MAGNETIC RESONANCE IN CHEMISTRY
Magn. Reson. Chem. 2005; 43: 41–46
An intramolecular ionic hydrogen bond stabilizes a cis
amide bond rotamer of a ring-opened
rapamycin-degradation product
Casey Chun Zhou,1∗ Kent D. Stewart2 and Madhup K. Dhaon3
1
D-R418, Structural Chemistry, Global Pharmaceutical Research and Development, Abbott Laboratories, North Chicago, IL 60064-4000, USA
D-R46Y, Structural Biology, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, North Chicago, IL 60064-6100,
2
USA
3
D-R450, Process Chemistry, Global Pharmaceutical Research and Development, Abbott Laboratories, North Chicago, IL 60064-4000, USA
Received 16 June 2004; Revised 9 August 2004; Accepted 8 September 2004
Rapamycin (1), a macrolide immunosuppressant, undergoes degradation into ring-opened acid products
2 and 3 under physiologically relevant conditions. The unsaturated product (3) was isolated and studied
in this work. Unlike 1, which has its amide primarily in a trans conformation in solution, 3 has both
cis and trans conformations in approximately a 1 : 1 ratio in dimethyl sulfoxide (DMSO). The amount
of cis rotamer was increased dramatically in the presence of an organic base such as triethylamine. The
detailed NMR results indicate that the cis rotamer is stabilized through an intramolecular ionic hydrogen
bond of the carboxylate anion with the tertiary alcohol as part of a nine-membered ring system. This
hydrogen bond was characterized further in organic media and the trans–cis rotamer equilibria were used
to estimate the relative bond strengths in several solvents. The additional stabilization arising from this
ionic hydrogen bond in the cis rotamer was determined to be 1.4 kcal mol−1 in DMSO-d6, 2.0 kcal mol−1
in CD3CN and 1.1 kcal mol−1 in CD3OD. Copyright 2004 John Wiley & Sons, Ltd.
KEYWORDS: NMR; 1H NMR; 13C NMR; amide bond rotamers; ionic hydrogen bond; rapamycin degradation product
metabolite in vitro as shown in Scheme 1.12–14 There is less
information about the trans and cis rotamers of the acyclic
tertiary amide.
INTRODUCTION
A majority of molecules containing amide bonds show trans
and cis rotamers in solution due to a partial double-bond
character of the C–N bond. Secondary amides typically exist
mainly as the trans rotamer to avoid steric repulsion between
the nitrogen atom and the substituent on the carbonyl carbon.
However, there are several reports in the literature that show
the cis rotamer can be stabilized through non-covalent inter-
actions such as hydrogen bonding,1 hydrophobic effects,2
C–H . . . ꢀ interactions3 and other factors.4 In contrast, the
stability of the trans and cis rotamers is hard to predict for
tertiary cyclic amides. For acyclic tertiary amides, the trans
and cis rotamers are expected to be populated to similar
extents in the absence of driving forces such as hydrogen
bonding, steric and hydrophobic effects.5
Rapamycin is a tertiary cyclic amide that exhibits
significant immunosuppressant activities.6,7 In solution, two
amide bond rotamers are observed.8 The predominant
rotamer is the trans conformation, which is consistent with
the X-ray crystal structure of free or bound rapamycin.9–11
The ring-opened acid form of rapamycin (2 and 3) is an
acyclic tertiary amide, which has been identified as the major
In this paper, compound 3 was isolated and studied
in organic solvents by NMR. In comparison to rapamycin,
there is a large difference in the ratio of trans to cis rotamers
in 3. Interestingly, the ratio changes dramatically in the
presence of organic bases such as triethylamine (TEA) or 1,8-
diazabicyclo[5.4.0]undec-7-ene (DBU). The detailed NMR
analysis indicates that an ionic hydrogen bond stabilizes the
cis rotamer. This is a good model system for assessing the
relative strengths of ionic hydrogen bonds through analysis
of the trans–cis rotamer equilibria in various solvents. Factors
that potentially contribute to the hydrogen bond strength,
such as the hydrogen bond angle and the pKa difference of
the hydrogen bond donor and acceptor, will be discussed.
EXPERIMENTAL
Rapamycin easily degrades in the presence of acid or base in
organic solvents.15–18 The reaction of rapamycin with DBU
efficiently provides the degradation product 3.16 Rapamycin
(1.0 g, 1.09 mM) was dissolved in tetrahydrofuran (THF) at
°
0 C in an ice bath, DBU (0.15 g, 1 mM) was added and the
ŁCorrespondence to: Casey Chun Zhou, D-R418, Structural
Chemistry, Global Pharmaceutical Research and Development,
Abbott Laboratories, North Chicago, IL 60064-4000, USA.
E-mail: chun.zhou@abbott.com
°
reaction mixture was stirred at 0–5 C for 6 h. The reaction
mixture was diluted with ethyl acetate (25 ml), washed with
1 N hydrochloric acid ꢁ2 ð 25 mlꢂ and water ꢁ2 ð 25 mlꢂ,
Copyright 2004 John Wiley & Sons, Ltd.