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Crystallographic and conformational analysis of 1,3-bis(2,4-
dimethoxyphenyl)imidazolidine-2-thione
ARTICLE in JOURNAL OF CHEMICAL CRYSTALLOGRAPHY · APRIL 2006
Impact Factor: 0.5 · DOI: 10.1007/s10870-005-9005-0
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Hasan Karabıyık Dokuz Eylul University 41 PUBLICATIONS 241 CITATIONS
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Muhittin Aygün Dokuz Eylul University 81 PUBLICATIONS 334 CITATIONS
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Crystallographic and conformational analysis
of 1,3-bis(2,4-dimethoxyphenyl)imidazolidine-2-thione
Hasan Karabıyık,(1)∗ M. Emin G ¨unay,(2) Muhittin Ayg ¨un,(1) Bekir C¸ etinkaya,(3)and Canan Kazak(4)
Received February 2, 2005; accepted June 10, 2005 Published Online May 24, 2006
The molecular and crystal structures of the title compound, C19H22N2O4S, were deter- mined by single crystal X-ray diffraction technique. The title compound crystallizes in space group F d d 2, with a= 30.785(3) ˚A, b = 10.6455(9) ˚A, c = 11.0036(8) ˚A, Z = 8, Dcalc= 1.379(2) g cm−3, µ(Mo-Kα)= 0.207 mm−1, and its crystal system is orthorhombic.
The structure was solved by direct methods and refined to a final R= 0.042 for 1530 reflections with I > 2σ (I). There is a half-independent molecule in the asymmetric unit.
The title molecule has twofold rotational symmetry along with the C–S bond. Classically no hydrogen bond is found in the crystal structure. The crystal structure is stabilized by π–π stacking and edge to face (C–H. . .π -ring) interactions. To elucidate conformational features and steric hindrances of the title molecule, selected torsion angle is varied from
−180◦ to+180◦ in every 10◦ and thus molecular energy profile is calculated by PM3 semi-empirical method.
KEY WORDS: Crystal structure; N-Heterocyclic Carbene (NHC); PM3; conformational analysis.
Introduction
Cyclic thioureas are important classes of compounds with a wide variety of applications.1 However, synthetic routes to these compounds are associated with some shortcomings such as long reaction times, harsh reaction conditions,
(1)Department of Physics, Faculty of Arts and Sciences, Dokuz Eyl¨ul University, Buca 35160 ˙Izmir Turkey.
(2)Department of Chemistry, Faculty of Arts and Sciences, Adnan Menderes University, Aydın, Turkey.
(3)Department of Chemistry, Faculty of Sciences, Ege University, Bornova ˙Izmir, Turkey.
(4)Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey.
∗ To whom correspondence should be addressed; e-mail: hasan.
karabiyik@ deu.edu.tr
low product yields and lack of generality. Pre- viously we have shown that metal derivatives of 1,3-bis(2,4-dimethoxyphenyl)imidazolidin-2- ylidene can be generated in high yield from the corresponding 2-tricholoromethyl- 1,3-bis(2,4-dimethoxyphenyl)imidazolidin (1) by simple thermal decomposition via α-elimination of chloroform.2 Recently, we have found that the carbene can be trapped by sulfur to give the cyclic thioure 2.3 The structure of 2 was established on the basis of elemen- tal analysis, NMR spectroscopic and X-ray structural studies and conformational flexibil- ity of the title compound was investigated by the PM3 semi-empirical molecular orbital method.
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1074-1542/06/0400-0243/0C2006 Springer Science+Business Media, Inc.
244 Karabıyık, G ¨unay, Ayg ¨un, C¸ etinkaya, and Kazak
N
N H
CCl3
Ar
Ar
S8 , PhMe
-CHCl3
Ar=2,4-(OCH3)2C6H3 1
N N Ar
Ar S
2 Scheme 1. Synthesis scheme of the title compound.
Experimental
Preparation and spectral measurements for the title compound
Synthesis scheme of the title compound has been illustrated in see Scheme 1. All reactions were carried out under argon atmosphere with the use of Schlenk techniques. The solvents were dried and deoxygenated by standard procedures. 1H and 13C NMR spectra were recorded on a Bruker DPX-400 MHz or Varian mercury +400 MHz spectrometer. J values are given in Hz. Elemental analyses were performed via CHNS-932 (LECO) in T ¨UB˙ITAK Microlab and melting points were determined by electrothermal melting point detection apparatus.
A 50 mL Schlenk tube was charged with 1 (0.200 g, 0.43 mmol), S8 (0.014 g, 0.44 mmol) and 5 mL toluene. The solution was heated under reflux for 4 h. Upon cooling to the room temperature, hexane (10 mL) was added into the solution. The solid was filtered off and then was recrystallized in CH2Cl2/Et2O. Yield:
0.110 g (68%), m.p.: 252–254◦C. Anal. Cal. for C19H22N2O4S; C: 60.94; H: 5.92; N: 7.48; found C: 60.18; H: 6.47; N: 7.54.1H NMR (δ, CDCl3):
3.81 [s, 6H, 2,4-(OCH3)2C6H3]; 3.85 [s, 6H, 2,4-(OCH3)2C6H3]; 4.01 [s, 4H, NCH2CH2N];
6.53 [d, 2H, J= 6.80 Hz, 2,4-(OCH3)2C6H3];
7.25 [s, 2H, 2,4-(OCH3)2C6H3]; 7.35 [d, 2H, J= 8.40 Hz, 2,4-(OCH3)2C6H3]. 13C NMR (δ, CDCl3): 49.3 [NCH2CH2N]; 55.7 [2,4- (OCH3)2C6H3]; 56.1 [2,4-(OCH3)2C6H3]; 100.2
[2,4-(OCH3)2C6H3]; 104.7 [2,4-(OCH3)2C6H3];
122.8 [2,4-(OCH3)2C6H3]; 131.2 [2,4- (OCH3)2C6H3]; 156.7 [2,4-(OCH3)2C6H3];
160.5 [2,4-(OCH3)2C6H3]; 184.6 [s, C= S].
X-ray crystallography
A suitable single crystal of size 0.30 mm× 0.23 mm × 0.20 mm for the title compound was selected for the crystallographic study and then mounted on goniometer of a STOE IPDS II diffractometer. All diffraction measure- ments were performed at the room temperature [293(2) K] using graphite monochromated MoKαradiation (λ= 0.71073 ˚A). The systematic absences and intensity symmetries indicated the orthorhombic F d d 2 space group. A total of 16495 reflections [2.64◦< θ <28.51◦] were collected in the rotation mode. The intensities col- lected were corrected for Lorentz and polarization factors, absorption correction (µ= 0.207 mm−1) by integration method via X-RED software4 and cell parameters were determined by using X-AREA software.4 The structure was solved by direct methods using SHELXS-97.5 The refinement was carried out by full-matrix least- squares method on the positional and anisotropic temperature-dependent parameters of the non- hydrogen atoms, or equivalently corresponding to 120 crystallographic parameters. The positions of H atoms bonded to C atoms were calculated (respective bond lenghts of methylene, methyl and aromatic C–H are 0.97, 0.96 and 0.93 ˚A) and included in the structure factor calculation using a riding model. Atom displacement parameters of all hydrogen atoms were restricted to be 1.2 Ueq of the parent atom. Using SHELXL-97,5 the structure was refined to R1= 0.042 for observed 1530 reflections which obey to the condition of I > 2σ (I) and to R1= 0.0733 for all 2376 data used in refinement process. The maximum peaks and deepest hole observed in the final ρ map were 0.17 and −0.26 e ˚A−3, respectively. The scattering factors were taken from SHELXL-97.5 The data collection conditions and parameters of refinement process are listed in Table 1. R(int)
Table 1. Crystal Data and Details of the Structure Refinement for the Title Compound
CCDC deposit no. CCDC 261789
Color/shape Colorless/prismatic
Chemical formula C19H22N2O4S
Formula weight 374.46
Crystal system Orthorhombic
Space group F d d 2
Unit cell dimensions
a ( ˚A) 30.785(3)
b ( ˚A) 10.6455(9)
c ( ˚A) 11.0036(8)
Volume ( ˚A3) 3606.1(5)
Z 8
Density (calculated, g cm−3) 1.379 Absorption coefficient (mm−1) 0.207 Calculated Tmin, Tmax 0.944, 0.959
R(int) 0.107
Diffractometer/measured method
STOE IPDS II/rotation
Unique reflections measured 2376 Independent/observed
reflections
2376/1530
Data/parameters 2376/131
Extinction coefficient 0.0026(3) Goodness of fit on F2 1.010
R indices [I > 2σ (I)] R1= 0.042, wR2= 0.086 R indices (all data) R1= 0.073, wR2= 0.094 Weighting scheme w= 1/[s(Fo2)+ (0.0394P )2]
where P= (Fo2+ 2Fc2)/3
value is higher than 0.1 due to poor quality of the crystal.
Conformational analysis
The geometry optimization of the title molecule leading to energy minima in vacuo was achieved by using PM3 self-consistent field molecular orbital6,7 method at the restricted Hartree-Fock (RHF) level8 with the aid of Win- Mopac 7.21 package.9 Polak-Ribiere conjugate gradient method was used in the optimization pro- cedure with RMS gradient of 0.001 kcal/ ˚Amol and convergence criteria of 0.01 kcal/ ˚Amol. The crystallographic coordinates were used as starting geometry for the calculations. The structure asso- ciated with the lowest energy according to the PM3 optimization was compared with the X-ray structure. To elucidate conformational features of the title molecule, the selected torsion angle was
varied from −180◦ to +180◦ in every 10◦ and the molecular energy profile was obtained by per- forming single-point calculations on the calcu- lated potential energy surface.
Results and discussion
An Ortep drawing10 with the atom- numbering scheme and packing drawing of the molecular structure of the title compound in the unit cell are shown in Figs.1and2, respectively.
The results obtained from X-ray crystallographic and computational studies are presented in Table2for comparison. The title compound which adapts to C2molecular point group crystallizes in space group F d d 2 and there is a half indepen- dent molecule in the asymmetric unit of the crys- tal structure. The molecule has a twofold sym- metry axis along the C1–S1 bond bisecting the NHC ring and thus whole molecular structure is completed by the symmetry operation [symmetry code:−x−1/2, −y−3/2, z]. C1–S1 bond length is 1.650(3) ˚A. Due to the fact that five membered ring which adapts to the twisted conformation on C2i–C2 bond has a twofold rotational symmetry axis along the C1–S1 bond, N1i/N1 and C2i/C2 atom pairs have the same deviations in magnitude from the average ring plane of the NHC, in which atom S1 is included without any deviation, but the deviations of these symmetrically equivalent atoms have opposite signs. Respective deviations of atoms N1 and C2 from the average ring plane of NHC are found as 0.065(2) and−0.094(3) ˚A.
C–N bonds in the NHC ring are different in terms of its bond distances. Although both C–N bonds are of single bond character, their bond dis- tances are considerably different from each other.
Excess charge transfer from nitrogen atoms in NHC ring to the carbon atom linked to the sulphur atom occurs. Indeed, excess charge located on the carbene carbon atom (C1) linked to the sulphur atom is relatively higher than on the other carbon atoms in the molecule.11 The theoretical studies have indicated that the stability of these carbenes is due to electron donation from the nitrogen lone pairs into the formally vacant p(π ) orbital of the
246 Karabıyık, G ¨unay, Ayg ¨un, C¸ etinkaya, and Kazak
C2i C2 N1i
C3i C4i C5i
C6i
C7i C8i
O1i
C9i O2i
C10i
N1
C1
S1
C3
C8 C7
C6
C5
C4 O2
C10 O1
C9
Fig. 1. An ORTEP III view of the title molecule with the atomic numbering scheme of non-hydrogen atoms. Displacement ellipsoids are drawn at the 50% probability level.
carbene carbon.11,12N1–C1 and N1–C2 bond dis- tances are 1.359(3) and 1.453(3) ˚A, respectively and these bond lengths are in agreement with the literature values.12–16
The angle between NHC and 2,4 dimethoxyphenyl ring (R1) planes is 83.57(12)◦. For this reason, it can be stated that 2,4- dimethoxyphenyl rings are nearly perpendicular to NHC average ring plane. Moreover, 2,4- dimethoxyphenyl rings are linked to NHC ring pseudo-equatorially. In conventional sense, neither inter- nor intramolecular hydrogen bond is found in the structure, since there are no O–H or N–H bonds in the compound. Two edge to face C–H. . .(π -Ring) interactions which R1 ring [fractional centroid coordinates: 0.17822(3), 0.46158(8), 0.09492(10)] participates are ob-
served in the crystal structure. The perpendicular distances of H. . .(π -Ring) and C–H. . .(π -Ring) angles for these interactions of C9–H9c. . .R1, C10–H10c. . .R1 are found as 2.832, 2.906 ˚A and 150.06◦, 137.69◦, with the respective symmetry codes; [1/4−x, 1/4+y, 1/4+z] and [1/4−x,
−1/4+y, −1/4+z]. There are two weak π–π stacking interactions between R1 rings in the crystal structure (see Fig. 2). The perpendicular distances of these π –π stacking interactions (R1–R1) are found as 3.528 and 3.207 ˚A and their symmetry codes; [1/4−x, 1/4+y, 1/4+z]
and [1/4−x, −1/4+y, −1/4+z]. Since both perpendicular distances between the interacting π-rings are smaller than 3.8 ˚A, it can be stated that both stacking interactions in addition to the edge to face interactions mentioned above supply
Fig. 2. Orientations of the non-H atoms in the unit cell. Dashed lines indicate weak π –π interactions.
Table 2. Some Selected Geometrical Parameters of the Title Compound ( ˚A,◦) Ob- tained from the X-ray Crystallographic and Theoretical Studies
Bond lengths X-ray PM3 Bond angles X-ray PM3
S1–C1 1.650(3) 1.639 S1–C1–N1 126.57(2) 127.21
O1–C8 1.363(3) 1.383 N1–C1–N1i 106.9(3) 105.58
N1–C1 1.359(3) 1.413 N1–C2–C2i 102.41(2) 103.76
N1–C2 1.453(3) 1.494 C2–N1–C3 120.42(2) 117.88
N1–C3 1.420(3) 1.450 C8–O1–C9 117.89(2) 116.03
C2–C2i 1.523(3) 1.525 N1–C3–C8 120.52(2) 123.32
Torsion angle X-ray PM3 Torsion angle X-ray PM3
C2–N1–C1–N1i −5.9(2) 3.68 C3–N1–C1–N1i −171.24(2) −165.58 C1–N1–C2–C2i 14.4(2) −9.15 C3–N1–C2–C2i −179.58(2) −162.66 N1–C2–C2i–N1i −16.1(2) 10.33 C2–N1–C1–S1 174.05(13) 176.32 C2–N1–C3–C8 −71.5(3) 73.40 N1–C3–C4–C5 −175.8(3) −179.98
non-negligible contributions to the stabilization of the crystal structure.
According to the crystallographic study, T(C2-N1-C3-C8) is obtained as −71.5(3)◦, whereas this torsion angle in the optimized molec- ular structure is 73.40◦. Another remarkable dif- ferentiation in the optimized structure from the crystallographic study is observed in the confor- mation of the five membered ring (see Table2).
The five membered NHC ring is slightly twisted conformation on C2i–C2 according to the results suggested by PM3 semi-empirical calculation, whereas this ring evidently adapts to the twisted conformation in the crystallographic study. PM3 method, which is a semi empirical method, can not represent comprehensively structural proper- ties of the crystalline materials, since this method has some shortcomings such as partial ignorance of overlap of the atomic orbitals in addition to the fact that the molecule is regarded as isolated (or single) molecule throughout the computations.
For these reasons, some conformational discrep- ancies between the optimized and X-ray crystallo- graphic structures are observed. These conforma- tional differences in the optimized structure are presumably due to the contributions from the π – π stacking, edge to face interactions and packing of the molecules which are obeyed to the space group symmetry operations.
In addition, the semi-empirical PM3 molecular orbital calculations were carried out
in order to define the conformational flexibility of the title molecule as a function of the selected torsion angle T(C2–N1–C3–C8) (see Fig.3). The energy profile as a function of T(C2–N1–C3–C8) shows evident a maximum in vicinity of 160◦ due to the steric hindrance between sulphur atom and ortho-methoxy groups. The heat of formation values corresponding to the most unfavorable conformer, X-ray crystallographic and the optimized structures are obtained as
−32,256, −58.714, and −60.618 kcal/mol, respectively. As seen from these results, X-ray crystallographic and the optimized structures are
Fig. 3. Variation of heat of formation versus the selected torsion angle.
248 Karabıyık, G ¨unay, Ayg ¨un, C¸ etinkaya, and Kazak
of no considerable difference in terms of energy.
In addition, there is a small potential barrier (approximately 6 kcal/mol) between the crystal- lographic and optimized structures. This barrier indicates an unfavorable conformer whose the orientations of the 2,4-methoxyphenyl rings are nearly perpendicular to the those of the optimized structure, but when it is compared with the most unfavorable conformer, it can be stated that the barrier is fairly small and has not considerable effects on the synthesis or purification of the title compound.
Acknowledgments
Dokuz Eyl¨ul University Fund is grate- fully acknowledged for its financial sup- port (Project No: 04.KB.FEN.100), additionally Hasan Karabıyık would like to thank T ¨UB˙ITAK (The Scientific and Technical Research Council of Turkey) for partial financial support.
Supplementary materials CCDC 261789 contains the supplemen- tary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data request/cif, by email-
ing data [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: $+$44 1223 336033.
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