Hybride interactions (stacking + H-bonds) between molecules bearing benzyl groups

J o u r n a l of

MOLECULAR STRUCTURE ELSEVIER

Journal of Molecular Structure 442 (1998) 115-119

Hybride interactions (stacking + H-bonds) between molecules bearing benzyl groups Zbigniew Ciunik a'*, Stawomir Jarosz h aFaculty of Chemistry, University of Wroetaw, F. Joliot-Curie 14, 50-383 Wroctaw, Poland blnstitute of Organic Chemistry, Polish Academy of Science, Kasprzaka 44, 01-224 Warsaw, Poland

Received 14 April 1997; accepted 17 July 1997

Abstract

In this paper, the crystal structure of the 3-O-benzyl-1,2-O-isopropylidene-5,6-dideoxy-c~-D-ribo-hex-5-yno-1,4-furanoseis presented. This is the first noticed example in which weak hydrogen bonds prevail over the 7r-Tr stacking interactions of the aromatic rings. As a result, the hybride interactions are formed by the 7r-o stacking and the C-H...Tr hydrogen bonds. The analysis of molecular packing of crystal structures collected in the Cambridge Crystallographic Database shows that hybride interactions occur in infinite columns ofbenzyl groups or in binary complexes of organic molecules. Semiempirical calculations suggest that the ~r-ostacking interactions and the C-H... r hydrogen bonds have a synergic character. Probably they are the key factor which stimulates the growth of crystals. © 1998 Elsevier Science B.V. Keywords: Hydrogen bonds; Stacking interactions

I. I n t r o d u c t i o n

The ability o f the C-H groups to act as donors in the hydrogen bonds was a matter o f debate and controversy in the past. This debate was initiated 60 years ago [1]. At present, such hydrogen bonds are relatively well known [2-5]. Their donor capability decreases in the series [6]: Csp--H > Csp2--H > Csp3--H

where the Csp-H group is the most acidic one. W e a k hydrogen bonds and other interactions are sometimes in competition. Such phenomena can be observed in crystals o f small molecules, macromolecules and in biological systems. Effective molecular recognition * Corresponding author.

requires a precise complementarity between several binding regions on the receptor and various chemical features o f the substrate. Self-assembly often operates under equilibrium control. Thus, a growing structure can recognize different types o f interactions during assembly to maximize complementary surface contacts [7]. A multi-site approach was undertaken to examine the nucleotide bases in which the hydrogen bonding and the aromatic stacking groups within a macrocyclic receptor bind simultaneously to the substrate [8,9]. In a series o f benzoic and cinnamic acid donor-acceptor complexes, all crystals consist o f acid dimers which are themselves stacked to optimize the 7r-a- interactions [10]. Therefore, the authors pointed out, the stacking o f the aromatic rings can prevail over other types o f interactions such as C - H . . . O and even O - H . . . O , and such effects should be included

0022-2860/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved PH S0022-2860(97)00285-8

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Z Ciunik, S. Jarosz/Journal t?/'Molecular Structure 442 (1998) 115-119

O

O

Scheme 1.

when the structures of biomolecules are modelled [5,11]. In this article we present the crystal structure of the 3-O-benzyl- 1,2-O-isopropylidene-5,6-dideoxyC~-D-ribo-hex-5-yno-l,4-furanose (Scheme 1). The packing diagram of these crystals shows the presence of several weak hydrogen bonds and stacking interactions of aromatic rings, but a precise analysis reveals some deviations from the geometry of the 7r-Tr stacking interactions. 2. Experimental The compound under investigation was prepared according to ref. [12]. Preliminary oscillation and Weissenberg photographs showed the crystal system and the space group. Intensity data were measured on a Kuma KM4 computer-controlled r-axis diffractometer using graphite-monochromated MoKc~ radiation at 150 K using an Oxford Cryosystem adapter. The cell constants were obtained from a least-squares refinement of the setting angles of 45 reflections in the 0 range 10-15 °. The data were collected with the ~o/20 scan techniques. The stability of intensities was monitored by the measurements of three standards every 100 reflections. No decay of intensity of the standard reflections was observed. The data were corrected for Lorentz and polarization effects. No absorption correction was applied. The structure was solved by direct methods (program SHELXS86 [13]). The positions of the hydrogens were found from the AF maps. A full-matrix least-squares refinement (program SHELXL93 [14]) of all the non-H atom co-ordinates and anisotropic displacement parameters and hydrogen co-ordinates with isotropic displacement parameters yielded the final Rl(F) = 0.0455 and wR2 (F 2) = 0.1028. A weighting scheme based on the function w = 1/ [or2(Fo) 2 + (0.06555P) 2] where P = [(Fo) 2 + 2 ( F c ) 2 ] / 3 was used to minimize ~w(AF2) 2. The crystallographic data are given in Table 1. The anisotropic

Table 1 Crystal data and structure refinement Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions

C 16H~O4 274.30 150(2)K 0.71069 ,~. orthorhombic P21212 a = 5.203(1),~ b = 13.424(3) ,~, c = 20.224(5) A. Volume 1412.5(5) A.~ Z 4 Density (calculated) 1.290 Mg/m 3 Absorption coefficient 0.092 mm -t F(000) 584 Crystal size 0.30 x 0.30 x 0,30 mm Diffractometer Kuma KM4 No. of standard reflections 3 Decay of standards < 3% 0 range for data collection 2 to 30 Index ranges h: 0 ---* 7, k: 0 ~ 18, l: 0 ~ 28 Reflections collected 2431 Independent reflections 2406 Observed reflections (1 > 2cq) 1496 Refinement method Full-matrix least-squares on F 2 Used programs SHELXS86, SHELXL93 Data/parameters 2406/253 Goodness-of-fit on F 2 1.019 Final R indices RL(F) = 0.0455, wR2(F z) = 0.1028 Largest diff. peak and hole 0.30 and -0.21 e.A 3

displacement parameters and the list of observed and calculated structure amplitudes are available on request from ZC.

3. Results and discussion The numbering scheme and overall conformation of the studied furanose are shown in Fig. 1. The geometry of the hydrogen bonds is presented in Table 2. The conformation of the molecule is partly determined by the isopropylidene substituent which fixes t h e 3T 4 twisted conformation of the furanoid ring [ 15] and the intramolecular C(33)-H(33)...O(3) hydrogen bond. This interaction stabilizes the conformation of the O-benzyl group with one, perpendicularly directed to the aromatic ring C-H bond from the methylene group. The C(33)-C(32)-C(31)-H(311) torsion angle is equal to 92(2) ° . Such geometry is one of the

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Z Ciunik. S. Jarosz/Journal o f Molecular Structure 442 (1998) 1 1 5 - 1 1 9

C6c5

C34

Fig. 1. View of the molecule with crystallographic numbering scheme. The dotted line represents the intramolecular H-bond. The ellipsoids correspond to 30% probability contours of atomic displacement. several observed conformations o f the O-benzyl groups [ 16]. All molecules generated in the studied crystals by the identity period along the [100] direction (lattice vector a) form infinite columns (Fig. 2). The result o f the above is that all the aromatic rings in one column are parallel. The interplanar distance 3.732(5),~ is longer than the separations observed for stacking interactions (3.3-3.6,~) [17]. Two other important factors which characterize these interactions, an overlap diagram and a ring offset in columns [3.625(5) A], show that the 7r-a interactions rather than the 7r-r ones dominate in the columns o f the aromatic rings [18]. The main reason for this phenomenon is a net o f intermolecular hydrogen bonds (Fig. 3, Table 2). The three-centred C(6)-H(6)...O(2')/O(3') hydrogen bond formed between columns has a minor significance for stacking interactions. Three other hydrogen bonds [C(2)-H(2)...O(1"), C(4)-H(4)...O(3"') and C(31)-H(311)...M"' where M denotes a midpoint o f the aromatic ring] are formed between molecules

Fig. 2. The packing diagram of studied crystals. in one column. This means that each molecule is connected with its two neigbours, a low and an upper one, via three weak hydrogen bonds. The aromatic rings can hypothetically diminish the offset by a small rotation around the C(3)-O(3) or 0(3)C(31) bond, but the molecules in these crystals optimize the net of hydrogen bonds rather than the 7r-Tr stacking interactions. One o f the results o f this optimization is a very weak Csp3-H...'n" interaction [C(31)-H(311)...M"'] which is formed by the methylene donor from the O-benzyl substituent (the C-H bond perpendicular to the phenyl ring). The above consideration suggests that one, two or three weak hydrogen bonds destroy the r-Tr stacking interactions. The answer for the question: which of them has the crucial role in this competition was found after a systematic analysis o f the data collected in the Cambridge Structural Database (October 1996) [ 19]. For this analysis there were selected c a . 1300

Table 2 Geometry of the hydrogen bonds (A,°), M = centroid of the phenyl ring D-H...A

D...A

D-H

H...A

AD-H...A

C(6)-H(6)...O(2') C(6)-H(6)...0(3') C(33)-H(33)...O(3) C(2)-H(2)...O(1") C(4)-H(4)...O(3"') C(31)-H(311)... M"'

3.165(3) 3.558(3) 2.806(3) 3.524(3) 3.472(3) 3.79

0.97(4) 0.97(4) 1.00(4) 1.05(4) 1.00(3) 1.05(4)

2.31 (4) 2.69(4) 2.36 (4) 2.52 (4) 2.76 (3) 2.75

145 (3) 148 (3) 106 (3) 159 (3) 128 (2) 175

Symmetry equivalent atoms: (none) x, y, z; (') -x, 0.5 + y, 0.5 z; (") -1 + x, y,z;

("') 1 + x, y, z.

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Z, Ciunik, S. Jarosz/Journal of Molecular Structure 442 (1998) 115 119

i H

H !

x"J ~ Scheme 3. Fig. 3. Stereoview of the intermolecular contacts. The dotted lines represent the H-bonds.

error-free organic monomers (with all positional atomic parameters available and R-factor < 0.1) containing the X-benzyl group (C6HsCH2X- where X = C, N, O). In these crystals we have found two types of interactions. The first type (in 17 crystal structures) is formed by molecules related by the shortest lattice vector (between 4.57 and 5.21 A) or a half of the lattice vector in two structures with two crystallographically independent molecules in the unit cell. All these columns are almost identical. The interplanar distances between the planes defined by aromatic rings and the ringoOffset in columns are within the range of 3.4-3.7 A [the average value (av.) 3.57(11)A] and 2.9-3.8.~ [av. 3.3(3),~], respectively. Distances and angles of the C-H...~r interactions (C-H = 1.08 ,~ after normalization) are within the range of 2.5-3.0 A and 120-160 °, respectively (Scheme 2). The second type of interactions (in 18 crystal structures) is frequently centrosymmetric and formed between two molecules (Scheme 3). The interplanar distances and the ring offset are within the range of 3.4-3.9 _A [av. 3.57(14)A] and 2.7-3.6 [av. 3.3(3) ,~]. The geometry of the C-H...Tr hydrogen bonds is similar to the one in the first type of x

Q>x Q>x ! I

Scheme 2.

interactions. The X-benzyl groups adopt in crystals all possible conformations [ 16]. This means that one of two dihedral angles C-C-C-Xcan be equal to 0, 30, 60 or 90 °. Presented parameters, particularly the values of the ring offset show explicitly that in the analysed crystals the 7r-a stacking interactions are dominant. Finally, quite simple models of binary interactions were analysed using semiempirical methods (PM3 [20] and AM 1[21 ]/MOPAC6122]). Calculations performed for several typical binary models with hybride interactions of the O-benzyl groups and models of the same molecules but with another packing diagram, with the 7r-Tr stacking interactions only (without any H-bond), showed that weak Csp-H...Tr hydrogen bonds stabilize the stacking interactions of benzyl groups of about 1 kcal/mol.

4. C o n c l u s i o n

In this paper, an intermolecular, hybride interaction between benzyl groups in crystals is presented, which is formed by two synergic components: the C-H...~r weak hydrogen bond (between the methylene group and the aromatic ring) and the 7r-or stacking interactions (between the aromatic rings). These hybride interactions stabilize infinite columns or binary complexes of molecules. In the case of infinite columns, molecules are related by the shortest lattice vector. The parallel orientation of the column axes and the shortest lattice vectors suggest that the hybride interactions control the growth of'crystals as its key factor.

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