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Structure and characterization of N-(2-hydroxy-1-naphthylidene)threonine
Journal of Molecular Structure 658 (2003) 207–213 www.elsevier.com/locate/molstruc
Structure and characterization of N-(2-hydroxy-1naphthylidene)threonine ¨ zcana,*, Semra ˙Idea, I˙ffet S¸akıyanb, Elif Logoglub Yusuf O a
Department of Engineering Physics, Hacettepe University, 06532 Beytepe, Ankara, Turkey b Department of Chemistry, Ankara University, 06100 Tandogan, Ankara, Turkey Received 2 December 2002; revised 27 March 2003; accepted 1 July 2003
Abstract Threonine Schiff base derived 2-hydroxy-1-naphthaldehyde and threonine has been isolated and investigated. The stoichiometry of this compound was derived from the results of elemental analyses, IR, 1H-NMR and UV spectroscopic techniques. X-ray diffraction method was also used to obtain the single-crystal structure. The compound crystallizes in the and b ¼ 91ð3Þ8 with Z ¼ 2: The molecule space group P21 with cell dimensions a ¼ 5:109ð2Þ; b ¼ 11:334ð2Þ; c ¼ 11:155ð3Þ A has phenol-imine tautomeric form in the crystal structure. Some of bond lengths and angles found in the molecular structure are distorted due to p-electron delocalization and steric effect of naphthylidene and threonine groups. q 2003 Elsevier B.V. All rights reserved. Keywords: Naphthylidene; Threonine; Schiff base; X-ray; Spectroscopic studies
1. Introduction Amino acids and their derivatives are very important in molecular biology because of their roles in biochemical reactions. We need more information about their molecular structures to learn their functional role in biological systems. The formation of amino acid Schiff base intermediates in reactions of biological importance, transamination, racemization, and decarboxylation is well documented [1]. Recently, years amino acids Schiff bases have been used as ligand in coordination chemistry [2 – 5]. In the literature, some researchers have synthesized amino acid Schiff bases and their metal complexes as * Corresponding author. Fax: þ 90-531-482-0860. ¨ zcan). E-mail address: [email protected] (Y. O 0022-2860/$ - see front matter q 2003 Elsevier B.V. All rights reserved. doi:10.1016/S0022-2860(03)00455-1
a mimic model of some enzymes cofactors [2]. In order to determine interaction between amino acid residue groups and metals, it is necessary more synthesis of model compounds and characterization of their structures. In this work we synthesized threonine Schiff base (Scheme 1) and characterized its structure by elemental analyses, IR, 1H-NMR, and UV spectroscopic techniques and X-ray diffraction method.
2. Experimental 2.1. Reagents and techniques The 1H-NMR spectrum (Fig. 1) was acquired from a Bruker GMbH Dpx-400 MHz High Performance
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hydrogen analyses were obtained by microanalyses on Leco 932 elementer analyzer. Electronic spectra of the Schiff bases were obtained from an Unicam UV2100 UV/Visible spectrophotometer. L -threonine, methanol and n-heptane were purchased from Merck, 2-hydroxy-1-naphthaldehyde was purchased from Aldrich. 2.2. Synthetic procedures
Scheme 1. Chemical diagram of the compound.
Digital FT-NMR spectrometer (SiMe4 with standard). Infrared absorption spectrum (Fig. 2) was obtained from 4000 to 350 cm21 in KBr pellet using a Mattson FT IR 1020 spectrophotometer. Carbon, nitrogen and
2-hydroxy-1-naphthaldehyde (10 mmol 1.72 g) was dissolved in 100 ml methanol and threonine (10 mmol 1.19 g) was added. This solution was refluxed for 3 h and filtered. After 1 day, yellow crystals were obtained and recrystallized from methanol/n-heptane. M.p. 180 8C, yield. Found: C, 65.35; H, 5.67; N, 5.18. Calc. for C15H15NO4: C, 65.93; H, 5.49; N, 5.12.
Fig. 1. 400.1 MHz H-NMR spectra of threonine Schiff base in DMSO-d6.
¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
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Fig. 2. FT-IR spectrum for threonine Schiff base in KBr pellet.
2.3. Crystallography
Table 1 Crystal and relevant X-ray data for the compound
Single crystal which are suitable for X-ray analysis were obtained by recrystallization from methanol/nheptane by slow-diffusion method. All X-ray measurements were made at room temperature on an Enraf-Nonius CAD4 Diffractometer operating in the w=2u scanning mode. Accurate lattice parameters were determined from least-squares refinement of 25 well centered reflection in the range 8:2 # u # 16:48: During data collection, three standard reflections were periodically measured and the results showed no significant intensity variations. The detailed knowledge about crystal and X-ray data for the studied compound were summarized in Table 1. The observed (1041) reflection was used for structure determination and refinement. Corrections for Lorentz and polarization factors were applied to the intensity values. The structure was determined by Direct Methods (SHELXS 97) [6] and refinement by full
Formula Crystal system Space group Molecular weight Crystal size (mm) a b c b V Dc Fð000Þ m(Mo Ka) Ntot N R, Rw ˚ 23) Drmax ; Drmin (e A l(Mo Ka) Weighting details w ¼ 1=½s2 ðFo2 Þ þ 0:0653P2 þ 0:0726P P ¼ ðFo2 þ 2Fc2 Þ=3
C15H15NO4 Monoclinic Z ¼ 2 P21 273.28 0.30 £ 0.25 £ 0.20 ˚ 5.109(2) A ˚ 11.334(2) A ˚ 11.155(3) A 91(3)8 ˚3 645.8(3) A 1.405 g cm3 288 0.103 mm21 1373 1041 ðI . 2sðIÞÞ 0.0438, 0.1058 0.286, 20.274 ˚ 0.71073 A
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matrix least squares methods (SHELXL 97) [7]. All nonH atoms were refined with anisotropic thermal parameters. Due to small positive electron densities in difference Fourier map, all H atom positions were calculated using a riding model and were considered with fixed isotropic U values to obtain more sensitive R value.
3. Results and discussion 3.1. IR, 1H-NMR and UV spectroscopies In the IR spectra of the Schiff base, an intensive band at 3455 cm21 was observed which ascribe threonine residue (OH) group. We also observed the stretching of carboxylic acid group nðCOOHÞ at 1714 cm21. The two bands at 1640 and 1620 were assigned to keto nðCyOÞ and imine nðCyNÞ groups of the Schiff base. It shows probably threonine Schiff base exist as keto-amine and phenol-imine tautomeric forms as glycine, alanine, phenylalanine, histidine, tryptophan Schiff bases with 2-hydroxy-1-naphthaldehyde synthesized in the previously work of Sakiyan et al. [5]. Their structures were determined using elemental analyses, IR, UV, 1H-NMR and found that
they exist in keto-amine, phenol-imine tautomeric forms. Although there have two tautomeric forms in free Schiff base, there exist only in the phenol-imine form in the manganese complexes. In the UV spectrum of this Schiff base, we observed two broad bands at , 300 and , 400 nm. These bands were assigned imine and keto form, respectively, according to the work of Heinert and Martell [8,9]. In the 1H-NMR spectrum of the Schiff base, a single small peak observed at d ¼ 14 ppm were assigned to OH group. The azomethyn (HCyN) proton appears at 9.3 ppm, as a doublet. These results show also that this Schiff base has tautomeric forms. 3.2. X-ray studies The refined molecule is shown in Fig. 3. The title compound is one of the rarely studied free Schiff base compounds and has naphthylidene and threonine molecular groups. These type compounds usually show tautomerism. Keto-amine and phenol-imine tautomerism of these compounds directly effect their activities. Similar compounds which given in Refs. [12 –15] generally include two types of intramolecular hydrogen bonds, either N –H· · ·O or N· · ·H – O and these hydrogen bonds cause to reversible proton
Fig. 3. ORTEP III [10,11] diagram of N-(2-hydroxy-1-naphthylidene)threonine, showing the molecular numbering scheme. Displacement ellipsoids are drawn at 50% probability for all atoms except H, for which they have been set artificially small.
¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
transfer between the amino N atom and the hydroxyl O atom. Briefly, according to Refs. [16,17], these Schiff bases usually have keto-amine tautomeric form, and show photochromism and thermochromism because of the above mentioned intramolecular hydrogen bonds. Similar proton transfer and intramolecular hydrogen bonds have not been determined in the molecular structure of our compound. The cause of this results may be explained by a steric effect between threonine and naphthylidene molecular groups. Due to this steric effect, different intra- and inter-molecular hydrogen bonds have been occurred in the molecular and crystallographic structure. According to the our crystallographic results, the title Schiff base has phenol-imine tautomeric form. There is no proton transfer between the amino N atom and the hydroxyl O atom. The final atomic coordinates and some of structural parameters were given in Tables 2 and 3. All structural parameters related with naphthylidene are as expected. The conformation at the C5yN1 double bond is trans with the torsion angle C6 –C5 – N1 – C1 ¼ 176.3(4)8. Two intra-molecular contacts [N1· · ·C4 ¼ 2.932(7) ˚ ] which observed in the and O2· · ·C3 ¼ 2.785(5) A molecular structure have changed some bond lengths and angles in the threonine group. These changes may be determined by comparing normal values of C –N ˚] [1.465(5)], CyN [1.279(4)] and C – O [1.440(6) A bonds lengths with observed values [18]. The observed values of these bonds are 1.45(1), 1.31(3) ˚ , respectively. The above-mentioned and 1.30(2) A bond lengths may be different from expected values, due to p-electron delocalization. As a result, the slight shortenings of the C2 – O2 and C1 – N1 bonds and the slight elongation of C5yN1 bond were obtained. The bond angles of N1 – C1 – C3 [108(1)], C1 – C3 –C4 [114(1)], C1 – C2 – O2 [112(2)] and C1 – C3 – O3 [107(1)8] were also effected by the mentioned intramolecular contacts. As a result of X-ray conformational analysis, it was shown that C6, C5, N1, C1 atoms; C4, C3, C1, C2 atoms and C1, C2, O1, O2 atoms formed plane 1, plane 2 and plane 3, respectively. The dihedral angles between plane 1 –2, plane 1 –3 and plane 2 –3 were determined as 74(1), 88(2) and 52(1)8. The molecular conformation of naphthylidene together O4 and C11 atoms is slightly distorted planar.
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Table 2 Final atomic coordinates Atom
x=a
y=b
z=c
N1 O1 O2 O3 O4 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 H1 H2 H3 H4 H5 H7 H8 H11 H12 H14 H15A H15B H15C
20.0961(6) 20.3832(6) 20.3713(6) 20.4979(5) 20.2711(6) 20.1235(7) 20.3074(7) 20.2420(7) 20.0747(9) 0.0764(7) 0.0732(7) 0.2478(7) 0.4464(7) 0.5966(8) 0.5558(8) 0.3700(8) 0.2126(8) 0.0214(8) 20.1314(8) 20.1150(7) 20.37042 20.51100 0.65354 0.34664 20.46937 0.00180 20.24985 0.20498 0.04844 20.25988 20.15937 20.05102 0.09268
0.4157(3) 0.2141(3) 0.2186(3) 0.4831(3) 0.5688(3) 0.3630(4) 0.2564(3) 0.4567(4) 0.5655(4) 0.3895(4) 0.4425(3) 0.4014(4) 0.3180(4) 0.2775(4) 0.3172(4) 0.4018(4) 0.4459(4) 0.5348(4) 0.5773(4) 0.5317(3) 0.61880 0.55430 0.28684 0.43076 0.16169 0.56455 0.63731 0.33388 0.33511 0.42249 0.62030 0.60161 0.54402
0.4737(3) 0.4885(2) 0.6891(2) 0.6255(3) 0.3324(3) 0.5915(3) 0.5834(3) 0.6733(3) 0.6880(4) 0.3922(3) 0.2787(3) 0.1856(3) 0.2056(4) 0.1133(4) 20.0026(4) 20.0249(4) 0.0678(4) 0.0452(4) 0.1311(4) 0.2500(4) 0.30382 0.61412 20.06485 20.10235 0.68180 20.03218 0.11297 0.41045 0.61987 0.75221 0.74017 0.61110 0.72201
There are 10 inter-molecular hydrogen bonds, which have types of O – H· · ·O and C –H· · ·O in the crystal structure. The contact distances are changing ˚ which occurred between from 2.50(1) to 3.55(4) A acceptor and donor atoms. The molecular packing of the compound as viewed down the a axis was given in Fig. 4 The 21 symmetry axis pass through the C10 –C11 bond. Translation symmetry in the crystal structure may be easily seen in the unit cell content along a and c axes. According to the general results of the present work, molecular structure of the studied threonine
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Table 3 Some geometrical parameters with estimated standard deviations Bond lengths (A˚) N1–C5 O1–C2 O3–C3 O4–C15
1.31(3) 11.22(2) 1.43(3) 1.30(3)
C1 –C2 C1 –C3 C1 –N1 C2 –O2
1.53(1) 1.53(2) 1.45(1) 1.30(2)
Bond angles (8) O1–C2 –O2 O3–C3 –C4 C1 –C2– O1 C1 –C2– O2 C1 –C3– O3 C1 –N1–C5
125(1) 112(1) 123(2) 112(2) 107(1) 128(1)
C2 –C1 –C3 C2 –C1 –N1 C3 –C1 –N1 C5 –C6 –C15 C6 –C5 –N1 C6 –C15–O4
109(1) 110(1) 108(1) 120(1) 122(1) 120(1)
Torsion angles (8) N1–C1 –C2– O1 N1–C1 –C2– O2 N1–C1 –C3– O3 N1–C1 –C3– C4 C1 –N1–C5– C6 C2 –C1– N1– C5 C2 –C1– C3–O3 C2 –C1– C3–C4
10.2(5) 2169.4(3) 64(4) 261(4) 176.3(4) 291.4(2) 255.8(6) 179.7(2)
C2 –C1 –N1–C5 C3 –C1 –N1–C5 C3 –C1 –C2 –O1 C3 –C1 –C2 –O2 C7 –C6 –C5 –N1 C7 –C6 –C15–O4 C13–C14 –C15–O4 C15–C6 –C5 –N1
291.4(2) 151.7(5) 128.2(2) 252.2(2) 2172.7(3) 2180.2(3) 2174.3(4) 5.7(6)
Fig. 4. A projection of the crystal structure along a axis.
Schiff base has phenol-imine tautomeric form in the crystal phase. In spectroscopic studies, some significant bands which show the presence of tautomerism were also recorded due to some intra and intermolecular hydrogen bonds as a result of p-electron delocalization.
Acknowledgements
We thank the Ankara University Research Foundation (No. 2001 070 5047) for financial support and TUBITAK (The Scientific and Technical Research
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Council of Turkey) for providing spectroscopy laboratory facilities. References [1] P.C. Wilkins, R.G. Wilkins, Inorganic Chemistry in Biology, Oxford University Press, Oxford, 1997, p. 9. [2] M.R. Mahmoud, S.A. El-Gyar, A.A. Moustafa, A. Shaker, Polyhedron 6 (5) (1987) 1017–1020. [3] P.K. Sharma, S.N. Dubey, Proc. Indian Acad. Sci. (Chem. Sci.) 106 (1) (1994) 23 –27. [4] H. Qing-Yu, M. Zhen-Hua, Z. Ya-Me, J. Coord. Chem. 21 (1990) 199–207. [5] I. Sakiyan, N. Gunduz, T. Gunduz, Synth. React. Inorg. Met.Org. Chem. 31 (7) (2001) 1175–1187. [6] G.M. Sheldrick, SHELXS 97, University of Go¨ ttingen, Germany, 1997. [7] G.M. Sheldrick, SHELXS 97, University of Go¨ ttingen, Germany, 1997.
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[8] D. Heinert, A.E. Martell, J. Am. Chem. Soc. 85 (1963) 183 –188. [9] D. Heinert, A.E. Martell, J. Am. Chem. Soc. 85 (1963) 188 –195. [10] L.J.J. Farrugia, Appl. Crystallogr. 30 (1997) 565. [11] L.J. Farrugia, J. Appl. Crystallogr. 32 (1999) 837–838. [12] L. Govindasamy, D. Velmurugan, T.M. Rejendran, Acta Crystallogr. C55 (1999) 1368–1369. [13] A. Elmalı, Y. Elerman, E. Kendi, Acta Crystallogr. C54 (1998) 1137–1139. [14] A. Elmalı, Y. Elerman, I. Svoboda, H. Fuess, Acta Crystallogr. C54 (1998) 974– 976. [15] Y. Elerman, M. Kabak, A. Elmalı, I. Svoboda, Acta Crystallogr. C54 (1998) 128–130. [16] D. Higelin, H. Sixl, Chem. Phys. 77 (1983) 391 –395. [17] M.D. Cohen, G.M.J. Schmidt, S. Flavian, J. Chem. Soc. (1964) 2041–2051. [18] A.G. Orpen, L. Brammer, F.H. Allen, O. Kennard, D.G. Watson, R. Taylor, J. Chem. Soc. Dalton Trans. Suppl. (1989) S1 –S83.
Structure and characterization of N-(2-hydroxy-1naphthylidene)threonine ¨ zcana,*, Semra ˙Idea, I˙ffet S¸akıyanb, Elif Logoglub Yusuf O a
Department of Engineering Physics, Hacettepe University, 06532 Beytepe, Ankara, Turkey b Department of Chemistry, Ankara University, 06100 Tandogan, Ankara, Turkey Received 2 December 2002; revised 27 March 2003; accepted 1 July 2003
Abstract Threonine Schiff base derived 2-hydroxy-1-naphthaldehyde and threonine has been isolated and investigated. The stoichiometry of this compound was derived from the results of elemental analyses, IR, 1H-NMR and UV spectroscopic techniques. X-ray diffraction method was also used to obtain the single-crystal structure. The compound crystallizes in the and b ¼ 91ð3Þ8 with Z ¼ 2: The molecule space group P21 with cell dimensions a ¼ 5:109ð2Þ; b ¼ 11:334ð2Þ; c ¼ 11:155ð3Þ A has phenol-imine tautomeric form in the crystal structure. Some of bond lengths and angles found in the molecular structure are distorted due to p-electron delocalization and steric effect of naphthylidene and threonine groups. q 2003 Elsevier B.V. All rights reserved. Keywords: Naphthylidene; Threonine; Schiff base; X-ray; Spectroscopic studies
1. Introduction Amino acids and their derivatives are very important in molecular biology because of their roles in biochemical reactions. We need more information about their molecular structures to learn their functional role in biological systems. The formation of amino acid Schiff base intermediates in reactions of biological importance, transamination, racemization, and decarboxylation is well documented [1]. Recently, years amino acids Schiff bases have been used as ligand in coordination chemistry [2 – 5]. In the literature, some researchers have synthesized amino acid Schiff bases and their metal complexes as * Corresponding author. Fax: þ 90-531-482-0860. ¨ zcan). E-mail address: [email protected] (Y. O 0022-2860/$ - see front matter q 2003 Elsevier B.V. All rights reserved. doi:10.1016/S0022-2860(03)00455-1
a mimic model of some enzymes cofactors [2]. In order to determine interaction between amino acid residue groups and metals, it is necessary more synthesis of model compounds and characterization of their structures. In this work we synthesized threonine Schiff base (Scheme 1) and characterized its structure by elemental analyses, IR, 1H-NMR, and UV spectroscopic techniques and X-ray diffraction method.
2. Experimental 2.1. Reagents and techniques The 1H-NMR spectrum (Fig. 1) was acquired from a Bruker GMbH Dpx-400 MHz High Performance
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hydrogen analyses were obtained by microanalyses on Leco 932 elementer analyzer. Electronic spectra of the Schiff bases were obtained from an Unicam UV2100 UV/Visible spectrophotometer. L -threonine, methanol and n-heptane were purchased from Merck, 2-hydroxy-1-naphthaldehyde was purchased from Aldrich. 2.2. Synthetic procedures
Scheme 1. Chemical diagram of the compound.
Digital FT-NMR spectrometer (SiMe4 with standard). Infrared absorption spectrum (Fig. 2) was obtained from 4000 to 350 cm21 in KBr pellet using a Mattson FT IR 1020 spectrophotometer. Carbon, nitrogen and
2-hydroxy-1-naphthaldehyde (10 mmol 1.72 g) was dissolved in 100 ml methanol and threonine (10 mmol 1.19 g) was added. This solution was refluxed for 3 h and filtered. After 1 day, yellow crystals were obtained and recrystallized from methanol/n-heptane. M.p. 180 8C, yield. Found: C, 65.35; H, 5.67; N, 5.18. Calc. for C15H15NO4: C, 65.93; H, 5.49; N, 5.12.
Fig. 1. 400.1 MHz H-NMR spectra of threonine Schiff base in DMSO-d6.
¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
209
Fig. 2. FT-IR spectrum for threonine Schiff base in KBr pellet.
2.3. Crystallography
Table 1 Crystal and relevant X-ray data for the compound
Single crystal which are suitable for X-ray analysis were obtained by recrystallization from methanol/nheptane by slow-diffusion method. All X-ray measurements were made at room temperature on an Enraf-Nonius CAD4 Diffractometer operating in the w=2u scanning mode. Accurate lattice parameters were determined from least-squares refinement of 25 well centered reflection in the range 8:2 # u # 16:48: During data collection, three standard reflections were periodically measured and the results showed no significant intensity variations. The detailed knowledge about crystal and X-ray data for the studied compound were summarized in Table 1. The observed (1041) reflection was used for structure determination and refinement. Corrections for Lorentz and polarization factors were applied to the intensity values. The structure was determined by Direct Methods (SHELXS 97) [6] and refinement by full
Formula Crystal system Space group Molecular weight Crystal size (mm) a b c b V Dc Fð000Þ m(Mo Ka) Ntot N R, Rw ˚ 23) Drmax ; Drmin (e A l(Mo Ka) Weighting details w ¼ 1=½s2 ðFo2 Þ þ 0:0653P2 þ 0:0726P P ¼ ðFo2 þ 2Fc2 Þ=3
C15H15NO4 Monoclinic Z ¼ 2 P21 273.28 0.30 £ 0.25 £ 0.20 ˚ 5.109(2) A ˚ 11.334(2) A ˚ 11.155(3) A 91(3)8 ˚3 645.8(3) A 1.405 g cm3 288 0.103 mm21 1373 1041 ðI . 2sðIÞÞ 0.0438, 0.1058 0.286, 20.274 ˚ 0.71073 A
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matrix least squares methods (SHELXL 97) [7]. All nonH atoms were refined with anisotropic thermal parameters. Due to small positive electron densities in difference Fourier map, all H atom positions were calculated using a riding model and were considered with fixed isotropic U values to obtain more sensitive R value.
3. Results and discussion 3.1. IR, 1H-NMR and UV spectroscopies In the IR spectra of the Schiff base, an intensive band at 3455 cm21 was observed which ascribe threonine residue (OH) group. We also observed the stretching of carboxylic acid group nðCOOHÞ at 1714 cm21. The two bands at 1640 and 1620 were assigned to keto nðCyOÞ and imine nðCyNÞ groups of the Schiff base. It shows probably threonine Schiff base exist as keto-amine and phenol-imine tautomeric forms as glycine, alanine, phenylalanine, histidine, tryptophan Schiff bases with 2-hydroxy-1-naphthaldehyde synthesized in the previously work of Sakiyan et al. [5]. Their structures were determined using elemental analyses, IR, UV, 1H-NMR and found that
they exist in keto-amine, phenol-imine tautomeric forms. Although there have two tautomeric forms in free Schiff base, there exist only in the phenol-imine form in the manganese complexes. In the UV spectrum of this Schiff base, we observed two broad bands at , 300 and , 400 nm. These bands were assigned imine and keto form, respectively, according to the work of Heinert and Martell [8,9]. In the 1H-NMR spectrum of the Schiff base, a single small peak observed at d ¼ 14 ppm were assigned to OH group. The azomethyn (HCyN) proton appears at 9.3 ppm, as a doublet. These results show also that this Schiff base has tautomeric forms. 3.2. X-ray studies The refined molecule is shown in Fig. 3. The title compound is one of the rarely studied free Schiff base compounds and has naphthylidene and threonine molecular groups. These type compounds usually show tautomerism. Keto-amine and phenol-imine tautomerism of these compounds directly effect their activities. Similar compounds which given in Refs. [12 –15] generally include two types of intramolecular hydrogen bonds, either N –H· · ·O or N· · ·H – O and these hydrogen bonds cause to reversible proton
Fig. 3. ORTEP III [10,11] diagram of N-(2-hydroxy-1-naphthylidene)threonine, showing the molecular numbering scheme. Displacement ellipsoids are drawn at 50% probability for all atoms except H, for which they have been set artificially small.
¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
transfer between the amino N atom and the hydroxyl O atom. Briefly, according to Refs. [16,17], these Schiff bases usually have keto-amine tautomeric form, and show photochromism and thermochromism because of the above mentioned intramolecular hydrogen bonds. Similar proton transfer and intramolecular hydrogen bonds have not been determined in the molecular structure of our compound. The cause of this results may be explained by a steric effect between threonine and naphthylidene molecular groups. Due to this steric effect, different intra- and inter-molecular hydrogen bonds have been occurred in the molecular and crystallographic structure. According to the our crystallographic results, the title Schiff base has phenol-imine tautomeric form. There is no proton transfer between the amino N atom and the hydroxyl O atom. The final atomic coordinates and some of structural parameters were given in Tables 2 and 3. All structural parameters related with naphthylidene are as expected. The conformation at the C5yN1 double bond is trans with the torsion angle C6 –C5 – N1 – C1 ¼ 176.3(4)8. Two intra-molecular contacts [N1· · ·C4 ¼ 2.932(7) ˚ ] which observed in the and O2· · ·C3 ¼ 2.785(5) A molecular structure have changed some bond lengths and angles in the threonine group. These changes may be determined by comparing normal values of C –N ˚] [1.465(5)], CyN [1.279(4)] and C – O [1.440(6) A bonds lengths with observed values [18]. The observed values of these bonds are 1.45(1), 1.31(3) ˚ , respectively. The above-mentioned and 1.30(2) A bond lengths may be different from expected values, due to p-electron delocalization. As a result, the slight shortenings of the C2 – O2 and C1 – N1 bonds and the slight elongation of C5yN1 bond were obtained. The bond angles of N1 – C1 – C3 [108(1)], C1 – C3 –C4 [114(1)], C1 – C2 – O2 [112(2)] and C1 – C3 – O3 [107(1)8] were also effected by the mentioned intramolecular contacts. As a result of X-ray conformational analysis, it was shown that C6, C5, N1, C1 atoms; C4, C3, C1, C2 atoms and C1, C2, O1, O2 atoms formed plane 1, plane 2 and plane 3, respectively. The dihedral angles between plane 1 –2, plane 1 –3 and plane 2 –3 were determined as 74(1), 88(2) and 52(1)8. The molecular conformation of naphthylidene together O4 and C11 atoms is slightly distorted planar.
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Table 2 Final atomic coordinates Atom
x=a
y=b
z=c
N1 O1 O2 O3 O4 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 H1 H2 H3 H4 H5 H7 H8 H11 H12 H14 H15A H15B H15C
20.0961(6) 20.3832(6) 20.3713(6) 20.4979(5) 20.2711(6) 20.1235(7) 20.3074(7) 20.2420(7) 20.0747(9) 0.0764(7) 0.0732(7) 0.2478(7) 0.4464(7) 0.5966(8) 0.5558(8) 0.3700(8) 0.2126(8) 0.0214(8) 20.1314(8) 20.1150(7) 20.37042 20.51100 0.65354 0.34664 20.46937 0.00180 20.24985 0.20498 0.04844 20.25988 20.15937 20.05102 0.09268
0.4157(3) 0.2141(3) 0.2186(3) 0.4831(3) 0.5688(3) 0.3630(4) 0.2564(3) 0.4567(4) 0.5655(4) 0.3895(4) 0.4425(3) 0.4014(4) 0.3180(4) 0.2775(4) 0.3172(4) 0.4018(4) 0.4459(4) 0.5348(4) 0.5773(4) 0.5317(3) 0.61880 0.55430 0.28684 0.43076 0.16169 0.56455 0.63731 0.33388 0.33511 0.42249 0.62030 0.60161 0.54402
0.4737(3) 0.4885(2) 0.6891(2) 0.6255(3) 0.3324(3) 0.5915(3) 0.5834(3) 0.6733(3) 0.6880(4) 0.3922(3) 0.2787(3) 0.1856(3) 0.2056(4) 0.1133(4) 20.0026(4) 20.0249(4) 0.0678(4) 0.0452(4) 0.1311(4) 0.2500(4) 0.30382 0.61412 20.06485 20.10235 0.68180 20.03218 0.11297 0.41045 0.61987 0.75221 0.74017 0.61110 0.72201
There are 10 inter-molecular hydrogen bonds, which have types of O – H· · ·O and C –H· · ·O in the crystal structure. The contact distances are changing ˚ which occurred between from 2.50(1) to 3.55(4) A acceptor and donor atoms. The molecular packing of the compound as viewed down the a axis was given in Fig. 4 The 21 symmetry axis pass through the C10 –C11 bond. Translation symmetry in the crystal structure may be easily seen in the unit cell content along a and c axes. According to the general results of the present work, molecular structure of the studied threonine
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¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
Table 3 Some geometrical parameters with estimated standard deviations Bond lengths (A˚) N1–C5 O1–C2 O3–C3 O4–C15
1.31(3) 11.22(2) 1.43(3) 1.30(3)
C1 –C2 C1 –C3 C1 –N1 C2 –O2
1.53(1) 1.53(2) 1.45(1) 1.30(2)
Bond angles (8) O1–C2 –O2 O3–C3 –C4 C1 –C2– O1 C1 –C2– O2 C1 –C3– O3 C1 –N1–C5
125(1) 112(1) 123(2) 112(2) 107(1) 128(1)
C2 –C1 –C3 C2 –C1 –N1 C3 –C1 –N1 C5 –C6 –C15 C6 –C5 –N1 C6 –C15–O4
109(1) 110(1) 108(1) 120(1) 122(1) 120(1)
Torsion angles (8) N1–C1 –C2– O1 N1–C1 –C2– O2 N1–C1 –C3– O3 N1–C1 –C3– C4 C1 –N1–C5– C6 C2 –C1– N1– C5 C2 –C1– C3–O3 C2 –C1– C3–C4
10.2(5) 2169.4(3) 64(4) 261(4) 176.3(4) 291.4(2) 255.8(6) 179.7(2)
C2 –C1 –N1–C5 C3 –C1 –N1–C5 C3 –C1 –C2 –O1 C3 –C1 –C2 –O2 C7 –C6 –C5 –N1 C7 –C6 –C15–O4 C13–C14 –C15–O4 C15–C6 –C5 –N1
291.4(2) 151.7(5) 128.2(2) 252.2(2) 2172.7(3) 2180.2(3) 2174.3(4) 5.7(6)
Fig. 4. A projection of the crystal structure along a axis.
Schiff base has phenol-imine tautomeric form in the crystal phase. In spectroscopic studies, some significant bands which show the presence of tautomerism were also recorded due to some intra and intermolecular hydrogen bonds as a result of p-electron delocalization.
Acknowledgements
We thank the Ankara University Research Foundation (No. 2001 070 5047) for financial support and TUBITAK (The Scientific and Technical Research
¨ zcan et al. / Journal of Molecular Structure 658 (2003) 207–213 Y. O
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