C-H?O hydrogen bond networks in E- and Z-unsaturated esters of C-glycosides

Article abstract of DOI:10.1007/s10870-005-3479-7

Methyl E(Z)-4,7 anhydro-5-benzamido-6,8-di-O-benzoyl-2,3,5-trideoxy-d-allo- oct-2-enoate have been synthesized like intermediates and isolated as single crystals during the synthesis of pyrazole-related C nucleosides as synthetic product with cytotoxic ac

Full text of DOI:10.1007/s10870-005-3479-7

ꢀC
Journal of Chemical Crystallography, Vol. 35, No. 9, September 2005 ( 2005)
DOI: 10.1007/s10870-005-3479-7
----
C H· · ·O hydrogen bond networks in E- and
Z-unsaturated esters of C-glycosides
Agnesˇ Kapor,(1)∗ Dieter Zobel,(2) Marianna Stru¨mpel,(2) Ljilja Torovic´,(1)
and Mirjana Popsavin(1)
Received October 15, 2004; accepted February 10, 2005
Methyl E(Z)-4,7 anhydro-5-benzamido-6,8-di-O-benzoyl-2,3,5-trideoxy-D-allo-oct-2-
enoate have been synthesized like intermediates and isolated as single crystals during the
synthesis of pyrazole-related C nucleosides as synthetic product with cytotoxic activity.1
Crystal structures of E(Z) isomers were determined by X-ray analysis. E isomer crystal-
˚
˚
lizes in the triclinic crystal system, space group P1, a = 5.319(1) A, b = 10.758(2) A,
c = 12.229(2) A, α = 72.38(2) , β = 89.97(2) , γ = 87.07(2) , Dx = 1.320 Mgm−3 and
◦
◦
◦
˚
˚
Z isomer in the orthorhombic crystal system, space group P212121, a = 5.1297(13) A,
b = 19.667(5) A, c = 25.871(6) A, Dx = 1.348 Mgm−3. The molecular structure was
solved by direct method on the basis of 2609 and 2727 unique reflections recorded at
the temperature 293 K (E-isomer) and 173 K (Z-isomer) up to the final R-factor 0.0378
˚
˚
---
and 0.0435, respectively. C H· · ·O contact networks were analyzed and the correlation
---
established between the existence of the weak C H· · ·O hydrogen bonds and the melting
point of the single crystals.
---
KEY WORDS: X-Ray crystallography; C-glycosides; weak C H· · ·O hydrogen bond networks.
Introduction
a mixture of CF3COOH-HCl-H2O and reacted
with carbomethoxymethylenetriphenylphospho-
C-Nucleosides and their analogues consti-
rane in methylene chloride to give the Z- and E-
unsaturated esters 3 and 4 as 2:1 mixture. After
effective separation on a column of silica gel, pure
Z- and E-isomers 3 and 4 were isolated in 56 and
29% yields, respectively. Herein we report the X-
ray structure and hydrogen-bonding network in
the E and Z-isomer.
tute targets in synthesis because of their biological
and pharmacological properties. As part of our
programme on the synthesis of pyrazole-related
C-nucleoside 51 from D-glucose (Scheme 1), we
have prepared two C-glycosyl derivatives 3 and
4, bearing the α,β-olefinic ester function at C4
of the 2-benzamido-2-deoxy-β-D-ribofuranosyl
moiety. The free aldehyde 2 was liberated from
its ethylene acetal derivative 1 by treatment with
Experimental
Pure Z-isomer 3 was isolated as a white
crystalline solid. Recrystallization from CH2Cl2-
hexane gave an analytical sample (m.p. 114–
115◦C). Further elution with 5:1 toluene-EtOAc
gave pure E-isomer 4 which crystallized from
CH2Cl2-hexane to produce colorless needless
(1) Faculty of Natural Sciences and Mathematics, Trg D. Obradovic´a
4, 21000 Novi Sad, Serbia and Montenegro.
(2) Institute fu¨r Kristallographie, Freie Universita¨t, Berlin, Takustraße
6, D-14195 Berlin, Germany.
∗ To whom correspondence should be addressed; e-mail: akapor@
uns.ns.ac.yu.
687
ꢀ
C
1074-1542/05/0900-0687/0 2005 Springer Science+Business Media, Inc.

688
Kapor, Zobel, Stru¨mpel, Torovic´, and Popsavin
Scheme 1. (a) 4:1 CF3CO2H-6M HCl, +4◦C, 96 h; (b) Ph3P:CHCO2Me, CH2Cl2, rt, 19 h, 85% from 1.
(m.p. 165◦C). The colorless crystal of E-isomer
of dimension 0.93 mm × 0.40 mm × 0.12 mm
was analyzed first at STOE four-circle diffrac-
tometer equipped with CuKα radiation and Ni-
filter at room temperature. Since we were dealing
with an organic crystal of small dimensions, no
absorption correction was performed. Very small
white needle-shaped crystals of Z-isomer were
rather fragile for the manipulation. Single crystal
of dimension 0.15 mm× 0.08 mm× 0.05 mm was
mounted at the STOE four circle diffractometer
with graphite-monochromated MoKα radiation.
The intensity of 14,271 reflections was recorded
with a CCD camera at the temperature of 173 K.
Recording conditions data and crystal unit cell
parameters are given in Table 1 for E and Z-
isomer. In both cases, reflections were recorded
with ꢀ-2θ scan. Data were corrected for Lorentz
and polarization effects.
least squares refinement of the fractional coordi-
nates of the non-hydrogen atoms with anisotropic
atomic displacement parameters was performed
with SHELXL933 and WinGX.4 Positions of H
atoms were generated from the assumed geom-
etry, checked in difference Fourier map and re-
fined isotropically with common displacement pa-
2
˚
rameters for methyl hydrogen U1 = 0.140(14) A
2
˚
(E-isomer), 0.067(12) A (Z-isomer), for phenyl
2
˚
hydrogen U2 = 0.107(5) A (E-isomer) 0.035(4)
2
˚
A (Z-isomer), and for other hydrogen’s U3 =
2
2
˚
˚
0.049(3) A (E-isomer), 0.016(5) A (Z-isomer).
Final R-factor was R = 0.0378, for 357 parame-
ters for E-isomer and R = 0.0435 for 423 param-
eters for Z-isomer, using the F2 values of 2609
and 2727 (I > 2σ(I)) reflections. The highest and
the lowest peaks in the final difference map were
−3
˚
0.157 (0.17) and −0.143(−0.18) eA , respec-
tively for E and Z-isomer. Scattering factors were
taken from SHELXL93. Details of structure solu-
tion and refinement are given in Table 1.
The structure of isomers was solved by
a direct method using program SHELXS86.2
The E-map computed from the phase set with
best combined figure of merit revealed the po-
sitions of all non-hydrogen atoms. Full-matrix
Atomic coordinates and equivalent isotropic
displacement coefficients for non-hydrogen atoms
are collected in Tables S1 and S2. Bond distances

---
C H···O hydrogen bond networks
689
Table 1. Crystal Data and Structure Refinement of E- and Z-isomer of C30H27NO8
CCDC deposit no.
Empirical formula
Formula weight
Melting point (K)
Temperature (K)
252513
30H27NO8,-E-isomer
529.53
m.p. 438
293(2)
252512
C30H27NO8,-Z-isomer
529.53
m.p. 387–388
173(2)
C
˚
Wavelength (A)
1.54178
Triclinic, P1
0.71073 (on CCD)
Orthorhombic, P212121
Crystal system, space group
Unit cell dimensions
˚
a (A)
5.319(1)
10.758(2)
12.229(2)
72.38(1)
89.97(2)
87.07(2)
665.9(3)
1, 1.320
5.1297(13)
˚
b (A)
19.6673(49)
25.8714(62)
90
90
90
2610.1(11)
4, 1.348
0.098
1112
˚
c (A)
α (◦)
β (◦)
γ (◦)
3
˚
Volume (A )
Z, Calculated density (Mg/m3)
Absorption coefficient (mm−1
F(000)
)
0.799
278
Crystal size (mm)
0.93 × 0.40 × 0.12
3.79 to 67.03
−6 ≤ h ≤ 0
0.15 × 0.08 × 0.05
1.30 to 20.81
−5 ≤ h ≤ 5
−19 ≤ k ≤ 19
−25 ≤ l ≤ 25
14271/2727 [Rint = 0.12(8)]
Full-matrix least-squares on F2
2727/0/423
θ range for data collection (◦)
Limiting indices
−12 ≤ k ≤ 12
−14 ≤ l ≤ 14
3257/2609 [Rint = 0.0748]
Full-matrix least-squares on F2
2609/3/357
Reflections collected/unique
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I > 2σ(I)]
R indices (all data)
1.066
1.032
R1 = 0.0378, wR2 = 0.1041
R1 = 0.0440, wR2 = 0.1082
0.0120(14)
0.157 and −0.143
R1 = 0.0435, [N = 1993]
R1 = 0.0756, wR2 = 0.0913
0.0053(6)
0.17 and −0.18
Extinction coefficient
Largest diff. peak and hole (eA )
3
˚
and bond angles are listed in Tables S3 and S4. The
H atom fractional atomic coordinates, anisotropic
atomic displacement parameters for non-
hydrogen atoms and other supplementary crystal-
lographic data for this paper have been deposited
at the Cambridge Crystallographic Data Center.
molecular conformation, on the basis of the val-
--- --- ---
ues of corresponding torsion angles O C4 C3
◦
◦
--- --- ---
C2 = 125.2(4) (E), −134.8(4) (Z); O C7 C8
O8 = −173.0(2)◦ (E), 175.5(4)◦ (Z)−173.0(2)◦
(E), 175.5(4)◦ (Z) −173.0(2)◦ (E), 175.5(4)◦ (Z)
−173.0(2)◦ (E), 175.5(4)◦ (Z) −173.0(2)◦ (E),
175.5(4)◦ (Z) confirmed that β bonding of C4
substituent occurs.
Results and discussion
The analysis of the molecular geometry has
The perspective views5 of the molecules are
depicted in Fig. 1 and Fig. 2. The “absolute config-
uration” of the C-nucleoside was taken from the
literature with C4 (sp3) chiral center possessing
the S configuration in both isomers because the
Flack parameter6 was inconclusive: 0.6(3) (for E)
and. 0.3(21) (for Z).
indicated to the presence of a large number of
---
C H· · ·O contacts within the molecule and be-
tween the symmetry related molecules within the
---
crystal unit cell. C H· · ·A (A/the proton accep-
tor) system are usually classified as weak hy-
drogen bonds.7 Systems with oxygen atom ac-
ceptors like in investigated structure are stronger
than that with sulfur atom ones. This is confirmed
not only by crystal structure results7 but also by
Bond lengths agree well with corresponding
data taken from the literature. The analysis of the

690
Kapor, Zobel, Stru¨mpel, Torovic´, and Popsavin
Table S1. Atomic Coordinates (×104) and Equivalent Isotropic
Table S2. Atomic Coordinates (×104) and Equivalent Isotropic
2
3
2
3
˚
˚
Displacement Parameters (A × 10 ) for E-isomer
Displacement Parameters (A × 10 ) for Z-isomer
Atom
x
y
z
Ueq
Atom
x
y
z
Ueq
O
O(1)
C(1)
C(2)
C(3)
C(4)
C(5)
N(5)
C(6)
O(6)
C(7)
C(8)
O(8)
O(9)
C(9)
C(10)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
O(16)
C(17)
C(18)
C(19)
C(20)
C(21)
C(22)
C(23)
O(23)
C(24)
C(25)
C(26)
C(27)
C(28)
C(29)
O(30)
C(30)
−3880(5)
−4325(6)
−6012(8)
−5960(7)
−4213(7)
−4151(6)
−1903(6)
−2270(5)
−1648(6)
−3471(4)
−2368(7)
−181(7)
1182(5)
3095(7)
2769(7)
4083(7)
5949(9)
7242(11)
6787(14)
4986(13)
3610(9)
−3213(7)
−1594(6)
−5164(7)
−7050(7)
−8855(9)
−8700(11)
−6811(12)
−5063(10)
−330(6)
1851(4)
3071(2)
732(3)
−2428(2)
−5385(3)
−5449(3)
−4940(3)
−4237(3)
−3638(3)
−3905(2)
−4970(2)
−2821(2)
−2923(2)
−1883(3)
−1308(3)
−642(2)
327(3)
155(3)
767(3)
1559(4)
2131(5)
1880(5)
1076(5)
522(4)
−2155(3)
−1434(2)
−2323(3)
−3145(3)
−3238(4)
−2508(5)
−1700(4)
−1598(4)
−5568(3)
−5235(2)
−6674(3)
−7548(4)
−8597(4)
−8783(3)
−7919(4)
−6854(3)
−5959(3)
−6450(5)
60(1)
84(1)
61(1)
59(1)
55(1)
47(1)
40(1)
44(1)
43(1)
50(1)
48(1)
53(1)
58(1)
88(1)
53(1)
51(1)
72(1)
97(2)
105(2)
97(2)
68(1)
51(1)
69(1)
54(1)
61(1)
77(1)
87(2)
87(2)
71(1)
43(1)
67(1)
42(1)
90(2)
111(2)
72(1)
81(1)
72(1)
80(1)
94(2)
O
C(1)
O(1)
C(2)
C(3)
C(4)
C(5)
N(5)
O(6)
C(6)
C(7)
C(8)
O(8)
C(9)
O(9)
C(10)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
O(16)
C(17)
C(18)
C(19)
C(20)
C(21)
C(22)
C(23)
O(23)
C(24)
C(25)
C(26)
C(27)
C(28)
C(29)
C(30)
O(30)
1265(7)
2461(13)
2599(10)
614(13)
6499(2)
6145(4)
5542(2)
6627(3)
6601(3)
6120(3)
5608(3)
4982(2)
5021(2)
5539(3)
6234(3)
6730(3)
6452(2)
6826(3)
7378(2)
6468(3)
6753(3)
6452(5)
5863(4)
5579(4)
5862(3)
4798(3)
5008(2)
4272(3)
4100(3)
3622(3)
3305(3)
3448(3)
3949(3)
4598(3)
4784(2)
3939(3)
3837(3)
3212(3)
2704(3)
2802(3)
3426(3)
6029(3)
6451(2)
9350(1)
10951(2)
10859(2)
10707(2)
10224(3)
9817(2)
9662(2)
9951(2)
8969(1)
9078(2)
8919(2)
8779(2)
8319(1)
8095(2)
8251(1)
7643(2)
7409(3)
6986(3)
6790(3)
7026(3)
7454(2)
8471(2)
8138(1)
8399(2)
8790(2)
8709(3)
8246(3)
7858(3)
7925(2)
10060(2)
9920(1)
10332(2)
10680(2)
10927(2)
10819(2)
10469(2)
10227(2)
11563(2)
11309(2)
31(1)
43(2)
65(2)
36(2)
36(2)
25(2)
22(2)
24(1)
26(1)
23(1)
27(2)
31(2)
33(1)
33(2)
42(1)
31(2)
44(2)
52(2)
55(2)
54(2)
39(2)
30(2)
40(1)
29(2)
29(2)
41(2)
54(2)
55(2)
43(2)
23(2)
28(1)
17(1)
24(2)
35(2)
30(2)
30(2)
25(1)
59(2)
51(1)
1543(4)
2623(4)
2720(3)
3732(3)
4611(3)
5657(2)
5014(3)
6075(2)
3787(3)
2872(3)
3509(2)
1623(3)
2770(3)
3540(3)
2926(5)
3617(6)
4929(6)
5565(6)
4882(4)
6752(3)
6479(3)
7838(3)
8087(4)
9098(4)
9861(4)
9630(5)
8612(4)
6257(3)
5935(3)
7294(3)
7463(5)
8377(7)
9149(4)
9025(4)
8100(4)
1556(3)
519(6)
−136(12)
755(12)
−1393(11)
−1212(9)
797(7)
−1154(11)
−147(11)
−2307(12)
−3484(8)
−5351(12)
−6009(8)
−6504(12)
−8656(14)
−9807(14)
−8761(17)
−6621(16)
−5485(13)
863(12)
−529(8)
2912(12)
4628(12)
6529(13)
6699(16)
5000(15)
3074(13)
−3337(12)
−5523(7)
−2930(10)
−930(11)
−710(13)
−2466(12)
−4452(12)
−4689(11)
5816(13)
3902(9)
−946(6)
719(9)
207(12)
−1935(9)
−3555(10)
−3099(9)
−8209(6)
−8577(10)
Note. Ueq is defined as one-third of the trace of the orthogonalized
Uij tensor.
Note. Ueq is defined as one-third of the trace of the orthogonalized
Uij tensor.
ab initio calculations.8 The proton donating abil-
of the relatively strong intramolecular hy-
---
---
---
ities of C H bond depend on the following order
drogen bond N5 H5· · ·. O1: (N5 H5N =
3
2
9,10
˚
˚
---
---
---
C(sp ) H<C(sp ) H<C(sp) H.
0.895(46) A, N5· · ·O1
=
3.248(6) A,
˚
---
The type and the length of the intramolecular
contacts are given in the Table 2 and it can be
seen that they are the same for both isomers
H5N· · ·O1 = 2.806(44) A, N5 H5N· · ·O1 =
111.9(33)◦) which is the consequence of the cis
geometry.
--- ---
except those related to the ester group CH CH
The very different geometries of the trans
---
and cis configurations about the C2 C3 double
CO2Me in Z-isomer due to the formation

---
C H···O hydrogen bond networks
691
◦
◦
˚
Table S4. Selected Bond Lengths [A] and Angles [ ] for Z-isomer
˚
Table S3. Selected Bond Lengths [A] and Angles [ ] for E-isomer
˚
˚
Bond lengths (A)
Bond lengths (A)
----
----
----
1.434(4) C(6) C(7)
----
----
----
1.430(6) O(6) C(6)
O
O
C(7)
C(4)
----
1.529(4)
1.362(4)
1.511(5)
1.431(4)
1.326(4)
1.191(4)
1.473(5)
1.193(4)
1.488(5)
1.227(4)
1.494(4)
1.438(5)
O
O
C(7)
C(4)
----
1.455(6)
1.519(7)
1.519(7)
1.443(6)
1.341(7)
1.206(6)
1.487(8)
1.192(6)
1.487(8)
1.234(6)
1.490(7)
1.444(7)
----
----
1.439(4) O(6) C(16)
1.443(6) C(6) C(7)
----
1.205(5) C(7) C(8)
----
1.213(7) C(7) C(8)
O(1) C(1)
----
C(1) O(30)
C(1) C(2)
----
C(2) C(3)
C(3) C(4)
----
C(4) C(5)
C(5) N(5)
----
C(5) C(6)
C(1) O(1)
----
C(1) O(30)
C(1) C(2)
----
C(2) C(3)
C(3) C(4)
----
C(4) C(5)
C(5) N(5)
----
C(5) C(6)
----
----
1.323(5) C(8) O(8)
1.329(7) C(8) O(8)
----
----
1.476(5) O(8) C(9)
----
----
1.482(9) O(8) C(9)
----
----
1.296(5) O(9) C(9)
1.309(8) C(9) O(9)
----
----
1.487(5) C(9) C(10)
----
----
1.487(8) C(9) C(10)
----
----
1.536(4) C(16) O(16)
1.546(8) C(16) O(16)
----
----
1.446(4) C(16) C(17)
----
----
1.443(6) C(16) C(17)
----
----
1.522(4) C(23) O(23)
1.522(7) C(23) O(23)
----
----
----
1.341(4) C(23) C(24)
----
----
----
1.356(7) C(23) C(24)
N(5) C(23)
C(6) O(6)
N(5) C(23)
O(6) C(16)
----
----
1.435(4) O(30) C(30)
1.362(6) C(30) O(30)
Bond angles (◦)
Bond angles (◦)
---- ----
----
----
----
----
---- ----
----
----
----
----
C(7)
O
C(4)
----
110.8(2)
124.0(4)
125.2(4)
110.7(3)
123.6(4)
126.0(3)
107.7(3)
103.7(2)
116.0(3)
116.5(2)
111.9(2)
102.6(2)
122.0(2)
106.7(2)
111.1(3)
102.4(2)
115.8(2)
106.5(3)
106.7(2)
C(8) C(7) C(6)
115.1(3)
C(7)
O
C(4)
----
111.9(4)
123.3(6)
125.4(6)
111.3(6)
124.7(6)
127.7(6)
108.6(4)
104.4(4)
112.3(5)
115.7(5)
112.0(5)
105.0(4)
122.1(5)
115.3(4)
110.1(4)
108.1(4)
102.5(4)
108.8(5)
106.8(4)
C(8) C(7) C(6)
113.2(5)
----
----
O(1) C(1) O(30)
---- ----
O(8) C(8) C(7)
---- ----
107.5(3)
117.2(2)
122.9(3)
125.1(3)
112.0(3)
O(1) C(1) O(30)
---- ----
O(8) C(8) C(7)
---- ----
104.9(5)
116.6(5)
123.3(6)
125.3(6)
111.4(6)
O(1) C(1) C(2)
---- ----
C(9) O(8) C(8)
---- ----
O(1) C(1) C(2)
---- ----
C(9) O(8) C(8)
---- ----
O(30) C(1) C(2)
---- ----
O(9) C(9) O(8)
---- ----
O(30) C(1) C(2)
---- ----
O(9) C(9) O(8)
---- ----
C(3) C(2) C(1)
---- ----
O(9) C(9) C(10)
---- ----
C(3) C(2) C(1)
---- ----
O(9) C(9) C(10)
---- ----
C(2) C(3) C(4)
O(8) C(9) C(10)
---- ----
C(2) C(3) C(4)
O(8) C(9) C(10)
---- ----
----
----
----
----
----
----
O
O
C(4) C(3)
C(11) C(10) C(9) 118.9(3)
---- ----
O
O
C(4) C(3)
C(15) C(10) C(9) 122.2(6)
---- ----
----
C(4) C(5)
----
C(4) C(5)
C(15) C(10) C(9) 122.1(3)
---- ----
O(16) C(16) O(6) 123.7(5)
---- ----
----
----
----
----
C(3) C(4) C(5)
---- ----
O(16) C(16) O(6) 122.5(3)
---- ----
C(3) C(4) C(5)
---- ----
O(16) C(16) C(17) 125.1(5)
---- ----
N(5) C(5) C(6)
---- ----
O(16) C(16) C(17) 125.1(3)
---- ----
N(5) C(5) C(6)
---- ----
O(6) C(16) C(17) 111.2(5)
---- ----
N(5) C(5) C(4)
---- ----
O(6) C(16) C(17) 112.4(3)
---- ----
N(5) C(5) C(4)
---- ----
C(22) C(17) C(16) 118.2(6)
---- ----
C(6) C(5) C(4)
---- ----
C(18) C(17) C(16) 122.9(3)
---- ----
C(6) C(5) C(4)
---- ----
C(18) C(17) C(16) 121.9(5)
---- ----
C(23) N(5) C(5)
---- ----
C(22) C(17) C(16) 117.5(4)
---- ----
C(23) N(5) C(5)
---- ----
O(23) C(23) N(5) 120.3(5)
---- ----
O(6) C(6) C(5)
---- ----
O(23) C(23) N(5) 121.2(3)
---- ----
C(16) O(6) C(6)
---- ----
O(23) C(23) C(24) 121.6(5)
---- ----
O(6) C(6) C(7)
---- ----
O(23) C(23) C(24) 121.9(3)
---- ----
O(6) C(6) C(7)
---- ----
N(5) C(23) C(24) 118.1(5)
---- ----
C(5) C(6) C(7)
---- ----
N(5) C(23) C(24) 117.0(3)
---- ----
O(6) C(6) C(5)
---- ----
C(29) C(24) C(23) 116.8(5)
---- ----
C(25) C(24) C(23) 122.7(5)
C(16) O(6) C(6)
C(25) C(24) C(23) 118.4(3)
---- ----
C(7) C(6) C(5)
----
----
----
----
----
----
----
----
O
O
C(7) C(8)
C(29) C(24) C(23) 123.4(3)
O
O
C(7) C(8)
C(1) O(30) C(30) 115.8(5)
----
C(7) C(6)
----
----
----
C(7) C(6)
C(1) O(30) C(30) 117.0(4)
---
˚
˚
the crystal unit cell. The geometry of C H· · ·.O
intermolecular contacts is given in the Table 3a
and 3b. The contacts are grouped into those
which bond the molecules parallel to each others
bond (1.296(5) A (E), 1.309(8) A (Z) and
◦
--- --- ---
torsion angle C1 C2 C3 C4 = −175.6(4)
(E), −3.2(11)◦ (Z)) cause the variation in
intermolecular contacts and in packing of the
molecules of Z-isomer with respect to E-isomer in
Fig. 2. ORTEP drawing of Z-isomer with non-H labeling
scheme. The displacement ellipsoids were drawn at 40%
probability.
Fig. 1. ORTEP drawing of E-isomer with non-H labeling
scheme. The displacement ellipsoids were drawn at 40%
probability.

692
Kapor, Zobel, Stru¨mpel, Torovic´, and Popsavin
---
Table 2. The Type and the Geometry of the Intramolecular C H· · ·O Contacts in E- and Z-Isomer of
C
30H27NO8
◦
˚
˚
˚
----
----
----
D
N
D
H· · ·A
Isomer
D
H (A)
H· · ·A (A)
D· · ·A (A)
H· · ·A ( )
----
1
C3 H3· · ·O1
E(trans) 0.930
2.603
2.528(42)
2.354
2.464
2.794
2.362(41)
2.443
2.388(49)
2.698
2.614(40)
2.407
2.350(50)
2.440
2.518(45)
2.558
2.596(54)
2.464
2.379(43)
2.792
2.731(42)
2.729
2.628(51)
2.535
2.572
2.488
2.471(45)
2.590
2.895(6)
3.074(7)
2.664(7)
2.639(8)
2.945(5)
2.438(6)
2.758(4)
2.713(7)
3.022(4)
2.916(6)
2.711(6)
2.721(7)
2.642(5)
2.665(7)
2.835(6)
2.846(8)
2.643(5)
2.664(6)
3.153(5)
3.151(7)
3.656(5)
3.524(8)
2.829(5)
2.839(7)
2.747(4)
2.749(7)
2.855(5)
2.819(7)
98.8
111.1(28)
98.1
89.2
89.0
82.7(25)
99.8
97.3(31)
99.7
96.4(26)
98.9
104.3(37)
91.0
87.6(27)
97.6
97.0(36)
89.4
94.3(26)
102.6
106.6(28)
174.6
168.3(43)
98.6
96.4
94.6
97.4(32)
96.9
----
C4 H4· · ·O1
Z(cis)
1.060(43)
----
2
3
C30 H30C· · ·O1
E(trans) 0.960
Z(cis)
0.980
----
C4 H4· · ·O6
E(trans) 0.980
----
C7 H7· · ·O6
Z(cis)
0.975(45)
----
4
C18 H18· · ·O6
E(trans) 0.930
Z(cis)
1.021(48)
----
5
C6 H6· · ·O8
E(trans) 0.980
Z(cis)
1.035(44)
----
6
C15 H15· · ·O8
E(trans) 0.930
Z(cis)
0.909(52)
----
7
C8 H81· · ·O9
E(trans) 0.970
Z(cis)
0.985(44)
----
8
C11 H11· · ·O9
E(trans) 0.930
Z(cis)
0.892(51)
----
9
C6 H6· · ·O16
E(trans) 0.980
Z(cis)
1.035(44)
----
10
11
12
13
14
C7 H7· · ·O16
E(trans) 0.980
Z(cis)
0.975(45)
----
C15 H15· · ·O16
E(trans) 0.930
Z(cis)
0.909(52)
----
C22 H22· · ·O16
E(trans) 0.930
Z(cis)
0.950
----
C5 H5· · ·O23
E(trans) 0.980
Z(cis)
0.929(46)
----
C25 H25· · ·O23
E(trans) 0.930
Z (cis)
1.073(49)
2.523(46)
94.6(28)
---
into stacks (Table 3a) and those which bond these
stacks within bc plane (Table 3b and Figs. 3 and
4. The mark number of the contacts is the same in
Table and Figure).
Intermolecular hydrogen bond N5
H5· · ·O23 in both isomers (symmetry
transformation 1 + x, y, z) have the geome-
˚
˚
---
try: N5 H5N = 0.860 A (E), 0.895(46) A (Z);
----
Table 3a.The Geometry of C H· · ·O Intermolecular Contacts in E- and Z-isomer of C30H27NO8 Which
Are the Same or Similar in Both Isomers
◦
˚
˚
˚
----
----
----
D ..A ( )
N
D
H · · · A
Isomer
D
H (A)
H · · · A (A) D.· · ·(A)
----
1
2
3
4
C4 H4· · ·O23 (2)
E (trans)
Z (cis)
E (trans)
Z (cis)
E (trans)
Z (cis)
E (trans)
Z (cis)
0.980
1.060(43)
0.930
1.021(48)
0.960
0.975(45)
0.970
2.415
2.298(42)
2.847
2.199(48)
2.566
2.952(47)
2.877
3.262(4)
3.258(7)
3.602(5)
3.219(7)
3.347(7)
3.778(7)
3.612(5)
3.641(7)
144.3
149.8(33)
139.1
176.1(39)
138,6
143.1(35)
133.3
----
C4 H4· · ·O23 (1)
----
C2 H2· · ·O23 (2)
----
C18 H18· · ·O23 (1)
----
C30 H30B· · ·O1 (2)
----
C7 H7· · ·O8 (1)
----
C8 H82· · ·O (1)
----
C8 H82· · ·O (2)
0.994(44)
2.777(45)
145.7(34)
Note. Equivalent positions: (1) x + 1, +y, +z (2) x − 1, +y, +z.

---
C H···O hydrogen bond networks
693
----
Table 3b. The Geometry of C H· · ·O Intermolecular Contacts in the E- and Z-isomer of C30H27NO8 Which
Belong Only to the One Isomer
◦
˚
˚
˚
---
---
----
D
N
D
H · · · A
Isomer
D
H (A) H · · · A (A) D· · ·A (A)
H· · ·A ( )
----
5
6
7
5
6
7
8
9
C12 H12· · ·O30 (3)
E(trans)
E(trans)
E(trans)
Z(cis)
Z(cis)
Z(cis)
0.930
0.930
0.930
0.950
2.630
2.810
2.648
2.657
3.542(6)
3.736(7)
3.384(5)
3.595(8)
3.563(8)
3.434(7)
3.638(7)
3.715(9)
166.9
173.6
136.6
169.2
----
C21 H21· · ·O9 (4)
----
C28 H28· · ·O9 (5)
----
C21 H21· · ·O9 (6)
----
C30 H30A· · ·O9 (7)
0.980
2.752
140.5
----
C2 H2· · ·O9 (8)
0.968(43)
0.985(44)
1.110(48)
2.509(42)
2.702(44)
2.969(47)
159.9(34)
158.9(34)
124.7(30)
----
C8 H8B· · ·O30 (9)
Z(cis)
Z(cis)
----
C13 H13· · ·O1 (10)
Note. Equivalent positions: (3) x − 2, +y, +z − 1; (4) x + 1, +y + 1, +z; (7) x + 1/2 + 1, −y + 1/2 +
1,−z + 2; (8) x + 1/2, −y + 1/2 + 1, −z + 2; (9) x − 1/2, −y + 1/2 + 1, −z + 2; (10) −x − 1/2, −y +
1,+z − 1/2; (5) x + 1, +y + 1, +z + 1; (6) −x, +y − 1/2, −z + 1/2 + 1.
˚
˚
˚
of the molecule, and these contacts are rather
similar in both isomers. Oxygen atoms O1, O8,
O9 and O23 realize several contacts of both inter-
and intramolecular type. The contact that might
be treated separately is the bond, which has a
H5N· · ·O23 = 2.323 A (E), 2.117(47) A (Z);
˚
N5· · ·O23 = 3.133(3) A (E), 2.945(6) A (Z);
◦
◦
---
N5 H5N· · ·O23 = 157.1 (E), 153.4(42) (Z).
The existence of these bond which are stronger
---
than C H· · ·O hydrogen bond networks,
---
single acceptor in the C H· · ·O intermolecular
determines the molecular packing in first step.
Table 4 presents the analysis of the number
of acceptor contacts realized by oxygen atoms
in both isomers. The oxygen atoms O6 and
contacts and satisfies the geometrical criteria of
existence of the hydrogen bond. Such contacts
2
---
are: the hydrogen bond C12(sp ) H· · ·O30 in E
˚
˚
---
---
isomer (C O = 3.542(6) A, H· · ·O = 2.630 A,
O16 possess only intramolecular C H· · ·O
◦
3
---
---
C H· · ·O = 166.86 ) and C8(sp ) H· · ·O30
contacts, which determine the conformation
Fig. 3. Crystal packing for unit cell projected along the a-axis for
E-isomer.

694
Kapor, Zobel, Stru¨mpel, Torovic´, and Popsavin
Fig. 4. Crystal packing for unit cell projected along the a-axis for Z-isomer.
(Z)) where oxygen atom belongs to glycoside
ring.
˚
---
---
in Z isomer (C O = 3.638(7) A, H· · ·O =
◦
˚
2.702(44) A, C H· · ·O = 158.9(34) ) which
is both with oxygen atom O30 from the side
3
---
chain of esters group and also C8(sp ) H82· · ·O
Conclusions
˚
---
in both isomers (C8 O = 3.612(5) A, (E),
˚
˚
3.641(7) A (Z); H· · ·O = 2.877 A (E), 2.777(45)
The analysis of the crystal and molecular
structures of Methyl E(Z)- 4,7 anhydro-5-ben-
zamido-6,8-di-O-benzoyl-2,3,5-trideoxy-D-allo-
oct-2-enoate isomers shows that there is a large
◦
◦
˚
---
A (Z); C8 H· · ·O = 133.3 (E), 145.7(34)
----
Table 4. Acceptors of C H· · ·O Contacts in
---
number of C H· · ·O noncovalent contacts
E- and Z-isomer of C30H27NO8
and possible week hydrogen bonds within the
molecule and between the symmetry related
molecules within the crystal unit cell. Packing of
the molecules of Z- and E-isomer in the crystal
unit cell was analyzed with respect to the type
and the length of the possible intermolecular
hydrogen bonds. The contacts that might induce
Oxygen atoms
E-isomer
Z-isomer
O
1-inter∗
—
1-inter
—
1-inter
3-intra
—
2-intra ∗
1-inter
2-intra
3-inter
2-intra
—
4-intra
3-inter
2-intra
1-inter
—
O1
1-inter
2-intra
—
O6
2-intra
—
---
the difference in melting point are the C H· · ·O
O8
hydrogen bonds whose single acceptor in the
intermolecular contacts is oxygen atom O30
from the side chain of esters group and O
from glycoside ring and which do fulfill the
geometrical criteria of existence of the hydrogen
bond. These hydrogen bonds are shorter in E
isomer than in Z isomer, since O30 is in contact
with C12(sp2)-H in E isomer and with C8(sp3)-H
2-intra
2-inter
2-intra
—
4-intra
3-inter
2-intra
1-inter ∗
—
O9
O16
O23
O30

---
C H···O hydrogen bond networks
695
in Z isomer that agrees with literature data.9,10
The existence of shorter bond is correlated with
higher bonding energy of the interaction between
molecules in the crystal unit cell and maybe
resulting also in higher melting point temperature,
which is measured in the case of E isomer.
References
1. Popsavin, M.; Torovic´, L.j.; Spaic´, S; Stankov, S.; Kapor, A.;
Tomic´, Z.; Popsavin, V. Tetrahedron 2002, 58, 569.
2. Sheldrick, G.M. SHELXS86, In Crystallographic Computing 3;
Sheldrick, G.M.; Kruger, C.; Goddard, R., Eds; Oxford Univer-
sity Press, UK 1985; pp. 175–189.
3. Sheldrick, G.M. SHELXL93, Program for the Refinement
of Crystal Structures; University of Go¨ttingen, Germany,
1993.
4. Farrugia, L.J. WinGX, J. Appl. Cryst. 1999, 32, 837.
5. Farrugia, L.J. ORTEP-3 for Windows, J. Appl. Cryst. 1997, 30,
565.
6. Flack, H.D. Acta Crystallogr. 1983, A39, 876.
7. Desiraju, G.R.; T. Steiner, The Weak Hydrogen Bond in Struc-
tural Chemistry and Biology; Oxford University Press, New
York, 1999.
Supplementary Material CCDC 252512 & 252513. These data can
be obtained free of charge via www.ccdc.cam.ac.uk/data request/
cif, by e-mailing data request@ccdc.cam.ac.uk, or by contacting
The Cambridge Crystallographic Data Center, 12 Union Road, Cam-
bridge CB2 1EZ, UK; fax: +44(0)1223-336033.
Acknowledgments
8. Novoa, J.J.; Planas, M.; Rovira, M.C. Chem. Phys. Lett. 1996,
251, 33.
This work was supported by a research grant from
the Ministry of Science and Environmental Protection
of the Republic of Serbia.
9. Allerhand, A.; Schleyer, R. J. Am. Chem. Soc. 1963, 85,
1715.
10. Scheiner, S.; Grabowski, S.J.; Kar, T. J. Phys. Chem. A 2001,
105, 10607.