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Gemcitabine hydro­chloride (2′-deoxy-2′,2′-di­fluoro­cytidine hydro­chloride), C9H12N3F2O4+·Cl, is a β-nucleoside that is of pharmaceutical interest as an antitumor agent. The N atom of the cytidine ring is protonated due to salt formation. The sugar residue adopts a C3′-endo and C4′-exo conformation. In the asymmetric unit, gemcitabine cations and chloride ions are linked by N—H...Cl hydrogen bonds. In the crystal structure, screw-related gemcitabine cations are linked by O—H...O hydrogen bonds to form molecular columns along the c axis and adjacent columns are interlinked by N—H...Cl and O—H...Cl hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803018816/ci6255sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536803018816/ci6255Isup2.hkl
Contains datablock I

CCDC reference: 225693

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.060
  • wR factor = 0.060
  • Data-to-parameter ratio = 10.9

checkCIF/PLATON results

No syntax errors found



Alert level A PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low ....... 0.96 PLAT052_ALERT_1_A (Proper) Absorption Correction Method Missing .. ?
Alert level C PLAT057_ALERT_3_C Correction for Absorption Required RT(exp) = 1.11 PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 5 PLAT431_ALERT_2_C Short Inter HL..A Contact F1 .. O2 = 2.92 Ang. PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 2 Cl
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 67.86 From the CIF: _reflns_number_total 2108 Count of symmetry unique reflns 1283 Completeness (_total/calc) 164.30% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 825 Fraction of Friedel pairs measured 0.643 Are heavy atom types Z>Si present yes
2 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1994); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation, 1995); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: CRYSTALS (Watkin et al., 1996); molecular graphics: CrystalStructure (Rigaku/MSC, 2003); software used to prepare material for publication: CrystalStructure.

2'-deoxy-2',2'-difluorocytidine monohydrochloride top
Crystal data top
C9H12F2N3O4+·ClF(000) = 616.00
Mr = 299.66Dx = 1.659 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2ac 2abCell parameters from 25 reflections
a = 11.4680 (7) Åθ = 22.6–24.8°
b = 15.5987 (9) ŵ = 3.27 mm1
c = 6.706 (2) ÅT = 298 K
V = 1199.6 (4) Å3Block, colourless
Z = 40.50 × 0.50 × 0.40 mm
Data collection top
Rigaku AFC-7S
diffractometer
2032 reflections with F2 > 2σ(F2)
Radiation source: X-ray tubeRint = 0.028
Graphite monochromatorθmax = 67.9°, θmin = 2.8°
ω–2θ scansh = 1313
Absorption correction: ψ scan
(North et al., 1968)
k = 1818
Tmin = 0.175, Tmax = 0.271l = 77
2540 measured reflections3 standard reflections every 150 reflections
2083 independent reflections intensity decay: 1.3%
Refinement top
Refinement on F(Δ/σ)max = 0.041
R[F2 > 2σ(F2)] = 0.060Δρmax = 0.77 e Å3
wR(F2) = 0.060Δρmin = 0.57 e Å3
S = 1.13Extinction correction: Larson (1970), eq. 22
2082 reflectionsExtinction coefficient: 110 (9)
191 parametersAbsolute structure: Flack (1983), 828 Friedel pairs
H atoms treated by a mixture of independent and constrained refinementAbsolute structure parameter: 0.00 (3)
Chebychev polynomial with 3 parameters (Carruthers & Watkin, 1979): 2.0710, 1.3167 and 0.0135
Special details top

Experimental. The scan width was (0.94 + 0.14tanθ)° with an ω scan speed of 16° per minute (up to 5 scans to achieve I/σ(I) > 15). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement using all reflections. The weighted R-factor (wR), goodness of fit (S) and R-factor (gt) are based on F, with F set to zero for negative F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.28824 (8)0.32194 (6)0.4814 (2)0.0519 (3)
F10.2745 (2)0.0581 (2)0.2133 (5)0.0624 (8)
F20.3973 (3)0.0299 (2)0.0220 (4)0.0642 (9)
O20.2558 (2)0.1739 (2)0.0510 (4)0.0414 (9)
O1'0.4719 (2)0.0592 (2)0.4248 (4)0.0405 (8)
O3'0.4475 (2)0.1666 (2)0.3127 (5)0.0449 (9)
O5'0.6978 (2)0.0162 (2)0.4448 (6)0.0587 (13)
N10.4392 (2)0.1239 (2)0.1166 (5)0.0357 (9)
N30.4038 (2)0.2137 (2)0.1546 (5)0.0361 (9)
N40.5456 (3)0.2519 (2)0.3770 (6)0.0473 (12)
C20.3600 (3)0.1713 (2)0.0061 (6)0.0317 (8)
C40.5166 (3)0.2106 (2)0.2169 (6)0.0357 (10)
C50.5958 (3)0.1621 (2)0.0999 (6)0.0377 (12)
C60.5561 (3)0.1200 (2)0.0610 (6)0.0360 (10)
C1'0.3942 (3)0.0638 (2)0.2623 (6)0.0370 (12)
C2'0.3848 (3)0.0274 (2)0.1796 (6)0.0403 (12)
C3'0.4747 (3)0.0792 (2)0.2913 (6)0.0363 (12)
C4'0.4883 (3)0.0290 (2)0.4822 (6)0.0350 (12)
C5'0.6065 (4)0.0360 (3)0.5778 (7)0.0483 (14)
H10.351400.248100.229500.0434*
H20.676100.159600.134600.0450*
H30.608700.086600.138200.0440*
H40.624100.250700.422500.0570*
H50.488500.283200.449100.0570*
H60.319900.082400.307500.0450*
H90.546100.075400.219900.0430*
H100.429700.045400.574600.0422*
H110.616800.093000.624600.0580*
H120.609900.002600.687200.0580*
H130.384 (6)0.169 (4)0.400 (3)0.10 (2)*
H140.709 (5)0.0425 (13)0.460 (10)0.10 (2)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0417 (5)0.0547 (6)0.0594 (7)0.0008 (4)0.0157 (5)0.0127 (5)
F10.0353 (12)0.0560 (10)0.096 (2)0.0140 (10)0.0137 (13)0.0210 (10)
F20.096 (2)0.0560 (10)0.0406 (13)0.0140 (10)0.0130 (10)0.0013 (12)
O20.0243 (11)0.0478 (13)0.052 (2)0.0051 (10)0.0004 (10)0.0037 (12)
O1'0.0440 (10)0.0345 (12)0.043 (2)0.0044 (10)0.0051 (12)0.0029 (10)
O3'0.0438 (13)0.0309 (11)0.060 (2)0.0003 (10)0.0000 (10)0.0007 (13)
O5'0.0330 (13)0.058 (2)0.085 (3)0.0011 (12)0.0030 (10)0.015 (2)
N10.0266 (13)0.0324 (13)0.048 (2)0.0028 (11)0.0010 (13)0.0075 (13)
N30.0292 (13)0.0312 (13)0.048 (2)0.0024 (11)0.0036 (13)0.0063 (12)
N40.037 (2)0.048 (2)0.057 (2)0.0000 (10)0.005 (2)0.014 (2)
C20.0290 (10)0.0260 (10)0.040 (2)0.0015 (11)0.0010 (10)0.001 (2)
C40.029 (2)0.0290 (10)0.049 (2)0.0026 (13)0.002 (2)0.0020 (10)
C50.026 (2)0.037 (2)0.050 (2)0.0023 (13)0.000 (2)0.000 (2)
C60.0230 (10)0.034 (2)0.051 (2)0.0041 (13)0.001 (2)0.007 (2)
C1'0.030 (2)0.041 (2)0.040 (2)0.0020 (10)0.002 (2)0.008 (2)
C2'0.037 (2)0.047 (2)0.037 (2)0.010 (2)0.000 (2)0.004 (2)
C3'0.030 (2)0.036 (2)0.043 (2)0.0002 (13)0.005 (2)0.001 (2)
C4'0.033 (2)0.034 (2)0.038 (2)0.0018 (13)0.004 (2)0.006 (2)
C5'0.048 (2)0.045 (2)0.052 (3)0.006 (2)0.010 (2)0.000 (2)
Geometric parameters (Å, º) top
F1—C2'1.371 (4)N4—H40.95
F2—C2'1.360 (5)N4—H50.95
O2—C21.233 (4)C4—C51.419 (5)
O1'—C1'1.409 (5)C5—C61.343 (5)
O1'—C4'1.441 (4)C1'—C2'1.531 (5)
O3'—C3'1.406 (4)C2'—C3'1.509 (5)
O5'—C5'1.410 (6)C3'—C4'1.509 (5)
O3'—H130.94 (5)C4'—C5'1.503 (6)
O5'—H140.93 (2)C5—H20.95
N1—C61.393 (4)C6—H30.95
N1—C21.386 (5)C1'—H60.95
N1—C1'1.449 (5)C3'—H90.95
N3—C41.360 (4)C4'—H100.95
N3—C21.361 (5)C5'—H110.95
N4—C41.295 (5)C5'—H120.95
N3—H10.95
Cl1···N33.068 (3)N4···Cl13.224 (4)
Cl1···N43.224 (4)N4···Cl1xiv3.158 (4)
Cl1···C43.608 (4)N4···O3'iii3.187 (5)
Cl1···N4i3.158 (4)C2···F23.173 (5)
Cl1···C5i3.580 (4)C2···F1vi3.058 (5)
Cl1···O5'ii3.212 (3)C4···O3'iv3.345 (5)
Cl1···H12.1691C4···Cl13.608 (4)
Cl1···H52.3846C4···O1'vii3.408 (5)
Cl1···H2i2.8927C5···Cl1xiv3.580 (4)
Cl1···H4i2.2896C5···O2xii3.165 (4)
Cl1···H14ii2.31 (3)C5···O5'xiii3.297 (4)
Cl1···H9iii2.9549C5···O3'iv3.331 (5)
Cl1···H11iv2.9447C6···F23.016 (5)
F1···O3'2.692 (4)C6···O5'xiii3.346 (4)
F1···C2v3.058 (5)C6···C3'3.593 (5)
F1···F2v2.986 (4)C3'···C63.593 (5)
F1···O2v2.918 (4)C2···H13vi2.89 (7)
F2···C63.016 (5)C4···H13iv3.06 (5)
F2···O3'3.149 (4)C5···H12vii2.8731
F2···N12.617 (4)C5···H13iv2.97 (6)
F2···C23.173 (5)H1···Cl12.1691
F2···F1vi2.986 (4)H1···H52.2227
F1···H132.48 (6)H2···H42.4703
F2···H10vii2.7413H2···O5'xiii2.7163
F2···H6vi2.8605H2···Cl1xiv2.8927
O2···F1vi2.918 (4)H2···O2xii2.8098
O2···O3'vi2.829 (4)H3···O1'2.5175
O2···C5ii3.165 (4)H3···O5'2.8005
O1'···C4viii3.408 (5)H3···H142.5403
O1'···O5'2.848 (4)H3···O5'xiii2.7950
O3'···O2v2.829 (4)H4···H22.4703
O3'···F12.692 (4)H4···Cl1xiv2.2896
O3'···C5ix3.331 (5)H5···Cl12.3846
O3'···F23.149 (4)H5···H12.2227
O3'···N4x3.187 (5)H5···O3'iii2.6641
O3'···C4ix3.345 (5)H6···O22.3529
O5'···C5xi3.297 (4)H6···F2v2.8605
O5'···Cl1xii3.212 (3)H9···O5'2.4807
O5'···O1'2.848 (4)H9···Cl1x2.9549
O5'···C6xi3.346 (4)H10···F2viii2.7413
O2···H62.3529H10···H132.3158
O2···H13vi1.90 (6)H11···Cl1ix2.9447
O2···H2ii2.8098H12···C5viii2.8731
O1'···H142.74 (6)H12···O5'xi2.8094
O1'···H32.5175H13···F12.48 (6)
O3'···H5x2.6641H13···H102.3158
O5'···H92.4807H13···O2v1.90 (6)
O5'···H2xi2.7163H13···C2v2.89 (7)
O5'···H3xi2.7950H13···C4ix3.06 (5)
O5'···H12xiii2.8094H13···C5ix2.97 (6)
O5'···H32.8005H14···O1'2.74 (6)
N1···F22.617 (4)H14···H32.5403
N3···Cl13.068 (3)H14···Cl1xii2.31 (3)
C1'—O1'—C4'109.7 (3)F2—C2'—C1'112.3 (3)
C3'—O3'—H13106 (4)F2—C2'—C3'114.0 (3)
C5'—O5'—H14104 (4)O3'—C3'—C2'114.7 (3)
C2—N1—C1'118.2 (3)O3'—C3'—C4'116.1 (3)
C6—N1—C1'119.7 (3)C2'—C3'—C4'102.4 (3)
C2—N1—C6120.7 (3)O1'—C4'—C3'104.8 (3)
C2—N3—C4125.2 (3)O1'—C4'—C5'107.5 (3)
C2—N3—H1117.40C3'—C4'—C5'114.7 (3)
C4—N3—H1117.36O5'—C5'—C4'112.6 (4)
H4—N4—H5119.99C4—C5—H2120.44
C4—N4—H5120.06C6—C5—H2120.34
C4—N4—H4119.95N1—C6—H3119.28
O2—C2—N3122.4 (3)C5—C6—H3119.38
O2—C2—N1121.5 (3)O1'—C1'—H6109.63
N1—C2—N3116.2 (3)N1—C1'—H6109.70
N3—C4—N4118.8 (3)C2'—C1'—H6109.65
N3—C4—C5117.3 (3)O3'—C3'—H9107.64
N4—C4—C5124.0 (3)C2'—C3'—H9107.77
C4—C5—C6119.2 (3)C4'—C3'—H9107.82
N1—C6—C5121.3 (3)O1'—C4'—H10109.83
O1'—C1'—N1109.2 (3)C3'—C4'—H10109.93
O1'—C1'—C2'106.1 (3)C5'—C4'—H10109.90
N1—C1'—C2'112.5 (3)O5'—C5'—H11108.76
C1'—C2'—C3'105.6 (3)O5'—C5'—H12108.62
F1—C2'—F2104.5 (3)C4'—C5'—H11108.71
F1—C2'—C1'109.3 (3)C4'—C5'—H12108.68
F1—C2'—C3'111.2 (3)H11—C5'—H12109.45
C4'—O1'—C1'—N1136.1 (3)C4—C5—C6—N10.8 (5)
C4'—O1'—C1'—C2'14.6 (4)O1'—C1'—C2'—F1112.5 (3)
C1'—O1'—C4'—C3'30.9 (3)O1'—C1'—C2'—F2132.0 (3)
C1'—O1'—C4'—C5'153.3 (3)N1—C1'—C2'—C3'112.1 (3)
C6—N1—C2—O2178.4 (3)O1'—C1'—C2'—C3'7.2 (4)
C1'—N1—C2—O212.1 (5)N1—C1'—C2'—F1128.2 (3)
C1'—N1—C2—N3167.3 (3)N1—C1'—C2'—F212.7 (4)
C6—N1—C2—N30.9 (5)F2—C2'—C3'—O3'85.0 (4)
C2—N1—C1'—O1'147.2 (3)F2—C2'—C3'—C4'148.4 (3)
C2—N1—C6—C50.3 (5)C1'—C2'—C3'—O3'151.3 (3)
C1'—N1—C6—C5166.5 (3)F1—C2'—C3'—C4'93.7 (3)
C6—N1—C1'—C2'71.2 (4)F1—C2'—C3'—O3'32.9 (5)
C2—N1—C1'—C2'95.3 (4)C1'—C2'—C3'—C4'24.7 (4)
C6—N1—C1'—O1'46.3 (4)O3'—C3'—C4'—O1'159.2 (3)
C2—N3—C4—N4177.6 (3)O3'—C3'—C4'—C5'83.1 (4)
C4—N3—C2—O2177.1 (3)C2'—C3'—C4'—C5'151.1 (3)
C2—N3—C4—C52.8 (5)C2'—C3'—C4'—O1'33.5 (3)
C4—N3—C2—N12.3 (5)C3'—C4'—C5'—O5'52.9 (5)
N3—C4—C5—C61.9 (5)O1'—C4'—C5'—O5'63.2 (4)
N4—C4—C5—C6178.4 (4)
Symmetry codes: (i) x1/2, y+1/2, z1; (ii) x1/2, y+1/2, z; (iii) x+1, y+1/2, z1/2; (iv) x+1, y+1/2, z+1/2; (v) x+1/2, y, z+1/2; (vi) x+1/2, y, z1/2; (vii) x, y, z1; (viii) x, y, z+1; (ix) x+1, y1/2, z+1/2; (x) x+1, y1/2, z1/2; (xi) x+3/2, y, z+1/2; (xii) x+1/2, y+1/2, z; (xiii) x+3/2, y, z1/2; (xiv) x+1/2, y+1/2, z1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H1···Cl10.952.173.068 (3)157
N4—H4···Cl1xiv0.952.293.158 (4)151
N4—H5···Cl10.952.383.224 (4)147
O3—H13···O2v0.94 (5)1.90 (6)2.829 (4)173 (5)
O5—H14···Cl1xii0.93 (2)2.31 (3)3.212 (3)165 (5)
C1—H6···O20.952.352.734 (5)103
C3—H9···O50.952.482.928 (4)109
Symmetry codes: (v) x+1/2, y, z+1/2; (xii) x+1/2, y+1/2, z; (xiv) x+1/2, y+1/2, z1.
 

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