Crystal chemistry of 1:1 molecular complexes of carbamate salts formed by slow aerial carbonation of amines

Article abstract of DOI:10.1007/s10870-008-9391-1

Amines do have rare tendency to undergo aerial carbonation to form carbamic acid. Four different 1:1 molecular complex of carbamate salts reported herein obtained by the aerial carbonation of cyclic amines. X-ray crystal structures show a systematic change in the molecular structure did bring some gradual supramolecular change from one structural motif to another.

Full text of DOI:10.1007/s10870-008-9391-1

J Chem Crystallogr (2008) 38:787–792
DOI 10.1007/s10870-008-9391-1
ORIGINAL PAPER
Crystal Chemistry of 1:1 Molecular Complexes of Carbamate
Salts Formed by Slow Aerial Carbonation of Amines
Raju Mondal Æ Manas Kumar Bhunia
Received: 4 July 2007 / Accepted: 2 April 2008 / Published online: 18 April 2008
Ó Springer Science+Business Media, LLC 2008
Abstract Amines do have rare tendency to undergo aerial
carbonation to form carbamic acid. Four different 1:1
molecular complex of carbamate salts reported herein
obtained by the aerial carbonation of cyclic amines. X-ray
crystal structures show a systematic change in the molec-
ular structure did bring some gradual supramolecular
change from one structural motif to another.
crystallisation is initiated by nucleation wherein the
pre-nuclear molecular aggregates or embryo grow into
nuclei that subsequently lead to crystal. This pre-nucleation
aggregates is believe to be driven by a molecular recog-
nition process which not necessarily be initiated by the
molecule (to be crystallised) itself. The initiator could be a
foreign molecule as well, which may act as some sort of a
catalyst towards the molecular recognition and subse-
quently crystallization [3].
Keywords Amine carbonation Á Crystal growth Á
Molecular structure and crystal engineering
The present work is very much related to the assistance
of a ‘foreign’ molecule to the crystallisation process of
molecular complexes of carbamate salts, which are other-
wise been known to form powder [4]. Diffraction quality
single crystal was obtained with ease for four different
carbamate salts (1–4) (Scheme 1) when they were crys-
tallised in presence of a diol (for 4, the diol is a part of the
molecular complex itself) which otherwise form white
powder.
Introduction
Crystallisation is often considered as an art. Notwith-
standing, even a highly skilled artist on this field frequently
finds it hard, sometime even impossible to obtain a dif-
fraction quality single crystal. The major reason could be
attributed to the fact that although the process of crystal-
lisation been known historically, the underlying theory of
crystallisation process or crystal growth, at the molecular
level, is still a murkier subject [1].
Amines has a rare tendency to undergo aerial carbon-
ation to form carbonated adducts. One such report on
ammonium carbamate salt by Adams and Small [4b] shows
a similar hydrogen bonding pattern to that of extensively
studied primary amide group. Hanessian et al. [5] carried
out a systematic study while serendipitously came across
carbonation of amine compounds while working on the
molecular recognition study of some supraminols. How-
ever, they were unable to obtain any diffraction quality
single crystal from slow ‘natural’ atmospheric carbonation;
instead they reported crystal structure obtained by ‘forced’
carbonation. Notwithstanding, their observation that a
diol play a crucial role during the crystallisation of the
resultant carbamate salt is highly relevant to the present
work. The present work highlight similar occurrences,
except the carbonation take place before crystallisation and
not the product of any solid state transformation.
Even with advent of highly sophisticated instruments,
we are still a far way off from probing or observing a
crystallisation process at the molecular level. Instead
the popular crystallisation theories are usually based on
imagination with the background of chemical and physical
knowledge [2]. According to one such popular theory,
R. Mondal (&) Á M. K. Bhunia
Department of Inorganic Chemistry, Indian Association for the
Cultivation of Science, Raja S.C. Mullick Road,
Kolkata 700032, India
e-mail: icrm@iacs.res.in
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J Chem Crystallogr (2008) 38:787–792
Scheme 1 Schematic
representation of the
carbonation reaction and
compounds 1–4
H
Cl
HO
NH-CO2-
NH2
CO
H3N+
+
2
+
OH
Cl
H
DDDA
H3N+
NH-CO2-
NH-CO2-
H3N+
+
+
1
2
CO2-
NH
N-CO2-
N+
H3N+
OH
+
HO
H2O
+
4
3
Experimental
A comparison of 1 with that of Hanessian’s report
reveals remarkable similarity, with the protonated amine
(ammonium) group adopt a tetrahedral arrangement, form
a somewhat distorted square motif with N+–H_-O bonds
X-ray Crystallography
˚
˚
˚
Reflections were collected at 120 K using a Bruker
(1.87 A, 173.5°; 1.58 A, 177.7°; 2.44 A, 141.8°) supported
˚
SMART 6000 CCD area detector, and Mo Ka radiation
˚
with a wavelength of 0.71073 A. Structure solution was via
by amidic N–H_O bond (2.43 A, 167.0°) (Fig. 1a).
Interestingly, even one of the ammonium hydrogen atom
˚
˚
direct methods, and full matrix anisotropic least square
refinement of all non-hydrogen atoms was carried out with
SHELX-97 [13]. All hydrogen atoms were located in the
electron density difference maps and their positional and
isotropic thermal parameters were refined. Crystallographic
data and final refinement details are given in Table 1.
Crystallographic data (excluding structure factors) for the
structures reported in this paper have been deposited with
the Cambridge Crystallographic Data Centre. Deposition
No. are given in Table 1. Copies of the data can be
obtained, free of charge, on application to the CCDC, 12
Union Road, Cambridge CB2 lEZ, UK (Fax: +44-1223-
336033; e-mail: deposit@ccdc.cam.ac.uk).
forms a bifurcated N–H_O bond (2.44 A, 141.8°; 1.88 A,
157.4°), similar to that of Hanessian’s report. With a
striking similarity in structural topology showing ‘‘a
pleated sheet-like central core motif consisting of fused
square planar eighth-membered H-bonded units, run along
the vertical ‘b’ axis of the assemblage’’ (Fig. 2) [5]. It is
imperative to note here that both the square motif and the
fused eight membered motifs are observed frequently for
supraminols [7]. However there is a subtle difference,
being an ionic molecular complex, here the square motifs
are ‘by-default’ comprised of N+–H_-O bond only rather
than alternative N–H_O and O–H_N bonds as observed
for supraminols.
With this background, we then start looking for new
carbamate salts for some 20 plus different amines that we
have used for our studies of amine solvates of DDDA [6].
For acyclic amines we routinely obtained the correspond-
ing DDDA-amine solvate crystals but even after using
several crystallisation batches we did not obtain any car-
bamate salt. Results with cyclic amines, on the other hand,
are much more encouraging.
Result and Discussion
The diol of interest, 1,5-dichloro-trans-9,10-diethynyl-9,10-
dihydroanthracene-9,10-diol (DDDA) (Scheme 1) shows a
unusual tendency to form solvates, especially with organic
bases, such as amines [6]. It is when we were trying to
crystallise DDDA with cyclohexyl amine, we experience a
concomitant crystallisation lead to two distinctly different
morphologies. While one of them is the corresponding
amine solvate [6b] of DDDA, the other one appears to be a
1:1 molecular complex of carbamate salt (1).
We were successful in obtaining good diffraction quality
single crystals (2) along with the corresponding DDDA-
amine solvate crystal while working with cycloheptyl
amine. The crystal structure of 2 is almost similar to that of
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J Chem Crystallogr (2008) 38:787–792
789
Table 1 Crystallographic data
and structure refinement
parameters for the titled
1
2
3
Empirical formula
C13H26N2O2
242.36
C15H30N2O2
270.41
C11H24N2O3
232.32
compounds
Formula wt.
Crystal system
Space group
Monoclinic
P2(1)/n
Triclinic
P-1
Triclinic
P-1
˚
a [A]
10.9742(7)
5.3297(3)
23.7760(14)
90
5.3762(2)
12.3344(6)
12.3848(6)
75.892(2)
79.001(2)
77.821(2)
770.11(6)
1.166
6.4425(2)
7.8889(2)
13.4873(4)
96.666(1)
101.129(1)
105.347(1)
638.40(3)
1.209
˚
b [A]
˚
c [A]
a [°]
b [°]
c [°]
Volume [A ]
Dcalc [g/cm3]
96.602(2)
90
3
˚
1381.42(14)
1.165
l [mm-1
]
0.078
0.077
0.087
2h [°]
6.0–55
5.3–55
5.4–55
Range h
Range k
Range l
-13 to 14
-6 to 6
-30 to 30
12228
-6 to 6
-15 to 15
-16 to 16
10347
-8 to 8
-10 to 10
-17 to 17
6801
Reflns. collected
Unique reflns.
R1 [I [ 2 r(I)]
wR2 [all]
3150
3491
2938
0.0396
0.0391
0.0380
0.0628
0.0909
0.1011
Goodness-of-fit
0.815
1.020
1.046
-3
)
˚
Largest diff. peak and hole (e A
CCDC number
0.163 and -0.175
634154
0.334 and -0.166
634153
0.235 and -0.187
* For details of compounds 4
see ref
634155
Fig. 1 (a) Crystal packing of 1
and (b) 2 showing the square
motifs with the tetrahedral
arrangement of the protonated
amine group highlighted with
bold bonds for 1. Notice that
some hydrogen atoms are
omitted for clarity
a
b
+
-
˚
1 with a cartwheel arrangement of the molecules centering
the square motif. Again a columnar arrangement of fused
square planar eight-membered hydrogen bonded network
dominates the interaction pattern (N –H_ O, 1.78 A,
˚
˚
168.5°; 1.85 A, 165.6°; 2.29 A, 130.1°) (Fig. 1b). The
sheet-like central core for 2, same as in 1, also stacked
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J Chem Crystallogr (2008) 38:787–792
Fig. 2 Packing diagram of (a) 1
and (b) 2, showing the columnar
arrangement of the non-polar
parts centering the square motifs
a
b
˚
along the shortest axis (Fig. 2), i.e., ‘a’ axis (5.376 A),
which is, surprisingly, almost same as the shortest axis (‘b’
˚
axis, 5.329 A) of 1.
All the three carbamate salts show a common trend of
crystallising in presence of DDDA along with the corre-
sponding DDDA-amine solvates. Whereas several attempts
to obtain crystals of carbamate salt by taking only amine,
amine with solvent but without DDDA or alcohol or any
hydroxyl group, at best, resulted in white powder. These
findings suggest that the diol may provide some impetus
during aggregation, which subsequently breaks up into two
aggregates. One of them forms ionic salts comprised of
carbamate ions while the other one with favourable molec-
ular recognition process leads to DDDA-amine solvate.
The prospect of a diol being of some assistance to
crystallisation for carbamate salts with basic chair confor-
mation of cyclohexyl ring is even more prominent for 4
(Fig. 4). The 1:1 molecular complex was obtained during
one of our study of 4-amino cyclohexanol [9] and not while
using DDDA. In other words we obtained crystal of the
Appearance of crystal for 3 only further emphasizes the
importance of cyclohexyl ring skeleton towards carbonation
and subsequent crystallization. Dreele et al. has reported a
similar structure of morpholine carboxylate with basic
chair conformation [8]. Interestingly, unlike 1 and 2, 3
crystallized as a hydrate, understandably to compensate the
absence of one amine proton and henceforth the deficiency
of N–H_O bonds compared to that of the carbamate salts
resulted from primary amines. As evidently two O–H_O
bonds involving water molecules provide the extra stability.
The crystal packing can envisage as an extended version of
the square motif which are cross-linked by two water
˚
˚
molecules with O–H_O (1.95 A, 168.5°, 1.94 A, 172.2°)
bonds (Fig. 3). Topologically, there is little difference from
1 or 2, with almost similar stacking along shortest axis and a
cartwheel arrangement of molecules around the square
motif. The only difference is the changeover from two
bifurcated N–H_O bonds to two ‘stand alone’ N–H_O
˚
˚
(1.76 A, 170.6°; 1.80 A, 176.8°) bonds, with both the car-
boxylate oxygen atoms are now involved instead of only
one carboxylate oxygen atom. In effect, the square motif is
no longer embedded in the extended square motif but
expands to an ‘extended’ square motif.
Fig. 3 Extended motif observed for 3, notice how two water
molecules are bridging between two motifs
Fig. 4 Crystal Structure of 4 showing both square and extended
square motif
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J Chem Crystallogr (2008) 38:787–792
791
carbamate salt in absence of DDDA, yet, interestingly not
in absence of any diol. This self assistance perfectly make
sense considering the fact that usually other amines of
interest are exist in liquid state and do not crystallize on
their own, they usually require a diol (e.g. DDDA) for
supramolecular recognition that could led to crystallisation
(transform in to solid state). However, for 4-amino cyclo-
hexanol being solid, molecular recognition become more
of a self-recognition and not dependent of location and
direction of any other molecule.
equatorial substituent is one of the most stable conforma-
tions known for organic molecules. Naturally, a reaction
coordinate would be expected to shifts towards the product
if the product generates any extra stability, such as adopting
a chair form with equatorial substituent. This is probably the
reason why the molecular complexes obtained for this work
mostly consist of cyclohexane ring wherein carbamic
groups are at the equatorial position of a chair form.
Conformations of cyclopentyl amine and cycloheptyl
amine support the same only from the opposite directions.
The half-envelop conformation of cyclopentyl amine is
more rigid than that of chair form of cycloheptyl ring, yet
the later undergo carbonation and subsequently crystallised
and not the former. The reason could be attributed to the
fact that while the amine group occupied the pseudo-
equatorial position in cyclohetyl amine, the same occupied
the axial position for cyclopentyl amine.
Usually, molecules with rigid conformation such as the
chair conformation of cyclohexyl ring tend to crystallize
much more easily than that of a flexible conformation. At
the same time, conformational flexibility would certainly
have a role to play on the rate of carbonation. Probability
of aerial carbonation, being a very slow reaction, would
certainly be greater for a conformationally ‘steady’ mole-
cule than that of a molecule with conformational ‘flip-flop’,
which is much faster compared to carbonation time
scale. Two different conformational pseudopolymorphs of
DDDA-cyclooctylamine are important in this regard [6a].
Wherein the presence two different conformations of cyc-
looctylamine would have certainly reduced the chances of
carbonation while the strong and directional hydrogen
bonding in the resultant conformational pseudopolymorphs
would certainly have affected the nucleation-assistant role
of DDDA, as a result no carbamate salt was obtained.
Again, molecular conformation of the resultant carba-
mate salt is also an important factor. Chair form with
Structural Changeover
Supramolecular changes in from one structural motif to
another are no longer an uncommon territory for structural
chemists. Recently we have witnessed such occurrences
wherein systematic change in the molecular structures did
bring some rational change in the supramolecular structure
in a highly comprehensible manner [10].
A closer look at the four crystal structures reported
herein shows a gradual change in the supramolecular
structure. Starting with the structure 1 showing a somewhat
Fig. 5 Illustration of gradual
structural changeover from
square motif to extended square
motif using the central core
from 1 ? 2 ? 3 ? 4
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J Chem Crystallogr (2008) 38:787–792
References
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resulting a central core comprised of extended square
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Conclusion
Amines containing cyclic rings often undergo aerial car-
bonation resulting white powder, however diffraction
quality single crystals are seldom obtained. We have been
successful in obtaining single crystals for four 1:1 molec-
ular complexes of carbamate salt. Crystallisation of all four
carbamate salts reported herein are apparently influenced
either externally or internally by diol, while absence of
which resulted in white powder.
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However one should be careful before making such cor-
relation, for instance we were unable to reproduce the
carbamate salt reported earlier using cyclohexyl-1,2-dia-
mine. Several attempts yield only the DDDA-Amine solvate.
Nevertheless, repetitive crystallisation of 1:1 molecular
complexes of carbamate salts in presence of DDDA does
vindicate our hypothesis that diol being of assistance
towards nucleation, just as the importance of stereochem-
istry of the non-polar parts dictating the directionality of
the non-bonded interactions.
123