Crystal structure of ethyl 6-(2-fluoro-phen-yl)-4-hy-droxy-2-sulfanyl-idene-4-tri-fluoro-meth-yl-1,3-diazinane-5-carboxyl-ate.

In the title compound, C14H14F4N2O3S, the central di-hydro-pyrimidine ring adopts a sofa conformation with the C atom bearing the 2-fluoro-benzene ring displaced by 0.596 (3) Å from the other five atoms. The 2-fluoro-benzene ring is positioned axially and bis-ects the pyrimidine ring with a dihedral angle of 70.92 (8)°. The mol-ecular conformation is stabilized by an intra-molecular O-H⋯O hydrogen bond, generating an S(6) ring. The crystal structure features C-H⋯F, N-H⋯S and N-H⋯O hydrogen bonds, which link the mol-ecules into a three-dimensional network.

Related literature

For the bioactivity of di­hydro­pyrimidines, see: Atwal et al. (1989 ▸); Brier et al. (2004 ▸); Cochran et al. (2005 ▸); Moran et al. (2007 ▸); Zorkun et al. (2006 ▸). For the bioactivity of organofluorine compounds, see: Hermann et al. (2003 ▸); Ulrich (2004 ▸). For related structures, see: Mosslemin et al. (2009 ▸); Li et al. (2011 ▸); Huang et al. (2012 ▸).

Experimental

Crystal data

C14H14F4N2O3S

M = 366.33

Monoclinic,

a = 10.937 (3) Å

b = 9.934 (3) Å

c = 14.629 (4) Å

β = 108.239 (5)°

V = 1509.7 (8) Å3

Z = 4

Mo Kα radiation

μ = 0.28 mm−1

T = 100 K

0.15 × 0.12 × 0.09 mm

Data collection

Bruker SMART APEX CCD detector diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 1998 ▸) T min = 0.952, T max = 0.957

7619 measured reflections

2646 independent reflections

2138 reflections with I > 2σ(I)

R int = 0.034

Refinement

R[F 2 > 2σ(F 2)] = 0.046

wR(F 2) = 0.141

S = 1.03

2646 reflections

219 parameters

H-atom parameters constrained

Δρmax = 0.64 e Å−3

Δρmin = −0.29 e Å−3

Data collection: SMART (Bruker,1998 ▸); cell refinement: SAINT-Plus (Bruker, 1998 ▸); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸) and CAMERON (Watkin et al., 1996 ▸); software used to prepare material for publication: WinGX (Farrugia, 2012 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015005836/hb7389sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015005836/hb7389Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989015005836/hb7389Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S2056989015005836/hb7389fig1.tif

The mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.

Click here for additional data file.

. DOI: 10.1107/S2056989015005836/hb7389fig2.tif

Unit-cell packing of the title compound showing C—H⋯F inter­actions as dotted lines. H atoms not involved in hydrogen bonding have been excluded.

Click here for additional data file.

. DOI: 10.1107/S2056989015005836/hb7389fig3.tif

Unit-cell packing depicting the N—H⋯S and N—H⋯O inter­actions with dotted lines. H atoms not involved in hydrogen bonding have been excluded.

CCDC reference: 1055499

Additional supporting information: crystallographic information; 3D view; checkCIF report

C14H14F4N2O3S	F(000) = 752
Mr = 366.33	Dx = 1.612 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2646 reflections
a = 10.937 (3) Å	θ = 2.0–25.0°
b = 9.934 (3) Å	µ = 0.28 mm−1
c = 14.629 (4) Å	T = 100 K
β = 108.239 (5)°	Block, colourless
V = 1509.7 (8) Å3	0.15 × 0.12 × 0.09 mm
Z = 4

Bruker SMART APEX CCD detector diffractometer	2646 independent reflections
Radiation source: fine-focus sealed tube	2138 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.034
ω scans	θmax = 25.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 1998)	h = −12→13
Tmin = 0.952, Tmax = 0.957	k = −11→7
7619 measured reflections	l = −17→17

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)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.141	H-atom parameters constrained
S = 1.03	w = 1/[σ2(Fo2) + (0.0939P)2 + 0.0341P] where P = (Fo2 + 2Fc2)/3
2646 reflections	(Δ/σ)max < 0.001
219 parameters	Δρmax = 0.64 e Å−3
0 restraints	Δρmin = −0.29 e Å−3

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

Refinement. 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 > 2σ(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.

	x	y	z	Uiso*/Ueq
S1	0.09623 (6)	0.40020 (7)	0.12780 (4)	0.0190 (2)
O1	−0.35850 (17)	0.71225 (18)	0.25205 (13)	0.0243 (5)
O2	−0.44764 (17)	0.50537 (18)	0.22450 (13)	0.0214 (4)
O3	−0.18273 (16)	0.75721 (18)	0.15250 (12)	0.0194 (4)
H3	−0.2203	0.7777	0.1926	0.029*
N1	−0.10705 (19)	0.5616 (2)	0.09977 (14)	0.0177 (5)
H1	−0.0968	0.5790	0.0436	0.021*
N2	−0.0313 (2)	0.4589 (2)	0.24785 (14)	0.0178 (5)
H2	0.0244	0.4048	0.2875	0.021*
F1	−0.36294 (14)	0.50800 (15)	−0.00967 (10)	0.0242 (4)
F2	−0.29456 (14)	0.70124 (16)	−0.04041 (10)	0.0238 (4)
F3	−0.42992 (13)	0.68945 (15)	0.03915 (10)	0.0225 (4)
F4	−0.18118 (15)	0.23990 (15)	0.27621 (10)	0.0270 (4)
C1	−0.3263 (2)	0.6310 (3)	0.02677 (18)	0.0183 (6)
C2	−0.0206 (2)	0.4780 (2)	0.16074 (18)	0.0165 (6)
C3	−0.3585 (2)	0.5968 (3)	0.22634 (18)	0.0189 (6)
C6	−0.1299 (2)	0.5223 (3)	0.28213 (17)	0.0182 (6)
H6	−0.0996	0.6145	0.3062	0.022*
C5	−0.2516 (2)	0.5364 (3)	0.19469 (17)	0.0164 (6)
H5	−0.2787	0.4454	0.1664	0.020*
C4	−0.2143 (2)	0.6238 (3)	0.12085 (18)	0.0163 (6)
C7	−0.5546 (3)	0.5477 (3)	0.2590 (2)	0.0270 (7)
H7A	−0.6337	0.4981	0.2234	0.032*
H7B	−0.5711	0.6451	0.2465	0.032*
C8	−0.5230 (3)	0.5208 (3)	0.3643 (2)	0.0334 (7)
H8A	−0.5017	0.4254	0.3770	0.050*
H8B	−0.5975	0.5433	0.3851	0.050*
H8C	−0.4493	0.5761	0.3999	0.050*
C9	−0.1537 (2)	0.4440 (3)	0.36335 (17)	0.0163 (6)
C10	−0.1553 (2)	0.5097 (3)	0.44637 (17)	0.0182 (6)
H10	−0.1368	0.6033	0.4530	0.022*
C11	−0.1832 (2)	0.4416 (3)	0.51975 (18)	0.0210 (6)
H11	−0.1870	0.4889	0.5752	0.025*
C12	−0.2054 (2)	0.3050 (3)	0.51222 (19)	0.0235 (6)
H12	−0.2225	0.2579	0.5634	0.028*
C13	−0.2031 (2)	0.2362 (3)	0.43111 (17)	0.0214 (6)
H13	−0.2176	0.1418	0.4259	0.026*
C14	−0.1794 (2)	0.3073 (3)	0.35795 (18)	0.0199 (6)

	U11	U22	U33	U12	U13	U23
S1	0.0188 (4)	0.0194 (4)	0.0211 (4)	0.0030 (3)	0.0096 (3)	0.0022 (3)
O1	0.0242 (10)	0.0196 (11)	0.0303 (10)	0.0003 (8)	0.0104 (8)	−0.0030 (8)
O2	0.0194 (10)	0.0217 (10)	0.0250 (10)	−0.0018 (8)	0.0098 (8)	0.0004 (8)
O3	0.0205 (10)	0.0177 (10)	0.0216 (10)	−0.0009 (8)	0.0089 (8)	−0.0010 (8)
N1	0.0208 (11)	0.0191 (12)	0.0152 (11)	0.0020 (9)	0.0086 (9)	0.0033 (9)
N2	0.0176 (11)	0.0212 (12)	0.0139 (11)	0.0037 (9)	0.0040 (9)	0.0029 (9)
F1	0.0250 (8)	0.0219 (9)	0.0227 (8)	−0.0002 (7)	0.0035 (7)	−0.0039 (7)
F2	0.0231 (8)	0.0304 (9)	0.0186 (8)	0.0043 (7)	0.0074 (6)	0.0092 (7)
F3	0.0169 (7)	0.0278 (9)	0.0232 (8)	0.0058 (6)	0.0071 (6)	0.0019 (7)
F4	0.0400 (9)	0.0207 (9)	0.0240 (8)	−0.0038 (7)	0.0154 (7)	−0.0038 (7)
C1	0.0189 (13)	0.0156 (13)	0.0225 (14)	0.0026 (11)	0.0097 (11)	0.0005 (11)
C2	0.0163 (13)	0.0144 (13)	0.0189 (13)	−0.0023 (10)	0.0055 (11)	0.0011 (10)
C3	0.0158 (13)	0.0224 (16)	0.0166 (13)	−0.0023 (11)	0.0023 (10)	0.0026 (11)
C6	0.0175 (13)	0.0159 (14)	0.0207 (13)	−0.0004 (11)	0.0052 (11)	0.0001 (11)
C5	0.0185 (13)	0.0155 (13)	0.0155 (12)	0.0016 (11)	0.0058 (11)	0.0004 (10)
C4	0.0170 (13)	0.0136 (13)	0.0189 (13)	0.0016 (10)	0.0066 (11)	−0.0009 (10)
C7	0.0168 (14)	0.0304 (16)	0.0372 (17)	0.0008 (12)	0.0134 (13)	−0.0010 (13)
C8	0.0311 (16)	0.046 (2)	0.0301 (16)	−0.0089 (15)	0.0197 (14)	−0.0049 (14)
C9	0.0127 (12)	0.0202 (14)	0.0156 (12)	0.0032 (11)	0.0041 (10)	0.0031 (11)
C10	0.0144 (13)	0.0177 (14)	0.0207 (14)	0.0010 (10)	0.0030 (11)	−0.0020 (11)
C11	0.0206 (14)	0.0273 (15)	0.0160 (13)	0.0013 (12)	0.0070 (11)	−0.0014 (11)
C12	0.0243 (14)	0.0253 (16)	0.0235 (14)	0.0033 (12)	0.0111 (11)	0.0080 (12)
C13	0.0281 (14)	0.0154 (14)	0.0228 (14)	0.0002 (12)	0.0110 (11)	0.0038 (11)
C14	0.0229 (14)	0.0183 (14)	0.0186 (13)	0.0014 (11)	0.0068 (11)	−0.0032 (11)

S1—C2	1.688 (3)	C6—H6	1.0000
O1—C3	1.207 (3)	C5—C4	1.537 (3)
O2—C3	1.327 (3)	C5—H5	1.0000
O2—C7	1.473 (3)	C7—C8	1.494 (4)
O3—C4	1.411 (3)	C7—H7A	0.9900
O3—H3	0.8400	C7—H7B	0.9900
N1—C2	1.361 (3)	C8—H8A	0.9800
N1—C4	1.442 (3)	C8—H8B	0.9800
N1—H1	0.8800	C8—H8C	0.9800
N2—C2	1.329 (3)	C9—C10	1.384 (3)
N2—C6	1.466 (3)	C9—C14	1.384 (4)
N2—H2	0.8800	C10—C11	1.381 (4)
F1—C1	1.343 (3)	C10—H10	0.9500
F2—C1	1.337 (3)	C11—C12	1.377 (4)
F3—C1	1.335 (3)	C11—H11	0.9500
F4—C14	1.365 (3)	C12—C13	1.377 (4)
C1—C4	1.531 (3)	C12—H12	0.9500
C3—C5	1.510 (3)	C13—C14	1.373 (4)
C6—C9	1.509 (3)	C13—H13	0.9500
C6—C5	1.537 (3)
C3—O2—C7	117.0 (2)	N1—C4—C1	107.66 (19)
C4—O3—H3	109.5	O3—C4—C5	113.1 (2)
C2—N1—C4	124.5 (2)	N1—C4—C5	108.7 (2)
C2—N1—H1	117.8	C1—C4—C5	110.1 (2)
C4—N1—H1	117.8	O2—C7—C8	110.5 (2)
C2—N2—C6	124.1 (2)	O2—C7—H7A	109.6
C2—N2—H2	117.9	C8—C7—H7A	109.6
C6—N2—H2	117.9	O2—C7—H7B	109.6
F3—C1—F2	107.4 (2)	C8—C7—H7B	109.6
F3—C1—F1	106.8 (2)	H7A—C7—H7B	108.1
F2—C1—F1	107.3 (2)	C7—C8—H8A	109.5
F3—C1—C4	111.9 (2)	C7—C8—H8B	109.5
F2—C1—C4	111.5 (2)	H8A—C8—H8B	109.5
F1—C1—C4	111.7 (2)	C7—C8—H8C	109.5
N2—C2—N1	117.7 (2)	H8A—C8—H8C	109.5
N2—C2—S1	120.65 (19)	H8B—C8—H8C	109.5
N1—C2—S1	121.70 (19)	C10—C9—C14	117.0 (2)
O1—C3—O2	125.8 (2)	C10—C9—C6	120.0 (2)
O1—C3—C5	123.3 (2)	C14—C9—C6	122.9 (2)
O2—C3—C5	110.9 (2)	C11—C10—C9	121.2 (3)
N2—C6—C9	112.0 (2)	C11—C10—H10	119.4
N2—C6—C5	107.03 (19)	C9—C10—H10	119.4
C9—C6—C5	112.6 (2)	C12—C11—C10	119.8 (2)
N2—C6—H6	108.4	C12—C11—H11	120.1
C9—C6—H6	108.4	C10—C11—H11	120.1
C5—C6—H6	108.4	C13—C12—C11	120.5 (2)
C3—C5—C6	109.46 (19)	C13—C12—H12	119.7
C3—C5—C4	113.1 (2)	C11—C12—H12	119.7
C6—C5—C4	106.6 (2)	C14—C13—C12	118.4 (3)
C3—C5—H5	109.2	C14—C13—H13	120.8
C6—C5—H5	109.2	C12—C13—H13	120.8
C4—C5—H5	109.2	F4—C14—C13	118.4 (2)
O3—C4—N1	109.9 (2)	F4—C14—C9	118.5 (2)
O3—C4—C1	107.2 (2)	C13—C14—C9	123.0 (2)
C6—N2—C2—N1	−0.1 (4)	F3—C1—C4—C5	62.6 (3)
C6—N2—C2—S1	−179.87 (18)	F2—C1—C4—C5	−177.09 (19)
C4—N1—C2—N2	−4.3 (4)	F1—C1—C4—C5	−57.1 (3)
C4—N1—C2—S1	175.49 (18)	C3—C5—C4—O3	54.3 (3)
C7—O2—C3—O1	−1.5 (4)	C6—C5—C4—O3	−66.0 (2)
C7—O2—C3—C5	176.6 (2)	C3—C5—C4—N1	176.62 (19)
C2—N2—C6—C9	157.1 (2)	C6—C5—C4—N1	56.3 (2)
C2—N2—C6—C5	33.2 (3)	C3—C5—C4—C1	−65.6 (3)
O1—C3—C5—C6	69.9 (3)	C6—C5—C4—C1	174.1 (2)
O2—C3—C5—C6	−108.2 (2)	C3—O2—C7—C8	−90.8 (3)
O1—C3—C5—C4	−48.7 (3)	N2—C6—C9—C10	131.1 (2)
O2—C3—C5—C4	133.1 (2)	C5—C6—C9—C10	−108.2 (3)
N2—C6—C5—C3	178.0 (2)	N2—C6—C9—C14	−51.4 (3)
C9—C6—C5—C3	54.5 (3)	C5—C6—C9—C14	69.3 (3)
N2—C6—C5—C4	−59.4 (2)	C14—C9—C10—C11	−0.9 (3)
C9—C6—C5—C4	177.1 (2)	C6—C9—C10—C11	176.7 (2)
C2—N1—C4—O3	98.7 (3)	C9—C10—C11—C12	2.3 (4)
C2—N1—C4—C1	−144.9 (2)	C10—C11—C12—C13	−1.6 (4)
C2—N1—C4—C5	−25.5 (3)	C11—C12—C13—C14	−0.6 (4)
F3—C1—C4—O3	−60.8 (3)	C12—C13—C14—F4	−178.0 (2)
F2—C1—C4—O3	59.5 (3)	C12—C13—C14—C9	2.2 (4)
F1—C1—C4—O3	179.53 (18)	C10—C9—C14—F4	178.7 (2)
F3—C1—C4—N1	−179.01 (19)	C6—C9—C14—F4	1.2 (4)
F2—C1—C4—N1	−58.7 (3)	C10—C9—C14—C13	−1.4 (4)
F1—C1—C4—N1	61.3 (3)	C6—C9—C14—C13	−178.9 (2)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1	0.84	2.07	2.787 (3)	143
C10—H10···F2i	0.95	2.62	3.285 (6)	128
C13—H13···F1ii	0.95	2.56	3.262 (8)	131
N1—H1···S1iii	0.88	2.52	3.389 (2)	171
N2—H2···O3iv	0.88	2.23	3.079 (3)	162

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
O3H3O1	0.84	2.07	2.787(3)	143
C10H10F2i	0.95	2.62	3.285(6)	128
C13H13F1ii	0.95	2.56	3.262(8)	131
N1H1S1iii	0.88	2.52	3.389(2)	171
N2H2O3iv	0.88	2.23	3.079(3)	162

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .