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  • 1. ISSN (Print): 2328-3777, ISSN (Online): 2328-3785, ISSN (CD-ROM): 2328-3793 American International Journal of Research in Formal, Applied & Natural Sciences AIJRFANS 14-259; © 2014, AIJRFANS All Rights Reserved Page 114 Available online at http://www.iasir.net AIJRFANS is a refereed, indexed, peer-reviewed, multidisciplinary and open access journal published by International Association of Scientific Innovation and Research (IASIR), USA (An Association Unifying the Sciences, Engineering, and Applied Research) Crystal structure of [(2E)-6,6-dimethylhept-2-en-4-yn-1- yl](methyl)(naphtha-1-ylmethyl)amine( Terbinafine) Tiwari R.K., MishraBharti Department of Physics, Jiwaji University-474011, Gwalior (M.P.), India I. Introduction Title compound (Terbinafine) C21H25N became available first time in 1991 in Europe and in 1996 in USA. It is a synthetic allylamine antifungle compound. It is recently introduced, orally active, antifungal belonging to the allylamines class1 of synthetic antifungal agents. The structurally related topical antifungal naftifine 2 was the prototype of these compounds from which it was developed during a programme of chemical synthesis3 . The biological and clinical properties of the allylamines have recently been reviewed4 . Title compound in common with naftifine and related allylamines, acts by blocking fungal ergosterol biosynthesis5-7 . Terbinafine is highly lipophilic in nature and tends to accumulate in skin, nails and fatty tissues. It prevents conversion of squalene to lanosterol. The present paper is related with its three- dimensional structure. II. Experimental Details Nice beautiful colorless crystals of title compound were grown by the slow evaporation from its solution in Acetone at room temperature. The density of the crystals was measured by floatation method in a mixture of Benzene and Carbon tetra chloride. The measured density was 1.054 mg/m3 whereas calculated density is 1.0966 mg/m3 . The molecular weight of the sample is 291.43 g/mol. and melting point is 193˚C. The IUPAC name of Terbinafine is [(2E)-6, 6-dimethylhept-2-en-4-yn-1-yl] (methyl) (naphtha-1-ylmethyl) amine. The unit cell parameters were determined by a computerized automatic Bruker axs Kappa apex 2 CCD diffractometer at Sardar Patel University, Vallabh Vidyanagar, Gujurat e ell pa amete s a e a 91 1 3 9 39 1 11 93 and β 97 9 ˚ 0 us t e spa e g oup was dete mined to e P 1/n with monoclinic crystal system and Z=4. The preliminary crystal data is given in Table 1. III. Data collection and structure solution The complete three dimensional intensity data collection was done at Sardar Patel University, Vallabh Vidyanagar, Gujarat on a computerized automatic Bruker axs Kappa apex 2 CCD diffractometer. The temperature of crystal during data collection was 293K. The X- ay adiation used was Mokα (0.7107 Å). All the data were corrected for Lorentz and polarization effects but no absorption correction was done because of very small absorption coefficient. The data collection was done y a θ ange of 1 to 7 ˚ e enti e data we e collected where h varies from -6 to 7, k from -38 to 38 and l from -14 to 7. In all 17396 reflection were measured out of which 4512 were unique reflections. Each intensity measurement involved in a scan over the reflection peak height. The structure was solved by direct method using SHELXS-978 . IV. Refinement The positional parameters which were obtained from SHELXS-97 and their isotropic temperature factors were subjected to refinement by SHELXL-979 refinement program. After 4 cycles of refinement the R factor dropped to 0.1154. Further refinement of the structure was carried out with individual anisotropic temperature factors of the form: Exp.[(U11h2 +U22k2 +U33l2 +2U12hk+2U23kl+2U13hl)] reduced R-factor to 0.1007. At this stage the hydrogen atoms were fixed by geometrical considerations and refined subsequently with isotropic temperature factors which were taken from the corresponding non- hydrogen atoms. Abstract: The title molecule [(2E)-6,6-dimethylhept-2-en-4-yn-1-yl ](methyl)(naphtha-1-ylmethyl)amine, C21H25N (Terbinafine) is characterized by X-ray single crystal diffraction analysis. The compound crystallizes in the monoclinic space group P21/n with a=5.9181(3)Å, b=29.4239(14)Å, c=11.429 β=97.92˚(0), Volume 1971.24(16) Å3 and Z=4. The two Benzene rings in the structure are essential planer, but the side chain is inclined with a gle of 7.21˚. There is i teresti g observ tio i this structure. During crystallization, two water molecules have shown their presence in the unit cell. These water molecules are engaged in hydrogen bonding and thus providing the stability to the structure. Keywords: Single crystal diffraction, Hydrogen bond, Crystallization etc.
  • 2. R.K Tiwari et al., American International Journal of Research in Formal, Applied & Natural Sciences, 6(2), March-May 2014, pp. 114-118 AIJRFANS 14-259; © 2014, AIJRFANS All Rights Reserved Page 115 Refinement of the structure was terminated after three more cycles of refinement when all the s ifts in t e pa amete s e ame mu small t an t e o esponding e s d’s e final R-value was 0.0951 for all the 17396 observed unique reflections. The final positional and thermal parameters of non-hydrogen atoms are listed in Table 2. V. Results and discussion The ORTEP10 view of the molecule with numbering scheme is shown in Fig 2. The bond lengths and angles involving non-hydrogen atoms are listed in Table 3. The two Benzene rings in the structure are essential plane ut t e side ain is in lined wit an angle of 37 1˚ The bond lengths and angles in the Benzene ring have usual variations, but the C(1)-C(11) bond in unusually long of 1.499(4) Å. This elongation may be due to extension of Benzene ring electrons delocalization along this bond. Similarly the chain from C(11)-C(23) is a stretched one having normal bond distances. There is also nothing unusual about the tetrahedral geometry around C(23). All the bond lengths and angles are normal. The relevant torsional angles are shown in Table 4. There is an interesting observation in this structure. During crystallization, two water molecules have shown their presence in the unit cell. These water molecules are engaged in hydrogen bonding and thus providing the stability to the structure. The possible hydrogen bonds are listed in Table 5. The packing of the molecules viewed along a, b and c axes are shown in Figs 3, 4, 5 and 6 respectively. References [1] G.Petranyi, N.S.Ryder, A.Stutz, Allylamine derivatives new class of synthetic antifungal agents inhibiting fungal squalene epoxidase Science, 1984, 224, 1239-41 [2] A.Georgopoulos, G.Petranyi, H.Mieth, J.Drews, in vitro activity of naftiline, a new antifungal agent, Antimicrob agents chemother, 1981, 19, 386-9 [3] A.Stutz, Synthesis and structure- activity correlations within allylamine antimycotics, Ann N Y Acad Sci, 1988, 544, 46-62 [4] N.S.Ryder, H.Mieth, Allylamine antifungal drugs Curr Top Med Mycol, 1991, 4, 158-88 [5] N.S.Ryder, G.Seidl, P.F.Troke, Effect of the antimycotic drug naftifine on growth of and sterol biosynthesis in candida albicans, Antimicrob Agents Chemother, 1984, 25, 483-7 [6] N.S.Ryder, Specific inhibition of fungal biosynthesis by SF 86-327,a new allylamine antimycotic agent, Antimicrob Agents Chemother, 1985, 27, 252-6 [7] N.S.Ryder, M-C Dupont, Inhibition of squalene epoxidase by allylamine antimycotic compounds, a comparative study of the fungal andmammalian enzymes Biochem J, 1985, 230, 765-70 [8] G M S eld i “ SHELXS-97 P og am fo t e solution of ystal st u tu e” 1997 [9] G M S eld i “SHELXL-97 P og am fo ystal st u tu e dete mination” 1997 [10] C K Jo nson “OR EP Repo t ORNL-3794 Ook Ridge National La o ato y ennessee U S A” 19 Fig.1 Molecular structure of compound Table 1: Crystallographic data for title compound Empirical formula C21 H25N Formula weight 325.45 Temperature 293(2) K Wavelength 0.71073 Å (Mokα Crystal system, space group monoclinic, P21/n Unit cell dimensions a=8.89 aa a=5.9181(3) Å, b=29.4239(14)Å 11 93 β 97 9 0 ˚ Volume 1971.24(16) Å3 Z, Calculated density 4, 1.0966 Mg/m3 Absorption coefficient 0.070 mm-1 F(000) 704 Theta range for data collection 1.4 to 27.5 deg Limiting indices -6<=h<=7, -38<=k<=38, -14<=l<=7 Reflections collected / unique 17396 / 4512 [R(int) = 0.027] Completeness to theta 27.5 99.0 % Refinement method Full-matrix least-squares on F2
  • 3. R.K Tiwari et al., American International Journal of Research in Formal, Applied & Natural Sciences, 6(2), March-May 2014, pp. 114-118 AIJRFANS 14-259; © 2014, AIJRFANS All Rights Reserved Page 116 Data / restraints / parameters 4512 / 0 / 233 Goodness-of-fit on F2 1.065 Final R indices [I>2sigma (I)] R1 = 0.0683, wR2 = 0.1939 R indices (all data) R1 = 0.0951, wR2 = 0.2146 Largest diff. peak and ho 0.53 and -0.32 e.Å Fig. 2 ORTEP view of molecule Fig. 3 Packing seen down a-axis Fig. 4 Packing seen down b-axis Fig. 5 Packing seen down c-axis Fig. 6 Packing of the unitcell Table 2: Atomic coordinates (x 104 2 x103 ) for non-hydrogen. U (eq) is defined as one third of the trace of the orthogonalized Uij tensor. X Y Z Ueq OW(2) 0.740 (2) 0.2441 (5) 0.139 (2) 0.050 (3) OW(1) 0.743 (2) 0.2414 (5) 0.147 (2) 0.0426 (17) C(12) 1.1656 (5) 0.23898 (10) −0 0 61 3 0.0595 (7) N(1) 0.9532 (3) 0.26658 (6) −0 071 17 0.0447 (5) C(13) 0.8008 (4) 0.24985 (7) −0 17 3 0.0462 (5) C(6) 0.7372 (4) 0.36422 (7) −0 1 0.0523 (6) C(1) 0.8127 (5) 0.34646 (8) −0 1060 0.0522 (6) C(16) 0.7217 (5) 0.12353 (9) −0 1 0.0613 (7) C(15) 0.7940 (5) 0.16986 (9) −0 1 0.0573 (7) C(11) 1.0157 (4) 0.31568 (8) −0 0 0.0541 (6) C(14) 0.7379 (5) 0.20124 (9) −0 1690 3 0.0534 (6) C(17) 0.6573 (5) 0.08516 (9) −0 1 3 0.0645 (7) C(7) 0.8548 (5) 0.35660 (9) −0 319 0.0608 (7) C(8) 0.7725 (7) 0.37409 (11) −0 3 0.0808 (10) C(3) 0.5005 (7) 0.38507 (11) −0 0316 0.0849 (11)
  • 4. R.K Tiwari et al., American International Journal of Research in Formal, Applied & Natural Sciences, 6(2), March-May 2014, pp. 114-118 AIJRFANS 14-259; © 2014, AIJRFANS All Rights Reserved Page 117 C(5) 0.5344 (5) 0.39082 (8) −0 391 3 0.0665 (8) C(18) 0.5693 (6) 0.03833 (9) −0 99 3 0.0725 (9) C(10) 0.4556 (7) 0.40692 (11) −0 3 30 0.0894 (12) C(2) 0.6968 (6) 0.35758 (9) −0 01 1 3 0.0687 (8) C(9) 0.5696 (8) 0.39871 (12) −0 0.0960 (13) C(4) 0.4209 (6) 0.40035 (10) −0 1 07 0.0820 (10) C(21) 0.6751 (15) 0.0120 (2) −0 3 13 7 0.198 (4) C(19) 0.6519 (17) 0.01448 (19) −0 13 9 6 0.217 (5) C(20) 0.3262 (9) 0.03818 (18) −0 7 1 0.311 (8) Table 3: ] b ˚] f - hydrogen atoms C(12)—N(1) 1.491 (3) N(1)—C(13) 1.497 (3) N(1)—C(11) 1.501 (3) C(13)—C(14) 1.485 (3) C(6)—C(7) 1.415 (4) C(6)—C(5) 1.424 (4) C(6)—C(1) 1.432 (4) C(1)—C(2) 1.371 (4) C(1)—C(11) 1.499 (4) C(16)—C(17) 1.190 (4) C(16)—C(15) 1.429 (4) C(15)—C(14) 1.311 (4) C(17)—C(18) 1.471 (4) C(7)—C(8) 1.371 (4) C(8)—C(9) 1.393 (6) C(3)—C(4) 1.349 (6) C(3)—C(2) 1.407 (5) C(5)—C(10) 1.404 (5) C(5)—C(4) 1.414 (5) C(18)—C(20) 1.427 (6) C(18)—C(19) 1.473 (6) C(18)—C(21) 1.505 (7) C(10)—C(9) 1.345 (6) C(7)—C(6)—C(5) 118.2 (3) C(7)—C(6)—C(1) 123.1 (2) C(5)—C(6)—C(1) 118.7 (3) C(2)—C(1)—C(6) 119.6 (3) C(2)—C(1)—C(11) 118.8 (3) C(12)—N(1)—C(13) 112.14 (19) C(12)—N(1)—C(11) 109.24 (19) C(13)—N(1)—C(11) 112.00 (18) C(14)—C(13)—N(1) 112.8 (2) Table 4: Torsion angles [deg] C(12)—N(1)—C(13)—C(14) 56.5 (3) C(11)—N(1)—C(13)—C(14) 179.7 (2) C(7)—C(6)—C(1)—C(2) 176.2 (2) C(5)—C(6)—C(1)—C(2) −3 3 C(7)—C(6)—C(1)—C(11) − 1 3 C(5)—C(6)—C(1)—C(11) 175.9 (2) C(17)—C(16)—C(15)—C(14) 110 (10) C(2)—C(1)—C(11)—N(1) 76.9 (3) C(6)—C(1)—C(11)—N(1) −10 3 C(12)—N(1)—C(11)—C(1) −17 C(13)—N(1)—C(11)—C(1) 56.3 (3) C(16)—C(15)—C(14)—C(13) −17 7 3 N(1)—C(13)—C(14)—C(15) −117 3 C(15)—C(16)—C(17)—C(18) − 16 C(5)—C(6)—C(7)—C(8) −0 7 C(1)—C(6)—C(7)—C(8) 179.2 (2) C(6)—C(7)—C(8)—C(9) −1 C(7)—C(6)—C(5)—C(10) 2.2 (4) C(1)—C(6)—C(5)—C(10) −177 7 (2) C(7)—C(6)—C(5)—C(4) −177 3 C(1)—C(6)—C(5)—C(4) 2.8 (4) C(16)—C(17)—C(18)—C(20) 6 (9) C(16)—C(17)—C(18)—C(19) −11 9 C(16)—C(17)—C(18)—C(21) 129 (9) C(4)—C(5)—C(10)—C(9) 177.9 (3) C(6)—C(5)—C(10)—C(9) −1 6 C(6)—C(1)—C(11) 121.6 (2) C(17)—C(16)—C(15) 178.0 (3) C(14)—C(15)—C(16) 124.9 (3) C(1)—C(11)—N(1) 113.30 (19) C(15)—C(14)—C(13) 123.1 (3) C(16)—C(17)—C(18) 178.0 (3) C(8)—C(7)—C(6) 120.4 (3) C(7)—C(8)—C(9) 120.7 (4) C(4)—C(3)—C(2) 120.0 (3) C(10)—C(5)—C(4) 122.5 (3) C(10)—C(5)—C(6) 118.8 (3) C(4)—C(5)—C(6) 118.7 (3) C(20)—C(18)—C(17) 110.6 (3) C(20)—C(18)—C(19) 111.9 (6) C(17)—C(18)—C(19) 109.9 (3) C(20)—C(18)—C(21) 111.5 (6) C(17)—C(18)—C(21) 109.2 (3) C(19)—C(18)—C(21) 103.4 (6) C(9)—C(10)—C(5) 121.7 (4) C(1)—C(2)—C(3) 121.2 (3) C(10)—C(9)—C(8) 120.2 (3) C(3)—C(4)—C(5) 121.7 (3)
  • 5. R.K Tiwari et al., American International Journal of Research in Formal, Applied & Natural Sciences, 6(2), March-May 2014, pp. 114-118 AIJRFANS 14-259; © 2014, AIJRFANS All Rights Reserved Page 118 C(6)—C(1)—C(2)—C(3) 1.9 (4) C(11)—C(1)—C(2)—C(3) −177 C(4)—C(3)—C(2)—C(1) 1.1 (5) C(5)—C(10)—C(9)—C(8) −0 6 6 C(7)—C(8)—C(9)—C(10) 2.2 (5) C(2)—C(3)—C(4)—C(5) − C(10)—C(5)—C(4)—C(3) −179 3 C(6)—C(5)—C(4)—C(3) 0.3 (4) Table 5: Possible Hydrogen Bonds (Å) D-H D….A H...A ∟D-H......A C(12)-H(12A) C(12 )...OW(2) (1) H(12A)...OW(2) (1) C(12)-H(12A) ...OW(2) (1) 0.960(.003) 3.734(.013) 2.968(.012) 137.65( 0.33) C(12)–H(12B) C(12)...OW(2) (2) H(12B)...OW(2) (2) C(12)-H(12B)...OW(2) (2) 0.960(.003) 3.736(.018) 2.891(.017) 147.41( 0.37) C(12)-H(12B) C(12)...OW(1) (2) H(12B)...OW(1) (2) C(12) -H(12B)...OW(1) (2) 0.960(.003) 3.628(.018) 2.779(.017) 147.76( 0.38) C(13)-H(13B) C(13)...OW(2) (2) H(13B)...OW(2) (2) C(13) –H(13B)...OW(2) (2) 0.970(.003) 3.561(.016) 2.661(.015) 154.50( 0.35) C(13)-H(13B) C(13)...OW(1) (2) H(13B)...OW(1) (2) C(13)-H(13B)...OW(1) (2) 0.970(.003) 3.509(.016) 2.622(.015) 152.17( 0.35) C(7)-H(7) C(7)...OW(2) (2) H(7)...OW(2) (2) C(7)-H(7)...OW(2) (2) 0.930(.003) 3.805(.014) 2.975(.014) 149.33( 0.32) C(7)-H(7) C(7)...OW(1) (2) H(7)...OW(1) (2) C(7)-H(7)...OW(1) (2) 0.930(.003) 3.738(.014) 2.893(.013) 151.68( 0.32) C(13) -H(13A) C(13)...OW(2) (3) H(13A)...OW(2) (3) C(13)-H(13A)...OW(2) (3) 0.970(.003) 3.691(.013) 3.000(.013) 129.29( 0.30) C(13)-H(13A) C(13)...OW(1) (3) H(13A)...OW(1) (3) C(13)-H(13A)...OW(1) (3) 0.970(.003) 3.605(.013) 2.889(.013) 131.42( 0.30) Equivalent positions: ( 1) x+1,+y,+z ( 2) x+1/2,-y+1/2,+z-1/2 ( 3) x-1/2,-y+1/2,+z-1/2