Crystal structure of the nucleoside 2′-de­oxy­guanosine dimethyl sulfoxide disolvate

Spingler, B.

doi:10.1107/S2056989023007405

Crystal structure of the nucleoside 2′-deoxyguanosine dimethyl sulfoxide disolvate

The first high-quality crystal structure of unmodified 2′-deoxyguanosine is reported. The isolated crystals are the dimethyl sulfoxide disolvate.

Keywords: crystal structure; nucleoside; guanine; guanosine; purine.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989023007405/zv2028sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989023007405/zv2028Isup2.hkl Contains datablock I
	Portable Document Format (PDF) file https://doi.org/10.1107/S2056989023007405/zv2028sup3.pdf Figures S1 and S2

CCDC reference: 2290127

checkCIF report

Key indicators

Structure: I

Single-crystal X-ray study
T = 183 K
Mean (C-C) = 0.003 Å
R factor = 0.030
wR factor = 0.073
Data-to-parameter ratio = 21.7

checkCIF/PLATON results

No syntax errors found



Alert level G
PLAT398_ALERT_2_G Deviating  C-O-C   Angle From 120 for O14      .      109.1 Degree
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          5 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   0 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   3 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 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
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

2'-Deoxyguanosine dimethyl sulfoxide disolvate top

Crystal data top

C₁₀H₁₃N₅O₄·2C₂H₆OS	D_x = 1.459 Mg m⁻³
M_r = 423.51	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 11856 reflections
a = 9.7590 (1) Å	θ = 2.4–32.7°
b = 11.7951 (2) Å	µ = 0.32 mm⁻¹
c = 16.7553 (2) Å	T = 183 K
V = 1928.68 (4) Å³	Needle, colourless
Z = 4	0.44 × 0.24 × 0.17 mm
F(000) = 896

Data collection top

Oxford Diffraction Xcalibur Ruby diffractometer	5874 independent reflections
Radiation source: Enhance (Mo) X-ray Source	5295 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
Detector resolution: 10.4498 pixels mm^-1	θ_max = 30.5°, θ_min = 2.4°
ω scans	h = −13→13
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008)	k = −14→16
T_min = 0.909, T_max = 1.000	l = −22→23
19896 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.030	w = 1/[σ²(F_o²) + (0.045P)²] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.073	(Δ/σ)_max < 0.001
S = 1.01	Δρ_max = 0.30 e Å⁻³
5874 reflections	Δρ_min = −0.27 e Å⁻³
271 parameters	Absolute structure: Flack x determined using 2107 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: 0.022 (14)
Primary atom site location: structure-invariant direct methods

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C2	0.35188 (19)	0.60776 (14)	0.66640 (9)	0.0159 (3)
C4	0.31935 (18)	0.42499 (14)	0.64001 (9)	0.0157 (3)
C5	0.40248 (18)	0.38572 (15)	0.70072 (10)	0.0163 (3)
C6	0.47568 (18)	0.46616 (14)	0.74730 (10)	0.0183 (3)
C8	0.32641 (18)	0.23836 (15)	0.64098 (10)	0.0184 (3)
H8	0.308547	0.161923	0.626466	0.022*
C11	0.17747 (19)	0.33364 (15)	0.53323 (10)	0.0192 (3)
H11	0.101178	0.388127	0.543999	0.023*
C12	0.2513 (2)	0.36613 (16)	0.45639 (10)	0.0242 (4)
H12A	0.190773	0.410232	0.420577	0.029*
H12B	0.334890	0.410942	0.467733	0.029*
C13	0.2870 (2)	0.25191 (18)	0.42025 (10)	0.0243 (4)
H13	0.370902	0.219466	0.445824	0.029*
C14	0.16057 (19)	0.18386 (15)	0.44271 (11)	0.0212 (4)
H14	0.084806	0.204527	0.405249	0.025*
C15	0.1745 (2)	0.05766 (16)	0.44360 (13)	0.0296 (4)
H15A	0.088134	0.023128	0.462851	0.035*
H15B	0.191768	0.029894	0.388760	0.035*
C23	0.0397 (2)	0.63289 (18)	0.47584 (13)	0.0280 (4)
H23A	0.093 (3)	0.593 (2)	0.5123 (15)	0.042*
H23B	0.010 (3)	0.585 (2)	0.4328 (16)	0.042*
H23C	−0.038 (3)	0.668 (2)	0.4972 (15)	0.042*
C24	0.2803 (3)	0.6683 (2)	0.40425 (16)	0.0438 (6)
H24A	0.248599	0.617530	0.361775	0.066*
H24B	0.319500	0.623323	0.447802	0.066*
H24C	0.350235	0.719659	0.382971	0.066*
N1	0.44138 (16)	0.57763 (13)	0.72580 (8)	0.0173 (3)
H1	0.483 (2)	0.6326 (19)	0.7512 (13)	0.021*
N2	0.32939 (19)	0.71824 (13)	0.65567 (9)	0.0218 (3)
H2A	0.281 (3)	0.737 (2)	0.6175 (13)	0.026*
H2B	0.367 (3)	0.771 (2)	0.6808 (13)	0.026*
N3	0.28910 (16)	0.53300 (12)	0.61976 (8)	0.0169 (3)
N7	0.40557 (16)	0.26752 (12)	0.70054 (8)	0.0187 (3)
N9	0.27173 (15)	0.33028 (12)	0.60156 (8)	0.0168 (3)
O6	0.56048 (15)	0.44860 (12)	0.80073 (7)	0.0270 (3)
O13	0.3041 (2)	0.26086 (16)	0.33678 (8)	0.0432 (4)
H13A	0.363 (4)	0.215 (3)	0.3158 (18)	0.065*
O14	0.12431 (14)	0.22319 (10)	0.52196 (7)	0.0219 (3)
O15	0.28382 (17)	0.02499 (13)	0.49400 (10)	0.0385 (4)
H15	0.275 (3)	−0.048 (3)	0.5060 (16)	0.058*
O21	0.50822 (19)	0.11673 (15)	0.28913 (10)	0.0440 (4)
O22	0.19120 (17)	0.80671 (12)	0.51554 (8)	0.0318 (3)
S22	0.13986 (5)	0.74863 (4)	0.44083 (3)	0.02532 (11)
S21	0.53507 (5)	0.01236 (4)	0.24068 (3)	0.02556 (11)
C22	0.4129 (2)	0.0115 (2)	0.16179 (12)	0.0362 (5)
H22A	0.431974	0.074434	0.125214	0.054*
H22B	0.320604	0.020153	0.183990	0.054*
H22C	0.418952	−0.060392	0.132742	0.054*
C21	0.4665 (3)	−0.1037 (2)	0.29503 (13)	0.0396 (5)
H21A	0.371508	−0.087110	0.309943	0.059*
H21B	0.521108	−0.116028	0.343349	0.059*
H21C	0.469085	−0.172052	0.261807	0.059*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C2	0.0194 (8)	0.0140 (8)	0.0144 (7)	0.0000 (6)	0.0000 (6)	−0.0005 (6)
C4	0.0175 (8)	0.0146 (8)	0.0150 (7)	−0.0013 (6)	0.0000 (6)	−0.0009 (6)
C5	0.0184 (8)	0.0146 (8)	0.0158 (7)	0.0009 (6)	−0.0004 (6)	0.0015 (6)
C6	0.0216 (8)	0.0172 (8)	0.0160 (7)	0.0014 (7)	0.0003 (7)	0.0009 (6)
C8	0.0208 (8)	0.0115 (8)	0.0231 (8)	−0.0016 (7)	0.0007 (6)	0.0026 (6)
C11	0.0211 (9)	0.0129 (8)	0.0235 (8)	0.0001 (6)	−0.0063 (7)	−0.0033 (6)
C12	0.0327 (10)	0.0191 (9)	0.0207 (8)	−0.0027 (8)	−0.0048 (7)	0.0022 (7)
C13	0.0301 (9)	0.0238 (9)	0.0189 (7)	0.0038 (8)	−0.0012 (7)	0.0018 (7)
C14	0.0247 (9)	0.0165 (9)	0.0224 (8)	0.0042 (7)	−0.0097 (7)	−0.0051 (7)
C15	0.0368 (11)	0.0169 (9)	0.0350 (10)	0.0027 (8)	−0.0101 (9)	−0.0059 (8)
C23	0.0255 (10)	0.0275 (11)	0.0310 (10)	−0.0040 (9)	0.0012 (9)	−0.0017 (8)
C24	0.0400 (13)	0.0350 (13)	0.0564 (14)	−0.0071 (11)	0.0217 (11)	−0.0083 (11)
N1	0.0228 (8)	0.0124 (7)	0.0166 (6)	−0.0014 (6)	−0.0055 (6)	−0.0015 (5)
N2	0.0317 (9)	0.0118 (7)	0.0218 (7)	−0.0004 (6)	−0.0091 (7)	−0.0011 (6)
N3	0.0208 (7)	0.0127 (7)	0.0171 (6)	0.0010 (6)	−0.0035 (5)	−0.0001 (5)
N7	0.0223 (7)	0.0125 (7)	0.0212 (7)	0.0005 (6)	0.0001 (6)	0.0032 (5)
N9	0.0191 (7)	0.0120 (7)	0.0195 (6)	−0.0018 (6)	−0.0031 (5)	−0.0003 (5)
O6	0.0339 (8)	0.0236 (7)	0.0234 (6)	0.0003 (6)	−0.0129 (6)	0.0019 (5)
O13	0.0663 (12)	0.0431 (10)	0.0201 (7)	0.0143 (9)	0.0066 (7)	0.0027 (7)
O14	0.0225 (6)	0.0156 (6)	0.0275 (6)	−0.0048 (5)	−0.0010 (5)	−0.0059 (5)
O15	0.0365 (8)	0.0198 (8)	0.0592 (10)	0.0036 (7)	−0.0145 (7)	0.0086 (7)
O21	0.0483 (11)	0.0361 (9)	0.0477 (10)	0.0013 (8)	−0.0043 (8)	−0.0179 (7)
O22	0.0463 (9)	0.0188 (7)	0.0302 (7)	−0.0004 (7)	−0.0144 (7)	−0.0014 (5)
S22	0.0316 (2)	0.0205 (2)	0.0239 (2)	−0.0008 (2)	−0.00666 (18)	0.00218 (18)
S21	0.0255 (2)	0.0264 (3)	0.0248 (2)	−0.00201 (19)	−0.00031 (19)	−0.00260 (17)
C22	0.0353 (11)	0.0424 (13)	0.0310 (10)	−0.0071 (10)	−0.0079 (9)	0.0039 (9)
C21	0.0464 (14)	0.0379 (13)	0.0345 (11)	−0.0042 (11)	0.0051 (11)	0.0076 (9)

Geometric parameters (Å, º) top

C2—N1	1.371 (2)	C15—H15A	0.9900
C2—N2	1.334 (2)	C15—H15B	0.9900
C2—N3	1.328 (2)	C15—O15	1.414 (2)
C4—C5	1.381 (2)	C23—H23A	0.93 (3)
C4—N3	1.351 (2)	C23—H23B	0.96 (3)
C4—N9	1.371 (2)	C23—H23C	0.94 (3)
C5—C6	1.421 (2)	C23—S22	1.778 (2)
C5—N7	1.395 (2)	C24—H24A	0.9800
C6—N1	1.404 (2)	C24—H24B	0.9800
C6—O6	1.237 (2)	C24—H24C	0.9800
C8—H8	0.9500	C24—S22	1.775 (2)
C8—N7	1.308 (2)	N1—H1	0.87 (2)
C8—N9	1.377 (2)	N2—H2A	0.83 (2)
C11—H11	1.0000	N2—H2B	0.83 (2)
C11—C12	1.525 (2)	O13—H13A	0.87 (3)
C11—N9	1.469 (2)	O15—H15	0.89 (3)
C11—O14	1.415 (2)	O21—S21	1.4978 (17)
C12—H12A	0.9900	O22—S22	1.5124 (14)
C12—H12B	0.9900	S21—C22	1.780 (2)
C12—C13	1.518 (3)	S21—C21	1.775 (2)
C13—H13	1.0000	C22—H22A	0.9800
C13—C14	1.520 (3)	C22—H22B	0.9800
C13—O13	1.412 (2)	C22—H22C	0.9800
C14—H14	1.0000	C21—H21A	0.9800
C14—C15	1.495 (3)	C21—H21B	0.9800
C14—O14	1.450 (2)	C21—H21C	0.9800

N2—C2—N1	117.13 (15)	H23A—C23—H23B	111 (2)
N3—C2—N1	123.30 (15)	H23A—C23—H23C	115 (2)
N3—C2—N2	119.57 (16)	H23B—C23—H23C	108 (2)
N3—C4—C5	129.01 (15)	S22—C23—H23A	107.2 (17)
N3—C4—N9	125.20 (15)	S22—C23—H23B	111.7 (15)
N9—C4—C5	105.78 (15)	S22—C23—H23C	103.7 (16)
C4—C5—C6	118.42 (16)	H24A—C24—H24B	109.5
C4—C5—N7	110.26 (15)	H24A—C24—H24C	109.5
N7—C5—C6	131.13 (16)	H24B—C24—H24C	109.5
N1—C6—C5	111.38 (14)	S22—C24—H24A	109.5
O6—C6—C5	128.47 (16)	S22—C24—H24B	109.5
O6—C6—N1	120.15 (15)	S22—C24—H24C	109.5
N7—C8—H8	123.6	C2—N1—C6	125.52 (14)
N7—C8—N9	112.82 (15)	C2—N1—H1	117.2 (14)
N9—C8—H8	123.6	C6—N1—H1	117.3 (15)
C12—C11—H11	110.1	C2—N2—H2A	117.4 (17)
N9—C11—H11	110.1	C2—N2—H2B	125.9 (17)
N9—C11—C12	111.64 (15)	H2A—N2—H2B	116 (2)
O14—C11—H11	110.1	C2—N3—C4	112.18 (14)
O14—C11—C12	106.99 (14)	C8—N7—C5	104.58 (15)
O14—C11—N9	107.98 (14)	C4—N9—C8	106.55 (13)
C11—C12—H12A	111.2	C4—N9—C11	123.81 (14)
C11—C12—H12B	111.2	C8—N9—C11	129.61 (14)
H12A—C12—H12B	109.1	C13—O13—H13A	116 (2)
C13—C12—C11	102.84 (15)	C11—O14—C14	109.10 (14)
C13—C12—H12A	111.2	C15—O15—H15	109 (2)
C13—C12—H12B	111.2	C24—S22—C23	97.37 (11)
C12—C13—H13	110.9	O22—S22—C23	104.88 (9)
C12—C13—C14	100.59 (15)	O22—S22—C24	105.77 (12)
C14—C13—H13	110.9	O21—S21—C22	106.85 (11)
O13—C13—C12	110.84 (16)	O21—S21—C21	106.85 (11)
O13—C13—H13	110.9	C21—S21—C22	97.15 (12)
O13—C13—C14	112.36 (17)	S21—C22—H22A	109.5
C13—C14—H14	108.4	S21—C22—H22B	109.5
C15—C14—C13	117.04 (17)	S21—C22—H22C	109.5
C15—C14—H14	108.4	H22A—C22—H22B	109.5
O14—C14—C13	104.83 (14)	H22A—C22—H22C	109.5
O14—C14—H14	108.4	H22B—C22—H22C	109.5
O14—C14—C15	109.36 (16)	S21—C21—H21A	109.5
C14—C15—H15A	109.6	S21—C21—H21B	109.5
C14—C15—H15B	109.6	S21—C21—H21C	109.5
H15A—C15—H15B	108.1	H21A—C21—H21B	109.5
O15—C15—C14	110.24 (16)	H21A—C21—H21C	109.5
O15—C15—H15A	109.6	H21B—C21—H21C	109.5
O15—C15—H15B	109.6

C4—C5—C6—N1	4.3 (2)	N3—C4—C5—C6	−4.4 (3)
C4—C5—C6—O6	−175.47 (17)	N3—C4—C5—N7	−179.94 (17)
C4—C5—N7—C8	0.2 (2)	N3—C4—N9—C8	−179.89 (17)
C5—C4—N3—C2	0.6 (3)	N3—C4—N9—C11	−1.5 (3)
C5—C4—N9—C8	0.69 (18)	N7—C5—C6—N1	178.83 (18)
C5—C4—N9—C11	179.13 (15)	N7—C5—C6—O6	−1.0 (3)
C5—C6—N1—C2	−1.6 (2)	N7—C8—N9—C4	−0.6 (2)
C6—C5—N7—C8	−174.68 (18)	N7—C8—N9—C11	−178.96 (16)
C11—C12—C13—C14	36.85 (17)	N9—C4—C5—C6	175.04 (15)
C11—C12—C13—O13	155.88 (17)	N9—C4—C5—N7	−0.55 (19)
C12—C11—N9—C4	77.0 (2)	N9—C4—N3—C2	−178.67 (16)
C12—C11—N9—C8	−104.9 (2)	N9—C8—N7—C5	0.3 (2)
C12—C11—O14—C14	0.18 (18)	N9—C11—C12—C13	93.88 (17)
C12—C13—C14—C15	−159.00 (16)	N9—C11—O14—C14	−120.12 (15)
C12—C13—C14—O14	−37.66 (16)	O6—C6—N1—C2	178.24 (16)
C13—C14—C15—O15	55.1 (2)	O13—C13—C14—C15	83.1 (2)
C13—C14—O14—C11	23.95 (18)	O13—C13—C14—O14	−155.58 (16)
C15—C14—O14—C11	150.21 (15)	O14—C11—C12—C13	−24.05 (18)
N1—C2—N3—C4	2.6 (2)	O14—C11—N9—C4	−165.65 (15)
N2—C2—N1—C6	178.46 (17)	O14—C11—N9—C8	12.4 (2)
N2—C2—N3—C4	−178.00 (16)	O14—C14—C15—O15	−63.8 (2)
N3—C2—N1—C6	−2.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C23—H23B···O6ⁱ	0.96 (3)	2.35 (3)	3.239 (3)	153 (2)
N1—H1···N7ⁱⁱ	0.87 (2)	2.09 (2)	2.962 (2)	173 (2)
N2—H2A···O22	0.83 (2)	2.09 (2)	2.902 (2)	168 (2)
N2—H2B···O6ⁱⁱ	0.83 (2)	2.24 (2)	3.012 (2)	155 (2)
O13—H13A···O21	0.87 (3)	1.88 (4)	2.738 (3)	169 (3)
O15—H15···O22ⁱⁱⁱ	0.89 (3)	1.91 (3)	2.752 (2)	159 (3)

Symmetry codes: (i) −x+1/2, −y+1, z−1/2; (ii) −x+1, y+1/2, −z+3/2; (iii) x, y−1, z.

Sugar conformations in 2'-deoxyguanosine, its supramolecular complexes and guanosine top

Compound	Space group	Sugar conformation	χ (O4'—C1'—N1—C6) (°)	Reference
2'-Deoxyguanosine·2(DMSO)	P2₁2₁2₁	Envelope, C3'-endo	-165.6 (1)	This work
(Actinomycin D)·2(2'-deoxyguanosine)·12(H₂O)	P2₁2₁2₁	Envelope, C3'-endo; Twisted, C1'-exo/C2'-endo	-86.5; -90.6	Jain & Sobell (1972)
(7-Bromoactinomycin D)·2(2'-deoxyguanosine)·11(H₂O)	P2₁2₁2₁	Twisted, C2'-exo/C3'-endo; Twisted, C1'-exo/C2'-endo	-86.5; -88.9	Jain & Sobell (1972)
(2'-Deoxyguanosine)·(5-bromo-2'-deoxycytidine)	P2₁2₁2	Envelope, C2'-endo	56.7	Haschemeyer et al. (1965)
(Guanosine)₂·4(H₂O)	P2₁	Envelope, C2'-endo; Twisted, C1'-exo/C2'-endo	-58.1; -137.2	Thewalt et al. (1970)

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Crystal structure of the nucleoside 2′-de­oxy­guanosine dimethyl sulfoxide disolvate

Supporting information

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Crystal structure of the nucleoside 2′-deoxyguanosine dimethyl sulfoxide disolvate