Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids

Article abstract of DOI:10.1039/c4ce00605d

Four linear connecting amino acid derived ligands, 1-4, and one potentially three connecting, 5, were prepared by the reaction of the appropriate terephthaloyl dichloride or benzene-1,3,5-tricarbonyl trichloride with the methyl ester protected amino acid.

Full text of DOI:10.1039/c4ce00605d

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Crystal structures and hydrogen bond analysis of
five amino acid conjugates of terephthalic and
benzene-1,2,3-tricarboxylic acids†
Cite this: DOI: 10.1039/c4ce00605d
Anirban Karmakar,‡ a Clive L. Oliver,b Ana E. Platero-Prats,c Elina Laurilaa
*
a
*
and Lars Öhrström
Four linear connecting amino acid derived ligands, 1–4, and one potentially three connecting, 5, were
prepared by the reaction of the appropriate terephthaloyl dichloride or benzene-1,3,5-tricarbonyl
trichloride with the methyl ester protected amino acid. Amino acids used here were alanine (1, 5),
isoleucine (2), leucine (3) and valine (4). Crystalline forms of four amino acid substituted terephthalamides
(2,2′-(terephthaloylbis(azanediyl))dipropanoic acid dihydrate 1; 2,2′-(terephthaloylbis(azanediyl))bis(3-
methylpentanoic acid) monohydrate 2; 2,2′-(terephthaloylbis(azanediyl))bis(4-methylpentanoic acid)
dihydrate 3; 2,2′-(terephthaloylbis(azanediyl))bis(3-methylbutanoic acid) dihydrate 4) and one benzene-
1,3,5-tricarboxamide molecule (2,2′,2″-((benzene-1,3,5-tricarbonyl)tris(azanediyl))tripropionic acid
hemihydrate 5) were characterised and the single crystal structures were solved. All the compounds form
hydrogen bonded 2D and 3D nets. Linear connecting amino acid derivatives can be categorised into three
groups depending on the hydrogen bond patterns and final structures. Compounds 1 and 2 form
3D structures but the final structure is different due to the different hydrogen bond synthons.
Compounds 3 and 4 are isostructural and form 2D hydrogen bonded structures while 5 forms a
hydrogen bonded pcu-net. Intermolecular interactions have been analysed with Hirshfeld surfaces
and graph set symbols.
Received 24th March 2014,
Accepted 27th May 2014
DOI: 10.1039/c4ce00605d
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assemblies.5–11 These molecules have a benzene ring core
and usually contain flexible functional groups. In addition to
Introduction
Understanding the driving forces of the formation of extended
assemblies is important for designing molecule based mate-
rials, be these for potential electronic,1 magnetic2 or porous3,4
applications. Often, the idea is to preprogram the building
blocks to interact with each other in a certain way to give larger
entities with the desired location and geometric relationships
between them. In other words, the interaction behaviour is
based on the functional groups of the molecules.
stronger interactions such as coordination and hydrogen
bonds, the role of non-covalent interactions is also important
in the assembly of molecules. For example, the benzene
ring in these systems offers the possibility of aromatic
interactions.
The assembly process of benzene-1,3,5-tricarboxamide
derivatives has been studied widely by using not only
different techniques such as CD and UV-Vis but also
theoretical methods.10,12,13 Terephthalamides and benzene-
1,3,5-tricarboxamides have produced nanostructured mate-
rials, for instance nano-staircases and fibres are among the
reported architectures.5,6,14–17 Spontaneous formation of
hydrogels and their encapsulation and sorption properties of
both di- and tri-substituted carboxamides have also been
studied.6,18,19 In addition, terephthalamides and benzene-
1,3,5-tricarboxamides derivatives have been reported to form
liquid columnar crystal phases (LC), preorganized surfactants
and multi-component organic cages within dynamic combi-
natorial libraries.20–23
Terephthalamides and benzene-1,3,5-tricarboxamides are
examples of building blocks used in preparing extended
a Chemical and Biological Engineering, Physical Chemistry, Chalmers University of
Technology, Kemivägen 10, Gothenburg, Sweden. E-mail: anirbanchem@gmail.com,
ohrstrom@chalmers.se
b Centre for Supramolecular Chemistry Research, Department of Chemistry,
University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
c Department of Materials and Environmental Chemistry (MMK) and Department
of Organic Chemistry (OC), Stockholm University, Sweden
† Electronic supplementary information (ESI) available: CIF files, additional
structures and Hirshfeld plots. CCDC 993036–993040. For ESI and crystallographic
data in CIF or other electronic format see DOI: 10.1039/c4ce00605d
‡ Present address: Centro de Química Estrutural, Instituto Superior Técnico,
University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
Introduction of amino acids into terephthalamide and
benzene-1,3,5-tricarboxamides offers the possibility of pro-
ducing enantiopure chiral building blocks and structures5,7,24
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hydrochlorides were prepared according to the literature.40
Triethyl amine (99.5%), terephthaloyl dichloride (99%),
benzene-1,3,5-tricarbonyl trichloride (98%) and d-chloroform
(99.8%) were manufactured by Aldrich. Anhydrous magne-
sium sulfate (98%) and sodium hydroxide (98%) were pro-
duced by Scharlau. Hydrochloric acid (≥37%), potassium
bromide (99%) and methanol (99.7%) were manufactured by
Sigma Aldrich. Dichloromethane (p.a.) was produced by
Merck. Dimethylsulfoxide-d6 (99.8%) was produced by
Armar Chemicals.
Experimental methods
The elemental analysis was performed by H. Kolbe
Mikroanalytisches Laboratorium, Germany. The FTIR spec-
troscopy measurements were performed using a Bruker
1
IFS-125 spectrometer in a KBr pellet. The H- and 13C-NMR
Fig. 1 Schematic presentation of the molecules of the studied
compounds 1–5.
spectra were analysed using an Agilent 400 MHz spectrome-
ter operating at 400 and 100 MHz for proton and carbon,
respectively.
with potential applications in enantioselective synthesis,
separation and detection. The amino acid part can also
stabilise the assemblies via hydrogen bonding and moreover
provide metal coordination sites.5,11,16,17,24–26
The complexing abilities of amino acid substituted
terephthalamide and benzene-1,3,5-tricarboxamides have
been studied by preparing network structures with metals
such as copper, cobalt, manganese, nickel, cadmium, zinc,
lantanoids, and calcium.7,11,17,24–31 These studies have
focused on non-chiral glycine (–H) substituted ligands,
but alanine (–CH3) and phenylalanine (–CH2(C6H5)) examples
are also known, although reported X-ray structures of such
network compounds are rare.32,33
The choice of the ligand and metal is essential in produc-
ing such metal–organic frameworks (MOFs)34 that can
have application in gas sorption, catalysis and molecular
recognition.27,35–39 These properties are incorporated into the
material during preparation using different building blocks.
Therefore, the design of new materials with desired proper-
ties requires understanding and control of the interactions of
the building blocks.
We report here the preparation and crystal structures
of the amino acid derivatives 1–5 of terephthalamide and
benzene-1,3,5-tricarboxamides (Fig. 1). These closely related
molecules give structures with differences and similarities
that are investigated not only by traditional means, but also
graph set and Hirshfeld surface analyses.
X-ray crystal structure determination
The crystallographic details of compounds 1–5 are summa-
rized in Table 1. The crystals of 1–5 were immersed in cryo-
oil, mounted in a Nylon loop, and measured at a temperature
of 293(2) K (1, 5) and 173(2) K using an Oxford Cryostream
600 (3) and 700 (2, 4). The X-ray diffraction data were col-
lected using an Xcalibur Sapphire3 diffractometer (1, 5),
a Nonius Kappa CCD diffractometer (3) and a Bruker DUO
APEX II CCD diffractometer (2, 4) with Mo Kα radiation
(λ = 0.71073 Å). For 1 and 5, the CrysAlisPro programme
package was used for cell refinement and data reduction,41
whilst for 3, DENZO was used, and for 2 and 4 data reduction
and cell refinement were performed using SAINT-Plus.42
Space groups were determined from systematic absences
using XPREP43 and confirmed using the program layer for
2–4.44 The structures were solved by direct methods using
the SHELXS-97 (ref. 45) program. Semi-empirical or numeri-
cal absorption (SCALE3 ABSPACK (1), SADABS46 (2–5)) was
applied to all of the data. Structural refinement was carried
out using SHELXL-97 (1–5).47 The refinement procedure by
full-matrix least-squares methods, based on F2 values
against all reflections was performed using SHELXL-97,
including the anisotropic displacement parameters for all
non-H atoms. Hydrogen atoms were placed geometrically,
except for O–H, N–H and water hydrogen atoms which were
located in difference Fourier maps. All other hydrogen
atoms were positioned geometrically and constrained to
ride on their parent atoms Uiso = 1.2Ueq(parent atom). The
crystals of 5 have an asymmetric carbon that is disordered
over two sites with equal occupancies. It also contains
electron density, interpreted as residual water molecules,
that cannot be refined properly. This electron density excess
was cleaned using the SQUEEZE routine of PLATON.48 CCDC
numbers 993036–993040.
Experimental
Materials
Amino acids L-phenylalanine (≥99%), L-leucine (≥99%),
L-isoleucine (≥99%) and DL-valine (≥99%) were produced
by Fluka. L-alanine methyl ester hydrochloride (≥99%) was
purchased from Aldrich and other amino acid methyl ester
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Table 1 Crystal data for compounds 1–5
1
2
3
4
5
Empirical formula
Fw
Temp (K)
l (Å)
Cryst. syst.
Space group
a (Å)
C14H20N2O8
344.32
293(2)
0.71073
Orthorhombic
P212121
7.7195(5)
8.2128(5)
26.453(2)
90
90
90
1677.1(2)
4
1.364
C20H30N2O7
410.46
173(2)
0.71073
Orthorhombic
P212121
6.9544(5)
11.7552(8)
26.872(2)
90
90
90
2196.8(3)
4
1.241
C20H32N2O8
428.47
173(2)
0.71073
Monoclinic
P21
12.374(3)
7.675(2)
12.714(3)
90
107.15(3)
90
1153.9(4)
2
1.233
0.095
25 132
C18H28N2O8
400.42
173(2)
0.71073
Monoclinic
P21
10.5665(10)
7.6596(7)
12.871(1)
90
106.949(2)
90
996.5(2)
2
1.335
0.105
C18H21.57N3O9.28
423.38
293(2)
0.71073
Trigonal
¯
R3
18.3488(5)
18.3488(5)
11.1379(6)
90
90
120
3247.5(2)
6
1.315
0.107
1468
b (Å)
c (Å)
a (deg)
b (deg)
g (deg)
V (Å3)
Z
rcalc (Mg m3)
m (Mo Kα) (mm−1
No. reflns.
Unique reflns.
GooF
)
0.113
31 431
5974
0.094
19 064
6670
9773
6055
1.016
4723
1.217
1468
1.250
1.084
1.016
Rinat
0.0771
0.0678
0.1084
0.0605
0.0615
0.1383
0.047 (Rmerge)
0.0489
0.1206
0.0286
0.0817
0.2048
R1 (I3 2s)
0.0889
0.2394
wR2 (I3 2s)
b
P
P
P
P
a
2
R1 = ||Fo| − |Fc||/ |Fo|. b wR2 = [ [w(Fo − Fc2)2]/ [w(Fo2)2]]1/2
.
Synthesis of dimethyl 2,2′-
(terephthaloylbis(azanediyl))dipropionate
pressure. The solid product was dissolved in 10 mL of water
and the solution was acidified (pH = 2) with dilute
hydrochloric acid solution. The obtained white solid product
was filtered and washed with water. (0.9 g, 62%). (Found:
C 48.61, H 5.81, N 8.11 calc. for C14H16N2O6·2H2O C 48.83,
H 5.85, N 8.14) νmax (KBr)/cm−1 3394 (bs), 3060 (w), 2982 (w),
2931 (w), 2542 (mb), 2019 (mb), 1732 (s), 1705 (s), 1639 (s),
1542 (s), 1500 (m), 1456 (m), 1406 (w), 1381 (w), 1345 (m),
1323 (m), 1289 (m), 1269 (s), 1240 (s), 1181 (s), 1039 (w),
1017 (w), 945 (w), 869 (s), 829 (m), 743 (s), 646 (m), 596 (m),
555 (w). δH (400 MHz; DMSO) 12.54 (s, 2H, –COOH), 8.77 (d,
2H, –NH, J = 8Hz), 7.95 (s, 4H, Bn), 4.42 (m, 2H, –CH), 1.39
(d, 6H, –CH3 J = 8Hz). δC (100 MHz; DMSO) 174.5, 165.9,
136.7, 127.8, 48.7, 17.3.
L-Alanine methyl ester hydrochloride (1.39 g, 10 mmol) and
triethylamine (2.52 g, 25 mmol) were placed in a round bottom
flask and then dissolved in dry 20 ml of dichloromethane.
Terephthaloyl dichloride (1.11 g, 5 mmol) in 2 ml of dry
dichloromethane was added dropwise to this mixture with
continuous stirring. The reaction mixture was stirred for
24 hours. Then the solvent was removed under reduced
pressure and a white solid was obtained. The white solid was
washed with water and then extracted with dichloromethane.
The organic extracts were collected and dried over anhydrous
magnesium sulfate. The solvent was evaporated under reduced
pressure and the product was obtained as a white solid.
(2.4 g, 73%). νmax (KBr)/cm−1 3294 (s), 3077 (w), 3001 (w),
2954 (w), 2850 (w), 1735 (s), 1637 (s), 1546 (s), 1500 (m),
1452 (m), 1441 (m), 1372 (w), 1345 (m), 1319 (m), 1288 (m),
1230 (s), 1170 (s), 1116 (m), 1052 (m), 1017 (w), 980 (w),
928 (w), 874 (s), 836 (w), 747 (m), 678 (s), 574 (w), 501 (w).
δH (400 MHz; CDCl3) 7.87 (s, 4H, Bn), 6.84 (d, 2H, –NH,
J = 8Hz), 4.82 (m, 2H, –CH), 3.81 (s, 6H, –COOCH3), 1.55
(d, 6H, –CH3, J = 8Hz). δC (100 MHz; CDCl3) 173.6, 165.8,
136.7, 127.3, 52.7, 48.6, 18.6.
Synthesis and analysis of dimethyl 2,2′-
(terephthaloylbis(azanediyl))bis(3-methylpentanoate)
Dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(3-methylpentanoate)
was synthesized following the synthesis of dimethyl 2,2′-
(terephthaloylbis(azanediyl))dipropionate, but using L-leucine
methyl ester hydrochloride (1.8 g, 10 mmol) instead of L-alanine
methyl ester hydrochloride. (2.7 mg, 64%). νmax (KBr)/cm−1
3325 (s), 3086 (w), 3043 (w), 2956 (s), 2871 (m), 1746 (s),
1635 (s), 1550 (s), 1503 (s), 1469 (w), 1437 (w), 1340 (s),
1278 (s), 1211 (s), 1163 (s), 1122 (w), 1088 (w), 1048 (w),
1018 (m), 991 (w), 872 (m), 847 (m), 748 (m), 730 (m), 642 (bs),
480 (w). δH (400 MHz; CDCl3) 7.77 (s, 4H, Bn), 6.94 (d, 2H, –NH,
J = 8Hz), 4.87 (m, 2H, –CH), 3.78 (s, 6H, –COOCH3), 1.82–1.65
(m, 6H, –CH2 and –CH), 0.98 (d, 12H, –CH3, J = 8Hz). δC (100 MHz;
CDCl3) 174.1, 166.1, 136.4, 127.3, 52.5, 51.1, 41.4, 25.0, 22.9,
21.8. The NMR shifts were in agreement with the literature.16
Synthesis of 2,2′-(terephthaloylbis(azanediyl))dipropionic
acid (1)
Dimethyl 2,2′-(terephthaloylbis(azanediyl))dipropionate (1.68 g,
5 mmol) and sodium hydroxide (0.6 g, 15 mmol) were
dissolved in 20 mL of methanol : water mixture (4 : 1). The
reaction mixture was stirred for eight hours at room temper-
ature. Then the solvent was evaporated under reduced
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Synthesis of 2,2′-(terephthaloylbis(azanediyl))bis(3-
methylpentanoic acid) (2)
(m, 2H, –CH2), 1.26 (m, 2H, –CH2), 0.92 (d, 6H, –CH3, J =
8Hz), 0.85 (t, 6H, –CH3, J = 8Hz). δC (100 MHz; DMSO) 173.5,
166.6, 136.8, 127.9, 57.8, 36.1, 25.6, 16.1, 11.5.
2,2′-(Terephthaloylbis(azanediyl))bis(3-methylpentanoic acid)
was synthesized following the synthesis of 2,2′-
(terephthaloylbis(azanediyl))dipropionic acid, but using
dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(3-methyl-
pentanoate) (2.1 g, 5 mmol) instead of dimethyl 2,2′-
(terephthaloylbis(azanediyl))dipropionate. (1.5 g, 77%).
(Found: C 55.67, H 7.25, N 6.38 calc. for C20H28N2O6·2H2O C
56.06, H 7.53, N 6.54) νmax (KBr)/cm−1 3367 (bs), 3060 (w),
2962 (s), 2575 (mb), 1728 (s), 1632 (s), 1545 (s), 1499 (m),
1471 (w), 1451 (w), 1387 (w), 1338 (m), 1270 (s), 1252 (s),
1180 (m), 1169 (m), 1089 (w), 1017 (w), 967 (w), 870 (s), 854 (s),
736 (s), 600 (m). δH (400 MHz; DMSO) 12.61 (bs, 2H, –COOH),
8.71 (d, 2H, –NH, J = 8Hz), 7.95 (s, 4H, Bn), 4.44 (m, 2H, –CH),
1.80–1.55 (m, 6H, –CH2 and –CH), 0.91 (d, 6H, –CH3, J = 8Hz),
0.86 (d, 6H, –CH3, J = 8Hz). δC (100 MHz; DMSO) 174.5, 166.2,
136.7, 127.8, 51.4, 24.9, 23.4, 21.6.
Synthesis of dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(3-
methylbutanoate)
Dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(3-methylbutanoate)
was synthesized following the synthesis of dimethyl 2,2′-
(terephthaloylbis(azanediyl))dipropionate, but using DL-valine
methyl ester hydrochloride (1.7 g, 10 mmol) instead of L-alanine
methyl ester hydrochloride. (2.9 g, 75%). νmax (KBr)/cm−1
3298 (s), 3031 (w), 2965 (s), 2875 (m), 1744 (s), 1642 (s),
1537 (s), 1501 (s), 1468 (m), 1435 (m), 1347 (s), 1321 (s),
1295 (m), 1261 (s), 1201 (s), 1160 (s), 1121 (w), 1070 (m),
1020 (s), 1002 (m), 923 (w), 862 (s), 826 (w), 737 (m), 681 (bs),
577 (w). δH (400 MHz; CDCl3) 7.86 (d, 4H, Bn, J = 8Hz), 6.66
(2H, m, –NH), 4.77 (m, 2H, –CH), 3.77 (s, 6H, –COOCH3),
2.27 (m, 2H, –CH), 0.99 (m, 12H, –CH3). δC (100 MHz; CDCl3)
172.5, 166.2, 136.9, 127.4, 57.5, 52.4, 31.6, 18.9, 17.9.
Synthesis of dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(4-
methylpentanoate)
Synthesis of 2,2′-(terephthaloylbis(azanediyl))bis(3-
methylbutanoic acid) (4)
Dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(4-methyl-
pentanoate) was synthesized following the synthesis of
dimethyl 2,2′-(terephthaloylbis(azanediyl))dipropionate, but
using L-isoleucine methyl ester hydrochloride (1.8 g,
10 mmol) instead of L-alanine methyl ester hydrochloride.
(2.7 mg, 64%). νmax (KBr)/cm−1 3345 (s), 3051 (w), 2966 (s),
2877 (m), 1746 (s), 1638 (s), 1547 (s), 1503 (s), 1459 (m),
1434 (m), 1372 (m), 1342 (s), 1298 (s), 1254 (m), 1201 (s), 1155 (s),
1117 (w), 1089 (w), 1008 (m), 964 (w), 878 (m), 847 (m), 769 (m),
731 (s), 679 (w), 619 (bs), 589 (m), 505 (w). δH (400 MHz; CDCl3)
7.86 (s, 4H, Bn), 6.72 (d, 2H, –NH, J = 8Hz), 4.82 (q, 2H, –CH, J =
8Hz), 3.78 (s, 6H, –COOCH3), 2.03 (m, 2H, –CH), 1.53 (m, 2H,
–CH2), 1.25 (m, 2H, –CH2), 0.97 (m, 12H, –CH3). δC (100 MHz;
CDCl3) 172.5, 166.1, 136.9, 127.4, 56.9, 52.3, 38.2, 25.4, 15.5,
11.6. The NMR shifts were in agreement with the literature.16
2,2′-(Terephthaloylbis(azanediyl))bis(3-methylbutanoic acid)
was synthesized following the synthesis of 2,2′-
(terephthaloylbis(azanediyl))dipropionic acid, but using
dimethyl 2,2′-(terephthaloylbis(azanediyl))bis(3-methyl-
butanoate) (1.9 g, 5 mmol) instead of dimethyl 2,2′-
(terephthaloylbis(azanediyl))dipropionate. (1.5 g, 84%).
(Found: C 59.15, H 6.49, N 7.55 calc. for C18H24N2O6 C 59.33,
H 6.64, N 7.69) νmax (KBr)/cm−1 3444 (bs), 3325 (bs), 2967 (s),
2936 (w), 2573 (bm), 1731 (s), 1629 (s), 1537 (s), 1499 (m), 1470 (w),
1394 (w), 1375 (w), 1368 (m), 1322 (s), 1253 (w), 1236 (s), 1193 (s),
1161 (s), 1033 (w), 1017 (w), 977 (m), 915 (m), 865 (s), 815 (s),
733 (s), 636 (m), 576 (w). δH (400 MHz; DMSO) 8.56 (d, 2H, –NH,
J = 8Hz), 7.94 (s, 4H, Bn), 4.28 (tr, 2H, –CH, J = 8Hz), 2.19
(m, 2H, –CH), 0.95 (tr, 12H, –CH3, J = 8Hz). δC (100 MHz;
DMSO) 173.5, 166.7, 136.9, 127.9, 58.9, 29.9, 19.8, 19.3.
Synthesis of 2,2′-(terephthaloylbis(azanediyl))bis(4-
methylpentanoic acid) (3)
Synthesis of trimethyl 2,2′,2″-((benzene-1,3,5-
tricarbonyl)tris(azanediyl))tripropionate
2,2′-(Terephthaloylbis(azanediyl))bis(4-methylpentanoic acid)
was synthesized following the synthesis of 2,2′-
(terephthaloylbis(azanediyl))dipropionic acid, but using dimethyl
2,2′-(terephthaloylbis(azanediyl))bis(4-methylpentanoate) (2.1 g,
5 mmol) instead of dimethyl 2,2′-(terephthaloylbis(azanediyl))
dipropionate. (1.6 mg, 83%). (Found: C 58.47, H 7.28, N 6.87 calc.
for C20H28N2O6·H2O C 58.52, H 7.37, N 6.83) νmax (KBr)/cm−1
3463 (bs), 3411 (s), 3315 (bs), 2967 (s), 2937 (m), 2546 (w),
1725 (s), 1630 (s), 1552 (s), 1524 (s), 1495 (m), 1458 (w),
1418 (w), 1385 (w), 1348 (m), 1241 (s), 1210 (s), 1168 (m), 1083 (w),
1017 (w), 974 (w), 869 (s), 728 (s), 697 (m), 600 (w), 568 (w).
δH (400 MHz; DMSO) 12.61 (bs, 2H, –COOH), 8.71 (d, 2H,
–NH, J = 8Hz), 7.95 (s, 4H, Bn), 4.44 (m, 2H, –CH), 1.80–1.55
(m, 6H, –CH2 and –CH), 0.91 (d, 6H, –CH3, J = 8Hz), 0.86
(d, 6H, –CH3, J = 8Hz). 8.57 (d, 2H, –NH, J = 8Hz), 7.93 (s, 4H,
Bn), 4.32 (t, 2H, –CH, J = 8Hz), 1.94 (m, 2H, –CH), 1.50
L-Alanine methyl ester hydrochloride (1.39 g, 10 mmol) and
triethylamine (3.53 g, 35 mmol) were placed in a round
bottom flask and then dissolved in dry 20 ml of
dichloromethane. Benzene-1,3,5-tricarbonyl trichloride
(0.8 g, 3 mmol) in 2 ml of dry dichloromethane was added
dropwise to this mixture with continuous stirring. The reac-
tion mixture was stirred for 24 hours. Then, the solvent was
removed under reduced pressure and a white solid was
obtained. The white solid was washed with water and then
extracted with dichloromethane. The organic extracts were
collected and dried over anhydrous magnesium sulphate.
The solvent was evaporated under reduced pressure and
the product was obtained. (3.2 mg, 69%). νmax (KBr)/cm−1
3235 (s), 3066 (s), 2991 (s), 2952 (s), 1751 (s), 1643 (s),
1562 (s), 1457 (s), 1437 (m), 1381 (m), 1318 (s), 1282 (m),
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1212 (s), 1165 (s), 1133 (w), 1054 (s), 986 (m), 933 (w),
849 (m), 828 (w), 723 (s), 692 (s).δH (400 MHz; CDCl3) 8.13
(s, 3H, Bn), 7.72 (d, 3H, –NH, J = 8Hz), 4.73 (m, 3H, –CH),
3.79 (s, 9H, –COOCH3), 1.58 (d, 9H, –CH3, J = 8Hz).
δC (100 MHz; CDCl3) 173.7, 165.9, 134.8, 128.6, 52.5, 48.8, 17.4.
Synthesis of 2,2′,2″-((benzene-1,3,5-
tricarbonyl)tris(azanediyl))tripropionic acid (5)
Trimethyl 2,2′,2″-((benzene-1,3,5-tricarbonyl)tris(azanediyl))
tripropionate (2.3 g, 5 mmol) and sodium hydroxide (0.6 g,
15 mmol) were dissolved in 20 mL of methanol : water mixture
(4 : 1). The reaction mixture was stirred for eight hours at room
temperature. Then the solvent was evaporated under reduced
pressure. The solid product was dissolved in 10 mL of water
and the solution was acidified (pH = 2) with dilute hydrochloric
acid solution. The obtained white solid product was filtered
and washed with water. (1.9 mg, 91%). (Found: C 50.12, H 5.04,
N 9.47 calc. for C18H21N3O9·0.5H2O C 50.00, H 5.13, N 9.72) νmax
(KBr)/cm−1 3393 (bs), 3233 (m), 3066 (s), 2992 (s), 2942 (s),
1722 (s), 1644 (s), 1544 (s), 1458 (m), 1412 (w), 1382 (w),
1289 (w), 1240 (s), 1167 (s), 1053 (w), 966 (w), 922 (w), 836 (w),
741 (m), 692 (w),607 (s). δH (400 MHz; DMSO) 8.20 (s, 3H, Bn),
4.45 (m, 3H, –CH), 1.43 (d, 9H, –CH3, J = 8Hz). δC (100 MHz;
DMSO) 176.5, 168.3, 134.1, 129.4, 49.4, 15.9. The NMR shifts
were in agreement with the literature.24
Scheme 2 The synthesis of racemic 5.
and they form chains along the b-axis. In addition, two
lattice water molecules strengthen the connection of the
molecules within the chain {O(7)–H(7B)⋯O(4)#2 2.816(3) Å,
O(7)–H(7A)⋯O(1)#3 2.830(3) Å, #2 x − 1, y, z, #3 −x, y − 1/2,
−z + 1/2}. These chains are further connected to other
chains with lattice water to form a three dimensional net
via hydrogen bonding {N(2)–H(2A)⋯O(8)#4 3.090 Å,
O(6)–H(6A)⋯O(8)#5 2.611(2) Å, O(2)–H(2B)⋯O(7)#6 2.574(3) Å,
O(8)–H(8B)⋯O(3)#7 2.711(2) Å, O(8)–H(8A)⋯O(5)#8 2.730(3) Å
#4 x, y, z − 1, #5 x + 1, y, z − 1, #6 x, y + 1, z, #7 x + 1/2, −y + 3/2,
−z + 1, #8 x − 1/2, −y + 3/2, −z + 1}.
Compound 2 monohydrate. Compound 2 also forms a
1D chain structure along the b-axis via hydrogen bonding
between the carboxylic group and the ketone group
{O(6)–H(6A)⋯O(1)#1 2.579(3) Å, #1 −x + 1, y − 1/2, −z + 3/2}.
Lattice water links the chains together, forming a hydrogen
bonded 3D net. Lattice water interacts with the amine groups,
the ketone groups and the carboxylic groups, and acts as both
hydrogen bond donors and acceptors {O(3)–H(3A)⋯O(W1)#2
2.618(4) Å, O(W1)–H(2W1)⋯O(2)#3 2.748(3) Å, O(W1)–
H(1W1)⋯O(4)#4 2.676 (3) Å, N(1)–H(1A)⋯O(W1) 2.948(4) Å,
#2 x − 1, y, z; #3 x + 1/2, −y + 3/2, −z + 1; #4 x − 1/2, −y + 3/2,
−z + 1}.
Results
Synthesis and crystallization
Compounds 1–5 were prepared in two steps at room tempera-
ture. In the first step, the protected amino acid methyl ester is
introduced to terephthaloyl dichloride (1–4) or benzene-1,3,5-
tricarbonyl trichloride (5) and in the next step the amino acid
is deprotected (Schemes 1 and 2). The compounds were
recrystallized from methanol (1, 2), H2O (3, 4) or from D2O (5)
for single crystal X-ray diffraction studies. 1–3 were obtained
enantiomerically pure while racemic valine was used to
prepare 4 and 5 was obtained as a racemate.
Compound 3 dihydrate and compound 4 dihydrate.
Compounds
3 and 4 are isostructural. Molecules are
connected to each other via hydrogen bonding with lattice
water forming a 2D hydrogen bonded network. For 3 {O(W1)–
H(2W1)⋯O(4) 2.756(4) Å, O(W2)–H(2W2)⋯O(1) 2.649(4) Å,
O(W1)–H(1W1)⋯O(2)#1 2.724(4) Å, O(3)–H(3O)⋯O(W1)#2
2.619(4) Å, N(1)–H(1N)⋯O(W1)#3 3.131(4) Å, O(W2)–
H(1W2)⋯O(5)#4 2.705(4) Å, O(6)–H(6O)⋯O(W2)#5 2.609(4) Å,
N(2)–H(2N)⋯O(W2)#6 2.909(5) Å, #1 x, y − 1, z; #2 −x + 1, y + 3/2,
−z + 1; #3 −x + 1, y + 1/2, −z + 1; #4 x, y + 1, z; #5 −x + 1, y − 3/2,
−z + 2; #6 −x + 1, y − 1/2, −z + 2). For 4 (O(W1)–H(2W1)⋯O(5)#1
2.754(5) Å, O(W1)–H(1W1)⋯O(1) 2.731(6) Å, N(2)–
H(2N)⋯O(W1)#2 3.135(6) Å, O(6)–H(6O)⋯O(W1)#3 2.633(5) Å,
O(W2)–H(1W2)⋯O(4) 2.711(5) Å, O(3)–H(3O)⋯O(W2)#4
2.599(6) Å, O(W2)–H(2W2)⋯O(2)#5 2.737(6), #1 x, y − 1, z;
#2 −x + 1, y + 1/2, −z + 2, −z + 1; #3 −x + 1, y + 3/2, −z + 2;
#4 −x + 1, y − 3/2, −z + 1; #5 x, y + 1, z). There are no direct
intermolecular hydrogen bonds between the amino acid
derivatives.
Structure descriptions
A complete set of ORTEP and packing diagrams can be found
in the ESI.†
Compound 1 dihydrate. The molecules of compound 1 are
connected to each other via hydrogen bonding of N–H⋯O
{N(1)–H(1A)⋯O(2)#1 3.132 Å, #1 −x + 1, y − 1/2, −z + 1/2}
Compound 5. This compound has a crystallographically
imposed threefold symmetry. The methyl groups in this
Scheme 1 The synthesis of compounds 1–4.
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Table 2 Graph set symbols for compounds 1–5
Comp.
Graph set symbol
Disubst.
1
2
R3,3(15); R4,4(13); R4,4(18); R3,4(17); R4,4(21)
R4,4(13); R4,4(18); R3,4(17); R4,4(21)
3
4
6
R4,4(13); R4,4(18); R3,4(17); R4,4(18); R4,4(21); R3,4(23)
R4,4(13); R4,4(18); R3,4(17); R4,4(18); R4,4(21); R3,4(23)
R4,4(18); R2,4(28); R3,4(17); R4,4(21); R3,4(23)
Trisubst.
5
7
R2,2(16); R2,2(22) R3,4(23);
R2,2(16); R2,2(22); R4,4(18); R4,4(20)
We note first that there are no directly hydrogen bonded
dimers in the 1–4 compounds, because that would have
implied a 2,2 designation, (i.e. two donor atoms D and two
acceptor atoms H as in the acetic acid dimer with symbol
R2,2(8)). Compound 1 forms hydrogen bonds directly to
another building block with a loop-back via hydrogen bonded
water, the R3,3 assignment. This does not happen for com-
pound 2 that has chains of building block–water–building
block instead.
Then we can also see a number of recurring motifs in the
different structures, the shorter circuits, i.e. the number in
parenthesis, likely the most significant. Thus, the R4,4(13)
motif is recurring in 1–4 but is absent in 6 and the R2,2(16)
motif is found in both 5 and 7. An illustration of some of
these motifs can be found in the ESI.†
Fig. 2 Schematic presentation of dimeric units (blue and black) of 5
forming via π–π stacking and hydrogen bonding (dotted line). Graph set
symbol R2,2,(16).
structure are disordered over two positions and it is therefore
evident that the alanine units became racemic during
preparation. This compound forms dimeric units via a
completely symmetric π–π stacking (3.5 Å). In addition to
aromatic interaction, the building blocks of the dimeric unit
are hydrogen bonded, as shown in Fig. 2 {N(2)–H(2A)⋯O(2)#1
2.888(4) Å, #1 1/3 + x − y, −1/3 + x, 2/3 − z}. The hydrogen
bonding also causes the substituents of the benzene rings to
have the same orientation within the dimers. The substituent
chains of two stacked benzene rings are anti-eclipsed/staggered.
These units further connect via hydrogen bonding of O–H⋯O
{O(3)–H(3A)⋯O(1)#2 2.641(4) Å, #2 1/3 − x + y, 2/3 − x, −1/3 + z}
to a 3D network.
Comparison of compounds 1–4, and 6
Before we examine in more detail the structures of 1–4 and 6,
a few remarks are needed. These compounds, differing only
in the amino acid chain part (R, Fig. 1), all contain three dis-
tinct entities, and each of them has different intermolecular
“preferences”. Thus we have a flat benzene ring that we often
find either π-stacked or with C–H σ–π interactions. Then we
have aliphatic groups (except for 6) that will normally prefer
to be in the presence of each other, and finally the polar
hydrogen bond donors and acceptors that will generally
“want” to have all free electron pairs and acidic hydrogens in
bonding interactions.
A convenient way to get an overall picture is to use
Hirshfeld surfaces. The Hirshfeld surface reveals the inter-
molecular interactions, and even the weaker secondary inter-
actions such as C–H⋯π, C⋯H and H⋯H contacts.51–53 This
surface represents the volume where, inside, electron density
is dominated by the atoms in the molecule in focus, while
outside, electron density is dominated by all other components
of the crystal. Each point on the surface has one closest
atom inside and one closest atom outside the surface. We can
therefore determine what percentage of the surface that
originates from O⋯H, C⋯C or any other close interaction.
This could be a crude first way of comparing similar structures
and a diagram of these percentages for compounds 1–4§ and
6–7 are found in Fig. 3.
Discussion
What we want to do here is to perform a structure compari-
son between our compounds using first the “big picture”
methods graph set and Hirshfeld surface analyses and then,
when needed, look into the structural details. For more
general applicability we also include in our discussion of the
compounds the earlier published structures of the glycine
terephthalamide derivative 6 (ref. 32) and the glycine
benzene-1,3,5-tricarboxamides derivative 7.33
General hydrogen bond analysis by the graph set method
Graph set analysis is a general method to investigate the
recurring hydrogen bond motifs and hydrogen bond patterns
in discrete and extended assemblies.35,49,50 It does not discern
the different atom types such as N or O, but once the criteria
for hydrogen bonding are set, the analysis will generate the
motifs such a chains (C) and rings (R) with the number of
atoms directly involved in the bonding as well as the number
of atoms linking these (in, for example, a ring). Table 2 shows
the graph set symbols for 1–7 as calculated using Mercury.
We chose to show only the ring-forming motifs as we believe
these to be fairly distinct.
§ The disorder of 5 makes a Hirshfeld surface difficult to compare and interpret.
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Fig. 3 The major contributions to the Hirshfeld surfaces in terms of
closest atom–atom interactions for compounds 1–4 and the glycine
derivative of terephthalamide 6 and benzene-1,3,5-tricarboxamide 7,
a rough first way to compare intermolecular interactions.
We immediately observe that the derivatives with longer
aliphatic chains, 2–4, have a higher proportion of H⋯H interac-
tions (blue), which is reasonable as these groups, as stated above,
will tend to interact with each other, but also, simply, because
of the higher percentage of hydrogen in these molecules.¶
Another notable feature is the higher proportion of C⋯O
(purple) in the glycine derivative 6 compared especially to
1–2. This stems from the interaction of the carbonyl groups
with the flat side of the benzene ring in 6, an arrangement
we suggest arises because 6 lacks the CH3 groups that tend
to come close to the aromatic ring in the alanine derivative 1.
One thing that is not picked up so clearly in these plots is
the difference between on one side compounds 3 and 4 that
form the same hydrogen bonded assemblies in unit cells that
are close to identical, and compound 2.
Both structures 3 and 4 contain two lattice water mole-
cules that connect the building blocks to form a 2D hydrogen
bonded net. The interactions between the building blocks are
all lattice water based. In other words there are no direct
intermolecular hydrogen bonds between the actual building
blocks. This is in contrast to 2 that has direct hydrogen bonds
between the building blocks and only one water molecule.
It is worth noting here that 3 and 4 pack with the aliphatic
groups facing each other, as shown in Fig. 4, just as intuition
would suggest. This leaves the aromatic ring exposed and
instead of CH3 interactions as in 1 it adopts the carbonyl
interaction as in 6.
Another property of 3 and 4 that has some implications is
chirality. As racemic valine was used, 4 is a racemic compound,
the crystals obtained are of the R,S molecule, and a non-
chirodescriptive space group would have been expected. How-
ever, solutions in P2/1c give a significantly higher R-factor than
when solved and refined in the space group P21, and the apparent
centre of symmetry is only pseudo. The abnormal anisotropic
displacement parameters of the C8-carbon (see Fig. S18†) could
be due to some minor R/S disorder present at the chiral
carbon, however this could not be satisfactorily modelled.
Fig. 4 Packing diagrams of 3 and 4. Note how the aliphatic groups
assemble and are kept separate from the hydrogen bonding parts.
On the other hand, 3 is enantiomerically pure (some indi-
cation of very minor isomerisation can be detected and
again, solutions in P2/1c give a significantly higher R-factor)
and having the chirodescriptive space group P21 is logical.
Somehow there is thus a chiral arrangement of 4. This riddle
is solved when one realizes first that the R-side is always
facing another R-side and vice-versa and that the aliphatic
groups meet around a screw axis parallel to the b-axis, thus
arranging these groups in a chiral, helical way.
This observation then begs the question why compound 2
does not form the same kind of structure, being an isomer
of 3. It is hard to fathom why the same packing and chiral
arrangement would not be possible, but we refrain from
further speculation, as this may simply be a question of
crystallization conditions.
Comparing compound 5 and compound 7
¶ Possible ways to account for the difference in composition are to weigh the
contributions by atom percentages or to calculate interactions only for the part
that is common to all molecules.
The local molecular structure of 5 resembles that of the
earlier published glycine derivative 2,2′,2″-((benzene-1,3,5-
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In contrast to the glycine derivative 7, in compound 5
these dimers are connected to each other via hydrogen
bonds and form a 3D pcu-net. Hirshfeld surface analyses of
compounds 1–7 indicate that some of the differences between
these systems and graph set symbols are also helpful in
categorising and discovering differences and similarities.
From a synthesis point of view, for the further use
of these ligands in building MOFs, it will be important to
have complete control of the stereochemistry and less harsh
conditions may be needed.
Acknowledgements
LÖ, EL and AK thank the Swedish Research Council, LÖ and
CLO thank the Swedish Research Links program for Southern
Africa, AK also expresses his gratitude to the Foundation for
Science and Technology (FCT), Portugal, for post-doctoral
fellowship (SFRH/BPD/76192/2011), AEPP was supported by
the CMCSU project, the Knut and Alice Wallenberg Foundation
and the MATsynCELL project, Röntgen–Ångström Cluster.
Fig. 5 The hydrogen bonded pcu-net formed by the dimeric units of
5 with disordered water molecules (blue spheres) in the roughly 3·3 Å
wide channels.
Notes and references
tricarbonyl)tris(azanediyl))triacetic acid trihydrate33 7 as they
both form the R2,2(19) based dimers as shown in Fig. 2.
However, the absence of methyl groups makes it possible for
the protruding chains to pack closer in 7. In addition, the
glycine derivative has lattice water in the structure that
participates in a hydrogen bond network.
In contrast to 7, the dimeric units in 5 are further
connected to six other dimers units via hydrogen bonding
of O–H⋯O O(3)–H(3A)⋯O(1)#2 2.641(4) Å, #2 1/3 − x + y,
2/3 − x, −1/3 + z} forming a pcu-net, the most common of the
six-connected nets,54 as shown in Fig. 5.
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