Download citation
Download citation
link to html
The title compound, C10H7Cl2NSe, crystallizes with two crystallographically independent mol­ecules in the asymmetric unit. All atoms in each mol­ecule are nearly coplanar, except for H2Cl of the chloro­methyl group. The mol­ecular structure presents two weak intra­molecular C—H...Se and C—H...Cl hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807036409/bh2124sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807036409/bh2124Isup2.hkl
Contains datablock I

CCDC reference: 657870

Key indicators

  • Single-crystal X-ray study
  • T = 296 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.035
  • wR factor = 0.098
  • Data-to-parameter ratio = 19.8

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 300 Deg. PLAT322_ALERT_2_C Check Hybridisation of Se1 in Main Residue . ? PLAT322_ALERT_2_C Check Hybridisation of Se2 in Main Residue . ? PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 1 C10 H7 Cl2 N Se
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

Selenium-containing molecules are of considerable biochemical and pharmacological relevance. A prominent example is the antitumor and antiviral active C-glycosyl selenazole selenazofurin (Koketsu & Ishihara, 2003; Geisler et al., 2004). In order to prepare compounds with higher anticancer activity, we planed to synthesize some selenazole derivatives containing amino acids. By reacting 2-phenyl-1,3-selenazole methanol with glycine in sulfuryl dichloride, we unexpectedly obtained the title compound, (I), and obtained single crystals suitable for X-ray diffraction.

The asymmetric unit of (I) contains two independent molecules, quoted 1 and 2 for Se1 and Se2 containing molecules, respectively (Fig. 1). The dihedral angle between phenyl and selenazole rings are 7.25 (9) and 7.47 (9)° for molecules 1 and 2, respectively. The Se—C distances, 1.852 (4), 1.883 (3) Å as well as the bond angle C—Se—C, 83.79 (14) ° in molecule 1, are slightly different than corresponding bond lengths [1.851 (3) and 1.878 (3) Å] and angle [83.25 (13)°] in molecule 2. The NC and N—C distances in molecule 1 are 1.282 (4) and 1.386 (4) Å; the corresponding distances in molecule 2 are 1.291 (3) and 1.372 (4) Å.

In the asymmetric unit, the dihedral angle between two neighboring phenyl rings is 65.79 (11)°, and angle between two neighboring selenazole rings is 51.12 (9)°. Furthermore, there are weak C—H···Se and C—H···Cl intramolecular hydrogen bonds, involving C6 and Se1, C16 and Se2, C1 and Cl2, C11 and Cl3, forming five-membered rings. Via hydrogen bond interactions, all the skeletal atoms in each independent molecule, except for chloromethyl Cl atoms, are approximately coplanar, with maximum deviations of -0.112 Å for C20 and 0.102 Å for C7.

Related literature top

For related literature, see: Koketsu & Ishihara, 2003; Geisler et al., 2004.

Experimental top

Glycine (5 mmol) was refluxed in sulfuryl dichloride (10 ml) for 6 h., and then 2-phenyl-1,3-selenazole methanol was added to the solution. The mixture was refluxed for 4 h., sulfuryl dichloride was evaporated and the residue was washed with water. The residue was dissolved in ether, giving a yellow solution, which afforded yellow single crystals after 7 days.

Refinement top

All H atom were positioned geometrically and refined using a riding model. Constrained C—H bond lengths: 0.93 (aromatic CH) or 0.97 Å (methylene CH2). isotropic displacement parameters for H atoms: Uiso(H) = 1.2Ueq(carrier C).

Structure description top

Selenium-containing molecules are of considerable biochemical and pharmacological relevance. A prominent example is the antitumor and antiviral active C-glycosyl selenazole selenazofurin (Koketsu & Ishihara, 2003; Geisler et al., 2004). In order to prepare compounds with higher anticancer activity, we planed to synthesize some selenazole derivatives containing amino acids. By reacting 2-phenyl-1,3-selenazole methanol with glycine in sulfuryl dichloride, we unexpectedly obtained the title compound, (I), and obtained single crystals suitable for X-ray diffraction.

The asymmetric unit of (I) contains two independent molecules, quoted 1 and 2 for Se1 and Se2 containing molecules, respectively (Fig. 1). The dihedral angle between phenyl and selenazole rings are 7.25 (9) and 7.47 (9)° for molecules 1 and 2, respectively. The Se—C distances, 1.852 (4), 1.883 (3) Å as well as the bond angle C—Se—C, 83.79 (14) ° in molecule 1, are slightly different than corresponding bond lengths [1.851 (3) and 1.878 (3) Å] and angle [83.25 (13)°] in molecule 2. The NC and N—C distances in molecule 1 are 1.282 (4) and 1.386 (4) Å; the corresponding distances in molecule 2 are 1.291 (3) and 1.372 (4) Å.

In the asymmetric unit, the dihedral angle between two neighboring phenyl rings is 65.79 (11)°, and angle between two neighboring selenazole rings is 51.12 (9)°. Furthermore, there are weak C—H···Se and C—H···Cl intramolecular hydrogen bonds, involving C6 and Se1, C16 and Se2, C1 and Cl2, C11 and Cl3, forming five-membered rings. Via hydrogen bond interactions, all the skeletal atoms in each independent molecule, except for chloromethyl Cl atoms, are approximately coplanar, with maximum deviations of -0.112 Å for C20 and 0.102 Å for C7.

For related literature, see: Koketsu & Ishihara, 2003; Geisler et al., 2004.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SMART (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXTL (Bruker, 2004); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. A view of the molecule of (I) showing the atom-labeling scheme, with displacement ellipsoids drawn at the 30% probability level. dashed lines represent intramolecular hydrogen bonds.
5-Chloro-4-chloromethyl-2-phenyl-1,3-selenazole top
Crystal data top
C10H7Cl2NSeZ = 4
Mr = 291.03F(000) = 568
Triclinic, P1Dx = 1.773 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.1640 (5) ÅCell parameters from 5903 reflections
b = 10.4050 (6) Åθ = 1.6–27.7°
c = 13.7225 (7) ŵ = 3.89 mm1
α = 76.264 (3)°T = 296 K
β = 74.357 (3)°Block, yellow
γ = 86.475 (3)°0.57 × 0.30 × 0.22 mm
V = 1090.39 (11) Å3
Data collection top
Bruker APEX2 area-detector
diffractometer
5021 independent reflections
Radiation source: fine-focus sealed tube3550 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.028
φ and ω scansθmax = 27.7°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1010
Tmin = 0.256, Tmax = 0.423k = 1313
17299 measured reflectionsl = 1717
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0445P)2 + 0.4631P]
where P = (Fo2 + 2Fc2)/3
5021 reflections(Δ/σ)max = 0.001
253 parametersΔρmax = 0.42 e Å3
0 restraintsΔρmin = 0.48 e Å3
Crystal data top
C10H7Cl2NSeγ = 86.475 (3)°
Mr = 291.03V = 1090.39 (11) Å3
Triclinic, P1Z = 4
a = 8.1640 (5) ÅMo Kα radiation
b = 10.4050 (6) ŵ = 3.89 mm1
c = 13.7225 (7) ÅT = 296 K
α = 76.264 (3)°0.57 × 0.30 × 0.22 mm
β = 74.357 (3)°
Data collection top
Bruker APEX2 area-detector
diffractometer
5021 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
3550 reflections with I > 2σ(I)
Tmin = 0.256, Tmax = 0.423Rint = 0.028
17299 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.098H-atom parameters constrained
S = 1.03Δρmax = 0.42 e Å3
5021 reflectionsΔρmin = 0.48 e Å3
253 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Se11.37993 (5)1.00206 (4)0.11871 (3)0.06946 (13)
Se20.72129 (4)0.96216 (3)0.65950 (2)0.06129 (12)
Cl11.2736 (2)1.44955 (11)0.02164 (11)0.1177 (5)
Cl21.43418 (18)1.27694 (13)0.27490 (8)0.1086 (4)
Cl30.56928 (17)0.69066 (11)0.79275 (8)0.1012 (4)
Cl40.70828 (12)0.54767 (9)0.52221 (9)0.0791 (3)
N11.1682 (3)1.1290 (2)0.01349 (19)0.0552 (6)
N20.6747 (3)0.8781 (2)0.49813 (19)0.0500 (6)
C11.1660 (6)1.3615 (3)0.0819 (3)0.0866 (12)
H1A1.04531.35920.04770.104*
H1B1.18111.40750.15400.104*
C21.2296 (4)1.2242 (3)0.0772 (3)0.0601 (8)
C31.3401 (4)1.1821 (3)0.1550 (3)0.0650 (8)
C41.2275 (3)1.0130 (3)0.0093 (2)0.0488 (6)
C51.1829 (4)0.8961 (3)0.0952 (2)0.0498 (7)
C61.2630 (5)0.7759 (3)0.0919 (3)0.0771 (10)
H6A1.34660.76610.03290.093*
C71.2180 (6)0.6693 (4)0.1774 (4)0.0937 (13)
H7A1.27400.58890.17600.112*
C81.0924 (6)0.6819 (4)0.2632 (3)0.0832 (11)
H8A1.06170.60980.31940.100*
C91.0126 (5)0.7990 (4)0.2667 (3)0.0712 (9)
H9A0.92690.80700.32540.085*
C101.0572 (4)0.9069 (3)0.1840 (2)0.0577 (7)
H10A1.00270.98740.18780.069*
C110.5462 (4)0.6569 (3)0.5694 (3)0.0686 (9)
H11A0.47690.68340.52070.082*
H11B0.47330.61070.63530.082*
C120.6184 (3)0.7770 (3)0.5839 (3)0.0543 (7)
C130.6302 (4)0.7979 (3)0.6745 (3)0.0599 (8)
C140.7312 (3)0.9791 (3)0.5186 (2)0.0455 (6)
C150.7991 (3)1.0989 (3)0.4403 (2)0.0464 (6)
C160.8770 (4)1.1978 (3)0.4642 (3)0.0589 (8)
H16A0.88281.19040.53200.071*
C170.9459 (4)1.3072 (3)0.3878 (3)0.0716 (10)
H17A0.99821.37310.40430.086*
C180.9374 (5)1.3189 (3)0.2881 (3)0.0776 (11)
H18A0.98551.39220.23670.093*
C190.8585 (5)1.2234 (4)0.2632 (3)0.0740 (10)
H19A0.85151.23280.19540.089*
C200.7894 (4)1.1132 (3)0.3388 (2)0.0581 (8)
H20A0.73621.04840.32170.070*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Se10.0758 (2)0.0742 (2)0.0559 (2)0.00109 (17)0.00420 (16)0.02466 (17)
Se20.0703 (2)0.0623 (2)0.0538 (2)0.00479 (15)0.01144 (15)0.02474 (15)
Cl10.1783 (13)0.0675 (7)0.1169 (10)0.0122 (7)0.0441 (9)0.0301 (6)
Cl20.1377 (10)0.1113 (9)0.0589 (6)0.0308 (8)0.0132 (6)0.0084 (6)
Cl30.1291 (9)0.0759 (6)0.0670 (6)0.0129 (6)0.0058 (6)0.0052 (5)
Cl40.0805 (6)0.0569 (5)0.1084 (8)0.0072 (4)0.0265 (5)0.0352 (5)
N10.0638 (15)0.0485 (14)0.0533 (15)0.0038 (12)0.0148 (12)0.0136 (12)
N20.0474 (12)0.0482 (14)0.0561 (15)0.0012 (10)0.0112 (11)0.0185 (12)
C10.117 (3)0.055 (2)0.088 (3)0.005 (2)0.040 (2)0.0034 (19)
C20.073 (2)0.0517 (18)0.059 (2)0.0047 (15)0.0263 (16)0.0078 (15)
C30.076 (2)0.070 (2)0.0488 (18)0.0167 (17)0.0182 (16)0.0062 (16)
C40.0501 (15)0.0526 (17)0.0481 (16)0.0009 (13)0.0135 (12)0.0193 (13)
C50.0538 (16)0.0471 (16)0.0545 (17)0.0025 (12)0.0197 (13)0.0160 (13)
C60.089 (2)0.052 (2)0.085 (3)0.0110 (18)0.013 (2)0.0213 (19)
C70.122 (4)0.045 (2)0.116 (4)0.012 (2)0.042 (3)0.014 (2)
C80.113 (3)0.058 (2)0.078 (3)0.017 (2)0.035 (2)0.000 (2)
C90.083 (2)0.073 (2)0.056 (2)0.0168 (19)0.0186 (17)0.0083 (17)
C100.0669 (18)0.0546 (18)0.0531 (18)0.0008 (14)0.0164 (15)0.0142 (15)
C110.0552 (17)0.0511 (18)0.096 (3)0.0055 (14)0.0069 (17)0.0230 (18)
C120.0448 (15)0.0468 (17)0.067 (2)0.0047 (12)0.0049 (13)0.0179 (15)
C130.0588 (18)0.0527 (18)0.0571 (19)0.0058 (14)0.0010 (14)0.0089 (15)
C140.0391 (13)0.0483 (16)0.0517 (16)0.0072 (11)0.0091 (11)0.0217 (13)
C150.0411 (13)0.0422 (15)0.0564 (17)0.0070 (11)0.0096 (12)0.0177 (13)
C160.0584 (17)0.0489 (17)0.073 (2)0.0038 (14)0.0169 (15)0.0215 (16)
C170.065 (2)0.0465 (19)0.103 (3)0.0019 (15)0.020 (2)0.0188 (19)
C180.071 (2)0.0480 (19)0.097 (3)0.0032 (16)0.009 (2)0.0001 (19)
C190.084 (2)0.064 (2)0.065 (2)0.0100 (18)0.0134 (18)0.0054 (18)
C200.0585 (17)0.0553 (18)0.061 (2)0.0048 (14)0.0126 (15)0.0198 (15)
Geometric parameters (Å, º) top
Se1—C31.852 (4)C7—H7A0.9300
Se1—C41.883 (3)C8—C91.351 (5)
Se2—C131.851 (3)C8—H8A0.9300
Se2—C141.878 (3)C9—C101.379 (5)
Cl1—C11.773 (4)C9—H9A0.9300
Cl2—C31.706 (3)C10—H10A0.9300
Cl3—C131.703 (3)C11—C121.490 (4)
Cl4—C111.779 (3)C11—H11A0.9700
N1—C41.282 (4)C11—H11B0.9700
N1—C21.386 (4)C12—C131.341 (4)
N2—C141.291 (3)C14—C151.464 (4)
N2—C121.372 (4)C15—C161.386 (4)
C1—C21.482 (5)C15—C201.389 (4)
C1—H1A0.9700C16—C171.380 (5)
C1—H1B0.9700C16—H16A0.9300
C2—C31.342 (5)C17—C181.365 (6)
C4—C51.464 (4)C17—H17A0.9300
C5—C61.380 (4)C18—C191.371 (5)
C5—C101.388 (4)C18—H18A0.9300
C6—C71.393 (6)C19—C201.381 (5)
C6—H6A0.9300C19—H19A0.9300
C7—C81.364 (6)C20—H20A0.9300
C3—Se1—C483.79 (14)C9—C10—H10A119.8
C13—Se2—C1483.25 (13)C5—C10—H10A119.8
C4—N1—C2113.8 (3)C12—C11—Cl4111.8 (2)
C14—N2—C12113.7 (3)C12—C11—H11A109.3
C2—C1—Cl1112.0 (3)Cl4—C11—H11A109.3
C2—C1—H1A109.2C12—C11—H11B109.3
Cl1—C1—H1A109.2Cl4—C11—H11B109.3
C2—C1—H1B109.2H11A—C11—H11B107.9
Cl1—C1—H1B109.2C13—C12—N2115.9 (3)
H1A—C1—H1B107.9C13—C12—C11125.9 (3)
C3—C2—N1116.1 (3)N2—C12—C11118.1 (3)
C3—C2—C1125.5 (3)C12—C13—Cl3126.1 (3)
N1—C2—C1118.3 (3)C12—C13—Se2112.4 (2)
C2—C3—Cl2126.1 (3)Cl3—C13—Se2121.5 (2)
C2—C3—Se1111.7 (2)N2—C14—C15124.0 (3)
Cl2—C3—Se1122.1 (2)N2—C14—Se2114.8 (2)
N1—C4—C5124.1 (3)C15—C14—Se2121.2 (2)
N1—C4—Se1114.5 (2)C16—C15—C20118.8 (3)
C5—C4—Se1121.3 (2)C16—C15—C14121.7 (3)
C6—C5—C10118.7 (3)C20—C15—C14119.5 (3)
C6—C5—C4122.4 (3)C17—C16—C15120.4 (3)
C10—C5—C4118.9 (3)C17—C16—H16A119.8
C5—C6—C7119.7 (4)C15—C16—H16A119.8
C5—C6—H6A120.2C18—C17—C16120.1 (3)
C7—C6—H6A120.2C18—C17—H17A120.0
C8—C7—C6120.5 (4)C16—C17—H17A120.0
C8—C7—H7A119.7C17—C18—C19120.4 (3)
C6—C7—H7A119.7C17—C18—H18A119.8
C9—C8—C7120.1 (4)C19—C18—H18A119.8
C9—C8—H8A119.9C18—C19—C20120.1 (4)
C7—C8—H8A119.9C18—C19—H19A120.0
C8—C9—C10120.5 (4)C20—C19—H19A120.0
C8—C9—H9A119.7C19—C20—C15120.2 (3)
C10—C9—H9A119.7C19—C20—H20A119.9
C9—C10—C5120.5 (3)C15—C20—H20A119.9
C4—N1—C2—C30.2 (4)C14—N2—C12—C130.0 (4)
C4—N1—C2—C1178.5 (3)C14—N2—C12—C11178.4 (2)
Cl1—C1—C2—C3100.3 (4)Cl4—C11—C12—C13100.8 (3)
Cl1—C1—C2—N181.6 (4)Cl4—C11—C12—N281.0 (3)
N1—C2—C3—Cl2179.5 (2)N2—C12—C13—Cl3179.6 (2)
C1—C2—C3—Cl21.3 (5)C11—C12—C13—Cl31.4 (5)
N1—C2—C3—Se10.4 (4)N2—C12—C13—Se20.2 (3)
C1—C2—C3—Se1177.8 (3)C11—C12—C13—Se2178.1 (2)
C4—Se1—C3—C20.6 (2)C14—Se2—C13—C120.2 (2)
C4—Se1—C3—Cl2179.7 (2)C14—Se2—C13—Cl3179.7 (2)
C2—N1—C4—C5179.6 (3)C12—N2—C14—C15179.6 (2)
C2—N1—C4—Se10.6 (3)C12—N2—C14—Se20.2 (3)
C3—Se1—C4—N10.7 (2)C13—Se2—C14—N20.2 (2)
C3—Se1—C4—C5179.5 (2)C13—Se2—C14—C15179.6 (2)
N1—C4—C5—C6172.8 (3)N2—C14—C15—C16172.1 (3)
Se1—C4—C5—C67.4 (4)Se2—C14—C15—C167.7 (4)
N1—C4—C5—C106.2 (4)N2—C14—C15—C206.4 (4)
Se1—C4—C5—C10173.6 (2)Se2—C14—C15—C20173.8 (2)
C10—C5—C6—C70.8 (5)C20—C15—C16—C171.1 (4)
C4—C5—C6—C7178.2 (3)C14—C15—C16—C17177.4 (3)
C5—C6—C7—C81.7 (6)C15—C16—C17—C180.2 (5)
C6—C7—C8—C91.2 (7)C16—C17—C18—C190.9 (5)
C7—C8—C9—C100.1 (6)C17—C18—C19—C201.1 (6)
C8—C9—C10—C51.1 (5)C18—C19—C20—C150.2 (5)
C6—C5—C10—C90.6 (4)C16—C15—C20—C190.9 (4)
C4—C5—C10—C9179.6 (3)C14—C15—C20—C19177.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1B···Cl20.972.783.213 (5)108
C6—H6A···Se10.932.793.219 (4)109
C11—H11B···Cl30.972.803.222 (4)107
C16—H16A···Se20.932.763.200 (3)110

Experimental details

Crystal data
Chemical formulaC10H7Cl2NSe
Mr291.03
Crystal system, space groupTriclinic, P1
Temperature (K)296
a, b, c (Å)8.1640 (5), 10.4050 (6), 13.7225 (7)
α, β, γ (°)76.264 (3), 74.357 (3), 86.475 (3)
V3)1090.39 (11)
Z4
Radiation typeMo Kα
µ (mm1)3.89
Crystal size (mm)0.57 × 0.30 × 0.22
Data collection
DiffractometerBruker APEX2 area-detector
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.256, 0.423
No. of measured, independent and
observed [I > 2σ(I)] reflections
17299, 5021, 3550
Rint0.028
(sin θ/λ)max1)0.653
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.098, 1.03
No. of reflections5021
No. of parameters253
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.42, 0.48

Computer programs: APEX2 (Bruker, 2004), SMART (Bruker, 2004), SAINT (Bruker, 2004), SHELXTL (Bruker, 2004), SHELXTL.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1B···Cl20.972.783.213 (5)107.7
C6—H6A···Se10.932.793.219 (4)109.3
C11—H11B···Cl30.972.803.222 (4)107.4
C16—H16A···Se20.932.763.200 (3)110.2
 

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds