Axel Drefahl • www.axeleratio.com/axel
A state and shape annotation is indicated by a two-character annotation marker. Letters of a state and shape annotation marker (SSAM) are in lowercase. In the following, SSAMs are listed alphabetically along with their meaning.
al
atomic layer
am
amorphous state
an
antimatter (see
examples)
aq
in aqueous solution
at
single atom
ay
alloy
az
azeotrope or component of azeotrope
br
branch or branch-like structuce (mesoscale)
cl
cluster (small nanoparticle containing fewer than 104 atoms or molecules)
co
core (in core-shell composite)
cp
colloidal particle
cr
crystalline state
db
distributed
dp
dispersed
ds
dissolved (if in water, aq
is preferred)
el
chemical element, generic; anchored to sole square-bracket-enclosed element symbol
fw
framework structure (at supramolecular level)
gr
grain
gs
gaseous state
ic
intercalated
in
incorporated (in matrix)
ip
ion pair
lc
liquid crystalline state
lq
liquid state
ma
matrix
mc
micelle
ml
material
mp
mesoporous material
mx
mixture
nb
nanobelt
nc
nanocrystal
nd
nanodisc
nf
nanoflower
nh
nanowhisker
nk
nanoflake
nl
nanocluster
nm
nanoframe
no
nanoporous material
np
nanoparticle, generic
nr
nanorod
ns
nanostructure, generic
nt
nanotube
nw
nanowire
pa
particle
pc
poly-crystalline state
po
porous material
qc
quasicrystalline state
qd
quantum dot
s2
salt that contains two different cations or anions (double salt)
sc
single-crystalline (monocrystalline) solid
sd
solid state
sh
shell (in core-shell composite)
su
substance
tf
thin film
tw
twinned crystal
In a notation of a multi-species material, such as a salt in solution,
the SSAM is
only attached once—preferably to the right-most species.
For example, the system “sodium chloride in aqueous solution”
is encoded with aq
anchored to the chloride ion
subnotation:
[Na+].[Cl-]{aq}
“NaCl dissolved in aqueous methanol” is encoded as
[Na+].[Cl-]{dsslv=O,CO}
where the dictionary entry with key slv
specifies the two solvents—comma-separated—in SMILES notation:
O
for water and CO
for methanol.
[1] Drefahl, A.
CurlySMILES: a chemical language to customize and annotate encodings
of molecular and nanodevice structures.
J. Cheminf. 2011, 3:1.
DOI:
10.1186/1758-2946-3-1.
[2] Weininger, D.
SMILES, a Chemical Language and Information System. 1. Introduction
to Methodology and Encoding Rules
Chem. Inf. Comput. Sci 1988, 28, pp. 31-36.
DOI:
10.1021/ci00057a005.
[3] SMILES - A Simplified Chemical Language.
DAYLIGHT Chemical Information Systems, Inc.
URL:
https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html.
© 2010- Axel Drefahl. All rights reserved.