Modulation of Pharmacologically Relevant Properties of Piperidine Derivatives by Functional Groups in an Equatorial or Axial β-Position to the Amino Group

Article abstract of DOI:10.1002/cbic.201900474

Thirteen epimeric pairs of 5-substituted N-piperonyl-3-phenylpiperidine derivatives were synthesized in order to explore the stereospecific modulation of basicity, lipophilicity, aqueous solubility, and membrane permeation by functional groups in equatorial or axial positions beta to the amine unit. While this comprehensive data set provides enhanced insight into multiple factors that affect basicity and lipophilicity, it fills an important knowledge gap, providing a frame of reference for the property-based design of bioactive compounds. Impacts on amine basicity are very pronounced for the β-equatorial functional groups and parallel basicity-lowering effects known for acyclic amine derivatives. For β-axial functional groups, the basicity-lowering effects are generally decreased, with the nitrile group as the only exception. Basicity and lipophilicity modulations observed for β-axial functional groups are quite diverse and rationalized in terms of intramolecular hydrogen bonding, dipolar interactions, and special solvation effects. Aqueous solubility and (artificial) membrane permeability are discussed with reference to lipophilicity.

Full text of DOI:10.1002/cbic.201900474

Accepted Article
Title: Modulation of Pharmacologically Relevant Properties of
Piperidine Derivatives by Functional Groups in Equatorial or Axial
β-Position to the Amino Group
Authors: Patrick Schnider, Cosimo Dolente, Henri Stalder, Rainer E.
Martin, Viktoria Reinmüller, Roman Marty, Caroline Wyss
Gramberg, Björn Wagner, Holger Fischer, André M. Alker,
and Klaus Müller
This manuscript has been accepted after peer review and appears as an
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of the final Version of Record (VoR). This work is currently citable by
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published online in Early View as soon as possible and may be different
to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published
to ensure accuracy of information. The authors are responsible for the
content of this Accepted Article.
To be cited as: ChemBioChem 10.1002/cbic.201900474
Link to VoR: http://dx.doi.org/10.1002/cbic.201900474
A Journal of
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ChemBioChem
10.1002/cbic.201900474
Modulation of Pharmacologically Relevant Properties of Piperidine
Derivatives by Functional Groups in Equatorial or Axial beta-Position to the
Amino Group
[
a]
[a]
[a]†
[a]
Patrick Schnider* , Cosimo Dolente , Henri Stalder , Rainer E. Martin* , Viktoria
[
a]‡
[a]‡‡
[a]
[a]
[a]
Reinmüller , Roman Marty , Caroline Wyss Gramberg , Björn Wagner , Holger Fischer ,
[
a]
[b]
André M. Alker , Klaus Müller*
[
a] Dr. Patrick Schnider,
Mr. Cosimo Dolente,
Dr. Henri Stalder,
Dr. Rainer E. Martin,
Dr. Viktoria Reinmüller,
Dr. Roman Marty,
Dr. Caroline Wyss Gramberg,
Mr. Björn Wagner,
Dr. Holger Fischer,
Dr. André M. Alker,
F. Hoffmann-La Roche AG, Pharmaceutical Research & Early Development, Roche
Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
[
b] Prof. (emer.) Dr. Klaus Müller,
ETH Zürich, Laboratorium für Organische Chemie, Vladimir-Prelog-Weg 3, 8093 Zürich,
Switzerland
†
‡
‡
current address: Beim Goldenen Löwen 12, 4052 Basel, Switzerland; e-mail:
henri.stalder@balcab.ch
current address: Auxenion Research AG, Gewerbestrasse 18, 4123 Allschwil, Switzerland;
e-mail: viktoria.reinmuller@auxenion-research.com
‡
current address: Auxenion Research AG, Gewerbestrasse 18, 4123 Allschwil, Switzerland;
e-mail: roman.marty@auxenion-research.com
1
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ChemBioChem
10.1002/cbic.201900474
Keywords:
piperidine derivatives
physicochemical properties
stereospecific group interactions
basicity
lipophilicity
Text to Table-of-Contents
A set of amine basicity and lipophilicity data for -substituted piperidine derivatives provide
enhanced insight into the stereospecific modulation of pharmacologically relevant properties by
small substituents and prototypic functional groups, establishing a valuable reference base for
molecular design.
Graphic Icon for Table-of-Contents
2
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ChemBioChem
10.1002/cbic.201900474
Abstract
Thirteen epimeric pairs of 5-substituted N-piperonyl-3-phenylpiperidine derivatives were
synthesized in order to explore the stereospecific modulation of basicity, lipophilicity, aqueous
solubility, and membrane permeation by functional groups in equatorial or axial positions beta to
the amine unit. While this comprehensive data set provides enhanced insight into multiple factors
affecting basicity and lipophilicity, it fills an important knowledge gap providing a reference
frame for the property-based design of bioactive compounds. Impacts on amine basicity are very
pronounced for the -equatorial functional groups and parallel basicity-lowering effects known
for acyclic amine derivatives. For -axial functional groups, the basicity-lowering effects are
generally reduced, with the nitrile group as the only exception. Basicity and lipophilicity
modulations observed for -axial functional groups are quite diverse and rationalized in terms of
intramolecular hydrogen bonding, dipolar interactions, and special solvation effects. Aqueous
solubility and (artificial) membrane permeability are discussed with reference to lipophilicity.
1
.
Introduction
Piperidine is a favorite building block in Drug Discovery. Two independent surveys of ring
systems contained in FDA-approved small-molecule drugs identified piperidine together with
[
1]
pyridine as the most frequently occurring N-heterocyclic ring systems. The piperidine unit has
[
2]
also been found in a number of ‘privileged scaffolds’ for library design and drug discovery.
[
3]
Recent searches (March 2019) in Clarivate Analytics Integrity for launched small-molecule
drugs or drug candidates in clinical development (phases I-III) containing a saturated piperidine
unit in their molecular structures revealed, respectively, 243 and 583 records. The overwhelming
majority of these drugs and drug candidates contain N-alkylated or N-unsubstituted piperidine
units (together close to 70 % in both groups) whereas N-acylated or N-(hetero)aryl-substituted
piperidine units are much less common (details are given in Supporting Information [SI], Fig.
S1). Likewise, monocyclic piperidine derivatives represent the overwhelming majority of
compounds (approximately 60 % in both groups), followed by bicyclic, spirocyclic, and more
complex bridged oligocyclic derivatives with embedded saturated piperidine units. Among the
bicyclic derivatives with one or more saturated piperidine substructural units, the
azabicyclo[3.2.1]octane scaffold is the most prominent one, followed by azadecaline and
quinuclidine units. In both groups of launched drugs and drug candidates in clinical
development, N-substituted terminal piperidine units carrying no further ring substituents are
encountered in about 10 % of all cases, whereas the great majority of cases contain saturated
piperidine units with one (ca. 40 %), two (ca. 25 %), or three (ca. 15 %) substituents at the ring
carbon atoms.
In contrast to the planar pyridine system with all its possible substituent bond exit vectors in the
same plane, the piperidine ring generally adopts one of two well-puckered chair conformations
with substituents in either equatorial or axial positions offering opportunities for molecular shape
design to deviate significantly from overall flat architectures. Furthermore, double substitution at
a given ring carbon atom opens the door to spirocyclic connections with its unique possibilities
3
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ChemBioChem
10.1002/cbic.201900474
for non-flat geometries (see SI, Chapt. 2, for illustrative examples). Whereas piperidine chair
conformations can interconvert rapidly at room temperature with concomitant exchange of axial
and equatorial positions, certain structural features keep substituents in their axial positions.
Thus, N-acyl or N-aryl substitution forces a substituent in -position to the piperidine nitrogen
into the axial position. This may then also put other substituents on the piperidine ring into axial
positions depending on their relative configurations (see SI, Chap. 2.3, for illustrative examples).
For N-alkyl-substituted piperidines, chair conformations are preferred which keep a further ring
substituent in an equatorial position. However, for two or more substituents, appropriate relative
configurations may assure that one or more substituents will adopt axial positions (see SI, Chap.
2
.2, for illustrative examples). This offers remarkable molecular design opportunities to avoid
[
4]
‘flatland’ chemistry.
[
5]
Remarkably, the intrinsic lipophilicity of (neutral) piperidine (logP = 0.84 ) is only slightly
[
5]
[6]
higher than that of pyridine (logP = 0.65 ). Whereas the weakly basic pyridine (pK
a
= 5.2 )
remains essentially unprotonated at a physiological pH of 7.4, the strongly basic piperidine (pK
a
[
6]
=
11.1 ) is fully protonated at this pH. Assuming that charged species essentially do not enter an
[
7]
organic phase such as n-octanol, the water/n-octanol distribution coefficient of piperidine can
pH=7.4
be estimated as logD
~ -3.0, which reflects its essential preference for the water phase. N-
alkyl substitution of piperidine produces a tertiary amine with basicity characteristically reduced
[
8]
from that of the parent secondary amine. Further substitution at the piperidine ring or in the N-
[
9]
alkyl group will modulate both lipophilicity and amine basicity. Thus, N-piperonyl-piperidine
and further derivatives, as exemplified in Scheme 1, exhibit increased intrinsic lipophilicity and
reduced amine basicity with resulting n-octanol/water distribution coefficients (effective
pH=7.4
lipophilicities logD) in a pharmacologically favorable range of 0 < logD
< 2.5.
Scheme 1: Experimental amine basicity (pK
),[6b, 8, 9] effective and intrinsic lipophilicities
a
pH=7.4
(logD
and logP, respectively) for selected piperidine derivatives; a) derived from logP and
pK
logD
a
according to reference [7]; b) experimental values from reference [5]; c) experimental
pH=7.4
; logP values derived from logDpH=7.4 and pK
.
[9]
a
4
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ChemBioChem
10.1002/cbic.201900474
Basicity modulation by polar substituents like fluorine or hydroxyl in -position to the piperidine
nitrogen atom exhibits strong configurational/conformational dependency. Thus, basicity
reductions are significantly smaller for these substituents in axial than in equatorial positions.
Ring-substituted piperidine derivatives can be used prototypically for the rationalization of
[8]
basicity effects in acyclic amine derivatives with staggered conformations, particularly in those
cases where one or more conformations dominate conformational averaging. This has provided
consistent interpretation of unusually small amine basicity lowering effects by single -fluorine
[8]
or -hydroxy substituents in N-alkyl amine derivatives. There are various other substituents
common in Medicinal Chemistry that are known to modulate amine basicity significantly.
However, to the best of our knowledge, no information is available on their
configuration/conformation-dependent modulation of amine basicity and other
pharmacologically relevant properties.
Therefore, we set out to synthesize pairs of racemic N-piperonyl-substituted piperidine
derivatives carrying a phenyl unit in position 3 and different functional substituents in position 5
in either a cis- or trans-configuration (Scheme 2) and to determine various pharmacologically
relevant properties as a function of the configuration/conformation of the functional group
relative to the piperidine amino group. The piperonyl group was chosen for the N-alkyl group as
[
9]
in previous work in place of an N-benzyl or N-methyl group to aid analytical measurements.
With an anticipated piperidine chair conformation and phenyl substituent in an equatorial
position, the cis- and trans-configured derivatives will have the substituent at C-5 fixed in,
respectively, the equatorial and axial positions.
Scheme 2: Phenyl-substituted N-piperonyl-piperidine derivatives synthesized and analyzed in
this work; all derivatives are racemic.
5
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ChemBioChem
10.1002/cbic.201900474
X =
H
cis-series
1
trans-series
(1)
F
OH
OMe
OAc
CH
cis-2
cis-3
cis-4
cis-5
cis-6
cis-7
cis-8
cis-9
cis-10
cis-11
cis-12
cis-13
cis-14
trans-2
trans-3
trans-4
trans-5
trans-6
trans-7
trans-8
trans-9
trans-10
trans-11
trans-12
trans-13
trans-14
2
OH
OMe
CH
2
COOMe
CONH
CONHMe
CONMe
COOH
C≡N
2
2
C≡CH
In this report, we include the results of a smaller parallel study on racemic tert-butyl-substituted
piperidines (Scheme 3). Although this study was not expanded for synthetic and analytical
reasons, the available data provide valuable complementary information.
Scheme 3: tert-Butyl-substituted N-methylpiperidine derivatives synthesized and analyzed in
this work. All derivatives are racemic.
X =
H
cis-series
15
trans-series
(15)
Cl
OH
OMe
cis-16
cis-17
cis-18
trans-16
trans-17
trans-18
6
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ChemBioChem
10.1002/cbic.201900474
2
.1
Synthesis of N-Piperonyl-3-phenylpiperidine Derivatives
All epimeric N-piperonyl-3-phenylpiperidine derivatives of Scheme 2 were prepared as
racemates. They were available in short sequences of standard chemical transformations from
commercial or readily available building blocks described in the literature. Thus, reference
[
10]
compound 1 and cis-3/trans-3 derivatives were obtained by direct alkylation of precursors 19
[
11]
and 20 , respectively (Scheme 4). The cis-3 and trans-3 epimers could be easily separated and
purified by chromatography. Individual acetylation then provided the epimeric acetates cis-5 and
trans-5. The methoxy derivatives cis-4 and trans-4 were prepared by O-methylation of the N-
Boc-protected cis- and trans-21 followed by a standard two-step sequence of N-deprotection and
alkylation by piperonyl chloride. Since the latter epimers could not be accessed directly by
chromatographic separation of their ~ (5:2) cis-/trans-mixture (21), they were obtained after
saponification of the chemically more differentiated and hence chromatographically readily
separable O-benzoyl esters, cis- and trans-22 (Scheme 4).
Scheme 4: Synthesis of racemic reference compound 1 and N-piperonyl-3-phenylpiperidine
derivatives with oxy-functional groups at position 5, cis-/trans-3, cis-/trans-4, and cis-/trans-5.
7
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ChemBioChem
10.1002/cbic.201900474
t
a) piperonyl chloride, K
dioxane, rt; c) benzoyl chloride, cat. DMAP, Et
chromatography); d) aq. NaOH, dioxane, rt; e) NaH, DMF, MeI, rt; f) 4 M HCl/dioxane, rt; g)
piperonyl chloride, K CO , DMF, rt; h) piperonyl chloride, K CO , DMF, rt (separation of cis-
and trans-products by chromatography); i) Ac O, DMAP, DCM, rt; procedures d-g and i are
2
CO
3
, DMF, rt; for 19 see ref. [10]; b) ( BuOCO)
2
O, 2 M aq. NaOH,
3
N, THF (separation of cis- and trans-products by
2
3
2
3
2
applied to epimeric starting materials individually; abbreviations see Experimental Part; for more
details see SI (Chap. 10.1).
Scheme 5: Preparation of racemic N-piperonyl-3-phenyl-5-fluoropiperidines cis-2 and trans-2
by deoxyfluorination.
®
a) DAST, DCM, 0-5 °C; b) XtalFluor-E , DBU, DCM, rt; c) 4M HCl/dioxane, rt; d) piperonyl
chloride, K
0.1).
2
CO , DMF, rt; abbreviations see Experimental Part; for more details see SI (Chap.
3
1
Deoxyfluorination of the secondary alcohol cis-3 gave cis-2 in excellent yield using
diethylamino)sulfur trifluoride (DAST) in dichloromethane (Scheme 5). The reaction proceeded
(
with complete retention of configuration. Whereas deoxyfluorination of secondary alcohols
under various conditions typically proceeds under inversion of configuration at the stereogenic
[
12]
center, anchimeric participation of nucleophilic groups in -position to the reaction site has
been shown to enable a double-inversion mechanism with overall retention of
[
13][14]
configuration.
In particular, Cossy et al. found that treatment of (R)-1-benzylpiperidin-3-ol
with DAST gave 55 % of an inseparable mixture of (R)-1-benzyl-3-fluoro-piperidine and (S)-1-
[
13a]
benzyl-2-(fluoromethyl)pyrrolidine.
The finding that both products were formed under
retention of configuration suggested that the reaction proceeded via an aziridinium intermediate
resulting from nucleophilic attack of the piperidine nitrogen at C-3. Aziridinium intermediates
8
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ChemBioChem
10.1002/cbic.201900474
have also been postulated in the deoxyfluorination of two epimeric N-(2-hydroxybutyl)piperidine
[
14]
derivatives by nonaflyl fluoride with clean retention of configuration for each epimer. In
contrast, treatment of trans-3 with DAST in dichloromethane did not yield any fluorination
product due to rapid elimination, presumably favored by the axial orientation of the -hydroxy
group, whereas formation of an aziridinium intermediate would require unfavorable
conformational changes in the piperidine unit. In another attempt towards trans-2, treatment of
®
the N-Boc-protected trans-21 with XtalFluor-E and DBU in dichloromethane gave the
deoxyfluorinated trans-24 in 16 % (Scheme 5) and the 5,6-elimination product in 14 % yield
along with approximately 20 % of a mixture, consisting of two further uncharacterized
elimination products and a small amount of the cis deoxyfluorination product. Using our
standard two-step N-deprotection and N-alkylation protocol, trans-24 was converted to trans-2.
Since optimization of synthetic accessibility was not the focus of this work, further mechanistic
investigations or different synthetic access routes to trans-2 remain to be undertaken.
Scheme 6: Synthesis of racemic 5-carboxamide derivatives cis-/trans-9 starting from 5-phenyl-
[
15]
nicotinamide (25), and conversion to epimeric nitrile derivatives cis-/trans-13, as well as
synthesis of cis-/trans-10 and cis-/trans-11 starting from cis/trans-28 (see Scheme 7).
a) Pd/C, MeOH/HCl, H
and trans-products by chromatography); c) TFAA, pyridine, THF, rt (procedure applied to
epimeric starting materials individually); d) aq. LiOH, THF, MeOH, rt; e) (COCl) , cat. DMF,
DCM; f) Et N, MeNHR (R = H or Me)/THF, DCM, rt (separation of cis- and trans-products by
2
(1 bar), rt; b) piperonyl chloride, K
2
CO
3
, DMF, rt (separation of cis-
2
3
chromatography); abbreviations see Experimental Part; for more details see SI (Chap. 10.1).
9
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The carboxamide derivatives cis-9 and trans-9 were readily available in two steps from phenyl-
[
15]
nicotinamide 25 by hydrogenation over Pd/C, resulting in an approximate (1:5) cis/trans-
mixture of the 3,5-disubstituted piperidine derivative, 26, followed by N-alkylation with
piperonyl chloride and subsequent chromatographic separation of the cis- and trans-isomers
(Scheme 6). Dehydration of either carboxamide isomer furnished the corresponding nitrile
derivatives cis-13 and trans-13 in good yields. The N-methylated and N,N-dimethylated
carboxamide derivatives cis-/trans-10 and cis-/trans-11, respectively, were prepared via the
carboxylate derivatives cis-/trans-12. The latter is available in three straightforward steps from
[
16]
methyl phenyl-nicotinate 27 (Scheme 7) by hydrogenation, followed by introduction of the N-
piperonyl group, and subsequent saponification of the methyl ester group resulting in an
approximate (1:4) mixture of the carboxylate derivatives cis-12 and trans-12. This mixture was
directly converted to either the N-methyl or the N,N-dimethyl amide derivatives, at which stage
the separation into the epimeric cis- and trans-isomers could be easily achieved by
chromatography (Scheme 6).
Scheme 7: Synthesis of epimeric carboxylic ester cis-/trans-8 and acid derivatives cis-/trans-12,
hydroxymethyl and methoxymethyl piperidine derivatives cis-/trans-6 and cis-/trans-7, as well
as epimeric acetylene derivatives cis-/trans-14, starting from methyl 5-phenyl-nicotinate (27[16]).
1
0
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ChemBioChem
10.1002/cbic.201900474
t
a) PtO
trans-products by chromatography); c) piperonyl chloride, K
and trans-products by chromatography); d) aq. LiOH, THF, MeOH, rt; e) LiBH
2
, MeOH/H
2
SO
4
, H
2
(1 bar), rt; b) ( BuOCO)
2
O, Et
3
N, THF, rt (separation of cis- and
CO , DMF, rt (separation of cis-
, Et O, toluene,
, DMF, rt; h) NaH, THF, MeOTs,
N, -55 °C → rt; j) B-O reagent, MeOH, K CO , rt;
2
3
4
2
1
00 °C; f) 4M HCl/dioxane, rt; g) piperonyl chloride, K
°C → rt, 36 h; i) (COCl) /DMSO, DCM, Et
2
CO
3
0
2
3
2
3
procedures d-j are applied to epimeric starting materials individually; abbreviations see
Experimental Part; for more details see SI (Chap. 10.1).
The epimeric carboxylic ester and acid derivatives cis-8/trans-8 and cis-12/trans-12,
respectively, were directly available from methyl 5-phenyl-nicotinate 27[16] by Pt(IV) dioxide-
catalyzed hydrogenation resulting in a cis/trans-mixture of the disubstituted piperidine derivative
[
17]
2
8
(Scheme 7). This was then either N-alkylated to yield the derivatives cis-8/trans-8, and
after saponification cis-12/trans-12, or N-Boc-protected to produce the key intermediate cis-
trans-30 after lithium borohydride reduction of cis-/trans-29. The separation of cis- and trans-
/
epimers was readily achieved by chromatography after N-alkylation or N-Boc protection. All
subsequent transformations (steps d-j of Scheme 5) were then carried out individually for the cis-
and trans-isomers. Swern oxidation of the hydroxymethyl group in cis-/trans-30 to the
corresponding aldehyde and transformation of the latter by means of Bestmann-Ohira reagent
furnished the N-Boc-protected phenyl-ethynyl piperidine derivatives cis-/trans-32. The latter
were easily converted to the desired cis-14 and trans-14 by N-deprotection and alkylation. The
last two steps were also applied to the hydroxymethyl intermediates cis-/trans-30, furnishing the
products cis-/trans-6, and subsequent Williamson methylation yielded the methoxymethyl
derivatives cis-/trans-7, respectively.
2
.2
Synthesis of N-methyl-3-tert-butyl-piperidine derivatives
The piperidine derivatives cis-17 and trans-17 (Scheme 3) are available in five steps from -tert-
[
18]
butyl-butyrolactone 33 (Scheme 8) by first boron tribromide-promoted lactone opening with
concomitant intramolecular bromination[ to generate the -bromoester 34 in good yields.
Whereas the transformation of butyrolactones to -bromoesters by anhydrous hydrobromic acid
19]
[
20]
is well described in the literature , this alternative route involving an intermolecular
bromination proceded only with low yields in the presence of the bulky -tert-butyl group in 33.
Substitution of bromide by sarcosine ethyl ester to produce the diester 35 and subsequent
cyclization by Dieckmann condensation furnished the intermediate 36, which was subjected to
microwave-assisted hydrolysis and decarboxylation in aqueous HCl to provide the piperidone
derivative 37. Subsequent reduction of the latter with sodium borohydride in methanol produced
an approximate (3:2)-mixture of the diastereomeric cis-17 and trans-17, which could be
separated by preparative HPLC.
1
1
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ChemBioChem
10.1002/cbic.201900474
Scheme 8: Synthetic access to cis-17 and trans-17.
a) BBr
3
, MeCN, 0 °C  rt, 2 d; EtOH; b) ethyl 2-(methylamino)acetate, K
2
CO
3
, acetone, MW
1
40 °C, 14 h; c) NaH, cat. EtOH, toluene, 0 °C, 2 h; d) 37 % aq. HCl, benzophenone, MW 170
°
C, 1.5 h; e) NaBH , MeOH, 0 °C  rt, 12 h, (3:2) cis/trans mixture, separation by
4
chromatography; abbreviations see Experimental Part; for more details see SI (Chap. 10.1).
The reference compound, N-methyl-3-tert-butyl-piperidine (15) was prepared in two steps from
commercially available tert-butylpyridine (38) by N-methylation and subsequent hydrogenation
over PtO /C in good overall yield (Scheme 9, top).
2
The synthesis of the 3-(tert-butyl)-5-methoxypiperidine derivatives cis-18 and trans-18 was
achieved over three steps starting from commercially available 3-bromo-5-methoxy-pyridine 40
(Scheme 9, bottom). Grignard alkylation of 40 to the tert-butyl pyridine derivative 41 was
achieved only in very low yields that could not be further improved even using a large excess of
a 2:1 mixture of tert-butylmagnesium chloride and copper (I) cyanide as proposed by Bell et
[21]
al.. The main side-product formed under these conditions was 3-methoxypyridine. -
Elimination in alkyl Grignard reagents with concomitant reduction of the aryl halide has
[
22]
previously been reported in the case of nickel catalysts and is known to be a major
[23]
decomposition pathway for alkyls bearing hydrogens in -position. N-Methylation of tert-
butyl methoxypyridine 41 and subsequent hydrogenation of 42 over PtO /C produced an
2
approximate (7:3)-mixture of the desired tert-butyl-methoxypiperidines cis-18 and trans-18,
which could be separated by HPLC.
1
2
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ChemBioChem
10.1002/cbic.201900474
Scheme 9: Syntheses of reference compound 15 and -methoxypiperidine derivatives cis-18 and
trans-18.
a) MeI, toluene, reflux, 1.5 h; b) H
2
(3 bar), PtO
2
/C, MeOH, 50 °C, 14 h; c) tert-BuMgCl, CuCN,
THF, 0 °C  rt, 12 h; d) H (3 bar), PtO
2
2
/C, MeOH, 50 °C, 14 h, (7:3) cis/trans-mixture,
separation by chiral chromatography into all four stereoisomers; yields for cis-18 and trans-18
are combined yields for both optical antipodes in each case; abbreviations see Experimental Part;
for more details see SI (Chap. 10.1).
The synthesis of the epimeric N-methyl 3-(tert-butyl)-5-chloropiperidines, cis-16 and trans-16,
[
18b]
respectively, involved essentially a five-step synthesis starting from the readily available
methyl 2-tert-butylpent-4-enoate 43 (Scheme 10), involving reduction of the methyl ester to the
primary alcohol 44, Swern oxidation to the aldehyde 45, and reductive amination to the N-
[
24]
methylamine 46 with good overall yield. The latter was subjected to N-chlorination using N-
chlorosuccinimide providing the N-chloroamine 47 in nearly quantitative yield. Due to chemical
instability, this compound had to be used immediately without further purification. Cyclization to
the epimeric cis- and trans-pyrrolidine derivatives cis/trans-48 was then achieved at low
[24]
temperature using BF
3
∙OEt
2
with a catalytic amount of TiCl
3
.
The pyrrolidine product mixture
was used without further purification and allowed to stand in chloroform at room temperature for
about 3.5 days, after which their stereospecific rearrangements[25][26] to the corresponding more
1
3
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ChemBioChem
10.1002/cbic.201900474
stable epimeric -chloropiperidine derivatives, cis-16 and trans-16, were complete. The epimers
could be easily separated by HPLC chromatography.
Scheme 10: Synthetic access to tert-butyl--chloropiperidine derivatives cis-16 and trans-16.
a) DIBAL, THF, -10 °C  rt, 1 h; b) (COCl)
MeNH , DCM, rt, 1 h; d) Na(CH COO) BH, AcOH, DCM, 0 °C  rt, 14 h; e) NCS, DCM, -40
C, 15 min; crude product used immediately in subsequent step; f) BF ˑEt O, TiCl , DCM, -78
C, 1 h,; g) CDCl , rt, 86 h, separation and purification of cis and trans products by
2
/DMSO, Et
3
N, DCM, -78 °C  rt, 14 h; c)
2
3
3
°
°
3
2
3
3
chromatography; abbreviations see Experimental Part; for more details see SI (Chap. 10.1).
2
.3
Assignment of Relative Configurations
Scheme 11: Proton-proton coupling patterns in cis- and trans-configured 3,5-disubstituted
1
2
1
2
piperidine derivatives; R = piperonyl, R = phenyl for derivatives of Scheme 2; R = methyl, R
tert-butyl for derivatives of Scheme 3. The signal patterns that discriminate between cis- and
=
trans-configurations are highlighted in red (for abbreviations, see Experimental Part). For certain
groups X (see Schemes 2 and 3), additional spin coupling is observed (see text); the actual signal
1
patterns are listed in the SI, Chap. 10.2, Table S5. The H NMR spectra are compiled in the
Experimental Part and full spectroscopic characterization is given in the SI, Chap. 10.1.
1
4
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ChemBioChem
10.1002/cbic.201900474
The relative configurations of the 3,5-disubstituted piperidine derivatives of Schemes 2 and 3
1
could all be assigned unambiguously by analyses of proton-proton coupling patterns in the H
1
NMR spectra (the H NMR spectra of the disubstituted piperidine derivatives are compiled in
the Experimental Part and the SI, Chap. 10.1; the configuration-determining coupling patterns
are listed in the SI, Chap. 10.2, Table S5). With an equatorial phenyl or tert-butyl group at
position 3, the axial methine proton H3ax (Scheme 11) displays a characteristic triplet-triplet
3
pattern with large trans-diaxial coupling constants JHH,diax (10.0 - 12.5 Hz) to the two adjacent
axial protons, H2ax and H4ax, and smaller synclinal coupling constants 3JHH,syncl (3.0 - 4.5 Hz) to
3
the two adjacent equatorial protons, H2eq and H4eq. In a few cases, where the two JHH,diax
coupling constants differ sufficiently, the large triplet splits into a doublet-doublet pattern. The
axial position of the methine proton at C-3 is further corroborated by a clear triplet pattern for the
2
axial proton at C-2, H2ax, with a geminal coupling JHH,gem and vicinal trans-diaxial coupling
3
constant JHH,diax of similar (absolute) magnitude (10 - 12.5 Hz).
Analogous patterns can be identified for the methine proton at C-5, H5ax, and the adjacent axial
proton H6ax in the set of cis-piperidine derivatives. This confirms the equatorial placement of the
substituent X at C-5 and thus the cis-configuration of these piperidine derivatives. In a few cases,
these characteristic signal patterns exhibit additional spin coupling to nuclei in the group X.
Thus, in the fluorine derivative cis-2, the coupling patterns of H5ax and H6ax are split by
2
3
substantial JHF,gem and JHF,syncl couplings to the equatorial fluorine. In the hydroxy derivative
cis-3, the coupling pattern for H5ax is split into a doublet-doublet-doublet-doublet, due to
3
inequalities of the two large diaxial coupling constants ( JHH,diax = 10.7 Hz and 10.1 Hz) and the
3
two smaller synclinal proton-proton coupling constants ( JHH,syncl = 6.1 Hz and 4.0 Hz); in
addition, the pattern is further split by a coupling between the methine and the hydroxyl protons
3
of similar magnitude ( JH,OH = 5.1 Hz). Finally, in cis-14, the characteristic triplet-triplet pattern
of H5ax is further split by the characteristic 4JHH coupling constant (2.5 Hz) to the acetylenic
proton.
For the set of epimeric trans-piperidine derivatives, the equatorial methine proton at C-5, H5eq
,
uniformly displays a very narrow mutiplet pattern, with relatively small coupling constants to the
1
5
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ChemBioChem
10.1002/cbic.201900474
four adjacent synclinal protons (3JHH,syncl 2.3 – 5.4 Hz), either appearing as a quintet or a doublet-
quartet depending on similarity or dissimilarity of coupling constants (for details, see SI, Table
S5). These patterns confirm both the equatorial position of the methine proton and the axial
placement of the substituent X at C-5, and thus the trans-configuration of the piperidine
2
derivatives in this set. This pattern is further split by a large JHF,gem coupling between the
methine proton and the geminal fluoro substituent in trans-2. For trans-3 an additional signal
3
splitting is observed due to the coupling between the methine and hydroxyl protons ( JH,OH = 9.5
Hz). For the methoxymethyl-substituted derivative trans-7 individual coupling constants of the
3
methine proton with the two exocyclic methylene protons ( JHH = 8.1 Hz and 6.5 Hz) can also be
observed. As discussed above, the splitting patterns for the methine proton at C-5 are
complemented by characteristic signal patterns for the adjacent axial proton H6ax, confirming the
equatorial position of the methine proton at C-5 in the trans-piperidine derivatives. In contrast to
the triplet splitting observed for H2ax in both cis- and trans-piperidine derivatives and for H6ax for
the cis-derivatives, the latter displays a doublet-doublet pattern with an (absolutely) large and a
2
small coupling constant due to its coupling to the geminal proton H6eq (│ JHH,gem│= 11.4 - 12.7
3
Hz) and the adjacent equatorial proton H5eq ( JHH,syncl = 1.4 – 3.9 Hz).
Important additional pieces of information come from the splitting patterns observed for the axial
proton at C-4. In the set of cis-piperidine derivatives, H4ax displays a quartet due to a geminal and
2
3
two trans-diaxial couplings of similar absolute magnitude ((│ JHH,gem│~ JHH,diax = 11.4 - 12.8
Hz). Only in the hydroxy and methoxy-piperidine derivatives (cis-3 and cis-4), the corresponding
signal patterns are doublet-doublet-doublet due to three different coupling constants in the range
of (absolutely) 10.7 - 13.2 Hz (for details, see SI, Table S5). Furthermore, in the case of the
fluorine derivative cis-2, the signal of H4ax appears as a quintet due to its additional coupling
3
with the equatorial fluorine substituent ( JHF,syncl ~ 11.1 Hz).
In the set of trans-piperidine derivatives H4ax couples with one geminal proton (H4eq), one
adjacent axial proton (H3ax), and one equatorial proton (H5eq). Thus, the appearance of this proton
signal is, in most cases, a triplet-doublet with a large coupling constant for the triplet and a small
coupling constant for the doublet, in clear contrast to the corresponding signal patterns in the cis-
epimers. In a few cases, the triplet part is split into a doublet-doublet due to inequality of the
large coupling constants. In the case of trans-2, H4ax experiences an additional substantial trans-
3
diaxial coupling to the fluorine substituent ( JHF,diax = 42.4 Hz).
Not all signals of the methine protons at C-3 and C-5 and the axial protons at C-2, C-4, and C-6
1
are fully visible in the H NMR spectra of all piperidine derivatives either due to signal overlap
or because they appear as complex, insufficiently resolved multiplets (for a tabulation of all
signals, see SI, Chap. 10.2, Table S5). However, the great majority of signals are well resolved.
As discussed above, they provide complementary information and, together, provide clear
support to the assignments of cis- and trans-configuration in each case.
1
6
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ChemBioChem
10.1002/cbic.201900474
3
.
Results and Discussion
For the (racemic) compounds of Scheme 2, the aqueous amine basicities (pK
a
) and the n-
octanol/water distribution coefficients (effective lipophilicities logD) at pH = 7.4 were
determined. They are compiled in Table 1 together with the intrinsic lipophilicities (logP)
[7]
derived from the experimental logD and pK values. Aqueous solubility at pH = 6.5 and
a
artificial membrane permeation (PAMPA) data for the same compounds are given in Table 2.
Table 1: Experimental amine basicity, effective lipophilicity, and derived intrinsic lipophilicity
of compounds listed in Scheme 2 (all data are rounded to one digit after the decimal point; the
original data are compiled in the SI, Tables S1 and S2).
comp
#
eq
ax
pK
a
pK
a
e)
logD
logD logD
logP
logP logP
-Xb)
pK
a
c)
5
a)
d)
f)
g)
h)
i)
j)
k)
ax-eq
ax-eq
ax-eq
1
(ref)
H
F
F
-
8.7
6.2
7.0
7.1
8.3
7.0
8.0
6.5
7.1
8.1
8.2
8.0
8.1
7.1
7.4
7.0
7.9
7.2
8.0
7.2
8.9
8.1l)
-
-
3.1
3.7
3.6
3.1
2.5
3.7
3.1
3.7
3.5
2.8
3.2
3.4
3.7
3.8
3.7
2.9
2.8
3.2
3.0
3.1
2.0
0.7
0.6
3.6
3.6
3.7
3.6
-
-
-
4.4
3.8
3.8
3.3
3.4
3.8
3.7
3.8
3.6
3.5
4.0
4.1
4.5
4.0
4.0
3.1
3.4
3.4
3.6
3.3
3.6
-
-
-
-
cis-2
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
-2.5
-1.7
-1.6
-0.4
-1.7
-0.7
-2.2
-1.6
-0.6
-0.5
-0.7
-0.6
-1.6
-1.3
-1.7
-0.8
-1.5
-0.7
-1.5
+0.2
-0.6
0.6
0.5
0.0
-0.6
0.6
0.0
0.7
0.4
-0.3
0.1
0.3
0.6
0.7
0.6
-0.2
-0.3
0.1
-0.1
0.0
-1.1
-2.4
-2.5
0.5
0.5
0.6
0.5
-0.6
-0.6
-1.1
-1.0
-0.6
-0.6
-0.6
-0.8
-0.9
-0.4
-0.3
0.1
trans-2
cis-3
0.8
-
-0.1
-
0.0
-
OH
OH
trans-3
cis-4
1.2
-
-0.6
-
0.1
-
OMe
OMe
OAc
OAc
trans-4
cis-5
1.0
-
-0.6
-
-0.1
-
trans-5
cis-6
0.6
-
-0.3
-
-0.1
-
CH
CH
2
2
OH
OH
trans-6
cis-7
0.1
-
0.4
-
0.5
-
CH
CH
2
2
OMe
OMe
trans-7
cis-8
0.1
-
0.3
-
0.4
-
COOMe
COOMe
-0.4
-0.4
-1.3
-1.0
-1.0
-0.8
-1.1
-0.8
-
trans-8
cis-9
0.3
-
-0.1
-
0.0
-
CONH
CONH
2
2
trans-9
cis-10
0.9
-
-0.1
-
0.3
-
CONHMe
trans-10 CONHMe
0.8
-
-0.2
-
0.3
-
cis-11
trans-11
cis-12
CONMe
CONMe
COO-
2
2
1.7
-
-1.1
-
0.2
-
COO-
9.5l) +0.8
1.4
-
-0.1
-
-
-
-
trans-12
cis-13
C≡N
5.8
5.6
7.1
7.4
-2.9
-3.1
-1.6
-1.3
3.6
3.6
3.9
3.9
-0.8
-0.8
-0.5
-0.5
-
trans-13
cis-14
C≡N
-0.2
-
-0.1
-
-0.1
-
C≡CH
C≡CH
trans-14
0.3
-0.1
0.1
1
7
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10.1002/cbic.201900474
a) Compound identifiers (see Scheme 2); b) substituent in 5-position, either equatorial (eq) or
axial (ax); c) pK , determined by multiplexed capillary electrophoresis and spectrophotometric
a
titration (for details see SI, Chap. 4.1-4.3); d) change of basicity relative to 5-unsubstituted
reference compound 1; e) basicity difference in epimeric pairs of 5-axially and 5-equatorially
substituted compounds; f) logarithmic n-octanol/water distribution coefficient (logD) at pH = 7.4
determined by CAMDIS method (for details see SI, Chap. 5, Table S2); g) change of logD
relative to 5-unsubstituted reference compound 1; h) logD difference in epimeric pairs of 5-
axially and 5-equatorially substituted compounds (see SI, Table S2); i) intrinsic lipophilicity,
logP, of neutral compounds according to logP = logD + log10(1 + 10(pKa-pH))[7] (see SI, Table S2);
j) change of logP relative to 5-unsubstituted reference compound 1; k) logP difference in
epimeric pairs of 5-axially and 5-equatorially substituted compounds; l) pK
a
(-eq COOH) = 3.1;
hence pI = 5.6; pK (-ax COOH) = 2.9; hence pI = 6.2.
a
Table 2: Experimental aqueous solubility and effective artificial membrane permeation of
racemic) compounds listed in Scheme 2.
(
comp
#
eq
ax
S
logS
logS
logS
P
e
h)
P
e
P
e
5
-Xb)
a)
c)
d)
e)
f)
j)
k)
ax-eq
ax-eq
1
(ref)
H
F
F
-
860
< 3
2.9
< 0.5
2.2
-
-
8.4
0.0 i)
7.5*
10.0*
9.1
-
-
-
cis-2
eq
ax
eq
< -2.4
-0.7
+0.1
> +0.2
-0.7
0.0
-8.4
-0.9
1.6
0.7
-3.1
0.6
-6.1
-2.3
-2.8
1.0
-
trans-2
cis-3
150
900
> 1.7
7.5
-
OH
OH
3.0
-
trans-3
cis-4
ax > 1140
> 3.1
2.2
> 0.1
(-0.9)
OMe
OMe
OAc
OAc
eq
ax
eq
ax
eq
ax
eq
ax
eq
ax
145
890
< 3
290
830
930
n.d.
n.d.
75
-
5.3*
9.0*
2.3i)
6.1
-
trans-4
cis-5
2.9
0.7
(3.7)
< 0.5
2.5
< -2.4
-0.4
0.0
-
-
trans-5
cis-6
> 2.0
3.8
CH
CH
2
2
OH
OH
2.9
-
0.1
-
5.6*
9.4*
n.d.
n.d.
5.4
-
trans-6
cis-7
3.0
+0.1
-
3.8
CH
CH
2
2
OMe
OMe
-
-
trans-7
cis-8
-
-
-
-
-
COOMe
COOMe
1.9
-1.0
-1.0
> 0.2
> 0.2
-0.1
-0.3
-0.2
-0.1
> 0.2
-
-3.0
-2.5
-5.1
-4.4
-0.6
1.4
-0.9
1.2
-3.1
-
0.5
-
trans-8
cis-9
85
1.9
0.0
-
(-)g)
5.9
CONH
CONH
2
2
eq > 1200
ax > 1200
> 3.1
> 3.1
2.8
3.3
trans-9
cis-10
trans-10
cis-11
trans-11
cis-12
4.0*
7.8
(0.7)
-
CONHMe
CONHMe
eq
ax
eq
ax
700
390
500
580
-
2.6
-0.2
-
9.8
2.0
-
CONMe
CONMe
COO-
2
2
2.7
7.5
2.8
0.1
-
9.6
2.1
-
eq > 1180
> 3.1
5.3
1
8
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COO-
C≡N
ax > 1270
> 3.1
< 0.5
< 0.5
0.8
> 0.2
< 2.4
< 2.4
-2.1
(-)g)
-
(-)g)
2.6
-5.8
-2.8
-5.2
-7.5
-7.5
-2.7
-
trans-12
cis-13
eq
ax
eq
ax
< 3
< 3
6
5.6 i)
3.2* i)
0.9* i)
0.9*
trans-13
cis-14
C≡N
-2.4
-
C≡CH
C≡CH
-
trans-14
25
1.4
-1.5
0.6
(0.0)
a) Compound identifiers (see Scheme 2); b) substituent in 5-position, either equatorial (eq) or
axial (ax); c) molar aqueous solubility determined by the LYSA method at pH = 6.5 [mol/L]
(for details see SI, Chap. 6), estimated standard deviations (esd) ≤ 10 % of given value; d) log10
of molar aqueous solubility; e) difference of logarithmic molar solubility with respect to
reference compound 1; f) difference of logarithmic molar solubility in epimeric pairs of 5-
axially and 5-equatorially substituted compounds; g) difference undetermined due to unknown
upper limits (see SI, Chapt. 6); h) effective artificial membrane permeation (PAMPA, for details
-6
see SI, Chap. 7) in [cm/s∙10 ], esd’s typically between 5-10 % of given value, except where
marked with * (for more details, see SI, Chap.7, Table S3); i) partial precipitation of analyte
during measurements; j) change of PAMPA value with respect to reference compound 1; k)
PAMPA value difference in epimeric pairs of 5-axially and 5-equatorially substituted
compounds; parenthetical differences are less meaningful due to overlapping standard errors (see
SI, Chap.7, Table S3).
Table 3: Experimental amine basicities of (racemic) piperidine derivatives listed in Scheme 3.
eq
ax
pK
a
pK
a
e)
comp-#a)
5 (ref)
5-Xb)
pK
c)
a
d)
ax-eq
1
H
Cl
-
10.3
7.8
8.4
8.6
9.8
8.4
9.5
-
cis-16
trans-16
cis-17
eq
ax
eq
ax
eq
ax
-2.5
-1.9
-1.7
-0.5
-1.9
-0.8
-
Cl
0.6
-
OH
OH
OMe
OMe
trans-17
cis-18
1.2
-
trans-18
1.1
a) Compound identifiers (see Scheme 3); b) substituent in 5-position, either equatorial (eq) or
axial (ax); c) aqueous basicity determined by spectrophotometric titration (see SI, Chap. 4.2); d)
change of basicity relative to 5-unsubstituted reference compound 15; e) basicity difference in
epimeric pairs of 5-axially and 5-equatorially substituted compounds.
The 5-fluorine case: To the best of our knowledge, the compound pair cis-2/trans-2 represents
the first case in which the fluorine substituent in -position to the piperidine amine unit is firmly
fixed in either an equatorial or axial position, respectively, by the bulky non-interfering 3-phenyl
1
9
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ChemBioChem
10.1002/cbic.201900474
substituent. As anticipated, the pK
a
-lowering effect by the equatorial fluorine is much more
pronounced than for the axial fluorine substituent. Gratifyingly, the difference in basicity-
[
8]
reducing effects (pK
a
(ax-eq) ~ 0.8) is essentially the same as that estimated earlier on the
basis of analyses of poly-hydroxylated piperidine derivatives carrying a single (equatorial)
[
27]
fluorine substituent, and from the difference of this value to the pK
the corresponding 3,3-difluoropiperidine derivative (Scheme 12), assuming approximate
additivity of pK effects. However, the basicity depressions for both the equatorial and axial -
a
depression determined for
a
fluorine substituent are somewhat more pronounced in the present study than those derived
earlier.
Scheme 12: Top: Derivation of amine basicity changes (pK
equatorial and axial positions of piperidine derivatives.
a
) for -fluorine substituent in
Bottom: comparison with directly
for 1, cis-2, and trans-2 (see Table 1), and derived basicity changes (pK ). The
[
8][27]
determined pK
a
a
differences in basicity changes, pK (Fax-Feq), as obtained by both approaches, are
a
essentially the same.
The 5-unsubstituted reference compound 1 is more basic than most of the 5-substituted
derivatives. It is about 95 % protonated at pH = 7.4. This explains the substantial difference
between intrinsic and effective lipophilicities of 1 (logP – logD = 1.3). Introduction of one
fluorine substituent in the -position reduces the intrinsic lipophilicity significantly. Both
epimeric fluorine derivatives exhibit very similar lipophilicities. As they are both very weakly
basic, their intrinsic lipophilicities (logP) differ only slightly from their logD values. The
2
0
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ChemBioChem
10.1002/cbic.201900474
essentially equal logP values for the two neutral epimeric -fluoro derivatives may come as a
surprise at first sight, but could hint at two counteracting factors (Scheme 13). Based on simple
[
28]
bond polarity vector analysis one might have anticipated a more pronounced polarity effect for
the -axial fluorine derivative since here the C-F bond dipole is properly aligned with the
resulting dipole moment of the trialkylamine fragment (Scheme 13A). This would predict a
lipophilicity difference of logP ~ -0.4 between the two epimers, placing trans-2 below cis-2.
On the other hand, the -axial fluorine substituent is partially shielded by the axial methine C-H
unit at the phenyl substitution site (Scheme 13B). To appreciate this latter effect, it is instructive
to note that, in both cis-2 and trans-2, the 5-fluoro substituent is embedded in a 1-fluoropropane
subunit either in an anti (extended) or a gauche (endo) conformation (Scheme 13 middle). For 1-
fluoropropane in the gas phase, the gauche-endo conformation is energetically preferred by
almost 0.5 kcal/mol and less polar (el = 1.90 D) than the extended anti-conformation (el = 2.05
D) as determined by microwave spectroscopy.[ This can be rationalized by favorable (1,3)-
29]
[30]
antiparallel C-F/H-C dipole-dipole or (1,5) F∙∙∙H partial charge interactions that are not
available in the anti-conformation of 1-fluoropropane or in cis-2.
Scheme 13: Two counteracting polarity factors that provide a rationale for the similar intrinsic
lipophilicities of the two epimeric -fluoro derivatives.
(
A) Simplified polar bond vector model[28a][31] applied to the -fluoroamines cis-2 and trans-2:
the three CN bond vectors (CN) are drawn in light red; for a tetrahedral arrangement, the three
CN vectors add up to a resultant C3N vector (red) which equals in length to CN; the CF bond
2
1
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ChemBioChem
10.1002/cbic.201900474
vector (green) is aligned with C3N in trans-2, but encloses a tetrahedral angle in cis-2. Assuming
[
31]

CN ~ 0.35 CF
,
as well as tetrahedral and perfectly staggered arrangements, the difference of
the magnitudes of the resultant polarity vectors is res(trans-cis) ~ 0.4 CF which translates to
logP(trans-cis) ~ -0.4, trans-2 being more polar. (B) On the other hand, cis-2 and trans-2

contain an embedded 1-fluoropropane substructural unit (shown in bold). The microwave
spectroscopic data for 1-fluoropropane in the gas-phase[ (inserted in the middle) indicate a
preference for the less polar gauche-conformation (corresponding to the subunit in trans-2) over
the more polar anti- conformation (corresponding to the subunit in cis-2); this result may be
interpreted in terms of favorable (1,3)-antiparallel C-F/H-C dipolar or (1,5) F∙∙∙H partial charge
interactions in trans-2.
29]
Consistent with their enhanced effective lipophilicity, both 5-fluoropiperidine derivatives are
much less soluble in aqueous buffer at pH = 6.5 than the 5-unsubstituted reference compound 1
(Table 2). Whereas trans-2 is moderately soluble under these conditions, cis-2 remains
essentially insoluble. However, we should caution that effective lipophilicity is only one of
several factors that contribute to aqueous solubility. The multi-factorial nature of aqueous
solubility has been noted earlier for partially fluorinated alkyl amines.[ Looking through the
solubility data of Table 2, it is apparent that for several cis/trans-pairs of 5-substituted piperidine
derivatives the trans-isomer displays higher solubility than its cis-counterpart (see e.g., cis/trans-
14]
2
, -3, -4, -5, -6, -11, -14). This may encourage molecular design with -axial substitution patterns
in quest of improved solubility.
The moderate solubility of trans-2 results in effective (artificial) membrane permeability (P )
e
similar to that of the 5-unsubstituted reference compound 1 (Table 2). For cis-2 no permeability
could be measured. However, these observations have to be taken with a grain of salt as for the
poorly soluble cis-2 partial precipitation during the PAMPA experiments was observed, and
repeated measurements of P
e
for trans-2 resulted in unusually large standard deviations (P
e
~ 7.5
-6
±
5.3 cm/s∙10 , see SI, Chap. 7, Table S3).
2
2
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Figure 1: Comparison of piperidine basicity-lowering effects by -equatorial (black bars) and -
axial substituents X (grey bars) in the series of, respectively, cis- and trans-N-piperonyl-3-phenyl
derivatives, for X = F, OH, OMe, OAc (left, data from Table 1), and N-methyl-3-(tert-butyl)
derivatives for X = OH, OMe, Cl (right, data from Table 3).
Oxy-functional groups: Some similarity between C-F and C-O bond units have been noted
[
8][32][33]
based on arguments of polarity and aggregate size of the two units.
On the basis of carbon
to oxygen electronegativity differences, the polarity of a C-O bond is reduced compared to a C-F
[
28]
bond. It has been estimated to be ~2/3 of that of a C-F bond. Accordingly, reduced -polarity
effects are expected and observed for -hydroxy, -methoxy, or -acetoxy groups in equatorial
positions of the piperidine ring. Whereas -hydroxy and -methoxy groups exert similar pK
a
effects (-1.6 in cis-3 and -1.7 in cis-4, Table 1), the basicity depression is more pronounced for
the equatorial -acetoxy group (-2.2 in cis-5), indicating increased -electron withdrawal due to
the additional carbonyl group (Fig. 1). The pattern for pK
a
effects of cis-3, cis-4, and cis-5
resembles remarkably that of acyclic tertiary amines with the same substituents in -position,
[
8]
except that corresponding pK effects are less pronounced (Scheme 14). This may indicate
a
possible anti-gauche conformational averaging, which is absent in the piperidine analogs.
2
3
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Scheme 14: Comparison of amine basicity depression (pK
a
) effects by -hydroxy, -methoxy,
or -acetoxy groups in equatorial positions of the piperidine ring (top row, Table 1) and in
[
8]
corresponding N,N-dimethyl-N-ethylamine derivatives (bottom row); the possibility of anti-
gauche conformational flexibility in acyclic amine derivatives is indicated by the curved arrows;
this may result in reduced pK effects due to conformational averaging.
a
More differentiation between basicity effects for the three oxy-substituents is expected in the
trans-axial series due to the close juxtaposition of the protonated or unprotonated amino unit.
Less prominent basicity reductions are expected due to the gauche-arrangement of the O-C-C-N
-backbone attenuating the electron withdrawing effect on the amino group and, in addition,
favorable (1,3)-antiparallel H-N/C-O dipole-dipole or (1,5) O∙∙∙H partial charge interactions.
However, two observations are counterintuitive: the first concerns the relatively strong basicity
reduction by the -axial acetoxy group in trans-5, the second is the unexpectedly small basicity
lowering by introducing an axial -hydroxy group in trans-3 (Fig. 1, left part).
Regarding the -axial acetoxy group, we might have anticipated a significant stabilization of the
protonated amine unit by intramolecular hydrogen bonding to the carbonyl oxygen with
concomitant increase in basicity. However, such an hydrogen bond interaction would involve a
somewhat unfavored seven-membered cyclic arrangement, its accommodation requiring valence
deformations as suggested by modeling (Fig. 2A). Furthermore, ester carbonyl groups exhibit a
[
35a]
rather modest avidity for hydrogen bonding,
that of amide carbonyl groups
more than an order of magnitude weaker than
[35b]
(see below). In this context, the X-ray crystal structure of the
hydrogen chloride salt of trans-5 is instructive (Fig. 2B). It shows tight chloride-piperidinium
ion pairs, with the chloride anion making further favorable intermolecular H-C contacts. The
acetoxy group, on the other hand, turns away from the protonated amine unit. It engages only in
two possibly favorable electrostatic contacts between the carbonyl oxygen and two polar H-C
bonds adjacent to the amine unit of a neighboring molecule, but enjoys no conspicuous
intramolecular interactions. Although direct ion pair contacts between chloride and
trialkylammonium ions are observed in the majority of cases of crystal structures of HCl salts of
organic amines, as verified by a search in the CSD[ , strong hydrogen bond acceptor groups can
compete with chloride ions. A particularly nice illustration is provided by such interactions
between cyclic trialkylammonium and carboxamide units in -position in a bis-HCl salt of a
cyclic bis-(lactam-ammonium) derivative, corresponding closely to the case of trans-10 (see
below and SI, Chap. 9, Fig. S21 and S22). It may thus be argued that, in aqueous conditions,
36]
2
4
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there would probably be little contribution to basicity modulation by intramolecular hydrogen
bonding in trans-5, as the -axial acetoxy group would not compete effectively with solvation or
chloride interaction with the piperidinium ion. In this regard, the -acetoxy group modulates
amine basicity in a comparable manner as a -fluorine substituent (Table 1, Fig. 1).
Figure 2: (A) X-ray molecular structure of HCl salt of trans-5 (black, for details see SI, Chap.
[
34]
8
); superposition of protonated trans-5 (blue), modeled by MOLOC removing the chloride ion
and turning the acetoxy group inside to enable intramolecular hydrogen bonding of the
piperidinium N-H to the carbonyl group; the fully energy-minimized model displays significant
valence geometry distortions for the -axial acetoxy group in order to accommodate the
intramolecular hydrogen bond with a seven-membered cyclic arrangement. (B) X-ray crystal
structure of the HCl salt of trans-5 showing a close ion pair contact (red) between the
piperidinium cation and the chloride anion (green); the latter engages in several non-bonded
intra- and intermolecular H-C contacts (blue) at or below van der Waals contact distance (dvdW,
Cl∙∙∙H ~ 3.0 Å); the axial -acetoxy group has two close intermolecular contacts (green) between
the carbonyl group and two polar H-C bonds adjacent to the protonated amino unit of a
neighboring molecule; all distances are in Å.
Concerning the axial -hydroxy group, its basicity reducing effect in trans-3 is marginal. This is
particularly evident when comparing the effect (pK
a
~ -0.4) with that of the axial -methoxy
group in trans-4 (pK ~ -0.7). The presence of a hydroxy group might imply intramolecular
a
hydrogen bonding effects. However, in aqueous medium, neither an N∙∙∙HO interaction in the
neutral state of trans-3 (which would stabilize, rather than destabilize, the neutral form) nor a
+
(
basicity increasing) N-H∙∙∙OH interaction in the protonated form are expected to contribute
significantly for geometrical reasons. On the other hand, a special solvation effect of the
protonated form of trans-3 may provide a possible explanation. The gauche-arrangement of the

-hydroxy group could allow a water molecule to bridge between the protonated piperidinium
unit and the axial hydroxy group as suggested by modeling (Fig. 3). With an additional water
2
5
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ChemBioChem
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molecule forming an external O-H∙∙∙OH
2
interaction, a local H-bond network could be formed in
which both the bridging water molecule and the -hydroxy group engage with reinforcing
[
37]
cooperative H-bonds, further stabilizing the protonated form of trans-3. Such a solvation
network would not be available for the (axial) methoxy group.
Figure 3: Moloc-optimized[34] model of trans-3 with two water molecules, one interacting
externally with the exo-oriented O-H unit, the other bridging between the protonated
+
piperidinium unit and OH group in a N-H∙∙∙O(H)H∙∙∙O-H∙∙∙OH
2
interaction pattern; in this H-
bond network both the bridging water molecule and the -OH group are involved with
reinforcing cooperative hydrogen bonds;[ all distances are in Å.
37]
The outstandingly small basicity reduction in trans-3 is not unique to the current series of N-
piperonyl-3-phenylpiperidine derivatives. A similar pattern of pK effects can be seen in the
a
short series of N-methyl-3-tert-butylpiperidine derivatives with -hydroxy and -methoxy
substituents in 5-equatorial or 5-axial position (Table 3 and Fig. 1). For the equatorial
derivatives, the basicity reduction is very pronounced and increases from the -hydroxy (cis-17)
to -methoxy case (cis-18). The very small basicity downshift for the axial -hydroxy group in
trans-17 and the comparatively larger downshift for the axial -methoxy substituent in trans-18
are identical to those in the corresponding phenyl-substituted piperidine series. Very pronounced
similar effects of axial versus equatorial -hydroxy substituents have been reported for a pair of
[
8]
N-alkyl-3,4-disubstituted piperidine derivatives (see SI, Chap. 3, Fig. S18). The characteristic
basicity modulation results in a substantial difference between axial and equatorial pK effects
a
which are consistent with the average difference, pK (ax-eq) ~ 1.0 ± 0.3, observed for a subset
a
of epimeric pairs of hydroxylated piperidines,[ differing only in the equatorial or axial position
27]
of a -hydroxy group (see SI, Chap. 3, Fig. S17).
2
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In this context, we include the pK values measured for the -chloride derivatives in the small
a
parallel series of N-methyl-3-(tert-butyl)-piperidines, cis- and trans-16 (Scheme 3). Although the
electronegativity of chlorine is lower than that of fluorine, the polarizing effect by organic
chlorine is substantial. Thus, -equatorial chlorine reduces piperidine basicity to a similar extent
as fluorine (Tables 1 and 3, Fig. 1). As may be expected, the effect for the -axial chlorine is
reduced; however, it is much more pronounced than the corresponding effects of -axial hydroxy
or methoxy substituents in trans-17 and trans-18, respectively, and again similar to the effect
exerted by a -axial fluorine substituent. Thus, the patterns of piperidine basicity reductions for
equatorial and axial fluorine, chlorine, and acetoxy substituents in -position are remarkably
similar (Fig. 1).
Moving the -hydroxy or methoxy function to an exocyclic -position as in cis-6/trans-6 or cis-
7
/trans-7 significantly attenuates the basicity decrements. The effects for the equatorial
hydroxymethyl or methoxymethyl groups are virtually identical to basicity modulations observed
[
8]
for -OH or -OMe groups in acyclic amines. The corresponding effects by axial -CH
-CH OMe groups in the epimers trans-6 or trans-7, respectively, are only marginally different.
This may indicate that, in aqueous solution, intramolecular interactions between the protonated
2
OH or

2
or unprotonated amine unit with the -oxy functions of -axial CH
2
OR (R = H, CH ) groups are
3
of minor importance.
The similarity between C-F and C-O bond units is best reflected by the intrinsic lipophilicities
logP) of the -methoxy derivatives, cis-4 and trans-4, which are very similar to those of the
(
corresponding -fluorine analogs, cis-2 and trans-2, respectively (Table 1, Fig. 4). However, the
similarity concept is not reflected by the corresponding lipophilicity downshifts exhibited by the

-hydroxy derivatives, cis-3 and trans-3, which are much stronger than those of their methylated
counterparts. The differences can be traced in part to the additional saturated carbon unit in going
from hydroxy to methoxy and in part to the protection of the solvation-enabling hydroxyl
function, which differentiates the latter from the fluorine and methoxy cases that are essentially
devoid of hydrogen-bonding capacity.
2
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7
.4
Figure 4: Intrinsic and effective lipophilicities (logP and logD , respectively) for cis- and
trans-5-substituted N-piperonyl-3-phenylpiperidine derivatives with fluorine and oxy-functional
groups X (X = F, OH, OMe, OAc, CH
2
OH, CH OMe) in position 5 (Table 1); lipophilicity
2
changes relative to the reference compound 1 are indicated with black bars for cis-derivatives (X
group equatorial) and grey bars for trans-derivatives (X group axial).
Remarkably, the -acetoxy group in either equatorial or axial orientation induces similar intrinsic
lipophilicity changes as the methoxy group in the corresponding positions (Table 1). Thus, the
presence of the polar carbonyl group appears to be counterbalanced by the larger size of the
acetoxy group. Except for the -axial hydroxy and methoxy groups, all other oxy-substituents
and fluorine in -position lower basicity below 7.4. Therefore, the patterns of effective and
intrinsic lipophilicities for these derivatives are very similar, logD being slightly lower than
corresponding logP values by approximately 0.1 log units (Table 1). For the slightly more basic

-axial hydroxy and methoxy piperidine derivatives (trans-3 and trans-4), however, significant
protonation shifts effective lipophilicities (logD) more than half a log unit below their respective
intrinsic lipophilicities (logP). Judging from the resulting logD pattern, the -hydroxy derivative
again clearly differentiates itself from the fluorine case (Fig. 4). The pharmacologically favorable
downshift in effective lipophilicity by introducing a -axial hydroxy group into the piperidine
ring deserves attention in molecular design. The cases of cis-3 and trans-4 stand out by their
vanishing effective lipophilicity changes upon replacing the corresponding hydrogen atoms in 1
by a -equatorial hydroxy or -axial methoxy group, respectively. The latter case is of particular
relevance when considering piperidine derivatives with -axial alkoxy substituents other than the
prototypic methoxy group.
2
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Shifting the hydroxy or methoxy unit from the ring -position to an exocyclic -position affects
both intrinsic and effective lipophilicities. Considering the equatorial -hydroxymethyl case (cis-
6
), we note a modest logP increase of 0.2 relative to cis-3 and a logP reduction of -0.3 compared
to the -equatorial methoxy derivative cis-4. Both methoxy and hydroxymethyl substituents
differ from the -equatorial hydroxy group in cis-3 by an additional saturated carbon unit.
Whereas methylation of the hydroxy function has a dual effect of raising lipophilicity by volume
increase and protection of the solvation-enabling hydroxyl functionality, as discussed above, the
insertion of a methylene unit, while also increasing volume to a similar extent, preserves or even
enhances the polar character of the hydroxy functionality due to enhanced exposure of the latter.
Turning to the corresponding axial cases, logP of trans-6 differs substantially from its -axial
hydroxy congener, trans-3, which may reflect, apart from the volume increase, the loss of a
special solvation effect as discussed above for the -axial hydroxy group. On the other hand, the

-axial hydroxymethyl unit may adopt different conformations and engage in weak hydrogen
bond interactions either to the protonated or neutral piperidine amino group. While these
interactions are possibly weak with small and opposing effects on amine basicity they may favor
compact cyclic arrangements of increased lipophilicity, particularly in the case where the neutral
amino group would shield the -hydroxy functionality by engaging in an intramolecular
hydrogen bond. Methylation of the -hydroxy group increases lipophilicity values significantly
for both the equatorial and axial cases (cis-7 and trans-7, respectively), while reducing the logP
difference between them slightly. Both epimeric pairs of -hydroxymethyl and -methoxymethyl
piperidine derivatives are weakly basic with pK
results in effective lipophilicities (logD
0
a
values around 8.1 ± 0.1. Partial protonation then
) for these piperidine derivatives, consistently 0.7-
.8 log units below their corresponding logP values (Table 1). This has remarkable consequences
pH=7.4
for their effective lipophilicities (Fig. 4). First, the -equatorial hydroxymethyl derivative,
although homologous to the -equatorial hydroxy derivative, is more polar than the latter.
Second, the -axial hydroxymethyl derivative, contrary to its -axial hydroxy congener, exhibits
an effective lipophilicity close to the reference compound 1. Third, both -equatorial and -axial
methoxymethyl derivatives are more lipophilic than the reference compound, being in the same
logD range of 3.6 ± 0.1 as the epimeric -fluoro and -acetoxy derivatives, as well as the -
equatorial methoxy derivative, thus are approximately 0.5 log units more lipophilic than the
unsubstituted parent compound 1 (Fig. 4).
All derivatives with -oxy functionalities (cis-/trans-3, cis-/trans-4, and cis-/trans-5) exhibit the
characteristic trend of higher aqueous solubility for the axial derivatives compared to their
equatorial counterparts (Table 2). Whereas solubility decreases in both the -equatorial and -
axial series, OH > OMe > OAc, the ratio of axial/equatorial solubility increases in the same
series, OH < OMe < OAc, the latter exceeding two orders of magnitude.
Regarding artificial membrane permeation (PAMPA, Table 2 and SI Table S3), all derivatives
with - or -oxy functionalities (cis-/trans-3, cis-/trans-4, cis-/trans-5, and cis-/trans-6) show
significant permeation rates, comparable to and, within estimated standard deviations, not
exceeding the rate of the unsubstituted reference compound 1. For the -hydroxy derivatives
(cis-/trans-3), permeation rates are essentially equal within standard deviations. For the epimeric
2
9
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