The Development of Novel Antibiotics Using ... - Jacobs University

2
Similar to the case of trianglimine chemistry, macrocycles A
and B form under conformational bias of dicarbohydrazides. 32-40
2. Results and discussion
2.1. Synthesis and molecular modeling
In continuation to our work with cyclophane macrocycles A and
B, we decided to synthesize a class of two-armed receptors which
simulates the structural framework of macrocycle B. Receptors
with such structural features are expected to be more flexible and
to show improved molecular recognition abilities. Two-armed
receptors 7-13 were synthesized from chiral dicarbohydrazides 1-
3 by reacting with substituted aromatic isocyanate 4-6 in
anhydrous THF (Fig. 1). The sidewalls of the receptors are made
of amide moieties, which function as the receptor binding motifs,
while dioxolane rings constitute the spacer units. The recognition
affinity of the novel receptors in the gas phase to a selection of
chiral carboxylic acids and oligopeptides is demonstrated by
using electrospray ionization time of flight mass spectrometry
(ESI-TOF/MS) and tandem MS. Structures of the novel receptors
were fully assigned by various spectroscopic techniques such as
FT IR, 1 H NMR, 13 C NMR, 2D ROESY, Circular Dichroism
spectroscopy (CD), ESI-TOF/MS and MS/MS.
for subsequent structure modeling calculations. Structure of
receptor 7 was energy-minimized using HyperChem software
(Release 8.0) at the Austin Model 1 level (AM1). 41,42 Molecular
modeling calculations are in good agreement with data from 2D
ROESY NMR and suggests a spiral-like structure for receptor 7
in which the NH moieties are syn/syn oriented. Structures of
receptors 7-13 are stabilized by intramolecular hydrogen bonds as
shown in Figure 3.
Table 1. High resolution ESI-TOF/MS data for receptors 7-13
Entry
Molecular
formula
Calcd. m/z
a Meas. m/z
Error
[ppm]
Yield
%
7 C 21H 24N 6O 8 487.1583 487.1588 –1.0 78
8 C 26H 32N 6O 8 555.2209 555.2224 –2.8 74
9 C 23H 28N 6O 10 547.1794 547.1782 2.2 93
10 C 23H 30N 8O 6 513.2216 513.2240 –4.8 89
11 C 21H 24N 6O 8 487.1583 487.1570 2.7 96
12 C 23H 28N 6O 10 547.1794 547.1799 –1.0 99
13 C 23H 30N 8O 6 513.2216 513.2233 –3.5 93
a Product ions appeared as [M – H] –
Fig. 2 2D ROESY NMR spectrum for receptor 7 (DMSO-d 6).
2.2. Molecular recognition and self-assembly in the gas phase
Fig. 1 Two-armed receptors 7-13, which were synthesized from chiral
dicarbohydrazides 1-3 and substituted aromatic isocyanates 4-6.
1 H NMR spectrum for (i.e., chiral receptor 7) showed three broad
signals at 10.05, 8.54 and 8.04 ppm corresponding to the amide
NH protons. FT IR spectrum showed a strong absorption band at
ν 1689 cm −1 corresponding to the stretching vibration of the ν
C=O. ESI-TOF/MS showed the expected pseudo-molecular ion
peak at m/z 487.1588 [M–H] – in the negative ion mode. High
resolution mass spectrometry (HRMS) data for the new receptors
are shown in table 1. 2D ROESY spectrum for receptor 7 (Fig. 2)
showed through space interactions between H d -H c and H d -H e ,
which suggests a syn/syn conformation of the NH moieties.
Unlike receptor 7, the NH moieties in macrocycle B assume a
syn/anti conformation. 29 Data from 2D ROESY NMR were used
Electrospray ionization (ESI-MS) has been widely used as a
versatile soft ionization method in studying weak non-covalent
interactions and molecular recognition in the gas phase. 43-45 The
ability of the technique to provide precise mass values, high
resolution and little or almost no fragmentations make it an indispensable
tool in supramolecular analysis. Recently, we reported on the
use of ESI-TOF/MS in probing the mechanism of trianglimine
formation in real-time and studying dynamic reversibility and
molecular recognition of tetra-carbohydrazide cyclophanes in the
gas phase to oligopeptides. 31,46 Two-armed receptor 7 showed
interesting molecular self-assembly both in solution and in the
gas phase to form dimeric, trimeric and tetrameric supramolecular
associations. Molecular self-assembly has been confirmed
in solution by variable temperature NMR (VT NMR) and in the
gas phase by ESI-TOF and tandem MS. VT NMR was performed
from 313 to 413 K in DMSO-d 6 . A downfield in chemical shift
(δ) for NH c , NH e and NH d , with increasing temperature, has
been observed (Fig. 4). The decrease in δ is an indication of
breaking inter- and intramolecular hydrogen bonding interactions
(NH…O=C) for the associated receptor molecules. Cooling the
NMR to 298 K yields the same spectrum as first recorded as a
consequent of re-establishment of the hydrogen bonds. Tandem