org.gennbo.help.show.txt Maven / Gradle / Ivy
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Jmol: an open-source Java viewer for chemical structures in 3D
SHOW (create a molecule model from
its 'formula')
SHOW ...\n"
(create supramolecular model from\n"
radical 'acceptor' and ligand\n"
'donor-i' formulas)\n"
The chemical 'formula' is a valid Lewis-type"
line formula, similar to textbook examples."
Use colons to denote multiple bonds (C::O double"
bond, C:::N triple bond, etc.) and parentheses"
to identify repeat units or side groups."
Atomic symbols in the range H-Cf (Z = 1-98)"
and repetition numbers 1-9 are allowed."
Chemical formula symbols are case-sensitive.\n"
Ligated free radicals (with free-valent acceptor"
sites) can also be formed in specified hapticity"
motifs with chosen molecular ligands. Radical"
and ligand monomers are"
specified by valid line formulas, with each"
ligand formula preceded by a number of"
colons (:) representing the number of 2e sites"
in the desired ligand denticity (such as ':NH3'"
for monodentate ammine ligand, '::NH2CH::CH2'"
for bidentate vinylamine ligand, or ':::Bz' for"
tridentate benzene ligand). Each such ligation"
symbol may be prefixed with a stoichiometric"
coefficient 2-9 for the number of ligands.\n"
In both molecular and supramolecular formulas,"
valid transition metal duodectet structures"
are also accepted. For d-block molecular species,"
the default idealized metal hybridization isomer"
can be altered with the REBOND command."
For d-block species one can also include"
coordinative ligands (:Lig), enclosed in"
parentheses and preceded by a colon symbol."
Formal 'ylidic' charges are allowed only for"
adjacent atom pairs (e.g., dative pi-bonds).\n"
Models may also be specified by using acronyms"
from a library of pre-formed species (many"
at B3LYP/6-31+G* optimized level). Each such"
acronym can also be used as a monovalent ligand"
in MUTATE commands, as illustrated below.\n"
Common cyclic aromatic species\n"
Bz C6H6 benzene\n"
A10R2L C10H8 naphthalene\n"
A14R3L C14H12 anthracene\n"
A18R4L C18H16 tetracene\n"
A22R5L C22H20 pentacene\n"
A14R3 C14H10 phenanthrene\n"
A14R4 C14H12 chrysene\n"
A16R4 C16H10 pyrene\n"
A18R4 C18H12 triphenylene\n"
A20R5 C20H12 benzopyrene\n"
A20R6 C20H10 corannulene\n"
A24R7 C24H12 coronene\n"
A32R10 C32H14 ovalene\n"
Common cyclic saturated species\n"
R6C C6H12 cyclohexane (chair)\n"
R6B ' ' (boat t.s.) \n"
R6T ' ' (twist-boat)\n"
R5 C5H10 cyclopentane\n"
R4 C4H8 cyclobutane\n"
R3 C3H6 cyclopropane\n"
RB222 [2,2,2]bicyclooctane\n"
RB221 [2,2,1]bicycloheptane (norbornane)\n"
RB211 [2,1,1]bicyclohexane\n"
RB111 [1,1,1]bicyclopentane (propellane)\n"
R5S spiropentane\n"
RAD adamantane\n"
\n"
Common inorganic ligands\n"
acac acetylacetonate anion (bidentate)\n"
bipy 2,2\"\"-bipyridine (bidentate)\n"
cp cyclopentadienyl anion (:, ::, :::)\n"
dien diethylenetriamine (tridentate)\n"
dppe 1,2-bis(diphenylphosphino)ethane\n"
(bidentate)\n"
edta ethylenediaminetetraacetate anion\n"
(hexadentate)\n"
en ethylenediamine (bidentate)\n"
phen 1,10-phenanthroline (bidentate)\n"
tren tris(2-aminoethyl)amine (tetradentate)\n"
trien triethylenetetramine (tetradentate)\n"
Peptide fragments (HC::ONHCH2R)\n"
GLY glycine\n"
ALA alanine\n"
VAL valine\n"
LEU leucine\n"
ILE isoleucine\n"
PRO proline\n"
PHE phenylalanine\n"
TYR tyrosine\n"
TRP tryptophan\n"
SER serine\n"
THR threonine\n"
CYS cysteine\n"
MET methionine\n"
ASN asparagine\n"
GLN glutamine\n"
ASP aspartate\n"
GLU glutamate\n"
LYS lysine\n"
ARG argenine\n"
HIS histidine\n"
Nucleic acid fragments\n"
NA_G guanine\n"
NA_C cytosine\n"
NA_A adenine\n"
NA_T thymine\n"
NA_U uracil\n"
NA_R ribose backbone fragment\n"
In addition, the SHOW command recognizes\n"
'D3H' (trigonal bipyramid) or 'D4H' (octahedral)\n"
species, created as SF5, SF6, respectively.\n"
('SHOW' and 'FORM' are synonymous commands.) \n"
Molecular examples:\n"
SHOW CH3C::OOH acetic acid\n"
SHOW CH3(CH2)4CH3 n-hexane\n"
SHOW WH2(:NH3)2 diammine of WH2\n"
SHOW NA_C cytosine\n"
SHOW CH4 methane\n"
MUTATE 3 RAD methyladamantane\n"
SHOW ALA alanine\n"
MUTATE 7 ALA ala-ala\n"
MUTATE 17 ALA ala-ala-ala, etc.\n"
Supramolecular examples:\n"
SHOW CH3 :H2O hydrated methyl radical\n"
SHOW Cr 2:::Bz dibenzene chromium\n"
SHOW CrCl3 2:H2O :NH3\n"
SHOW Cr 3::acac\n"
SHOW Cr ::::::edta\n",