Daron E Janzen1, Maya S Butler1, Eric W Reinheimer2. 1. Dept. of Chemistry & Biochemistry, St. Catherine University, 2004 Randolph Avenue, St. Paul, MN 55105, USA. 2. Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX 77381, USA.
Cinchona-derived enantioselective phase-transfer catalysts have been used in a variety of applications including [2,3]-Wittig rearrangements (Denmark & Cullen, 2015 ▸), synthesis of unnatural α-amino acids (O’Donnell et al., 1989 ▸), and even industrial-scale synthesis of pharmaceuticals (Moccia et al., 2015 ▸). As this class of phase-transfer catalysts are easy to prepare from the parent natural product alkaloids, and demonstrate aspects of green and sustainable chemistry, they are attractive organocatalysts for further development. Mechanistic studies of N-benzylcinchonidinium bromide and substrates in solution provide evidence for the importance of quaternary ammonium benzylic C—H hydrogen-bond donor interactions as well as the classical OH donor (Bencivenni et al., 2021 ▸). Anion effects also demonstrate differences in the binding mode of substrates with mechanistic implications and potential enantioselectivity.While structures are reported for analogs of this cation, that of the commercially available bromide salt is unpublished. We report here the structures of N-benzylcinchonidinium bromide (I) and the sesquihydrate (II).
Structural commentary
The anhydrous compound (I) (Fig. 1 ▸) crystallizes in the monoclinic space group P21. The asymmetric unit of (I) consists of one molecular cation and one bromide anion. The sesquihydrate (II) (Fig. 2 ▸) crystallizes in the tetragonal space group P41212. The asymmetric unit of (II) consists of one molecular cation, one bromide anion, and one water on a general position and one half water, as O3 lies on a twofold axis at z = 0.5. For (I) and (II), the absolute configuration of chiral atoms N1, C2, C3, C7, and C8 are determined as S, R, S, S, and R, respectively, by anomalous dispersion and are consistent with previous structures of cinchonidine.
Figure 1
Molecular structure of (I) with displacement ellipsoids drawn at the 50% probability level.
Figure 2
Molecular structure of (II) with displacement ellipsoids drawn at the 50% probability level.
Most analogous bond lengths in (I) and (II) show only minor differences, with two exceptions (Tables 1 ▸ and 2 ▸). The largest differences in bond lengths occur for C6—C7 [1.510 (4) Å (I), 1.553 (8) Å (II)] and N2—C11 [1.282 (6) Å (I), 1.319 (9) Å (II)]. The quinuclidine intramolecular N1⋯C3 distances show small expansion of this bicyclic ring system from (I) [2.534 (5) Å] to (II) [2.591 (8) Å]. Overlap of the N-benzylcinchonidinium cation atom coordinates of (I) and (II) (Fig. 3 ▸) shows significant conformational differences. While the quinuclidine, benzyl, and vinyl functionalities adopt very similar conformations for (I) and (II), larger changes are observed in the alcohol and quinoline groups. Torsion angles that highlight the largest conformational changes include C7—C8—C13—C12 [107.9 (3)° (I); 101.3 (7)° (II)], C8—C7—N1—C20 [−39.0 (3)° (I); −53.6 (7)° (II)], and O1—C8—C13—C12 [−11.7 (4)° (I); −19.2 (8)° (II)]. These torsion-angle differences result in large changes in the relative angles between least-squares planes of the phenyl and quinoline groups in (I) [14.8 (2)°] and (II) [41.8 (3)°]. Intramolecular C—H⋯O contacts C5—H5A⋯O1 are found in both (I) and (II), but (I) shows an additional benzylic C20—H20B⋯O1 contact (Tables 3 ▸ and 4 ▸, Figs. 4 ▸ and 5 ▸).
Table 1
Selected geometric parameters (Å, °) for (I)
N2—C11
1.282 (6)
C6—C7
1.510 (4)
C12—C13—C8—O1
−11.7 (4)
C20—N1—C7—C8
−39.0 (3)
C12—C13—C8—C7
107.9 (3)
Table 2
Selected geometric parameters (Å, °) for (II)
N2—C11
1.319 (9)
C7—C6
1.553 (8)
O1—C8—C13—C12
−19.2 (8)
C20—N1—C7—C8
−53.6 (7)
C7—C8—C13—C12
101.3 (7)
Figure 3
Overlap of quinuclidine non-H atom coordinates (C1–C7, N1) of the N-benzylcinchonidinium cation of (I) (red) and (II) (green).
Table 3
Hydrogen-bond geometry (Å, °) for (I)
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
O1—H1⋯Br1
0.73 (5)
2.45 (5)
3.149 (3)
162 (5)
C15—H15⋯Br1i
0.93
2.90
3.644 (4)
137
C12—H12⋯O1
0.93
2.39
2.739 (5)
102
C6—H6A⋯O1
0.97
2.58
2.967 (4)
104
C2—H2⋯Br1ii
0.98
2.83
3.779 (3)
164
C26—H26⋯Br1i
0.93
2.87
3.738 (4)
155
C5—H5A⋯O1
0.97
2.36
3.024 (4)
125
C20—H20A⋯Br1i
0.97
2.91
3.800 (3)
153
C20—H20B⋯O1
0.97
2.64
3.198 (4)
117
C10—H10A⋯Br1i
0.93
3.02
3.943 (4)
172
Symmetry codes: (i)
; (ii)
.
Table 4
Hydrogen-bond geometry (Å, °) for (II)
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
O1—H1⋯O2i
0.89 (8)
1.75 (8)
2.629 (7)
168 (8)
O2—H2A⋯N2ii
0.88 (10)
1.97 (10)
2.824 (8)
161 (9)
O2—H2B⋯Br1
0.75 (9)
2.48 (9)
3.202 (5)
160 (10)
C7—H7⋯Br1
1.00
2.99
3.894 (6)
151
C12—H12⋯O1
0.95
2.44
2.771 (8)
101
C2—H2⋯Br1iii
1.00
2.98
3.811 (7)
142
C1—H1B⋯Br1
0.99
2.88
3.779 (7)
152
C5—H5A⋯O1
0.99
2.29
2.836 (8)
114
C5—H5B⋯O3
0.99
2.56
3.464 (6)
151
C17—H17⋯O1iv
0.95
2.61
3.500 (8)
157
C6—H6A⋯O1
0.99
2.70
3.016 (8)
99
C4—H4A⋯Br1iii
0.99
2.94
3.785 (7)
144
C20—H20A⋯Br1
0.99
2.89
3.794 (7)
152
C10—H10A⋯Br1
0.95
3.01
3.960 (8)
176
C23—H23⋯O2v
0.95
2.71
3.518 (11)
143
O3—H3A⋯Br1iii
0.90 (10)
2.61 (10)
3.499 (6)
170 (11)
Symmetry codes: (i)
; (ii)
; (iii)
; (iv)
; (v)
.
Figure 4
Intra- and intermolecular interactions of (I). Symmetry codes: (i) 1 − x, y −
, 1 - z; (ii) 1 + x, y, z.
Figure 5
Intra- and intermolecular interactions of (II). Symmetry codes: (i) x, 1 + y, z; (ii) 1 + x, y, z; (iii) y, −1 + x, 1 − z; (iv)
+ x,
− y,
− z; (v) −1 + x, y, z
Supramolecular features
The extended structure of (I) displays a simple isolated charge-assisted hydrogen bond with the alcohol donor O1 and Br1 anion acceptor (Table 3 ▸, Fig. 4 ▸). The quinoline N2 acceptor does not participate in any hydrogen-bonding interactions. Each bromide also has four short C—H⋯Br contacts with the same cation (phenyl, benzyl, quinoline, and vinyl) as well as an additional quinuclidine methine C—H.The sesquihydrate (II) shows very different hydrogen-bonding interactions (Table 4 ▸, Fig. 5 ▸). The alcohol group O1 acts as a donor with a water acceptor, O2. Water O2 hydrogen bonds as donor with Br1 and quinoline N2, while water O3 acts a donor to two bromide acceptors. This pattern of hydrogen bonds forms a chain with terminal O1 donors and water and bromide links, with the water O2 relating the two halves of the chain. Quinoline N2 acceptors of O2 hydrogen-bond donors link the chains forming an extended network. Each bromide also has four short C—H⋯Br contacts with the same cation (benzyl, vinyl, and two quinuclidine) as well as two additional quinuclidine contacts with a neighboring molecular cation (Figs. 5 ▸ and 6 ▸).
Figure 6
Intermolecular hydrogen-bonding pattern of (II). Symmetry codes: (i) 1 − y, 1 − x,
− z; (ii)
+ y,
− x, −
+ z; (iii)
+ y,
− x, −
+ z; (iv)
+ x,
− y,
− z; (v)
+ x,
− y,
− z; (vi) −
+ y,
− x, −
+ z
Database survey
A search of the Cambridge Structural Database (ConQuest version 2022.1.0; Groom et al., 2016 ▸) yields several related analogs of both N-benzylcinchonidinium salts as well as the pseudo-enantiomer N-benzylcinchoninium. The 2-fluorobenzyl bromide sesquihydrate analog XUNQIG (Jew et al., 2002 ▸) is isostructural with (II) though additional C—H⋯F intra- and intermolecular interactions are present. Introduction of the aromatic 2-fluoro substituent yielded enhanced enantioselectivity in catalytic phase-transfer alkylation reactions, with possible origins related to more conformational or dipole changes to enhance substrate binding. Other closely related N-benzylcinchonidinium chloride salts have been employed in co-crystal resolution of a chiral spirocyclic diol (GAJBOJ01; Zhang et al., 2006 ▸), atropisomeric chiral diols (HADSIS; Walsh et al., 2021 ▸ and JAPGIR; Sweetman et al., 2005 ▸) and a related mixed chiral amine/alcohol (GOSWIU; Ding et al., 1999 ▸). Even in the presence of multiple additional hydrogen-bond donors in these co-crystals, short benzylic C—H⋯Cl contacts are retained in GAJBOJ01 and JAPGIR, though not in HADSIS or GOSWIU. The N-benzylcinchonidinium cation has also been employed in resolution of chiral halogenated phosphates (GARJUF, GAWSUT; Frantz et al., 2005 ▸). Short benzylic C—H⋯O contacts are found in these chiral phosphate salts.Closely related cinchoninium anhydrous bromide structures with phenyl substituents [2-bromobenzyl, QEDZAC (Skórska-Stania et al. 2012 ▸) and 3,5-bistrifluoromethyl, UHINUV (Kawai et al., 2009 ▸)] show similar O—H⋯Br hydrogen bonding to (I). However, the C—H⋯Br interactions differ. In QEDZAC, each bromide has quinuclidine, quinoline, and benzyl C—H⋯Br contacts with the same cation. In UHINUV, quinoline, benzyl, and phenyl C—H⋯Br contacts with the same cation are found. The N-benzylcinchoninium chloride salt has also been employed in a co-crystal resolution of BINOL (WOMQUK01; Walsh et al., 2021 ▸).
Synthesis and crystallization
N-benzylcinchonidinium bromide was purchased from Sigma-Aldrich (St. Louis, Missouri, USA). Crystals of the anhydrous form (I) were obtained by vapor diffusion of diethyl ether into an acetonitrile solution of N-benzylcinchonidinium bromide. Crystals of the sesquihydrate (II) were obtained by slow evaporation of an ethanol solution of N-benzylcinchonidinium bromide.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 5 ▸. The O—H hydrogen positions were assigned from residual electron-density peaks and positions were refined. All remaining hydrogen atoms were placed in calculated positions and refined in the riding-model approximation with distances of C—H = 0.93, 0.93, 0.93, 0.97, and 0.98 Å for the aromatic C—H, terminal vinyl CH2, vinyl C9—H9, methylene C—H, and methine C—H, respectively, and with U
iso(H) = k·U
eq(C), k = 1.2 for all C—H and 1.5 for the hydroxyl H1.
Table 5
Experimental details
(I)
(II)
Crystal data
Chemical formula
C26H29N2O+·Br−
2C26H29N2O+·2Br−·3H2O
Mr
465.42
984.89
Crystal system, space group
Monoclinic, P21
Tetragonal, P41212
Temperature (K)
173
173
a, b, c (Å)
11.2574 (7), 8.8445 (5), 11.9039 (9)
9.9254 (2), 9.9254 (2), 47.1267 (14)
α, β, γ (°)
90, 110.126 (8), 90
90, 90, 90
V (Å3)
1112.85 (14)
4642.6 (2)
Z
2
4
Radiation type
Mo Kα
Mo Kα
μ (mm−1)
1.87
1.80
Crystal size (mm)
0.61 × 0.25 × 0.15
0.52 × 0.36 × 0.36
Data collection
Diffractometer
XtaLABmini
XtaLABmini
Absorption correction
Multi-scan (CrysAlis PRO; Rigaku OD, 2020 ▸)
Multi-scan (CrysAlis PRO; Rigaku OD, 2020 ▸)
Tmin, Tmax
0.610, 1.000
0.281, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections
15118, 7531, 5890
36339, 4154, 3919
Rint
0.030
0.078
(sin θ/λ)max (Å−1)
0.765
0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.041, 0.084, 1.01
0.051, 0.111, 1.05
No. of reflections
7531
4154
No. of parameters
274
297
No. of restraints
1
0
H-atom treatment
H atoms treated by a mixture of independent and constrained refinement
H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)
0.54, −0.29
0.35, −0.40
Absolute structure
Flack x determined using 2185 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013 ▸)
Flack x determined using 1347 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013 ▸)
Absolute structure parameter
−0.011 (5)
0.005 (7)
Computer programs: CrysAlis PRO (Rigaku OD, 2020 ▸), SHELXT (Sheldrick, 2015a
▸), SHELXL (Sheldrick, 2015b
▸), and OLEX2 (Dolomanov et al., 2009 ▸).
Crystal structure: contains datablock(s) I, II. DOI: 10.1107/S2056989022005096/pk2664sup1.cifStructure factors: contains datablock(s) I. DOI: 10.1107/S2056989022005096/pk2664Isup2.hklStructure factors: contains datablock(s) II. DOI: 10.1107/S2056989022005096/pk2664IIsup3.hklCCDC references: 2172120, 2172119Additional supporting information: crystallographic information; 3D view; checkCIF report
H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.041
w = 1/[σ2(Fo2) + (0.0383P)2 + 0.0838P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.084
(Δ/σ)max = 0.001
S = 1.01
Δρmax = 0.54 e Å−3
7531 reflections
Δρmin = −0.29 e Å−3
274 parameters
Absolute structure: Flack x determined using 2185 quotients
[(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
1 restraint
Absolute structure parameter: −0.011 (5)
Primary atom site location: dual
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.051
w = 1/[σ2(Fo2) + 19.0784P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.111
(Δ/σ)max < 0.001
S = 1.05
Δρmax = 0.35 e Å−3
4154 reflections
Δρmin = −0.40 e Å−3
297 parameters
Absolute structure: Flack x determined using 1347 quotients
[(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
0 restraints
Absolute structure parameter: 0.005 (7)
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
Authors: Richard Frantz; André Pinto; Samuel Constant; Gérald Bernardinelli; Jérôme Lacour Journal: Angew Chem Int Ed Engl Date: 2005-08-12 Impact factor: 15.336