A Comparative X-ray Diffraction Study and Ab Initio Calculation on RU60358, a New Pyrethroid

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A Comparative X-ray Diffraction Study and Ab Initio Calculation on RU60358, a New Pyrethroid
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     Int. J. Mol. Sci.   2006 , 7  , 255-265 International Journal of Molecular Sciences   ISSN 1422-0067 © 2006 by MDPI www.mdpi.org/ijms/ A Comparative X-ray Diffraction Study and  Ab Initio  Calculation on RU60358, a New Pyrethroid Fodil Hamzaoui 1 , Abdelkader Chouaih 1 , Philippe Lagant 2 , Ouassila Belarbi 1  and Gérard Vergoten 2, * 1   Laboratoire SEA2M, Département de Chimie, Université de Mostaganem, 27000 Mostaganem, Algeria; E-mail: aek_chouaih@yahoo.fr for Abdelkader Chouaih 2   UMR CNRS 8576 Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies, 59655 Villeneuve d’Ascq, France * Author to whom correspondence should be addressed; E-mail: Gerard.Vergoten@univ-lille1.fr   Received: 28 February 2006, in Revised Form: 12 April 2006 / Accepted: 30 July 2006 / Published: 9  August 2006 Abstract:  The crystal structure of RU60358, C 20 H 21 NO 3 , has been determined using X-ray diffraction to establish the configuration and stereochemistry of the molecule around the C15-C16 triple bond. The compound crystallises in the orthorhombic space group P2 1 2 1 2 1 , a = 7.7575, b = 11.3182, c = 21.3529Å, V = 1874.80Å3 and Z = 4. The structure has been refined to a final R = 0.068 for the observed structure factors with  I    ≥  3 σ   (  I  ). The refined structure was found to be significantly non planar. A comparative study, using the ab initio  calculations of the structure at B3LYP/6-31G** levels of theory, shows good geometrical agreement with the X-ray diffraction data. Standard deviations between the calculated and experimental bond values have been shown to be 0.01 Å and 0.5° for bond angles. Vibrational wavenumbers were obtained from a normal mode analysis using the ab initio  calculations. Keywords:  X-ray diffraction,  Ab initio  calculation, organic compounds, pyrethroid. 1. Introduction The structures of pyrethroids compounds obtained from experimental X-ray diffraction data has been investigated by several authors [1-4]. Considerable progress has been made in relating the structure of pyrethroids with their biological activity, but improvement of such concepts requires reliable information on molecular shape (configuration, bond lengths and angles and conformation).   Int. J. Mol. Sci.   2006  ,7 256 Biological activity in pyrethroids is related to molecular structure and depends strongly on the stereochemistry adopted by the asymmetric centers [5-7]. In this context the compound RU60358 appears as an useful intermediate in the synthesis of some pyrethroid insecticides [8]. The study of the conformation of this molecule may yield information about the mechanism of its biological activity [9,10]. In this paper, we propose a comparative study between the experimental X-ray diffraction data and the optimized geometry predicted from ab initio  molecular orbital calculations performed on the compound RU60358. Vibrational wavenumbers were then consequently predicted and correct assignments obtained. RU60358 2. Results and discussion 2.1. Description of the crystal structure The displacement ellipsoid plot with the numbering scheme for the title compound is shown in Figure 1. Figure 2 shows a perspective view of the crystal packing in the unit cell. Selected X-ray diffraction data summarize bond lengths in Table 1 and bond angles in Table 2. Figure 1. Perspective view of the molecule showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.   Int. J. Mol. Sci.   2006  ,7 257   Figure 2. A perspective view of the crystal packing in the unit cell. Table 1. Selected bond distances (Å) by X-ray and theoretical calculations Distance (Å) Atom 1 Atom 2 X-ray B3LYP/6-31G** C1 C2 1.395 (10) 1.433 C1 C10 1.395 (11) 1.381 C1 C11 1.474 (12) 1.472 C2 C3 1.410 (09) 1.416 C2 C7 1.395 (11) 1.433 C3 C4 1.395 (13) 1.388 C4 C5 1.395 (10) 1.428 C4 C15 1.429 (10) 1.428 C5 C6 1.395 (10) 1.371 C6 C7 1.395 (09) 1.422 C7 C8 1.395 (11) 1.418 C8 C9 1.395 (11) 1.375 C9 C10 1.395 (09) 1.412 C11 N 1.278 (13) 1.290 C11 C12 1.514 (15) 1.497 C12 O1 1.292 (10) 1.351 C12 O2 1.152 (10) 1.210 C13 O1 1.439 (12) 1.436 N O3 1.376 (09) 1.374 C14 O3 1.427 (11) 1.467 C15 C16 1.163 (13) 1.213 C16 C17 1.467 (12) 1.459 C17 C18 1.439 (12) 1.548 C17 C19 1.469 (11) 1.541 C17 C20 1.531 (13) 1.549   Int. J. Mol. Sci.   2006  ,7 258   Table 2. Selected bond angles (°) by X-ray and theoretical calculations Angle (°) Atom 1 Atom 2 Atom 3 X-ray B3LYP/6-31G** C2 C1 C10 120.0 (8) 119.8 C2 C1 C11 123.5 (5) 121.1 C10 C1 C11 116.2 (8) 119.1 C1 C2 C3 120.2 (6) 122.6 C1 C2 C7 120.0 (7) 118.5 C3 C2 C7 119.8 (7) 118.7 C2 C3 C4 120.0 (5) 121.5 C3 C4 C5 120.0 (5) 119.2 C3 C4 C15 122.1 (6) 120.9 C5 C4 C15 117.9 (8) 119.9 C4 C5 C6 120.0 (8) 120.4 C5 C6 C7 120.4 (7) 121.2 C2 C7 C6 119.8 (9) 118.8 C2 C7 C8 120.0 (5) 119.6 C6 C7 C8 120.2 (6) 121.6 C7 C8 C9 120.0 (5) 120.6 C8 C9 C10 120.0 (7) 120.1 C16 C17 C19 111.5 (9) 109.4 C16 C17 C20 107.7 (9) 109.3 C18 C17 C19 110.5 (8) 109.7 C18 C17 C20 107.3 (5) 109.6 C19 C17 C20 107.2 (4) 109.5 C1 C10 C9 120.0 (6) 121.2 C1 C11 N 126.9 (8) 125.7 C1 C11 C12 121.6 (5) 121.4 N C11 C12 111.5 (4) 112.9 C12 O1 C13 117.0 (9) 115.0 N O3 C14 108.5 (5) 109.2 C11 N O3 110.8 (7) 112.6 C11 C12 O1 110.6 (7) 110.5 C11 C12 O2 126.0 (9) 125.7 O1 C12 O2 123.4 (5) 123.8 C4 C15 C16 174.8 (9) 180.5 C15 C16 C17 179.3 (6) 180.1 C16 C17 C18 112.6 (7) 109.6   Int. J. Mol. Sci.   2006  ,7 259 2.2. Optimized geometry Calculated geometric parameters at B3LYP/6-311G** are equally displayed into Tables 1 and 2. From the theoretical values, it is noteworthy that most of the optimized bond lengths have slightly larger values than the corresponding experimental ones, due to the fact that theoretical calculations imply isolated molecules in gaseous phase state while experimental results refer to molecules in the solid state. Comparing theoretical bond angles with those given in experimental data, the B3LYP calculated values correlate in a good agreement. In spite of the differences, calculated geometric parameters represent a good approximation and can provide a starting point to calculate other parameters, such as vibrational wavenumbers, as will be described below. 2.3. Vibrational wavenumbers The theoretically derived DFT vibrational wavenumbers corresponding to the optimized geometry can be expressed in the more convenient internal coordinate space for a description of the potential energy distribution (PED) via the Redong Program [11]. This algorithm uses least square methods to fit the theoretical vibrational wavenumbers to the experimental ones by introducing scaling factors associated to the various types of force constants. Table 3 displays the potential energy distribution among internal coordinates obtained for the scaled DFT normal modes analysis (scaling factor = 0.962). This last value is currently recommended to obtain correct vibrational wavenumbers and adequate assignments of the PED [12]. The  ν C=N stretching mode of the imine part is generally observed in the 1665-1675 cm-1 range by Raman spectroscopy. The presence of neigbouring aryl groups lowers this value by 10-20 cm-1. Using a general scaling factor of 0.962 leads to the 1594 cm -1  DFT theoretical wavenumber (1657 cm -1  without scaling). This assignment is in accordance with the Raman wavenumbers as reported by Dollish et al. [13]. The imine moiety participates also to Raman bands around 1274 cm -1 , presently calculated at 1266 cm -1 . Other vibrational modes of interest implying the imine group are predicted to occur at 314 cm -1  ( δ (N-O-CH 3 ), at 971.6 cm -1  (  ν N-O) and at 997 cm -1  for the (  ν O-CH 3 ) stretching mode. The alkyne  ν C Ξ C stretching mode displays intense Raman bands in the 2220-2240 cm -1  range. The DFT corresponding wavenumber is obtained presently at 2243 cm -1 . Keeping the same 0.962 scaling factor, the δ C-C Ξ C in plane bending mode is predicted to occur at 474.6 cm -1 , this frequency being quite comparable to the experimental range centered at 484 cm -1  [13]. The ester group gives a predicted DFT  ν C=O stretching mode located at 1749 cm -1  corresponding to current experimental bands obtained in the 1730-1750 cm -1  range. The associated  ν C-O stretching mode is predicted at 1215 cm -1 , this value appearing quite consistent with experimental data (1200-1220 cm -1 ). The in plane δ (O-C=O) bending mode is observed in the 750-775 cm -1  range using Raman spectroscopy and the DFT derived corresponding wavenumber is obtained here at 752 cm -1 . The δ (C-C=O) and δ (C-O-CH 3 ) in plane bending motions are predicted to stand at 374 and 298 cm -1  respectively, these two wavenumbers being very close to the experimental data (300-340 cm -1 ). For the aromatic part of the molecule, we can observe a rough accordance between the DFT predicted wavenumbers (and corresponding vibrational assignments) and the experimental data obtained from vibrational analyses on benzene derivatives [14]. The pyrethoid molecule displays numerous and complex mixings of vibrational modes between the two rings and their substituents. The  ν 8 degenerate (8a, 8b) mode (in Wilson’s notation) [14] implying  ν CA-CA ring stretching
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