Cytosinium N-benzoyl­glycinate monohydrate, a redetermination at 105 K

The crystal structure of the title complex, C₄H₆N₃O⁺·C₉H₈NO₃^-·H₂O, has been redetermined as part of an electron paramagnetic resonance (EPR) study of the effect of radiation on such systems. Protonated cytosine and the deprotonated carboxyl­ate group of the amino acid form a typical eight-membered hydrogen-bonded ring motif.

Key indicators

• Single-crystal X-ray study
• T = 105 K
• R factor = 0.033
• wR factor = 0.092
• Data-to-parameter ratio = 15.7

checkCIF/PLATON results

No syntax errors found



Alert level B
CRYSS02_ALERT_3_B  The value of _exptl_crystal_size_mid is > 0.8
   Mid crystal size given     =   0.950
CRYSS02_ALERT_3_B  The value of _exptl_crystal_size_max is > 1.0
   Maximum crystal size given =   1.050

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

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

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Computing details

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

cytosine N-benzoylglycine monohydrate

Crystal data

C9H8NO3·C4H6N3O·H2O	F(000) = 648
Mr = 308.30	Dx = 1.412 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 6264 reflections
a = 11.4821 (2) Å	θ = 1.9–28.3°
b = 7.2107 (1) Å	µ = 0.11 mm^−1
c = 18.2817 (3) Å	T = 105 K
β = 106.692 (1)°	Block, colourless
V = 1449.83 (4) Å^3	1.05 × 0.95 × 0.22 mm
Z = 4

Data collection

Siemens SMART CCD diffractometer	3603 independent reflections
Radiation source: fine-focus sealed tube	3354 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.018
Detector resolution: 8.3 pixels mm^-1	θmax = 28.3°, θmin = 1.9°
Sets of exposures each taken over 0.3° ω rotation scans	h = −15→14
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −9→9
Tmin = 0.816, Tmax = 0.976	l = −19→24
13211 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.033	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.092	w = 1/[σ^2(Fo^2) + (0.0477P)^2 + 0.4875P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max = 0.012
3603 reflections	Δρmax = 0.37 e Å^−3
230 parameters	Δρmin = −0.26 e Å^−3
0 restraints	Extinction correction: SHELXTL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0199 (18)

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. Data were collected by measuring five sets of exposures; two with the detector set at 2θ = 29° and three with 2θ = 55°, crystal-to-detector distance 5.00 cm. Refinement of F² against ALL reflections.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O8A	0.45862 (7)	1.21529 (10)	0.39978 (5)	0.02693 (18)
N1A	0.56816 (7)	1.03457 (11)	0.34117 (5)	0.02109 (18)
H1A	0.6058 (13)	1.133 (2)	0.3308 (8)	0.025*
N3A	0.44267 (7)	0.90339 (10)	0.40698 (5)	0.01778 (17)
H3A	0.3876 (12)	0.9213 (18)	0.4338 (7)	0.021*
N7A	0.42465 (8)	0.58902 (12)	0.41828 (5)	0.02420 (19)
H71A	0.3705 (13)	0.610 (2)	0.4463 (8)	0.029*
H72A	0.4465 (13)	0.476 (2)	0.4100 (8)	0.029*
C2A	0.48918 (8)	1.06172 (13)	0.38369 (5)	0.01927 (19)
C4A	0.47444 (8)	0.72824 (12)	0.39255 (5)	0.01852 (18)
C5A	0.55994 (9)	0.70653 (13)	0.34968 (6)	0.0219 (2)
H5A	0.5841 (12)	0.5851 (19)	0.3396 (8)	0.026*
C6A	0.60371 (9)	0.86145 (14)	0.32578 (6)	0.0228 (2)
H6A	0.6609	0.8500	0.2974	0.027*
O1B	0.26393 (7)	0.64887 (10)	0.50238 (5)	0.02592 (17)
O2B	0.27520 (6)	0.95479 (9)	0.48376 (4)	0.02223 (16)
O3B	0.29065 (6)	0.67759 (10)	0.68514 (4)	0.02376 (17)
N1B	0.10942 (7)	0.69880 (12)	0.59320 (5)	0.02063 (18)
H1B	0.0391 (13)	0.6689 (19)	0.5804 (8)	0.025*
C1B	0.23597 (8)	0.81349 (13)	0.51056 (5)	0.01905 (19)
C2B	0.14518 (8)	0.85632 (13)	0.55571 (6)	0.02079 (19)
H21B	0.0726 (12)	0.9012 (19)	0.5193 (8)	0.025*
H22B	0.1778 (12)	0.9540 (19)	0.5921 (8)	0.025*
C3B	0.18638 (8)	0.61736 (13)	0.65378 (5)	0.01910 (18)
C4B	0.14347 (8)	0.44383 (13)	0.68277 (5)	0.01820 (18)
C5B	0.05472 (9)	0.32875 (14)	0.63609 (5)	0.02133 (19)
H5B	0.0161	0.3631	0.5847	0.026*
C6B	0.02306 (10)	0.16374 (15)	0.66513 (6)	0.0253 (2)
H6B	−0.0374	0.0857	0.6335	0.030*
C7B	0.07965 (10)	0.11288 (15)	0.74038 (6)	0.0269 (2)
H7B	0.0593	−0.0012	0.7596	0.032*
C8B	0.16595 (9)	0.22883 (16)	0.78747 (6)	0.0277 (2)
H8B	0.2031	0.1955	0.8392	0.033*
C9B	0.19784 (9)	0.39373 (15)	0.75871 (6)	0.0235 (2)
H9B	0.2570	0.4727	0.7909	0.028*
O1C	0.14587 (7)	0.30238 (11)	0.47806 (4)	0.02487 (17)
H11C	0.1884 (15)	0.402 (2)	0.4913 (9)	0.037*
H12C	0.1942 (15)	0.207 (2)	0.4834 (9)	0.037*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O8A	0.0242 (4)	0.0127 (3)	0.0433 (4)	0.0008 (3)	0.0087 (3)	−0.0022 (3)
N1A	0.0191 (4)	0.0168 (4)	0.0266 (4)	−0.0021 (3)	0.0054 (3)	0.0005 (3)
N3A	0.0164 (3)	0.0126 (3)	0.0235 (4)	0.0009 (3)	0.0045 (3)	−0.0016 (3)
N7A	0.0304 (4)	0.0122 (4)	0.0321 (4)	0.0012 (3)	0.0122 (4)	−0.0007 (3)
C2A	0.0150 (4)	0.0147 (4)	0.0248 (4)	−0.0003 (3)	0.0006 (3)	−0.0008 (3)
C4A	0.0181 (4)	0.0140 (4)	0.0209 (4)	0.0015 (3)	0.0015 (3)	−0.0017 (3)
C5A	0.0220 (4)	0.0172 (4)	0.0261 (5)	0.0027 (3)	0.0061 (4)	−0.0039 (3)
C6A	0.0200 (4)	0.0233 (5)	0.0252 (5)	0.0006 (4)	0.0063 (3)	−0.0034 (4)
O1B	0.0267 (4)	0.0164 (3)	0.0381 (4)	−0.0003 (3)	0.0147 (3)	−0.0009 (3)
O2B	0.0223 (3)	0.0169 (3)	0.0288 (4)	0.0001 (2)	0.0094 (3)	0.0018 (3)
O3B	0.0168 (3)	0.0220 (3)	0.0306 (4)	−0.0029 (3)	0.0038 (3)	0.0011 (3)
N1B	0.0136 (4)	0.0209 (4)	0.0274 (4)	−0.0007 (3)	0.0059 (3)	0.0026 (3)
C1B	0.0151 (4)	0.0179 (4)	0.0226 (4)	0.0000 (3)	0.0029 (3)	0.0003 (3)
C2B	0.0171 (4)	0.0176 (4)	0.0276 (5)	0.0025 (3)	0.0064 (3)	0.0029 (4)
C3B	0.0164 (4)	0.0183 (4)	0.0237 (4)	0.0009 (3)	0.0077 (3)	−0.0013 (3)
C4B	0.0157 (4)	0.0197 (4)	0.0207 (4)	0.0007 (3)	0.0076 (3)	−0.0005 (3)
C5B	0.0230 (4)	0.0233 (5)	0.0189 (4)	−0.0031 (4)	0.0081 (3)	−0.0013 (3)
C6B	0.0271 (5)	0.0247 (5)	0.0266 (5)	−0.0070 (4)	0.0118 (4)	−0.0023 (4)
C7B	0.0264 (5)	0.0278 (5)	0.0312 (5)	−0.0007 (4)	0.0157 (4)	0.0072 (4)
C8B	0.0233 (5)	0.0367 (6)	0.0238 (5)	0.0025 (4)	0.0078 (4)	0.0085 (4)
C9B	0.0174 (4)	0.0291 (5)	0.0229 (5)	−0.0001 (4)	0.0039 (3)	0.0003 (4)
O1C	0.0186 (3)	0.0204 (3)	0.0337 (4)	−0.0010 (3)	0.0044 (3)	−0.0017 (3)

Geometric parameters (Å, º)

O8A—C2A	1.2228 (12)	N1B—H1B	0.802 (15)
N1A—C6A	1.3675 (13)	C1B—C2B	1.5355 (13)
N1A—C2A	1.3675 (13)	C2B—H21B	0.961 (14)
N1A—H1A	0.880 (15)	C2B—H22B	0.968 (14)
N3A—C4A	1.3613 (11)	C3B—C4B	1.4965 (13)
N3A—C2A	1.3786 (12)	C4B—C9B	1.3963 (13)
N3A—H3A	0.913 (14)	C4B—C5B	1.3985 (13)
N7A—C4A	1.3077 (13)	C5B—C6B	1.3931 (14)
N7A—H71A	0.925 (15)	C5B—H5B	0.9500
N7A—H72A	0.880 (16)	C6B—C7B	1.3913 (15)
C4A—C5A	1.4299 (13)	C6B—H6B	0.9500
C5A—C6A	1.3482 (14)	C7B—C8B	1.3900 (16)
C5A—H5A	0.953 (14)	C7B—H7B	0.9500
C6A—H6A	0.9500	C8B—C9B	1.3910 (15)
O1B—C1B	1.2497 (12)	C8B—H8B	0.9500
O2B—C1B	1.2681 (12)	C9B—H9B	0.9500
O3B—C3B	1.2476 (12)	O1C—H11C	0.860 (17)
N1B—C3B	1.3379 (12)	O1C—H12C	0.874 (17)
N1B—C2B	1.4457 (12)
C6A—N1A—C2A	122.24 (8)	N1B—C2B—H21B	106.5 (8)
C6A—N1A—H1A	119.9 (9)	C1B—C2B—H21B	106.5 (8)
C2A—N1A—H1A	116.9 (9)	N1B—C2B—H22B	110.6 (8)
C4A—N3A—C2A	124.01 (8)	C1B—C2B—H22B	109.2 (8)
C4A—N3A—H3A	120.0 (8)	H21B—C2B—H22B	108.6 (11)
C2A—N3A—H3A	116.0 (8)	O3B—C3B—N1B	123.10 (9)
C4A—N7A—H71A	120.4 (9)	O3B—C3B—C4B	119.89 (8)
C4A—N7A—H72A	118.3 (9)	N1B—C3B—C4B	116.99 (8)
H71A—N7A—H72A	121.2 (13)	C9B—C4B—C5B	119.51 (9)
O8A—C2A—N1A	123.32 (9)	C9B—C4B—C3B	118.03 (8)
O8A—C2A—N3A	120.81 (9)	C5B—C4B—C3B	122.43 (8)
N1A—C2A—N3A	115.85 (8)	C6B—C5B—C4B	119.89 (9)
N7A—C4A—N3A	118.25 (9)	C6B—C5B—H5B	120.1
N7A—C4A—C5A	123.57 (9)	C4B—C5B—H5B	120.1
N3A—C4A—C5A	118.17 (8)	C7B—C6B—C5B	120.20 (9)
C6A—C5A—C4A	117.74 (9)	C7B—C6B—H6B	119.9
C6A—C5A—H5A	122.8 (8)	C5B—C6B—H6B	119.9
C4A—C5A—H5A	119.4 (8)	C8B—C7B—C6B	120.08 (10)
C5A—C6A—N1A	121.91 (9)	C8B—C7B—H7B	120.0
C5A—C6A—H6A	119.0	C6B—C7B—H7B	120.0
N1A—C6A—H6A	119.0	C7B—C8B—C9B	119.88 (9)
C3B—N1B—C2B	121.82 (8)	C7B—C8B—H8B	120.1
C3B—N1B—H1B	119.6 (10)	C9B—C8B—H8B	120.1
C2B—N1B—H1B	118.1 (10)	C8B—C9B—C4B	120.39 (9)
O1B—C1B—O2B	125.80 (9)	C8B—C9B—H9B	119.8
O1B—C1B—C2B	119.52 (8)	C4B—C9B—H9B	119.8
O2B—C1B—C2B	114.67 (8)	H11C—O1C—H12C	109.6 (15)
N1B—C2B—C1B	115.21 (8)
O1B—C1B—C2B—N1B	6.87 (13)	C4A—C5A—C6A—N1A	−0.30 (14)
O2B—C1B—C2B—N1B	−173.87 (8)	C2A—N1A—C6A—C5A	2.10 (15)
C1B—C2B—N1B—C3B	70.48 (12)	C2B—N1B—C3B—O3B	4.80 (15)
C2B—N1B—C3B—C4B	−173.84 (8)	O3B—C3B—C4B—C9B	24.38 (13)
N1B—C3B—C4B—C5B	25.23 (13)	O3B—C3B—C4B—C5B	−153.46 (9)
N1B—C3B—C4B—C9B	−156.93 (9)	C9B—C4B—C5B—C6B	−1.29 (14)
C6A—N1A—C2A—O8A	178.05 (9)	C3B—C4B—C5B—C6B	176.52 (9)
C6A—N1A—C2A—N3A	−3.12 (13)	C4B—C5B—C6B—C7B	−0.14 (15)
C4A—N3A—C2A—O8A	−178.56 (9)	C5B—C6B—C7B—C8B	1.58 (16)
C4A—N3A—C2A—N1A	2.58 (13)	C6B—C7B—C8B—C9B	−1.57 (16)
C2A—N3A—C4A—N7A	179.42 (9)	C7B—C8B—C9B—C4B	0.13 (15)
C2A—N3A—C4A—C5A	−0.94 (13)	C5B—C4B—C9B—C8B	1.30 (14)
N7A—C4A—C5A—C6A	179.35 (9)	C3B—C4B—C9B—C8B	−176.61 (9)
N3A—C4A—C5A—C6A	−0.27 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1A—H1A···O3B^i	0.880 (15)	1.887 (15)	2.7595 (11)	170.8 (13)
N3A—H3A···O2B	0.913 (14)	1.799 (14)	2.7121 (11)	178.1 (12)
N7A—H71A···O1B	0.925 (15)	1.829 (15)	2.7543 (12)	179.3 (14)
N7A—H72A···O8A^ii	0.880 (16)	1.897 (16)	2.7576 (11)	165.6 (14)
C5A—H5A···O3B^iii	0.953 (14)	2.496 (14)	3.4128 (12)	161.3 (11)
N1B—H1B···O1C^iv	0.803 (15)	2.096 (15)	2.8453 (11)	155.4 (13)
O1C—H11C···O1B	0.861 (17)	1.968 (17)	2.8163 (10)	168.5 (15)
O1C—H12C···O2B^ii	0.874 (17)	2.039 (17)	2.8998 (10)	168.1 (15)

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