Crystal structures of the synthetic inter­mediate 3-[(6-chloro-7H-purin-7-yl)meth­yl]cyclo­butan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-di­hydro-7H-purin-7-yl)meth­yl]cyclo­butan-1-ol and 3-[(6-chloro-9H-purin-9-yl)meth­yl]cyclo­butan-1-ol

Yaseen, A.; Hassan, M.M.; Lee-Ruff, E.; Audette, G.F.

doi:10.1107/S2056989019004432

Crystal structures of the synthetic intermediate 3-[(6-chloro-7H-purin-7-yl)methyl]cyclobutan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-dihydro-7H-purin-7-yl)methyl]cyclobutan-1-ol and 3-[(6-chloro-9H-purin-9-yl)methyl]cyclobutan-1-ol

A. Yaseen, M. M. Hassan, E. Lee-Ruff and G. F. Audette

Two oxetanocin A derivatives have been synthesized stereospecifically. The crystal structures of both derivatives and a synthetic intermediate are reported on herein.

Keywords: crystal structure; oxetonacin; cyclobutanone; cyclobutanol; HIV; hydrogen bonding; offset π–π interactions; supramolecular framework.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989019004432/zp2033sup1.cif Contains datablocks global, I, II, IV
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989019004432/zp2033Isup2.hkl Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989019004432/zp2033IIsup3.hkl Contains datablock II
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989019004432/zp2033IIsup5.cml Supplementary material

CCDC references: 1907200; 1907199; 1907198

checkCIF report

Key indicators

Structure: I

Single-crystal X-ray study
T = 110 K
Mean (C-C) = 0.003 Å
R factor = 0.043
wR factor = 0.111
Data-to-parameter ratio = 17.3

Structure: II

Single-crystal X-ray study
T = 110 K
Mean (C-C) = 0.003 Å
Disorder in main residue
R factor = 0.037
wR factor = 0.098
Data-to-parameter ratio = 11.2

Structure: IV

Single-crystal X-ray study
T = 110 K
Mean (C-C) = 0.003 Å
R factor = 0.038
wR factor = 0.103
Data-to-parameter ratio = 11.9

checkCIF/PLATON results

No syntax errors found



Datablock: I


Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.15 Report
PLAT480_ALERT_4_C Long H...A H-Bond Reported H4'      ..CL1      .       2.97 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H6'B     ..N1       .       2.68 Ang.
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.801 Check

Alert level G
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          6 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          1 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          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
   4 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   4 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 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
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check




Datablock: II


Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full value Low .      0.959 Why?
PLAT921_ALERT_1_B R1  in the CIF and FCF Differ by ...............    -0.0128 Check
PLAT922_ALERT_1_B wR2 in the CIF and FCF Differ by ...............    -0.0385 Check
PLAT927_ALERT_1_B Reported and Calculated  wR2 Differ by .........    -0.0115 Check

Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.63 Report
PLAT410_ALERT_2_C Short Intra H...H Contact  H3'1     ..H4'B     .       1.97 Ang.
                                                      x,y,z  =      1_555 Check
PLAT410_ALERT_2_C Short Intra H...H Contact  H5'2     ..H4'B     .       1.96 Ang.
                                                      x,y,z  =      1_555 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.592         74 Report
PLAT923_ALERT_1_C S    Values in the CIF and FCF Differ by .......     -0.428 Check
PLAT928_ALERT_1_C Reported and Calculated    S value   Differ by .     -0.133 Check
PLAT934_ALERT_3_C Number of (Iobs-Icalc)/SigmaW > 10 Outliers ....          1 Check

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          2 Note
PLAT171_ALERT_4_G The CIF-Embedded .res File Contains EADP Records          2 Report
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          1 Report
PLAT301_ALERT_3_G Main Residue  Disorder ..............(Resd  1  )        13% Note
PLAT367_ALERT_2_G Long?  C(sp?)-C(sp?) Bond  C2'      - C3'      .       1.52 Ang.
PLAT367_ALERT_2_G Long?  C(sp?)-C(sp?) Bond  C2'      - C5'      .       1.53 Ang.
PLAT434_ALERT_2_G Short Inter HL..HL Contact Cl1      ..Cl1              3.37 Ang.
                                                 -x,1-y,1-z  =      2_566 Check
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........         11 Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          1 Note
PLAT909_ALERT_3_G Percentage of I>2sig(I) Data at Theta(Max) Still        83% Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          3 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          3 Info

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

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   9 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check




Datablock: IV


Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full value Low .      0.954 Why?

Alert level C
THETM01_ALERT_3_C  The value of sine(theta_max)/wavelength is less than 0.590
            Calculated sin(theta_max)/wavelength =    0.5875

Alert level G
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          1 Report
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          6 Note
PLAT933_ALERT_2_G Number of OMIT Records in Embedded .res File ...          4 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   1 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
   1 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
   1 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

Computing details top

For all structures, data collection: CrysAlis PRO (Rigaku OD, 2018); cell refinement: CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

3-[(6-Chloro-7H-purin-7-yl)methyl]cyclobutan-1-one (I) top

Crystal data top

C₁₀H₉ClN₄O	F(000) = 488
M_r = 236.66	D_x = 1.555 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 11.9736 (5) Å	Cell parameters from 9903 reflections
b = 6.8854 (4) Å	θ = 3.3–32.6°
c = 12.2746 (5) Å	µ = 0.36 mm⁻¹
β = 92.938 (4)°	T = 110 K
V = 1010.63 (8) Å³	Plate, pale_yellow
Z = 4	0.43 × 0.21 × 0.04 mm

Data collection top

Bruker APEXII CCD diffractometer	2508 independent reflections
Radiation source: sealed X-ray tube	2217 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
ω scans	θ_max = 28.3°, θ_min = 3.3°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	h = −15→15
T_min = 0.661, T_max = 1.000	k = −9→9
35539 measured reflections	l = −16→16

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.111	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0508P)² + 0.9477P] where P = (F_o² + 2F_c²)/3
2508 reflections	(Δ/σ)_max < 0.001
145 parameters	Δρ_max = 0.60 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³

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
Cl1	0.70136 (4)	0.21385 (7)	0.52904 (4)	0.02685 (14)
N1	0.81306 (13)	0.2530 (2)	0.35301 (12)	0.0230 (3)
N3	0.93051 (12)	0.5196 (2)	0.30500 (11)	0.0219 (3)
N7	0.84068 (11)	0.6388 (2)	0.56456 (11)	0.0183 (3)
N9	0.95030 (12)	0.7744 (2)	0.44062 (12)	0.0216 (3)
O1'	0.43878 (13)	0.6449 (3)	0.76126 (16)	0.0503 (5)
C2'	0.53242 (16)	0.6753 (3)	0.73657 (17)	0.0303 (4)
C3'	0.64220 (16)	0.7042 (3)	0.80129 (15)	0.0297 (4)
H3'A	0.670598	0.585740	0.839075	0.036*
H3'B	0.642461	0.816481	0.851695	0.036*
C4'	0.69801 (14)	0.7464 (3)	0.69174 (14)	0.0215 (4)
H4'	0.720328	0.885805	0.685533	0.026*
C5'	0.58520 (15)	0.7032 (3)	0.62724 (16)	0.0297 (4)
H5'A	0.554763	0.814870	0.584483	0.036*
H5'B	0.586295	0.584132	0.582080	0.036*
C6'	0.79428 (14)	0.6106 (3)	0.67259 (12)	0.0198 (3)
H6'A	0.854160	0.632156	0.729957	0.024*
H6'B	0.768262	0.474799	0.678746	0.024*
C2	0.88240 (14)	0.3491 (3)	0.28787 (13)	0.0230 (4)
H2	0.898377	0.285913	0.221649	0.028*
C4	0.90857 (13)	0.6006 (3)	0.40103 (13)	0.0183 (3)
C5	0.83895 (13)	0.5123 (2)	0.47653 (12)	0.0176 (3)
C6	0.79181 (14)	0.3358 (3)	0.44645 (13)	0.0198 (3)
C8	0.90917 (14)	0.7900 (3)	0.53629 (14)	0.0205 (3)
H8	0.925073	0.897356	0.583167	0.025*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0305 (2)	0.0264 (2)	0.0241 (2)	−0.00833 (17)	0.00535 (16)	0.00170 (17)
N1	0.0231 (7)	0.0246 (8)	0.0213 (7)	0.0002 (6)	0.0002 (6)	−0.0029 (6)
N3	0.0215 (7)	0.0272 (8)	0.0173 (7)	0.0026 (6)	0.0046 (5)	0.0014 (6)
N7	0.0202 (7)	0.0202 (7)	0.0146 (6)	0.0007 (5)	0.0030 (5)	0.0009 (5)
N9	0.0213 (7)	0.0210 (7)	0.0229 (7)	−0.0006 (6)	0.0036 (5)	0.0027 (6)
O1'	0.0302 (8)	0.0585 (12)	0.0639 (11)	−0.0075 (8)	0.0186 (8)	0.0010 (9)
C2'	0.0257 (9)	0.0282 (10)	0.0377 (10)	0.0011 (7)	0.0102 (8)	−0.0006 (8)
C3'	0.0284 (9)	0.0409 (12)	0.0207 (8)	0.0025 (8)	0.0091 (7)	0.0002 (8)
C4'	0.0198 (8)	0.0263 (9)	0.0187 (8)	0.0019 (6)	0.0046 (6)	0.0022 (6)
C5'	0.0215 (8)	0.0425 (12)	0.0251 (9)	0.0037 (8)	0.0000 (7)	−0.0010 (8)
C6'	0.0228 (8)	0.0253 (9)	0.0116 (7)	0.0016 (7)	0.0033 (6)	0.0011 (6)
C2	0.0229 (8)	0.0301 (9)	0.0162 (7)	0.0041 (7)	0.0021 (6)	−0.0038 (7)
C4	0.0177 (7)	0.0204 (8)	0.0168 (7)	0.0022 (6)	0.0003 (6)	0.0037 (6)
C5	0.0179 (7)	0.0213 (8)	0.0135 (7)	0.0035 (6)	0.0004 (6)	0.0011 (6)
C6	0.0195 (7)	0.0223 (8)	0.0175 (7)	0.0007 (6)	0.0015 (6)	0.0039 (6)
C8	0.0205 (7)	0.0176 (8)	0.0232 (8)	0.0009 (6)	−0.0014 (6)	−0.0022 (6)

Geometric parameters (Å, º) top

Cl1—C6	1.7372 (17)	C3'—H3'A	0.9900
N1—C6	1.317 (2)	C3'—H3'B	0.9900
N1—C2	1.354 (2)	C4'—C6'	1.512 (2)
N3—C2	1.320 (2)	C4'—C5'	1.559 (2)
N3—C4	1.342 (2)	C4'—H4'	1.0000
N7—C8	1.381 (2)	C5'—H5'A	0.9900
N7—C5	1.387 (2)	C5'—H5'B	0.9900
N7—C6'	1.4765 (19)	C6'—H6'A	0.9900
N9—C8	1.301 (2)	C6'—H6'B	0.9900
N9—C4	1.376 (2)	C2—H2	0.9500
O1'—C2'	1.195 (2)	C4—C5	1.415 (2)
C2'—C3'	1.514 (3)	C5—C6	1.382 (2)
C2'—C5'	1.524 (3)	C8—H8	0.9500
C3'—C4'	1.559 (2)

C6—N1—C2	117.04 (16)	C2'—C5'—H5'B	114.0
C2—N3—C4	113.96 (15)	C4'—C5'—H5'B	114.0
C8—N7—C5	105.24 (13)	H5'A—C5'—H5'B	111.2
C8—N7—C6'	125.49 (14)	N7—C6'—C4'	112.54 (14)
C5—N7—C6'	128.74 (15)	N7—C6'—H6'A	109.1
C8—N9—C4	104.09 (14)	C4'—C6'—H6'A	109.1
O1'—C2'—C3'	133.7 (2)	N7—C6'—H6'B	109.1
O1'—C2'—C5'	133.0 (2)	C4'—C6'—H6'B	109.1
C3'—C2'—C5'	93.29 (14)	H6'A—C6'—H6'B	107.8
C2'—C3'—C4'	88.33 (14)	N3—C2—N1	128.03 (16)
C2'—C3'—H3'A	113.9	N3—C2—H2	116.0
C4'—C3'—H3'A	113.9	N1—C2—H2	116.0
C2'—C3'—H3'B	113.9	N3—C4—N9	126.01 (15)
C4'—C3'—H3'B	113.9	N3—C4—C5	123.02 (16)
H3'A—C3'—H3'B	111.1	N9—C4—C5	110.96 (14)
C6'—C4'—C5'	116.77 (16)	C6—C5—N7	138.56 (15)
C6'—C4'—C3'	112.49 (15)	C6—C5—C4	116.68 (15)
C5'—C4'—C3'	90.22 (14)	N7—C5—C4	104.75 (14)
C6'—C4'—H4'	111.9	N1—C6—C5	121.22 (16)
C5'—C4'—H4'	111.9	N1—C6—Cl1	116.95 (14)
C3'—C4'—H4'	111.9	C5—C6—Cl1	121.83 (13)
C2'—C5'—C4'	87.96 (14)	N9—C8—N7	114.95 (15)
C2'—C5'—H5'A	114.0	N9—C8—H8	122.5
C4'—C5'—H5'A	114.0	N7—C8—H8	122.5

O1'—C2'—C3'—C4'	−175.7 (3)	C8—N7—C5—C6	179.2 (2)
C5'—C2'—C3'—C4'	3.32 (16)	C6'—N7—C5—C6	7.2 (3)
C2'—C3'—C4'—C6'	−122.53 (16)	C8—N7—C5—C4	0.10 (17)
C2'—C3'—C4'—C5'	−3.24 (16)	C6'—N7—C5—C4	−171.83 (15)
O1'—C2'—C5'—C4'	175.7 (3)	N3—C4—C5—C6	−0.8 (2)
C3'—C2'—C5'—C4'	−3.32 (16)	N9—C4—C5—C6	−179.83 (14)
C6'—C4'—C5'—C2'	118.72 (16)	N3—C4—C5—N7	178.47 (15)
C3'—C4'—C5'—C2'	3.22 (15)	N9—C4—C5—N7	−0.52 (18)
C8—N7—C6'—C4'	76.0 (2)	C2—N1—C6—C5	−0.4 (2)
C5—N7—C6'—C4'	−113.61 (19)	C2—N1—C6—Cl1	179.16 (13)
C5'—C4'—C6'—N7	72.5 (2)	N7—C5—C6—N1	−177.58 (18)
C3'—C4'—C6'—N7	174.86 (15)	C4—C5—C6—N1	1.4 (2)
C4—N3—C2—N1	2.1 (3)	N7—C5—C6—Cl1	2.9 (3)
C6—N1—C2—N3	−1.5 (3)	C4—C5—C6—Cl1	−178.08 (12)
C2—N3—C4—N9	178.09 (16)	C4—N9—C8—N7	−0.70 (19)
C2—N3—C4—C5	−0.8 (2)	C5—N7—C8—N9	0.4 (2)
C8—N9—C4—N3	−178.22 (16)	C6'—N7—C8—N9	172.66 (15)
C8—N9—C4—C5	0.74 (18)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6′—H6′B···Cl1	0.99	2.66	3.407 (2)	132
C4′—H4′···Cl1ⁱ	1.00	2.97	3.7889 (19)	140
C6′—H6′B···N1ⁱⁱ	0.99	2.68	3.343 (2)	124

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

3-[(6-Chloro-8,9-dihydro-7H-purin-7-yl)methyl]cyclobutan-1-ol (II) top

Crystal data top

C₁₀H₁₃ClN₄O	Z = 2
M_r = 240.69	F(000) = 252
Triclinic, P1	D_x = 1.488 Mg m⁻³
a = 6.1101 (4) Å	Cu Kα radiation, λ = 1.54184 Å
b = 8.6075 (5) Å	Cell parameters from 8605 reflections
c = 11.0083 (7) Å	θ = 4.3–65.4°
α = 68.957 (6)°	µ = 3.03 mm⁻¹
β = 83.799 (5)°	T = 110 K
γ = 87.189 (5)°	Plate, colorless
V = 537.15 (6) Å³	0.44 × 0.30 × 0.12 mm

Data collection top

Bruker–Nonius Kappa CCD diffractometer	1793 independent reflections
Radiation source: sealed X-ray tube, Enhance (Cu) X-ray Source	1681 reflections with I > 2σ(I)
Detector resolution: 7.9 pixels mm^-1	R_int = 0.028
ω scans	θ_max = 66.0°, θ_min = 4.3°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	h = −7→5
T_min = 0.771, T_max = 1.000	k = −10→10
9261 measured reflections	l = −13→12

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.037	Hydrogen site location: mixed
wR(F²) = 0.098	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0479P)² + 0.5464P] where P = (F_o² + 2F_c²)/3
1793 reflections	(Δ/σ)_max < 0.001
160 parameters	Δρ_max = 0.71 e Å⁻³
1 restraint	Δρ_min = −0.27 e Å⁻³

Special details top

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
Cl1	0.16834 (8)	0.41808 (6)	0.40624 (5)	0.02598 (19)
N1	0.4817 (3)	0.2850 (2)	0.28999 (16)	0.0208 (4)
C2	0.6669 (3)	0.2012 (3)	0.28642 (19)	0.0208 (4)
H2	0.719070	0.193795	0.204161	0.025*
N3	0.7920 (3)	0.1241 (2)	0.38609 (16)	0.0201 (4)
C4	0.7122 (3)	0.1387 (2)	0.49898 (19)	0.0181 (4)
C5	0.5139 (3)	0.2254 (2)	0.51675 (19)	0.0175 (4)
C6	0.4064 (3)	0.2984 (2)	0.40720 (19)	0.0185 (4)
N7	0.4843 (3)	0.2163 (2)	0.64573 (16)	0.0195 (4)
C8	0.6671 (3)	0.1184 (3)	0.71453 (19)	0.0217 (4)
H8A	0.750275	0.184768	0.750830	0.026*
H8B	0.612778	0.016417	0.786389	0.026*
N9	0.8027 (3)	0.0776 (2)	0.61286 (16)	0.0212 (4)
H9	0.916 (3)	0.018 (3)	0.627 (2)	0.021 (6)*
O1'	0.1576 (3)	0.2578 (2)	1.12373 (14)	0.0278 (4)
H1'	0.256 (5)	0.284 (4)	1.161 (3)	0.045 (8)*
C2'	0.2169 (4)	0.3455 (3)	0.9900 (2)	0.0273 (5)
H2'	0.230429	0.466833	0.973632	0.033*
C3'	0.4091 (4)	0.2873 (3)	0.9160 (2)	0.0346 (6)
H3'1	0.446403	0.167641	0.956402	0.041*
H3'2	0.541933	0.356932	0.895749	0.041*
C5'	0.0629 (4)	0.3203 (3)	0.8985 (2)	0.0277 (5)
H5'1	−0.044286	0.412524	0.866879	0.033*
H5'2	−0.011259	0.211215	0.933326	0.033*
C4'	0.2642 (4)	0.3281 (3)	0.7998 (2)	0.0240 (6)	0.858 (4)
H4'	0.288618	0.445876	0.739504	0.029*	0.858 (4)
C6'	0.2716 (4)	0.2157 (3)	0.7213 (2)	0.0229 (6)	0.858 (4)
H6'1	0.239112	0.100518	0.781565	0.027*	0.858 (4)
H6'2	0.155181	0.251106	0.660680	0.027*	0.858 (4)
C4'B	0.246 (3)	0.216 (2)	0.8417 (15)	0.0240 (6)	0.142 (4)
H4'B	0.228733	0.092243	0.870206	0.029*	0.142 (4)
C6'B	0.332 (3)	0.308 (2)	0.7043 (15)	0.0229 (6)	0.142 (4)
H6'3	0.206224	0.345077	0.650824	0.027*	0.142 (4)
H6'4	0.406521	0.409522	0.701360	0.027*	0.142 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0222 (3)	0.0321 (3)	0.0240 (3)	0.0101 (2)	−0.0049 (2)	−0.0110 (2)
N1	0.0227 (9)	0.0239 (9)	0.0162 (8)	0.0000 (7)	−0.0018 (7)	−0.0078 (7)
C2	0.0227 (11)	0.0255 (10)	0.0158 (10)	−0.0004 (8)	0.0012 (8)	−0.0104 (8)
N3	0.0198 (9)	0.0244 (9)	0.0173 (8)	0.0013 (7)	0.0010 (7)	−0.0100 (7)
C4	0.0171 (10)	0.0192 (10)	0.0186 (10)	−0.0008 (8)	−0.0003 (8)	−0.0080 (8)
C5	0.0181 (10)	0.0193 (9)	0.0166 (10)	−0.0025 (8)	0.0006 (8)	−0.0087 (8)
C6	0.0168 (10)	0.0204 (10)	0.0192 (10)	0.0014 (8)	−0.0004 (8)	−0.0087 (8)
N7	0.0173 (9)	0.0277 (9)	0.0155 (8)	0.0057 (7)	−0.0014 (7)	−0.0109 (7)
C8	0.0212 (11)	0.0293 (11)	0.0176 (10)	0.0059 (8)	−0.0036 (8)	−0.0121 (8)
N9	0.0181 (9)	0.0294 (10)	0.0181 (9)	0.0094 (7)	−0.0038 (7)	−0.0114 (7)
O1'	0.0275 (9)	0.0394 (9)	0.0177 (7)	0.0028 (7)	−0.0043 (6)	−0.0115 (7)
C2'	0.0286 (12)	0.0371 (12)	0.0179 (10)	−0.0017 (9)	−0.0008 (9)	−0.0119 (9)
C3'	0.0257 (12)	0.0522 (15)	0.0340 (13)	0.0000 (11)	−0.0030 (10)	−0.0253 (12)
C5'	0.0250 (11)	0.0400 (13)	0.0215 (11)	0.0119 (9)	−0.0052 (9)	−0.0157 (10)
C4'	0.0258 (13)	0.0263 (14)	0.0205 (12)	0.0035 (11)	0.0002 (10)	−0.0104 (11)
C6'	0.0164 (12)	0.0341 (16)	0.0216 (12)	0.0011 (11)	0.0000 (10)	−0.0147 (11)
C4'B	0.0258 (13)	0.0263 (14)	0.0205 (12)	0.0035 (11)	0.0002 (10)	−0.0104 (11)
C6'B	0.0164 (12)	0.0341 (16)	0.0216 (12)	0.0011 (11)	0.0000 (10)	−0.0147 (11)

Geometric parameters (Å, º) top

Cl1—C6	1.739 (2)	C2'—C3'	1.524 (3)
N1—C2	1.317 (3)	C2'—C5'	1.527 (3)
N1—C6	1.365 (3)	C2'—H2'	1.0000
C2—N3	1.355 (3)	C3'—C4'	1.561 (3)
C2—H2	0.9500	C3'—C4'B	1.626 (16)
N3—C4	1.332 (3)	C3'—H3'1	0.9900
C4—N9	1.342 (3)	C3'—H3'2	0.9900
C4—C5	1.424 (3)	C5'—C4'	1.537 (3)
C5—C6	1.366 (3)	C5'—C4'B	1.616 (15)
C5—N7	1.386 (2)	C5'—H5'1	0.9900
N7—C6'B	1.440 (15)	C5'—H5'2	0.9900
N7—C6'	1.465 (3)	C4'—C6'	1.508 (3)
N7—C8	1.471 (3)	C4'—H4'	1.0000
C8—N9	1.455 (3)	C6'—H6'1	0.9900
C8—H8A	0.9900	C6'—H6'2	0.9900
C8—H8B	0.9900	C4'B—C6'B	1.48 (2)
N9—H9	0.833 (17)	C4'B—H4'B	1.0000
O1'—C2'	1.407 (3)	C6'B—H6'3	0.9900
O1'—H1'	0.84 (3)	C6'B—H6'4	0.9900

C2—N1—C6	116.73 (17)	C2'—C3'—H3'1	114.0
N1—C2—N3	127.76 (18)	C4'—C3'—H3'1	114.0
N1—C2—H2	116.1	C2'—C3'—H3'2	114.0
N3—C2—H2	116.1	C4'—C3'—H3'2	114.0
C4—N3—C2	113.74 (17)	H3'1—C3'—H3'2	111.2
N3—C4—N9	126.70 (19)	C2'—C5'—C4'	88.64 (17)
N3—C4—C5	124.39 (18)	C2'—C5'—C4'B	92.8 (6)
N9—C4—C5	108.91 (17)	C2'—C5'—H5'1	113.9
C6—C5—N7	136.29 (19)	C4'—C5'—H5'1	113.9
C6—C5—C4	115.33 (18)	C2'—C5'—H5'2	113.9
N7—C5—C4	108.35 (17)	C4'—C5'—H5'2	113.9
N1—C6—C5	122.04 (18)	H5'1—C5'—H5'2	111.1
N1—C6—Cl1	115.38 (15)	C6'—C4'—C5'	118.5 (2)
C5—C6—Cl1	122.56 (15)	C6'—C4'—C3'	120.1 (2)
C5—N7—C6'B	128.7 (6)	C5'—C4'—C3'	87.40 (17)
C5—N7—C6'	125.55 (17)	C6'—C4'—H4'	109.7
C5—N7—C8	108.55 (16)	C5'—C4'—H4'	109.7
C6'B—N7—C8	121.7 (6)	C3'—C4'—H4'	109.7
C6'—N7—C8	118.33 (17)	N7—C6'—C4'	113.3 (2)
N9—C8—N7	103.41 (15)	N7—C6'—H6'1	108.9
N9—C8—H8A	111.1	C4'—C6'—H6'1	108.9
N7—C8—H8A	111.1	N7—C6'—H6'2	108.9
N9—C8—H8B	111.1	C4'—C6'—H6'2	108.9
N7—C8—H8B	111.1	H6'1—C6'—H6'2	107.7
H8A—C8—H8B	109.0	C6'B—C4'B—C5'	112.7 (13)
C4—N9—C8	110.76 (17)	C6'B—C4'B—C3'	99.0 (12)
C4—N9—H9	125.9 (17)	C5'—C4'B—C3'	82.6 (7)
C8—N9—H9	123.2 (17)	C6'B—C4'B—H4'B	118.5
C2'—O1'—H1'	103 (2)	C5'—C4'B—H4'B	118.5
O1'—C2'—C3'	121.1 (2)	C3'—C4'B—H4'B	118.5
O1'—C2'—C5'	114.52 (18)	N7—C6'B—C4'B	115.0 (14)
C3'—C2'—C5'	89.12 (16)	N7—C6'B—H6'3	108.5
O1'—C2'—H2'	110.1	C4'B—C6'B—H6'3	108.5
C3'—C2'—H2'	110.1	N7—C6'B—H6'4	108.5
C5'—C2'—H2'	110.1	C4'B—C6'B—H6'4	108.5
C2'—C3'—C4'	87.87 (18)	H6'3—C6'B—H6'4	107.5
C2'—C3'—C4'B	92.5 (5)

C6—N1—C2—N3	0.8 (3)	N7—C8—N9—C4	−1.3 (2)
N1—C2—N3—C4	−0.3 (3)	O1'—C2'—C3'—C4'	138.2 (2)
C2—N3—C4—N9	−178.94 (19)	C5'—C2'—C3'—C4'	19.78 (18)
C2—N3—C4—C5	0.4 (3)	O1'—C2'—C3'—C4'B	105.1 (6)
N3—C4—C5—C6	−1.1 (3)	C5'—C2'—C3'—C4'B	−13.3 (6)
N9—C4—C5—C6	178.36 (17)	O1'—C2'—C5'—C4'	−144.2 (2)
N3—C4—C5—N7	−179.35 (17)	C3'—C2'—C5'—C4'	−20.09 (19)
N9—C4—C5—N7	0.1 (2)	O1'—C2'—C5'—C4'B	−110.7 (6)
C2—N1—C6—C5	−1.6 (3)	C3'—C2'—C5'—C4'B	13.4 (6)
C2—N1—C6—Cl1	177.14 (14)	C2'—C5'—C4'—C6'	142.7 (2)
N7—C5—C6—N1	179.3 (2)	C2'—C5'—C4'—C3'	19.62 (18)
C4—C5—C6—N1	1.6 (3)	C2'—C3'—C4'—C6'	−141.4 (2)
N7—C5—C6—Cl1	0.7 (3)	C2'—C3'—C4'—C5'	−19.66 (18)
C4—C5—C6—Cl1	−176.96 (14)	C5—N7—C6'—C4'	−135.6 (2)
C6—C5—N7—C6'B	−10.1 (10)	C8—N7—C6'—C4'	78.4 (3)
C4—C5—N7—C6'B	167.6 (10)	C5'—C4'—C6'—N7	−171.4 (2)
C6—C5—N7—C6'	32.6 (4)	C3'—C4'—C6'—N7	−66.6 (3)
C4—C5—N7—C6'	−149.7 (2)	C2'—C5'—C4'B—C6'B	−109.4 (12)
C6—C5—N7—C8	−178.7 (2)	C2'—C5'—C4'B—C3'	−12.7 (6)
C4—C5—N7—C8	−0.9 (2)	C2'—C3'—C4'B—C6'B	124.6 (10)
C5—N7—C8—N9	1.3 (2)	C2'—C3'—C4'B—C5'	12.7 (6)
C6'B—N7—C8—N9	−168.2 (9)	C5—N7—C6'B—C4'B	146.2 (9)
C6'—N7—C8—N9	152.69 (18)	C8—N7—C6'B—C4'B	−46.6 (16)
N3—C4—N9—C8	−179.79 (18)	C5'—C4'B—C6'B—N7	−175.7 (10)
C5—C4—N9—C8	0.8 (2)	C3'—C4'B—C6'B—N7	98.5 (13)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of ring N1/C2/N3/C4/C5/C6.

D—H···A	D—H	H···A	D···A	D—H···A
C6′—H6′2···Cl1	0.99	2.64	3.390 (3)	132
N9—H9···N3ⁱ	0.83 (2)	2.14 (2)	2.952 (2)	166 (2)
O1′—H1′···N1ⁱⁱ	0.84 (3)	2.09 (3)	2.909 (2)	164 (3)
C4′—H4′···Cg1ⁱⁱⁱ	0.99	2.87	3.857 (3)	170

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

3-[(6-Chloro-9H-purin-9-yl)methyl]cyclobutan-1-ol (IV) top

Crystal data top

C₁₀H₁₁ClN₄O	F(000) = 496
M_r = 238.68	D_x = 1.482 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.54178 Å
a = 12.7276 (8) Å	Cell parameters from 4964 reflections
b = 5.9725 (4) Å	θ = 4.0–64.9°
c = 14.819 (1) Å	µ = 3.04 mm⁻¹
β = 108.250 (3)°	T = 110 K
V = 1069.81 (12) Å³	Plate, colourless
Z = 4	0.50 × 0.21 × 0.07 mm

Data collection top

Bruker APEXII CCD diffractometer	1732 independent reflections
Radiation source: sealed X-ray tube	1569 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.045
Detector resolution: 7.9 pixels mm^-1	θ_max = 64.9°, θ_min = 4.0°
ω scans	h = −14→14
Absorption correction: numerical (CrysAlisPro; Rigaku OD, 2018)	k = −4→7
T_min = 0.043, T_max = 0.741	l = −17→17
7078 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	H-atom parameters constrained
S = 0.94	w = 1/[σ²(F_o²) + (0.0599P)² + 1.4189P] where P = (F_o² + 2F_c²)/3
1732 reflections	(Δ/σ)_max < 0.001
146 parameters	Δρ_max = 0.35 e Å⁻³
0 restraints	Δρ_min = −0.31 e Å⁻³

Special details top

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

	x	y	z	U_iso*/U_eq
Cl1	0.65978 (4)	0.22748 (10)	0.21719 (4)	0.0258 (2)
O1'	−0.06577 (11)	0.5696 (3)	−0.19248 (10)	0.0233 (4)
H1'	−0.067187	0.456986	−0.226798	0.035*
N3	0.44729 (14)	0.7995 (3)	0.06539 (12)	0.0218 (4)
N1	0.61729 (14)	0.5895 (3)	0.11346 (12)	0.0196 (4)
N7	0.39848 (13)	0.3289 (3)	0.19580 (12)	0.0199 (4)
N9	0.30402 (13)	0.6280 (3)	0.11873 (11)	0.0186 (4)
C4	0.40817 (16)	0.6422 (4)	0.11001 (13)	0.0178 (5)
C5	0.46564 (16)	0.4569 (4)	0.15808 (13)	0.0168 (5)
C3'	0.12604 (16)	0.5194 (4)	−0.07173 (14)	0.0201 (5)
H3'A	0.090406	0.436047	−0.031431	0.024*
H3'B	0.179230	0.424010	−0.090614	0.024*
C6	0.57424 (16)	0.4399 (4)	0.15774 (13)	0.0180 (5)
C8	0.30351 (16)	0.4385 (4)	0.16970 (14)	0.0192 (5)
H8	0.240264	0.389301	0.185165	0.023*
C2	0.55210 (18)	0.7598 (4)	0.07007 (15)	0.0223 (5)
H2	0.584609	0.865250	0.038801	0.027*
C2'	0.04431 (16)	0.6477 (4)	−0.15487 (14)	0.0177 (5)
H2'	0.077386	0.673588	−0.206946	0.021*
C4'	0.17237 (18)	0.7495 (4)	−0.03173 (15)	0.0216 (5)
H4'	0.231950	0.796287	−0.058547	0.026*
C6'	0.21115 (17)	0.7800 (4)	0.07552 (15)	0.0208 (5)
H6'A	0.234806	0.936928	0.091463	0.025*
H6'B	0.149539	0.747512	0.100968	0.025*
C5'	0.05979 (17)	0.8537 (4)	−0.09087 (15)	0.0217 (5)
H5'A	0.005170	0.866225	−0.056036	0.026*
H5'B	0.066593	0.996160	−0.122717	0.026*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0169 (3)	0.0313 (4)	0.0291 (3)	0.0052 (2)	0.0069 (2)	0.0101 (2)
O1'	0.0144 (7)	0.0311 (10)	0.0231 (8)	−0.0006 (6)	0.0037 (6)	−0.0095 (7)
N3	0.0217 (9)	0.0229 (11)	0.0184 (9)	−0.0037 (8)	0.0027 (7)	0.0013 (8)
N1	0.0194 (9)	0.0206 (10)	0.0183 (8)	−0.0042 (8)	0.0051 (7)	−0.0005 (8)
N7	0.0155 (9)	0.0260 (11)	0.0177 (8)	−0.0011 (8)	0.0045 (7)	0.0024 (8)
N9	0.0142 (8)	0.0232 (11)	0.0160 (8)	0.0021 (8)	0.0013 (7)	−0.0017 (8)
C4	0.0169 (10)	0.0206 (12)	0.0129 (9)	−0.0030 (9)	0.0004 (8)	−0.0016 (8)
C5	0.0156 (9)	0.0207 (12)	0.0121 (9)	−0.0022 (8)	0.0014 (7)	−0.0014 (8)
C3'	0.0188 (10)	0.0231 (12)	0.0177 (10)	0.0034 (9)	0.0045 (8)	−0.0013 (9)
C6	0.0160 (10)	0.0219 (12)	0.0134 (9)	−0.0010 (9)	0.0006 (8)	−0.0002 (9)
C8	0.0159 (10)	0.0234 (13)	0.0177 (9)	−0.0013 (9)	0.0045 (8)	0.0003 (9)
C2	0.0230 (11)	0.0232 (13)	0.0193 (10)	−0.0064 (9)	0.0047 (9)	0.0015 (9)
C2'	0.0134 (9)	0.0220 (12)	0.0165 (10)	0.0005 (9)	0.0031 (8)	−0.0007 (9)
C4'	0.0186 (11)	0.0249 (13)	0.0194 (11)	0.0010 (9)	0.0035 (9)	0.0009 (9)
C6'	0.0193 (11)	0.0209 (12)	0.0194 (10)	0.0043 (9)	0.0021 (8)	0.0000 (9)
C5'	0.0206 (10)	0.0223 (13)	0.0185 (10)	0.0032 (9)	0.0011 (8)	0.0001 (9)

Geometric parameters (Å, º) top

Cl1—C6	1.723 (2)	C3'—C2'	1.544 (3)
O1'—C2'	1.415 (2)	C3'—H3'A	0.9900
O1'—H1'	0.8400	C3'—H3'B	0.9900
N3—C4	1.332 (3)	C8—H8	0.9500
N3—C2	1.335 (3)	C2—H2	0.9500
N1—C6	1.325 (3)	C2'—C5'	1.528 (3)
N1—C2	1.342 (3)	C2'—H2'	1.0000
N7—C8	1.321 (3)	C4'—C6'	1.520 (3)
N7—C5	1.388 (3)	C4'—C5'	1.556 (3)
N9—C8	1.362 (3)	C4'—H4'	1.0000
N9—C4	1.374 (3)	C6'—H6'A	0.9900
N9—C6'	1.469 (3)	C6'—H6'B	0.9900
C4—C5	1.393 (3)	C5'—H5'A	0.9900
C5—C6	1.388 (3)	C5'—H5'B	0.9900
C3'—C4'	1.539 (3)

C2'—O1'—H1'	109.5	N3—C2—H2	116.0
C4—N3—C2	111.81 (19)	N1—C2—H2	116.0
C6—N1—C2	117.32 (17)	O1'—C2'—C5'	115.42 (17)
C8—N7—C5	103.39 (18)	O1'—C2'—C3'	119.16 (18)
C8—N9—C4	106.00 (17)	C5'—C2'—C3'	88.88 (16)
C8—N9—C6'	127.78 (17)	O1'—C2'—H2'	110.6
C4—N9—C6'	126.10 (18)	C5'—C2'—H2'	110.6
N3—C4—N9	127.7 (2)	C3'—C2'—H2'	110.6
N3—C4—C5	126.60 (19)	C6'—C4'—C3'	118.02 (19)
N9—C4—C5	105.69 (18)	C6'—C4'—C5'	118.75 (18)
C6—C5—N7	134.5 (2)	C3'—C4'—C5'	88.05 (16)
C6—C5—C4	114.87 (19)	C6'—C4'—H4'	110.1
N7—C5—C4	110.64 (17)	C3'—C4'—H4'	110.1
C4'—C3'—C2'	86.87 (17)	C5'—C4'—H4'	110.1
C4'—C3'—H3'A	114.2	N9—C6'—C4'	109.58 (17)
C2'—C3'—H3'A	114.2	N9—C6'—H6'A	109.8
C4'—C3'—H3'B	114.2	C4'—C6'—H6'A	109.8
C2'—C3'—H3'B	114.2	N9—C6'—H6'B	109.8
H3'A—C3'—H3'B	111.3	C4'—C6'—H6'B	109.8
N1—C6—C5	121.3 (2)	H6'A—C6'—H6'B	108.2
N1—C6—Cl1	117.18 (15)	C2'—C5'—C4'	86.82 (16)
C5—C6—Cl1	121.52 (16)	C2'—C5'—H5'A	114.2
N7—C8—N9	114.28 (18)	C4'—C5'—H5'A	114.2
N7—C8—H8	122.9	C2'—C5'—H5'B	114.2
N9—C8—H8	122.9	C4'—C5'—H5'B	114.2
N3—C2—N1	128.1 (2)	H5'A—C5'—H5'B	111.3

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of ring N1/C2/N3/C4/C5/C6.

D—H···A	D—H	H···A	D···A	D—H···A
O1′—H1′···N7ⁱ	0.84	2.03	2.853 (3)	168
C8—H8···O1′ⁱⁱ	0.95	2.27	3.148 (2)	153
C2—H2···N3ⁱⁱⁱ	0.95	2.48	3.311 (3)	146
C2′—H2′···Cg1^iv	0.99	2.84	3.628 (2)	136

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

Geometric parameters (Å, °) about atom C8 for compounds (I), (II) and (IV) top

Bond/angle	(I)	(II)	(IV)
C8—N7	1.381 (2)	1.471 (3)	1.362 (3)
C8—N9	1.301 (2)	1.455 (3)	1.321 (3)
N7—C8—N9	114.95 (15)	103.41 (15)	114.28 (18)

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Crystal structures of the synthetic inter­mediate 3-[(6-chloro-7H-purin-7-yl)meth­yl]cyclo­butan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-di­hydro-7H-purin-7-yl)meth­yl]cyclo­butan-1-ol and 3-[(6-chloro-9H-purin-9-yl)meth­yl]cyclo­butan-1-ol

Supporting information

Key indicators

checkCIF/PLATON results

Crystal structures of the synthetic intermediate 3-[(6-chloro-7H-purin-7-yl)methyl]cyclobutan-1-one, and of two oxetanocin derivatives: 3-[(6-chloro-8,9-dihydro-7H-purin-7-yl)methyl]cyclobutan-1-ol and 3-[(6-chloro-9H-purin-9-yl)methyl]cyclobutan-1-ol