text:
What's the difference between ΔG° and ΔG°'?
In biochemistry contexts, one often sees $\Delta G^{\circ\prime}$ ("delta G naught prime"), rather than the normal standard free energy change $\Delta G^{\circ}$ ("delta G naught").
What's the difference between the two quantities?
Is there a formal definition of the two terms?

Can you give us a quote in context, perhaps from one of the books in which you've seen it? That would help in getting an answer, I think.

I don't think it is a useful question for the simple reason similar notation nuances appears in all kinds of texts with wide variety of meaning.

The prime usually denotes a standard free energy that corresponds to an apparent equilibrium constant where the concentration (or activity) of one or more constituents is held constant.
For example, for $\ce{HA <=>A- + H+}$ the equilibrium constant is $K=\frac{[\ce{A-}][\ce{H+}]}{[\ce{HA}]}$ and the corresponding standard free energy change is $\Delta G^\circ=-RT \ln(K)$. If you know the value of $K$ and the start concentration of $\ce{HA}$ then you can compute the equilibrium concentrations of $\ce{HA}$, $\ce{A-}$, and $\ce{H+}$.
However, if the pH is held constant then $[\ce{H+}]$ is no longer a free variable and the apparent equilibrium constant is $K'=\frac{[\ce{A-}]}{[\ce{HA}]}$ and the corresponding standard free energy change is $\Delta G'^\circ=-RT \ln(K')$. So $\Delta G'^\circ=-RT \ln(K/[\ce{H+}])=\Delta G^\circ+RT\ln[\ce{H+}]$
In biochemistry there is often several important constituents in addition to  $\ce{H+}$ that are held constant such as $\ce{Mg++}$, phosphate, etc.

If you could list the constituents in biochemistry which are normally considered to have constant (unit) activity, that would improve the answer.

Is there a formal definition of the two terms?

One form of the fundamental equation of thermodynamics is:
$$dU = TdS - P dV + \sum_{i}\mu_i dN_i$$
In this equation, the total internal energy has canonical variables $V$, $S$, and $dN_i$, where $S$ is the total entropy (in units of $\frac{\mathrm J}{\mathrm K}$), $V$ is the total volume, and $N_i$ is the number of moles of each molecular species present.  $T$ is temperature; $P$ is pressure, and $\mu_i$ is the chemical potential of species $i$.  The equation implies that if we were to know an equation that gave $U$ as a function of $S$, $V$, and all the $N_i$ we would know everything about the system.  However, this is inconvenient for two reasons.  First, $S$ and $V$ are extensive variables.  Make the system bigger without changing its composition, and $S$ and $V$ increase.  Second and more importantly, it is often difficult to hold $S$ constant when doing experiments.  The same is true of $V$.  (We live in a constant pressure atmosphere.)
Taking the Legendre transform of $U$ with respect to variables $S$ and $V$ gives a new fundamental equation:
$$dG = -S dT  + V dP + \sum_{i}\mu_i dN_i$$
This equation means that if we knew a function that gave the Gibbs free energy as a function of $T$, $P$, and all the $N_i$, we could easily compute all thermodynamic properties of the system.
Say we're interested in the thermodynamics of ATP hydrolysis:
$\ce{ATP + H2O <=> ADP + Pi}$
This equation is really better written as
$\ce{A-P3O10H3 + H2O -> A-P2O7H2 + H3PO4}$
But of course in a buffer at pH 7, the conditions where many biochemical reactions occur, there really won't be $\ce{H3PO4}$ etc., there will be dissociation of protons $\ce{H+}$ and formation of anions like $\ce{H2PO4-}$ etc.  So now all those reactions will have to be tracked too. The number of protons released by ATP is not the same as released by inorganic phosphate, and this is generally true.  During a reaction, it is difficult to hold the number $N_{\ce{H+}}$ of protons constant, but through judicious choice of buffers etc. it is possible to hold the chemical potential of protons constant (i.e. do experiments at constant pH). Under such conditions, it makes sense to continue the Legendre transformations one step further:
$$dG^\prime = -S dT + V dP - N_{\ce{H+}} d\mu_{\ce{H+}} + \sum_{i \neq \ce{H+}}\mu_i dN_i$$
$\Delta G^{\circ \prime}$ is a Legendre transform of $\Delta G^{\circ}$ with respect to the number of protons in the system.
Robert Alberty's paper from 1994 is a good place for further reading.

If I could accept two answers, I'd also accept yours for the Alberty reference, in particular as he apparently was the head of the IUPAC-IUBMB (International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology) panel on Biochemical Thermodynamics nomenclature (official panel recommendations), which also has a discussion of the issue.

@Curt F. I really like your answer since it takes into account of the Legendre transformation. Could you please elaborate on the intuition or motivation behind using such a transformation? Thanks for your answer.

The biochemistry convention does not assume all solutions are 1 M. If you did this then you would have [H+] = 1 M. This simply never happens in biochemical reactions. Instead, we assume pH = 7. We also assume that water has an activity of 1 even though its concentration is 55 M.

The use of $\Delta G^\circ$ does not assume that all solutions are 1 M.  It assumes that the standard state is 1 M ideal solution.  Also, activity is always defined as $\gamma [X]/[X]^\circ$ which is always 1 for pure substances.

Delta G naught means that the reaction is under standard conditions (25 celsius, 1 M concentraion of all reactants, and 1 atm pressure). Delta G naught prime means that the pH is 7 (physiologic conditions) everything else is the same. The concentration of [H+] now isn't 1 molar because 1 molar concentration would be an extremely low pH (0). Delta G naught prime is just like Delta G naught but for biology.

The prime has nothing to do with whether a concentration is held constant. The prime is used to indicate that some species, typically protons or ions such as Mg, are being set to a value other than the standard 1M concentration for use in a reference free energy. Although the prime has been adopted by some in the biochemical community and was endorsed in 1994 by IUPAC, the prime is not used in other communities for good reason - it is much better to explicitly state what concentrations are being used for the reference free energy. When using a reference free energy other than the standard free energy, concentrations can vary or be held fixed. In most biochemical situations, it is useful to keep the pH fixed since buffers are used. But this is a separate issue.

The key difference between ΔG° and ΔG°' is the concentration of protons, or [H+], in the solution. ΔG° is the standard Gibbs free energy change, which is measured under standard conditions, which include a temperature of 298 K, a pressure of 1 atm, and all reactants and products at a concentration of 1 M. ΔG°', on the other hand, is the standard Gibbs free energy change under physiological conditions, which means that the pH of the solution is 7.


text:
why does milk of magnesia have an expiration date?
I noticed an old bottle of milk of magnesia in my refrigerator and saw that it had an expiration date printed: January 2015.  Checking the ingredients, I saw only three: magnesium hydroxide, purified water, sodium hypochlorite.  I understand that milk of magnesia is more or less a mineral solution.  How could this require an expiration date?  What would be the consequences of taking milk of magnesia past the expiration date?
(I see that this page discusses expiry dates on chemicals in the abstract; I don't know which of these arguments apply to milk of magnesia in particular, or any other over-the-counter dietary supplement or drug.  As an IT professional, I have absolutely no experience or expertise in the physical or life sciences.)

Has nothing to do with chemistry: Laws in many countries require almost anything sold as edible to have an expiry date. Even white sugar.

While I agree in general with @KarlRatzsch, there is the issue in that the efficacy of a product (as determined by the manufacturer, in accordance with some guidelines - such as antacid strength as in the present case) cannot be guaranteed past a certain date. These factors will depend on things like humidity, temperature, whether or not you've left the cap on tightly, and other variables.

And you are saying that white sugar does not spoil?  That's new information to me... what, then, does spoil?  Only fats and proteins?  Or do complex carbohydrates (such as those found in flour) also not spoil?

Hm. Of course you can store even sugar in a way that it "spoils". But if you keep it reasonably dry, it will be good in fifty or fivehundred years. Flour will keep good as long, if it is kept so dry that the proteins in it can't get to work.

And as for the magnesia milk: It will keep good as long as there is enough hypochlorite in it to kill off anything that tries to live in there. Keep the lid tightly on and that is forever. If you trust that lid. ;-)

Milk of magnesia is not a solution, but a suspension. Over time, the suspension may segregate; also, the solid phase (being slightly soluble) may recrystallize into larger grains. This is yet another possible reason for the product to have an expiration date. On a side note, once I was surprised to see the expiration date on table salt (NaCl). Can someone think of a chemical reason behind it?

I had seen expiry date on calcium carbonate tablets as well. But I generally don't care about it.

@KarlRatzsch You did indirectly answer the question already, why not copy-edit it into an answer and liberate the comments section?

@ Ivan Neretin Same here, and no, I don't. Cannot, because there isn't.

Why, actually there is. In my country, table salt is mostly iodised, and it may lose iodine, so...

Guys, even alcohol has expiration data. Don't hang up on law.

It won't, unless you leave it in the sunlight, and you could even then still eat it without any foreseeable problem.

@Greg  Liquor has no expiration date, and neither has wine (although it should). For beer see my answer below.

Of course the salt would remain good. It's just that it says "iodised" on the pack, and it will no longer be true, and the manufacturer doesn't want to get sued over that tiny detail.

@KarlRatzsch It was confusing: I was talking about lab alcohol. It is not for human consumption - on the other hand it really doesn't have anything to get spoiled in any sense.

@Greg Lab solvents with an expiry date? Alcohol can get spoiled, google "isopropanole peroxide", but that is up to the user, not time.

@KarlRatzsch It may depend on country, but I have seen expiry date for lab alcohol as well as pharmaceutical alcohol. And I was talking about ethyl-alcohol.

Let's can this here, but pharmaceutical ethanol legally is both a drug and a beverage. Same for pure, non-denaturised ethanol. You even pay liquor taxes on it. But the ordinary, methylated lab-rotgut?

generally organic molecules require this expiry date. Simple inorganic salts, mostly, dont need expiry.

Wouldn't another consideration be that the plastic container in which the liquid is contained is not inert and can over time contaminate the medicine?

Many countries require anything marketed as edible to have an expiry date. You can speculate about what might spoil your Magnesia (see comments above), but likely it will be good four or fourty times as long as indicated.
Of course the lid might not be perfectly tight, and it could dry up or get contaminated by bacteria, but this can happen anytime. And certainly after some time it will separate into clear water and a thick suspension of magnesia particles and you'll have to shake or stir it very thoroughly before consummation.
Anyway these expiry dates are 99% baloney. Very few things really get bad before you see the mould grow on them.
Fun fact and (german) exemption to that rule: After six months at the latest, the taste of beer (the non-pasteurised stuff) starts to deteriorate. Yet, according to the date on the bottle, you have 12 more weeks to drink the remainder of that crate with increasing disgust before it "expires".

Expiry dates also helps companies avoid getting sued by someone who felt unresistable desire to consume something obviously spoiled. No one wants to be responsible to some 50 years old table salt.

Even in the US at least higher courts still believe in the concept of responsible adults and educated consumers. You don't actually get those millions for dryfrying your cat in the microwave. ;-)

I wasn't speaking about US exclusively. Or you meant the US is a unique exception? Anyway, I think we can agree on that companies have tendencies to extremely undershoot realistic expiry dates, often 1-2 order of magnitude. Doing so makes no significant cost to them: no one wants sell 50 years old SPAM in their shop, and most accounting system write such down as loss.  Trashing old, unsold stocks is actually cheaper than keeping them around. Making our costumers trashing their old stock is not a cost for the company neither. On the other hand, if anything happens, they can loose a lot.

If you actually tried to sell 50 year old spam, you'll be liable for your customers upturned stomachs, with or without an expiry date on the can. If a stupid customer finds it in his basement in 2045, it will make no difference either.

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sort: votes


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Cinnamaldehyde -> trans-3-phenylprop-2-enal
When was the name cinnamaldehyde officially changed to trans-3-phenylprop-2-enal?

You can call it as you wish. Also there were lots of nomenclature changes

Wouldn't it be generally when IUPAC nomenclature was introduced and adopted ?

The rules for systematic nomenclature in organic chemistry have changed several times. They were first issued in Geneva in 1892, followed by the Liége Rules in 1930. The IUPAC rules were issued in 1957 (Sections A and B), 1969 (Sections A, B, and C), and 1979 (Sections A, B, C, D, E, F, and H). The rules were revised in the 1993 Guide to IUPAC Nomenclature of Organic Compounds and amended by official publications from 1993 through 2002. The current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book) was published in December 2013.
According to the current IUPAC recommendations, the preferred IUPAC name (PIN) of cinnamaldehyde is (2E)-3-phenylprop-2-enal.

However, many compounds can have two or more systematic names in accordance with several methods recommended by IUPAC. Other names (that are not preferred IUPAC names but that are generated in accordance with IUPAC recommendations) may be used in general nomenclature. In addition, various traditional names are retained for use in IUPAC nomenclature, though the number of retained names has been reduced with each succeeding edition of the IUPAC recommendations.
According to the following subsections of the current IUPAC recommendations, the traditional name cinnamaldehyde may still be used in general nomenclature.

P-65.1.1.2 Retained names only for general nomenclature
(…)
P-65.1.1.2.2 The following names are retained for general nomenclature with
functionalization but no substitution is allowed. (…)
(…)
cinnamic acid
(…)

P-66.6.1.2 Names of aldehydes derived from retained names of carboxylic acids
Names of aldehydes derived from retained names are formed by changing the ‘ic acid’ or ‘oic acid’ ending of the retained names of carboxylic acids to ‘aldehyde’. (…)
(…)
P-66.6.1.2.3 Aldehydes derived from retained acid names given in P-65.1.1.2 are only used in general nomenclature; no substitution is allowed. Preferred IUPAC names are systematic names (…).

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Basis for the hydrophobic effect?
I'm confused about why hydrophobic molecules, which do not have high polarity, would have a tendency to attract and cluster with themselves. It is easier to understand the hydrophilic as long as one believes that positive charges attract negative charges. Anyone have any insights?

related: http://chemistry.stackexchange.com/questions/26544/how-do-transmembrane-protein-alpha-helixes-bind-to-the-membrane

The driving force behind the hydrophobic effect is entropy. Suppose I put several hydrophobic molecules in water. These molecules have two choices. (1) The molecules can stay separate from each other and randomly move around in solution. (2) They can group together and form a cluster. It turns out that it is entropically favorable to cluster. The reason is that it takes more water to individually solvate the separate molecules. It takes less water to solvate a cluster of the molecules. When water solvates these molecules, it is ordering itself. In fact, it is believed that water forms cages around hydrophobic molecules in solution. Therefore, if the molecules cluster, less water will have to order itself. Less ordering means greater entropy (randomness).
It also true that London dispersion forces will occur in these clusters. However, this is not the driving force for the hydrophobic effect. The driving force is entropy.

There are other intermolecular forces besides dipole-dipole forces (which is what polar molecules primarily use) that allow molecules to come together. For nonpolar molecules, they use dispersion (London) forces. Dispersion forces come from random movements of electrons which cause temporary dipoles. Due to the large amount of electrons in the molecules, lots of these temporary dipoles exist at all times, keeping the molecules together.


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Probablity distribution of bend angle in gromacs
In an analysis I got the probability distribution of a bend angle $P(\theta)$ with respect to time. However, I need to plot $P(\theta)$ with respect to $1- \cos(\theta)$ where $\theta$ refers to the bend angle in B-DNA.
Is there any command or procedure employed for it in GROMACS?

Why won't you export data to do it externally?


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Structure of Buckminsterfullerene
In several pictures that I have seen of buckminsterfullerene and graphite (such as below), each carbon is bonded to only 3 other carbons, so it only forms 3 covalent bonds.

I asked my teacher about this and he says that each carbon only make 3 bonds and has a lone pair. These lone pairs are de-localised hence, that is why buckminsterfullerene is able to conduct electricity.
However, I am doubtful about this as how can a lone pair on an atom be de-localised. Would the electrons be in their orbitals, and not be able to freely move around the compound. I try searching the internet for any information, but there is no mention on how many bonds each carbon atoms makes.
I am guessing that there is alternating double bonds between each carbon so that each carbon has 4 bonds. It is these pi bonds which along the compound that makes it a  hyper-conjugated compound. This would explain why buckminsterfullerene and graphite are able to conduct electricity. Am I correct?

Have you ever seen a picture of graphite, to begin with? It shares the same feature, i.e., that each carbon is bonded to exactly 3 other carbons. You may call it "alternating double bonds", but this is not quite correct either, because in fact all bonds are equal. Think of it as a resonance structure, much like benzene. This is the reason for graphite conductivity, too.
The idea about that lone pair is plain wrong. Carbon has but 4 valence electrons; once 3 of them are spent for sigma bonds, how could it have a lone pair?
Pure buckminsterfullerene does not conduct electricity (strictly speaking, it is a semiconductor, not a conductor like any metal). Some of its derivatives do, but that's another story.

Thanks. So, if graphite and buckminsterfullerene both have the same structure, why is only graphite able to conduct electricity, but not buckminsterfullerene?

Because they don't have the same structure. Look again at that picture of graphite. Look at them layers, they are infinite. It's a huge system of conjugated pi bonds, from one end to another. That's what conducts electricity. With fullerene, it's just a system of such bonds within one molecule. Supposedly it could conduct electricity from one side of molecule to another, but that's about it.

Fun fact: Graphite (at least an ideally layered) is only a conductor in two dimensions.

Yes, of course. And nanotubes (at least some of them) are 1D conductors.

Fun fact: Calculations gave me alternating single and double bonds along the six-membered rings and the five-membered rings of fullerene were exclusively single-bonds.

True, the bonds in fullerene (unlike graphite) are not equal, and the so-called 6/6 bonds (those which are shared between two hexagons) have more of the "double" character, while the 5/6 bonds are more like "single". Still, it's a conjugated $\pi$ system all over. Think of butadiene: its central bond is kinda "single", but it's quite different from the true single bond in butane.

Fun fact. Fullerene is called a zero- dimensional compound


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Flow cup viscometer vs rotational viscometer: limitations and use cases for each
What are the limitations of an inexpensive flow cup viscometer (or any other manual test viscometer) when compared to an expensive digital rotational viscometer?


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Resources for learning Chemistry
Based on various other Stack exchange site (Mandarin Chinese, Russian and German), we adapt this project here for chemistry, since it's a great idea to have all kinds of resources in one place.
This is a specifically created Community Wiki which gathers resources for learning Chemistry. The lists are a community maintained project, hence everybody with more than 100 reputation points can contribute edits to the appropriate sections. If you feel something is missing, just fill it in. To avoid multiple answers for similar branches, we decided on a general outline, which is locked, i.e. no new answers can be added.
If you have concerns or questions, you can discuss this list on its parent meta post. If they are of a more general concern, you can also post a new question on chemistry.meta.se. This procedure is used, so the comment section here does not become too overcrowded. If you do choose the second option, please leave the link to it in the comments to this post.
Organization

Answers have a type of resource each.
If possible, state whether the material is directed towards a beginner, intermediate or an advanced audience.
Do not include links that lead to illegal content or sites that host such content. If you see any, please flag for moderator attention and choose "other" so you can point us to the content. We'll delete it as soon as we see the flag. (You can of course also delete it yourself. If you do, please flag it anyway, so that we are aware of it. In this case it is crucial you fill in the edit summary with something like: Removed link to illegal content.)
Both free and commercial resources are allowed, but make sure to include a note if they are the latter. Remember the rules about self-promotion. Include also if registration is required.
Include links to the sites only, don't post images, they would take too much space.
Add the resources in alphabetical order so they're easier to find.
For the resources, a short summary is very much appreciated.

If you have questions about these guidelines, please head to meta to make yourself heard. The above points are not set in stone and might change in the future.
Alphabetical Index

(Text)Books: All books that teach you chemistry with theory and exercises. The subcategories are:

General Chemistry
Inorganic, Organic and Physical Chemistry
Analytical Chemistry, Biochemistry and Chemical Biology, Chemical Engineering, Computational and Quantum Chemistry, Theoretical Chemistry
You can add any subcategory to this post if it is missing.

Online courses and Websites: Free or paid services online that teach you chemistry through lessons as well as sites that give help for learning chemistry. They give material, tips, hints, and various help for self-learners or regular students.
Software: This can be any software ranging from plugins for the browser over mobile apps up to standalone applications for the computer. Pure 2D or 3D visualization programs as well as quantum chemistry programs might not fit in this category, as they are not primarily focused on teaching chemistry.
Video Resources & TV: Video resources which help learning chemistry.
References about Nomenclature: Successful communication requires an agreed set of definitions compiled as nomenclature. An example for such compilations are IUPAC's Color Books, named by the color of their book cover.

Currently those are all categories. If you think, that a new one should be added, please submit an answer in the corresponding meta thread. (A comment is probably not sufficient, as it does "bump" the question on the active tab.

Official chat room for this thread: http://chat.stackexchange.com/rooms/29685/discussion-about-resources-for-learning-chemistry (Ping a moderator in [chat] if frozen.)

Books about Inorganic Chemistry

General texts

Housecroft, C. E.; Sharpe, A. G. Inorganic Chemistry, 4th ed.; Prentice Hall: Upper Saddle River, NJ, 2012.

Weller, M.; Overton, T.; Rourke, J.; Armstrong, F. Inorganic Chemistry, 6th ed; Oxford UP: Oxford, U.K., 2014.
This is the latest version of the textbook commonly known as Shriver & Atkins.

Miessler, G. L.; Fischer, P. J.; Tarr, D. A. Inorganic Chemistry, 5th ed.; Prentice Hall: Upper Saddle River, NJ, 2014.
A relatively shorter text, but explains chemical bonding extremely well.

Ghosh, A.; Berg, S. Arrow Pushing in Inorganic Chemistry: A Logical Approach to the Chemistry
of the Main-Group Elements, 1st ed.; Wiley: Hoboken, NJ, 2014.
A mechanistic approach to reactions in inorganic chemistry with emphasis on the mechanisms.

Lee, J. D. Concise Inorganic Chemistry, 5th ed; Wiley: Hoboken, NJ, 1999.
A classic introductory inorganic chemistry textbook.

Bauer, G Handbook of Preparative Inorganic Chemistry, 2nd ed; Academic Press: New York, 1963
A two volume compendium about small-scale syntheses of elements, maingroup and transition element inorganic compounds.

Books about Organic Chemistry

General texts

Carey, F. A.; Sundberg, R. J. Advanced Organic Chemistry, Part A: Structure and Mechanisms, 5th ed.; Springer: New York, 2007.
Carey, F. A.; Sundberg, R. J. Advanced Organic Chemistry, Part B: Reactions and Synthesis, 5th ed.; Springer: New York, 2007.
Carey & Sundberg is a classic two-volume text with an extremely in-depth discussion. Mechanisms are elucidated in great detail (primarily via MO theory, with results from both ab initio and semi-empirical methods), and the exposition of pericyclic reactions is notably excellent. It also contains a great deal of illuminating content on conformational analysis. Definitely not appropriate for a first textbook, but essential reading for advanced undergraduates and above.
Carey, F. A.; Giuliano, R. M. Organic Chemistry, 9th ed.; McGraw-Hill: New York, NY, 2014.
Clayden, J.; Greeves, N.; Warren, S. Organic Chemistry, 2nd ed.; Oxford UP: Oxford, U.K., 2012.
Excellent first textbook for organic with lucid explanations. It's worth noting that the first edition, while slightly more verbose, contains more information than the second, where some chapters and sections were cut.
Smith, M. B. March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 7th ed.; Wiley: Hoboken, NJ, 2013.
A comprehensive book that covers nearly every reaction under the sun, with appropriate references to primary literature. Arguably best used as a reference and not as study material, but it is also surprisingly readable.
Solomons, T. W. Graham; Fryhle, C. B.; Organic Chemistry, 10th ed.; Wiley: Hoboken, NJ, 2011.
Introductory textbook for organic chemistry.
Wade, L. G. Organic Chemistry, 8th ed.; Pearson Education: Glenview, IL, 2013.
A systematic introductory textbook for organic chemistry. Follows the traditional functional group approach.

Organic synthesis

Warren, S.; Wyatt, P. Organic Synthesis: The Disconnection Approach, 2nd ed.; Wiley: Chichester, U.K., 2008.
A step-by-step introduction to organic retrosynthetic analysis and the construction of different relations between functional groups. Do also get the accompanying workbook (the solutions are discussed immediately after problems).
Kürti, L.; Czakó, B. Strategic Applications of Named Reactions in Organic Synthesis; Elsevier: Amsterdam, 2005.
An incredible compilation of 250 named reactions, with discussion of mechanisms and examples of application to total synthesis. Nearly 10,000 references to primary literature.
Mundy, B. P.; Ellerd, M. G.; Favaloro, F. G., Jr. Name Reactions and Reagents in Organic Synthesis, 2nd ed.; Wiley: Hoboken, NJ, 2005.
A reference book for numerous reaction mechanisms and common reagents.
Nicolaou, K. C.; Sorensen, E. J. Classics in Total Synthesis; Wiley: Weinheim, Germany, 1996.
Thorough discussion of the retrosynthesis and forward synthesis of 36 molecules, by one of the most well-known synthetic chemists of recent years and (at the time) his Ph.D. student. Examples are taken from almost the entire history of organic synthesis: from Woodward's 1954 synthesis of strychnine to the author's own 1995 synthesis of brevetoxin B. Also check out the sequels, Classics in Total Synthesis II and Classics in Total Synthesis III.
Wuts, P. G. M. Greene's Protective Groups in Organic Synthesis, 5th ed.; Wiley: Hoboken, NJ, 2014.
Comprehensive listing of protecting groups, protection and deprotection conditions with references to primary literature, and handy reactivity charts which assess the stability of protecting groups towards various reagents and conditions.
Zubrick, James W. The Organic Chem Lab Survival Manual: A Student's Guide to Techniques; Wiley: Hoboken, NJ, 2019.  This primer introduces students to basic equipment and techniques in the organic lab. Topics considered include literature search, general safety, microscale operation, product isolation / purification / characterization (e.g., melting point, IR and NMR), and record keeping.

Spectroscopy

Pavia, D. L.; Lampman, G. M.; Kriz, G. S.; Vyvyan, J. A. Introduction to Spectroscopy, 5th ed.; Cengage Learning: Stamford, CT, 2015.
Excellent introductory text with good coverage of all the typical structure determination techniques: elemental analysis, NMR, IR, MS, and UV-Vis.

Silverstein, R. M.; Webster, F. X.; Kiemle, D. J.; Bryce, D.L. Spectrometric Identification of Organic Compounds, 8th ed.; Wiley: Hoboken, NJ, 2014.
Perhaps a slightly more in-depth discussion than Pavia, but without sacrificing any clarity. Includes a large number of tables and charts of spectroscopic data, making it also very valuable as a reference.

Claridge, T. D. W. High-Resolution NMR Techniques in Organic Chemistry, 3rd ed.; Elsevier: Amsterdam, 2016.
A much more involved (graduate level) discussion of how NMR experiments are designed and how we extract information from them. Along with the more physchem-oriented NMR books, this is recommended for those who want to know what is actually going on in their NMR machine.

Field, L. D.; Li, H. L.; Magill, A. M. Organic Structures from Spectra, 6th edition; Wiley, 2020  Brief theory of UV-Vis, MS, IR, and NMR followed by training sets of experimentally recorded data with focus on the combination of these techniques in the process of structure elucidation.  Instructors may obtain an answer key.

Field, L. D.; Li, H. L.; Magill, A. M. Organic Structures from 2D NMR Spectra, Wiley, 2016 While (newer editions) of their other book about structure elucidation contains some 2D NMR spectra, this book now emphasises the training how to interpret correlation NMR spectra.  Equally available as instructor's guide including the answers.

Books about Physical Chemistry

General texts

Atkins, P.; de Paula, J. Physical Chemistry, 10th ed; Oxford UP: Oxford, U.K., 2014.
Classic physical chemistry textbook, but can sometimes be difficult to follow, especially for first-time students.
Atkins, P.; de Paula, J. Elements of Physical Chemistry, 7th ed.; Oxford UP: Oxford, U.K., 2016.
A less detailed book than Physical Chemistry. Can be used for introductory physical chemistry courses.
Engel, T.; Reid, P. Physical Chemistry, 3rd ed.; Prentice Hall: Upper Saddle River, NJ, 2012.
Levine, I. N. Physical Chemistry, 6th ed.; McGraw-Hill: New York, 2009.

Statistical mechanics

Chandler, D. Introduction to Modern Statistical Mechanics; Oxford UP:Oxford, U.K., 1987
Useful for undergraduate and early graduate study of both classical and quantum statistical mechanics, as well as for reference.
McQuarrie, D. A. Statistical Mechanics; University Science Books: Mill Valley, CA, 2000.

Nuclear magnetic resonance

Keeler, J. Understanding NMR Spectroscopy, 2nd ed.; Wiley: Chichester, U.K., 2010.
An extremely accessible and readable introduction to the theory behind NMR experiments. Describes nearly every important aspect of NMR, from basic quantum mechanics to the vector model, product operators, and a range of NMR experiments. It seems to be a conscious choice on the part of the author to not delve too deep into the quantum mechanics, in the interests of clarity and understanding.
Levitt, M.H. Spin Dynamics, 2nd ed.; Wiley: Chichester, U.K., 2008.
An extremely in-depth treatment of the quantum mechanics of NMR, which goes well beyond the level of Keeler's book.
Gunther, H. NMR Spectroscopy, 3rd ed.; Wiley: Weinheim, Germany, 2013.

Computational and Quantum Chemistry

Levine, I. N. Quantum Chemistry, 7th ed.; Pearson: Upper Saddle River, NJ, 2012.
This book acts as a first introduction to quantum chemistry and computational methods for students who do not have prior experience with the field.

Atkins, P. W.; Friedman, R. S. Molecular Quantum Mechanics, 5th ed.; Oxford UP: Oxford, U.K., 2010.
Realizes a more extensive coverage than Levine.

Cohen-Tannoudji, C.; Diu, B.; Laloe, F. Quantum Mechanics; Wiley: New York, 1977.
This book is a very good book on quantum mechanics that is often used by physics majors to learn the subject. Reading it is necessary if a better understanding than that provided by previous books is desired.

McWeeny, R. Symmetry; Dover, 2002.

Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford UP: Oxford, U.K., 1996.
The first book on DFT and by leaders in the field, still unbeatable.

Jensen, F. Introduction to Computational Chemistry; Wiley, 2007
This books treats the computational methods at a beginner level.

Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory; Dover, 1996

Helgaker, T.; Jorgensen, P; Olsen, J. Molecular Electronic-Structure Theory.
This is the reference book on wavefunction methods.

Cancès, E; Defranceschi, M; Kutzelnigg, W.; Le Bris, C.; Maday, Y. Computational Quantum Chemistry: A primer.
A sophisticated mathematical analysis of wavefunction methods and density functional theory.

Solid State Chemistry and Crystallography

West, A. R. Solid State Chemistry and Its Applications, 2nd ed.; John Wiley & Sons, Inc: Chichester, West Sussex, 2014.

Simon, S. H. The Oxford Solid State Basics, 1st ed.; Oxford University Press: Oxford, 2013.

Smart, L.; Moore, E. Solid State Chemistry: An Introduction, 4th ed.; CRC Press: Boca Raton, FL, 2012.

Tilley, R. J. D. Understanding Solids: The Science of Materials; J. Wiley: Chichester, West Sussex, England; Hoboken, NJ, USA, 2004.

Hoffmann, R. How Chemistry and Physics Meet in the Solid State; DOI: 10.1002/anie.198708461.
Learning solid state theory is difficult for a chemist in part because it is primarily ridden by a different community (physicists) that have a different language and way to understand bonding. This review helps in bridging the gap.

Ashcroft, N. S.; Mermin, N. Solid State Physics; Cengage Learning, 1976.
This textbook is primary reference to learn solid state physics.

Evarestov, R. A. Quantum Chemistry of Solids: LCAO Treatment of Crystals and Nanostructures, Springer, 2012.

Fundamentals of Crystallography, 3th ed., Oxford University Press, 2011

Müller, Ulrich Symmetry Relationships between Crystal Structures.
Applications of Crystallographic Group Theory in Crystal Chemistry, 2nd ed., Oxford University Press, 2017
A rigorous yet accessible explanation of the foundations of crystallography and symmetry relationships with a large collection of exercises to practice. Good for self-study.

Müller, U. Anorganische Strukturchemie, 6., aktualisierte Aufl., unveränd. Nachdr.; Studium; Vieweg + Teubner: Wiesbaden, 2009. (in German)

Dronskowski, R. Computational Chemistry of Solid State Materials: A Guide for Materials Scientists, Chemists, Physicists and Others; Wiley-VCH: Weinheim, 2005.

Molecular Orbital Theory

Fleming, I. Molecular Orbitals and Organic Chemical Reactions: Student Edition; Wiley: Chichester, 2009.
A readable introduction to molecular orbital theory with an emphasis on its application to simple organic chemical reactions (SN1/SN2 etc). Suitable for undergraduates wanting a more detailed understanding of organic reactivity. Also widely considered to be the book for the molecular orbital treatment of pericyclic reactions.

Fleming, I. Molecular Orbitals and Organic Chemical Reactions: Reference edition; Wiley: Chichester, 2009.
An expanded version of Molecular Orbitals and Organic Chemical Reactions: Student Edition with a full list of references and additional coverage of some material. More suited to graduate students / instructors who might want to read deeper into a topic.

Albright, T. A.; Burdett, J. K.; Whangbo, M-H. Orbital Interactions in Chemistry, 2nd ed.; Wiley: Hoboken, NJ, 2013.
Arguably the best book on the subject, both in terms of depth (some mathematical treatment of the topics) and coverage (organic and inorganic molecules are discussed). Given the size (over 800 pages), Albright is more of a reference text than Fleming which can easily be read cover-to-cover, and the level of discussion is more geared towards graduate students / undergraduates in later years who already have some understanding of molecular orbitals.

Jean, Y. Molecular Orbitals of Transition Metal Complexes; Oxford, 2005.
An undergraduate level textbook covering the fundamentals of molecular orbital theory applied to transition metal complexes. The derivations of the MO diagrams for various coordination geometries is provided along with a chapter on 'applications' of MO theory such as how complexes react.

Electrochemistry

Elgrishi, N. et al. A Practical Beginner’s Guide to Cyclic Voltammetry; J. Chem. Educ. 2018, 95, 197–206. (open access)
A short introduction teaching the very basics about CV's theory, supplemented with tips and warnings for pitfalls recording and interpreting the experimental data.  The supplementary information contains five training modules to walk through the more typical minutiae one encounters.

For Organic chemistry I really like "Organic Chemistry" by Brown, Iverson, Anslyn and Foote

Umm...Paula Bruice would be a good book for beginners..to get the basics clear..and for further reading Peter Sykes is also good.

I found McQuarrie's Quantum Chemistry to be very helpful for quantum mechanics. Especially the "math chapters", which reviewed pertinent math techniques before they are required for each quantum topic.

Video Resources (online)

The University of Nottingham's Periodic Videos
The periodic table of videos includes introductions to all elements. The molecular videos section focuses on interesting chemical reactions. Apart from having quite some entertaining value, they visualise a lot of reactions that can only safely be carried out in a laboratory environment. The videos are hosted on their YouTube channel.

Khan Academy
Khan Academy is a site, which is explaining many different subjects to all who are eager to learn. Those subjects are explained through video lessons on youtube, on which the speaker uses a virtual blackboard to draw and clarify the explanations for a deeper understanding. As those videos cover basic theories, it is probably more helpful for the beginner as for the advanced student. There are two channels for chemistry:

Khan Academy - Chemistry
Did you know that everything is made out of chemicals? Chemistry is the study of matter: its composition, properties, and reactivity. This material roughly covers a first-year high school or college course, and a good understanding of algebra is helpful.

Khan Academy - Organic Chemistry
Topics covered in college organic chemistry course are explained. Basic understanding of basic high school or college chemistry assumed (although there is some review).

Organic Chemistry 1 by University of New Orleans
This is the first semester of sophomore Organic Chemistry.This course completes most chemistry requirements for pre-professional degree programs and science degrees.  This course will cover the introduction of basic fundamental topics of organic chemistry.  Specifically the structure-activity relationship and spectroscopy of organic functional groups will be investigated.  Starting with simple organic models, we will cover structures of organic chemicals from basic connectivity to three- dimensional spatial alignments.  Nomenclature and spectroscopy of the different groups will be covered along with reactivity of those groups.

Organic Chemistry 2 by University of New Orleans
This is the second semester of sophomore Organic Chemistry.  This course completes most chemistry requirements for pre-professional degree programs and science degrees. This course will cover the reactions, mechanisms and properties of various functional groups including dienes, arenes, carbonyls, carboxylic acid and their derivatives, phenols, amines as well as biochemicals such as carbohydrates, lipids, amino acids and proteins.

General Organic Chemistry 2 Course by Arizona State University
This is the complete set materials used in the second semester of Organic Chemistry. It includes home works, video lectures, notes, exams, etc.

Chemistry Courses by University of Massachusetts - Boston
Offers both Organic Chemistry 1 and 2.

“Organic Chemistry – Structure and Reactivity” by UC Berkeley professor Peter C. Vollhardt
An Excellent Resource for Organic Chemistry. It is different from other courses, in the manner the of approach to the topic.

Organic Reactions and Pharmaceuticals by Professor Hardinger, UCLA
The lectures are lot more exciting than others due to the method of teaching of the professor.Organic Reactions and Pharmaceuticals is a class that provides an in-depth analysis of organic reactions, nucleophilic and electrophilic substitutions and additions; electrophilic aromatic substitutions, carbonyl reactions, catalysis, molecular basis of drug action, and organic chemistry of pharmaceuticals.

UC Irvine OpenCourseWare
This is mother of all resources. OpenChem by UCI offers a course on each and every aspect of chemistry. It has 6 different courses for organic chemistry whose levels vary from undergraduate to graduate.

The youtube channel of the Australian and New Zealand Society for Magnetic Resonance
Presented briefly by Kwan et al. in the Journal of Chemical Education, basic and advanced principles of NMR / MRI and EPR are lectured.

MIT 5.60 Thermodynamics and Kinetics, Spring 2008
The above course is available as a part of MIT OCW. Links in the description of video lectures includes lecture notes, readings, exams and course materials available for download. Covers a basic to intermediate introduction to thermodynamics and kinetics at the undergraduate level.

TMP Chem
Trent M. Parker's youtube channel about quantum chemistry, spectroscopy, chemical thermodynamics, kinetics, theoretical/computational chemistry, reviewing mathematics for physical chemistry.  Computations centre on Python.

Television

Uranium- Twisting the Dragon's Tail
Host and physicist Dr. Derek Muller unlocks the mysteries of uranium, one of the Earth's most controversial elements. Born from the collapse of a star, uranium has brought hope, progress and destruction. It has revolutionized society, from medicine to warfare. It is an element that has profoundly shaped the past, will change the future and will exist long after humans have left the Earth.

Books about Analytical Chemistry

Schwarzenbach, G.; Flaschka, H. A. Complexometric Titrations; Methuen: London, 1957 (translated by H. Irving in 1969).
Skoog, D. A.; West, D. M.; Holler, F. J.; Crouch, S. R. Fundamentals of Analytical Chemistry, 9th ed.; Brooks/Cole: Pacific Grove, CA, 2013.
Elgrishi et al., A Practical Beginner’s Guide to Cyclic Voltammetry, J. Chem. Educ. 2018, 95, 2, 197-206, doi 10.1021/acs.jchemed.7b00361. A short introduction, indicating tips and pitfalls, published as open access.

Books about Biochemistry and Chemical Biology

Voet, D.; Voet, J. G. Biochemistry, 4th ed.; Wiley: Hoboken, NJ, 2011.
Nelson, D.; Cox, M. Lehninger Principles of Biochemistry, 7th ed.;  Macmillan Higher Education: Houndmills, UK, 2017.
Berg, J.; Tymoczko, J.; Gatto Jr., G; Stryer L. Biochemistry, 9th ed.; Macmillan Higher Education: Houndmills, UK, 2019.

Books about Chemical Engineering

The probably most comprehensive reference for chemical engineering is the McGraw-Hill Chemical Engineering Series, which contains more than you should know as a student. After all a strong knowledge in all areas of chemistry is necessary. As an engineer, and a chemist especially, if you are looking for sizing operations, you'll need to think about details, which are not in the books unfortunately.
For the related question, see: What are introductory level books on chemical engineering?

The Visual Encyclopedia of Chemical Engineering is a project hosted by the Department of Chemical Engineering, University of Michigan.  By text, illustration, and video, typical applications of devices and processes, their advantages and disadvantages are presented.  Equally, means to monitor processes are shown and literature references (pointing e.g. to Perry's Chemical Engineering Handbook) provided.

Books about Computational Chemistry and Quantum Chemistry
Introductory

Atkins, P.; Friedman, R. Molecular Quantum Mechanics, 5th ed.; Oxford UP: Oxford, U.K., 2010.
Oxford University Press,
Amazon.
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Cramer, C. J. Essentials of Computational Chemistry: Theories and Models, 2nd ed.; Wiley: Chichester, U.K., 2004.
Wiley,
Amazon.
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Jensen, J.H. Molecular Modeling Basics; CRC Press: Boca Raton, FL, 2010.
CRC Press,
Amazon.
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Levine, I. N. Quantum Chemistry, 7th ed.; Prentice Hall: Upper Saddle River, NJ, 2014.
Prentice Hall,
Amazon.
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McQuarrie, D. A. Quantum Chemistry, 2nd ed.; University Science Books: Mill Valley, CA, 2007.
University Science Books (https not available),
Amazon.
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Koch, W.; Holthausen , M. C. A Chemist’s Guide to Density Functional Theory, 2nd ed.; Wiley-VCH: Weinheim, 2001. ISBNs: 3-527-30372-3 (Softcover); 3-527-60004-3 (Electronic). DOI: 10.1002/3527600043.
Introductory text for chemists familiar with conventional quantum mechanics. The book introduces density functional theory: its basis, concepts, terms, implementation, and performance in diverse applications. This includes the usage of DFT for structure, energy, and molecular property computations, as well as reaction mechanism studies, etc.

Intermediate

Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, U.K., 1987. <Links>.
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Bachrach, S. M. Computational Organic Chemistry, 2nd ed.; Wiley: Hoboken, NJ, 2014.
Wiley (https not available),
Amazon.com.
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Jensen, F. Introduction to Computational Chemistry, 3rd ed.; Wiley: Chichester, U.K., 2017.
Wiley (https not available),
Amazon.com.
Provides a good overview/introduction to many aspects of QC. The focus is on concepts, not on mathematical rigour.

Szabo, A.; Ostlund, N.S. Modern Quantum Chemistry: Introduction to Advanced Electronic Stucture Theory; Dover: Mineola, NY, 1989 (revised in 1996).
Dover Publications (https not available),
Amazon.com.
A classic introduction to the ab initio wave-function-based methods of electronic structure theory. Contains detailed discussions of the Hartree-Fock and post-Hartree-Fock methods such as Møller–Plesset perturbation theory, configuration interaction, and coupled cluster. The latter discussions are correct, but sometimes a bit dated.

Tuckerman M.E; Statistical Mechanics: Theory and Molecular Simulation, 1st ed.; Oxford University Press: Oxford, U.K., 2010.
Oxford UP,
Amazon.com.

Helgaker T.; Jørgensen P.; Olsen J. Molecular Electronic-Structure Theory; Wiley: Chichester, U.K. 2000.
Wiley
(https not available), Amazon.
An in-depth description of the inner workings of all the common modern wavefunction based methods - Hartree-Fock and multi-reference self-consistent field, perturbation theory, configuration interation and coupled cluster.

Books about Theoretical Chemistry

Cotton, F. A. Chemical Applications of Group Theory, 3rd ed.; Wiley: New York, 1990.
Vincent, A. Molecular Symmetry and Group Theory: A Programmed Introduction to Chemical Applications, 2nd ed.; Wiley: Chichester, U.K., 2000.

related: List of important publications in chemistry on Wikipedia

There is an excellent course available for free at compmatphys.org . I am not sure if the videos will be available afterwards.

Can someone mention what are the standard undergraduate level (up to 4th year) analytical chemistry textbooks used in Germany?

Online Courses

Chemistry LibreTexts
This collection was formerly known as UC Davis' ChemWiki: The Dynamic Chemistry Hypertext. It is a collaborative approach toward chemistry education where an Open Access textbook environment is constantly being written and re-written by students and faculty members resulting in a free Chemistry textbook to supplant conventional paper-based books.

Jim Clark's Chemguide
An in-depth overview of many areas of basic chemistry, including organic, inorganic, physical, and instrumental. Forgoes mathematical treatments of chemistry in favor of teaching an intuitive understanding for how chemical systems behave. Targeted at UK A-level students, but useful for anyone who wants to shore up their fundamentals.

Virtual Textbook of Organic Chemistry
A very useful introduction to principles in organic chemistry and the reactions of common functional groups.

Websites

IUPAC Compendium of Chemical Terminology - the Gold Book
A concise compendium of the most common terminology that is used in chemical and related sciences.

NIST Chemistry WebBook
A searchable database for standard reference data of chemical compounds by the National Institute of Standards and Technologies.

Symmetry@Otterbein
An interactive tutorial (by Otterbein University) about molecular, as well as crystallographic symmetry.

A Hypertext Book of Crystallographic Space Group Diagrams and Tables
The Space group diagrams you find in the in the International Tables of Crystallography.  It equally considers standard settings (e.g., $P2_1/c$) and alternatives like $P2_1/a$, $P2_1/n$, $B2_1/a$, $B2_1/d$ -- all of the  filed under #14.

Online Dictionary of Crystallography
The dictionary is provided by the International Union of Crystallography (IUCr). It is a curated glossary about the more frequently met crystallographic concepts.

Organic Chemistry Lab Techniques
An illustrated collection of basic techniques met in the organic chemistry lab.  The content naturally shows some overlaps with / complements to print primers like the one by Zubrick.

Organic Chemistry Data & Info
A site of general interest about chemical and reaction data, cross-link to literature references (like the Hans Reich collection) useful for the chemist in the lab as well as educators/students.  Moderated by the Division of Organic Chemistry of the American Chemical Society.

hyperphysics.phy-astr.gsu.edu - Chemistry
A hierarchical set of compact cheat-cards, navigated along a "bubble tree", intended for quick learning/reminding/overview of basics of many chemical concepts, rules and topics.

Wikipedia Chemical Structure Explorer
Query more than 20k chemicals in the English edition of Wikipedia by drawing a structure which either is a substructure, or exactly the structure you look for, or is just similar to the one in mind.  If there is a match, the lower part of the page displays the corresponding entry in Wikipedia.

Is there a clean difference between an online course a website, or is it somewhat fuzzy?

For me, the online courses are a special subset of websites that are explicitly for teaching conceptual stuff and not only for giving some information. E.g., the mentioned Goldbook and the Webbook both give information from which you can learn, but they are not teaching like what you'd expect from a school lesson. And then there are sites like Khan Acadamy on youtube, which besides other subjects is about teaching chemistry and should be classified as an online course. But I guess you are right, when saying it can be quite fuzzy. (Please ask about such things in the meta thread next time.)

Another great website is the eBook Principles of General Chemistry

Software

ChemOffice Professional
Commercial software for drawing molecular structures, 3D models and many more. High price but most higher education institutes will provide students/staff with free institutional licenses. The molecular sketcher now has a free online version (built using HTML$5$ and JS): ChemDraw online
MarvinSketch (desktop) & MarvinJS (web)
Freeware (closed-source) for drawing molecular structures with a wide feature set. In addition to just being able to draw Lewis structures, the software includes plugins to name what you have drawn (systematic/traditional), predict properties, change atom and bond properties, generate stereoisomers, and much more. Desktop version is Java based so works on Mac, Windows, Linux.
ChemDoodle
Commercial software for 2D and 3D molecular structures and diagrams and much more. Also has versions for tablet/mobile. An online free version of ChemDoodle is here: ChemDoodle Web Components
ACD/ChemSketch
Commercial software for Windows only. Includes a free version with fewer features.
chemfig
Free $\mathrm\LaTeX$ package distributed under the LATEX Project Public License 1.3c developed by Christian Tellechea for creating 2D chemical structures with seamless integration into any type of a document, from a standalone illustration to a textbook or a poster. Since TikZ is used for graphics generation, the functionality of chemfig can be greatly extended. PDF output can also be rasterized by using external tools such as ImageMagick. Also, see chemfig questions on TeX.SE.
Avogadro
Free, open source software for generating 3D models and computational chemistry.
GAMESS
Free ab initio molecular quantum chemistry program.
ORCA
Free for academic use ab initio/DFT quantum chemistry program. Has a nice tutorial on basic molecular modelling here.
Open Babel: The Open Source Chemistry Toolbox
Free "Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas."
RDKit: Open-Source Cheminformatics Software
Odyssey by Wavefunction
Commercial software designed to be used for teaching and learning chemistry. Includes high quality molecular simulations of many materials, in-built virtual labs. Excellent animations of many physical and chemical processes.

Related questions: - What free software exists to view molecule pictures within a file explorer? - How do I take chemistry notes on Mac? - How do I make 3d molecular graphics similar to those shown on Wikipedia?

Also related on our meta: Software to name compounds

Books about General Chemistry

Atkins, P. W.; Jones, L. L.; Laverman, L. E. Chemical Principles: The Quest for Insight, 6th ed.; W. H. Freeman: New York, 2012.

Silberberg, M.; Amateis, P. Chemistry: The Molecular Nature of Matter and Change, 7th ed.; McGraw-Hill: New York, 2014.

Oxtoby, D. W.; Gillis, H. P.; Campion, A. Principles of Modern Chemistry, 8th ed.; Cengage Learning: Boston, MA, 2015.

Zumdahl, S. S.; Zumdahl, S. A. Chemistry, 9th ed.; Brooks/Cole: Pacific Grove, CA, 2013.

Whitten, K. W.; Davis, R. E.; Peck, L.; Stanley, G. G. Chemistry, 10th ed.; Brooks/Cole: Pacific Grove, CA, 2013.

Munowitz, M. Principles of Chemistry, W. W. Norton and Co.: New York, NY, 2000.

References about Nomenclature
Successful communication requires an agreed set of definitions compiled as nomenclature.  An example for such compilations are IUPAC's Color Books, named by the color of their book cover.  Below, they are listed in alphabetic order of their color.

Favre, H. A. Powell W. H. (eds.) Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013, IUPAC Blue book, RSC Publishing
It is noteworthy that there is a searchable compilation of these rules on-line prepared by G. P. Moss here.
The sub-set about substitutive nomenclature is nicely illustrated by Hellwich et al. in the Brief guide to the nomenclature of organic chemistry as open access publication, altogether with a   four-page SI (pdf) summary this article.

McNaught, A. D. and Wilkinson, A. (eds.) Compendium of Chemical Terminology, The Gold Book, Blackwell Science, Oxford 1997.  The perhaps most elemental compilation about terms, synonyms, acronyms, and abbreviations by IUPAC equally may be consulted as online reference.

Cohen, E. R. et al. (eds.) Quantities, Units and Symbols in Physical Chemistry, IUPAC Green Book.  A joint effort by IUPAC, IUPAP, and ISO about quantities, constants, units and their recommended symbolization.  The conversion of units, scientific typography and uncertainty are addressed, too.  The content of the second reprint is available online (pdf). Equally, Stohner and Quack prepared a four-page summary (pdf).

Inczedy, J.; Lengyel, T. and Ure, A. M. IUPAC Compendium on Analytical Nomenclature, Definitive Rules 1997 3rd edition, Blackwell Science, 1998. Equally known as Orange Book, it addresses topics like the (statistical) representation of results, terms and definitions of classical wet chemistry like titrimetry, thermo- and electrochemical analysis, separations (chromatography and extraction), spectroscopic and spectrometric techniques; kinetic, radiochemical or surface analytical characterizations; as well as quality assurance.  The publication of its fourth edition is scheduled for January 27th, 2023 (landing page).
Between 2000 and 2003, IUPAC's Analytical Chemistry Division set up a public searchable online compendium.  To ease the compilation of .pdf files, there is a searchable index.  There are concepts considered important (PCA / principal component analysis, PLS / partial least squares, or chemometrics) for which the current edition does not (yet) contain a proper dedicated keyword.

Jones, R. G. et al. Compendium of Polymer Terminology and Nomenclature, IUPAC Recommendations 2008, RSC Publishing, 2009.
The Purple Book addresses both general as well as specific terms about the nomenclature of polymers, their graphical representation.  In addition, copolymers and blends of polymers; liquid crystals; sols, gels, networks, inorganic organic hybrid materials; reactions and aging of polymers are among the topics addressed.
Since June 2014, there is searchable online pdf compendium by IUPAC, too.

Connelly, N. G.; Damhus, T.; Hartshorn, R. M.; Hutton, A. T. (eds.) Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005, RSC publishing, 2005.  The Red Book compiles the rules about elements, isotopes, simple inorganic compounds, coordination compounds, metalorganic compounds, and solids.
There is a freely available online release (pdf) by IUPAC, as well as a public site about errors and updates.  Similar to the Blue Book, there equally is a Brief guide to the nomenclature of inorganic chemistry with examples of application illustrated in colour, as well as a 4-page summary (pdf).

Férard, G.; Dybkaer, R.; Fuentes-Arderiu X. Compendium of Terminology and Nomenclature of Properties Clinical Laboratory Sciences, Recommendations 2016, RCS publishing, 2016.  The Silver Book is a joint effort by IUPAC and IFCC, and to be understood as one interface between laboratory scientists and medical professionals.
A 4-page summary (pdf) is available.

Liébecq, C. Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992.  For this reference known as White Book, G.P. Moss set up an on-line companion site.

If used critically, the non-exhaustive listing about software to name [organic] compounds mentioned in a comment by @Gaurang Tandon may be of interest, too.

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


text:
How much hydrogen or oxygen will be produced in the electrolysis of water?
Is there a way to exactly calculate the quantity of hydrogen or oxygen in a water electrolysis? I am thinking of a plain and simple electrolysis like an anode and cathode in salted water separating oxygen and hydrogen.
I am looking for the relation between the amounts of hydrogen $n(\ce{H2})$ or oxygen $n(\ce{O2})$ and the amounts of water and salt, current, voltage and time of electrolysis.

I'm not sure it's appropriate to explain the relationship between all the variables above, here, as there are a lot of concepts that would need to be explored. However, fundamentally (assuming there are no other reactions apart from the electrolysis) the charge passed through the cell is proportional to the amount of products formed, described by Faraday's laws of electrolysis. Here is a useful rearrangement:
$$n = \frac{Q}{Fz}$$
Where $Q$ is the charge passed, $F$ is the Faraday constant and $z$ is the number of electrons transferred per redox reaction. For example, $z = 2$ for hydrogen because it takes two electrons to convert $\ce{H+}$ to $\ce{H2}$ as $\ce{2H+ + 2e- <=> H2}$. Therefore, for every coulomb of charge, we get: $$\begin{align}
  n &= \frac{1\ \mathrm{C}}{(96.485\ \mathrm{kC/mol})(2)}\\
    &= 5.18\ \mathrm{µmol}
\end{align}$$ of hydrogen gas produced. So if we can measure the charge (or current integrated over time), we can calculate the amount of product produced. This is true no matter what voltage is applied or what the electrolyte content of the solution is, however if more than one reaction is occurring at an electrode, you won't be able to separate the contributions from each reaction with only the charge as information. There will also be a minor contribution from charging the double layer capacitance when the potential is first applied.
Where things become less straightforward is understanding how changing the potential or the solution resistance affects the amount of charge that flows, but the charge itself is directly related to how much product is being produced.

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


text:
Osmotic Pressure
If the osmotic pressure of a 0.010 M aqueous solution of sucrose at 27˚C is 0.25 atmosphere, then the osmotic pressure of a 0.010 M aqueous solution of NaCl at 27˚C is
(a) 0.062 atm
(b) 0.12 atm
(c) 0.25 atm
(d) 0.50 atm
(e) 1.0 atm
The correct answer is (d).  However, I'm not entirely sure why.
I know that the osmotic press $\Pi$ = MRT where M is the concentration, R is the ideal gas constant, and T is the absolute temperature.
Thus:
$\Pi_{NaCl} = M_{NaCl}RT = (0.01 M)RT = M_{sucrose}RT = 0.25$
So why isn't the osmotic pressure of NaCl at 27˚C 0.25 atm?

The expression you need is
$$\Pi = i\mathrm{MRT}$$
where $i$, the van't Hoff factor, describes the degree of ionization of the solute (for sucrose, it's 1; for $\ce{NaCl}$, it's 2, since we get 2 moles of ions for each mole of salt we dissolve). The other variables are as you describe. Thus, the osmotic pressure for your salt solution is twice that of your sucrose solution.
See this page for a nice explanation and worked examples for sucrose and salt.


text:
Geometry of AsF5 molecule

Which of the following is the best description of the arragement of fluorine atoms around the arsenic atom in a molecule of $\ce{AsF5}$?
  (a) trigonal bipyramid
  (b) octahedron
  (c) tetrahedron
  (d) square pyramid
  (e) planar pentagon

The correct answer is (a).
I know that the answer can't be (b), (c), or (e) since octahedron requires 6 ligands and tetrahedron requires 4 ligand, and planar pentagon is only observed in $\ce{[IF5]-}$ and $\ce{[XeF5]-}$. I recall that first row transition metals prefer trigonal bipyramidal configurations, thus trigonal bipyramidal is the more likely geometry, but I'm not sure why this is true?
Any help would be greatly appreciated.

You'd need lone pairs to be different.

Please avoid using Latex in titles due to searching issues

There should be a bonding argument for one case that doesn’t fit with the other if I am informed correctly. But then again, $\ce{AsF5}$ pseudorotates, doesn’t it?

$\ce{AsF5}$ has a trigonal bipyramid structure with the axial bonds slightly longer than the equatorial bonds.  The $\ce{As}$ atom is $\ce{sp^2}$ hybridized and hypervalent bonding is involved in the two axial bonds.  Take a look at this earlier description of the hypervalent bonding in $\ce{PCL5}$ to understand what is going on here.

There are no lone pairs in $\ce{As}$ after it forms a bond with each of the five $\ce{F}$.
Hence, the number of lone pairs of electron around the central atom ($\ce{As}$) is zero, and the number of sigma bonds the central atom forms is five (a single bond has one $\sigma$-bond only).
Hence the hybridization number of $\ce{As}$ in $\ce{AsF5}$ is $0+5=5$ and it follows $\ce{sp^3d}$ hybridization geometry with no change in actual shape because of absence of lone pairs.
So, it has a trigonal bipyramidal structure: two $\ce{F}$ ions in the axial positions and three others in equitorial positions.

While hybridisation is a very common (but by far too simple) concept and the question was asked in terms of VSEPR theory, it is essential to point out, that there is little to no involvement of the d orbitals in the bonding of that molecule.

@Nij Please make sure you use mhchem for any occurrences of chemical elements, don't just leave them in plain maths mode.


text:
Equilirium mixture of nitrogen dioxide and its dimer

When an equilibrium mixture of gaseous, colorless $\ce{N2O4}$ and brown $\ce{NO2}$ is warmed at constant volume, which of the following is correct?

The density remains constant.
The degree of dissociation decreases.
The average molar mass increases.
The pressure decreases.
The color becomes lighter.

The correct answer is (1).  But all the other answers except (4) seem reasonable to me.
The equilibrium we are looking at is: $\ce{N2O4<=>2NO2}$
Upon heating at constant volume, the pressure will increase, and so the equilibrium will shift to the left, which means that there is less dissociation of $\ce{N2O4}$, the average molar mass will be closer to the molar mass of $\ce{N2O4}$, than before warming, thus the average molar mass will increase.
Finally, as the equilibrium shifts to the left, more colorless $\ce{N2O4}$ will be present, lightening the color of the gaseous mixture.
Obviously, the density will also remain constant, as density of gas = $\frac {\text{mass}}{\text{volume}}$ and since no mass is lost and we are at constant volume, the density remains constant.

Are you sure about the direction of the shift in equilibrium? True, increased pressure favors association and thus shifts it to the left; but increased temperature favors entropy and thus shifts it to the right. Which influence will prevail?

What is the $\Delta H^\circ$ of the reaction? If the reaction has $\Delta_r H^\circ <0$, then increasing the temperature (adding heat) can cause the equilibrium to shift to the left.

@IvanNeretin So, because we don't necessarily know if entropy or pressure wins out in the end, the only thing we do know is that no mass can escape, ergo, the density is constant?


text:
Is phosphorus trichloride really a stronger Lewis acid than antimony pentafluoride?
The following was a question from the ETS Chem GRE guide and apparently this was an actual question on an exam a few decades ago. Unfortunately, no explanation for the answer was given, and I couldn't find anything more helpful on the internet.

Which of the following molecules is the strongest Lewis acid?
  (a) $\ce{NF3}$
  (b) $\ce{SbF5}$
  (c) $\ce{NaCl}$
  (d) $\ce{PCl3}$
  (e) $\ce{SnCl2}$

The correct answer is supposed to be (d), which I find very surprising.  I thought it should be (b), since I know that $\ce{SbF5}$ has an empty orbital that can facilitate electron donation.  I also know it is a strong Lewis acid.
What orbital on $\ce{PCl3}$ is empty and why would $\ce{PCl3}$ be stronger than $\ce{SbF5}$?

It may be strongest base, definitely not strongest acid.

Related: https://chemistry.stackexchange.com/q/41556/44877

Such a question is really quite interesting... Typically, we would consider electron-deficient Group 3 compounds, e.g. AlCl3, BCl3 etc. as Lewis acids and would usually consider these Group 15 compounds to be Lewis bases. Considering acidity of these compounds is rather weird...


text:
Points needed to come up with a calibration curve
Usually when you are doing your masters, what are the minimum points that you can have when doing a calibration curve?

There is not really a simple answer to this—it depends on what you're doing and what level of error your application can tolerate. If you've characterized the response of your instrument and you know that it's linear within a certain range but the response has a variable offset, even a single-point calibration may be sufficient. On the other hand, if you just built an instrument and have no idea of its response characteristics but need very accurate results, you're best to take measurements at many different points (and over a length of time to see how stable the response is) to accommodate the possibility of non-linear response in the range of interest.
Occasionally, if you need to follow a measurement standard (e.g. the ITS-90 standard for temperature), you may be constrained to doing it a certain way so your data can be directly compared with that of other labs but in general, do enough to get the results you need, but not so much that you're just wasting your time. This might mean taking a few well-separated calibration points to get a ball-park value for an unknown sample, then bracketing the value with more calibration points near it to get a better measurement.

Your question contains very little about the analytical method you deploy; hence I agree with the answer by Michael "it depends on what you aim for".
On the other hand: assuming you know (almost) nothing about the relationship between the concentration of the analyte (like an $x$ in mathematics), on one side, and the response by the method deploy (like $f(x)$ in mathematics) I recommend to collect data for at least five different analyte concentrations that are not "too close to each other" to construct your calibration curve.
Why at least five?  For me it appears to be the smallest number of data points to figure out if there is a linear relationship between $x$ and $f(x)$, like $f(x) = ax + b$ with a direct proportion factor $a$ (slope) and an absolute term of $b$ (intersection with the ordinate) including to calculate an estimate for the standard deviation of them and a regression coefficient.
But perhaps the relationship between $f(x)$ and $x$ is not strongly linear and another model fits better? This could be spotted for example by plotting the data in a diagram, where the attempt to draw a straight line across all of them with a ruler fails.  Then, with five different values on your abscissa you may attempt transformations into a linear form and check if this significantly fits better  For example:

$f(x) = y = a \cdot e^{bx}$  transformed into a form of: $\lg y = \lg{a} + bx$
$y = a^{bx}$ transformed into a form of: $\lg{y} = bx \cdot \lg{a}$
$y = a \cdot x^b$ transformed into a form of: $\lg{y} = \lg{a} + b \cdot \lg{x}$

This still is limited (on a shoestring) and of course with the limitation to cover only about the region covered by the data, being descriptive rather than predictive.  Collecting more data (both repeated at one abscissa value, as well as at different abcissa values) may then become the next thing to do to support your analytical model.


text:
Need to dissolve glue placed intentionally in a lock
Someone intentionally sabotaged the lock on the front door of my house by putting glue inside it apparently, I have no idea what type of glue it is. Is there any chemical substance I can use to dissolve the glue instead of having to replace the entire lock?
Also, would heating the lock work?
I took a look at this, the heating option wasn't possible since they're talking about paper, but I was wondering if it'll work before trying any of the chemicals mentioned.
Please consider that I don't have much experience in Chemistry while answering, thank you for your time.

If it's superglue, it should be dissolved pretty easily by acetone (i.e. nail polish remover), though it'll take a while. Superglue is, in my experience, the weapon of choice for vandals since it's cheap and hardens quickly, so that's a good starting point. On the other end of the spectrum, if they used casting polymers, you might just be out of luck.

To paraphrase the link you mentioned,
Without knowing the specific glue, you should try different solvents to see if it dissolves the glue:

Start with a mild, non-polar solvent like paint thinner.
If that doesn't work, try a polar solvent like acetone.
If that doesn't work, try tetrahydrofuran (PVC pipe solvent)

All of these solvents are flammable and pretty nasty if you get them on you. To minimise risk, use small quantities at a time, minimise the time that the lid is off the container. The fumes shouldn't be too much of a problem if you're outside, but still take care.


text:
Why does Brady's reagent include sulfuric acid and methanol?
I'm supposed to explain why sulfuric acid and methanol are used in combination with 2,4-dinitrophenylhydrazine to form Brady's reagent. Are they just used as a solvent system for the hydrazine? Also, wouldn't sulfuric acid react with methanol?

2,4-DNPH is usually dissolved in an alcoholic solvent, together with sulfuric acid, when used as a reagent to detect aldehydes and ketones (Brady's reagent). The sulfuric acid is a source of $\ce{H+}$, which catalyses the reaction between the hydrazine group and the carbonyl compound, as depicted in the mechanism below:

The final hydrazone product is the precipitate which signals a positive test.
The solvent used is typically methanol or ethanol. You are correct that these could theoretically react with sulfuric acid: dimethyl ether is the most likely product. However, the concentration of sulfuric acid is typically not sufficiently high, and these side reactions do not take place.

2,4-Dinitrophenylhydrazine is available as a powder, synthesised from hydrazine sulphate and 2,4-dinitrochlorobenzene (Wikipedia).
Brady's reagent is prepared by dissolving the powder in a solution of methanol and concentrated sulfuric acid.
Although sulfuric acid and methanol react, the reaction is not 'big enough' to interfere with the 2,4-DNP reaction.


text:
Would the density and radius of your metal appear to be higher or lower if you forgot to tap the flask to release air bubbles?
For this lab we had to measure out copper in flasks, but tap them out before so no air bubbles would affect the weight. We have this question at the end of the lab and so I wasn't sure if the density/radius would be higher or lower if I didn't tap them out and why.
We were trying to figure out the size on an atom of copper. To find the density of the sample, we had to add about 1/3 of copper to an empty flask and weigh it with the metal. Then after we had to add enough water to just cover the metal, then gently tap and rotate the volumetric flask to remove any air bubbles. Then fill to the calibration mark with water and reweigh the volumetric flask containing the water solid mixture.

In short, you were measuring the mass and volume of copper. Which of these measurements would be affected by the air bubbles, and how?

Yes. We are trying to figure out if those and density would be higher or lower based on if I hadn't tapped out the bubbles.

In this experiment, you were determining the average volume that a copper atom occupied in your sample of copper.  In order to do this, you had to know the number of copper atoms and the volume that number of copper atoms occupied.
The moles of copper was measured by gravimetrically determining the mass of the copper (e.g. by weighing it). From that you determined the number of moles of copper using it's atomic weight, and from there you calculated the number of copper atoms using Avogadro's number.
The volume occupied by your copper sample was determined by measuring how much water the copper displaced. So, if the volume of water increased by 10 $\mathrm{cm^3}$, then you knew your volume of copper was $\mathrm{cm^3}$. But air bubbles occupy space also.  If, for example, 1 $\mathrm{cm^3}$ of the total displaced volume were actually due to air bubbles, then you would actually only have 9 $\mathrm{cm^3}$ of copper, but you would mistakenly have used a value of 10 $\mathrm{cm^3}$.
So, the bottom line is that because you were calculating the molecular volume as the volume occupied by the copper per molar quantity of copper, your calculated molar volume would have been proportionally higher than the true value.


text:
Why does electronegativity create a stronger acid, but so does greater electron distribution?
I just learned that:
Acids get stronger with:

Increasing electronegativity of atom bonded to $\ce{H}$.
Size of atom bearing negative charge.
Hybridization of negative charge (more s character, $\ce{e-}$ closer to nucleus, more acidic).
Resonance stabilization (like size, greater distribution of electrons).

So basically, the  more concentrated the negative charge (think $\ce{F-}$, $-1$ and very small), the tighter it's going to "hold on" to the proton. With resonance and large negative groups, the charge is less concentrated, so it's not going to "hold on" to the proton as well.
However, electronegativity is the tendency for an atom to "hog" electrons. Therefore, the more electronegative, the more electrons there are in a similarly sized space.
More concentrated electrons = more stable base = weaker acid.
But electronegativity = more concentrated electrons (even though size trumps it).
And electronegativity = stronger acid.
Feel free to edit if you see what I'm trying to say but can say it better!

You're overlooking the decisive step: An acid is the stronger, the more energy it gains by becoming an anion.  With that, you can rationalise. Chemistry is 95% pure logic.

Hey, more stable base means stronger acid!

Well, $\ce{HF}$ is a weak acid ...

The main point about strong acids is ‘how stable is the conjugate base?’
The better stabilised the negative charge on a conjugate base of a neutral acid is, the happier the species will be to loose a proton and thus the more acidic the proton is. All of the points you noted just emphasise that.
Therefore, the only wrong assumption you are making is:

more stable base = weaker acid.

The correct way is:

more stable base = stronger acid.

Increasing EN means less acidic.
Refer to the $\mathrm{p}K_\mathrm{a}$ values below.
$$
\begin{array}{l|rrrr}
\hline
\ce{HX} & \ce{HF} & \ce{HCl} & \ce{HBr} & \ce{HI} \\
\hline
\mathrm{p}K_\mathrm{a} & 3.2 & -7 & -9 & -10 \\
\hline
\end{array}
$$


text:
Titration of magnesium sulfate with potassium permangante
One common method for measuring the amount of $\ce{Fe^2+}$ in $\ce{FeSO4}$ is by dissolving it with $\ce{H2SO4}$ and then titrating with $\ce{KMnO4}$.
However, is it possible to measure the amount of $\ce{Mg^2+}$ ion in magnesium sulfate by dissolving it in $\ce{H2SO4}$ and then titrating it with $\ce{KMnO4}$? Why or why not?

Do you know about redox reactions? It looks like you'd like to oxidate sth that can't be oxidated...

The $\ce{Fe^2+}$ concentration can be measured in this fashion since the iron(II) cation can be oxidized by a suitable oxidant, like the permanganate ion $\ce{MnO4-}$.
$$\ce{MnO4- +4H+ +3Fe^2+ -> MnO2 + 2H2O + 3Fe^3+}$$
Since permanganate is purple, and manganese dioxide is an insoluble brown solid, we have a built in indicator for redox titrations like these.
However, magnesium ion content cannot be determined this way since $\ce{Mg^2+}$ is the highest usual oxidation state for magnesium. The electron configuration for magnesium is $1s^2 2s^2 2p^6 3s^2$ or $[\ce{Ne}]3s^2$. The $\ce{Mg^2+}$ ion has the electron configuration of $\ce{[Ne]}$, which is relatively stable. Remove an additional electron from $\ce{Mg^2+}$ to get $\ce{Mg^3+}$, you get an ion with the electron configuration of $1s^2 2s^2 2p^5$, which is the same electron configuration as electron-hungry fluorine atoms, but with a nucleus containing three more protons. $\ce{Mg^2+}$ cannot be chemically oxidized further.
Now, one could use this method to determine the concentration of many other metal ions that can be oxidized, including even $\ce{Mn^2+}$.
$$\ce{3Mn^2+ + 2MnO4- + 2H2O -> 5MnO2 + 4H+}$$

Thank you so much! It was actually more simple than I thought it would be. Thank you for your very helpful explanation.


text:
Skipping the defatting stage in extraction of alkaloids
I am attempting to extract certain alkaloids from green plant matter, which is very high in waxes and fats.
I understand that in this scenario it is common to first acidify and then use a non-polar solvent to de-fat the solution.
I am curious though: say I were to basicify and extract alkaloids without any de-fatting. If I were then to add HCl solution to the non-polar solvent which now contains the alkaloids, wouldn't this in theory be equivalent to the de-fatting stage? Wouldn't the alkaloids would now be in the aqueous layer, and the lipids would be stuck in the non-polar layer?
As the acid/base method is so common, I am wondering if there are any downsides to the method described above that I am unaware of. I only have enough material for one shot so I would just like to hear some input before I attempt this expedited method.
May main fear would be emulsions that wouldn't break up. Is this a valid concern that is remedied by a preliminary de-fatting stage? Are there other concerns I should be wary of?

You need to allow your aqueous solvent to gain access to the regions that contain alkaloids. If these are occluded by fatty matter then you have to remove them otherwise your extraction would be inefficient. The emulsions do break up, you can centrifuge to separate the phases efficiently.

I am no chemist, but a biologist. I routinely extract alkaloids from some insects. We don't follow this defatting protocol you describe to rid the mix of waxes, in fact I had never heard of it. We just use silica column separation by affinity -- our alkaloids get captured in the silica by a strongly apolar solvent which will carry the fats off, and then the silica can be washed with a more polar solvent to release alkaloids. Acidification helps a lot in removing them from the silica. Does that sound helpful?

One big risk with the method you propose is foaming and gellation turning your extractions into a huge mess.  Under basic conditions, the fats (e.g. triacylglycerols or TAGs) are likely to hydrolyze, forming carboxylate salts of fatty acids.  "Carboxylate salts of fatty acids" is a long way of saying soap.  These soap-like compounds could lead to excessive foaming or gellation of the sample, which will hinder phase separation and gunk up your apparatus.


text:
Molecules aren't the same as atoms?
Question is simple but tricky, for example my chemistry teacher says that preservatives on food for example Nitrate N3 are not good in excess for your body (like everything else), but if Nitrogen is in the air, and we breath it what is the real difference in this case between Nitrate and Nitrogen.
Lets formulate the final question:
Is there any difference between taking 3 Nitrates (9 Nitrogen atoms) and taking 9 Nitrogen atoms?

First I will clear up a few misconceptions you have:

Nitrate is actually the ion $\ce{NO3-}$, not $\ce{N3}$. Three nitrogens exist in the ion $\ce{N3-}$ which is called an azide ion. Nitrates are indeed used as food preservatives, e.g. sodium nitrate $\ce{NaNO3}$.
Nitrogen in the air is in a diatomic form, i.e. $\ce{N2}$. Nitrogen is more stable this way because it can share electrons between the two atoms in the form of a triple bond. This gives each nitrogen a full 8 electrons in its valence shell, making it more stable than free nitrogens which have only have 5.

Since nitrogens are so stable being diatomic, if any two come into contact they will likely react to form $\ce{N2}$, so it is hard to have free nitrogen atoms by themselves. $\ce{N3-}$ is a negatively charged ion so it will usually be ionically bonded to a positive ion e.g. $\ce{Na+}$ in sodium azide $\ce{NaN3}$, which is very toxic but now isn't purely nitrogen. So I think as a better example to answer your question, I will compare $\ce{O2}$ (oxygen in the air) with $\ce{O3}$ (ozone). Is there a difference between inhaling 3 $\ce{O2}$ and 2 $\ce{O3}$ if it means you're taking 6 oxygens in both cases?
For the same reasons as nitrogen, oxygen is very stable as $\ce{O2}$. Since it's so stable, it is unlikely to react with anything unless given a lot of energy, i.e. it is inert. Therefore we can breathe in oxygen safely, and it can safely be carried around the body until it reaches places where it can be given enough energy to react in processes that keep us alive.
Now with ozone, this molecule is less stable than $\ce{O2}$. The electrons in the bonds need to be shared amongst 3 nucleuses, while trying to have a full octet. This gives something called a resonance structure which stabilises the ozone, but it is still less stable than $\ce{O2}$. This means it is more reactive! And if it's more reactive, it means it can react much quicker than $\ce{O2}$ and with molecules in our body that we don't want it to react with. It can also decompose to the $\ce{O2}$ and an oxygen free radical $\ce{O.}$, which is a free oxygen atom with a single unpaired electron, making it extremely reactive. Breathing in ozone can cause throat irritation and chest discomfort among other symptoms, caused by ozone reacting with molecules in the lungs.
So the way the atoms are bonded matter. Their bonding gives them different reactivities and other properties like boiling point and solubility, which make molecules behave differently to free atoms or other molecules made of the same atom.


text:
What does the "s" mean in s-cis and s-trans conformations
I am learning about conjugated unsaturated systems, and came upon s-cis and s-trans conformations in conjugated dienes.
So what does the "s" mean in s-cis and s-trans conformations?

The s stands for single, as in single bond. It means the double bonds are cis or trans to each other based around the single bond.

It is a common enough expression to search for, if more information is required.


text:
How does the equipartition theorem apply to vibrational modes?
Specifically, how, based on the idea that energy will be shared equally among all degrees of freedom, does one come to the conclusion that each vibrational mode of a molecule will occupy $kT$ units of energy?
When learning statistical thermodynamics, classes often spend a lot of time talking about the Maxwell-Boltzmann distribution and even deriving that the expectation value for the energy of a monoatomic ideal gas is $\frac{3}{2}kT$ where $\frac12 kT$ comes from energy distributed to each cartesian coordinate plane.
Now, I find that I learn a whole lot from mathematical derivations of these types of things, and from simply working through the math and understanding its physical meaning.
So, I want to know, both on a conceptual level and through some sort of mathematical explanation, why does each vibrational mode of a molecule contribute $kT$ to the overall energy of the molecule when those modes are occupied?

My only guess is that one degree of freedom is kinetic energy (associated with the moving atoms) and the other is potential energy (analogy with a spring works here) but, if that is true, much clarity would be gained from a mathematical demonstration of this.

The following article explains it well (and also has some nice visuals for the vibrational degrees of freedom): https://www.tec-science.com/thermodynamics/kinetic-theory-of-gases/equipartition-theorem/

As you probably already know, the equipartition theorem states that each quadratic
degree of freedom will, on average, possess an energy $\frac{1}{2}kT$, where a ‘quadratic degree of freedom’ is one for which the energy depends on the square of some property.
Now lets consider the kinetic and potential energies associated with translational, rotational and vibrational energy:

Translational degrees of freedom:  $~E = \frac{1}{2}mv^2$

Rotational degrees of freedom:  $~E = \frac{1}{2}Iω^2$

Vibrational degrees of freedom: $~E = \frac{1}{2}mv^2 + \frac{1}{2}kx^2$

As you can see that for translational and rotational degrees of freedom, there is only one quadratic. Hence each translational and rotational state will contain $\frac{1}{2}kT$ energy.
However for vibrational states, the energy contains two quadratic contributions. Therefore each vibrational state will contain $kT$ energy.
Now lets consider the reasoning behind this. You are right when you say that the vibrational degree of freedom depends on kinetic and potential energy and hence has 2 quadratic contributions. In the equation for the energy of the vibrational state, $\frac{1}{2}mv^2$ represents the kinetic energy and $\frac{1}{2}kx^2$ represents the potential energy.
A molecule in the vibrational state acts like a harmonic oscillator. So let consider $H_2$. You can imagine that the bond between the 2 hydrogen atoms is like a spring which contracts and expands in length.

The average bond length can be thought as the equilibrium length of the bond. When the bond the contracts, the displacement from this equilibrium length is known as 'x'. Now using Hooke's Law, the potential energy of the system is $\frac{1}{2}kx^2$ where k is the spring constant while the kinetic energy is $\frac{1}{2}mv^2$. Hence the total energy of the system is given by: $~E = \frac{1}{2}mv^2 + \frac{1}{2}kx^2$


text:
Is silicon oxide=rock?
Are common rock (I.e. Rock from mountain, river, bricks, or even concrete) actually silicon oxides? Or it is just one of compositions?

You ask:

Are common rocks (e.g. rock from mountains or rivers, bricks, or even concrete) actually silicon oxides? Or it is just one of compositions?

Rocks can contain silicon oxides, but that's not part of what the definition of a "rock" implies. From an introductory course in geology at the University of Texas at Austin, a rock is defined as:

Any coherent, naturally occurring substance generally composed of minerals.

That's all there is to it. Whether or not the minerals include silicon oxides has nothing to do with a rock being called a rock.

The latter statement is more accurate. Rocks are mostly silicates and aluminosilicates; though they do contain silicon and oxygen, they also contain other elements. Silicon oxide per se, albeit not uncommon, is a relative minority.
Upd. Thought I'd rather include a quote from the link above.

More than 90% on the crust is composed of silicate minerals. Most
abundant silicates are feldspars (plagioclase (39%) and alkali
feldspar (12%)). Other common silicate minerals are quartz (12%)
pyroxenes (11%), amphiboles (5%), micas (5%), and clay minerals (5%).
The rest of the silicate family comprises 3% of the crust. Only 8% of
the crust is composed of non-silicates — carbonates, oxides, sulfides,
etc.

Quartz is $\ce{SiO_2}$; the rest is more complicated.

Small addition: concrete which is made of cement is essentially CaO hardened to calcium carbonate. Also has gypsum. There are silicate additives but the main components are not silicates.


text:
Nomenclature priorities with ethers, acyl groups and ketones
$\hspace{6cm}$
(2-oxopropionyl)oxy butanoic acid
$\hspace{6.5cm}$
3,4-dioxo 4-methoxy butanoic acid
$\hspace{6.3cm}$
3-(2-oxopropyl),6-oxo heptanoic acid
$\hspace{6.25cm}$
3-propionyl,6-oxo heptanoic acid
$\hspace{6.3cm}$
3-(3-oxobutyl),6-oxo hexanoic acid
Aldehyde takes priority over ketone, yes?
Have I got these right?
PS: With the third molecule, wouldn't it be convenient if we could have a ketonyl group so that instead of 2-oxopropyl , one could say propanonyl?

In principle, your assumptions about the order of priority for classes is correct. According to the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book), the order of seniority of classes in decreasing order of seniority is as follows.

(…)
  7. acids
  (…)
  9. esters
  (…)
  15. aldehydes
  16. ketones
  (…)
  42. ethers
  (…)

Thus, it is correct that the names for all compounds given in the question have the suffix ‘oic acid’.
However, the names proposed by you still contain a few errors.
Your name “(2-oxopropionyl)oxy butanoic acid” is ambiguous since the locant for the complex substituent group ‘(2-oxopropionyl)oxy’ is missing.
The complete name is “4-[(2-oxopropionyl)oxy]butanoic acid”.
However, the preferred name is 4-[(2-oxopropanoyl)oxy]butanoic acid.
Your other names include the correct suffixes and locants; however, the suffixes are not cited in alphabetical order. The correct names are

4-methoxy-3,4-dioxobutanoic acid (not “3,4-dioxo 4-methoxy butanoic acid”)
6-oxo-3-(2-oxopropyl)heptanoic acid (not “3-(2-oxopropyl),6-oxo heptanoic acid”)
6-oxo-3-propanoylheptanoic acid (not “3-propionyl,6-oxo heptanoic acid”)
6-oxo-3-(3-oxopropyl)heptanoic acid (not “3-(3-oxobutyl),6-oxo hexanoic acid”)

Sorry, I drew the first one wrong. Edited now.  Anyway, the the whole point I drew that one was I wanted to know, whenever there is an oxygen atom double bonded to the end carbon of a substituent group, does it automatically become an acyl?


text:
Ordering the activity of metals

So I'm stuck on this question because I'm having trouble breaking it down. So I know the answer already but like most stuck students I'm not sure how to get to it.
The problem is that I am not sure how to break this question down.

Can you please type the question in? Images are not searchable. And could you please be elaborate about what part confuses you?

The activity series summarizes the experimental behavior of metals and their cations. A more active metal will displace the cation of a less reactive metal from solution.
Let's consider the case of zinc and copper. Zinc is higher on the activity series than copper. Zinc will displace copper ions from solution:
$$\ce{Zn(s) + Cu^2+ (aq) -> Zn^2+ (aq) + Cu(s)}$$
If we place a strip of zinc metal into a solution containing $\ce{Cu^2+}$ ions, the some of the zinc will dissolve into the solution, while some of the copper will plate onto the zinc.
What happens if we put a copper strip into a solution of $\ce{Zn^2+}$? Very little. Copper is less active than zinc. Copper metal will not displace zinc ions from solution.
$$\ce{Cu^2+ (aq) + Zn(s) -> No\ reaction}$$
If you did not know which was more active, copper or zinc, these two experiments would give you the information you need. Zinc displaces copper from solution. Copper does not displace zinc. Zinc is more active than copper $(\ce{Zn>Cu})$.
How can you apply this logic to your question?


text:
Calculating solubility in water with other species present
I'm very confused about calculating solubility.
Everything is in temperature of $298\ \mathrm K$
From Atkins's book, exercise 16.83:
Based on solubility constant, calculate solubility of $\ce{Al(OH)3}$ in acid solution of $\mathrm{pH}=4.5$, $K_{\rm s}=1\cdot10^{-33}$.
Using stoichiometry and equilibrium constants I proceed as follows:
$\mathrm{pH}=4.5$ corresponds to $\mathrm{pOH}=9.5$ and
$$\ce{Al(OH)3 (s) \rightarrow Al^3+ (aq) + 3OH- (aq)}$$
$$K_{\rm s}=\ce{[Al^3+][OH- ]^3}$$
Let's call $\ce{[Al^3+]} = x$.
From stoichiometry and the assumption that $\ce{[OH- ]} >> 10^{-7}$ we know that $\ce{[OH- ]} \approx 3x+10^{-9.5}$.
We get a equation like
$$x(3x+10^{-9.5})^3=K_{\rm s}$$
which I solve as $x=2.39\cdot10^{-9}$, but Atkins's answer is $3.0\cdot10^{-5}$.
Atkins's solution looks like:
$$K_{\rm s}=\ce{[Al^3+][OH- ]^3}$$
$${K_{\rm s}\over[\ce{OH-}]^3}=[\ce{Al^3+}] = 3.0\cdot10^{-5}$$
It looks like Atkins assumes that $[\ce{OH-}]=10^{-9.5}$.
I have two questions:

Why does Atkins assume that $\ce{Al(OH)3}$ doesn't affect $\mathrm{pH}$?
Which one is correct?

There might very well be an issue with the value of $K_{\rm s}$ you're using - are you certain you've copied it correctly from the book? Also, see this relevant post on the vagaries of the solubility constant for $\ce{AlOH3}$.

@ToddMinehardt
It's $1\cdot 10^{-33}$ for sure. I have double checked.

Since the solution is acidic you have to consider $\ce{[OH- ]}$ concentration to be $10^{-7}$
Then solubility product: $$k_\text{sp} = \ce{[Al^3+ ] [OH- ]^3}$$
And if $x$ amount dissociated: $$k_\text{sp} = x \cdot (3x)^3$$
Then we have,
$$10^{-33} = 27 \cdot x^4$$
So $$x = 2.466 \cdot 10^{-9}~\mathrm{mol/L}$$

"Since the solution is acidic you have to consider [OH−] concentration to be 10−7" It shouldn't cointain then $[OH−] = \frac{K_w}{[H3O^+]}=10^{-9.5}$ or i think wrong ?
Anyway, then why Atkins says in his book that answer is $3.0⋅10^{−5}? mol/l $

Clearly you can't make an acidic solution by dissolving Al(OH)3. Either the question is wrong or you're holding back essential facts. And I assume latter to be the case

It may as well be the case where temperature is not 298K (25°C). So you ought to subtract the pH value from the specific pKw value given