Topological correspondence between crystal structure of 2,4,6-trimethylbenzene-1,3,5-tris(methanaminium) 2,4,6-trimethylbenzene-1,3,5-triacetate and cesium chloride

Article abstract of DOI:10.1135/cccc20001587

Solid-state self-assembly of 2,4,6-trimethylbenzene-1,3,5-tris(methanaminium) 2,4,6-trimethylbenzene-1,3,5-triacetate is mediated by hydrogen bonding. It gives rise to three-dimensional network of hydrogen bonds in which each trication is coordinated with

Full text of DOI:10.1135/cccc20001587

Crystal Structure
1587
TOPOLOGICAL CORRESPONDENCE BETWEEN CRYSTAL STRUCTURE
OF 2,4,6-TRIMETHYLBENZENE-1,3,5-TRIS(METHANAMINIUM)
2,4,6-TRIMETHYLBENZENE-1,3,5-TRIACETATE
AND CESIUM CHLORIDE
a
b2
Jaroslav PODLAHA , Ivana CÍSAŘOVÁa1, Daniel ALEXANDERb1, Petr HOLÝ
,
b3
b4,
Tomáš KRAUS and Jiří ZÁVADA
*
a
Department of Inorganic Chemistry, Charles University, Hlavova 2030, 128 40 Prague 2,
Czech Republic; e-mail: cisarova@prfdec.natur.cuni.cz
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic,
Flemingovo nám. 2, 166 10 Prague 6, Czech Republic; e-mail: dalex@uochb.cas.cz,
1
b
1
2
3
4
petrholy@uochb.cas.cz, kraus@uochb.cas.cz, zavada@uochb.cas.cz
Received Jun e 30, 2000
Accepted August 25, 2000
Solid-state self-assem bly of 2,4,6-trim eth ylben zen e-1,3,5-tris(m eth an am in ium ) 2,4,6-trim eth yl-
ben zen e-1,3,5-triacetate is m ediated by h ydrogen bon din g. It gives rise to th ree-dim en sion al
n etwork of h ydrogen bon ds in wh ich each trication is coordin ated with eigh t trian ion s an d
vice versa. Th e resultin g crystal structure topologically correspon ds to th e sim ple in organ ic
cesium ch loride type.
Key w ord s: Carboxylic acids; Am in es; Hydrogen bon ds; Crystal en gin eerin g; X-Ray diffrac-
tion ; Supram olecular ch em istry; Self assem bly.
Majority of inorganic ionic com poun ds of th e M+X– type exists in th e cesium
ch loride or sodium ch loride crystal type, each ion in th e form er structure
bein g coordin ated with eigh t, wh ereas in th e latter with six coun ter-ion s
(Figs 1a, 1b). For a given salt, th e m axim um coordin ation n um ber is pre-
ferred, wh ich allows a close con tact between opposite-ch arge ion s with out
com pressin g ion s of th e sam e ch arge. Relative size of th e coun ter-ion s is th e
decisive factor. A sim ple geom etric an alysis1 sh ows th at th e ratio of th e ra-
dii of th e oppositely ch arged ion s, r–/r+ m ust be equal or less th an 1.37 in
order to secure effective coordin ation of th e an ion with eigh t cation s, an d
vice versa. In prin ciple, an an alogous situation can be also expected for th e
correspon din g polyvalen t salts, M(n+)X(n–), provided th at th e participatin g
ion s possess sph erical sym m etry an d un iform ch arge distribution .
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

1588
Podlaha et al.:
Such a stipulation does n ot h old for organic ionic com poun ds sin ce th ey
usually do n ot exh ibit eith er sph erical sym m etry or un iform ch arge distri-
bution . Form ation of crystal structures of such com poun ds is accordin gly
con trolled by oth er (m ore com plex) rules an d forces. Does it, h owever, ex-
clude an alogies with sim ple crystal structures of th e in organ ic salts?
Desiraju, in h is pen etratin g study2a on crystal en gin eerin g poin ted out th at
any organ ic crystal (ion ic as well as n on -ion ic) m ay be depicted as a n et-
work with th e m olecules as n odes an d sh owed, at th e sam e tim e, th at th e
n ext logical step in th is visualization is to search for th e topological corre-
spon den ces with its in organ ic coun terpart. So far, on ly on e pertin en t exam -
ple of such correspon den ce h as been reported2b
.
In th is paper, we wish to report on an un expected case of a topological
correspon den ce between crystal structure of a com plex triple-ch arged or-
gan ic an d a sim ple sin gle-ch arged in organ ic salt.
RESULTS AND DISCUSSION
Self-assem bly of organ ic salts in crystal is often organ ized by ion ic h ydro-
gen bon din g3–5 allowin g th e sim ultan eous use of direction al h ydrogen
bon ds an d less direction al electrostatic in teraction between th e opposite-
ch arge un its. As a part of our in terest in th is self-assem bly, we h ave exam -
in ed th e h ydrogen bon din g pattern in th e organ ic salt 1 arisin g by triple
proton tran sfer from 2,4,6-trim eth ylben zen e-1,3,5-triacetic acid 2 to
2,4,6-trim eth ylben zen e-1,3,5-tris(m eth an am in e) 3 in th e solid state. Th e
startin g com poun ds 2 an d 3 were prepared from th e correspon din g
tribrom ide 6 by sim ple procedures outlin ed in Sch em e 1.
b
a
FIG. 1
Cesium ch loride (a) an d sodium ch loride (b) crystal type
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

Crystal Structure
1589
N3
NH2
CH3
H3C
N3
CH3
N3
H3C
H2N
ii or iii
i
CH3
NH2
CH3
Br
4
3
H3C
Br
CH3
Br
CH3
CN
COOH
iv
6
H3C
NC
CH3
CN
H3C
HOOC
CH3
v
CH3
COOH
CH3
5
2
i
: NaN3, DMSO
iv : NaCN, DMSO
v : NaOH, H2O/EtOH; HCl
ii : PPh3; NH4OH; HCl; DOWEX OH-
iii : H2, Pd/C
SCHEME 1
Mixin g of equim olar am oun t of 2 an d 3 in water followed by crystalliza-
tion of th e resultin g precipitate from aqueous eth an ol gave th e triple-
ch arged salt 1. Accordin g to elem en tal an alysis supported by NMR spectra
an d X-ray data, th e obtain ed salt
C
1 correspon ds to th e form ula
12H24N33+·C15H15O63–·3H2O·0.5C2H5OH. X-Ray diffraction an alysis of th e
sin gle crystal con firm s th at all carboxylic groups are ion ized an d all am in o
groups are proton ized.
Molecular Structure
Lookin g at th e m olecular structure of both participatin g triple-ch arged ion s
in a crystal of salt 1 (Fig. 2), on e fin ds n oth in g un usual with th e bon d dis-
tan ces an d an gles. Th e carbon atom s of th e ben zen e rin gs plus th e directly
bon ded carbon atom s are alm ost exactly plan ar an d th e am m on ium as well
as th e carboxylate groups are distributed in th e “up-up-down ” m an n er,
taken relatively to th e correspon din g ben zen e rin g. Th e geom etry of th e
positively ch arged n itrogen atom s is rough ly tetrah edral, supportin g th e
form ulation of th e trication . In th e trian ion , th e m etric param eters of th e
carboxy groups are close, but n ot iden tical, to th ose of th e isolated dissoci-
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

1590
Podlaha et al.:
ated carboxyl6. Th e differen ce m ay be due to th e perturbation caused by
h ydrogen bon din g.
Hydrogen Bonding Pattern
In teraction between th e opposite triple-ch arged ion s resultin g from 2 an d 3
in th e salt crystal is m ediated by h ydrogen bon din g. Th ere is a variety of
h ydrogen bon ds sum m arized in Table I. Alth ough som e of th em sh ould be
taken with caution due to th e problem associated with th e h ydrogen atom s
at N1 an d, in part, also on O9, m ost of th em are un am biguous. Lin ks be-
tween th e am m on ium an d carboxy groups are eith er direct or by m ean s of
+
water m olecules. Th e direct NH···O lin ks (Fig. 3) are m arkedly asym m etric,
in accordan ce with th e ch arge of th e participatin g ion s. Th e sh ortest h ydro-
gen -bon d con tacts between th e opposite ion s give rise, via th e +NH···O
bon ds, to zig-zag ladders wh ich are placed in parallel in xz plan e (Fig. 4)
an d stacked in th e perpen dicular plan e (Fig. 5). A close an alysis reveals th at
th e n eigh bourin g ladders are lin ked by lon ger h ydrogen bon d in teraction s
(+NH···O, +NH···OH2···OH2···–O2C, +NH···OH2···C2H5OH···–O2C). Th is gives
rise to th e th ree-dim en sion al n etwork of h ydrogen bon ds (Fig. 6) in wh ich
each trication is coordin ated with eigh t trian ion s an d vice versa (Fig. 7). In
th is way, th e situation closely resem bles th e crystal packin g of cesium ch lo-
ride (Fig. 1a).
FIG. 2
Sin gle-crystal m olecular structure of salt 1 with atom labellin g
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

Crystal Structure
1591
FIG. 3
Direct ion ic h ydrogen bon ds –+NH3···–OOC– in th e crystal structure of salt 1
FIG. 4
Sch em atic represen tation of zig-zag ladders form ed by th e sh ortest ion ic h ydrogen bon ds (cf.
Fig. 3) in xz plan e. Th e opposite triple-ch arged ion s are represen ted by blue an d red sph eres
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

1592
Podlaha et al.:
FIG. 5
Stackin g of zig-zag ladders in perpen dicular (xy) plan e
FIG. 6
Lin kin g of th e n eigh bourin g ladders by solven t m olecules (H2O, EtOH) gives rise to th e
th ree-dim en sion al n etwork of h ydrogen bon ds
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

Crystal Structure
1593
FIG. 7
In th e resultin g th ree-dim en sion al n etwork, each trication is coordin ated with eigh t
trian ion s an d vice versa
EXPERIMENTAL
1,3,5-Tris(azidom eth yl)-2,4,6-trim eth ylben zen e (4)
Sodium azide (5.2 g, 80 m m ol) was added to
a solution of 1,3,5-tris(brom om eth yl)-
2,4,6-trim eth ylben zen e 6 (ref.7; 7.98 g, 20 m m ol) in dim eth ylform am ide (100 m l). Th e m ix-
ture was stirred at room tem perature for 5 h an d poured in to cold water (400 m l). Th e re-
sultin g precipitate was filtered off an d wash ed with water. After dryin g it was crystallized
from m eth an ol; yield 5.5 g (96%), m .p. 64–65 °C. 1H NMR (CDCl3): 4.45 s, 6 H (CH2); 2.48 s,
9 H (CH3). EI-MS, m/z (rel.%): 285 (M+, 43), 243 (72), 200 (100), 185 (38), 172 (63), 158 (77),
157 (84), 144 (66), 130 (57), 115 (40), 91 (44), 77 (41), 65 (28), 51 (28), 39 (34). (Caution:
Explosion occurred in the course of elemental analysis.)
2,4,6-Trim eth ylben zen e-1,3,5-tris(m eth an am in e) (3)
Procedure A (trihydrochloride). Triph en ylph osph in e (15.17 g, 57.8 m m ol) was slowly added
to a stirred solution of triazide 4 (5.5 g, 19.3 m m ol) in tetrah ydrofuran e (150 m l). After 2 h ,
con cen trated am m on ium h ydroxide (22 m l) was added, th e m ixture was stirred for 15 h an d
evaporated to dryness. The residue was suspended in water (500 ml) and neutralized with 1 M HCl
to pH 5. Th e suspen sion was extracted with toluen e (3 × 250 m l), th e aqueous layer was fil-
tered th rough cellite an d evaporated to dryn ess; yield 5.8 g (95%). 1H NMR (D2O): 4.24 s,
6 H (CH2); 2.50 s, 9 H (CH3). Positive spectrum FAB-MS, m/z: 208 ([MH]+ – 3 HCl). For
C
12H24Cl3N3 (316.7) calculated: 45.51% C, 7.64% H, 13.27% N; foun d: 45.13% C, 7.95% H,
12.95% N.
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

1594
Podlaha et al.:
Procedure B (free base). A gen tle stream of h ydrogen was bubbled in to a m ixture of triazide
4 (2.85 g, 10 m m ol) an d palladium catalyst (10% Pd/C, 50 m g) in m eth an ol (30 m l). After
th e sligh tly exoth erm ic reaction ceased (approxim ately 40 m in ), th e catalyst was rem oved
by filtration , th e reaction m ixture was evaporated to dryn ess an d th e solid residue was dis-
solved in h ot toluen e (50 m l). After coolin g, th e crystals were collected an d dried in vacuo.
Yield 1.87 g (90.2%), m .p. 143–145 °C. 1H NMR (CDCl3): 3.93 s, 6 H (CH2); 2.46 s, 9 H
(CH3); 1.27 br s, 6 H (NH2). EI-MS, m/z (rel.%): 207 (M+, 6), 191 (13), 190 (100), 175 (45),
171(14), 170 (20), 158 (49), 156 (13), 144 (10), 131 (10), 91 (10). For C12H21N3 (207.3) calcu-
lated: 69.52% C, 10.21% H, 20.27% N; foun d: 69.52% C, 10.27% H, 19.94% N.
1,3,5-Tris(cyan om eth yl)-2,4,6-trim eth ylben zen e (5)
Potassium cyan ide (31.24 g, 451 m m ol) was treated with 1,3,5-tris(brom om eth yl)-
2,4,6-trim eth ylben zen e 6 (ref.7; 39.9 g, 100 m m ol) in dim eth yl sulfoxide (300 m l) at room
tem perature for 24 h . Usual work-up an d crystallization (eth an ol) afforded 19.9 g (84%) of
TABLE I
Possible h ydrogen bon ds. Sym m etry code: i, 1 – x, –y, 1 – z; ii, 0.5 – x, y, 0.5 – z; iii, x – 0.5,
–y, z + 0.5; iv, 1 – x, 1 – y, 1 – z; v, x, 1 + y, z; vi, 0.5 – x, 1 + y, 0.5 – z; vii, 1 – x, y, z; viii,
1.5 – x, 1 + y, 0.5 – z
Atom
H
Distan ce, Å
An gle, °
X–H
Y
X
Y
X–H
H
Y
X Y
N1
N1
N1
N2
N2
N2
N3
N3
N3
O7
O7
O8
O8
O9
O9
H1NA
H1NB
H2NC
H2NA
H2NB
H2NC
H3NA
H3NB
H3NC
H7OA
H7OB
H8OA
H8OB
H9OA
H9OB
O1i
O6
0.89
1.93
1.98
1.92
2.741(8)
2.830(7)
2.801(6)
2.76(1)
150
159
170
0.89
O6i
O3ii
O8
0.89
0.74(7)
1.0(1)
0.92(9)
1.00(8)
0.88(6)
0.93(7)
0.81
2.11(8)
1.9(1)
1.86(10)
2.04(8)
1.91(6)
1.73(8)
1.91
146(7)
163(8)
173(7)
166(6)
160(5)
169(6)
177.2
147.2
156.7
172.0
172.7
147.3
2.82(1)
O4iii
2.777(9)
3.013(8)
2.752(8)
2.649(9)
2.720(8)
2.855(7)
2.862(8)
2.880(8)
2.744(8)
2.705(8)
O7
O1iv
O5v
O9iv
O9vi
O7
0.81
2.4
0.81
2.10
O9vii
0.81
2.08
O2
0.81
1.94
O4viii
0.81
1.99
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

Crystal Structure
1595
th e product, m .p. 256–258 °C (ref.9 251–253 °C). 1H NMR (CDCl3): 3.74 s, 6 H (CH2); 2.46 s,
9 H (CH3). EI-MS, m/z (rel. %): 237 (M+, 50), 210 (100), 197 (35), 183 (12), 170 (18), 154 (7),
128 (11), 115 (11), 91 (5), 77 (6), 63 (4), 51 (5), 39 (6). IR (KBr): 2 978 m , 2 957 m (νas CH3);
2 882 w sh (νs CH3); 2 248 s (ν CN); 1 574 w, 1 471 w sh (ν rin g); 1 454 m (δas CH3); 1 428 vs
(βs CH2); 1 386 m (δs CH3); 1 311 w (γs CH2); 1 298 w, 1 101 w, 1 023 m (arom atics); 1 232 w
(γas CH2); 935 w, 922 w, 907 w (ν C–CN); 803 m (βas CH2). For C15H15N3 (237.3) calculated:
75.92% C, 6.37% H, 17.71% N; foun d: 75.62% C, 6.43% H, 17.92% N.
2,4,6-Trim eth ylben zen e-1,3,5-triacetic Acid (2)
Th e tris(cyan om eth yl) derivative 5 (6.7 g, 28.2 m m ol) was h eated un der reflux with 20%
aqueous sodium h ydroxide in eth an ol (28 m l) for 14 h . Th e reaction m ixture was acidified
with con cen trated h ydroch loric acid, th e precipitate was filtered off, wash ed with water an d
recrystallized from water. Yield 6.82 g (82%), m .p. 282–284 °C (ref.5 283–285 °C). 1H NMR
(CD3SOCD3): 12.27 s, 3 H (COOH); 3.63 s, 6 H (CH2); 2.16 s, 9 H (CH3). EI-MS, m/z (rel.%):
294 (M+, 4), 256 (22), 213 (8), 185 (8), 167 (9), 149 (28), 129 (21), 111 (14), 97 (28), 83 (34),
69 (51), 57 (93), 43 (100). IR (KBr): 3 479 w (ν OH, COOH m on om er); 3 073 s, 3 002 s (ν OH,
COOH dim er); 2 975 s (νas CH3); 2 893 s sh (νs CH3); 2 738 s, 2 645 s, 2 548 m (dim er);
1 697 vvs, 1 655 s (ν C=O); 1 572 w, 1 477 m sh (ν rin g); 1 458 m (δas CH3); 1 438 m sh (βs
CH2); 1 412 s, 1 288 s, 1 243 s (ν C–O + δ COH, COOH dim er); 1 393 s, 1 378 s sh (δs CH3);
1 323 m (γs CH2); 1 227 s (γas CH2); 1 303 s sh , 1 189 s, 1 243 s (arom atics); 1 075 w, 1 066 w
(δas CH3); 930 s br (γ COH, COOH dim er); 799 w (βas CH2). For C15H18O6 (294.3) calculated:
61.22% C, 6.16% H; foun d: 60.96% C, 6.14% H.
X-Ray Diffraction An alysis
Sin gle crystal X-ray diffraction data: C12H24N33+·C15H15O63–·3H2O·0.5C2H5OH, M.w. 578.7,
m on oclin ic, space group P2/n (n on -stan dard settin g of P2/c, No. 13), a = 17.476(1) Å, b =
9.103(2) Å, c = 18.908(2) Å, β = 100.583(7)°, V = 2 957.3(5) Å–3, Z = 4, Dc = 1.300 g cm –3
,
F(000) = 1 252. A prism atic crystal of th e dim en sion s 0.2 × 0.1 × 0.3 m m (grown from 20%
aqueous eth an ol) was m easured at 293 on CAD4 diffractom eter with graph ite-
K
a
m onochrom ated MoKα radiation (λ = 0.71073 Å). Absorption was neglected (µ = 0.10 m m –1).
Th e lattice param eters were determ in ed from 25 reflection s in th e 12–13° θ-ran ge. Th e in ten -
sities of reflection s were m easured by θ–2θ scan between h –16,16 , k 0,8 , l 0,18 . Th ree
stan dard reflection s m on itored durin g th e m easurem en t in 1 h in tervals sh owed an in ten sity
variation of 2%. From 3 090 m easured reflection s, 2 097 were un ique (R = 0.0513) an d 1 553
in t
were regarded as “observed” accordin g to th e I ≥ 2σ(I) criterion . Th e structure was solved by
direct m eth ods9 (SHELXS86) an d refin ed by SHELXL93 (ref.10) usin g a full-m atrix least
squares procedure based on F2. Th ere rem ain ed sign ifican t region s of electron den sity on th e
differen ce m ap, wh ich were in terpreted as on e h alf of disordered eth an ol per form ula un it
(origin ated from th e solven t used for obtain in g th e sin gle crystal). Th e disorder was m odeled
with two position s of eth an ol related by sligh tly m utually displaced (by 0.45 Å) cen tral car-
bon atom s an d term in al atom s of 0.5 relative occupan cy or carbon an d/or oxygen , i.e., th ese
atom s are in terch an ged in th e two position s. Th is m odel appears justified sin ce (i) it leads to
con siderable lowerin g of th e R-factor, (ii) th e resultin g m etric param eters of eth an ol are
quite reason able: th e cen tral-term in al in teratom ic distan ce (i.e., th e m ean of C–C an d C–O)
is 1.43 Å an d th e bon d an gle on th e cen tral carbon is 122°, (iii) th e presen ce of eth an ol was
con firm ed by NMR spectroscopy. From th e crystallograph ic poin t of view, its m olecule is lo-
Collect. Czech. Chem. Commun. (Vol. 65) (2000)

1596
Podlaha et al.:
cated in a ch an n el with in th e structure displayin g n o close in term olecular con tacts, h en ce
th e disorder. No attem pt was m ade to locate th e h ydrogen atom s of eth an ol. All oth er h y-
drogen s were clearly visible in th e differen ce m ap. Th ey were refin ed isotropically except for
th e h ydrogen s at N1 an d for th ose in water m olecules wh ich , for un kn own reason s, beh aved
erratically on refin em en t. Th ese h ydrogen atom s were even tually fixed at th e position s
foun d from th e differen ce m ap an d given th e isotropic tem perature factor of N1 an d of water
oxygen s m u ltip lied by 1.2. All th e n on -h ydrogen atom s were refin ed an isotrop ically.
Th e fun ction m in im ized was Σw(F2 – F2 )2, wh ere w = 1/[σ 2(F2) + (0.104P)2 + 1.670P], P = (F2
+
o
o
c
o
2F2)/3. Th is m odel con verged for 417 param eters to R = 0.056, Rw = 0.145, GOF = 1.066 and
c
(∆/σ)m ax = ±0.02 for n on -H atom s. Th e fin al differen ce electron den sity m ap displayed ex-
trem e values of 0.82 e Å–3 (n ear th e eth an ol m olecule) an d –0.34 e Å–3. Th e tables of ob-
served an d calculated structure factors an d of an isotropic displacem en t param eters, as well
as th e stan dard CIF file produced by SHELXL93, can be obtain ed from th e auth or (I. C.)
upon request. Crystallograph ic data for th e structure reported in th is paper h ave been depos-
ited with th e Cam bridge Crystallograph ic Data Cen tre as supplem en tary publication n um ber
CCDC-145738. Copies of th e data can be obtain ed free of ch arge on application to CCDC,
e-m ail: deposit@ccdc.cam .ac.uk.
This work was supported by the Grant Agency of the Czech Republic (grants No. 203/97/0025 and
No. 203/00/0138).
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