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There is an excellent introduction to the use of abbreviations in general at http://www.chem.qmul.ac.uk/iupac/misc/symbols.html. We probably want to steal some of it.

Other lists of abbreviations: http://www.chem.qmul.ac.uk/iupac/AminoAcid/A1819.html, http://www.27eps.unina.it/manuscripts3.htm, http://themerckindex.cambridgesoft.com/TheMerckIndex/AdditionalTables/pdfs/AbbreviationsandSelectedDefinitions.pdf, http://scooter.cyto.purdue.edu/pucl_cd/flow/vol4/4_teach/data/acronyms/acron.htm, http://www.chem.ucalgary.ca/courses/551/listofabbreviations.pdf, http://www.users.totalise.co.uk/~tbroom/acrobat/chem.pdf, http://www.galchimia.com/downloads/files/200Problems.pdf, https://paragon.acs.org/paragon/ShowDocServlet?contentId=paragon/menu_content/authorchecklist/jo_authguide.pdf

The following nicknames (with capitalization as shown) may be used without further explanation to refer to the structures shown. In all cases, the nicknames should be used to refer only to the specific structures shown, without further substitution and without the presence of further charges, radicals, or non-natural isotopy.

Authors are welcome to create their own abbreviations as well, but any abbreviations not included in the list below should be defined clearly when they are used. When creating new abbreviations, it is recommended that an all-caps style be used for abbreviations that are formed as acronyms (BOM = Benzyl Oxy Methyl), while an initial-caps style should be used for abbreviations that are formed simply by shortening a longer word (Ac = Acetyl).

Several of the abbreviations listed below include portions of the text in italics. The italicization shown is the preferred formatting of those abbreviations. However, the corresponding forms without capitalization are also acceptable. [Yes? Or should we recommend only one or the other?]

The first column in the table below indicates whether it is listed at http://www.chem.qmul.ac.uk/iupac/misc/symbols.html. The second column indicates whether we want to continue to recommend that that abbreviation can be used without further explanation..

Listed?	Recommend?	Abbreviation	Other Abbreviations	Full structure
yes	yes	Ac
	yes?	Acm
yes	?	Act
	yes?	9-BBN
	yes?	Bn
yes	yes	Boc BOC	t-BOC
	yes?	BOM
	yes?	BPOC
	yes?	Bs
	yes?	Bt
yes	yes	BTM
yes	yes	Bu (recommended)	Bun n-Bu
	yes?	Bui	i-Bu  (recommended) iBu
	yes?	Bun	Bu  (recommended) n-Bu nBu
	yes?	Bus	s-Bu (recommended) sBu
yes	yes	But	t-Bu  (recommended) tBu
yes	yes	Bz
yes	?	Bza
yes	?	Cam
yes	?	Cbm
	yes?	Cbz CBZ
yes	yes	cHx	Cy (recommended)
yes	?	Cm
	yes	Cp
yes	yes	cPe
	yes	Cy (recommended)	cHx
	yes?	Ddz
yes	yes	DEAE
yes	yes	DNP
yes	yes	Dns
yes	yes	Et
	yes?	FMOC
	yes?	i-Bu (recommended)	Bui iBu
	yes?	i-Pr (recommended)	iPr Pri
	yes?	iBu	Bui i-Bu (recommended)
	yes?	iPr	i-Pr (recommended) Pri
yes	?	Ips
yes	?	Mal
yes	yes	Me
	yes?	MEM
	yes?	Mes
	yes?	MOM
	yes?	Ms
yes	?	Mtc
	yes?	MTM
yes	?	Mz
	yes?	n-Bu	Bu (recommended) Bun nBu
	yes?	n-Pr	nPr Pr (recommended) Prn
	yes?	nBu	Bu (recommended) Bun n-Bu
	yes?	nPr	n-Pr Pr (recommended) Prn
	yes?	Nb
yes	?	Nbs
yes	?	NSu
	yes?	PCP
yes	?	Pe
yes	yes	Ph
yes	yes	Pht
yes	?	Pip
	yes?	Piv
	yes?	PMB
yes	yes	POC
yes	yes	Pr	n-Pr nPr (recommended) Prn
	yes?	Pri	i-Pr (recommended) iPr
	yes?	Prn	n-Pr nPr Pr (recommended)
yes	?	Ptc
yes	?	Pz
yes	?	Qu
	yes?	s-Bu (recommended)	Bus sBu
	yes?	sBu	Bus s-Bu (recommended)
yes	?	Suc
	yes?	t-BOC	BOC (recommended) Boc
	yes?	t-Bu (recommended)	But tBu
	yes?	tBu	But t-Bu (recommended)
	yes?	TBDMS (recommended)	TBS
	yes?	TBDPS
	yes?	TBS	TBDMS (recommended)
	yes?	TES
	yes?	Tf
	yes?	THP
	yes?	TIPS
	yes?	TMS
yes	yes	Tos	Ts (recommended)
	yes?	Tr	Trt (recommended)
	yes?	TROC
yes	yes	Trt (recommended)	Tr
	yes?	Ts (recommended)	Tos

The following abbreviations have been used in some circumstances, but it is proposed that they no longer be recommended:

Listed?	Recommend?	Abbreviation	Other Abbreviations	Full structure	Comments
yes?	no?	Z	Cbz CBZ		Andrey: I'd say No for "Z" (Cbz) seems better as soon as Z has some meaning of variable group, as X, Y, Z... Jonathan: I've also seen it used in circumstances where it can be confused with a stereochemical indicator SUGGESTED: The use of the abbreviation "Z", for benzoxycarbonyl-, is not recommended. If an abbreviation for that structure is desired, "CBZ" should be used instead. [Note: this is a departure from the recommendations at http://www.chem.qmul.ac.uk/iupac/misc/symbols.html.]
yes	no?	Bzl	Bn		Andrey: not sure that it is used often and close to Bz -- benzoyl SUGGESTED: The use of the abbreviation "Bzl", for benzyl-, is not recommended, in large part because of its easy confusion with "Bz" for benzoyl-. If an abbreviation for that structure is desired, "Bn" should be used instead. [Note: this is a departure from the recommendations at http://www.chem.qmul.ac.uk/iupac/misc/symbols.html.]
yes	no?	Np			Andrey: I vote by two hands against Np and Nps/NpS/SNp. The reason is that even for IUPAC page there are: -SNp          for 4-nitrophenylthio and NpS-/Nps- for 2-nitrophenylthio If it is not a misprint, it is very bad that simple changes of direction lead to different structures. (Also in general case, abbreviation that imply but doesn't cite exact position of substitutent could be less preferred if we need reason for our decision about some of them.)
yes	no?	Nps			(see previous)
yes	no?	Snp			(see previous)
yes	yno?	Bzh			Andrey: Not sure about Bzh (benzhydryl) - quite rare and may be simply drawn with common Ph labels. Jonathan: Yup: only five pages on google have "Bzh" and "benzhydryl"
	yes?	TCP			Andrey: TCP in chemistry is most often used for substances and most often for 2,4,5-trichlorophenol an dless for tricresyl phosphate (also found for 2,3,5,6-tetrachloropyridine) (even most hits with both "TCP" and "trichlorophenyl" mention TCP only for 2,4,5-trichlorophenol) this abbreviation itself doesn't state the positions of chloro in phenyl "T" can be used both for tri and tetra Not sure that it is often used. Keith: In the Auk,TCP is also an OTC antiseptic. Yes, the active ingredient is trichlorophenol. So best avoided.

Should we list amino acids here or just reference the amino acids doc?
Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val (see longer list at http://www.chem.qmul.ac.uk/iupac/misc/symbols.html)

How about inorganic ligands (cross-ref to the revised Red Book)?

What about ISIS/Draw, ChemSketch, etc?