A weak attractive interaction between organic fluorine and an amide group

Article abstract of DOI:10.1002/anie.200460781

A combination of a chemical double-mutant cycle and a linear free energy relationship has demonstrated that a weak attractive interaction (-0.8 to -1.5 kJ mol^-1) exists between an organic fluorine substituent and the face of an amide functional

Full text of DOI:10.1002/anie.200460781

Communications
Noncovalent Interactions
approaches the plane of the carbonyl group from an angle
between 1008 and, at very short F···C distances, 1408.[3a]
Herein we report the first model system to evaluate the
A Weak Attractive Interaction between Organic
Fluorine and an Amide Group**
ꢁ
energetics of the proposed C F···amide interactions.
ꢁ
The distinct geometry of the orthogonal C F···amide
interaction presented an unusual challenge. We found an
answer in the “molecular torsion balance” derived by Wilcox
et al. from the Tröger base—a system designed for the
accurate measurement of edge-to-face aromatic–aromatic
interactions by the observation of a simple conformational
equilibrium.[4] We found through examination of existing
crystal structures[5] that appropriate substitution of the Tröger
base skeleton would provide the perpendicular arrangement
of functional groups required for our study (Scheme 1). The
Fraser Hof, Denise M. Scofield, W. Bernd Schweizer,
and François Diederich*
Questions regarding the nature and strength of noncovalent
interactions formed by organic fluorine atoms are increas-
ingly being addressed and debated in the literature.[1] We have
been exploring noncovalent interactions of fluorine by
carrying out a systematic fluorine scan[2] at the active site of
thrombin.[3] While exploring the hydrophobic D pocket of this
serine protease, we noticed that the potency of a closely
related family of fluorinated inhibitors was strongly influ-
enced by the position of the fluorine atom (Figure 1).[3a] The
4-fluorobenzyl derivative (ꢀ )-4 exhibits fivefold better
inhibition than any other member of the family. The X-ray
structure of the (+)-4–enzyme complex showed two close
ꢁ
contacts between the fluorine atom and the Ca H atom as
well as the carbonyl C atom of Asn98 (Figure 1b). Subse-
quent searches in the Cambridge Structural Database and
RCSB Protein Data Bankprovided numerous examples of
similar sub van der Waals contacts between organic fluorine
atoms and carbonyl carbon atoms in chemical and biological
samples. These interactions have a characteristic geometry:
the fluorine atom tends to reside orthogonally above the
Scheme 1. The torsion balance of Wilcoxand co-workers. Modeling
studies predict both edge-to-face aromatic–aromatic interactions and
close contacts between substituents R1 and R2 for the folded state.
use of a trifluoromethyl group was required to approximate
ꢁ
ꢁ
pseudotrigonal axis of the carbonyl group, and the C F bond
the optimal C F···amide geometry. Based on the similarity of
the results obtained from database
searches for fluorine atoms attached to
sp2- and sp3-hybridized carbon atoms, we
anticipated that this substitution would
have a negligible effect on the energetics
of the proposed interaction.
The second challenge in characteriz-
ing fluorine–amide interactions is their
expected weakness. The relative Ki val-
ues for compounds (ꢀ )-1–(ꢀ )-7 suggest
that the fluorine substitution provides
approximately 4 kJmolꢁ1 of stabilizing
energy. Hunter and co-workers have
popularized chemical double-mutant
cycles for the measurement of very
small interaction energies in supramolec-
Figure 1. a) A family of inhibitors designed to probe the fluorophilicity of the D pocket at the
thrombin active site. b) X-ray structure showing close contacts between the fluorine atom of
inhibitor (+)-4 and the protein backbone of thrombin.
ular systems, and have used this method to accurately
measure various noncovalent interactions as weakas
1 kJmolꢁ1.[6] The application of this strategy to the Wilcox
torsion balance is straightforward. The edge-to-face aro-
matic–aromatic interaction is the primary force behind the
folding of the molecule, and the effect of each substitution on
this primary force must be accounted for to determine the
incremental folding free enthalpy provided by the two
[*] Dr. F. Hof, D. M. Scofield, Dr. W. B. Schweizer, Prof. Dr. F. Diederich
Laboratorium für Organische Chemie
ETH-Hönggerberg, HCI
8093 Zürich (Switzerland)
Fax: ( +41)1-632-1109
E-mail: diederich@org.chem.ethz.ch
[**] F.H. thanks the Novartis Foundation and the Human Frontier
Science Program for postdoctoral fellowship support. This research
was supported by the ETH Research Council and F. Hoffmann-
La Roche Ltd.
appended functional groups.
A
double-mutant cycle
(Scheme 2) can be used to determine the influence of each
appended group on the edge-to-face interaction independ-
ently from their interaction with each other. When the folding
energies of all four molecules in the double-mutant cycle have
Supporting information for this article (synthesis and character-
ization of compounds (ꢀ)-8–(ꢀ)-10 and (ꢀ)-13 as well as
complete error analysis of the physical data) is available on the
WWW under http://www.angewandte.org or from the author.
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DOI: 10.1002/anie.200460781
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Angewandte
Chemie
be determined with well-defined estimations of error. The
singlets corresponding to the methyl resonances of each
folded state are resolved at 300 MHz, and the identity of each
conformer is easily determined by analogy with related
compounds (Figure 2).[4] A summary of the folding energies
Scheme 2. Double-mutant cycle for determining the magnitude of the
attraction between orthogonally oriented CF3 and NHCOCH3 groups.
Figure 2. 1H NMR spectra (methyl region, C6D6, c=10 mm) of: a) (ꢀ)-
8, b) (ꢀ)-9, c) (ꢀ)-10, d) (ꢀ)-11. The sensitivity of the acetamide
COCH3 resonance to the proximity of the trifluoromethyl group in the
folded state is highlighted.
been determined, the interaction energy of the two appended
functional groups (DGCF ···NHCOCH ) is given by Equation (1).
3
3
for compounds (ꢀ )-8–(ꢀ )-11 in three different solvents is
given in Table 1. The application of the double-mutant cycle
in the form of Equation (1) provides the incremental free
enthalpy for the interaction of the two appended functional
groups. The interaction is weak, but measurable, in CDCl3
(ꢁ1.05 ꢀ 0.25 kJmolꢁ1) and C6D6 (ꢁ0.85 ꢀ 0.25 kJmolꢁ1),
while the value is essentially zero in CD3OD (ꢁ0.10 ꢀ
0.25 kJmolꢁ1).
DG
¼ DGðꢀÞ-8ꢁDGðꢀÞ-9ꢁDGðꢀÞ-10 þ DGðꢀÞ-11
ð1Þ
CF3ꢂꢂꢂNHCOCH3
The four molecules of interest were synthesized as shown
in Scheme 3. The nitrocarboxylic acid intermediate (ꢀ )-12,
prepared in thirteen steps using literature methods,[7] was
esterified with 4-(trifluoromethyl)phenol and phenol to give
(ꢀ )-13 and (ꢀ )-14, respectively.
Table 1: Folding free enthalpies for compounds (ꢀ)-8–(ꢀ)-11.
Compound
DG [ꢀ0.12 kJmolꢁ1 [a]
]
CDCl3
C6D6
CD3OD
(ꢀ)-8
ꢁ2.46
ꢁ1.95
ꢁ0.45
ꢁ1.00
ꢁ3.78
ꢁ3.31
ꢁ1.46
ꢁ1.84
ꢁ2.88
ꢁ2.37
ꢁ1.72
ꢁ1.31
(ꢀ)-9
(ꢀ)-10
(ꢀ)-11
[a] Determined by integration of signals in the NMR spectra of 10 mm
solutions at 298 K. For a complete error analysis, see the Supporting
Information.
Scheme 3. Synthesis of (ꢀ)-8–(ꢀ)-11. a) Et3N, BOP, 4-(trifluorome-
thyl)phenol or phenol, CH2Cl2, RT, 71–97%. b) H2 (atm), RaNi, EtOAc/
EtOH, RT, 90–100%. c) Ac2O, CH2Cl2, RT, 20–72%. d) 1. HCl, NaNO2,
58C; 2. H3PO2, 58C, 25–63%. BOP=Benzotriazol-1-yloxy-tris(dimethy-
lamino)phosphonium hexafluorophosphate, RaNi=Raney Nickel.
Two main conditions must be satisfied for a double-
mutant cycle to be valid. Firstly, the core must not undergo
major structural rearrangements between different members
of the cycle. With few degrees of freedom, the scaffold of
Wilcox and co-workers derived from the Tröger base is
exceptionally well organized. To determine the effect of
trifluoromethyl substitution on the folded structure we solved
the crystal structure of synthetic precursor (ꢀ )-13
(Figure 3).[9] Comparison with several existing crystal struc-
tures[5] of related torsion-balance molecules shows there is
little deviation in the folded edge-to-face geometry through-
out the series. The crystal structure of precursor (ꢀ )-13 also
Reduction of the nitro group with H2/RaNi gives the
corresponding anilines. In divergent steps, each aniline is then
acetylated to yield target compounds (ꢀ )-8 and (ꢀ )-10, or
converted into its corresponding diazonium salt, which is in
turn reduced with H3PO2 to afford compounds (ꢀ )-9 and
(ꢀ )-11.
The interconversion between the two conformations of
each molecule is slow on the NMR timescale (Ea = 65–
75 kJmolꢁ1).[4a,8] Direct integration of the 1H and/or 19F reso-
nances for each conformer allows the folding equilibrium to
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pound (ꢀ )-11 to (ꢀ )-9) causes a much larger favorable
secondary effect (D(DG) = ꢁ1.5 kJmolꢁ1 in C6D6). This
difference arises from the acidification of the neighboring
ortho proton, which increases the strength of the CH–
p interaction at the heart of the folded conformation.
To get a better understanding of the effect of the
trifluoromethyl group on the core edge-to-face interaction
we synthesized a series of compounds in which the “face”
component bears different substituents. The folding equili-
brium constant of each was determined by using the same
method as for compounds (ꢀ )-8–(ꢀ )-11, and the entire series
was examined using a linear free energy relationship between
the folding free enthalpy and the Hammett constants smeta
(Figure 4).[10] The correlation is excellent (R2 > 0.98), thus
Figure 3. ORTEP plot with ellipsoids at 50% level showing the folded
state of (ꢀ)-13. Distances between F(32) and the atoms of the nitro
group are given in Š.
displays the desired perpendicular approach of the appended
functional groups (in this case a trifluoromethyl and a nitro
group). The trifluoromethyl group experiences no attraction
to the adjacent nitro group (see below), and accordingly the
close interatomic contacts involving F(32) are greater than
the sum of van der Waals radii (Figure 3). Modeling studies
on (ꢀ )-8 suggest that the minute (< 0.3 Š) vertical adjust-
ment required to bring the fluorine atom close to the plane of
the acetamide group can be accommodated, despite the
rigidity of the scaffold. However, the modeling study also
shows that for (ꢀ )-8 the fluorine atom closest to the
acetamide group may not reach its ideal position above the
pseudotrigonal axis of the carbonyl unit. Instead, it may lie
somewhere above the bond connecting the nitrogen atom to
the carbonyl carbon atom, which suggests there is a geometric
factor that can account for the slightly weaker than expected
value measured for the fluorine–amide interaction.
In the absence of an X-ray structure of (ꢀ )-8, we turned
to NMR studies to provide evidence for the proximity of the
trifluoromethyl and acetamide groups in solution. The differ-
ence in the chemical shifts observed for the acetamide CH3
group in the folded and unfolded states is larger for (ꢀ )-8
(Dd = 0.30 ppm) than for control compound (ꢀ )-10 (Dd =
0.14 ppm), which suggests that the acetamide residue expe-
riences decreased shielding in the folded state of (ꢀ )-8
because of the nearby fluorine atoms (Figure 2).
Figure 4. A linear free energy relationship showing substituent effects
for edge-to-face interactions in a family of trifluoromethyl-substituted
molecules.
showing that the primary CH–p interaction follows a well-
behaved continuum that depends on the electronic properties
of the “face” component. The sole significant departure from
this trend arises for the acetamide-substituted compound
(ꢀ )-8.[11] This compound is more folded by 1.5 ꢀ 0.7 kJmolꢁ1
than substituent effects would predict—this value is similar to
that obtained from the double-mutant cycle analysis.
What is the origin of the attraction between the appended
trifluoromethyl and acetamide groups? It is unlikely that the
amide NH group can be appropriately oriented to donate a
hydrogen bond to the fluorine atoms, and the lackof any
attraction for the more acidic phenol compound (Figure 4)
confirms that this mode of weakhydrogen bonding does not
stabilize the folded state.[1a] It is possible that the model
suggested by our previous database findings, in which the
electronegative end of the carbon–fluorine dipole interacts
favorably with the electropositive carbonyl carbon atom, is
operative.[3a] This dipolar electrostatic model accounts for the
absence of any measurable attraction in the polar solvent
CD3OD. Alternatively, one can consider the approach of the
unpolarizable, partially negative surface of the trifluoro-
The validity of a double-mutant cycle also rests on the
linear additivity of the secondary energy perturbations arising
from each functional group mutation. A closer analysis of the
data in Table 1 shows that the addition of an acetamide group
to the “face” component of the primary edge-to-face inter-
action (from compound (ꢀ )-11 to (ꢀ )-10) causes a small
unfavorable change in the folding free enthalpy (D(DG) =
+ 0.4 kJmolꢁ1 in C6D6). In comparison, the addition of a
trifluoromethyl group to the “edge” component (from com-
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Angewandte
Chemie
methyl group[12] close to the polarizable delocalized p cloud of
the amide group. Attraction arises in this model from charge-
induced dipole and dipole-induced dipole interactions. Argu-
ments against such a model are indicated by a recent study in
which a trifluoromethyl group is not attracted by the face of
an aryl ring, regardless of the electrostatic potential of the
ring.[13] In the absence of structural information for compound
(ꢀ )-8, it is impossible to conclude whether an atom-centered
model or a functional-group-scale model of this attraction is
more appropriate. We hope that further studies using differ-
ent fluorine-containing functional groups and different car-
bonyl functional groups will shed light on this issue.
In summary, we have presented the first efforts to quantify
the interactions of organic fluorine with the face of an amide
functional group. A novel combination of the torsion balance
developed by Wilcox and co-workers with two distinct
physical methods—a double-mutant cycle and a linear free
energy relationship—provided the initial measurement of an
attractive interaction with a value of 0.8–1.5 kJmolꢁ1 in
nonpolar solvents. The effects of fluorination on the hydro-
phobicity, distribution, metabolism, and pharmacokinetics of
potential drug molecules are increasingly well understood.[14]
Model studies such as those presented here help clarify the
role played by fluorine atoms in altering the binding affinity
and selectivity[3,14d] of enzyme inhibitors.
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[7] E.-I. Kim, PhD thesis, University of Pittsburgh (USA), 1996.
[8] S. Paliwal, PhD thesis, University of Pittsburgh (USA), 1996.
[9] Crystals of (ꢀ )-13 were grown by vapor diffusion of pentane
into a solution of (ꢀ )-13 in EtOAc: yellow prism, 0.4 ” 0.1 ”
0.1 mm; orthorhombic, space group F2dd; a = 10.36, b = 25.37,
c = 38.17 Š, V= 10030 Š3; 1calcd = 1.445 Mgmꢁ3; 2qmax = 60.068;
MoKa radiation, l = 0.71073 Š; T= 152 K; 7164 independent of
7301 measured reflections Rint = 0.032, no absorption correction
applied (m = 0.113 mmꢁ1); structure solution using SIR97 (A.
Altomare, M. C. Burla, M. Camalli, G. L. Cascarano, C.
Giacovazzo, A. Guagliardi, A. G. G. Moliterni, R. Spagna, J.
Appl. Crystallogr. 1999, 32, 115 – 119); 5402 reflections with I >
3s(I) refined on j F2 j using SHELXL-97 (G. M. Sheldrick,
SHELXL97, Program for the Refinement of Crystal Structures,
University of Göttingen, Göttingen (Germany), 1997); D/smax
=
0.299, D1max = 0.734 eŠ3, D1min = ꢁ0.482 eŠ3; 449 parameters,
all hydrogen atom parameters refined;, R(all) = 0.0953, R(gt) =
0.0653, wR(ref) = 0.1920, wR(gt) = 0.1603. CCDC-239177 con-
tains the supplementary crystallographic data for this paper and
is available free of charge from the Cambridge Crystallographic
Data Centre (CCDC, 12 Union Road, Cambridge CB2 1EZ
(UK); Tel.: (+ 44) 1223-336-408, Fax: (+ 44) 1223-336-033, E-
mail: deposit@ccdc.cam.ac.uk).
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constants smeta were obtained from: D. H. McDaniel, H. C.
Brown, J. Org. Chem. 1958, 23, 420 – 427.
[11] The trifluoromethyl group should experience some repulsion
when brought close to the large iodine atom. This effect is
evident in the slightly under-folded state of the iodo compound.
[12] J. C. Biffinger, H. W. Kim, S. G. DiMagno, ChemBioChem 2004,
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Received: May 25, 2004
Keywords: amides · fluorine · molecular recognition ·
.
noncovalent interactions
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