that a bond can cover multiple linkages, not just a single pair of atoms; therefore an atom can be joined to more neighbors than the number of bonds it forms. When you learn about molecular orbitals you can see how this happens.

@andselisk I am talking of dodecahedron structure of boron-12 and not of isotopes .

@Get_Maths You've probably misread my comment. "Boron-12" is a notation for isotope that is equivalent to $\ce{^{12}B}.$ In the context of recent edit, you should refer to your composition as to dodecaborate, not boron-12 since the latter causes confusion.

Boron makes not five but six bonds in compounds such as dodecaborate or boron carbide. Boron carbide is a semiconductor, so it has aspects of a metal and a non-metal. For actual metals such a elemental sodium, you have to explain twelve nearest neighbors with only 1 outer electron, so there is no way to describe it with covalent bonds. For boron carbide, you can get away with invoking 3 center 2 electron bonds, but it is not clear if there is much insight to be gained.
Roald Hoffmann wrote a detailed account of bonding in boron carbide here. Even if all you get out of it is that boron makes beautiful intricate structures, and 2 electron bonds do not do justice to all compounds known, it is worthwhile taking a look.

I don't think any of the bonding models make use of the inner electrons.

But if boron's maximum covalency is 4 , then how can it make 6 bonds

Call it advanced inorganic chemistry. Either you need less than 2 electrons per bond, or a bond connects more than two atoms. The existence and structure of the boron icosahedra is well supported by experiment. If your bonding model cannot explain it, you need a more sophisticated bonding model.


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Will Lithium displace a sodium salt?
This question is based on a discrepancy I have observed in my limited knowledge about the reactivity and electrochemical series.
In the reactivity series it is mentioned that Na>Li in reactivity which is understandable considering the higher ionization energy of Li. This property is shown in various situations such as the more vigorous reaction of Na with water.
On the other hand, in the electrochemical series, Li is given as a stronger reducing agent than Na.
So, my question is whether Li will displace an aqueous solution of a sodium salt, for example, sodium sulphate to form lithium sulphate(typically the outcomes of these displacement reactions are explained on the basis of the reactivity series, not the electrochemical series-at least at my level). Also, will Li displace sodium oxide?
If so, is the higher value of Na in the reactivity series just an indication of the rate of the reaction as opposed to the outcome of the reaction?

Sodium reacts and releases energy faster, lithium releases more energy (in water environment). As the higher released hydration energy of lithium gets the upper hand over higher consumed ionization energy. Lithium will not displace sodium in water solutions, but hydrogen.

@Poutnik Please could you elaborate.

Reactivity serie is matter of kinetics, electrochemical serie is matter of thermodynamics.

On the other hand, I would be pleased to simply know how the redox potentials of alcaline metals have been practically measured. Because they cannot be determined in water, because in electrolysis, water is reduced at the cathode before $\ce{Na^+}$ or $\ce{Li^+}$ . Does anybody which solvant or which technique was used to get $\ce{Li^+}$ at $-3.04$V ?

@Poutnik Then why doesn't lithium displace sodium in an aqueous of sodium sulphate(as per your comment)? How is that linked to kinetics?

Think longer. This is linked to thermodynamics. What are standard redox potentials of Lithium, sodium and hydrogen?

@Poutnik Yes, wouldn't Lithium sulphate be thermodynamically more stable considering the high hydration energy released? So, shoudn't Li displace sodium to form the more thermodynamically stable product?

Hydrogen + lithium hydroxide are thermodynamically much more preferred to lithium sulphate + sodium.

@Poutnik Ok, understood. One final question-Does the greater reducing power of Li compared to Na influence the outcome of any reaction and is there any chemical application/observation to this? If not, can I safely ignore the higher reducing power of Li when dealing with inorganic reaction prediction and work solely on the reactivity series?

@Poutnik Also, if I replace the situation with Li(s) added to molten Na2SO4(l) (not aqueous), will Li now displace sodium?

Consider, in solution, all those alkali metals are not bound, but are ions.


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Selectivity in dehydration of isopropyl alcohol to diisopropyl ether
Can isopropyl alcohol be dehydrated by sulfuric acid to diisopropyl ether in a similar way as to how ethanol can? Is there a way to avoid or at least minimize the inevitable dehydration to propylene?

In addition to the necessity of a proper title please refrain from salutations ("hi", "thanks", "hope this helps" etc. are noise) and note that IUPAC discourages use of the name "isopropanol".

Who cares what IUPAC says?  Isopropanol is a universally used name, far more commonly used than whatever IUPAC says it should be @andselisk.  Link https://books.google.com/ngrams/graph?content=isopropanol%2C+propan-2-ol%2C+2-propanol&year_start=1800&year_end=2019&corpus=26&smoothing=3&direct_url=t1%3B%2Cisopropanol%3B%2Cc0%3B.t1%3B%2Cpropan%20-%202%20-%20ol%3B%2Cc0%3B.t1%3B%2C2%20-%20propanol%3B%2Cc0

@CurtF. "Isopropanol is a universally used name, far more commonly used than whatever IUPAC says it should be" is not true. I suggest you do a slightly better background check before posting snarky comments like this solely reflecting personal preferences. Also, please make sure your edits are complete.

@CurtF. I recall an old comment of yours demonstrating another disagreement with IUPAC recommendations regarding units for $m/z$. I'm not sure what your problem with IUPAC is, but please refrain from unsubstantiated criticism of recognized standards and recommendations that should at the very least least be brought to the attention of the questioner.

I will not refrain from criticizing IUPAC when their recommendations are pedantic, unhelpful, or wrong.  Also, my criticisms aren't unsubstantiated.

Also @andselisk, what was incomplete about my edits?

@CurtF. IUPAC (yes, sometimes pedantic to the extreme) at least provides a logical explanation as to why the name "isopropanol" is incorrect. Your argumentation is at the level of "a billion flies can't be wrong" and isn't even backed up by the usage statistics. This type of subjective critics appears quite unsubstantiated to me. I'm afraid I'm not going to continue this debate as I don't see any signs of mutual understanding so far. All I'm asking is to keep snarky comments to yourself or a personal blog. We have enough issues with terminology, formatting and notations to deal with.

Let us continue this discussion in chat.

Note that diisopropylether has reportedly much stronger tendency to form peroxide, similarly as diethylether does so. In both cases, before usage, it is recommended to treat the solvent with $\ce{FeSO4}$ solution to scavenge these peroxides. This  prevents accidental self-ignitions or in worst case explosions, especially if the solvent is treated thermally.

The acid catalyzed dehydration of secondary and tertiary alcohols to give corresponding ethers at room temperature and atmospheric pressure is unsuccessful as elimination competes over substitution and as a consequence, alkenes are easily formed.
However, in the presence of specific conditions such as low temperature and additional catalysts, isopropyl alcohol can get converted to diisopropyl ether.

Secondary alcohols are converted to symmetrical secondary alkyl ethers in high selectivity. The method employs acidic solid metallosilicate catalyst particles to accomplish the etherification in the presence of sulfuric acid by selective intermolecular dehydration of secondary alcohol to form di-secondary alkyl ethers. Preferably, the catalysts are solid shape selective aluminosilicate particles, especially zeolite such as ZSM-5, zeolite HY and zeolite Beta.

Another resource which talks about the preparation of diisopropyl ether is the following research https://www.researchgate.net/publication/251456024_The_mechanism_of_diisopropyl_ether_synthesis_from_a_feed_of_propylene_and_isopropanol_over_ion_exchange_resin

What I have inferred from these is that at standard conditions, a secondary alcohol like isopropyl alcohol will get dehydrated in the presence of $\ce{H2SO4}$ to propylene. But in the presence of an acid along with a metallosilicate catalyst such as zeolite beta or ZSM-5 and at highly specific conditions, we can minimize the inevitable dehydration to propylene.
Also, another method to synthesize diisopropyl ether from excess isopropyl alcohol is by simple dehydration and elimination at high temperatures to obtain propylene(step 1). The propylene is then separated and is subjected to indirect hydration. In the indirect-hydration process, propylene is further reacted with sulfuric acid to produce mono- and diisopropyl sulfates(step 2). The diisopropyl sulfates will then subsequently get hydrated to obtain diisopropyl ether(step 3). Step 2 and 3 occur at high sulfuric acid concentration (> 80% wt) and low temperature (e.g. 20–30 °C). It might appear that in this entire process, we are first dehydrating and and then rehydrating but the reaction conditions in step 1 are different from those in step 2 and 3 which results in the product being different from the compound we began with.
References

"Process for the production of symmetrical ethers from secondary alcohols", author = Brown, Stephen H. (Princeton, NJ), 1995 August

The mechanism of diisopropyl ether synthesis from a feed of propylene and isopropanol over ion exchange resin, Studies in Surface Science and Catalysis, F.P Heese, M.E Dry, K.P Moller


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Finding the ratio of acid and conjugate base from the absorbance equation

I am struggling on a question about acid dissociation constants.
Below is an image showing the problem but I will reiterate it here.
HX<->H+ + X-
Using the Beer-Law equation, derive that the ratio X- : HX is as follows:
A-A{HX}/A{X-}-A
Where A{HX} is the absorbance of the fully protonated solution
A{X-} is the absorbance of the fully deprotonated solution
My own attempts have been futile, for I keep getting:
epsilon{HX}(A-A{HX})/epsilon{X-}(A-A{X})
This equation would indicate that epsilon{HX}/epsilon{X-}=-1, which isn't possible
Any help would be appreciated

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Suitable formatting can be done according to formatting math/chem expressions/equations.

This makes no sense to me: the total absorbance, A, is the sum of the two absorbances for the weak acid and its conjugate base, and all of the terms are greater than zero at all pHs. So the ratio of concentrations must be greater than zero, but the right hand side of your last equation has a negative denominator, so the quotient is negative. Looks like a typo or something messed up.


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Comparing acidic strength of crotonic and isocrotonic acids

Compare acidic strength of crotonic acid (1) and isocrotonic acid (2):

On comparing $\mathrm{p}K_\mathrm{a}$ values, cis-form $(4.44)$ turns out to be more acidic than the trans-form $(4.69)$.
Most of the explanations I found on internet say that cis-form will be more acidic because in trans-form the $\ce{CH3}$ opposite to it, provides electrons by inductive effect directly in its direction (the dipole moment is almost directly in its direction) making the conjugate base unstable.
However, I am not convinced with this explanation as there's also a $\ce{C=C}$ bond between methyl group and $\ce{COOH}$ so same amount of electron density reaches $\ce{COOH}$ group via the double bond in both cases.
What's the flaw in my reasoning? How to compare the acidic strength correctly?

One possibility: in the cis anion a weak hydrogen bond forms between the carboxylate ion and the methyl group. A molecular orbital model where the oxygen lone pair overlaps a C-H antibonding orbitals could allow that.

0.25? That's hardly any difference at all.

@Mithoron I have asked this question to seek correct reason for a fact whose reasons that I found online seem incorrect to me

For a related discussion on the acidity of o-toluic acid look here.

Firstly, I've found many different pKa values for isocrotonic acid. For example, this website claims the pKa of isocrotonic acid to be $4.9$, so I'm not really sure which is more acidic.
If you look at the conjugate base of isocrotonic acid, due to the methyl group on the same side the conjugate base of isocrotonic acid could be less solvated compared to the conjugate base of crotonic acid, which has no such steric hindrance. This would mean that crotonic acid is more acidic.
I'm not really sure whether this is correct or not since I can't really predict how much of a role the methyl group will have in reducing the solvation of the conjugate base of isocrotonic acid, but this is the only factor which comes to my mind.
(I know this is more of a comment, but I have posted an answer so that more experienced users can talk about the correctness of this possibility and vote accordingly)

That makes sense logically, but the problem would just be that it's speculative. In my opinion, a 0.25 pKa difference can't be explained convincingly using the crude models of organic chemistry.

If one draws in all the hydrogens and rotates the position of the OH group in the carboxylic acid group we can see some steric hindrance between the methyl hydrogen and the acidic carboxyl hydrogen with cis isocrotonic acid.
This is one case where building a "full model" with the black, red, and white little balls and plastic connectors may be much more explanatory than
trying to understand the "skeleton" organic chemistry notations.


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Where do electrons jump to when they jump to next shell in emission spectrum? Why are there no emission lines for jumps btwn orbitals, same shell?
In the emission spectrum, do electrons that jump up to the next shell go to any orbital in that shell? Or if the electron is originally in say the p orbital, does it jump to the next p orbital in the next shell??
Also wouldn’t there be more colors on the emission spectrum if energy is emitted when electrons fall down from an excited orbital down to lower orbital in the same shell? Why does it seem like there are only colors for change in shell and not orbital within a shell?

See also wikipedia: Selection rule.

Yes there are emission lines for jumps between the orbitals for multi electron lines as seen in the form of doublets( two closely spaced lines) and triplets( three closely spaced lines).
Infact this is one of the reason why Bohr's model failed. Doublets and triplets appear in the spectra of some atoms as very close pairs of lines. Bohr's model cannot say why some energy levels should be very close together. These closely spaced lines corresponds to transition from one orbital to other.


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Is there a filtration method that can be used to separate solids and liquids without filter paper?
I am looking for a filter that can can be reused indefinitely like a strainer with very small gaps. Does such an equipment exist?

Glass filters are a thing.

Which objection to indefinitely as there is always the trouble  of clogging (Remember inkjet printers.) of small pores. Reverse washing helps just partially, can prolong the filter life, but it has its limits.

Be aware that laconic, not elaborated questions are usually closed on the StackExchange network.    How do I ask a good question?.
Describe the question well, search, think, refer and summarize.  Well elaborated questions have higher probability to  receive acceptable answers.

This is what you are looking for  https://www.fishersci.co.uk/shop/products/glass-funnel-filter-sintered-glass-disc/11922148

The Mr. Coffee Larger Gold Tone Reusable Coffee Filter is the answer.

Part of the trouble with the use of the word "filtration" is that it implies a specific method of separating solids from liquids. If you phrased the question without using the word "filtration" you might get more answers, for example some processes might use centrifugal processes (like Dyson vacuum cleaners) which can be used as both batch processes (a standard lab centrifuge) or continuously (in some industrial cyclones or, indeed, vacuum cleaners).

You neither state the size of the particles to retain/remove, nor the chemistry of the suspension you deal with; in this regard, your question should be improved.  E.g., is the solution acidic/neutral/basic, absence/presence of strong oxydants, temperature and intended processing parameters equally are worth an addition to yield a more specific answer.
The possibly most strainer-like approach is the use of metal or plastic as a sieve which may be performed in batches, or continuously.  The filter bed may be fix, or moving  as for e.g., centrifugal sieves / essoreuses:

(image edited; image credit to https://www.palamaticprocess.com/bulk-handling-equipment/centrifugal-sieve).
The material of the sieve may be e.g., metal (like a tea infuser, the oil filter in a car), plastic (like your essoreuse in the kitchen), or gravel (like the sand filters in a water purification plant).  This may be complemented by filtration across a fabric like cotton (removal of crud in artisanal cheese making), or polymers (polypropylene, polyamide) as seen for belt and pan filters acting by gravity or vacuum:

(image credit to http://www.solidliquid-separation.com/VacuumFilters/vacuum.htm)

I'm think of separating pasta and hot water with a strainer. Those strainers can be cleaned in the dishwasher, but I wouldn't say they last indefinitely...


text:
How is PEMFC not a violation of the Laws of thermodynamics
I was trying to understand how the proton-exchange membrane fuel cell works.
Online I read that in such a cell hydrogen is oxidized at an anode catalyst, mostly platinum, and a detached electron ends up going through the circuit.
My doubt is where is the energy coming from?
That the catalyst can split hydrogen molecules for ever, isn't this a violation of the Laws of Thermodynamics? If the platinum is oxidizing the hydrogen, it must get depleted some time later?
ps: im in high school

You should look for a reaction that depletes the platinum. Is there one?

If you want to understand the thermodynamics of a redox reaction, you have to look at both half-reactions. You are discussing the half-reaction that provides the electrons (and the protons):
$$\ce{H2 -> 2H+ + 2 e-}$$
There has to be a second half-reaction that consumes the electrons, e.g.
$$\ce{O2 + 4H+ + 4e- -> 2 H2O}$$
In combination, this is a redox reaction where the equilibrium lies on the side of the products.
$$\ce{O2 + 2H2 -> 2 H2O}$$
Those types of reactions can be used to generate electricity.

Like if this catalyst can split the hydrogen molecules for ever , then isn't this a violation of the Laws of Thermodynamics? If the Platinum is oxidizing the hydrogen , it must get depleted some time later?

The platinum is a catalyst. It affects the speed of the reaction (the kinetics), but not on which side the equilibrium lies (thermodynamics). The other half-reaction is oxidizing the hydrogen, and platinum is just a catalyst.


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Do fats in edible oils and ghee undergo oxidation or rancidation when cooked in pressure cooker along with rice?
In a lot of dishes, it's quite common to cook rice along with fats like edible oil or ghee(clarified butter), in a pressure cooker.
Now the pressure cooker can reach very high temperatures, to quickly cook the rice. But can this degrade and oxidize the oil and ghee?

Pressure cookers don't reach "very high" temperatures. A typical home pressure cooker reaches about 100 kPa above ambient atmospheric pressure. At 200 kPa, the boiling point of water is about 120 °C. Most effects happen at higher temperatures, like the Maillard reaction (~150 °C), oil smoke points (~200 °C).

@Nayuki thank you, but does the high pressure of 200kpa influence fat oxidation and rancidity?

@Nayuki so while cooking oil and ghee in pressure cooker can we assume that the structure is not so changed and its health impact is as before?

not sure, but the 2 times I tried rice cooked in pressure cooker with ghee given me very hard time (feeling of indigestion/fullness/discomfort/belches all the time and dullness for almost 48 hours). not sure what might be the reason or it's just a coincidence, I won't try again :)

By the semiempirical Van't Hoff rule, speed of chemical reactions increases typically 2-4 times by temperature increase by 10 deg C. There is no threshold temperature limit below which reactions do not happen. But there are conditional threshold limits below which reaction rate can be neglected. That is the case for pressure cooking.


text:
What's the difference between internal energy and average kinetic energy?
I was sent a problem which goes roughly like this:

There are 6 moles of diatomic nitrogen in a container at temperature T. Some heat is given to the gas such that 2 moles disociate into atomic nitrogen keeping the temperature constant. Calculate the heat given to the gas.

And the solution says that the change in internal energy would be equal to the heat provided and the change in internal energy can be calculated by comparing the average kinetic energies of the gases which are different since one is diatomic and one is monoatomic.
Is this explanation/solution correct? If yes/no then can you please explain why?

Internal energy will include a contribution from any interactions between the particles in the sample. If the gases are assumed ideal then you ignore these interactions and the internal energy is assumed equal to the kinetic energy.

Yes, it is correct for the sake of problem.
You can say that the total heat ( which causes change in U, internal energy) is solely responsible for the change in average kinetic energy, by assuming that there is no change in other type of potential energies. Hence, ∆KE becomes equal to ∆U as KE is also a constituent of U.

Internal energy : It is the total energy contained within the system .
i.e., It is the sum of all types of energies possessed by a system .

Kinetic energy : It is the energy possessed by a body by virtue of its motion.

Is this explanation is correct ?

Yes of course , but on one condition . We should treat the gas as an ideal gas. If it is an ideal gas then interaction potential energy in the system will be zero. Therefore , the change in internal energy is equal to the change in Kinetic energy of the system.  The work done on the system will be zero as the volume of container remains unchanged. So from the first law of thermodynamics the change in internal energy is equal to the heat supplied to the system.

I wonder if there is ambiguity sometimes in what counts as "kinetic" energy.  Sometimes I think people use it to include rotational and vibrational energies, and sometimes I think they use it just to mean translational energy.

Yes , but I here included vibration and rotation too


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Safe disposal of pyrolysis side products in production of wood gas
I am in the process of building a pyrolysis chamber producing wood gas for use in a generator.
The process involves heating a batch of biomass (wood) in absence of oxygen (air) in a closed vessel, and separating carbon monoxide, hydrogen, and other products gaseous in NTP conditions from heavier molecules in a heat exchanger.
The output will be further filtered for particulates, but that is not important for this question:
The heat exchanger stage produces two end products: The set of volatile flammable gases, and a liquid phase containing indeterminate combination of complex hydrocarbons and a large fraction of water.
This liquid is toxic, and harmful to the environment in its initial form. What would be the easiest way to dispose of this liquid waste?
I am building this system in a remote location, so I don't have access to municipal waste water system, and I cannot transport large amounts of waste to be processed elsewhere. I can use heat to decompose the waste.
I suspect the best (and only) way is to burn the toxic hydrocarbons in a furnace. What makes this hard is the water suspension.
If injected into a hot furnace as is, I suspect the water would flash boil, cooling its surroundings a lot, and produce a gas cloud of vapor where the nasty hydrocarbons are mostly left untouched. This could probably be mitigated through careful engineering of the furnace.
If I try to boil the water off first, I will certainly also evaporate many volatile hydrocarbons, producing equally toxic gas fumes.

Can you use a parallel process to make some sort of charcoal to which the hydrocarbon would adsorb and the burn that?

Yes. In fact as the biomass is I intend to use is wood, bark, and leaves, I am left with biochar in the primary process. Hovever, for this method to work, I would need to trust the charcoal scrubs the liquid so completely, it is essentially clean enough to be released to nature. How could I verify that if I tried?

Test the process in a lab? Use gas or liquid chromatography to check for the contamination before and after charcoal treatment

It might help to provide more context regarding constraints such as budget, location, volume of production, applicable ordinances, etc    The following gives ideas: DOI:10.3390/en13102594

What you are describing is an experiment similar to one which I did when I was about 12 years old. I took an old sweet tin and packed it with bits of wood (I think pine) and I had made a hole (about 5 mm) in the lid. I put the lid on as tightly as I could and then I heated it up by putting it on the red hot coals formed towards the end stage of a bonfire of garden waste. What happened was that the wood was pyrolyised and converted into a mixture of steam, hydrocarbons, some hydrogen, tars and charcoal. The gases came out of the hole and I ignited them with a flame and watched the flame burning.
What we were both doing was making something similar to coal gas but by heating wood instead.
Now there is your problem, the heat exchanger can be used to recover heat from the hot gases from the degradation of the wood, in the heat exchanger the water and the tars will condense away from the gases. The thing to be aware is that the tars from the degradation of coal tend to contain a lot of nasty carcinogens. Coal tar is well known to contain things like anilines, polycyclic aromatic hydrocarbons, benzene, thiophenes, phenols and other things.
Tars and oils from wood will be a bit different.
If you read Characterization of biomass-based flash pyrolysis oils by Kai Sipilä, Eeva Kuoppala, Leena Fagernäs and Anja Oasmaa in Biomass and Bioenergy, Volume 14, Issue 2, 23 March 1998, Pages 13-113
Then you will see how the degradation of pine wood forms formic and acetic acids along with smaller amounts of other oils. The water insoluble oil from pine was reported to be 69.3 % C, 6.4 % H, 0.2 % N and 24.1 % O (all are weight / weight %). The gas chromatography suggests that the oil was complex and packed with lots of oxygenated compounds including phenols. Some of these phenols are toxic.
I do not want to pour cold water on your ideas for renewable energy, but I worry that you might start to make a toxic mess. If you start trying to process the liquid which condenses from the heating of wood then you could expose yourself to a range of toxic substances. From reading the paper I think that most of the water soluble parts of the oil are things which would degrade with ease in soil. But the water insoluble part of the oil will be more toxic and I suspect that burning it on a fire at your site would not be a good method of dealing with it.
I think that the best way to make renewable energy from wood waste would be to do the processing on the small industrial scale where the plant can be professionally designed and a process devised which will take care of the tar. I think that the best small scale production of biofuel for a internal combustion engine would be biodiesel (FAME = Fatty Acid Methyl Esters) from waste cooking oil. Sadly that it is a bit harder than it is from unused cooking oil. But my thoughts on renewable / bio fuels are drifting a bit off topic from the question.
Sorry if my answer is a bit of a "mind dump".

Hmm. I should probably ask the pros in question. Oasmaa and some others mentioned in the paper you referred are still working at research center VTT that happens to be like 800m from my workplace in Espoo Finland. Small world. :D


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How does molecular structure contribute in the property of fluorescence?
Fluorescence is the property which is exhibited when electrons emit wavelength of light lower than the one they absorbed so does that mean we can make every molecule to become fluorescent? I wanted to know how does the molecular structure contribute in giving rise to this property and how it's different from substances that are non fluorescent I searched but couldn't find anything related to molecular structure.

Look up the structures of phenolphthalein, rhodamine B, anthracene, rubrene, and fluorescein. The first one, which is a common pH indicator, is non-fluorescent. All the others are. See any aromatic rings in those? Any planar portions with rings? Just take a look and see if anything suggests itself!

You may be interested by the book Molecular Fluorescence by Bernard Valeur and Mario Berberan-Santos (Wiley library), especially chapter 4 : "Structural Effects on Fluorescence Emission" which should answer your question perfectly. DOI : 10.1002/9783527650002.ch4.

Keep in mind a few things that must happen for an absorption process to result in fluorescence:
(1) the initial transition is to an excited electronic state that observes certain rules regarding the structure of the excited state (Franck-Condon principle). That requires that the light used to excite the molecule have a sufficient frequency to result in electronic excited states.
(2) The excited electronic state must not lead to dissociation, otherwise you end up with photodissociation, not fluorescence.
(3) after excitation the molecule must relax to a state lower in energy with the same electron spin (unlike in phosphorescence, where a conversion occurs), so a transition occurs to a different vibrational excited state.
(4) the molecule must now relax from the low lying vibrational state in the excited electronic manifold to the ground state. Note that this may not happen efficiently, for reasons that have to do with transition rules. The emission process competes with non-radiative relaxation processes. The extent to which the emission represents the pathway to the ground state is the quantum yield of the fluorescence process.
So in short, provided the molecule doesn't fall apart or react when you excite it, and doesn't find other ways to dissipate energy more efficiently, then you should observe fluorescence, although this may occur outside of the visible spectrum of course.

It is not an answer to the question. The question is : why are there no non-radiative relaxation processes in  fluorescent molecules ? Or : why are most molecules able to find non-radiative processes to dissipate energy, whereas fluorescent molecules do not find these relaxation modes ? Fluorescent molecules have something special. What ?

@Maurice I agree that my answer is not elaborate. I do not mention for instance that low energy $\pi\rightarrow\pi*$ transitions are important in many fluorescing molecules, as in many aromatics. Fluorescent molecules can however dissipate energy in non-radiative ways.

Thankyou i did not know about photodissociation so i suppose this is the factor that makes other molecules non fluorescent and it arises due to their molecular arrangement, is it right?

@25SimranTiwari You may want to look into the phenomenon of photobleaching, which can compete with fluorescence, and results in bond rupture or reactions. In order to make a molecule fluoresce you need to bring it into an electronic excited state. For many molecules that requires so much energy that it results in changes to structure or bonding in the molecule, rather than fluorescence.

The fluorescence yield is $\varphi =k_k/(k_f+k_n)$ where $k_f$ is the rate constant for fluorescence and $k_n$ that for non-radiative processes. If $k_n \gg k_f$ then the fluorescence yield dis very low and we might consider the molecule to be non-fluorescent.
The question is then what makes $k_n$ large and this is answered in large part here What makes a species "fluorescence quencher"?
Edit:
In addition, symmetry of the excited state vs. ground state is important as is internal molecular motion.
Symmetry restriction is most obvious in the carotenes for when the lowest excited singlet state has the wrong symmetry for absorption/emission to the ground state no fluorescence is observed.
Instead absorption occurs to the second excited singlet state which then non-radiatively crosses to the first singlet (which is close by in energy) and as this has a forbidden transition to the ground state beta carotene, for example, if effectively non-fluorescent. The lowest singlet is then rapidly deactivated non-radiatively to the ground state by twisting of the long single /double bonded chain.
In the triphenylmethanes,  such as malachite green, fluorescence is  allowed by symmetry, but as the phenyl groups rotate they open up  a non-radiative channel to the ground state and this quenches the fluorescence. Consequently in viscous solvents the fluorescence yield is high as molecular motion is slow, but the yield is low in mobile solvents when phenyl twisting is rapid.


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Density gradient vs. entropy of mixing
I was wondering how real gases would behave when they are released into a closed container with fixed volume.
For example, suppose we use chlorine and nitrogen gas. Obviously, chlorine has a higher density than nitrogen gas. Now suppose both are released in similar quantities into a container without air, we have a closed system.
From what I remember for ideal gases, they should mix because the entropy of mixing increases overall entropy. However, since the real gases have different densities and gravity is working on them, the nitrogen gas should be on top of the chlorine gas because of buoyancy.
For reference, mixing of liquids is easy to predict, for example water and ethanol mix because intermolecular interactions dominate and buoyancy does not. But what is up with gases?
Which effect prevails here? Or am I missing something? Thanks in advance.

Because of entropy of mixing, each gas fully distributes itself through the container.  Assuming ideality, each gas's distribution is independent of the presence of the other gas (neither gas "sees" the other).  This distribution, however, is subject to a Boltzmann gravity gradient: $\rho(h) = \rho(0) e^{\frac{-m g h}{RT}}$.  And since their masses are different, their distributions will be different: the density of the heavier gas will fall off more rapidly with elevation.   You can actually calculate what will happen to the composition of the mixture as a function of height.

Note that this assumes no turbulent mixing. You should do this calculation yourself.  You will see the change is composition is extremly small unless the column of gas is very tall.

@theorist Good comment! Note that T=T(h), for air at equilibrium it is dT/dh = -0.0098 K/m, Air with constant initial temperature will reach such T gradient at the equilibrium ( much faster than forming composition gradient).

@Poutnik  Thanks ;).  Note that the OP wasn't asking about open air, they were asking about air in a container, which presumably is building-sized or smaller.  Thus I don't think we don't need to concern ourselves with atmospheric temperature gradients.  The idea here is that if the OP does the calculation for any reasonably-sized container, they will see (as you know) that the gravitational gradient has only a miniscule effect.

@theorist It is not related specifically to atmosphere, which is just another, giant and open container. The point is, if you apply the Boltzmann formula for high enough container to have some noticable composition change, you cannot ignore temperature gradient either, but T(h) must be integrated in the computation. BUT I do agree that for the rough first picture, it is more than enough.

@Poutnik  Are you referrng to Tolman temperature gradients in a gravitational field, which are reported here to be a consequence of General Relativity?  Information on this phenomenon is sparse, so I don't know whether it is generally accepted https://static1.squarespace.com/static/5852e579be659442a01f27b8/t/5af9c04faa4a993b554df0e9/1526317136980/Santiago_Visser_2018.pdf

@theorist No, I mean the standard adiabatic mixing. Random fluctuations warm up lower layers and cool down upper layers until about 0.98 K/100 m is established. If it was mixed turbulently, it would be established quickly.

@Poutnik It sounds like you have in mind a different type of system from what I'm considering. Here's what I had in mind, which I think corresponds to what the OP was asking:  Suppose you have a large box of gas sitting in lab and maintained at thermodynamic equilibrium. The box contains two non-interacting gases, one light and one heavy. You want to know how the composition of the gas will change as you move from the bottom of the box (h=0 m) to the top (say, h = 3 m).  Outside of a hypothetical GR-based Tolman effect, how would gravity create a temp gradient in a sys at thermo equilibrium?

Let us continue this discussion in chat.

There would be (non-measurable on small scale) molar fraction gradient (Density gradient is always present due hydrostatic compression).
At this state, the rate of chlorine/nitrogen gravitational settling down/up is balanced by the diffusive mixing driven by molar fraction gradient.