A study of two geometric isomers of 1,1′-bi-3-cyanocyclohex-2-enylidene

Article abstract of DOI:10.1023/A:1009594532547

The preparation, separation, crystal structure and ¹H NMR spectra are reported for the two geometrical isomers of 1,1′-bi-3-cyanocyclohex-2-enylidene. The E-isomer crystallized as thin plates in the monoclinic space group P2₁,/n with a = 5.3980(5), b = 7.0757(7), c = 15.300(2) A, β = 94.571(2)°, and Z = 2. The structure has symmetry C_2h. The Z-isomer crystallized as needles in the triclinic space group PT with a = 7.0790(6), b = 11.3155(9), c = 15.386(1) A, α = 104.943° β= 90.164(2)°, γ = 99.494(2)°, and Z = 4. The compound crystallized with two molecules per asymmetric unit. In C₆D₆,¹H NMR signals of the 2-vinyl protons appear almost identical. However, in a mixture of C₆D₆ and pyridine-d₅, the 2-vinyl protons can be distinguished. The structures compare favorably with MM2 calculations.

Full text of DOI:10.1023/A:1009594532547

Journal of Chemical Crystallography, Vol. 29, No. 8, 1999
A study of two geometric isomers of 1,1؅-bi-3-
cyanocyclohex-2-enylidene
Yonghui Wang,(1) W.v.E. Doering,(1) and Richard J. Staples(1)*
Received July 1, 1999
The preparation, separation, crystal structure and 1H NMR spectra are reported for the two
geometrical isomers of 1,1Ј-bi-3-cyanocyclohex-2-enylidene. The E-isomer crystallized as
thin plates in the monoclinic space group P21/n with a ϭ 5.3980(5), b ϭ 7.0757(7), c ϭ
˚
15.300(2) A, ͱ ϭ 94.571(2)Њ, and Z ϭ 2. The structure has symmetry C2h. The Z-isomer
crystallized as needles in the triclinic space group P1 with a ϭ 7.0790(6), b ϭ 11.3155(9),
˚
c ϭ 15.386(1) A, Ͱ ϭ 104.943Њ ͱ ϭ 90.164(2)Њ, Ͳ ϭ 99.494(2)Њ, and Z ϭ 4. The compound
crystallized with two molecules per asymmetric unit. In C6D6, 1H NMR signals of the 2-vinyl
protons appear almost identical. However, in a mixture of C6D6 and pyridine-d5, the 2-vinyl
protons can be distinguished. The structures compare favorably with MM2 calculations.
KEY WORDS: Cyano allyl radical; thermal arrangement; crystal structure; isomer; NMR, MM2.
Introduction
In continuing studies of structural perturbations
on the transition region of the Cope rearrangement,1
cyano is a superior perturbing group due to its small
size (more suitable for theoretical calculation than
phenyl, for example), little, if any, steric interaction,
and good radical-stabilizing ability. In order to inter-
pret the effect of cyano group on the rearrangement2
and to predict activation parameters, the magnitude
of its stabilization of an allyl radical has to be deter-
mined. Access to this quantity can be obtained
through thermal interconversion of (E)- and (Z)-1,1Ј-
bi-3-cyanocyclohex-2-enylidenes (1). Activation pa-
rameters for isomerization of E-1 and Z-1 (Scheme
1) measure the difference in enthalpy and entropy
of formation of the planar triene 1 as educt and the
orthogonal, singlet diradical as transition state.3
Scheme 1
Detailed structures of E-1 and Z-1 are important
for both experimental and theoretical analysis. Since
E-1 and Z-1 can be separated by crystallization, their
structures can be determined by x-ray crystallogra-
phy. The assignment of the correct stereochemistry
of E-1 and Z-1 will allow the isomeric structures of
this type of compound (1,1Ј-bi-3-X-cyclohex-2-enyli-
denes) generally to be assigned by the relative chemi-
1
cal shift of 2-vinyl protons in H NMR.
Experimental
(E)- and (Z)-1,1Ј-Bi-3-cyanocyclohex-2-enylidenes
(1) Department of Chemistry and Chemical Biology, Harvard Uni-
versity, Cambridge, MA 02138.
* To whom correspondence should be addressed.
3-Cyano-2-cyclohexen-1-one4 (10 g, 0.083 mol),
prepared from monoethylene ketal of 1,3-cyclohex-
977
1074-1542/99/0800-0977$16.00/0  1999 Plenum Publishing Corporation

978
Wang, Doering, and Staples
Table 1. Crystal Data and Structure Refinement
Compound
(E)-1,1Ј-bi-3-cyanocyclohex-2-enylidene
(Z)-1,1Ј-bi-3-cyanocyclohex-2-enylidene
CCDC deposit no.
Color/shape
Empirical formula
Formula weight
Temperature
Crystal system
Space group
Unit cell dimensions
CCDC-1003/5643
colorless/plate
C14H14N2
210.27
213(2) K
CCDC-1003/5644
colorless/needle
C14H14N2
210.27
213(2) K
Triclinic
Monoclinic
P21/n
a ϭ 5.3980(5) A
P1
˚
˚
a ϭ 7.0790(6) A
Ͱ ϭ 90Њ
b ϭ 7.0757(7) A
ͱ ϭ 94.571(2)Њ
c ϭ 15.300(2) A
Ͱ ϭ 104.943(1)Њ
˚
˚
(2786 reflections in full
theta range for ANTI-1)
(3106 reflections in full
theta range for SYN-1)
Volume
b ϭ 11.3155(9) A
ͱ ϭ 90.164(2)Њ
˚
˚
c ϭ 15.386(1) A
Ͳ ϭ 90Њ
582.5(1) A
Ͳ ϭ 99.494(2)Њ
1173.2(2) A
3
3
˚
˚
Z
2
4
Density (calculated)
Absorption coefficient
Diffractometer
1.199 mg/m3
0.072 mmϪ1
1.191 mg/m3
0.071 mmϪ1
Bruker SMART/CCD
˚
Radiation/wavelength
Theta range for data collection
Index ranges
MoKͰ (graphite monochrom.)/0.71073 A
1.37 to 28.29Њ
Ϫ8 Ͻ ϭ h Ͻ ϭ 9, Ϫ15 Ͻ ϭ k
Ͻ ϭ 11, Ϫ17, Ͻ ϭ l Ͻ ϭ 20
7919
2.67 to 24.99Њ
Ϫ2 Ͻ ϭ h Ͻ ϭ 6, Ϫ7 Ͻ ϭ k
Ͻ ϭ 8, Ϫ18, Ͻ ϭ l Ͻ ϭ 17
3293
Reflections collected
Independent reflections
Data/restraints/parameters
Goodness-of-fit on F2
1027 [R(int) ϭ 0.0373]
1027/0/73
1.002
5489 [R(int) ϭ 0.0335]
5489/0/289
1.112
SHELX-97 weight parameters
Final R indices [I Ͼ 2␴(I)]
R indices (all data)
Largest diff. peak and hole
Completeness of data
0.0410
0.0431
R1 ϭ 0.0366, wR2 ϭ 0.0786
R1 ϭ 0.0631, wR2 ϭ 0.0847
0.101 and Ϫ0.141 e.A
100.0% to theta ϭ 24.99Њ
R1 ϭ 0.0572, wR2 ϭ 0.1199
R1 ϭ 0.1232, wR2 ϭ 0.1311
0.543 and Ϫ0.290 e.A
94.2% to theta ϭ 28.29Њ
Ϫ3
Ϫ3
˚
˚
a
˚
Table 3. Bond Lengths [A] and Angles [Њ] for E-1
anedione, in 50 mL THF was added to titanium
reagent [TiCl4 (23.6 g, 0.124 mol) was added to
400 mL THF at 0ЊC, followed by activated zinc-
dust (16.2 g, 0.124 mol) and 10 mL pyridine]. The
mixture was heated under reflux for 30 min, then
40 mL of 10% HCl was added dropwise at 0ЊC.
N(1)UC(7)
C(1)UC(1)#1
C(1)UC(2)
C(1)UC(6)
C(2)UC(3)
C(3)UC(7)
C(3)UC(4)
C(4)UC(5)
C(5)UC(6)
1.1474(18)
1.370(3)
1.4466(17)
1.5161(18)
1.3446(18)
1.436(2)
1.4991(19)
1.5146(19)
1.5255(19)
Table 2. Atomic Coordinates (ϫ104) and Equivalent Isotropic
2
3
˚
Displacement Parameters (A ϫ 10 ) for E-1
C(1)#1UC(1)UC(2)
C(1)#1UC(1)UC(6)
C(2)UC(1)UC(6)
C(3)UC(2)UC(1)
C(2)UC(3)UC(7)
C(2)UC(3)UC(4)
C(7)UC(3)UC(4)
C(3)UC(4)UC(5)
C(4)UC(5)U(6)
121.04(15)
123.69(15)
115.24(11)
123.31(12)
118.74(13)
123.45(12)
117.81(11)
109.86(11)
111.49(12)
112.41(11)
178.68(16)
x
y
z
U(eq)a
N(1)
C(1)
C(2)
C(3)
C(4)
C(5)
C(6)
C(7)
Ϫ1981(3)
4046(2)
2563(2)
643(2)
Ϫ74(2)
2113(2)
3266(3)
Ϫ798(3)
4910(2)
35(2)
1726(2)
1854(2)
307(2)
Ϫ1005(2)
Ϫ1626(2)
3561(2)
8809(1)
9677(1)
9532(1)
8919(1)
8278(1)
8196(1)
9093(1)
8865(1)
61(1)
31(1)
33(1)
33(1)
40(1)
38(1)
35(1)
41(1)
C(1)UC(6)UC(5)
N(1)UC(7)UC(3)
a U(eq) is defined as one-third of the trace of the orthogonalized
Uij tensor.
a Symmetry transformations used to generate equiv-
alent atoms: #1 Ϫx ϩ 1, Ϫy, Ϫz ϩ 2.

Two gemometrical isomers
979
Table 4. Atomic Coordinates (ϫ104) and Equivalent Isotropic
1H NMR (10:1 benzene-d6/pyridine-d5), ͳ 1.07 (tt,
J ϭ 5.9 Hz, J ϭ 6.2 Hz, 4H), 1.60 (t, J ϭ 6.2 Hz,
4H), 1.75 (t, J ϭ 5.9 Hz, 4H), 6.77 (s, 2H); MS
(EI) m/e 210 (M, 100).
2
3
˚
Displacement Parameters (A ϫ 10 ) for Z-1
x
y
z
U(eq)a
N(1)
N(2)
C(1)
C(2)
C(3)
C(4)
C(5)
C(6)
2371(3)
2308(3)
2615(2)
2489(2)
2457(2)
2473(3)
1779(3)
2800(3)
2408(3)
2632(3)
2515(2)
2459(3)
2529(3)
3460(4)
2730(3)
2374(3)
Ϫ1581(3)
6475(3)
4057(3)
2531(3)
1100(3)
855(4)
1991(4)
4023(3)
Ϫ354(3)
5407(3)
5387(3)
6671(3)
8285(3)
8740(3)
6960(3)
6519(3)
3841(2)
10388(2)
5100(2)
4978(2)
3897(2)
2685(2)
2761(2)
3923(2)
3879(2)
6204(2)
7342(2)
8427(2)
8582(2)
7590(2)
6309(2)
9499(2)
8843(2)
12032(2)
7623(2)
8232(2)
7670(2)
6336(2)
5644(2)
6331(2)
8345(2)
8160(2)
9373(2)
9882(2)
9274(2)
8357(2)
7483(2)
11074(2)
6901(1)
5672(1)
4110(1)
5022(1)
5234(1)
4542(1)
3632(1)
3400(1)
6165(2)
3899(1)
4581(1)
4392(1)
3453(1)
2862(2)
2944(1)
5110(2)
Ϫ1140(1)
3030(1)
Ϫ30(1)
Ϫ235(1)
Ϫ844(1)
Ϫ1360(2)
Ϫ896(2)
Ϫ641(2)
Ϫ1005(1)
657(1)
62(1)
78(1)
34(1)
36(1)
37(1)
48(1)
49(1)
44(1)
45(1)
33(1)
36(1)
40(1)
54(1)
64(1)
45(1)
51(1)
63(1)
62(1)
39(1)
38(1)
41(1)
66(1)
79(1)
60(1)
46(1)
38(1)
37(1)
38(1)
49(1)
54(1)
51(1)
45(1)
X-ray crystallographic analysis
Data were collected using a Bruker SMART
CCD based diffractometer equipped with an LT-2
low-temperature apparatus operating at 213 K. Suit-
able colorless crystals were chosen and mounted on
a glass fiber using grease. Data were measured using
omega scans of 0.3Њ per frame for 30 s, such that a
hemisphere was collected. A total of 1271 frames
C(7)
C(8)
C(9)
C(10)
C(11)
C(12)
C(13)
C(14)
N(1A)
N(2A)
C(1A)
C(2A)
C(3A)
C(4A)
C(5A)
C(6A)
C(7A)
C(8A)
C(9A)
C(10A)
C(11A)
C(12A)
C(13A)
C(14A)
˚
were collected with a maximum resolution of 0.75 A.
The first 50 frames were recollected at the end of
data collection to monitor for decay. Cell parameters
were retrieved using SMART5 software and refined
using SAINT on all observed reflections. Data reduc-
tion was performed using the SAINT software,6
which corrects for Lp and decay. Data for Z-1 was
˚
limited to 0.85 A since greater than 80% of the data
integrated to less than 2␴I. The structures were
solved by the direct method using the SHELXS-977
program and refined by least squares method on F2,
SHELXL-97,8 incorporated in SHELXTL-PC V
5.10.9
1265(1)
1962(1)
2172(1)
1328(1)
863(1)
The structures were solved in the space group
P21/n(# 14) for E-1 and P-1 (#2) for Z-1 as determined
by analysis of systematic absences. All nonhydrogen
atoms are refined anisotropically. Hydrogens were
calculated by geometrical methods and refined as a
riding model. The crystals used for the diffraction
studies showed no decomposition during data collec-
tion. Final refinement values are given in Table 1.
2549(1)
a U(eq) is defined as one-third of the trace of the orthogonalized
Uij tensor.
The dark brown solution was filtered through a
bed of celite. The filtrate was added saturated NaCl
aqueous solution and extracted with diethyl ether
several times. The ether solution was washed with
5% NaHCO3 solution, dried over MgSO4, and con-
centrated. The residual orange oil was passed
through a silica gel column using 1:1 petroleum/
CH2Cl2 as eluting solvents. The elute was concen-
trated to a solid, which was dissolved in hot ethyl
acetate and crystallized at 0Њ C. Pale-yellow crystals
were obtained (E-1) as plates. To the mother liquid
was gradually added petroleum ether and pale yel-
low needle crystals were obtained (Z-1). E-1: mp,
Discussion
1,1Ј-Bi-3-cyanocyclohex-2-enylidene was syn-
thesized by application of the Mukaiyama-Tyrlic-
McMurry reaction10 to 3-cyano-2-cyclohexen-1-one,
which was prepared by hydrolyzing the cyanohydrin
formed by reaction of NaCN with the monoethylene
ketal of 1,3-hexanedione obtained from 1,3-cyclohex-
anedione and ethylene glycol (Scheme 2). The re-
sulting mixture of E-1 and Z-1 can be separated by
crystallization. Less soluble E-1 crystallized first as
plates (mp 259.5ЊC) from ethyl acetate, and then
Z-1 was obtained as needles (mp 171.5ЊC) from the
mother liquid by gradual addition of petroleum ether.
1
259.5ЊC; H NMR (10:1 benzene-d6/pyridine-d5), ͳ
1.03 (tt, J ϭ 5.8 Hz, J ϭ 6.2 Hz, 4H), 1.57 (t, J
ϭ 6.2 Hz, 4H), 1.74 (t, J ϭ 5.8 Hz, 4H), 6.67 (s,
2H); MS (EI) m/e 210 (M, 100). Z-1: mp, 171.5ЊC;

980
Wang, Doering, and Staples
a
˚
Table 5. Bond Lengths [A] and Angles [Њ] for Z-1
N(1)UC(7)
N(2)UC(14)
C(1)UC(8)
C(1)UC(2)
C(1)UC(6)
C(2)UC(3)
C(3)UC(7)
C(3)UC(4)
C(4)UC(5)
C(5)UC(6)
C(8)UC(9)
C(8)UC(13)
C(9)UC(10)
C(10)UC(14)
C(10)UC(11)
C(11)UC(12)
C(12)UC(13)
1.145(2)
1.153(2)
1.367(2)
1.446(3)
1.514(2)
1.342(3)
1.438(3)
1.505(2)
1.510(3)
1.519(3)
1.451(2)
1.506(3)
1.340(3)
1.425(3)
1.500(3)
1.497(3)
1.494(3)
N(1A)UC(7A)
N(2A)UC(14A)
C(1A)UC(8A)
C(1A)UC(2A)
C(1A)UC(6A)
C(2A)UC(3A)
C(3A)UC(7A)
C(3A)UC(4A)
C(4A)UC(5A)
C(5A)UC(6A)
C(8A)UC(9A)
C(8A)UC(13A)
C(9A)UC(10A)
C(10A)UC(14A)
C(10A)UC(11A)
C(11A)UC(12A)
C(12A)UC(13A)
1.156(2)
1.149(2)
1.367(3)
1.449(3)
1.517(2)
1.335(3)
1.435(3)
1.495(3)
1.504(3)
1.516(3)
1.451(2)
1.515(3)
1.346(2)
1.438(3)
1.501(3)
1.511(3)
1.516(3)
C(8)UC(1)UC(2)
C(8)UC(1)UC(6)
C(2)UC(1)UC(6)
C(3)UC(2)UC(1)
C(2)UC(3)UC(7)
C(2)UC(3)UC(4)
C(7)UC(3)UC(4)
C(3)UC(4)UC(5)
C(4)UC(5)UC(6)
C(1)UC(6)UC(5)
N(1)UC(7)UC(3)
C(1)UC(8)UC(9)
C(1)UC(8)UC(13)
C(9)UC(8)UC(13)
C(10)UC(9)UC(8)
C(9)UC(10)UC(14)
C(9)UC(10)UC(11)
C(14)UC(10)UC(11)
C(12)UC(11)UC(10)
C(13)UC(12)UC(11)
C(12)UC(13)UC(8)
N(2)UC(14)UC(10)
122.87(17)
121.83(17)
115.27(16)
123.26(18)
119.11(18)
123.23(19)
117.66(17)
110.11(17)
111.48(16)
112.64(16)
178.6(2)
122.03(17)
122.13(16)
115.84(17)
123.38(18)
119.22(19)
123.06(18)
117.70(18)
109.91(17)
114.56(19)
114.21(17)
177.8(2)
C(8A)UC(1A)UC(2A)
C(8A)UC(1A)UC(6A)
C(2A)UC(1A)UC(6A)
C(3A)UC(2A)UC(1A)
C(2A)UC(3A)UC(7A)
C(2A)UC(3A)UC(4A)
C(7A)UC(3A)UC(4A)
C(3A)UC(4A)UC(5A)
C(4A)UC(5A)UC(6A)
C(1A)UC(6A)UC(5A)
N(1A)UC(7A)UC(3A)
C(1A)UC(8A)UC(9A)
C(1A)UC(8A)UC(13A)
C(9A)UC(8A)UC(13A)
C(10A)UC(9A)UC(8)
C(9A)UC(10A)UC(14A)
C(9A)UC(10A)UC(11A)
C(14A)UC(10A)UC(11A)
C(10A)UC(11A)UC(12A)
C(11A)UC(12A)UC(13A)
C(8A)UC(13A)UC(12A)
N(2A)UC(14A)UC(10A)
123.07(16)
122.80(18)
114.13(17)
123.37(17)
119.68(17)
123.87(19)
116.40(18)
110.11(18)
111.7(2)
111.72(17)
177.1(2)
122.68(17)
121.58(16)
115.65(17)
122.71(17)
119.26(17)
123.71(17)
117.03(17)
109.41(17)
112.06(17)
112.82(17)
177.2(2)
a Symmetry transformations used to generate equivalent atoms.
Fig. 2. Drawing showing both molecules of Z-1 drawn at
50% ellipsoids.
Fig. 1. Drawing at 50% ellipsoids showing E-1.

Two gemometrical isomers
981
Fig. 4. Drawing showing the intermolecular interactions of hydro-
˚
gen atoms (A) for Z-1. Those in parenthesis are those from
MM2 calculations.
Scheme 2. Synthesis of E-1 and Z-2.
The distances calculated by MM2 program (in paren-
theses) compare favorably with the X-ray distances.
The 1H NMR spectra of E-1 and Z-1 in benzene-
d6 are almost identical. However, in a mixture of
benzene-d6 and pyridine-d5 (10:1), two isomers can
be distinguished by the chemical shifts of 2-vinyl-
protons (6.67 ppm for E-1 and 6.77 ppm for Z-1).
Based on 1H NMR assignment of E-1 and Z-1 (helped
by X-ray structures), it is now possible to speculate
isomeric assignment for the other compounds with
the same type. The isomer that has a greater value
of chemical shift for the 2-vinyl hydrogen is assigned
to the Z-isomer and smaller value the E-isomer. The
speculation has been examined against the similar
types of compounds previously studied in this labora-
tory and appeared correct so far (for example, 1,1Ј-
bicyclohex-2-enylidene1 in benzene-d6: E-isomer,
6.59 ppm, Z-isomer, 6.77 ppm; 1,1Ј-bi-3-phenylcyclo-
hex-2-enylidene3 in benzene-d6: E-isomer, 7.10 ppm,
Z-isomer, 7.50 ppm).
E-1 crystallized in the monoclinic space group
P21/n with the molecule sitting on an inversion center
of the cell. Atomic positions are given in Table 2,
while bond distances and angles are shown in Table
3. The structure of E-1 is shown in Fig. 1. The mole-
cule has C2h symmetry. Z-1 crystallized in the space
group P1 (#2) and has two molecules per asymmetric
unit. Atomic positions are given in Table 4. The bond
distances and angles are shown in Table 5. Figure 2
shows Z-1 with thermal ellipsoids with its estab-
lished structure.
In E-1, the angle of twist along the central bond
is 0Њ (ЄC2UC1UC1AUC2A ϭ Ϫ180Њ). This is also true
of one of the molecule in the unit cell (ЄC2UC1U
C8UC9 ϭ Ϫ0.2Њ) and very nearly so of the other
(ЄC2AUC1AUC8AUC9A ϭ 2.5Њ). The other dihedral
angles define derivation of the triene system from
coplanarity are all close to 180Њ: E-1, ЄC1AUC1U
C2UC3
ϭ
Ϫ178.7Њ;
Z-1,
ЄC8UC1U
C2UC3 ϭ 179.5Њ, ЄC1UC8UC9UC10 ϭ Ϫ177.5Њ;
(Z-1)A, ЄC8AUC1AUC2AUC3A ϭ Ϫ173.1Њ, ЄC1AU
C8AUC9AUC10A ϭ 177.4Њ.
The structures formed by MM2 calculation are
confirmed by X-ray structures. Interannular interac-
tions of hydrogen atoms are noted in Figs. 3 and 4.
Acknowledgments
The work was supported by the Norman Fund in
organic chemistry in memory of Ruth Alice Norman
Weil Halsband. Support to the Department of Chem-
istry and Chemical Biology of Harvard University for
its NMR facility comes from the NIH (s10-RR01748)
and (s10-RR04870) and the NSE (CHE 88-14019).
The CCD based X-ray diffractometer at Harvard
University was purchased through NIH grant
(1S10RR1193701).
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