Tricoccin R2. Erratum

Abdul Ajees, A.; Sekar, K.; Parthasarathy, S.; Schenk, H.; Epe, B.; Mondon, A.

doi:10.1107/S010827010002045X

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addenda and errata

STRUCTURAL

CHEMISTRY

ISSN: 2053-2296

Volume 57| Part 4| April 2001| Page 499

https://doi.org/10.1107/S010827010002045X

Free

Tricoccin R2. Erratum

A. Abdul Ajees,^a K. Sekar,^a S. Parthasarathy,^a ^* H. Schenk,^b B. Epe ^c and A. Mondon ^c

^aDepartment of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, ^bLaboratory Voor Kristallografie, Nieuwe Achtergracht 166, 1018 WU, Amsterdam, The Netherlands, and ^cInstitute of Organic Chemistry, University of Kiel, D-2300 Kiel, Olshausenstrasse, Be 40-60, Germany

^*Correspondence e-mail: [email protected]

(Received 6 December 2000; accepted 18 December 2000)

The crystal structure of the title compound, C₂₅H₂₆O₇, was published with erroneous positions for a C atom and the O atom in ring F [Sekar et al. (1996 ). Acta Cryst. (1996), C52, 92–94]. This has now been corrected and leads to a more sensible bond length and angle geometry.

1. Comment

During a comparative study of the molecular structure of Tricoccin R6 (Abdul Ajees et al., 2001 ) with that of the related compound Tricoccin R2 (Sekar et al., 1996) it was found that

the geometry of the molecules in the two structures agreed well except in the region of ring F of Tricoccin R2

. This could be traced to a wrong assignment of two of the atoms in ring F of Tricoccin R2

. That is, the neighbours of atoms C21 and C22 in ring F of Tricoccin R2 are to be taken as O and C atoms, respectively, instead of C and O as in the original report. The structure of Tricoccin R2

thus modified was refined and converged to a lower R value and the final difference Fourier was better. There is now better agreement of the geometry of ring F of Tricoccin R2

with that of Tricoccin R6.

Figure 1

The molecular structure of the title compound with 30% probability displacement ellipsoids

2. Experimental

2.1.1. Crystal data

C₂₅H₂₆O₇
M_r = 438.46
Monoclinic, C2
a = 22.939 (1) Å
b = 6.574 (2) Å
c = 16.481 (2) Å
β = 114.67 (1)°
V = 2258.5 (7) Å³
Z = 4
D_x = 1.289 Mg m⁻³
Cu Kα radiation
Cell parameters from 25 reflections
θ = 20–30°
μ = 0.78 mm⁻¹
T = 293 (2) K
Needle, colourless
0.30 × 0.25 × 0.20 mm

2.1.2. Data collection

Enraf–Nonius CAD-4 diffractometer
ω/2θ scans
Absorption correction: empirical ψ scan (North et al., 1968 )T_min = 0.961, T_max = 0.991
2312 measured reflections
2230 independent reflections
2054 reflections with I > 2σ(I)
R_int = 0.027
θ_max = 70.3°
h = −25 → 27
k = 0 → 8
l = −19 → 0
2 standard reflections frequency: 120 min intensity decay: <1%

2.1.3. Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.103
S = 1.07
2230 reflections
293 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0588P)² + 0.6138P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.12 e Å⁻³
Extinction correction: SHELXL97
Extinction coefficient: 0.0018 (2)
Absolute structure: Flack (1983 )
Flack parameter = 0.1 (3)

Data collection: CAD-4 Software (Enraf–Nonius, 1989 ); cell refinement: SDP (Frenz, 1978 ); data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S010827010002045X/vj1131sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S010827010002045X/vj1131Isup2.hkl

Computing details top

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: SDP (Frenz, 1978); data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997).

(I) top

Crystal data top

C₂₅H₂₆O₇	F(000) = 928
M_r = 438.46	D_x = 1.289 Mg m⁻³
Monoclinic, C2	Cu Kα radiation, λ = 1.54180 Å
a = 22.939 (1) Å	Cell parameters from 25 reflections
b = 6.574 (2) Å	θ = 20–30°
c = 16.481 (2) Å	µ = 0.78 mm⁻¹
β = 114.67 (1)°	T = 293 K
V = 2258.5 (7) Å³	Needle, colourless
Z = 4	0.30 × 0.25 × 0.20 mm

Data collection top

Enraf-Nonius CAD-4 diffractometer	2054 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.027
Graphite monochromator	θ_max = 70.3°, θ_min = 3.0°
ω/2θ scans	h = −25→27
Absorption correction: empirical (using intensity measurements) ψ scan	k = 0→8
T_min = 0.961, T_max = 0.991	l = −19→0
2312 measured reflections	2 standard reflections every 120 min
2230 independent reflections	intensity decay: <1%

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.036	w = 1/[σ²(F_o²) + (0.0588P)² + 0.6138P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.103	(Δ/σ)_max < 0.001
S = 1.07	Δρ_max = 0.27 e Å⁻³
2230 reflections	Δρ_min = −0.12 e Å⁻³
293 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0018 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983)
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.1 (3)

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.5001 (2)	0.3359 (8)	0.1535 (2)	0.0884 (13)
H1	0.4821	0.4590	0.1589	0.106*
C2	0.5380 (3)	0.3143 (15)	0.1124 (3)	0.138 (3)
H2	0.5515	0.4171	0.0854	0.165*
C3	0.55499 (19)	0.0986 (16)	0.1168 (2)	0.136 (3)
C4	0.51095 (12)	−0.0319 (5)	0.35079 (16)	0.0495 (6)
C5	0.51555 (12)	0.1521 (4)	0.29493 (16)	0.0451 (6)
H5	0.4918	0.2628	0.3072	0.054*
C6	0.58606 (12)	0.2103 (6)	0.34162 (16)	0.0543 (7)
H6A	0.5919	0.3549	0.3360	0.065*
H6B	0.6114	0.1356	0.3170	0.065*
C7	0.60510 (12)	0.1507 (5)	0.44081 (16)	0.0506 (7)
C8	0.66748 (11)	0.2699 (4)	0.58414 (15)	0.0432 (6)
C9	0.69709 (11)	0.0774 (4)	0.56993 (15)	0.0453 (6)
H9	0.6873	−0.0349	0.6013	0.054*
C10	0.48957 (12)	0.1400 (5)	0.19060 (16)	0.0529 (7)
C11	0.76878 (11)	0.0952 (5)	0.60159 (16)	0.0517 (7)
H11A	0.7789	0.2061	0.5709	0.062*
H11B	0.7859	−0.0296	0.5888	0.062*
C12	0.79923 (11)	0.1359 (5)	0.70458 (16)	0.0516 (7)
H12A	0.7954	0.0136	0.7349	0.062*
H12B	0.8446	0.1639	0.7240	0.062*
C13	0.76875 (11)	0.3117 (5)	0.73265 (16)	0.0465 (6)
C14	0.70042 (11)	0.3743 (4)	0.67166 (16)	0.0431 (6)
C15	0.66908 (13)	0.4280 (4)	0.73307 (17)	0.0493 (6)
O16	0.71301 (9)	0.4229 (4)	0.82068 (12)	0.0587 (5)
C17	0.77399 (12)	0.3345 (5)	0.82997 (16)	0.0507 (6)
H17	0.8085	0.4311	0.8623	0.061*
C18	0.75748 (14)	0.5110 (5)	0.6846 (2)	0.0596 (7)
H18A	0.7700	0.5225	0.6354	0.072*
H18B	0.7630	0.6341	0.7195	0.072*
C19	0.42104 (14)	0.0723 (7)	0.14383 (18)	0.0683 (9)
H19A	0.4078	0.0792	0.0804	0.102*
H19B	0.3943	0.1595	0.1605	0.102*
H19C	0.4172	−0.0652	0.1606	0.102*
C20	0.78499 (13)	0.1459 (5)	0.88397 (16)	0.0528 (7)
C21	0.74541 (17)	−0.0300 (6)	0.8694 (2)	0.0687 (8)
H21	0.7064	−0.0541	0.8211	0.082*
C22	0.83659 (18)	0.1101 (6)	0.9619 (2)	0.0756 (10)
H22	0.8707	0.2000	0.9880	0.091*
O24	0.83239 (17)	−0.0739 (5)	0.99729 (18)	0.0999 (10)
C23	0.7759 (2)	−0.1549 (7)	0.9400 (3)	0.0874 (12)
H23	0.7601	−0.2800	0.9479	0.105*
O25	0.61416 (9)	0.4682 (4)	0.71455 (14)	0.0655 (6)
O26	0.66502 (8)	0.0429 (4)	0.47372 (11)	0.0558 (5)
O27	0.55533 (8)	0.0248 (4)	0.44137 (11)	0.0595 (6)
C28	0.44694 (13)	−0.0560 (6)	0.3563 (2)	0.0662 (8)
H28A	0.4516	−0.1489	0.4036	0.099*
H28B	0.4158	−0.1082	0.3007	0.099*
H28C	0.4330	0.0738	0.3682	0.099*
C29	0.5324 (2)	−0.2330 (6)	0.3265 (3)	0.0832 (11)
H29A	0.5747	−0.2179	0.3286	0.125*
H29B	0.5031	−0.2720	0.2673	0.125*
H29C	0.5330	−0.3359	0.3681	0.125*
C30	0.61627 (12)	0.3144 (5)	0.50991 (16)	0.0512 (7)
H30	0.5909	0.4297	0.5017	0.061*
O31	0.52773 (10)	−0.0018 (5)	0.16438 (13)	0.0861 (9)
O32	0.58593 (15)	0.0036 (14)	0.08401 (18)	0.219 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.098 (3)	0.100 (3)	0.0397 (16)	−0.021 (2)	0.0024 (17)	0.0130 (19)
C2	0.090 (3)	0.257 (9)	0.047 (2)	−0.057 (5)	0.009 (2)	0.037 (4)
C3	0.056 (2)	0.315 (11)	0.0362 (17)	0.033 (4)	0.0190 (14)	0.017 (4)
C4	0.0511 (13)	0.0536 (16)	0.0412 (12)	0.0019 (13)	0.0167 (11)	−0.0039 (12)
C5	0.0413 (12)	0.0560 (16)	0.0351 (12)	0.0055 (12)	0.0130 (10)	−0.0039 (11)
C6	0.0451 (13)	0.076 (2)	0.0357 (12)	−0.0020 (14)	0.0111 (10)	0.0050 (13)
C7	0.0429 (12)	0.0677 (19)	0.0373 (12)	0.0046 (13)	0.0130 (10)	0.0030 (13)
C8	0.0417 (11)	0.0492 (15)	0.0380 (12)	0.0029 (11)	0.0160 (10)	0.0047 (11)
C9	0.0441 (12)	0.0532 (16)	0.0335 (11)	0.0063 (12)	0.0110 (10)	0.0024 (11)
C10	0.0482 (13)	0.071 (2)	0.0347 (12)	0.0096 (14)	0.0128 (10)	−0.0019 (13)
C11	0.0433 (12)	0.0691 (19)	0.0422 (12)	0.0093 (13)	0.0174 (10)	0.0024 (13)
C12	0.0365 (11)	0.0706 (19)	0.0441 (12)	0.0059 (13)	0.0132 (10)	0.0039 (14)
C13	0.0392 (11)	0.0554 (16)	0.0398 (12)	−0.0049 (11)	0.0114 (10)	0.0011 (12)
C14	0.0412 (11)	0.0427 (14)	0.0424 (12)	−0.0001 (10)	0.0144 (10)	0.0031 (11)
C15	0.0547 (14)	0.0418 (14)	0.0486 (13)	0.0029 (12)	0.0186 (11)	−0.0009 (12)
O16	0.0614 (11)	0.0674 (14)	0.0441 (9)	0.0082 (10)	0.0188 (8)	−0.0053 (10)
C17	0.0443 (12)	0.0588 (17)	0.0410 (13)	−0.0051 (12)	0.0098 (10)	−0.0067 (12)
C18	0.0637 (16)	0.0551 (18)	0.0582 (16)	−0.0135 (15)	0.0235 (13)	0.0033 (14)
C19	0.0568 (15)	0.095 (3)	0.0409 (13)	0.0041 (17)	0.0088 (11)	−0.0081 (16)
C20	0.0542 (14)	0.0654 (18)	0.0383 (12)	0.0036 (14)	0.0188 (11)	−0.0014 (13)
C21	0.0706 (18)	0.073 (2)	0.0688 (19)	−0.0051 (18)	0.0352 (16)	0.0017 (18)
C22	0.082 (2)	0.079 (3)	0.0464 (16)	0.007 (2)	0.0073 (15)	0.0028 (17)
O24	0.135 (2)	0.091 (2)	0.0618 (14)	0.025 (2)	0.0296 (15)	0.0204 (15)
C23	0.131 (4)	0.067 (2)	0.091 (3)	0.007 (2)	0.072 (3)	0.014 (2)
O25	0.0542 (11)	0.0703 (14)	0.0711 (13)	0.0134 (11)	0.0251 (9)	−0.0040 (12)
O26	0.0495 (9)	0.0735 (14)	0.0363 (8)	0.0124 (10)	0.0099 (7)	−0.0062 (9)
O27	0.0553 (10)	0.0818 (15)	0.0365 (8)	−0.0099 (11)	0.0144 (8)	0.0048 (10)
C28	0.0594 (16)	0.082 (2)	0.0561 (16)	−0.0122 (17)	0.0236 (13)	−0.0050 (18)
C29	0.111 (3)	0.062 (2)	0.078 (2)	0.028 (2)	0.041 (2)	0.0074 (19)
C30	0.0467 (13)	0.0605 (18)	0.0420 (13)	0.0115 (13)	0.0142 (10)	0.0068 (13)
O31	0.0720 (13)	0.142 (3)	0.0431 (10)	0.0408 (16)	0.0228 (10)	−0.0083 (14)
O32	0.100 (2)	0.500 (12)	0.0690 (16)	0.110 (5)	0.0482 (16)	0.015 (4)

Geometric parameters (Å, º) top

C1—C2	1.312 (7)	C9—C11	1.508 (3)
C1—C10	1.488 (5)	C10—O31	1.462 (4)
C2—C3	1.464 (11)	C10—C19	1.501 (4)
C3—O32	1.228 (7)	C11—C12	1.566 (3)
C3—O31	1.360 (7)	C12—C13	1.520 (4)
C4—O27	1.461 (3)	C13—C18	1.497 (4)
C4—C28	1.517 (4)	C13—C14	1.523 (3)
C4—C29	1.522 (5)	C13—C17	1.565 (3)
C4—C5	1.550 (4)	C14—C15	1.508 (4)
C5—C6	1.522 (4)	C14—C18	1.527 (4)
C5—C10	1.569 (3)	C15—O25	1.195 (3)
C6—C7	1.556 (3)	C15—O16	1.374 (3)
C7—O27	1.413 (3)	O16—C17	1.463 (3)
C7—O26	1.437 (3)	C17—C20	1.485 (4)
C7—C30	1.509 (4)	C20—C22	1.355 (4)
C8—C30	1.328 (3)	C20—C21	1.427 (5)
C8—C14	1.487 (3)	C21—C23	1.355 (5)
C8—C9	1.500 (4)	C22—O24	1.364 (5)
C9—O26	1.461 (3)	O24—C23	1.354 (6)

C2—C1—C10	112.0 (5)	C9—C11—C12	108.48 (19)
C1—C2—C3	107.4 (5)	C13—C12—C11	114.0 (2)
O32—C3—O31	119.7 (9)	C18—C13—C12	120.3 (2)
O32—C3—C2	131.4 (8)	C18—C13—C14	60.76 (18)
O31—C3—C2	108.8 (4)	C12—C13—C14	118.8 (2)
O27—C4—C28	104.1 (2)	C18—C13—C17	112.4 (2)
O27—C4—C29	109.1 (3)	C12—C13—C17	122.5 (2)
C28—C4—C29	110.7 (3)	C14—C13—C17	105.6 (2)
O27—C4—C5	102.5 (2)	C8—C14—C15	124.6 (2)
C28—C4—C5	115.1 (2)	C8—C14—C13	118.8 (2)
C29—C4—C5	114.3 (2)	C15—C14—C13	105.5 (2)
C6—C5—C4	102.5 (2)	C8—C14—C18	117.7 (2)
C6—C5—C10	113.8 (2)	C15—C14—C18	112.9 (2)
C4—C5—C10	121.5 (2)	C13—C14—C18	58.75 (18)
C5—C6—C7	103.9 (2)	O25—C15—O16	120.4 (2)
O27—C7—O26	110.9 (3)	O25—C15—C14	128.9 (2)
O27—C7—C30	107.2 (2)	O16—C15—C14	110.7 (2)
O26—C7—C30	103.5 (2)	C15—O16—C17	111.70 (19)
O27—C7—C6	106.3 (2)	O16—C17—C20	108.1 (2)
O26—C7—C6	109.0 (2)	O16—C17—C13	105.65 (19)
C30—C7—C6	119.9 (3)	C20—C17—C13	117.1 (2)
C30—C8—C14	133.5 (3)	C13—C18—C14	60.49 (17)
C30—C8—C9	109.0 (2)	C22—C20—C21	105.1 (3)
C14—C8—C9	117.4 (2)	C22—C20—C17	125.1 (3)
O26—C9—C8	104.17 (19)	C21—C20—C17	129.7 (3)
O26—C9—C11	111.71 (19)	C23—C21—C20	106.4 (3)
C8—C9—C11	112.3 (2)	C20—C22—O24	111.7 (4)
O31—C10—C1	102.1 (3)	C23—O24—C22	105.6 (3)
O31—C10—C19	106.7 (3)	O24—C23—C21	111.2 (4)
C1—C10—C19	111.2 (3)	C7—O26—C9	107.59 (18)
O31—C10—C5	110.9 (2)	C7—O27—C4	111.29 (18)
C1—C10—C5	110.7 (3)	C8—C30—C7	110.1 (3)
C19—C10—C5	114.5 (2)	C3—O31—C10	109.7 (5)

References

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Frenz, B. A. (1978). The Enraf–Nonius CAD-4 SDP. Computing in Crystallography, edited by H. Schenk, R. Olthof-Hazekamp, H. van Koningsveld & G. C. Bassi, pp. 64–71. Delft University Press. Google Scholar

North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359. CrossRef IUCr Journals Web of Science Google Scholar

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ISSN: 2053-2296