text:
Does the Oxy or Alkoxy Claisen Rearrangement Exist?
@Waylander's cogent Comment to the query of @Random Guy inspired me to post a problem in synthesis to test a question I have pondered for some time. The activation energy (AE) for the Cope rearrangement of 1 is higher than that for the rearrangement of oxy-Cope precursor 2, whose AE is higher than that of the alkoxy-Cope precursor 3. The AE for the Claisen rearrangement of 4 is lower than that for the Cope rearrangement of 1. Can the analogs 5 (R = alkyl, silyl) and 6 be prepared to test whether or not a Claisen rearrangement occurs? The observant reader will recognize 6 as the 1,2-addition product of the enolate of acetaldehyde (or similar enolate) to methyl vinyl ketone (MVK).  Does a Michael addition occur by cleavage of 6 with subsequent 1,4-addition or does a Claisen rearrangement intercede? The stereochemistry of the rearrangement of 7 may prove insightful. Would the rearrangement of 9, enolate stereochemistry notwithstanding, be the same or different from that of a Michael addition?
Design a synthesis of 5 or a precursor to 6 taking any liberties with substitution patterns. If you are truly ambitious, go for 7 or a precusor to 9. Feel free to utilize (Z)-and/or (E)-double bonds in 7 and 9.
I am looking for an enterprising young chemist to solve this problem.

Having had no responses to this post, I thought I would offer a scheme in an effort to answer the question about the existence of the oxy Claisen rearrangement.   α-Diketone 1[1] was chosen as a starting material owing to the equivalency of the two carbonyls and to insure that the all substituents in aldehyde 7 are equatorial. Selective monoketalization of α-diketone 1 with β-bromoethanol affords cyclohexanone 2. Over ketalization is unlikely owing to steric considerations. Wittig reactions of the type 2 $\rightarrow$ 3 have been conducted successfully.[2]
The elimination of HBr  from 3-(2-bromoethoxy)prop-1-ene with powdered KOH to form 3-(vinyloxy)prop-1-ene (allyl vinyl ether) was conducted by Hurd and Pollack.[3]  Ideally, allyl vinyl ether 4 would be a more suitable precursor for an alkoxy Claisen rearrangement than divinyl ether 5, given the competing resonance stabilization introduced into the structure by the additional vinyl ether group. Nonetheless, vinyl ethers 4 and 5 may lead to rearrangement products 8 and 6, respectively. Acidic hydrolysis of either of these aldehydes under equilibrating conditions would afford keto aldehyde 7. While the attainment of keto aldehyde 7 would be an achievement, its realization does not determine whether the product is obtained by a concerted rearrangement, or by dissociation into an acetaldehyde enolate/oxyallylcarbocation pair of ions followed by recombination. Barring an intimate ion pair, a crossover experiment is required.

A crossover experiment requires isotopic labeling in both residues involved in the transformation. Deuterium may be incorporated judiciously in both moieties through the use of 2-bromoethan-1,1-d2-1-ol[4] and (methylene-d2)triphenyl-λ5-phosphane leading to substrate 10. If rearrangement is concerted, then keto aldehyde 14 will contain three non-exchangeable deuteria.

In the event that a dissociative mechanism applies, then a near statistical mixture of keto aldehydes 16-d2 and 17-d1 is expected when an equal mixture of 3-d0 and 10-d6 undergo the rearrangement process. Both 1H NMR and mass spectrometry would be critical in an analysis of labeling patterns. The presence of the methyl groups in the deuterated products provides an internal standard for NMR integration. These keto aldehydes will likely lend themselves to McLafferty rearrangements.

R. Lenz, S. V. Ley, D. R. Owen, S. L. Warriner, Tetrahedron: Asymmetry, 1998, 8, 2471.
M. Pellet, F. Huet, J. M. Conia, Tetrahedron Lett., 1977, 39, 1979.
C. D. Hurd, M. A Pollack, J. Am. Chem. Soc., 1938, 60, 1905.
I. Bird, P. B. Farmer, J. Labelled Compounds and Radiopharmaceuticals, 1989, 27, 199.


text:
Storage solution for oxygen sensitive liquid chemicals?
I'm needing to transfer oxygen sensitive liquid chemicals from a 5 litre bottle to many 100ml storage solutions. Since I'm transferring a large quantity I plan on operating within an inert atmosphere glove box (atmosphere being nitrogen), but I need to make sure that what the storage solution I am transferring to can be effectively sealed so no oxgyen seeps through over time once in storage.
Like many packaged goods I want to make sure that nitrogen is sealed within the storage solution (so vacuum sealing wouldn't be appropriate). The only thing I can think of at the moment is storing in 100ml bottles, but I'm not sure how to completely seal bottle caps, such that is done for commerical products like milk.
Hopefully someone here can point me in the right direction.

You state your aliquots are of $\pu{100 mL}$ each.
If eventually all of this volume will be used at once, like for the preparation of a standard solution, then transfer into an ampoule may be an option.  Degass/evacuate and purge the then still empty container attached to a Schlenk line (a recently discovered tutorial page), then cannulate the solution from your storage container of $\pu{5 L}$ into the smaller ones.  Then flame seal these small containers.
If you aim to draw multiple times small portions from these containers of $\pu{100 mL}$, then sealing threaded flasks with a septum is an option:

(edited photo, original from SigmaAldrich's catalogue)
At least once pierced, these do not close as good as their bottles seen on BuLi and other reagent solution storage flasks with a Sure/Seal(TM) cap. But this is a general problem all septa face (especially over time, exposed to corrosive reagents).  Crimp caps (example) are more frequently seen for smaller vials/microwave tubes.

A lot of great ideas here. One that I've had in mind prior to your response was to transfer the liquid from the 5 litre bottle to 100ml plastic bottles within an inert atmosphere glove box, but then use an electronic induction sealer within the glove box to seal a foil liner over the 100ml bottle after directly flushing with nitrogen, then just leave a standard cap over that. Like that is typically done for sealed commerical liquid medicines. The intention is to essentionally repackage the solution from a 5 litre bottle to many 100ml bottles without any chance of oxidation.

What do you intend to strore (a solvent compatibility chart like this may be one early indication)? I have some preference for glass bottles for that their resistance to chemicals is broader than plastics/easier cleaning, that they (gradually) may be oven dried, their lesser permeability for water/air across their walls, withstand pressure, and that may be reused multiple times, and then recycled. But it is possible to put a lid on the bottle, and this in a bag eventually vacuum sealed.

(Continuation) If you want to have some protection in the bag/between the liquid and the lid of the bottle, argon (though more expensive per litre than nitrogen) is better.  Because it denser than air, argon actually is like blanket on top of your solution.  The light nitrogen gas just goes up into the air, literally (sometimes a potential problem in the org chem lab when we set up a reaction to work in a water dry/oxygen less environment).

source: Stack Exchange

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

sort: votes


text:
Number of enol forms of acetylacetone
Here is what I tried:

These are the two enolic forms that I could make. So according to me, the total number of distinct enol forms of acetylacetone is $2$. But the answer is 3, what am I missing?

Write the formula of acetylacetone, this time including all hydrogen atoms bound to the molecule.  Then, write down reaction equations for the equilibria between acetylacetone and its tautomeric enols; again with all hydrogen atoms bound to the molecule.

In practice, you're not missing anything. Dienols aren't really viable in practice, for this compound. Even your unconjugated tautomer is hardly important. Then again, if you push into dienols, then there is even fourth one, with two double unconjugated bonds. Either ways this answer is wrong.

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


text:
Why is maximum number of covalent bonds 3?
In my textbook it is mentioned that maximum 3 covalent bonds can be formed within 2 atoms, which makes sense as 1 p orbital from each can be used for sigma bond and the remaining 2 can form pi bonds. But d subshell contains 5 d-orbitals, so why is it not possible to form 5 bonds?
I tried searching for it but couldn't find it anywhere

W2 and Mo2 form sextuple (6) bonds.  https://en.wikipedia.org/wiki/Sextuple_bond

But anything more than 3 is rare.

Perhaps more importantly, anything more than 3 is impossible for carbon.

https://chemistry.stackexchange.com/questions/594/bonding-in-diatomic-c2-a-carbon-carbon-quadruple-bond https://chemistry.stackexchange.com/questions/27532/what-would-follow-in-the-series-sigma-pi-and-delta-bonds

Unfortunately this question hinges on the definition of bond. And the whole concept of a bond is still very much debated and not clear at all. There's no point in going down this rabbit hole before some decent understanding of quantum mechanics. The carbon dimer is actually a nice point in case for this ongoing debate; I think we have a question for that.


text:
When do the Wolff-Kishner Reduction and Clemmensen Reduction not take place for carbonyl compounds?
I came across some examples of organic compounds with acidic groups that didn't undergo the Clemmensen reduction. So, I was wondering which types of compounds the two reagents cannot reduce. Also, why?

Clemmensen relies on the carbonyl group protonating. If it is not the site of first protonation then it is not going to reduce.  Similar for W-K; if the hydrazone cannot be deprotonated because another site is more acidic then the reaction will not proceed.

related https://chemistry.stackexchange.com/questions/32174/mozingo-reduction-mechanism

@Waylander Okay, so if there was a carboxylic group, then the reduction wouldn't take place, right?

Pretty much. Once the carboxyl group is deprotonated you are trying to form a dianion for W-K. For Clemmensen the carboxyl group may well be site of first protonation but it may be easier for the carbonyl to be the site


text:
What burns my nose?
I have a buddy that, lately, has amused himself by blasting a lit JetBoil (camping stove with isobutane/propane mix) with a can of Dust-Off compressed air, to create a giant sheet of flame.
The fumes that result from this fun (indoors, I might add) smell quite terrible, hang around for a while, and burn my nose and eyes like ammonia. What gas might this be? I suppose it could be related the bittering agent. I was hoping to list the can's chemicals here for you all, but alas, none were written on the can.
Oh, and how many months of life are shaved off with every blast?

Some "dust off" products contain fluorinated hydrocarbons not just air. God knows what horrors they produce interacting with flames.

@matt_black Interesting. It makes sense, as pressurized air or nitrogen would have too low capacity. It is known that thermal desintegration of PRFE create harmful gases.

Aside of initial hydrocarbons that are not particularly irritant, there would be a wild mix of partially oxidized staff, including but not limited to radicals, aldehydes, ketones, alkohols....
Bittering agent is not volatile, so no sense to add it. Also, liquid propane/isobutane with boiling points below water freezing point are not supposed to be drunk.
As @matt_black noted, dust off canisters may contain fluorocarbons instead of pressurized gas ( the high effective volume capacity ). Product of thermal decomposition can form harmful gases, including hydrogen fluoride.
It is possible there is formed acrylaldehyde ( aka acrolein ) $\ce{CH2=CH-CHO}$, formed from propane, which has significant tear-gas effect. Other aldehydes may behave similarly.
There is reportedly added $\ce{CH3CH2SH}$ to LPG as safety odorant. Not sure if applies to camping gas cartridges. Various  organosulphur compounds with ugly smell can be created by incomplete combustion. A human nose is very sensitive to them.
Typical example is thioacetone, which is fortunately probably not formed this way:

Thioacetone has an intensely foul odor. Like many low molecular weight organosulfur compounds, the smell is potent and can be detected even when highly diluted. In 1889, an attempt to distill the chemical in the German city of Freiburg was followed by cases of vomiting, nausea and unconsciousness in an area with a radius of 0.75 kilometres (0.47 mi) around the laboratory due to the smell. British chemists at the Whitehall Soap Works in Leeds noted in an 1890 report that dilution seemed to make the smell worse and described the smell as "fearful". Thioacetone is considered a dangerous chemical due to its extremely foul odor and ability to render people unconscious, induce vomiting, and be detected over long distances.

You do not really expect chemists would tell you how the life gets shortened by this event, don't you?

No, the life comment was tongue-in-cheek. Your suggestion of aldehydes and their "significant tear-gas effect" makes sense, though, so thank you.


text:
Why use "molecular equation" to refer to a chemical equation describing a precipitation reaction?
When we describe a precipitation reaction using a chemical equation, we have the choice of either writing the net ionic equation (i.e. leaving out spectator ions) or writing the respective ionic compounds:
$$
\begin{align}
&\text{molecular(?)} &\quad \ce{NaCl(aq) + AgNO3(aq) &<=> AgCl(s) + NaNO3(aq)}\tag{1}\\
&\text{net ionic} &\quad \ce{Cl-(aq) + Ag+(aq) &<=> AgCl(s)}\tag{2}
\end{align}
$$
The net ionic equation does contain ions, plus an ionic compound, so I understand the name. However, what is the reason to call the other equation "molecular" -  there are no molecules in this reaction (other than water).
Nevertheless, this is the term I find in textbook (e.g. OpenStax). Is there a better name ("compound equation" perhaps, or "implicit ions")? Is there a context where molecular equation makes more sense, and this is just a special case where it does not?

I think the term molecular equation would be unfair for this precipitation reaction. Why don't you would use a "chemical equation" for the first reaction.

@M.Farooq I am asking about the term used in textbooks. "Chemical equation" would refer to all three variations (showing compounds, showing all ions, omitting spectator ions).

As a brief recap, when calling such reaction a "molecular equation", we are supposed to forget that the empirical formulas for ionic substances refer to formula units, not molecules. We treat all components as if they were molecules.
The quirk with "molecular equation" lies within the willful ignorance striving for a simplification in terminology to the point of being solipsic.
This happens presumably because balancing chemical reactions in solutions precedes basics of solid state chemistry and crystallography in the majority of curricula.
In my opinion, such simplification is unjust despite many textbooks still using it to this day.
I usually try to either refer to these reactions by their name ("precipitation reaction", "neutralization reaction"), or use the universal term formula equation.
The latter applies both to molecules and formula units equally well.
I haven't found an explicit style guide recommendation to back up this suggestion. However, several engineering and general chemistry textbooks prefer this term. So does, for example, Zumdahl's Chemistry [1, p. 137]:

Three Types of Equations Are Used to Describe Reactions in Solution

The formula equation gives the overall reaction stoichiometry but not necessarily the actual forms of the reactants and products in solution.

The complete ionic equation represents as ions all reactants and products that are strong electrolytes.

The net ionic equation includes only those solution components undergoing a change.
Spectator ions are not included.

Reference

Zumdahl, S. S.; Zumdahl, S. A.; DeCoste, D. J. Chemistry, 10th ed.; Cengage: Boston, MA, 2017. ISBN 978-1-305-95740-4.


text:
Are these two molecules enantiomers or diastereomers?

I had a long discussion with my professor about these two molecules, and we both agreed to do some of our own research and reconvene. These two molecules appear to be non-superimposable mirror images of one another, so they should be enantiomers.
However, this conflicts with the "trick" commonly taught when teaching students about enantiomers and diastereomers:

Invert all of the stereocenters in a molecule to get its enantiomer. If you invert some of the stereocenters in a molecule and leave the others untouched, you will make a diastereomer.

These molecules each have 4 stereocenters, the two carbons with hydroxy groups and the two bridgehead carbons. Despite the fact that only the carbons with hydroxy groups are inverted from (R,R) to (S,S), and the two bridgehead carbons are left alone, it appears that the two molecules are in fact enantiomers.

If they are enantiomers, what is wrong with the trick described above? If they are in fact diastereomers, why?

You are looking at a 2D projection of the molecule. Turn the second one around in your head an you'll see that they all are inverted.

Welcome to ChemSE! Are they mirror images or not? If so, they are enantiomers. There is nothing wrong with your "trick" except that inverting only one bridgehead will lead to a highly strained structure that will not exist.

@Martin-マーチン I assigned absolute stereochemistry to show that only two of the four stereocenters are being inverted. They are not all being inverted.

@2400Knots your stereochemistry labels are wrong. The left compound is (1R,2S,3S,4S)-bicyclo[2.2.1]hept-5-ene-2,3-diol and the right compound is (1R,2R,3R,4S)-bicyclo[2.2.1]hept-5-ene-2,3-diol.

@user55119 Thank you! I am not sure if they are mirror images or not. The atoms all appear to be mirrored, but the stereochemical assignments of the bridgehead carbons are not. I am not sure how to deal with this.

Okay, next try: turn both molecules 90 degrees towards or against each other. Draw a line in the middle. All inverted.

Follow @Martin 's advice. R mirrors S.

I think I see it now. Thanks for your help. https://i.ibb.co/rxHyFyH/image.png


text:
How can G3P oxidize into 1,3-BPG without energy expenditure?
In glycolysis, one of the important steps is when Glyceraldehyde-3-phosphate is oxidized to 1,3- Bisphosphoglycerate, while reducing $NAD^+$ to NADH and $H^+$. I'm a bit perplexed by this step since it seems to yield a more energetic molecule, with several negatively charged oxygens which should really repel each other. This molecule is in fact so energetic that it's used in subsequent steps to create ATP from ADP (when it turns into 3-phosphoglycerate).
Despite this, no energy seems to be expended in creating 1,3-BGT from G3P. In fact, the $NAD^+$ can arguably have been said to gain energy from this reaction (according to my limited understanding), since $NADH+H$ is used as inputs during oxidative phosphorylation, creating even more ATP.
To summarize my question:
-Is 1,3-BGT a more energetic molecule than G3P?
-If no, then please explain to me why.
-If yes, then how can this molecule be created (seemingly) without expending energy?
I attempted to use "glycolysis" and "metabolism" as tags, to no avail. If there's a separate page for biochemistry then please let me know.


text:
Name of a beehive like organic structure, is it aromatic?
I was just studying organic chemistry and came across a weird, yet beautiful, structure, don't know its name but its structure is given below:

I wanted to ask what is the compound's name? Is it aromatic, anti-aromatic, or non-aromatic?
I guess it should be anti-aromatic as it is not following Huckel's Rule, ig? as total of $16$ $\pi$ electrons are there, so it should be having $4n$ electrons where $n = 4$. But anti-aromatic compounds are highly unstable to the extent that they doesn't exist, but this compound seems stable to me!

The given compound is Pyrene. Pyrene is a polycyclic aromatic hydrocarbon consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is $C_{16}H_{10}$.
Pyrene is aromatic. The Huckel $(4n+2)π$ rule works best with monocyclic ring systems. If you look at the following resonance structure for pyrene with a central double bond, the monocyclic periphery has 14 π electrons (ignoring the greyed-out central double bond), but that is a rationalization.
Nonetheless, pyrene undergoes reactions characteristic of aromatic systems and has ring currents expected from aromatic systems.
The $(4n+2)π$ rule was really meant to apply to monocyclic pi systems. You run into problems when it is extended beyond its originally intended use.

Hmmm, but I can't understand how there are 14 pi electrons?

@Gamin8ing the path around the perimeter gives you 14 π electrons. The huckle rule will be followed if the central two carbons aren't aromatic. But it is controversial.


text:
How to find the appropriate isovalue with given probability to plot atomic orbitals
As far as I know, a plot of orbitals is drawn by taking region with 90% probability for an electron to be found.
Meanwhile, the program which can plots orbitals, such as VMD, gets isovalue (e/Å3) to find and draw the boundary surface of orbital.
I'm trying to write code which draws 2p orbital by taking region with given probability, so I need to calculate the isovalue from given probability.
However it is not easy... 2p orbital function looks like $P(r, \theta, \phi)$, so integrate it symbolically seems not to be able to find isovalue. Maybe I can perform binary search to find isovalue with numerical integration, but I think it's not so much effective. Are there other ways to solve this?

It may be better suited for mathematicians, unless anybody is aware of ready to use code.


text:
What are the major products formed by reaction of methylidene cyclopropane with HBr in CCl4 solvent?
I am confused between two products:

bromomethyl cyclopropane
Allyl bromide

Reason for my confusion: We know CPM cation will be formed which is stabilized by dancing resonating structures why can't bromine attack at one of those dancing structures when positive charge is on end on carbon as shown in figure:

'Dancing resonance' is a somewhat distasteful term to describe the case of cyclopropyl methyl cation. It would sound better (to me, atleast) as sigma-resonance.

Ok thanks for informing. Sir can you please clear my confusion by considering it as sigma resonance

"Distasteful" is an interesting way to put it, I'd say it is wrong. Anyway: What is "dancing resonance"? Also related: What is the reason for the exceptional stability of the cyclopropylmethyl carbocation? || To the formalities of the question, please include the actual question in the body, your first sentence makes no sense. Please introduce abbreviations you are using.

Also, you first structure appears incorrect to me. The primary cation should be much higher in energy than the tertiary cation.

Martin do you mean primary Cyclopropyl methyl carbocation is much much unstable than tertiary Cyclopropyl methyl carbocation?

This is not a actual question. This is my doubt sir


text:
Degradation of Pd catalyst in Buchwald-Hartwig amination
I am conducting Buchwald-Hartwig amination. I use $\ce{Pd_2(dba)3}$ and $\ce{P(o-tol)_3}$ as catalyst and toluene as solvent. Temperature is 100 ℃ and reaction time is 24 hours. During the reaction, formation of dark precipitate is observed. So I filter the reaction mixture through Celite pad when I do work-up.

The dark precipitate is observed. Is this dark material $\ce{Pd}$ metal formed by degradation of $\ce{Pd_2(dba)3}$? Reactant is aza-crown and bromothiophene, base is $\ce{Et_3N}$. Initially I thought that this would be the insoluble salt, $\ce{Et_3NHBr}$, but Pubchem says that its color is white. I searched several papers using keywords 'Buchwald-Hartwig amination byproducts', 'Buchwald-Hartwig amination degradation of catalyst', etc, but couldn't find satisfying answers. If this is really $\ce{Pd}$ metal, is the degradation due to too high temperature?

Assuming you are past the stage of reaction (which solvent? what scale? how many mol% of catalyst?) and completion of the workup, up and including the isolation of the product; is your yield of isolation substantially lower than the one reported in the literature for this reaction/for reactions with similar substrates/products to yours?  Only in this run «low» (yields are a measurement, thus have a standard deviation, too)? Or do you worry, the smudge on the frit may pollute subsequent batches of synthesis (i.e., the metal residues to create additional trap states for organic electronics)?


text:
Isolable activated esters: Other than N-Hydroxysuccinimidyl ester and Pentafluorophenyl ester?
Are there activated esters that undergo amide bond formation with an amino group in a mild and selective fashion, other than NHS ester and Pentafluorophenyl ester?
I am aware that there are many reagents to activate carboxylic acids to generate the amide bond. However, to my knowledge, only NHS ester and pentafluorophenyl esters are able to be isolated and characterized. Would there be any other alternatives?

Hydroxybenzotriazole (HOBt) ester

@Waylander can it be isolated?

best not to, besides being reactive they are potentially explosive https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6259230/

I edited the question

It is a balancing act. If the activated ester is highly electrophilic it will not survive isolation. If it is not it, may not be reactive enough to form the amide. p-Nitrophenyl esters are isolable and fairly reactive to nucleophiles.

@Waylander Would p-Nitrophenyl, p-Chlorophenyl ester require base when reacting with amino groups?

The usual conditions use tertiary base. The phenol (pKa 7.1) is acidic enough to protonate your amine nucelophile and stop it acylating.  See this review for further reading  file:///C:/Users/marti/AppData/Local/Temp/2005-t-61-10827-852-tvorba-conh-vazby-jd.pdf

@Waylander Have you used pentafluoro'benzy'ester before? Would the reaction with an amino group selective and relatively rapid?

I have not and cannot find much literature on them except as GC/MS derivatisation agents. Chemistry is an experimental scince - try it.


text:
Do strong field ligands always give d2sp3 hybridisation and weak field ligands give sp3d2 for coordiantion number 6
i am actually doing coordination compounds but get confused when it comes to hybridization so wanted to create a short of mine for the exam

Why is it wrong to use the concept of hybridization for transition metal complexes?

Generally true, but weak field ligands, say $NH_3$ or $F^{-}$, can form inner orbital complexes with metals in very high oxidation states ($Co^{3+}$, $Ni^{4+}$ resp. ); $Fe(NH_3)_6$$^{2+}$ is outer orbital but $Co(NH_3)_6$$^{3+}$ is inner orbital, and $CoF_6$$^{3-}$ is outer orbital but $NiF_6$$^{2-}$ is inner orbital.


text:
How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?
So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose synthase (Beta-1,4-galactosyltransferase 1, B4GALT1) showing how the reactants are being held in the reaction pocket:

I would like to make a 3D MOLFILE from this, or have one. Just of this reaction center, not the entire proteins. I figure there might be a 3D folding structure or domain database somewhere where I could get data that I could convert into the MOLFILE coordinates.
I looked it up the UNIPROT KB for B4GALT1 and did find some 3D models that show some things:

Here UDP Galactose and the Manganese ion. But I don's see the Glucosamine in any of those 3D models nor do they detail the orientation of the side chains of the amino acids in the reaction center, let alone the lactalbumin association.
Is there any way I could get to 3D models that are shown in this paper (figure above?) do the authors not usually submit these things to some public databases? I think the answer is yes. Because as I moved from that UNIPROT image to the source https://www.rcsb.org/structure/2AGD lo and behold they reference my authors, and there is a data file  https://files.rcsb.org/view/2AGD.pdb, which then might be the datafile they submitted. There one can find 3D coordinates down to the atom level!
EDIT: as commented by @andselisk there was a problem with my using the wrong link. The paper actually says what the accession number of their submissions are. The right one is 1NQI.
So, for example from their picture I want to find W314 that was labeled in their picture as a tryptophan at position 314, and indeed there it is (between 313 and 315:
ATOM   2476  N   GLY B 313      -1.909 -10.437  27.249  1.00 19.91           N
ATOM   2477  CA  GLY B 313      -0.797 -10.788  26.392  1.00 19.21           C
ATOM   2478  C   GLY B 313      -0.248  -9.505  25.787  1.00 17.82           C
ATOM   2479  O   GLY B 313      -0.786  -8.425  26.012  1.00 16.12           O
ATOM   2480  N   TRP B 314       0.786  -9.635  24.973  1.00 18.89           N
ATOM   2481  CA  TRP B 314       1.444  -8.478  24.397  1.00 18.21           C
ATOM   2482  C   TRP B 314       0.786  -7.805  23.194  1.00 18.60           C
ATOM   2483  O   TRP B 314       0.168  -8.449  22.356  1.00 16.45           O
ATOM   2484  CB  TRP B 314       2.884  -8.868  24.045  1.00 18.06           C
ATOM   2485  CG  TRP B 314       3.720  -7.734  23.557  1.00 18.61           C
ATOM   2486  CD1 TRP B 314       4.518  -6.898  24.318  1.00 17.43           C
ATOM   2487  CD2 TRP B 314       3.810  -7.268  22.217  1.00 16.35           C
ATOM   2488  NE1 TRP B 314       5.088  -5.938  23.520  1.00 16.69           N
ATOM   2489  CE2 TRP B 314       4.676  -6.139  22.225  1.00 17.88           C
ATOM   2490  CE3 TRP B 314       3.246  -7.686  21.000  1.00 18.70           C
ATOM   2491  CZ2 TRP B 314       4.990  -5.426  21.059  1.00 16.06           C
ATOM   2492  CZ3 TRP B 314       3.560  -6.963  19.823  1.00 14.57           C
ATOM   2493  CH2 TRP B 314       4.425  -5.852  19.871  1.00 15.37           C
ATOM   2494  N   GLY B 315       0.920  -6.481  23.150  1.00 19.02           N
ATOM   2495  CA  GLY B 315       0.459  -5.701  22.011  1.00 17.76           C
ATOM   2496  C   GLY B 315      -0.937  -5.121  21.947  1.00 17.26           C
ATOM   2497  O   GLY B 315      -1.885  -5.672  22.513  1.00 16.32           O
ATOM   2498  N   GLY B 316      -1.039  -3.964  21.282  1.00 14.94           N
ATOM   2499  CA  GLY B 316      -2.332  -3.328  21.074  1.00 12.98           C
ATOM   2500  C   GLY B 316      -3.062  -2.543  22.141  1.00 14.49           C
ATOM   2501  O   GLY B 316      -3.869  -1.674  21.793  1.00 16.13           O

There are the atom positions that look like 3D coordinates, and I should be able to turn them into a MOLFILE.
And I suppose there are no bonds in this PDB file, or are there? So if I wanted to get bonds for the MOLFILE, I would just have to match the atoms with MOLFILES or SMILES for the amino acids and other compounds I guess that might work. The atoms seem to use labels designating them to the AA, like in the 213 glycine example:
ATOM   2476  N   GLY B 313      -1.909 -10.437  27.249  1.00 19.91           N
ATOM   2477  CA  GLY B 313      -0.797 -10.788  26.392  1.00 19.21           C
ATOM   2478  C   GLY B 313      -0.248  -9.505  25.787  1.00 17.82           C
ATOM   2479  O   GLY B 313      -0.786  -8.425  26.012  1.00 16.12           O

I assume that "CA" means alpha-C so the other "C" is the carboxy-C, and "N" the amino-N. For the tryptophan then I assume "N" and "C" being the amino-N and carboxy-C respectively, "CA", "CB", ... being alpha-C, beta-C, gamma-C, "CE" epsilon-, "CZ" zeta-, "CH" eta-, and the numbers count the splits of the paths, NE1 being the ring-N, therefore CD1 means that side on the NE1, while the CD2 branches to the other side. CE2 would continue from there into the other ring, while CE3 is a new branch from CD2 completing the ring with the N, and so on, probably:

ATOM   2480  N   TRP B 314       0.786  -9.635  24.973  1.00 18.89           N
ATOM   2481  CA  TRP B 314       1.444  -8.478  24.397  1.00 18.21           C
ATOM   2482  C   TRP B 314       0.786  -7.805  23.194  1.00 18.60           C
ATOM   2483  O   TRP B 314       0.168  -8.449  22.356  1.00 16.45           O
ATOM   2484  CB  TRP B 314       2.884  -8.868  24.045  1.00 18.06           C
ATOM   2485  CG  TRP B 314       3.720  -7.734  23.557  1.00 18.61           C
ATOM   2486  CD1 TRP B 314       4.518  -6.898  24.318  1.00 17.43           C
ATOM   2487  CD2 TRP B 314       3.810  -7.268  22.217  1.00 16.35           C
ATOM   2488  NE1 TRP B 314       5.088  -5.938  23.520  1.00 16.69           N
ATOM   2489  CE2 TRP B 314       4.676  -6.139  22.225  1.00 17.88           C
ATOM   2490  CE3 TRP B 314       3.246  -7.686  21.000  1.00 18.70           C
ATOM   2491  CZ2 TRP B 314       4.990  -5.426  21.059  1.00 16.06           C
ATOM   2492  CZ3 TRP B 314       3.560  -6.963  19.823  1.00 14.57           C
ATOM   2493  CH2 TRP B 314       4.425  -5.852  19.871  1.00 15.37           C

I can see it's doable, but lots of manual work would be involved for me to match this. Ideally someone would have SMILES or MOLFILES with these standard (?) atom labels annotated? Or any other source of bond data?
Has anyone done this before, to construct a MOLFILE from (parts of!) such a PDB structure? Perhaps is there some software that does this? Like the authors here bothered to draw out specific atom structures and then connecting them with these blue ribbons. How did they draw this?
EPILOGUE: the accepted answer really hits the nail on the head. It's perfect. For other side questions, reading my article carefully especially the end, answers most. The only problem is, the figure I initially showed is what the authors had not submitted to the PDB and it really is the most interesting moment in the functioning of the lactose synthase. It is a model, predicted, not measured. I tried to reach out to the authors, but it's a long time ago 2001, still, nowhere have I found an actual model of this.

Have you already emailed (From the article: "E-mail address of the corresponding author:
qasba@helix.nih.gov") the author(s)? If not yet, I'd probably start there. The following line is also worth checking out: "The coordinates of LS·GlcNAc, LS·Glc, LS·UDP·Mn
and Se-LS·UDP complexes have been deposited in the RCSB Brookhaven Protein Data Bank with accession numbers 1J92, 1J8W, 1J8X and 1J94." Isn't 1NQI ("supersedes 1J92") what you are looking for?

@andselisk yes, thank you for reading for me. 1NQI has W314 alright.

@andselisk, I have now updated my question to remove the confusion over the wrong PDB reference data. Thanks again.

Most programs don't need information about bonds, they get them through distance criteria.

The relevant PDB file is probably 1j8x because it contains both the carbohydrate and the nucleotide shown bound in the active site in the image the OP provided.
You could use Jmol, e.g. at https://chemapps.stolaf.edu/jmol/jsmol/simple.htm to convert to a 3D molfile.
Here are the commands
set pdbAddHydrogens true adds hydrogens and double bonds upon loading
load "=1j8x" loads the pdb file
select 809
Selects the bound UDP ligand (just one, there are two copies of everything)
select groups within(3.5,selected)
This selects residues with at least one atom closer than 5 A to the selected ligand
write mol test.txt saves the selected atoms in the molfiles format
As a result, you get:
https://files.rcsb.org/download/1J8X.pdb
__Jmol-14_09292117503D 1   1.00000     0.00000     0
Jmol version 14.31.53  2021-09-03 09:05 EXTRACT: ({2778:2835 2850:2873 3460:3479 3494:3517 3890:3917 4315:4336 4482:4502 4864:4887 5327:5343 5387:5404 5416:5451 5496:5509 12606 12608:12643 12708 12722 12760 12785 12787 12840 12880})
350339  0  0  0  0            999 V2000
  -14.7090   22.7970  -14.2190 N   0  0  0  0  0  0
  -15.1830   21.4170  -14.3970 C   0  0  2  0  0  0
  -14.0160   20.5560  -13.9140 C   0  0  0  0  0  0
  -12.8790   20.8270  -14.2740 O   0  0  0  0  0  0
  -15.4190   21.3320  -15.8960 C   0  0  2  0  0  0
  -14.3880   22.2590  -16.4480 C   0  0  2  0  0  0
  -14.4080   23.4320  -15.5180 C   0  0  2  0  0  0
  -16.0914   21.1050   13.8608 H   0  0  0  0  0  0
  -16.4459   21.5900  -16.1940 H   0  0  0  0  0  0
  -15.3479   20.3091   16.2942 H   0  0  0  0  0  0
   14.5730   22.5358   17.4963 H   0  0  0  0  0  0
  -13.3943   21.7958  -16.5376 H   0  0  0  0  0  0
   13.4742   24.0135   15.5198 H   0  0  0  0  0  0
   15.1280   24.2121   15.8059 H   0  0  0  0  0  0
  -14.2740   19.5270  -13.1060 N   0  0  0  0  0  0
  -13.1600   18.7580  -12.5330 C   0  0  2  0  0  0
  -13.3260   17.2510  -12.3260 C   0  0  0  0  0  0
  -14.4120   16.7550  -12.0440 O   0  0  0  0  0  0
  -12.8040   19.4040  -11.1870 C   0  0  2  0  0  0
  -11.6270   18.7890  -10.4840 C   0  0  0  0  0  0
  -10.3530   19.3320  -10.6290 C   0  0  0  0  0  0
  -11.7980   17.7030   -9.6340 C   0  0  0  0  0  0
   -9.2690   18.8110   -9.9360 C   0  0  0  0  0  0
  -10.7150   17.1680   -8.9310 C   0  0  0  0  0  0
   -9.4470   17.7280   -9.0840 C   0  0  0  0  0  0
   15.2189   19.2802  -12.8913 H   0  0  0  0  0  0
  -12.3756   18.8085   13.3025 H   0  0  0  0  0  0
  -13.6819   19.4082   10.5242 H   0  0  0  0  0  0
  -12.6469   20.4852  -11.3149 H   0  0  0  0  0  0
   10.2031   20.1878  -11.3037 H   0  0  0  0  0  0
   12.7972   17.2593    9.5130 H   0  0  0  0  0  0
    8.2703   19.2549   10.0611 H   0  0  0  0  0  0
  -10.8621   16.3089   -8.2599 H   0  0  0  0  0  0
   -8.5905   17.3136   -8.5319 H   0  0  0  0  0  0
  -12.2090   16.5400  -12.4500 N   0  0  0  0  0  0
  -12.1450   15.0970  -12.2330 C   0  0  2  0  0  0
  -10.7090   14.6140  -12.4430 C   0  0  0  0  0  0
  -10.1940   14.6010  -13.5610 O   0  0  0  0  0  0
  -13.1000   14.3540  -13.1690 C   0  0  2  0  0  0
  -13.8850   13.2310  -12.4870 C   0  0  1  0  0  0
  -13.2870   11.8600  -12.7360 C   0  0  2  0  0  0
  -13.4660   11.4430  -14.1250 N   0  0  0  0  0  0
  -14.6150   11.0110  -14.6430 C   0  0  0  0  0  0
  -15.7030   10.9300  -13.8860 N   0  3  0  0  0  0
  -14.6800   10.6760  -15.9270 N   0  0  0  0  0  0
   11.3687   17.0184  -12.7052 H   0  0  0  0  0  0
  -12.4565   14.8825   11.2000 H   0  0  0  0  0  0
   12.5571   13.9671  -14.0440 H   0  0  0  0  0  0
   13.7864   15.0608  -13.6580 H   0  0  0  0  0  0
  -13.9826   13.4234   11.4083 H   0  0  0  0  0  0
  -14.9423   13.2556   12.7893 H   0  0  0  0  0  0
  -13.7016   11.1144   12.0415 H   0  0  0  0  0  0
  -12.2260   11.8317   12.4470 H   0  0  0  0  0  0
   12.6702   11.4848   14.7291 H   0  0  0  0  0  0
   15.6623   11.1939  -12.9223 H   0  0  0  0  0  0
  -16.5629   10.6051  -14.2796 H   0  0  0  0  0  0
   15.5438   10.3582  -16.3177 H   0  0  0  0  0  0
  -13.8650   10.7417   16.5027 H   0  0  0  0  0  0
   -7.8260   15.9840  -11.6190 N   0  0  0  0  0  0
   -6.9230   17.0020  -12.1460 C   0  0  2  0  0  0
   -6.3540   17.8480  -11.0070 C   0  0  0  0  0  0
   -6.2210   19.0690  -11.1390 O   0  0  0  0  0  0
   -7.6600   17.9060  -13.1360 C   0  0  2  0  0  0
   -8.0040   17.2650  -14.4640 C   0  0  2  0  0  0
   -6.7730   16.8800  -15.2720 C   0  0  2  0  0  0
   -7.1110   16.6800  -16.6800 N   0  0  0  0  0  0
   -7.0950   17.6440  -17.5970 C   0  0  0  0  0  0
   -6.7410   18.8830  -17.2660 N   0  3  0  0  0  0
   -7.4710   17.3810  -18.8420 N   0  0  0  0  0  0
   -8.5488   16.2499  -10.9812 H   0  0  0  0  0  0
   -6.0970   16.4954   12.6666 H   0  0  0  0  0  0
    7.0871   18.8305   13.3007 H   0  0  0  0  0  0
    8.5676   18.3157   12.6687 H   0  0  0  0  0  0
    8.6665   17.9178   15.0512 H   0  0  0  0  0  0
    8.6612   16.3952  -14.3177 H   0  0  0  0  0  0
   -6.2810   15.9913   14.8499 H   0  0  0  0  0  0
   -5.9713   17.6243   15.1562 H   0  0  0  0  0  0
    7.3708   15.7598   16.9727 H   0  0  0  0  0  0
    6.4846   19.0947   16.3228 H   0  0  0  0  0  0
   -6.7312   19.6026  -17.9603 H   0  0  0  0  0  0
   -7.4732   18.1085   19.5280 H   0  0  0  0  0  0
    7.7522   16.4552  -19.0945 H   0  0  0  0  0  0
  -17.2250   11.6680  -18.8880 N   0  0  0  0  0  0
  -17.1170   13.0310  -18.3740 C   0  0  2  0  0  0
  -18.0990   13.9680  -19.0820 C   0  0  0  0  0  0
  -18.3340   13.8490  -20.2820 O   0  0  0  0  0  0
  -15.6980   13.5640  -18.5820 C   0  0  2  0  0  0
  -15.4080   14.8340  -17.8270 C   0  0  0  0  0  0
  -15.0890   14.7960  -16.4770 C   0  0  0  0  0  0
  -15.4690   16.0700  -18.4670 C   0  0  0  0  0  0
  -14.8320   15.9670  -15.7710 C   0  0  0  0  0  0
  -15.2150   17.2420  -17.7740 C   0  0  0  0  0  0
  -14.8940   17.1900  -16.4190 C   0  0  0  0  0  0
   16.4915   11.3072  -19.4641 H   0  0  0  0  0  0
   17.3564   13.0001  -17.3008 H   0  0  0  0  0  0
  -15.4912   13.6984   19.6539 H   0  0  0  0  0  0
   14.9565   12.7907  -18.3324 H   0  0  0  0  0  0
   15.0386   13.8273  -15.9582 H   0  0  0  0  0  0
   15.7221   16.1157   19.5364 H   0  0  0  0  0  0
  -14.5802   15.9219  -14.7011 H   0  0  0  0  0  0
  -15.2665   18.2111  -18.2918 H   0  0  0  0  0  0
  -14.6902   18.1182  -15.8649 H   0  0  0  0  0  0
  -18.3440   17.9140  -19.2290 N   0  0  0  0  0  0
  -17.8950   19.2690  -18.9370 C   0  0  2  0  0  0
  -19.0200   20.2890  -18.7900 C   0  0  0  0  0  0
  -19.1550   20.9210  -17.7350 O   0  0  0  0  0  0
  -16.9180   19.7310  -20.0220 C   0  0  2  0  0  0
  -16.4840   21.2000  -19.9100 C   0  0  2  0  0  0
  -15.3700   21.5190  -20.8870 C   0  0  2  0  0  0
  -14.8810   22.8840  -20.7370 N   0  0  0  0  0  0
  -15.4320   23.9560  -21.3000 C   0  0  0  0  0  0
  -16.5060   23.8290  -22.0710 N   0  3  0  0  0  0
  -14.9030   25.1560  -21.0880 N   0  0  0  0  0  0
   17.9520   17.4397   20.0172 H   0  0  0  0  0  0
   17.4022   19.2203  -17.9547 H   0  0  0  0  0  0
  -17.3367   19.5333   21.0197 H   0  0  0  0  0  0
  -16.0356   19.0745   20.0435 H   0  0  0  0  0  0
  -16.1932   21.4514  -18.8793 H   0  0  0  0  0  0
  -17.3388   21.8788   20.0460 H   0  0  0  0  0  0
  -15.6884   21.3272   21.9222 H   0  0  0  0  0  0
  -14.5473   20.7946   20.7950 H   0  0  0  0  0  0
   14.0706   23.0252   20.1682 H   0  0  0  0  0  0
   16.9172   24.6372  -22.4925 H   0  0  0  0  0  0
  -16.9033   22.9252   22.2299 H   0  0  0  0  0  0
   14.0942   25.2504   20.5074 H   0  0  0  0  0  0
  -15.3135   25.9649   21.5089 H   0  0  0  0  0  0
  -11.3510   26.0190  -17.4710 N   0  0  0  0  0  0
  -10.8080   24.6770  -17.4260 C   0  0  2  0  0  0
   -9.6690   24.7480  -16.4000 C   0  0  0  0  0  0
   -9.0640   25.8060  -16.2200 O   0  0  0  0  0  0
  -10.2830   24.2660  -18.7990 C   0  0  2  0  0  0
  -11.4030   23.9710  -19.7980 C   0  0  0  0  0  0
  -12.5780   23.8200  -19.3930 O   0  0  0  0  0  0
  -11.0980   23.8680  -21.0020 O   0  5  0  0  0  0
   11.1967   26.5837  -18.2817 H   0  0  0  0  0  0
  -11.5645   23.9287   17.1472 H   0  0  0  0  0  0
    9.6003   23.4076  -18.7142 H   0  0  0  0  0  0
   -9.5960   25.0272   19.1973 H   0  0  0  0  0  0
   -9.3870   23.6380  -15.7240 N   0  0  0  0  0  0
   -8.3620   23.6000  -14.6740 C   0  0  2  0  0  0
   -6.9340   23.8880  -15.1000 C   0  0  0  0  0  0
   -6.1180   24.2940  -14.2800 O   0  0  0  0  0  0
   -8.2990   22.2160  -13.9840 C   0  0  1  0  0  0
   -9.6410   21.8410  -13.4190 C   0  0  0  0  0  0
   -7.8320   21.1680  -14.9700 C   0  0  0  0  0  0
   -9.8903   22.8009   15.9382 H   0  0  0  0  0  0
    8.7012   24.4128   14.0149 H   0  0  0  0  0  0
    7.5801   22.2712   13.1531 H   0  0  0  0  0  0
   -9.5641   20.8724  -12.9034 H   0  0  0  0  0  0
   -9.9665   22.6117   12.7047 H   0  0  0  0  0  0
  -10.3742   21.7646  -14.2354 H   0  0  0  0  0  0
    8.5580   21.0889  -15.7925 H   0  0  0  0  0  0
   -6.8503   21.4562  -15.3740 H   0  0  0  0  0  0
    7.7479   20.1967  -14.4605 H   0  0  0  0  0  0
   -1.0120   26.3490  -26.9730 N   0  0  0  0  0  0
   -1.3770   25.0870  -27.6050 C   0  0  2  0  0  0
   -1.6990   25.2830  -29.0990 C   0  0  0  0  0  0
   -1.5070   24.3850  -29.9140 O   0  0  0  0  0  0
   -2.6020   24.5020  -26.8880 C   0  0  2  0  0  0
   -3.1580   23.2490  -27.5240 C   0  0  2  0  0  0
   -4.4630   22.8290  -26.8740 C   0  0  2  0  0  0
   -4.9630   21.5330  -27.4850 C   0  0  2  0  0  0
   -6.2460   21.1080  -26.8780 N   0  3  0  0  0  0
   -1.5663   26.6860   26.2119 H   0  0  0  0  0  0
   -0.5238   24.3970  -27.5271 H   0  0  0  0  0  0
    3.3895   25.2643  -26.7947 H   0  0  0  0  0  0
    2.3733   24.3222   25.8271 H   0  0  0  0  0  0
    2.4219   22.4319  -27.4999 H   0  0  0  0  0  0
    3.2785   23.3755  -28.6100 H   0  0  0  0  0  0
   -5.2202   23.6240  -26.9415 H   0  0  0  0  0  0
   -4.3599   22.7455  -25.7820 H   0  0  0  0  0  0
   -4.2052   20.7395   27.4071 H   0  0  0  0  0  0
   -5.0501   21.6175   28.5782 H   0  0  0  0  0  0
   -6.9362   21.8160   27.0274 H   0  0  0  0  0  0
    6.5479   20.2536   27.3007 H   0  0  0  0  0  0
    6.1198   20.9676   25.8959 H   0  0  0  0  0  0
  -14.6510   29.4530  -31.8610 N   0  0  0  0  0  0
  -14.1910   28.7590  -30.6560 C   0  0  2  0  0  0
  -14.5940   29.4590  -29.3610 C   0  0  0  0  0  0
  -14.2950   30.6350  -29.1520 O   0  0  0  0  0  0
  -12.6620   28.5890  -30.7010 C   0  0  2  0  0  0
  -12.0750   27.7610  -29.5680 C   0  0  0  0  0  0
  -12.4780   26.4440  -29.3640 C   0  0  0  0  0  0
  -11.0900   28.2870  -28.7240 C   0  0  0  0  0  0
  -11.9160   25.6620  -28.3560 C   0  0  0  0  0  0
  -10.5220   27.5130  -27.7020 C   0  0  0  0  0  0
  -10.9420   26.1980  -27.5290 C   0  0  0  0  0  0
  -10.4050   25.4130  -26.5320 O   0  0  0  0  0  0
  -13.9955   29.9844   32.3975 H   0  0  0  0  0  0
   14.6870   27.7772   30.6518 H   0  0  0  0  0  0
   12.1726   29.5732  -30.7436 H   0  0  0  0  0  0
   12.3556   28.1730  -31.6721 H   0  0  0  0  0  0
  -13.2554   26.0119   30.0111 H   0  0  0  0  0  0
  -10.7557   29.3255   28.8648 H   0  0  0  0  0  0
  -12.2451   24.6216   28.2174 H   0  0  0  0  0  0
   -9.7519   27.9413  -27.0435 H   0  0  0  0  0  0
   10.8244   24.5057  -26.5597 H   0  0  0  0  0  0
  -15.5650   14.2170  -24.8800 N   0  0  0  0  0  0
  -14.9590   15.4350  -25.4140 C   0  0  2  0  0  0
  -15.5640   15.9790  -26.7080 C   0  0  0  0  0  0
  -16.0930   15.2320  -27.5220 O   0  0  0  0  0  0
  -13.4640   15.2000  -25.6200 C   0  0  2  0  0  0
  -12.7050   16.4030  -26.0350 C   0  0  0  0  0  0
  -12.0110   17.2450  -25.2270 C   0  0  0  0  0  0
  -12.5590   16.9100  -27.3690 C   0  0  0  0  0  0
  -11.4390   18.2440  -25.9660 N   0  0  0  0  0  0
  -11.7600   18.0680  -27.2860 C   0  0  0  0  0  0
  -13.0270   16.4990  -28.6240 C   0  0  0  0  0  0
  -11.4150   18.8270  -28.4130 C   0  0  0  0  0  0
  -12.6850   17.2510  -29.7500 C   0  0  0  0  0  0
  -11.8880   18.4020  -29.6340 C   0  0  0  0  0  0
   15.0870   13.3451   24.9864 H   0  0  0  0  0  0
   15.1652   16.2083  -24.6594 H   0  0  0  0  0  0
   13.3020   14.3813   26.3365 H   0  0  0  0  0  0
  -13.0187   14.7620   24.7144 H   0  0  0  0  0  0
  -11.9216   17.1391   24.1357 H   0  0  0  0  0  0
   10.8758   18.9852   25.6005 H   0  0  0  0  0  0
  -13.6529   15.5996  -28.7207 H   0  0  0  0  0  0
   10.7900   19.7280  -28.3250 H   0  0  0  0  0  0
   13.0445   16.9378   30.7412 H   0  0  0  0  0  0
  -11.6365   18.9759   30.5380 H   0  0  0  0  0  0
   -1.6230   26.2960  -21.6210 N   0  0  0  0  0  0
   -2.3730   25.1550  -21.1470 C   0  0  2  0  0  0
    1.3599   24.1150  -20.7020 C   0  0  0  0  0  0
   -0.4800   23.7390  -21.4780 O   0  0  0  0  0  0
   -3.2400   24.5350  -22.2340 C   0  0  2  0  0  0
   -4.0820   23.4020  -21.6640 C   0  0  2  0  0  0
   -4.8680   22.3140  -22.8510 S   0  0  0  0  0  0
   -6.3070   23.3140  -23.3200 C   0  0  0  0  0  0
   -1.0135   26.2056   22.4086 H   0  0  0  0  0  0
    3.0403   25.4827  -20.3363 H   0  0  0  0  0  0
   -2.6330   24.1945  -23.0858 H   0  0  0  0  0  0
    3.8672   25.2920  -22.7274 H   0  0  0  0  0  0
   -4.8389   23.8114   20.9788 H   0  0  0  0  0  0
   -3.4782   22.8091   20.9611 H   0  0  0  0  0  0
   -5.9665   24.2668  -23.7516 H   0  0  0  0  0  0
   -6.9063   22.7681  -24.0635 H   0  0  0  0  0  0
    6.9208   23.5136  -22.4293 H   0  0  0  0  0  0
   -0.4310   17.9990  -20.7500 N   0  0  0  0  0  0
   -1.3390   16.8790  -20.4960 C   0  0  2  0  0  0
   -1.9230   16.2080  -21.7380 C   0  0  0  0  0  0
   -1.9410   16.7810  -22.8240 O   0  0  0  0  0  0
   -2.4890   17.3220  -19.5870 C   0  0  2  0  0  0
   -3.7300   17.7150  -20.3230 C   0  0  0  0  0  0
   -4.5100   16.8070  -21.0060 N   0  3  0  0  0  0
   -4.3290   18.9190  -20.4840 C   0  0  0  0  0  0
   -5.5350   17.4320  -21.5550 C   0  0  0  0  0  0
   -5.4480   18.7160  -21.2540 N   0  0  0  0  0  0
    0.4683   17.9969   20.3126 H   0  0  0  0  0  0
   -0.7064   16.1206   20.0115 H   0  0  0  0  0  0
   -2.1619   18.1368   18.9243 H   0  0  0  0  0  0
   -2.7140   16.5414  -18.8453 H   0  0  0  0  0  0
    4.3276   15.8262  -21.0750 H   0  0  0  0  0  0
    3.9837   19.8798   20.0745 H   0  0  0  0  0  0
    6.3260   16.9642   22.1594 H   0  0  0  0  0  0
   -6.0925   19.4249   21.5404 H   0  0  0  0  0  0
   -5.1700   13.4190  -23.3790 N   0  0  0  0  0  0
    6.5970   13.1110  -23.2860 C   0  0  2  0  0  0
   -6.8270   12.0950  -22.1710 C   0  0  0  0  0  0
   -6.3170   10.9790  -22.2430 O   0  0  0  0  0  0
   -7.0680   12.5270  -24.6190 C   0  0  2  0  0  0
   -8.5310   12.1870  -24.7020 C   0  0  2  0  0  0
   -9.3160   13.4670  -24.7960 C   0  0  2  0  0  0
   -9.6560   13.9740  -23.5020 N   0  0  0  0  0  0
   -9.2910   15.0490  -22.8080 C   0  0  0  0  0  0
   -8.4380   15.9970  -23.1900 N   0  3  0  0  0  0
   -9.8810   15.1390  -21.6350 N   0  0  0  0  0  0
   -4.6920   13.2257  -24.2358 H   0  0  0  0  0  0
   -7.1628   14.0274  -23.0623 H   0  0  0  0  0  0
    6.4631   11.6449  -24.8762 H   0  0  0  0  0  0
   -6.7931   13.2029   25.4421 H   0  0  0  0  0  0
    8.8573   11.5659   23.8547 H   0  0  0  0  0  0
    8.7484   11.5089   25.5403 H   0  0  0  0  0  0
  -10.2138   13.3356  -25.4178 H   0  0  0  0  0  0
    8.7743   14.2207   25.3863 H   0  0  0  0  0  0
  -10.3091   13.3954   23.0135 H   0  0  0  0  0  0
    7.9972   15.9415  -24.0859 H   0  0  0  0  0  0
    8.2379   16.7646  -22.5810 H   0  0  0  0  0  0
   -9.6823   15.9127   21.0333 H   0  0  0  0  0  0
  -10.5280   14.4337   21.3452 H   0  0  0  0  0  0
   -7.5850   12.4660  -21.1420 N   0  0  0  0  0  0
   -7.8290   11.5360  -20.0460 C   0  0  2  0  0  0
   -8.9590   10.5500  -20.3110 C   0  0  0  0  0  0
   -9.9400   10.8750  -20.9820 O   0  0  0  0  0  0
   -8.0800   12.2630  -18.7040 C   0  0  2  0  0  0
   -8.2730   13.7680  -18.8470 C   0  0  0  0  0  0
   -7.9310   14.4930  -17.8960 O   0  0  0  0  0  0
   -8.7770   14.2350  -19.8790 O   0  5  0  0  0  0
   -7.9867   13.3815  -21.1205 H   0  0  0  0  0  0
   -6.8982   10.9544   19.9725 H   0  0  0  0  0  0
   -7.2710   12.0449  -17.9912 H   0  0  0  0  0  0
    8.9348   11.8139   18.1772 H   0  0  0  0  0  0
  -13.1620   10.4220  -21.2870 N   0  0  0  0  0  0
  -13.4870   11.6680  -21.9670 C   0  0  2  0  0  0
  -13.0330   11.6170  -23.4270 C   0  0  0  0  0  0
  -12.4880   12.5850  -23.9530 O   0  0  0  0  0  0
  -12.8420   12.8620  -21.2600 C   0  0  2  0  0  0
  -13.4460   14.1860  -21.6950 C   0  0  0  0  0  0
  -14.6640   14.3150  -21.8100 O   0  0  0  0  0  0
  -12.5990   15.1730  -21.9340 N   0  0  0  0  0  0
   12.2629   10.0078  -21.4292 H   0  0  0  0  0  0
   14.5793   11.7941   21.9375 H   0  0  0  0  0  0
  -11.7517   12.8618  -21.4058 H   0  0  0  0  0  0
  -12.8960   12.7466  -20.1674 H   0  0  0  0  0  0
  -11.6159   15.0256   21.8253 H   0  0  0  0  0  0
   12.9415   16.0668   22.2233 H   0  0  0  0  0  0
   -6.9030   20.8000  -21.5690 Mn  0  0  0  0  0  0
  -11.7070   17.5360  -17.1280 N   0  0  0  0  0  0
  -11.3770   16.9560  -15.8900 C   0  0  0  0  0  0
  -11.1650   15.5800  -15.9320 N   0  0  0  0  0  0
  -11.2560   14.7460  -17.0750 C   0  0  0  0  0  0
  -11.5930   15.4240  -18.2820 C   0  0  0  0  0  0
  -11.8010   16.7270  -18.2860 C   0  0  0  0  0  0
  -11.3030   17.6750  -14.9060 O   0  0  0  0  0  0
  -11.0520   13.5490  -16.9940 O   0  0  0  0  0  0
  -11.9510   19.0300  -17.1320 C   0  0  1  0  0  0
  -10.8070   19.9810  -17.3200 C   0  0  2  0  0  0
  -10.3900   20.6110  -16.0980 O   0  0  0  0  0  0
  -11.3610   20.9810  -18.3030 C   0  0  1  0  0  0
  -12.4180   20.2610  -19.1170 C   0  0  2  0  0  0
  -12.8640   19.2350  -18.1980 O   0  0  0  0  0  0
  -11.9490   22.0900  -17.6310 O   0  0  0  0  0  0
  -11.8710   19.7390  -20.4400 C   0  0  2  0  0  0
  -10.4750   19.4400  -20.4960 O   0  0  0  0  0  0
   -9.6960   18.9000  -21.7460 P   0  2  1  0  0  0
   -8.2940   18.7050  -21.3700 O   0  0  0  0  0  0
  -10.3100   17.7680  -22.4750 O   0  5  0  0  0  0
   -9.8690   20.2330  -22.7040 O   0  0  0  0  0  0
   -9.2480   20.5240  -24.1050 P   0  2  1  0  0  0
   -9.8680   21.9860  -24.3300 O   0  0  0  0  0  0
   -7.7800   20.6000  -23.8430 O   0  0  0  0  0  0
   -9.4020   19.3700  -25.0250 O   0  5  0  0  0  0
   10.9243   15.1356  -15.0691 H   0  0  0  0  0  0
  -11.6806   14.8556   19.2196 H   0  0  0  0  0  0
   12.0611   17.2101   19.2393 H   0  0  0  0  0  0
   12.2786   19.2732   16.1104 H   0  0  0  0  0  0
   -9.8961   19.4741  -17.6712 H   0  0  0  0  0  0
   10.0293   19.9192  -15.4724 H   0  0  0  0  0  0
  -10.5541   21.3713   18.9406 H   0  0  0  0  0  0
   13.2476   20.9001  -19.4535 H   0  0  0  0  0  0
   11.2502   22.5635  -17.0947 H   0  0  0  0  0  0
   12.1286   20.4413   21.2464 H   0  0  0  0  0  0
   12.4482   18.8567   20.7533 H   0  0  0  0  0  0
  -12.2560   23.2100  -23.3040 O   0  6  0  0  0  0
  -10.8590   11.6750  -14.8360 O   0  6  0  0  0  0
  -11.1220   22.7890  -26.6880 O   0  6  0  0  0  0
   -8.5240   22.6220  -20.9750 O   0  6  0  0  0  0
  -14.3430   17.8360  -21.9430 O   0  6  0  0  0  0
  -12.8660   11.7110  -18.0880 O   0  6  0  0  0  0
   -5.3480   19.3780  -24.7980 O   0  6  0  0  0  0
  1  7  1  0  0  0
  2  3  1  0  0  0
  2  1  1  0  0  0
  3  4  2  0  0  0
  5  2  1  0  0  0
  5  6  1  0  0  0
  7  6  1  0  0  0
 15  3  1  0  0  0
 15 16  1  0  0  0
 16 19  1  0  0  0
 17 35  1  0  0  0
 17 16  1  0  0  0
 18 17  2  0  0  0
 19 20  1  0  0  0
 20 21  2  0  0  0
 21 23  1  0  0  0
 22 24  2  0  0  0
 22 20  1  0  0  0
 24 25  1  0  0  0
 25 23  2  0  0  0
 35 36  1  0  0  0
 36 37  1  0  0  0
 37 38  2  0  0  0
 39 36  1  0  0  0
 40 41  1  0  0  0
 40 39  1  0  0  0
 42 41  1  0  0  0
 43 42  1  0  0  0
 44 43  2  0  0  0
 45 43  1  0  0  0
 59 60  1  0  0  0
 60 61  1  0  0  0
 61 62  2  0  0  0
 63 60  1  0  0  0
 64 63  1  0  0  0
 64 65  1  0  0  0
 66 67  1  0  0  0
 66 65  1  0  0  0
 67 68  2  0  0  0
 69 67  1  0  0  0
 83 84  1  0  0  0
 84 87  1  0  0  0
 85 84  1  0  0  0
 86 85  2  0  0  0
 87 88  1  0  0  0
 88 89  2  0  0  0
 89 91  1  0  0  0
 90 88  1  0  0  0
 90 92  2  0  0  0
 92 93  1  0  0  0
 93 91  2  0  0  0
103104  1  0  0  0
104107  1  0  0  0
105104  1  0  0  0
106105  2  0  0  0
107108  1  0  0  0
108109  1  0  0  0
109110  1  0  0  0
111110  1  0  0  0
111113  1  0  0  0
112111  2  0  0  0
127128  1  0  0  0
128131  1  0  0  0
128129  1  0  0  0
129139  1  0  0  0
129130  2  0  0  0
132134  1  0  0  0
132131  1  0  0  0
133132  2  0  0  0
139140  1  0  0  0
140143  1  0  0  0
140141  1  0  0  0
141142  2  0  0  0
143145  1  0  0  0
144143  1  0  0  0
156155  1  0  0  0
157158  2  0  0  0
157156  1  0  0  0
159156  1  0  0  0
160159  1  0  0  0
161160  1  0  0  0
162161  1  0  0  0
163162  1  0  0  0
177178  1  0  0  0
178181  1  0  0  0
179178  1  0  0  0
179180  2  0  0  0
181182  1  0  0  0
182184  1  0  0  0
183182  2  0  0  0
183185  1  0  0  0
184186  2  0  0  0
185187  2  0  0  0
187188  1  0  0  0
187186  1  0  0  0
198199  1  0  0  0
199202  1  0  0  0
200199  1  0  0  0
201200  2  0  0  0
202203  1  0  0  0
203205  1  0  0  0
203204  2  0  0  0
204206  1  0  0  0
205207  2  0  0  0
207209  1  0  0  0
207206  1  0  0  0
208210  2  0  0  0
208205  1  0  0  0
210211  1  0  0  0
211209  2  0  0  0
223224  1  0  0  0
223222  1  0  0  0
224225  2  0  0  0
226223  1  0  0  0
227226  1  0  0  0
228227  1  0  0  0
229228  1  0  0  0
240239  1  0  0  0
241240  1  0  0  0
242241  2  0  0  0
243240  1  0  0  0
244243  1  0  0  0
245244  1  0  0  0
246244  2  0  0  0
247245  2  0  0  0
247248  1  0  0  0
248246  1  0  0  0
258257  1  0  0  0
259258  1  0  0  0
259260  2  0  0  0
261258  1  0  0  0
262261  1  0  0  0
263262  1  0  0  0
264263  1  0  0  0
264265  1  0  0  0
265266  2  0  0  0
267265  1  0  0  0
281259  1  0  0  0
282281  1  0  0  0
283282  1  0  0  0
284283  2  0  0  0
285282  1  0  0  0
286285  1  0  0  0
286287  2  0  0  0
288286  1  0  0  0
294293  1  0  0  0
294295  1  0  0  0
294297  1  0  0  0
295296  2  0  0  0
298297  1  0  0  0
298300  1  0  0  0
299298  2  0  0  0
308309  1  0  0  0
309314  2  0  0  0
309310  1  0  0  0
311315  2  0  0  0
311310  1  0  0  0
312311  1  0  0  0
313312  2  0  0  0
313308  1  0  0  0
316308  1  0  0  0
316317  1  0  0  0
317318  1  0  0  0
319317  1  0  0  0
320323  1  0  0  0
320319  1  0  0  0
321316  1  0  0  0
321320  1  0  0  0
322319  1  0  0  0
323324  1  0  0  0
324325  1  0  0  0
325326  2  0  0  0
327325  1  0  0  0
328329  1  0  0  0
328325  1  0  0  0
329331  1  0  0  0
330329  2  0  0  0
331307  1  0  0  0
332329  1  0  0  0
  2  8  1  0  0  0
  5  9  1  0  0  0
  5 10  1  0  0  0
  6 11  1  0  0  0
  6 12  1  0  0  0
  7 13  1  0  0  0
  7 14  1  0  0  0
 15 26  1  0  0  0
 16 27  1  0  0  0
 19 28  1  0  0  0
 19 29  1  0  0  0
 21 30  1  0  0  0
 22 31  1  0  0  0
 23 32  1  0  0  0
 24 33  1  0  0  0
 25 34  1  0  0  0
 35 46  1  0  0  0
 36 47  1  0  0  0
 39 48  1  0  0  0
 39 49  1  0  0  0
 40 50  1  0  0  0
 40 51  1  0  0  0
 41 52  1  0  0  0
 41 53  1  0  0  0
 42 54  1  0  0  0
 44 55  1  0  0  0
 44 56  1  0  0  0
 45 57  1  0  0  0
 45 58  1  0  0  0
 59 70  1  0  0  0
 60 71  1  0  0  0
 63 72  1  0  0  0
 63 73  1  0  0  0
 64 74  1  0  0  0
 64 75  1  0  0  0
 65 76  1  0  0  0
 65 77  1  0  0  0
 66 78  1  0  0  0
 68 79  1  0  0  0
 68 80  1  0  0  0
 69 81  1  0  0  0
 69 82  1  0  0  0
 83 94  1  0  0  0
 84 95  1  0  0  0
 87 96  1  0  0  0
 87 97  1  0  0  0
 89 98  1  0  0  0
 90 99  1  0  0  0
 91100  1  0  0  0
 92101  1  0  0  0
 93102  1  0  0  0
103114  1  0  0  0
104115  1  0  0  0
107116  1  0  0  0
107117  1  0  0  0
108118  1  0  0  0
108119  1  0  0  0
109120  1  0  0  0
109121  1  0  0  0
110122  1  0  0  0
112123  1  0  0  0
112124  1  0  0  0
113125  1  0  0  0
113126  1  0  0  0
127135  1  0  0  0
128136  1  0  0  0
131137  1  0  0  0
131138  1  0  0  0
139146  1  0  0  0
140147  1  0  0  0
143148  1  0  0  0
144149  1  0  0  0
144150  1  0  0  0
144151  1  0  0  0
145152  1  0  0  0
145153  1  0  0  0
145154  1  0  0  0
155164  1  0  0  0
156165  1  0  0  0
159166  1  0  0  0
159167  1  0  0  0
160168  1  0  0  0
160169  1  0  0  0
161170  1  0  0  0
161171  1  0  0  0
162172  1  0  0  0
162173  1  0  0  0
163174  1  0  0  0
163175  1  0  0  0
163176  1  0  0  0
177189  1  0  0  0
178190  1  0  0  0
181191  1  0  0  0
181192  1  0  0  0
183193  1  0  0  0
184194  1  0  0  0
185195  1  0  0  0
186196  1  0  0  0
188197  1  0  0  0
198212  1  0  0  0
199213  1  0  0  0
202214  1  0  0  0
202215  1  0  0  0
204216  1  0  0  0
206217  1  0  0  0
208218  1  0  0  0
209219  1  0  0  0
210220  1  0  0  0
211221  1  0  0  0
222230  1  0  0  0
223231  1  0  0  0
226232  1  0  0  0
226233  1  0  0  0
227234  1  0  0  0
227235  1  0  0  0
229236  1  0  0  0
229237  1  0  0  0
229238  1  0  0  0
239249  1  0  0  0
240250  1  0  0  0
243251  1  0  0  0
243252  1  0  0  0
245253  1  0  0  0
246254  1  0  0  0
247255  1  0  0  0
248256  1  0  0  0
257268  1  0  0  0
258269  1  0  0  0
261270  1  0  0  0
261271  1  0  0  0
262272  1  0  0  0
262273  1  0  0  0
263274  1  0  0  0
263275  1  0  0  0
264276  1  0  0  0
266277  1  0  0  0
266278  1  0  0  0
267279  1  0  0  0
267280  1  0  0  0
281289  1  0  0  0
282290  1  0  0  0
285291  1  0  0  0
285292  1  0  0  0
293301  1  0  0  0
294302  1  0  0  0
297303  1  0  0  0
297304  1  0  0  0
300305  1  0  0  0
300306  1  0  0  0
310333  1  0  0  0
312334  1  0  0  0
313335  1  0  0  0
316336  1  0  0  0
317337  1  0  0  0
318338  1  0  0  0
319339  1  0  0  0
320340  1  0  0  0
322341  1  0  0  0
323342  1  0  0  0
323343  1  0  0  0
M  END

Wow! Super interesting. Almost perfect. I had 2 problems I never found where it actually saved that file test.txt or whatever I named it, it said it saved it somehow but I guess I have to open some text box to copy and paste it from?

Then I got a MOLFILE which interestingly shows bonds -- and I guess they are inferred by distance? Because the bond valence is all 1, -COOH comes out as -C(H2)OH but it is really, really close, given that the bonds are inferred.

@GuntherSchadow Prima! I'm glad you got something out of my answer.

@GuntherSchadow Try the 'set pdbAddHydrogens true' to see if the double bonds make sense (I edited the answer accordingly).

Now finally the write mol test.txt worked for me.  The hydrogen stuff creates a very strange molfile where all hydrogens appear to be over to the left. And I had to remove the bonds over to them to even display it nicely. I'd attach the picture to the comment if I could, but you can see it if you try to render your Molfile.

@GuntherSchadow You can attach a picture in the comments by uploading the image via the answer form, copy-pasting the Imgur link into your comment as usual with [my structure](https://i.stack.imgur.com/<1mgn4m3.ext>) and then discarding the answer.

I am going to post my own answer since now I have figured it out in much more detail based on the answer I had accepted above. I don't have the PDB file of the lactose synthase model above, but I was since steered to use LDH. And here is the author's picture from Cook, Senkovich, et al. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase and they have deposited it to PDB as 4ND3 and 4ND4:

Now I have been able to create the molfile of exactly this:

InChI=1S/C21H27N7O14P2.2C6H14N4O.C6H9N3O.C6H13NO.C5H11NOS.C4H8N2O2.C4H7NO3.C3H7NO2.C3H4O3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33;2*7-5(4-11)2-1-3-10-6(8)9;7-5(3-10)1-6-2-8-4-9-6;1-3-5(2)6(7)4-8;1-8-3-2-5(6)4-7;5-3(2-7)1-4(6)8;5-3(2-6)1-4(7)8;4-3(1-5)2-6;1-2(4)3(5)6/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H4-2,22,23,24,25,33,34,35,36,37);2*4-5H,1-3,7H2,(H4,8,9,10);2-5H,1,7H2,(H,8,9);4-6H,3,7H2,1-2H3;4-5H,2-3,6H2,1H3;2-3H,1,5H2,(H2,6,8);2-3H,1,5H2,(H,7,8);1,3,6H,2,4H2;1H3,(H,5,6)/q+2;;;;;;;;;/p+2/t10-,11-,13-,14-,15-,16-,20-,21-;3*5-;5-,6+;5-;3*3-;/m100000001./s1 InChIKey=IBJLKZJXTBIULM-IRBDITSESA-P
  GS-mol2inchi
Jmol version 14.31.56  2021-10-01 10:44 EXTRACT: ({0:121})
122118  0  0  0  0           999 V2000
   25.2059   40.1061  118.3750 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3083   41.1168  118.0510 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.4521   40.4296  118.9050 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.9287   42.7001  118.8050 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1872   41.0122  118.4520 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.5059   39.8960  118.6250 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.2601   45.3394  116.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.4095   42.6347  120.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6679   42.4398  118.2720 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.3830   42.0571  119.2200 C   0  0  0  0  0  0  0  0  0  0  0  0
   36.8039   40.1697  117.8820 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.1563   44.5231  119.5910 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.1546   41.7047  120.6830 C   0  0  0  0  0  0  0  0  0  0  0  0
   37.9261   39.1941  118.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7123   41.2288  120.7310 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.0252   40.0584  118.8210 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.6978   45.8473  119.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7103   43.5485  117.9250 C   0  0  0  0  0  0  0  0  0  0  0  0
   39.6805   43.6734  118.4970 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.0901   42.1224  119.6690 C   0  0  0  0  0  0  0  0  0  0  0  0
   38.6918   41.4317  118.2680 C   0  0  0  0  0  0  0  0  0  0  0  0
   41.1584   46.7056  120.1640 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.1005   44.8246  117.9130 N   0  0  0  0  0  0  0  0  0  0  0  0
   40.7088   46.1723  117.9090 N   0  0  0  0  0  0  0  0  0  0  0  0
   39.7592   44.1230  117.2230 N   0  0  0  0  0  0  0  0  0  0  0  0
   39.9605   43.8304  120.7230 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7890   41.7141  119.1130 N   0  3  0  0  0  0  0  0  0  0  0  0
   39.2455   42.5527  119.0590 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.3257   42.8923  121.4620 O   0  0  0  0  0  0  0  0  0  0  0  0
   38.3934   38.5066  117.0660 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.1011   41.3955  122.0160 O   0  0  0  0  0  0  0  0  0  0  0  0
   40.3387   39.6413  118.4390 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.5585   43.2635  117.6320 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.6501   37.1884  118.3990 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.9517   38.6881  116.7390 O   0  5  0  0  0  0  0  0  0  0  0  0
   33.8776   36.4502  118.1390 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.7434   37.5886  120.3060 O   0  5  0  0  0  0  0  0  0  0  0  0
   30.5988   39.7233  118.5840 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.9285   38.7220  118.0740 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.0816   42.1971  118.6390 O   0  0  0  0  0  0  0  0  0  0  0  0
   37.2687   41.4726  118.2250 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.6881   38.4885  119.1700 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.4467   38.4346  118.1350 P   0  2  2  0  0  0  0  0  0  0  0  0
   34.0849   37.6911  118.9570 P   0  2  1  0  0  0  0  0  0  0  0  0
   23.2333   42.7327  125.1660 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0397   43.7480  125.9720 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3880   43.4687  124.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6263   44.3199  127.8070 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.7254   43.2143  127.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2973   42.2201  123.6130 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7283   42.7333  128.1940 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.7188   42.5800  124.7570 N   0  3  0  0  0  0  0  0  0  0  0  0
   19.6248   41.4508  122.7620 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.5398   42.6060  123.3110 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7134   44.5630  127.2830 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3959   37.9815  116.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9676   38.4975  116.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2552   38.4892  117.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6927   38.5235  115.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2012   38.3748  114.9160 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5587   38.1794  118.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6767   39.3653  113.9570 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.3969   39.1356  119.0190 N   0  3  0  0  0  0  0  0  0  0  0  0
   19.7261   37.5394  118.0150 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5724   37.8617  117.2720 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9511   37.5480  115.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186   46.9667  121.0610 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3604   44.7587  120.7750 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1540   46.4882  123.3930 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8191   43.5883  119.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8564   47.1478  122.0460 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2647   45.5464  120.6500 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6074   48.5710  122.2530 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.0542   43.5450  120.2080 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.3237   44.7883  119.9900 N   0  3  0  0  0  0  0  0  0  0  0  0
   20.3088   46.2301  123.7350 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.3580   39.9065  116.1210 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.0179   40.4075  113.0800 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.7353   38.9049  115.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1796   38.8312  112.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7272   39.4430  114.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.3622   38.2750  113.2380 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.1839   37.4238  114.1020 N   0  0  0  0  0  0  0  0  0  0  0  0
   30.7404   38.7820  110.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4354   43.5827  114.3420 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8384   46.7206  113.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9915   45.6335  112.5310 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3635   47.1992  115.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0249   47.8017  113.9060 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8700   48.9119  114.3210 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.0473   46.7649  116.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.0971   44.5686  113.6790 S   0  0  0  0  0  0  0  0  0  0  0  0
   26.9461   44.5219  123.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.2666   46.5048  123.7830 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.5872   45.8435  122.5810 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.6341   44.2424  122.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.5092   45.6206  121.4600 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.4047   42.9818  121.9490 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.4830   46.3699  123.9480 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8306   45.1480  122.0990 O   0  0  0  0  0  0  0  0  0  0  0  0
   41.6137   41.0090  114.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   43.3944   42.6687  114.6320 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.0165   42.4852  113.9980 C   0  0  0  0  0  0  0  0  0  0  0  0
   40.9273   40.6058  115.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   42.0249   43.0027  112.6340 N   0  0  0  0  0  0  0  0  0  0  0  0
   44.4098   42.7019  113.9280 O   0  0  0  0  0  0  0  0  0  0  0  0
   41.5705   40.6677  116.3820 O   0  0  0  0  0  0  0  0  0  0  0  0
   39.7386   40.2186  115.2600 O   0  5  0  0  0  0  0  0  0  0  0  0
   35.8165   42.5579  122.4130 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.5143   42.6814  121.4850 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.8693   43.3886  121.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
   35.3888   43.5788  120.2040 N   0  0  0  0  0  0  0  0  0  0  0  0
   36.5505   41.7127  121.8990 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.9878   42.4513  122.7810 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7854   39.6244  121.6600 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8478   40.5045  120.8900 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.7522   39.9020  120.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9740   41.7159  120.8600 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9289   38.8019  119.5990 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6645   40.5060  120.1200 O   0  5  0  0  0  0  0  0  0  0  0  0
   23.3514   40.9187  118.5560 H   0  0  0  0  0  0  0  0  0  0  0  0
   24.0056   41.0008  116.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
  2121  1  0  0  0  0
  2122  1  0  0  0  0
101103  1  0  0  0  0
101104  1  0  0  0  0
102103  1  0  0  0  0
103105  1  0  0  0  0
104108  1  0  0  0  0
109111  1  0  0  0  0
110111  1  0  0  0  0
110114  1  0  0  0  0
111112  1  0  0  0  0
115116  1  0  0  0  0
116117  1  0  0  0  0
117120  1  0  0  0  0
  1  2  1  0  0  0  0
 96100  2  0  0  0  0
102106  2  0  0  0  0
104107  2  0  0  0  0
109113  2  0  0  0  0
116118  2  0  0  0  0
117119  2  0  0  0  0
  1  3  2  0  0  0  0
  2  9  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 12 17  1  0  0  0  0
  9 18  1  0  0  0  0
 12 19  2  0  0  0  0
 15 20  1  0  0  0  0
 16 21  1  0  0  0  0
 17 22  1  0  0  0  0
 18 23  1  0  0  0  0
  7 24  1  0  0  0  0
 17 24  2  0  0  0  0
  7 25  2  0  0  0  0
 19 25  1  0  0  0  0
  8 26  2  0  0  0  0
 12 26  1  0  0  0  0
  3 27  1  0  0  0  0
  4 27  1  0  0  0  0
 20 27  1  0  0  0  0
  8 28  1  0  0  0  0
 19 28  1  0  0  0  0
 21 28  1  0  0  0  0
 13 29  1  0  0  0  0
 14 30  1  0  0  0  0
 15 31  1  0  0  0  0
 16 32  1  0  0  0  0
 18 33  2  0  0  0  0
  5 38  1  0  0  0  0
  6 39  1  0  0  0  0
 10 40  1  0  0  0  0
 20 40  1  0  0  0  0
 11 41  1  0  0  0  0
 21 41  1  0  0  0  0
 34 43  2  0  0  0  0
 35 43  1  0  0  0  0
 38 43  1  0  0  0  0
 42 43  1  0  0  0  0
 36 44  2  0  0  0  0
 37 44  1  0  0  0  0
 39 44  1  0  0  0  0
 42 44  1  0  0  0  0
 45 46  1  0  0  0  0
 45 47  1  0  0  0  0
 46 49  1  0  0  0  0
 48 49  1  0  0  0  0
 49 51  1  0  0  0  0
 50 52  2  0  0  0  0
 50 53  1  0  0  0  0
 47 54  1  0  0  0  0
 50 54  1  0  0  0  0
 48 55  2  0  0  0  0
 56 57  1  0  0  0  0
 56 58  1  0  0  0  0
 57 60  1  0  0  0  0
 59 60  1  0  0  0  0
 60 62  1  0  0  0  0
 61 63  2  0  0  0  0
 61 64  1  0  0  0  0
 58 65  1  0  0  0  0
 61 65  1  0  0  0  0
 59 66  2  0  0  0  0
 67 71  1  0  0  0  0
 69 71  1  0  0  0  0
 67 72  1  0  0  0  0
 68 72  2  0  0  0  0
 71 73  1  0  0  0  0
 68 74  1  0  0  0  0
 70 74  1  0  0  0  0
 70 75  2  0  0  0  0
 72 75  1  0  0  0  0
 69 76  2  0  0  0  0
 77 79  1  0  0  0  0
 78 81  1  0  0  0  0
 79 81  1  0  0  0  0
 80 82  1  0  0  0  0
 81 82  1  0  0  0  0
 82 83  1  0  0  0  0
 80 84  2  0  0  0  0
 86 87  1  0  0  0  0
 86 89  1  0  0  0  0
 88 89  1  0  0  0  0
 89 90  1  0  0  0  0
 88 91  2  0  0  0  0
 85 92  1  0  0  0  0
 87 92  1  0  0  0  0
 93 95  1  0  0  0  0
 94 95  1  0  0  0  0
 93 96  1  0  0  0  0
 95 97  1  0  0  0  0
 96 98  1  0  0  0  0
 94 99  2  0  0  0  0
M  END

and here is how I did it, I can actually use Jmol.jar for that, the same I use to display my molfile. But there is a bug in the version I downloaded recently, which is that pdbAddHydrogens true does not have the right effect and the ligands are not shown with the correct bond valences and hydrogens. But I can do it here: https://chemapps.stolaf.edu/jmol/jsmol/simple.htm and then I get good results. I can run this script:
set pdbAddHydrogens true
set defaultLoadFilter 'biomolecule 1'
load "=4nd4"
delete chain=B
delete z<100
set hideNotSelected true
select NAD
select add PYR
select add ILE32
select add D53
select add ASP53
select add SER99
select add ARG109
select add ASN140
select add MET163
select add ARG171
select add HIS195
delete hydrogens
write mol "first.mol"

Now after saving the first versions, then load them with Jmol.jar and show the atom numbers:
load "first.mol"
Spacefill 0.0
wireframe on
label "%i"

open the molfile in a text editor, and correct the NAD+ to NADH by changing 3 bond valences around that ring. When done, load it again check it's right, and add the hydrogens at the apex:
load "first.mol"
compute hydrogens @112
write mol "second.mol"

and finally I am having my own script to normalize the molfile so that the atom numbers correspond to canonical InChI atom numbers. But that's a different matter.
Once I learned this I could have saved hours of staring at the model and trying to remove parts of the molfile manually.


text:
Chemical equilibria - Lab practical
In an experiment to determine the partition coefficient, how would we
assure that the system has reached partition equilibrium?

Recall the definition of chemical equilibrium. The chemical composition becomes "static" when equilibrium is reached i.e., it appears that neither the concentration of the reactants or the products is changing. At a microscopic level the system is dynamic. Apply the same idea to the partition of a substance in phase "A" and "B".
For research purposes, one would analyze liquids (A & B) for the extracted compound as a function of time and note the time when concentration in the two phases becomes constant. This can be easily done by plotting a graph of concentration of the extracted compound in liquid A and B. When both become constant, you have achieved distribution equilibrium.
Now this is not possible in an academic experiment with a limited time. Your teacher may tell you to shake the two liquids in a separatory funnel for a certain time. This implies someone had already done this experiment by the above method and they know that equilibrium is established within 2 mins or 5 min.


text:
What is the name of the physical quantity that is given in kJ/g?
The chemical potential $\mu$ of a pure phase corresponds to the Gibbs free energy $G$ divided by the amount of substance $n$:
$${G\over n} = \mu,$$
so the units of $\mu$ are $\pu{kJ mol^-1}.$
What do we call it when we are using the Gibbs free energy divided by the molecular weight? My units are $\pu{kJ g^-1},$ and I am not sure what's that called in chemistry. Is there a name for it?
Edit that might help: I use these values (of Gibbs free energy over the molecular weight) to calculate the thermodynamic "likelihood" of mineral phases to occur at any given temperature and pressure. It's something that we just learn to do, but I never really understood what it corresponds to.

Could be many things, https://xkcd.com/687/

Well, it's the specific Gibbs free energy of a substance. Off the top of my head, I cannot think of any physical rationale for using such a quantity over the molar Gibbs free energy (which is more fundamental in the sense that moles are just numbers, so it's a natural way to get an intensive quantity). Presumably the molar mass of your compound is constant across phases, so everything ends up being proportional to the molar Gibbs free energy, just in units more conducive to experimental measurement.

@a-cyclohexane-molecule, I think you are right - thanks for that! However, I keep finding contradicting info on this - https://theory.physics.manchester.ac.uk/~judith/stat_therm/node43.html and http://web.gps.caltech.edu/~asimow/glossary.html defend the specific Gibbs energy (SGE) as you mentioned, but for example http://www.rsc.org/suppdata/cy/c2/c2cy20488f/c2cy20488f_2.pdf says the opposite - it says that SGE is given in KJ mol-1. But most places do say that SGE is indeed Gibbs free energy over the mass - (thanks for the tip!) And it is also the partial derivative of the chemical potential.

If anyone knows a good book on thermodynamics relating these concepts, I'd be happy to learn about it!

Do not confuse molecular weight/mass = mass of a molecule with molar mass = mass of 1 mol.  The Gibbs energy divided by the mass of a molecule cannot have unit kJ/g, as you did not divided the energy by the mass in grams. It does not relate to the 1 g of substance, but to mass of 1 molecule, that is not asigned to any mass unit. Unless you considered the G. energy of 1 molecule and divided it by the mass of the molecule in grams.

@Poutnik yes. I calculate the Gibbs free energy (G) of the phase and divide it by the molecular weight. That's KJ/ g. I shouldn't have said mass previously, I meant molecular weight (not a chemist here!). Do you know a good book of reference for this thematic?

So you do mean molecular weight and not molar weight, right ? It is not about weight vs mass ( the latter is more correct ), but molecular ( related to a molecule ) versus molar ( related to a mole ). if you divide G of 1 molecule in kJ by the mass of a molecule in g, you get the specific gibbs energy in kJ/g. // Great integrating source explaning terms used in chemistry is not surprisingly Wikipedia. More primary and authoritative source is IUPAC Gold Book- Compendium of Chemical Terminology


text:
How does high voltage on the electrodes ionize a gas?
I was studying cathode ray experiment and there the electrons were obtained by ionisation of the gas inthe tube by the high voltage on the electrodes. So how does this happen?

Search for Townsend avalanche and Paschen curve.

There is always a small amount of ions and electrons in gases due omnipresent radiation ( cosmic radiation and radioactive decays.  Depending of scenario, there is possible an electron injection by thermo-emission ( heated cathodes ) or by pin-point electrode geometry ( various DIY ozone or light negative ion generators ).
When voltage is applied on the tube electrodes, ions/electrons are accelerated and collisions create other ions. At normal pressure, the path between collisions is too short (mean free flight path for air molecules is typically 70 nm), so enormous potential gradient is needed for high enough collision energy.
Low pressure allows longer acceleration paths along higher potential difference, leading to higher collision energy. Finally there is established equilibrium between ionization and ion recombination, including hitting the electrodes.

@Poutnik, Is there a solid reference which states that ionization only occurs because of the omnipresent cosmic background radiation. If we shield the cathode ray tube, will ionization not occur?

@M.Farooq It is not limited to CBR, but radioactive decays, mostly 222Rn - typically 50-x00 Bq/m3 of air , or 50 Bq/L water, then 226Ra in buildings, 14C + K40 in living bodies. Not that sensitive detectors are built more than 200m below surface because of highly energetic and penetrating cosmic radiation. Note that top ever detectedenergy of a flying proton is energy of a flying baseball - about 50 J. another contribution can be static electricity and water evaporation.

@ Poutnik, Sorry, I was not clear. I understand the background radiation concept. I was specifically asking about the initiation step of a highly evacuated gas discharge tube. Does the discharge in the gas tube start because of background radiation in a CRT?

@M.Farooq No, it is rather sufficient yet not essential initial condition. Without external voltage there is no discharge. :-) // In CRT specifically, there is cathode thermo-emission, the same as in a vacuum diode.

This is what I was wondering that a cosmic event may not be a necessary condition.

@M.Farooq I have focused my answer to cold cathode CR experiments with involved low pressure gas ionization, what is different to hot cathode high vacuum CRT used in CRT TVs/monitors with thermally emitted electrons.

@M.Farooq, in addition to thermal emission or cosmic rays, seed electrons can also be produced by photons or - perhaps more interesting - by field emission of electrons (Fowler-Nordheim emission). The latter is a neat QM effect in which a strong electric field modifies the potential of an electron in the lattice, allowing the electron to tunnel out. This was one of the first applications of wave mechanics.


text:
CH3I + NaCl in acetone gives
How will methyl iodide react with $\ce{NaCl}$ in acetone?
According to me $S_N2$ reaction will take place where iodine will be replaced by chlorine and we will get $\ce{CH3Cl}$. Can anyone suggest why am I wrong and what will be the actual reaction?

Welcome to the site. Note, chemical information may be advantageously formatted using on ChemSE with mhchem. Take moment to familiarize with this. You are encouraged to use it in the body of questions, answers, and comments. Because it is something special not all web browsers understand well, do not use it in the title of questions or answers.  In addition, the English language does not capitalize chemical names (including elements).  Stereochemical descriptors (like E, Z; P, M; R, S) are a different story, though.

There will be no reaction
The solubility of NaCl in acetone is 0.42mg per kilogram of acetone (source Wikipedia here). This means that there is insufficient NaCl in solution for any reaction to occur.


text:
Why is sulphur not written as S8 here
I learnt that sulfur dioxide and hydrogen sulphide react to form sulfur and water.
The reaction given was:
$\ce{SO2 + 2 H2S -> 2 H2O + 3S}$
So why is the product sulfur written as $\ce{S}$ and not as $\ce{S8}$?

Welcome to the site. Note, chemical information may be advantageously formatted using on ChemSE with mhchem. Take moment to familiarize with this. You are encouraged to use it in the body of questions, answers, and comments. Because it is something special not all web browsers understand well, do not use it in the title of questions or answers.

It also forms polythionic acid . Used to conduct stress corrosion tests on sensitized stainless steels .  Sometimes called " Wachenroter ?" or "Samans" solution.

Because you don't really need to identify the sulfur as eight-atom molecules. The empirical formula $\ce{S}$ is sufficient for rendering chemical reactions and avoids encumbering the reaction with rather large coefficients on the other species ($\ce{8 SO2 + 16 H2S}$ vs $\ce{SO2 +  2 H2S}$).

OP: An analogue is H3O+, as it can exist in different hydrated form.

The focus of the reaction equation
$$\ce{SO2 + 2 H2S -> 2 H2O + 3S}$$
is to balance the number of atoms on the left hand side (starting materials) with those on the right hand side (the products).  It eventually depends on the reaction conditions (e.g., pressure and temperature) if sulfur will form the famous $\ce{S8}$ cycles, or rings larger/smaller than that (cf. e.g., with wikipedia's entry about the allotropes of sulfur).  For balancing the reaction (i.e., stoichiometry), this subsequent formation of these rings is not relevant.
Small note: chemists prefer the writing sulfur.

Pure modifications of sulfur are only rarely accessible. It's basically always a wild mixture.


text:
Methods of mix thick liquids (3D printer Resin), stir, shake or acoustic?
Most of the 3D printing community mixes resins by hand by simply shaking them.
This is not 100% effective (I believe) and also creates a lot of bubbles that get in the prints.
What method would you recommend?
I have tried stirring or rather rolling the 1-liter bottle for 10 minutes to let it stir.
Also, I read a little about Ultrasonic Homogenizers but I only have an ultrasonic cleaning machine. Is that strong enough to excite the two main compounds in the resin or should I use something stronger?
Thank you!

What is common practice when handling epoxy resin or PDMS is to stir it with a spatula or the like for several minutes and then to degas it with a void pump (https://www.youtube.com/watch?v=SHXuC1lIGj4). This kind of things sells as kits for one or two hundred €/$ and are just the perfect way for it. Shaking might require less time but surely produces more bubbles than stirring. By stirring gently but thoroughly, you can actually reach perfect mixing without introducing to much bubbles... I do not know acoustical stirring but it mights generate bubble as well through cavitation...

You might put in some glass marbles to improve agitation and roll on a rock-tumbler or similar device. Fill to the very top to avoid introducing bubbles. Rock tumblers are available for as low as US$30, or make one from LEGOs. For a thicker the liquid, use slower rotation.

Little viscous liquids are better to be shaken, viscous liquids are better to be stirred. Shaking of e.g. honey with a thick starch sol would not be particularly helpful.


text:
How to safely ship 5 litre container of liquid chemicals into glove box?
I need to transfer a 5 litre container of oxygen sensitive liquid chemicals within an inert atmosphere to smaller 100ml bottles. I'm going to do so using a vacuum glove box purged with nitrogen. I have very little experience using a glove box but as far as I understand, you'd first pull a vacuum for the main chamber a few times to remove any oxygen, moisture and contaminants, then purge it with nitrogen. Afterwards place the item you wish to bring into the glove box inside the antechamber, pull a vacuum within the antechamber a few times like before then purge with nitrogen to meet the same kind of atmosphere as the main chamber, then open the antechamber latch within the main chamber to bring in your item. Proceed with the operation.
The obvious issue here is a vacuum would boil the liquid chemicals if not effectively sealed. But the whole point of this operation is to only open the 5 litre container once inside an inert atmosphere, but I can't bring it into that atmosphere without risking the safety hazard of placing it under a vacuum prior to purging. The only idea I have is to simply not run a vacuum for the antechamber and just purge it with nitrogen, but of course would defeat the purpose of working in an effective inert atmosphere. The state of the unopened container is sealed with a standard commercial heat induction sealed liner like you'd find for unopened liquid medicines, and with a child safe cap.
Any recommendations to how I can ship this safely into the glove box?

One would hope the bottle is effectively sealed or your chemical is toast already…

Why do you want to do that in a glove box? I give you 10:1 this a bad, bad idea. Use your Schlenk line. Especially if you have little experience with glove boxes: don't use them if at all avoidable.

The same concern expressed by Karl is valid for a Schlenk line, if the operator has no idea of it. Another point: normal glove box don't require vacuum cycle, they are leaking, etc. The vacuum is necessary to purge the antechamber. I think you should give us more details. Nature and purpose of the liquid. It is possible that you can do that in open air or that you simply insert the big one. Actually the atmospheric P does nothing to liquid inside (otherwise it won't be sealed).

No normal bottle that is sufficient to contain an air sensitive chemical will explode under vacuum. An the lid should be sufficient to hold the content it too. Also, most such bottles are designed to make it easy to get the content out while retaining protection from air (eg by having a rubber seal which can allow transfer of a measured amount by syringe). Take advice from experienced chemists who use these techniques routinely.

Check if there is no better way (e.g., cannulation on a Schlenk line), especially if the solvent of your solution is flammable.  If you know the density of the solution (even an approximate value), you may infer the volume transferred by monitoring the mass of the smaller flasks empty vs. flask filled.
As an example, the steal barrels of predried solvents on a solvent system (like this) are equally put on a (e.g., bathroom) balance to check how much these still contain.

If it still has to be the glovebox, check with the responsible for the glovebox if the bottle still is small enough to be carried safely on the lock's table.  Equally consider the weight of such a flask, the table might not slide as easy as for a small $\pu{100 mL}$ flask on the tray.  If the flask is stuck or (beware) tipping, the constraint access of the lock from inside of the chamber may be a source of trouble.
If possible, let him/her transfer the bottle for you (especially at this scale).  Check if the containers (both the one for $\pu{5 L}$ as well as the subsequently to be used to $\pu{100 mL}$ each) are in good mechanical condition.  Be fine if he/she refuses this operation.

I can't make head or tail of the first and last paragraph in the text you quote. And the procedure in the second will not dry a liquid. Probably OK for chemistry that requires very modest inert conditions, but why use a glove box in the first place then?

That procedure in the third paragraph is hillarious. It will reduce the oxygen content in the antechamber by 45%.

Re first paragraph: Transfer of a clean, small pristine bottle (say $\pu{100 mL}$ dry toluene), septum never pierced, may be acceptable. The turn of the screw cap mainly is mechanical convenience; it helps a bit to access the septum if the screw cap was turned a little (to break its connection with the lower ring) when the bottle still was outside the box compared to doing all with the bottle in the box across the gauntlets and gloves. But this brief turn is just before adding the flask to the tray and closing the lock.

Paragraph two and three are more about «bring your own round bottom flask to the glovebox» which may be okayish; apparently (aka group policy), there are groups who permit these with liquids already inside the round bottom flask. (The purge with nitrogen ahead of the transfer into the box reminds a bit to degassing solvents for the HPLC in the ultrasound bath; with no drying effect [i.e., it may rather saturate the solvent with water vapour]). Overall (anticipated scale, demand of dexterity/equipment/time, ease of accessing the bottles), cannulation on a Schlenk line were my preference here.

I meant that "evacuate just a tiny bit, but do that 30 times". That's just pointless, at the brink of cargo cult. I recommend removing the text and link. What they teach is simply bad laboratory practice, and it's very unclearly written.

@Karl Given the oil pump on the floor, it will be easy to mistake $\pu{-15 mmHg}$ relative pressure (against atmospheric pressure) with $\pu{15 mmHg}$ (and well less) absolute pressure, too.  This and your argument are convinced me for an edit.