Experimental. Crystal data. C 37 H 38 N 4 O 6 M r = Monoclinic, P2 1 a = (2) Å b = (7) Å c = (2) Å = 112.
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1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN Pheophorbide b ethyl ester from a chlorella vulgaris dietary supplement Experimental Crystal data C 37 H 38 N 4 O 6 M r = Monoclinic, P2 1 a = (2) Å b = (7) Å c = (2) Å = (2) V = (7) Å 3 Z =2 Mo K radiation = 0.09 mm 1 T = 100 (2) K mm Chin Fei Chee, Noorsaadah Abdul Rahman, Sharifuddin M. Zain and Seik Weng Ng* Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia Correspondence seikweng@um.edu.my Received 10 September 2008; accepted 16 September 2008 Key indicators: single-crystal X-ray study; T = 100 K; mean (C C) = Å; R factor = 0.064; wr factor = 0.178; data-to-parameter ratio = 8.3. In the title compound, C 37 H 38 N 4 O 6, four five-membered nitrogen-bearing rings are nearly coplanar. Two N atoms in two these five-membered rings have attached H atoms, which contribute to the formation of intramolecular N HN hydrogen bonds [NN = (5) (6) Å]. Related literature For the crystal structure of pheophorbide a methyl ester, see: Fischer et al. (1972). For another example of a chlorin, see: Senge & Smith (1997). Data collection Bruker SMART APEX diffractometer Absorption correction: none measured reflections Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 438 parameters 3 restraints Table 1 Hydrogen-bond geometry (Å, ) independent reflections 3100 reflections with I > 2(I) R int = H atoms treated by a mixture of independent and constrained refinement max = 0.55 e Å 3 min = 0.38 e Å 3 D HA D H HA DA D HA N1 H1NN (3) 2.48 (9) (6) 111 (7) N1 H1NN (3) 2.42 (8) (6) 127 (8) N3 H3NN (3) 1.99 (4) (5) 139 (5) Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publcif (Westrip, 2008). We thank the University of Malaya (grant No. PS149/ 2007B) for supporting this study. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2447). References Barbour, L. J. (2001). J. Supramol. Chem. 1, Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Fischer, M. S., Templeton, D. H., Zalkin, A. & Calvin, M. (1972). J. Am. Chem. Soc. 94, Senge, M. O. & Smith, K. M. (1997). Acta Cryst. C53, Sheldrick, G. M. (2008). Acta Cryst. A64, Westrip, S. P. (2008). publcif. In preparation. o1986 Chee et al. doi: /s x Acta Cryst. (2008). E64, o1986
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3 Acta Cryst. (2008). E64, o1986 [ doi: /s x ] Pheophorbide b ethyl ester from a chlorella vulgaris dietary supplement C. F. Chee, N. A. Rahman, S. M. Zain and S. W. Ng Experimental A sample of the dietary supplement Chlorenergy (C'est Si Bon Co., USA) (20 g) was dissolved in 100 ml e thanol and 10 ml dilute sulfuric acid (10%, v/v). The mixture was heated at 323 K for 2 h. The solution was cooled and then stirred at room temperature for 3 days under normal day light (light intensity not measured), during which the solution turned green yellowish. The solvent was evaporated to dryness at reduced pressure. The crude product was purified by HPLC on an RP18e semi-preparative column (Merck Chromolith mm) with acetonitrile-water (90:10, v/v) as the eluent. Pheophorbide b ethyl ester was isolated as brownish plates. Single crystals were grown by slow evaporation of a mixture of acetone and chloroform solution. Refinement C-bound H-atoms were placed in calculated positions (C H 0.95 to 0.99 Å) and were included in the refinement in the riding model approximation, with U iso (H) set to U eq (C). The amino H-atoms were located on a difference Fourier map, and were isotropically refined with a distance restraint N H=0.88 (2) Å). In the absence of heavy scatterers, 3452 Friedel pairs were merged in the refinement. Figures Fig. 1. The molecular structure of the title compound showing the atomic numbering and 70% probability displacement ellipsoids. (I) Crystal data C 37 H 38 N 4 O 6 F 000 = 672 M r = Monoclinic, P2 1 Hall symbol: P 2yb D x = Mg m 3 Mo Kα radiation λ = Å a = (2) Å θ = º b = (7) Å c = (2) Å β = (2)º Cell parameters from 3714 reflections µ = 0.09 mm 1 T = 100 (2) K Plate, brown sup-1
4 V = (7) Å 3 Z = mm Data collection Bruker SMART APEX diffractometer Radiation source: fine-focus sealed tube R int = Monochromator: graphite θ max = 27.5º T = 100(2) K θ min = 1.3º ω scans Absorption correction: None 3100 reflections with I > 2σ(I) h = 9 9 k = measured reflections l = independent reflections Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement wr(f 2 ) = w = 1/[σ 2 (F o 2 ) + (0.0986P) P] where P = (F o 2 + 2F c 2 )/3 S = 1.17 (Δ/σ) max = reflections Δρ max = 0.55 e Å parameters Δρ min = 0.38 e Å 3 3 restraints Extinction correction: none Primary atom site location: structure-invariant direct methods Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq O (6) (12) (5) (8) O (6) (13) (6) (9) O (6) (11) (5) (8) O (5) (12) (5) (7) O (5) (12) (4) (7) O (7) (13) (5) (9) N (7) (14) (6) (8) H1N (11) (3) (3) 0.06 (3)* N (6) (13) (5) (8) N (6) (13) (5) (8) H3N (8) (19) (3) (15)* N (6) (13) (5) (8) C (7) (16) (6) (9) C (7) (17) (6) (9) sup-2
5 C (9) (19) (7) (12) H * C (11) (2) (8) (16) H4A * H4B * C (7) (16) (6) (9) C (8) (17) (6) (10) H6A * H6B * H6C * C (7) (16) (6) (9) C (7) (16) (6) (9) H * C (7) (16) (6) (9) C (7) (15) (6) (9) H * C (9) (16) (7) (10) H11A * H11B * H11C * C (7) (16) (6) (9) H * C (7) (15) (6) (9) H13A * H13B * C (8) (16) (7) (10) H14A * H14B * C (8) (16) (7) (10) C (9) (19) (7) (11) H16A * H16B * C (9) (2) (9) (12) H17A * H17B * H17C * C (7) (15) (6) (9) C (7) (15) (6) (9) C (7) (15) (6) (9) H * C (7) (15) (6) (9) C (8) (16) (7) (10) H22A * H22B * H22C * C (7) (16) (7) (9) C (7) (15) (6) (9) C (7) (16) (7) (9) C (7) (16) (6) (9) sup-3
6 C (8) (17) (7) (10) H27A * H27B * H27C * C (7) (16) (6) (9) C (7) (16) (7) (9) H * C (7) (16) (7) (9) C (7) (16) (7) (10) C (8) (17) (7) (10) H32A * H32B * C (9) (2) (9) (12) H33A * H33B * H33C * C (8) (17) (7) (11) C (9) (17) (7) (10) H * C (8) (17) (7) (10) C (8) (16) (7) (10) H * Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 O (18) (19) (17) (15) (14) (14) O (2) (2) (2) (16) (18) (17) O (19) (17) (19) (14) (15) (14) O (16) (18) (18) (14) (14) (14) O (17) (19) (16) (14) (13) (13) O (3) (2) (2) (18) (18) (16) N (19) (19) (19) (15) (16) (15) N (2) (2) (2) (15) (16) (15) N (19) (19) (19) (15) (16) (15) N (19) (2) (19) (15) (16) (15) C (2) (2) (2) (18) (17) (17) C (2) (2) (2) (18) (18) (18) C (3) (3) (2) (2) (2) (2) C (4) (3) (3) (3) (3) (2) C (2) (2) (2) (18) (18) (17) C (2) (3) (2) (19) (18) (18) C (2) (2) (2) (17) (17) (17) C (2) (2) (2) (17) (16) (17) C (2) (2) (2) (18) (17) (17) C (2) (2) (2) (18) (17) (17) C (3) (2) (2) (2) (2) (18) C (2) (2) (2) (17) (17) (17) sup-4
7 C (2) (2) (2) (18) (18) (17) C (3) (2) (2) (19) (19) (18) C (2) (2) (2) (18) (19) (19) C (3) (3) (3) (2) (2) (2) C (3) (3) (3) (2) (2) (2) C (2) (2) (2) (17) (18) (17) C (2) (2) (2) (17) (17) (17) C (2) (2) (2) (18) (17) (16) C (2) (2) (2) (17) (17) (17) C (2) (2) (3) (18) (2) (19) C (2) (2) (2) (18) (18) (18) C (2) (2) (2) (17) (17) (17) C (2) (2) (2) (18) (17) (18) C (2) (2) (2) (18) (18) (18) C (2) (3) (2) (2) (19) (19) C (2) (2) (2) (17) (17) (18) C (2) (2) (2) (17) (18) (18) C (2) (2) (2) (17) (19) (18) C (2) (2) (3) (18) (19) (2) C (2) (3) (3) (2) (2) (2) C (3) (3) (3) (2) (2) (2) C (3) (3) (2) (2) (2) (19) C (3) (2) (2) (2) (2) (19) C (2) (2) (2) (18) (19) (19) C (3) (2) (2) (2) (2) (18) Geometric parameters (Å, ) O1 C (6) C13 H13A O1 C (6) C13 H13B O2 C (6) C14 C (7) O3 C (6) C14 H14A O3 C (6) C14 H14B O4 C (6) C16 C (8) O5 C (6) C16 H16A O6 C (7) C16 H16B N1 C (6) C17 H17A N1 C (6) C17 H17B N1 H1N 0.88 (3) C17 H17C N2 C (6) C18 C (6) N2 C (6) C19 C (7) N3 C (6) C19 C (6) N3 C (6) C20 C (6) N3 H3N 0.88 (3) C20 C (6) N4 C (6) C20 H N4 C (6) C22 H22A C1 C (7) C22 H22B C1 C (6) C22 H22C C2 C (7) C23 C (7) sup-5
8 C2 C (7) C24 C (7) C3 C (9) C24 C (6) C3 H C26 C (6) C4 H4A C26 C (7) C4 H4B C27 H27A C5 C (6) C27 H27B C5 C (7) C27 H27C C6 H6A C28 C (7) C6 H6B C29 C (7) C6 H6C C29 H C7 C (7) C30 C (7) C8 C (6) C31 C (7) C8 H C31 C (7) C9 C (7) C32 C (8) C10 C (7) C32 H32A C10 C (6) C32 H32B C10 H C33 H33A C11 H11A C33 H33B C11 H11B C33 H33C C11 H11C C34 C (7) C12 C (7) C34 C (7) C12 C (6) C35 H C12 H C36 C (7) C13 C (7) C37 H C15 O1 C (4) C16 C17 H17B C21 O3 C (4) H17A C17 H17B C7 N1 C (4) C16 C17 H17C C7 N1 H1N 131 (6) H17A C17 H17C C1 N1 H1N 116 (6) H17B C17 H17C C9 N2 C (4) N2 C18 C (4) C25 N3 C (4) N2 C18 C (4) C25 N3 H3N 135 (4) C19 C18 C (4) C28 N3 H3N 115 (4) C18 C19 C (4) C36 N4 C (4) C18 C19 C (4) C37 C1 N (4) C25 C19 C (4) C37 C1 C (4) C19 C20 C (4) N1 C1 C (4) C19 C20 C (4) C5 C2 C (5) C21 C20 C (4) C5 C2 C (4) C19 C20 H C3 C2 C (5) C21 C20 H C4 C3 C (5) C23 C20 H C4 C3 H O4 C21 O (4) C2 C3 H O4 C21 C (4) C3 C4 H4A O3 C21 C (4) C3 C4 H4B O3 C22 H22A H4A C4 H4B O3 C22 H22B C2 C5 C (4) H22A C22 H22B C2 C5 C (4) O3 C22 H22C C7 C5 C (4) H22A C22 H22C sup-6
9 C5 C6 H6A H22B C22 H22C C5 C6 H6B O5 C23 C (5) H6A C6 H6B O5 C23 C (4) C5 C6 H6C C24 C23 C (4) H6A C6 H6C C26 C24 C (4) H6B C6 H6C C26 C24 C (4) N1 C7 C (4) C25 C24 C (4) N1 C7 C (4) N3 C25 C (5) C8 C7 C (4) N3 C25 C (4) C7 C8 C (4) C19 C25 C (4) C7 C8 H C24 C26 C (4) C9 C8 H C24 C26 C (4) N2 C9 C (4) C28 C26 C (4) N2 C9 C (4) C26 C27 H27A C8 C9 C (4) C26 C27 H27B C9 C10 C (4) H27A C27 H27B C9 C10 C (4) C26 C27 H27C C11 C10 C (4) H27A C27 H27C C9 C10 H H27B C27 H27C C11 C10 H C29 C28 N (4) C12 C10 H C29 C28 C (4) C10 C11 H11A N3 C28 C (4) C10 C11 H11B C28 C29 C (4) H11A C11 H11B C28 C29 H C10 C11 H11C C30 C29 H H11A C11 H11C N4 C30 C (4) H11B C11 H11C N4 C30 C (4) C18 C12 C (4) C29 C30 C (4) C18 C12 C (4) C34 C31 C (4) C13 C12 C (4) C34 C31 C (5) C18 C12 H C30 C31 C (5) C13 C12 H C31 C32 C (4) C10 C12 H C31 C32 H32A C14 C13 C (4) C33 C32 H32A C14 C13 H13A C31 C32 H32B C12 C13 H13A C33 C32 H32B C14 C13 H13B H32A C32 H32B C12 C13 H13B C32 C33 H33A H13A C13 H13B C32 C33 H33B C15 C14 C (4) H33A C33 H33B C15 C14 H14A C32 C33 H33C C13 C14 H14A H33A C33 H33C C15 C14 H14B H33B C33 H33C C13 C14 H14B C31 C34 C (4) H14A C14 H14B C31 C34 C (5) O2 C15 O (5) C36 C34 C (5) O2 C15 C (5) O6 C35 C (5) O1 C15 C (4) O6 C35 H O1 C16 C (5) C34 C35 H sup-7
10 O1 C16 H16A N4 C36 C (5) C17 C16 H16A N4 C36 C (4) O1 C16 H16B C37 C36 C (5) C17 C16 H16B C1 C37 C (5) H16A C16 H16B C1 C37 H C16 C17 H17A C36 C37 H C7 N1 C1 C (5) C19 C20 C21 O (4) C7 N1 C1 C2 0.6 (5) C23 C20 C21 O (4) C37 C1 C2 C (5) C19 C20 C23 O (4) N1 C1 C2 C5 0.0 (5) C21 C20 C23 O (6) C37 C1 C2 C3 4.1 (8) C19 C20 C23 C (4) N1 C1 C2 C (5) C21 C20 C23 C (4) C5 C2 C3 C (7) O5 C23 C24 C (10) C1 C2 C3 C4 9.4 (11) C20 C23 C24 C (6) C3 C2 C5 C (4) O5 C23 C24 C (5) C1 C2 C5 C7 0.5 (5) C20 C23 C24 C (5) C3 C2 C5 C6 4.8 (8) C28 N3 C25 C (5) C1 C2 C5 C (4) C28 N3 C25 C (5) C1 N1 C7 C (4) C18 C19 C25 N3 0.8 (9) C1 N1 C7 C5 0.9 (5) C20 C19 C25 N (5) C2 C5 C7 N1 0.9 (5) C18 C19 C25 C (4) C6 C5 C7 N (4) C20 C19 C25 C (5) C2 C5 C7 C (4) C26 C24 C25 N3 0.1 (5) C6 C5 C7 C8 2.7 (8) C23 C24 C25 N (4) N1 C7 C8 C9 3.0 (8) C26 C24 C25 C (4) C5 C7 C8 C (4) C23 C24 C25 C (5) C18 N2 C9 C (4) C25 C24 C26 C (5) C18 N2 C9 C (5) C23 C24 C26 C (6) C7 C8 C9 N2 0.3 (8) C25 C24 C26 C (4) C7 C8 C9 C (4) C23 C24 C26 C (9) N2 C9 C10 C (4) C25 N3 C28 C (4) C8 C9 C10 C (6) C25 N3 C28 C (5) N2 C9 C10 C (5) C24 C26 C28 C (5) C8 C9 C10 C (4) C27 C26 C28 C (8) C9 C10 C12 C (4) C24 C26 C28 N3 1.2 (5) C11 C10 C12 C (4) C27 C26 C28 N (4) C9 C10 C12 C (4) N3 C28 C29 C (7) C11 C10 C12 C (4) C26 C28 C29 C (4) C18 C12 C13 C (4) C36 N4 C30 C (4) C10 C12 C13 C (5) C36 N4 C30 C (5) C12 C13 C14 C (5) C28 C29 C30 N4 0.2 (7) C16 O1 C15 O2 1.7 (7) C28 C29 C30 C (5) C16 O1 C15 C (4) N4 C30 C31 C (6) C13 C14 C15 O (7) C29 C30 C31 C (5) C13 C14 C15 O (5) N4 C30 C31 C (5) C15 O1 C16 C (6) C29 C30 C31 C (8) C9 N2 C18 C (4) C34 C31 C32 C (7) C9 N2 C18 C (5) C30 C31 C32 C (6) C13 C12 C18 N (4) C30 C31 C34 C (5) sup-8
11 C10 C12 C18 N (5) C32 C31 C34 C (5) C13 C12 C18 C (6) C30 C31 C34 C (5) C10 C12 C18 C (4) C32 C31 C34 C (9) N2 C18 C19 C (7) C31 C34 C35 O (6) C12 C18 C19 C (4) C36 C34 C35 O6 4.9 (9) N2 C18 C19 C (4) C30 N4 C36 C (5) C12 C18 C19 C (7) C30 N4 C36 C (5) C18 C19 C20 C (6) C31 C34 C36 N4 0.3 (6) C25 C19 C20 C (4) C35 C34 C36 N (5) C18 C19 C20 C (4) C31 C34 C36 C (5) C25 C19 C20 C (5) C35 C34 C36 C (8) C22 O3 C21 O4 1.7 (7) N1 C1 C37 C (9) C22 O3 C21 C (4) C2 C1 C37 C (5) C19 C20 C21 O (6) N4 C36 C37 C1 1.1 (9) C23 C20 C21 O (5) C34 C36 C37 C (5) Hydrogen-bond geometry (Å, ) D H A D H H A D A D H A N1 H1N N (3) 2.48 (9) (6) 111 (7) N1 H1N N (3) 2.42 (8) (6) 127 (8) N3 H3N N (3) 1.99 (4) (5) 139 (5) sup-9
12 Fig. 1 sup-10
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