organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 6| June 2009| Pages o1298-o1299

5-[(3,4-Di­meth­oxy­benzyl)­amino­methyl­ene]-2,2-di­methyl-1,3-dioxane-4,6-dione

aState Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People's Republic of China, bDepartment of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China, and cState Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
*Correspondence e-mail: lirui@scu.edu.cn

(Received 29 April 2009; accepted 8 May 2009; online 14 May 2009)

The title compound, C15H17NO6, is approximately planar, with dihedral angles of 3.11 (4) and 2.12 (4)° between the connecting amino­methyl­ene unit and the planar part of the dioxane ring, and between the dimethoxy­benzyl ring and the amino­methyl­ene group, respectively. The dioxane ring exhibits a half-boat conformation, in which the C atom between the dioxane O atoms is 0.5471 (8) Å out of the plane. The mol­ecule has an intra­molecular N—H⋯O hydrogen bond which may stabilize the planar conformation. In the crystal, weak inter­molecular C—H⋯O hydrogen-bonding contacts, result in the formation of sheets parallel to the ab plane.

Related literature

For the synthesis of related compounds, see: Cassis et al. (1985[Cassis, R., Tapia, R. & Valderrama, J. A. (1985). Synth. Commun. 15, 125-133.]). For the synthesis of related anti­tumor precursors, see Ruchelman et al. (2003[Ruchelman, A. L., Singh, S. K., Ray, A., Wu, X. H., Yang, J. M., Li, T. K., Liu, A., Liu, L. F. & LaVoie, E. J. (2003). Bioorg. Med. Chem. 11, 2061-2073.]). For the structure of 5-(amino­methyl­ene)-2,2-dimethyl-1,3-dioxane-4,6-dione, see: da Silva et al. (2006[Silva, L. E. da, Joussef, A. C., Silva, L. L., Foro, S. & Schmidt, B. (2006). Acta Cryst. E62, o3866-o3867.]). For Meldrum's acid, see: Meldrum (1908[Meldrum, A. N. (1908). J. Chem. Soc. Trans. 93, 598-601.]).

[Scheme 1]

Experimental

Crystal data
  • C15H17NO6

  • Mr = 307.30

  • Monoclinic, P 21 /c

  • a = 6.270 (4) Å

  • b = 12.486 (4) Å

  • c = 19.529 (5) Å

  • β = 106.31 (3)°

  • V = 1467.3 (11) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 292 K

  • 0.44 × 0.38 × 0.18 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • Absorption correction: none

  • 2852 measured reflections

  • 2657 independent reflections

  • 1675 reflections with I > 2σ(I)

  • Rint = 0.008

  • 3 standard reflections every 150 reflections intensity decay: 1.8%

Refinement
  • R[F2 > 2σ(F2)] = 0.056

  • wR(F2) = 0.160

  • S = 1.03

  • 2657 reflections

  • 207 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N⋯O3 0.86 (3) 2.11 (3) 2.744 (3) 130 (2)
C9—H9⋯O4i 0.93 2.40 3.309 (4) 164
C15—H15C⋯O3ii 0.96 2.59 3.528 (4) 166
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: DIFRAC (Gabe & White, 1993[Gabe, E. J. & White, P. S. (1993). DIFRAC. American Crystallographic Association, Pittsburgh Meeting. Abstract PA104.]); cell refinement: DIFRAC; data reduction: NRCVAX (Gabe et al., 1989[Gabe, E. J., Le Page, Y., Charland, J.-P., Lee, F. L. & White, P. S. (1989). J. Appl. Cryst. 22, 384-387.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

The 4(1H)quinolone structure plays an extremely important role in the field of pharmaceutical chemistry. These compounds have been used as precursors for anticancer agents, anti-malarial agents and reversible (H+/K+) ATPase inhibitors (Ruchelman et al.,2003). 5-arylaminomethylene-2,2-dimethyl-1,3-dioxane-4,6-diones are the key intermediates which can be used to synthesize the 4(1H)quinolone derivatives by thermolysis (Cassis et al., 1985).

In the structure of the title molecule (Fig. 1), it is approximately planar with the dihedral angles of 3.11 (4)° and 2.12 (4)° between the connecting aminomethylene unit and the planar part of the dioxane ring, and between the dimethoxybenzyl ring and the aminomethylene group, respectively. Besides, the dioxane ring of the title compound exhibits a half-boat conformation, in which the C atom between the dioxane O atoms is -0.5471 (8) Å out-of-plane.

The intramolecular N—H···O hydrogen bond (Table 1) is stabilizing the planar conformation in the molecule. Intermolecular weak C—H···O hydrogen bonding contacts (Table 1) result in the formation of sheets running parallel to the a-b plane in the crystal structure (Fig. 2).

Related literature top

For the synthesis of related compounds, see: Cassis et al. (1985). For the synthesis of related antitumor precursors, see Ruchelman et al. (2003). For the structure of 5-(aminomethylene)-2,2-dimethyl-1,3-dioxane-4,6-dione, see: da Silva et al. (2006). For Meldrum's acid, see: Meldrum (1908).

Experimental top

A solution of 2,2-dimethyl-1,3-dioxane-4,6-dione (Meldrum's acid) and methylorthoformate was heated to reflux for two hours and immediately the arylamine was added in an equimolar amount relative to Meldrum's acid. The mixture was heated under reflux for another 5–8 h; single recrystallization from methanol gave the corresponding arylaminomethylene derivative as analytically pure material.

Refinement top

H atoms were positioned geometrically (C—H = 0.93–0.98 Å) and refined using a riding model, with Uiso(H) = 1.2–1.5Ueq(C).

Computing details top

Data collection: DIFRAC (Gabe & White, 1993); cell refinement: DIFRAC (Gabe & White, 1993); data reduction: NRCVAX (Gabe et al., 1989); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. A packing diagram of the title compound showing the layer-like aggregation of the title molecules in the unit cell.
5-[(3,4-Dimethoxybenzyl)aminomethylene]-2,2-dimethyl-1,3-dioxane-4,6-dione top
Crystal data top
C15H17NO6F(000) = 648
Mr = 307.30Dx = 1.391 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 6.270 (4) ÅCell parameters from 29 reflections
b = 12.486 (4) Åθ = 4.4–7.7°
c = 19.529 (5) ŵ = 0.11 mm1
β = 106.31 (3)°T = 292 K
V = 1467.3 (11) Å3Block, yellow
Z = 40.44 × 0.38 × 0.18 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.008
Radiation source: fine-focus sealed tubeθmax = 25.4°, θmin = 2.0°
Graphite monochromatorh = 77
ω/2θ scansk = 150
2852 measured reflectionsl = 238
2657 independent reflections3 standard reflections every 150 reflections
1675 reflections with I > 2σ(I) intensity decay: 1.8%
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)] = 0.056Hydrogen site location: mixed
wR(F2) = 0.160H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0954P)2]
where P = (Fo2 + 2Fc2)/3
2657 reflections(Δ/σ)max < 0.001
207 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
C15H17NO6V = 1467.3 (11) Å3
Mr = 307.30Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.270 (4) ŵ = 0.11 mm1
b = 12.486 (4) ÅT = 292 K
c = 19.529 (5) Å0.44 × 0.38 × 0.18 mm
β = 106.31 (3)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.008
2852 measured reflections3 standard reflections every 150 reflections
2657 independent reflections intensity decay: 1.8%
1675 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0560 restraints
wR(F2) = 0.160H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.21 e Å3
2657 reflectionsΔρmin = 0.26 e Å3
207 parameters
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
xyzUiso*/Ueq
O10.0589 (3)0.78796 (12)0.14968 (8)0.0456 (5)
O20.0296 (3)0.60397 (13)0.13307 (9)0.0489 (5)
O30.3798 (3)0.84242 (14)0.22145 (9)0.0522 (5)
O40.2084 (3)0.47579 (14)0.18214 (10)0.0623 (6)
O51.4467 (3)0.80170 (14)0.40934 (10)0.0544 (5)
O61.5852 (3)0.60587 (14)0.42558 (9)0.0503 (5)
N10.7059 (3)0.69339 (19)0.27469 (10)0.0403 (5)
H1N0.677 (4)0.761 (2)0.2721 (13)0.046 (8)*
C10.2969 (4)0.7333 (2)0.08019 (14)0.0523 (7)
H1A0.37970.67670.05130.078*
H1B0.32420.79940.05400.078*
H1C0.34270.74040.12290.078*
C20.0406 (5)0.7062 (3)0.03595 (15)0.0674 (9)
H2A0.19660.69030.05170.101*
H2B0.01870.77490.01310.101*
H2C0.03430.65230.00270.101*
C30.0529 (4)0.70753 (19)0.09947 (12)0.0411 (6)
C40.2670 (4)0.7662 (2)0.19222 (12)0.0389 (6)
C50.3347 (4)0.65633 (19)0.20110 (11)0.0374 (6)
C60.1782 (4)0.5710 (2)0.17241 (13)0.0422 (6)
C70.5461 (4)0.6272 (2)0.24184 (12)0.0398 (6)
H70.57780.55440.24640.048*
C80.9280 (4)0.66471 (19)0.31291 (11)0.0374 (6)
C91.0729 (4)0.74811 (19)0.34299 (11)0.0388 (6)
H91.02190.81840.33840.047*
C101.2914 (4)0.72663 (18)0.37956 (11)0.0392 (6)
C111.3659 (4)0.61937 (18)0.38805 (11)0.0370 (6)
C121.2204 (4)0.5382 (2)0.35779 (12)0.0442 (6)
H121.26960.46760.36260.053*
C131.0014 (4)0.5605 (2)0.32015 (12)0.0445 (6)
H130.90500.50510.30000.053*
C141.3812 (5)0.9112 (2)0.39922 (15)0.0588 (8)
H14A1.33070.92660.34910.088*
H14B1.50560.95620.42120.088*
H14C1.26310.92450.42050.088*
C151.6708 (4)0.4995 (2)0.43247 (14)0.0535 (7)
H15A1.59730.45770.46030.080*
H15B1.82750.50120.45570.080*
H15C1.64510.46810.38600.080*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0390 (10)0.0379 (10)0.0492 (10)0.0012 (8)0.0054 (8)0.0002 (7)
O20.0380 (10)0.0398 (10)0.0585 (11)0.0059 (8)0.0036 (8)0.0011 (8)
O30.0468 (11)0.0371 (10)0.0602 (11)0.0067 (8)0.0054 (9)0.0021 (8)
O40.0517 (12)0.0318 (11)0.0890 (14)0.0007 (8)0.0040 (10)0.0002 (9)
O50.0456 (11)0.0377 (10)0.0634 (11)0.0014 (8)0.0120 (8)0.0020 (8)
O60.0388 (10)0.0459 (11)0.0550 (10)0.0053 (8)0.0052 (8)0.0005 (8)
N10.0345 (12)0.0390 (13)0.0417 (11)0.0005 (9)0.0012 (9)0.0041 (9)
C10.0384 (15)0.0603 (18)0.0493 (15)0.0006 (13)0.0025 (12)0.0020 (13)
C20.0541 (18)0.097 (2)0.0504 (15)0.0023 (17)0.0130 (13)0.0022 (16)
C30.0356 (13)0.0432 (14)0.0392 (12)0.0032 (11)0.0017 (10)0.0001 (11)
C40.0371 (13)0.0408 (14)0.0357 (12)0.0019 (11)0.0050 (10)0.0021 (10)
C50.0334 (13)0.0383 (13)0.0366 (12)0.0023 (10)0.0034 (10)0.0010 (10)
C60.0338 (14)0.0417 (15)0.0471 (14)0.0016 (11)0.0045 (11)0.0025 (11)
C70.0364 (14)0.0424 (14)0.0382 (12)0.0001 (11)0.0063 (11)0.0013 (10)
C80.0329 (13)0.0404 (14)0.0346 (12)0.0006 (11)0.0024 (9)0.0052 (10)
C90.0410 (14)0.0334 (13)0.0377 (12)0.0042 (11)0.0038 (10)0.0017 (10)
C100.0413 (14)0.0378 (14)0.0329 (11)0.0028 (11)0.0011 (10)0.0024 (10)
C110.0335 (13)0.0419 (14)0.0320 (11)0.0059 (11)0.0031 (10)0.0034 (10)
C120.0432 (15)0.0351 (14)0.0492 (14)0.0050 (11)0.0045 (11)0.0021 (11)
C130.0425 (15)0.0371 (14)0.0468 (14)0.0042 (11)0.0011 (11)0.0043 (11)
C140.0604 (18)0.0389 (15)0.0644 (17)0.0048 (13)0.0030 (14)0.0025 (13)
C150.0455 (16)0.0508 (16)0.0572 (15)0.0149 (13)0.0030 (12)0.0028 (13)
Geometric parameters (Å, º) top
O1—C41.363 (3)C2—H2C0.9600
O1—C31.441 (3)C4—C51.432 (3)
O2—C61.376 (3)C5—C71.389 (3)
O2—C31.439 (3)C5—C61.450 (3)
O3—C41.227 (3)C7—H70.9300
O4—C61.211 (3)C8—C131.374 (4)
O5—C101.359 (3)C8—C91.398 (3)
O5—C141.425 (3)C9—C101.382 (3)
O6—C111.375 (3)C9—H90.9300
O6—C151.424 (3)C10—C111.413 (3)
N1—C71.318 (3)C11—C121.380 (3)
N1—C81.428 (3)C12—C131.392 (4)
N1—H1N0.86 (3)C12—H120.9300
C1—C31.504 (4)C13—H130.9300
C1—H1A0.9600C14—H14A0.9600
C1—H1B0.9600C14—H14B0.9600
C1—H1C0.9600C14—H14C0.9600
C2—C31.513 (4)C15—H15A0.9600
C2—H2A0.9600C15—H15B0.9600
C2—H2B0.9600C15—H15C0.9600
C4—O1—C3118.37 (18)N1—C7—C5126.0 (2)
C6—O2—C3118.82 (19)N1—C7—H7117.0
C10—O5—C14117.26 (19)C5—C7—H7117.0
C11—O6—C15117.28 (19)C13—C8—C9120.2 (2)
C7—N1—C8126.4 (2)C13—C8—N1122.7 (2)
C7—N1—H1N117.7 (17)C9—C8—N1117.1 (2)
C8—N1—H1N115.9 (17)C10—C9—C8120.4 (2)
C3—C1—H1A109.5C10—C9—H9119.8
C3—C1—H1B109.5C8—C9—H9119.8
H1A—C1—H1B109.5O5—C10—C9125.1 (2)
C3—C1—H1C109.5O5—C10—C11115.5 (2)
H1A—C1—H1C109.5C9—C10—C11119.5 (2)
H1B—C1—H1C109.5O6—C11—C12125.4 (2)
C3—C2—H2A109.5O6—C11—C10115.3 (2)
C3—C2—H2B109.5C12—C11—C10119.3 (2)
H2A—C2—H2B109.5C11—C12—C13121.0 (2)
C3—C2—H2C109.5C11—C12—H12119.5
H2A—C2—H2C109.5C13—C12—H12119.5
H2B—C2—H2C109.5C8—C13—C12119.7 (2)
O2—C3—O1110.38 (17)C8—C13—H13120.1
O2—C3—C1105.8 (2)C12—C13—H13120.1
O1—C3—C1106.7 (2)O5—C14—H14A109.5
O2—C3—C2110.5 (2)O5—C14—H14B109.5
O1—C3—C2109.8 (2)H14A—C14—H14B109.5
C1—C3—C2113.5 (2)O5—C14—H14C109.5
O3—C4—O1117.1 (2)H14A—C14—H14C109.5
O3—C4—C5125.1 (2)H14B—C14—H14C109.5
O1—C4—C5117.8 (2)O6—C15—H15A109.5
C7—C5—C4121.5 (2)O6—C15—H15B109.5
C7—C5—C6117.6 (2)H15A—C15—H15B109.5
C4—C5—C6120.7 (2)O6—C15—H15C109.5
O4—C6—O2117.6 (2)H15A—C15—H15C109.5
O4—C6—C5127.0 (2)H15B—C15—H15C109.5
O2—C6—C5115.4 (2)
C6—O2—C3—O148.6 (3)C6—C5—C7—N1176.7 (2)
C6—O2—C3—C1163.7 (2)C7—N1—C8—C130.4 (4)
C6—O2—C3—C273.1 (3)C7—N1—C8—C9179.0 (2)
C4—O1—C3—O245.3 (3)C13—C8—C9—C100.7 (4)
C4—O1—C3—C1159.8 (2)N1—C8—C9—C10178.8 (2)
C4—O1—C3—C276.8 (3)C14—O5—C10—C92.9 (4)
C3—O1—C4—O3162.7 (2)C14—O5—C10—C11177.2 (2)
C3—O1—C4—C519.1 (3)C8—C9—C10—O5178.4 (2)
O3—C4—C5—C73.9 (4)C8—C9—C10—C111.7 (3)
O1—C4—C5—C7178.1 (2)C15—O6—C11—C121.5 (3)
O3—C4—C5—C6171.1 (2)C15—O6—C11—C10177.0 (2)
O1—C4—C5—C66.9 (3)O5—C10—C11—O60.3 (3)
C3—O2—C6—O4158.5 (2)C9—C10—C11—O6179.6 (2)
C3—O2—C6—C524.7 (3)O5—C10—C11—C12178.3 (2)
C7—C5—C6—O42.9 (4)C9—C10—C11—C121.9 (4)
C4—C5—C6—O4172.3 (3)O6—C11—C12—C13179.4 (2)
C7—C5—C6—O2179.3 (2)C10—C11—C12—C131.0 (4)
C4—C5—C6—O24.2 (3)C9—C8—C13—C120.2 (4)
C8—N1—C7—C5175.7 (2)N1—C8—C13—C12179.6 (2)
C4—C5—C7—N11.6 (4)C11—C12—C13—C80.0 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O30.86 (3)2.11 (3)2.744 (3)130 (2)
C9—H9···O4i0.932.403.309 (4)164
C15—H15C···O3ii0.962.593.528 (4)166
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+2, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC15H17NO6
Mr307.30
Crystal system, space groupMonoclinic, P21/c
Temperature (K)292
a, b, c (Å)6.270 (4), 12.486 (4), 19.529 (5)
β (°) 106.31 (3)
V3)1467.3 (11)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.44 × 0.38 × 0.18
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2852, 2657, 1675
Rint0.008
(sin θ/λ)max1)0.603
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.056, 0.160, 1.03
No. of reflections2657
No. of parameters207
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.21, 0.26

Computer programs: DIFRAC (Gabe & White, 1993), NRCVAX (Gabe et al., 1989), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O30.86 (3)2.11 (3)2.744 (3)130 (2)
C9—H9···O4i0.932.403.309 (4)164
C15—H15C···O3ii0.962.593.528 (4)166
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+2, y1/2, z+1/2.
 

Acknowledgements

This research was supported financially by the State Key Laboratory of Drug Research (Shanghai Institute of Materia Medica, Chinese Academy of Sciences).

References

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Volume 65| Part 6| June 2009| Pages o1298-o1299
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