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IUMSC   Indiana University Molecular Structure Center

In order to be able to search for compounds of interest it is necessary to define a consistent set of definitions to be used in the data tables. Thus while H2O and HOH are both understood to be "water," knowing that you only have to search for H2O will certainly facilitate searching for compounds and ligands of interest. A glance at various journals reveals that a variety of conventions are used. For the purpose of the formula search in the IUMSC Data Server, the following practices, mostly those recommended by IUPAC, are proposed. A major difference, of course, is that no subscripts or superscripts are used. In the following rules and table, the five digit numbers in braces, {}, are examples of IUMSC usage and link to the example data page.

  • Lower case letters are used for all abbreviations, except for those of certain hydrocarbon radicals (Me, methyl; Et, ethyl; Ph, phenyl; etc) and Ac, the acetyl radical.
  • Ligands are set off with parentheses, with exceptions for simple (atomic) ligands such as oxides and chlorides that immediately follow the metal, for example [RuCl2(dmso)(C15H27N3), CH2Cl2] {99011}.
  • A specific isomer, such as t-Bu, that follows another symbol in a ligand should be preceded by a dash, e.g., (P-t-Bu..). Without it, in this example, (Pt-Bu..) would probably be flagged in a search for Pt compounds. If more than one of the isomer is present, parentheses should be used, e.g., P(t-Bu)2(Ph).
  • The atom or atoms of a ligand which coordinate to a metal atom are listed first, e.g., benzoate is (O2CPh). Acetonitrile, MeCN, as a ligand is (NCMe){94106}. Similarly the central atom of a separate ion or solvent molecule is listed first, e.g., [NMe4]+, CH2Cl2.
  • Solvent molecules involving oxygen are an exception. Thus methanol as a ligand is (OHMe) but as a solvent is MeOH {86107}. Water as a ligand is (OH2) {95170), but as a solvent it is H2O. Acetic acid as a ligand is OHAc, but as a solvent it is AcOH {94160}.
  • Those hydrogen atoms that can be replaced by the metal atom are shown by the symbol H. Thus the molecule Hacac forms an anionic ligand acac. Benzene is HPh {94049}. Toluene, MePh {94102}, is an exception (to avoid confusion between Htol and HBz).
  • Ions are set off with square brackets. Ionic charges greater than one are written as a number followed by a + or -, e.g., [ion]2-, not [ion]-2.
  • Ions are separated with a space, solvent molecules with a semi-colon+space, e.g., 5[N(Et)4]+ [V15O36]5-; 2MeCN
  • The empirical formula begins with carbon and hydrogen, if any, with the remaining atoms in alphabetical order. Single letter symbols precede two letter symbols with the same first letter, e.g., B before Ba.
  • The empirical formula will include all atoms in the title formula including those in solvent molecules that are clearly identified in the structure determination.
  • A ligand with a complicated formula should have an empirical type of formula, e.g., an adenine ligand with two ethyl substituents was simply listed as (C9H13N5) in IUMSC structure {96140}. Except for trivial cases, the compounds that we receive from organic chemists should also be listed in this way

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Reference:

International Union of Pure and Applied Chemistry. Commission on the Nomenclature of Inorganic Chemistry. Nomenclature of Inorganic Chemistry: Recommendations 1990. Boston: Blackwell Scientific, 1990.

The abbreviations in use are listed below. This will be expanded from time to time as needed.

Ac acetyl, CH3CO
acac acetylacetonate, CH3COCHCOCH3
bpy 2,2'-dipyridine, or bipyridine
Bu butyl (n-,i-,s-,t- : normal,iso,secondary,tertiary)
Bz benzyl, C6H5CH2
cod cycloocta-1,5,-diene, C8H12
cotcyclooctatetraene, C8H8
Cp cyclopentadienyl, C5H5
Cp*pentamethylcyclopentadienyl
Cy cyclohexyl, C6H11
dbm dibenzylmethyl, C6H5COCHCOC6H5
dmedimethoxyethane, CH3OCH2CH2OCH3
dmf N,N'-dimethylformamide, HCON(CH3)2
dmpe 1,2-bis(dimethylphosphino)ethane, (CH3)2PCH2CH2P(CH3)2
dmpm 1,2-bis(dimethylphosphino)methane, (CH3)2PCH2P(CH3)2
dmsodimethyl sulfoxide, (CH3)2SO
edtethane-1,2-dithiolate, SCH2CH2S
Et2dbm(see dbm) C6H4(C2H5)COCHCOC6H4(C2H5)
en ethylenediamine, H2NCH2CH2NH2
Et ethyl, C2H5
hmpa hexamethylphosphoric triamide, OP(N(CH3)2)3
Memethyl, CH3
MePhtoluene
Mesmesityl, 2,4,6-trimethylphenyl
Ntol NC6H4CH3 {94240}
OAcacetate, CH3CO2
OCH2-t-Buneopentoxide
O2CPh benzoate
ORalkoxides, e.g., OMe, O-t-Bu
O2Ctol CH3C6H4CO2 {94152)
ox oxalate, C2O4
Phphenyl, C6H5
phth phthalate, H2phth = phthalic acid, C6H4(COOH)2
pic picolinate, Hpic = picolinic acid, C5H4NCOOH
Pr propyl (n- or i- : normal or iso)
pypyridine, C5H5N
pzHpz = pyrazole, C3H4N2
ROHalcohols, e.g., MeOH, t-BuOH
sal salicylaldehyde, C6H4(OH)(CHO)
thftetrahydrofuran, C4H8O
tol tolyl, CH3C6H4
triflateCF3SO3 {94124}
18-crown-6 1,4,7,10,13,16-hexaoxacyclooctadecane {94049}

Author: W.E. Streib, IUMSC, March 19, 1997. Comments to webiumsc@indiana.edu.

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