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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

2-Amino-6-(2,6-di­fluoro­benzamido)­pyridinium chloride

aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bMalaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Block A, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 20 July 2010; accepted 26 July 2010; online 31 July 2010)

In the cation of the title compound, C12H10F2N3O+·Cl, the dihedral angle between the pyridine and benzene rings is 16.1 (1)°. In the crystal structure, mol­ecules linked into two-dimensional sheets parallel to the bc plane by inter­molecular N—H⋯Cl, C—H⋯Cl and C—H⋯F hydrogen bonds.

Related literature

For general background to 2,6-diflorobenzyl­chloride derivatives, see: Beavo (1995[Beavo, J. A. (1995). Physiol. Rev. 75, 725-748.]); Beavo & Reifsnyder (1990[Beavo, J. A. & Reifsnyder, D. H. (1990). Trends Pharmacol. Sci. 11, 150-155.]); Hidaka & Asano (1976[Hidaka, H. & Asano, T. (1976). Biochim. Biophys. Acta, 429, 485-497.]); Nicholson et al. (1991[Nicholson, C. D., Chaliss, R. A. & Shalid, M. (1991). Trends Pharmacol. Sci. 12, 19-27.]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C12H10F2N3O+·Cl

  • Mr = 285.68

  • Monoclinic, P 21 /c

  • a = 7.3196 (2) Å

  • b = 13.6314 (3) Å

  • c = 12.2892 (3) Å

  • β = 99.755 (1)°

  • V = 1208.44 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.34 mm−1

  • T = 100 K

  • 0.34 × 0.12 × 0.08 mm

Data collection
  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.895, Tmax = 0.972

  • 11996 measured reflections

  • 3524 independent reflections

  • 2628 reflections with I > 2σ(I)

  • Rint = 0.041

Refinement
  • R[F2 > 2σ(F2)] = 0.047

  • wR(F2) = 0.113

  • S = 1.07

  • 3524 reflections

  • 188 parameters

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

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.35 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N1⋯Cl1i 0.84 (3) 2.35 (2) 3.1622 (18) 163 (2)
N2—H1N2⋯Cl1 0.87 (2) 2.41 (2) 3.1678 (17) 146 (2)
N3—H1N3⋯Cl1ii 0.84 (2) 2.39 (2) 3.2140 (17) 166 (2)
N3—H2N3⋯Cl1 0.84 (2) 2.51 (2) 3.2346 (18) 145 (2)
C3—H3A⋯F2iii 0.93 2.52 3.414 (3) 162
C10—H10A⋯Cl1iv 0.93 2.74 3.581 (2) 151
Symmetry codes: (i) -x, -y+1, -z+1; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) [x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (iv) [-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Thr derivatives of 2,6-diflorobenzylchloride involved in the inhibition of phosphodiesterases (PDEs) are enzymes which catalyze PDEs. These derivatives are classified into seven families, five of which, PDE1–PDE5, have been characterized (Beavo, 1995). The hydrolysis of cyclic nucleotides was evaluated according to the methods of Beavo & Reifsnyder (1990); Hidaka & Asano, (1976); Nicholson et al. (1991).

The asymmetric unit of the title compound contains one protonated 2-amino-6-(2,6-difluorobenzamido)pyridin-1-ium cation and one chloride anion (Fig. 1). The cation molecule is twisted with the dihedral angle between the pyridine ring and the benzene ring being 16.1 (1)°. In the crystal structure, molecules are linked into infinite chains along c axis by intermolecular C3—H3A···F2 hydrogen bonds. The chloride anions link these chains into two-dimensional sheets parallel to the bc plane by intermolecular N—H···Cl and C—H···Cl hydrogen bonds (Fig. 2, Table 1).

Related literature top

For general background to 2,6-diflorobenzylchloride derivatives, see: Beavo (1995); Beavo & Reifsnyder (1990); Hidaka & Asano (1976); Nicholson et al. (1991). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).

Experimental top

2,6-Difluorobenzylchloride (0.01 mol, 1.7 g) was added drop-wise into a round bottom flask containing 25 ml mixture of tetrahydrofuran (THF) and 2,6-diamino pyridine (0.01 mol, 1.1 g) with stirring. The mixture was then refluxed for two and a half hours. The oily precipitate formed was filtrated and dissolved in water and then filtrated and evaporated. The green precipitate formed was dissolved in methanol. Green needle-shaped crystals which were formed at room temperature overnight and were filtrated and dried at 333 K.

Refinement top

The N-bound hydrogen atoms were located from a difference Fourier map and refined freely. The remaining H atoms were positioned geometrically [C–H = 0.93 Å and refined using a riding model, with Uiso(H) = 1.2Ueq(C)].

Structure description top

Thr derivatives of 2,6-diflorobenzylchloride involved in the inhibition of phosphodiesterases (PDEs) are enzymes which catalyze PDEs. These derivatives are classified into seven families, five of which, PDE1–PDE5, have been characterized (Beavo, 1995). The hydrolysis of cyclic nucleotides was evaluated according to the methods of Beavo & Reifsnyder (1990); Hidaka & Asano, (1976); Nicholson et al. (1991).

The asymmetric unit of the title compound contains one protonated 2-amino-6-(2,6-difluorobenzamido)pyridin-1-ium cation and one chloride anion (Fig. 1). The cation molecule is twisted with the dihedral angle between the pyridine ring and the benzene ring being 16.1 (1)°. In the crystal structure, molecules are linked into infinite chains along c axis by intermolecular C3—H3A···F2 hydrogen bonds. The chloride anions link these chains into two-dimensional sheets parallel to the bc plane by intermolecular N—H···Cl and C—H···Cl hydrogen bonds (Fig. 2, Table 1).

For general background to 2,6-diflorobenzylchloride derivatives, see: Beavo (1995); Beavo & Reifsnyder (1990); Hidaka & Asano (1976); Nicholson et al. (1991). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with atom labels and 50% probability ellipsoids for non-H atoms.
[Figure 2] Fig. 2. The crystal packing of title compound, viewed down the c axis, showing two 2-D planes parallel to bc plane.
2-Amino-6-(2,6-difluorobenzamido)pyridinium chloride top
Crystal data top
C12H10F2N3O+·ClF(000) = 584
Mr = 285.68Dx = 1.570 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3017 reflections
a = 7.3196 (2) Åθ = 3.4–30.0°
b = 13.6314 (3) ŵ = 0.34 mm1
c = 12.2892 (3) ÅT = 100 K
β = 99.755 (1)°Needle, green
V = 1208.44 (5) Å30.34 × 0.12 × 0.08 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3524 independent reflections
Radiation source: fine-focus sealed tube2628 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
φ and ω scansθmax = 30.0°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 710
Tmin = 0.895, Tmax = 0.972k = 1519
11996 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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.0421P)2 + 0.7252P]
where P = (Fo2 + 2Fc2)/3
3524 reflections(Δ/σ)max < 0.001
188 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = 0.35 e Å3
Crystal data top
C12H10F2N3O+·ClV = 1208.44 (5) Å3
Mr = 285.68Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.3196 (2) ŵ = 0.34 mm1
b = 13.6314 (3) ÅT = 100 K
c = 12.2892 (3) Å0.34 × 0.12 × 0.08 mm
β = 99.755 (1)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3524 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2628 reflections with I > 2σ(I)
Tmin = 0.895, Tmax = 0.972Rint = 0.041
11996 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.37 e Å3
3524 reflectionsΔρmin = 0.35 e Å3
188 parameters
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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
Cl10.00538 (7)0.25071 (3)0.48845 (3)0.02010 (13)
F10.25530 (18)0.41301 (9)0.78112 (10)0.0280 (3)
F20.45736 (17)0.69690 (9)0.61851 (10)0.0250 (3)
O10.3723 (2)0.41722 (10)0.57487 (11)0.0235 (3)
N10.2196 (2)0.55280 (13)0.49862 (13)0.0179 (3)
N20.1692 (2)0.42610 (12)0.36587 (13)0.0174 (3)
N30.1129 (3)0.29372 (13)0.24827 (14)0.0212 (4)
C10.3195 (3)0.50617 (15)0.78901 (16)0.0209 (4)
C20.3485 (3)0.55016 (18)0.89145 (16)0.0267 (5)
H2A0.32190.51700.95300.032*
C30.4181 (3)0.64466 (18)0.90068 (17)0.0284 (5)
H3A0.43960.67500.96950.034*
C40.4564 (3)0.69494 (16)0.80912 (17)0.0245 (4)
H4A0.50630.75780.81560.029*
C50.4181 (3)0.64856 (15)0.70798 (16)0.0193 (4)
C60.3492 (3)0.55372 (14)0.69319 (15)0.0175 (4)
C70.3170 (3)0.50038 (14)0.58476 (15)0.0176 (4)
C80.1933 (3)0.52380 (14)0.38828 (15)0.0164 (4)
C90.1878 (3)0.58888 (15)0.30421 (16)0.0195 (4)
H9A0.20190.65570.31870.023*
C100.1605 (3)0.55403 (15)0.19510 (16)0.0208 (4)
H10A0.15800.59810.13710.025*
C110.1375 (3)0.45590 (15)0.17297 (15)0.0188 (4)
H11A0.12150.43330.10060.023*
C120.1384 (3)0.38928 (14)0.26127 (14)0.0164 (4)
H1N10.181 (3)0.6086 (19)0.512 (2)0.031 (7)*
H1N20.166 (3)0.3855 (18)0.420 (2)0.027 (6)*
H1N30.095 (3)0.2722 (18)0.183 (2)0.030 (7)*
H2N30.105 (3)0.2579 (18)0.303 (2)0.025 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0327 (3)0.0136 (2)0.01412 (19)0.00100 (19)0.00408 (17)0.00081 (17)
F10.0345 (7)0.0215 (7)0.0282 (6)0.0066 (5)0.0053 (5)0.0033 (5)
F20.0321 (7)0.0177 (6)0.0235 (6)0.0045 (5)0.0004 (5)0.0025 (5)
O10.0313 (8)0.0155 (7)0.0210 (7)0.0069 (6)0.0038 (6)0.0023 (6)
N10.0250 (9)0.0120 (8)0.0155 (7)0.0029 (7)0.0005 (6)0.0011 (6)
N20.0245 (9)0.0145 (8)0.0130 (7)0.0002 (7)0.0027 (6)0.0010 (6)
N30.0359 (10)0.0154 (9)0.0124 (7)0.0024 (7)0.0048 (7)0.0008 (7)
C10.0200 (10)0.0200 (11)0.0222 (9)0.0002 (8)0.0020 (8)0.0003 (8)
C20.0256 (11)0.0372 (13)0.0173 (9)0.0028 (10)0.0037 (8)0.0016 (9)
C30.0273 (12)0.0364 (13)0.0205 (9)0.0056 (10)0.0009 (8)0.0120 (9)
C40.0244 (11)0.0202 (11)0.0271 (10)0.0047 (8)0.0011 (8)0.0085 (8)
C50.0214 (10)0.0160 (10)0.0193 (9)0.0018 (8)0.0006 (7)0.0013 (7)
C60.0189 (9)0.0160 (10)0.0166 (8)0.0025 (7)0.0002 (7)0.0019 (7)
C70.0181 (9)0.0167 (10)0.0170 (8)0.0012 (8)0.0003 (7)0.0007 (7)
C80.0175 (9)0.0148 (10)0.0159 (8)0.0007 (7)0.0001 (7)0.0025 (7)
C90.0244 (10)0.0127 (10)0.0208 (9)0.0005 (8)0.0019 (8)0.0008 (7)
C100.0255 (10)0.0183 (10)0.0180 (8)0.0001 (8)0.0025 (8)0.0046 (8)
C110.0233 (10)0.0199 (10)0.0130 (8)0.0012 (8)0.0024 (7)0.0005 (7)
C120.0186 (9)0.0152 (9)0.0150 (8)0.0007 (7)0.0017 (7)0.0007 (7)
Geometric parameters (Å, º) top
F1—C11.352 (2)C2—H2A0.9300
F2—C51.354 (2)C3—C41.386 (3)
O1—C71.217 (2)C3—H3A0.9300
N1—C71.373 (2)C4—C51.380 (3)
N1—C81.394 (2)C4—H4A0.9300
N1—H1N10.84 (3)C5—C61.388 (3)
N2—C121.363 (2)C6—C71.501 (3)
N2—C81.365 (2)C8—C91.357 (3)
N2—H1N20.87 (2)C9—C101.405 (3)
N3—C121.322 (3)C9—H9A0.9300
N3—H1N30.84 (3)C10—C111.370 (3)
N3—H2N30.84 (2)C10—H10A0.9300
C1—C21.378 (3)C11—C121.414 (3)
C1—C61.393 (3)C11—H11A0.9300
C2—C31.383 (3)
C7—N1—C8124.78 (17)C4—C5—C6123.94 (19)
C7—N1—H1N1117.9 (17)C5—C6—C1115.33 (17)
C8—N1—H1N1117.0 (17)C5—C6—C7124.48 (17)
C12—N2—C8123.00 (16)C1—C6—C7120.10 (18)
C12—N2—H1N2117.7 (16)O1—C7—N1123.10 (18)
C8—N2—H1N2119.2 (16)O1—C7—C6122.36 (17)
C12—N3—H1N3117.0 (17)N1—C7—C6114.54 (17)
C12—N3—H2N3120.1 (16)C9—C8—N2119.86 (17)
H1N3—N3—H2N3123 (2)C9—C8—N1122.45 (18)
F1—C1—C2118.17 (18)N2—C8—N1117.68 (16)
F1—C1—C6118.59 (17)C8—C9—C10119.13 (18)
C2—C1—C6123.2 (2)C8—C9—H9A120.4
C1—C2—C3118.5 (2)C10—C9—H9A120.4
C1—C2—H2A120.7C11—C10—C9120.84 (18)
C3—C2—H2A120.7C11—C10—H10A119.6
C2—C3—C4121.09 (19)C9—C10—H10A119.6
C2—C3—H3A119.5C10—C11—C12119.36 (17)
C4—C3—H3A119.5C10—C11—H11A120.3
C5—C4—C3117.8 (2)C12—C11—H11A120.3
C5—C4—H4A121.1N3—C12—N2118.32 (17)
C3—C4—H4A121.1N3—C12—C11123.91 (17)
F2—C5—C4118.02 (18)N2—C12—C11117.77 (17)
F2—C5—C6117.99 (16)
F1—C1—C2—C3178.58 (19)C5—C6—C7—O1131.1 (2)
C6—C1—C2—C32.9 (3)C1—C6—C7—O145.2 (3)
C1—C2—C3—C40.7 (3)C5—C6—C7—N149.3 (3)
C2—C3—C4—C51.7 (3)C1—C6—C7—N1134.4 (2)
C3—C4—C5—F2179.22 (18)C12—N2—C8—C90.2 (3)
C3—C4—C5—C62.1 (3)C12—N2—C8—N1178.56 (18)
F2—C5—C6—C1177.18 (17)C7—N1—C8—C9144.7 (2)
C4—C5—C6—C10.1 (3)C7—N1—C8—N236.5 (3)
F2—C5—C6—C70.7 (3)N2—C8—C9—C101.2 (3)
C4—C5—C6—C7176.40 (19)N1—C8—C9—C10179.89 (18)
F1—C1—C6—C5178.98 (17)C8—C9—C10—C110.8 (3)
C2—C1—C6—C52.5 (3)C9—C10—C11—C121.0 (3)
F1—C1—C6—C72.4 (3)C8—N2—C12—N3178.62 (18)
C2—C1—C6—C7179.1 (2)C8—N2—C12—C112.0 (3)
C8—N1—C7—O19.0 (3)C10—C11—C12—N3178.30 (19)
C8—N1—C7—C6171.45 (18)C10—C11—C12—N22.3 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···Cl1i0.84 (3)2.35 (2)3.1622 (18)163 (2)
N2—H1N2···Cl10.87 (2)2.41 (2)3.1678 (17)146 (2)
N3—H1N3···Cl1ii0.84 (2)2.39 (2)3.2140 (17)166 (2)
N3—H2N3···Cl10.84 (2)2.51 (2)3.2346 (18)145 (2)
C3—H3A···F2iii0.932.523.414 (3)162
C10—H10A···Cl1iv0.932.743.581 (2)151
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1/2, z1/2; (iii) x, y+3/2, z+1/2; (iv) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H10F2N3O+·Cl
Mr285.68
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)7.3196 (2), 13.6314 (3), 12.2892 (3)
β (°) 99.755 (1)
V3)1208.44 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.34
Crystal size (mm)0.34 × 0.12 × 0.08
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.895, 0.972
No. of measured, independent and
observed [I > 2σ(I)] reflections
11996, 3524, 2628
Rint0.041
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.113, 1.07
No. of reflections3524
No. of parameters188
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.37, 0.35

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···Cl1i0.84 (3)2.35 (2)3.1622 (18)163 (2)
N2—H1N2···Cl10.87 (2)2.41 (2)3.1678 (17)146 (2)
N3—H1N3···Cl1ii0.84 (2)2.39 (2)3.2140 (17)166 (2)
N3—H2N3···Cl10.84 (2)2.51 (2)3.2346 (18)145 (2)
C3—H3A···F2iii0.93002.52003.414 (3)162.00
C10—H10A···Cl1iv0.93002.74003.581 (2)151.00
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1/2, z1/2; (iii) x, y+3/2, z+1/2; (iv) x, y+1/2, z+1/2.
 

Footnotes

Thomson Reuters ResearcherID: A-5523-2009.

§Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

NM gratefully acknowledges funding from Universiti Sains Malaysia (USM) under the University Research Grant (No. 1001/PFARMASI/815025). HKF and CSY thank USM for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CSY also thanks USM for the award of a USM Fellowship.

References

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