[(1-Methyl­cytosine)₂H]I, an asymmetric base pair

The X-ray crystal structure of the title compound, 1-methyl­cytosinium iodide 1-methyl­cytosine, [(1-MeC)₂H]I (1-MeC is 1-methyl­cytosine) or C₅H₈N₃O⁺·I^-·C₅H₇N₃O, has been determined at 163 K. In this compound, one protonated (1-MeCH⁺) and one neutral methyl­cytosine (1-MeC) moiety form an asymmetric base pair comprising three hydrogen bonds. A previous structure determination [Krüger, Bruhn & Steinborn (2004). Org. Biomol. Chem. 2, 2513-2516] showed the same cell parameters but a centrosymmetric base pair in space group P2₁/c. At low temperature, however, we discovered the title compound to be a racemic twin showing pseudo-centrosymmetry.

Key indicators

• Single-crystal X-ray study
• T = 163 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.020
• wR factor = 0.043
• Data-to-parameter ratio = 13.8

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT035_ALERT_1_A No _chemical_absolute_configuration info given .          ?

Author Response: The presented compound is a racemic twin with twin fractions of 0.52(2) and 0.48(2), thus inversion of the structure yielded identical R values.

PLAT112_ALERT_2_A ADDSYM Detects Additional (Pseudo) Symm. Elem...          n

Author Response: The presented compound features a hemiprotonated cytosine- cytosine base pair with pseudo-centrosymmetry. Solution of the structure in the centrosymmetric space group P21/c with only one cytosine molecule yielded 114 systematic absence violations (62>3s):

    Systematic absence exceptions:
         -21-   -a-   -c-   -n-

  N         5    87    89    88
  N I>3s    0    73    62    75
  <I>     2.6 532.5  56.1 525.0
  <I/s>   0.7  18.1  12.0  18.4

 Refinement in P21/c converged against R1 = 0.0851 for 1192 Fo >
 4sig(Fo) and wR2 =  0.2085 (GooF = 1.484) with N1 and C6 NPD.

PLAT113_ALERT_2_A ADDSYM Suggests Possible Pseudo/New Spacegroup .      P21/c

Author Response: see response above.

Alert level B
PLAT111_ALERT_2_B ADDSYM Detects (Pseudo) Centre of Symmetry .....        100 PerFit

Alert level C
STRVA01_ALERT_4_C           Flack test results are ambiguous.
           From the CIF: _refine_ls_abs_structure_Flack    0.520
           From the CIF: _refine_ls_abs_structure_Flack_su    0.020
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.97
PLAT033_ALERT_2_C Flack Parameter Value Deviates from Zero .......       0.52
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N3     -   C2      ..       5.79 su
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C5     -   C6      ..       5.37 su
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          5
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1
              C5 H8 N3 O

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           25.35
           From the CIF: _reflns_number_total               2519
           Count of symmetry unique reflns         1396
           Completeness (_total/calc)            180.44%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1123
           Fraction of Friedel pairs measured     0.804
           Are heavy atom types Z>Si present        yes

   3 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   8 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   6 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: KappaCCD Software (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (VMS) (Sheldrick, 1990b); software used to prepare material for publication: SHELXL97.

1-Methylcytosinium iodide 1-methylcytosine

Crystal data

C5H8N3O^+·I^−·C5H7N3O	F(000) = 372
Mr = 378.18	Dx = 1.771 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71069 Å
Hall symbol: P 2yb	Cell parameters from 4452 reflections
a = 7.195 (1) Å	θ = 2.9–25.4°
b = 8.629 (2) Å	µ = 2.27 mm^−1
c = 11.522 (2) Å	T = 163 K
β = 97.59 (3)°	Block, colourless
V = 709.1 (2) Å^3	0.50 × 0.40 × 0.38 mm
Z = 2

Data collection

Nonius KappaCCD diffractometer	2519 independent reflections
Radiation source: fine-focus sealed tube	2291 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.022
Detector resolution: 44 pixels mm^-1	θmax = 25.4°, θmin = 2.9°
360 frames via ω–rotation (Δω1°) and two times 5s per frame scans	h = −8→8
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997)	k = −10→10
Tmin = 0.358, Tmax = 0.427	l = −13→13
4435 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.020	w = 1/[σ^2(Fo^2) + (0.0118P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.043	(Δ/σ)max = 0.001
S = 0.98	Δρmax = 0.31 e Å^−3
2519 reflections	Δρmin = −0.27 e Å^−3
183 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0174 (9)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 1166 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.52 (2)

Special details

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. Intensity data were collected on an Enraf–Nonius KappaCCD (Nonius BV, Netherlands) (Mo Kα, λ = 0.71069 Å, graphite-monochromator). The structure was solved by standard Patterson methods (Sheldrick 1990a) and refined by full-matrix least-squares based on F² using the SHELXTL-Plus (Sheldrick 1990b) and SHELXL97 (Sheldrick 1997) programs. The positions of all non-hydrogen atoms were deduced from difference Fourier maps and refined anisotropically. Initially, the Flack parameter was refined to a value of 0.51 (2) with: _refine_ls_R_factor_all 0.0263 _refine_ls_R_factor_gt 0.0220 _refine_ls_wR_factor_ref 0.0493 _refine_ls_wR_factor_gt 0.0485 and _refine_ls_goodness_of_fit_ref 1.040 Accordingly, subsequent application of the twin law (-1 0 0, 0 - 1 0, 0 0 - 1) resulted in a racemic twin fraction of 0.51881 with the R factors presented below. 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 (Ų)

	x	y	z	Uiso*/Ueq
H3'	0.163 (5)	−0.025 (5)	0.248 (3)	0.045 (10)*
I1	0.75919 (2)	0.00071 (13)	0.754516 (15)	0.03646 (9)
N1	0.6507 (4)	0.2149 (4)	0.2055 (4)	0.0297 (9)
C1	0.7037 (5)	0.3110 (5)	0.1102 (3)	0.0419 (10)
H1A	0.7033	0.2488	0.0410	0.048 (4)*
H1B	0.8270	0.3526	0.1325	0.048 (4)*
H1C	0.6157	0.3943	0.0946	0.048 (4)*
C2	0.4866 (4)	0.1298 (4)	0.1845 (3)	0.0261 (8)
O2	0.3983 (3)	0.1308 (3)	0.08405 (16)	0.0308 (6)
N3	0.4287 (3)	0.0467 (3)	0.27326 (19)	0.0230 (8)
C4	0.5352 (4)	0.0432 (4)	0.3781 (3)	0.0252 (10)
N4	0.4765 (3)	−0.0428 (3)	0.4622 (2)	0.0305 (9)
H4A	0.3733	−0.0939	0.4484	0.046 (5)*
H4B	0.5418	−0.0472	0.5302	0.046 (5)*
C5	0.7054 (4)	0.1272 (4)	0.4009 (3)	0.0313 (9)
H5	0.7789	0.1239	0.4736	0.041 (4)*
C6	0.7560 (5)	0.2133 (5)	0.3103 (6)	0.0334 (12)
H6	0.8655	0.2717	0.3218	0.041 (4)*
N1'	−0.1634 (4)	−0.2274 (4)	0.2974 (4)	0.0290 (9)
C1'	−0.2220 (5)	−0.3265 (5)	0.3885 (3)	0.0434 (11)
H1'1	−0.3459	−0.3653	0.3635	0.048 (4)*
H1'2	−0.2223	−0.2677	0.4592	0.048 (4)*
H1'3	−0.1364	−0.4118	0.4028	0.048 (4)*
C2'	0.0013 (4)	−0.1463 (4)	0.3218 (3)	0.0256 (8)
O2'	0.0890 (3)	−0.1442 (3)	0.41984 (17)	0.0319 (6)
N3'	0.0596 (4)	−0.0656 (3)	0.2310 (2)	0.0257 (8)
C4'	−0.0342 (4)	−0.0578 (4)	0.1211 (3)	0.0263 (10)
N4'	0.0347 (3)	0.0217 (6)	0.04203 (19)	0.0351 (8)
H4'1	0.1396	0.0694	0.0592	0.046 (5)*
H4'2	−0.0244	0.0269	−0.0278	0.046 (5)*
C5'	−0.2075 (4)	−0.1396 (4)	0.0995 (3)	0.0303 (9)
H5'	−0.2800	−0.1352	0.0265	0.041 (4)*
C6'	−0.2631 (5)	−0.2221 (5)	0.1857 (5)	0.0316 (12)
H6'	−0.3736	−0.2789	0.1707	0.041 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
I1	0.03211 (11)	0.04901 (13)	0.02584 (11)	−0.00791 (16)	−0.00519 (7)	0.00848 (13)
N1	0.0295 (16)	0.0269 (18)	0.0332 (19)	0.0005 (16)	0.006 (2)	0.0043 (18)
C1	0.0320 (16)	0.041 (2)	0.053 (2)	−0.0079 (16)	0.0045 (18)	0.010 (2)
C2	0.0184 (13)	0.0252 (19)	0.0337 (18)	0.0049 (13)	0.0000 (15)	−0.0023 (16)
O2	0.0299 (10)	0.0366 (14)	0.0247 (11)	0.0012 (10)	−0.0008 (10)	0.0042 (11)
N3	0.0246 (11)	0.023 (2)	0.0211 (11)	0.0006 (10)	0.0016 (10)	0.0003 (11)
C4	0.0220 (13)	0.026 (3)	0.0269 (15)	0.0071 (12)	−0.0003 (14)	−0.0073 (15)
N4	0.0298 (12)	0.036 (2)	0.0244 (13)	−0.0013 (12)	−0.0026 (12)	0.0021 (14)
C5	0.0274 (15)	0.035 (2)	0.0298 (17)	0.0036 (15)	−0.0040 (15)	−0.0060 (18)
C6	0.018 (2)	0.029 (2)	0.049 (3)	0.0022 (19)	−0.008 (2)	−0.011 (2)
N1'	0.0204 (15)	0.0280 (19)	0.0368 (19)	−0.0002 (16)	−0.0030 (18)	−0.0009 (18)
C1'	0.0327 (17)	0.047 (3)	0.052 (2)	−0.0041 (16)	0.0094 (18)	0.015 (2)
C2'	0.0262 (15)	0.0226 (19)	0.0279 (17)	0.0063 (13)	0.0032 (15)	0.0038 (16)
O2'	0.0305 (10)	0.0371 (15)	0.0264 (11)	0.0023 (10)	−0.0022 (10)	0.0046 (11)
N3'	0.0206 (11)	0.0295 (19)	0.0256 (14)	−0.0020 (11)	−0.0017 (12)	−0.0023 (12)
C4'	0.0258 (14)	0.028 (3)	0.0232 (16)	0.0053 (13)	−0.0024 (15)	−0.0042 (16)
N4'	0.0292 (11)	0.052 (2)	0.0220 (12)	−0.0027 (18)	−0.0041 (11)	−0.004 (2)
C5'	0.0224 (14)	0.034 (2)	0.0318 (18)	0.0028 (14)	−0.0043 (15)	−0.0063 (18)
C6'	0.031 (2)	0.026 (2)	0.036 (3)	0.0009 (19)	−0.001 (2)	−0.005 (2)

Geometric parameters (Å, º)

N1—C6	1.338 (9)	C5'—C6'	1.326 (6)
N1—C2	1.384 (5)	C1—H1A	0.9600
N1—C1	1.466 (5)	C1—H1B	0.9600
C2—O2	1.245 (3)	C1—H1C	0.9600
C2—N3	1.359 (4)	N4—H4B	0.8600
N3—C4	1.342 (3)	N4—H4A	0.8600
C4—N4	1.333 (4)	C5—H5	0.9300
C4—C5	1.417 (4)	C6—H6	0.9300
C5—C6	1.370 (7)	C1'—H1'3	0.9600
N1'—C2'	1.373 (4)	C1'—H1'2	0.9600
N1'—C6'	1.389 (9)	C1'—H1'1	0.9600
N1'—C1'	1.459 (6)	N3'—H3'	0.82 (4)
C2'—O2'	1.219 (3)	N4'—H4'2	0.8600
C2'—N3'	1.368 (4)	N4'—H4'1	0.8600
N3'—C4'	1.355 (3)	C5'—H5'	0.9300
C4'—N4'	1.291 (5)	C6'—H6'	0.9300
C4'—C5'	1.426 (4)
C6—N1—C2	121.4 (4)	H1'1—C1'—H1'3	109.00
C6—N1—C1	120.6 (3)	H1'2—C1'—H1'3	109.00
C2—N1—C1	118.0 (3)	C2'—N3'—H3'	113 (2)
O2—C2—N3	122.3 (3)	C4'—C5'—H5'	121.00
O2—C2—N1	118.6 (3)	C4'—N3'—H3'	122 (2)
N3—C2—N1	119.2 (3)	C6'—C5'—H5'	121.00
C4—N3—C2	119.6 (2)	C4'—N4'—H4'1	120.00
N4—C4—N3	117.9 (3)	C5'—C6'—H6'	119.00
N4—C4—C5	119.9 (2)	C4'—N4'—H4'2	120.00
N3—C4—C5	122.2 (3)	N1'—C6'—H6'	119.00
C6—C5—C4	116.5 (3)	H4'1—N4'—H4'2	120.00
N1—C6—C5	121.2 (3)	H4A—N4—H4B	120.00
C2'—N1'—C6'	120.0 (4)	C4—N4—H4B	120.00
C2'—N1'—C1'	118.4 (3)	C4—N4—H4A	120.00
C6'—N1'—C1'	121.5 (3)	N1—C1—H1A	109.00
O2'—C2'—N3'	121.8 (3)	N1—C1—H1B	109.00
O2'—C2'—N1'	121.7 (4)	N1—C1—H1C	109.00
N3'—C2'—N1'	116.5 (3)	H1A—C1—H1B	109.00
C4'—N3'—C2'	125.1 (3)	H1A—C1—H1C	109.00
N4'—C4'—N3'	119.7 (3)	H1B—C1—H1C	109.00
N4'—C4'—C5'	123.2 (3)	C4—C5—H5	122.00
N3'—C4'—C5'	117.0 (3)	C6—C5—H5	122.00
C6'—C5'—C4'	118.6 (3)	N1'—C1'—H1'1	109.00
C5'—C6'—N1'	122.8 (3)	N1—C6—H6	119.00
N1'—C1'—H1'3	109.00	N1'—C1'—H1'2	110.00
H1'1—C1'—H1'2	109.00	C5—C6—H6	119.00
C6—N1—C2—O2	−177.1 (3)	C6'—N1'—C2'—O2'	177.5 (3)
C1—N1—C2—O2	4.6 (5)	C1'—N1'—C2'—O2'	−6.9 (5)
C6—N1—C2—N3	2.0 (5)	C6'—N1'—C2'—N3'	−1.2 (5)
C1—N1—C2—N3	−176.4 (3)	C1'—N1'—C2'—N3'	174.4 (3)
O2—C2—N3—C4	176.3 (3)	O2'—C2'—N3'—C4'	−177.4 (3)
N1—C2—N3—C4	−2.7 (4)	N1'—C2'—N3'—C4'	1.3 (5)
C2—N3—C4—N4	−178.3 (3)	C2'—N3'—C4'—N4'	−179.8 (4)
C2—N3—C4—C5	1.6 (4)	C2'—N3'—C4'—C5'	0.5 (5)
N4—C4—C5—C6	−179.8 (3)	N4'—C4'—C5'—C6'	177.8 (4)
N3—C4—C5—C6	0.3 (5)	N3'—C4'—C5'—C6'	−2.4 (5)
C2—N1—C6—C5	0.0 (6)	C4'—C5'—C6'—N1'	2.6 (6)
C1—N1—C6—C5	178.3 (4)	C2'—N1'—C6'—C5'	−0.8 (6)
C4—C5—C6—N1	−1.2 (6)	C1'—N1'—C6'—C5'	−176.2 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3′—H3′···N3	0.82 (4)	1.99 (4)	2.808 (4)	171 (4)
N4′—H4′1···O2	0.86	1.92	2.762 (4)	166
N4—H4A···O2′	0.86	2.07	2.901 (3)	161
N4—H4B···I1	0.86	2.87	3.717 (2)	169
N4′—H4′2···I1^i	0.86	2.78	3.633 (2)	171
C5—H5···O2′^ii	0.93	2.47	3.088 (4)	124
C5′—H5′···O2^iii	0.93	2.48	3.085 (4)	123

Symmetry codes: (i) x−1, y, z−1; (ii) −x+1, y+1/2, −z+1; (iii) −x, y−1/2, −z.