Ethyl 6-methyl-4-[2-(4,4,5,5-tetra­methyl-1,3,2-dioxaborolan-2-yl)thio­phen-3-yl]-2-thioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

Decken, A.; Zamora, M.T.; Duguay, D.R.; Vogels, C.M.; Westcott, S.A.

doi:10.1107/S1600536808005965

organic compounds

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ISSN: 2056-9890

Volume 64| Part 5| May 2008| Page o929

doi:10.1107/S1600536808005965

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Ethyl 6-methyl-4-[2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)thiophen-3-yl]-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate

Andreas Decken,^a ^* Matthew T. Zamora,^b Dominique R. Duguay,^b Christopher M. Vogels ^b and Stephen A. Westcott ^b

^aDepartment of Chemistry, University of New Brunswick, Fredericton, NB, Canada E3B 6E2, and ^bDepartment of Chemistry, Mount Allison University, 63C York Street, Sackville, NB, Canada E4L 1G8
^*Correspondence e-mail: adecken@unb.ca

(Received 15 February 2008; accepted 3 March 2008; online 26 April 2008)

A new Biginelli compound, C₁₈H₂₅BN₂O₄S₂, containing a boronate ester group was synthesized from a lithium bromide-catalysed reaction. The compound crystallizes with two independent molecules in the asymmetric unit that differ mainly in the conformation of the ester functionality. The crystal structure is stabilized by intermolecular N—H⋯O and N—H⋯S hydrogen bonds involving the 3,4-dihydropyrimidine-2(1H)-thione NH groups as donors and the carbonyl O and thiophene S atoms as acceptors.

Related literature

Blacquiere et al. (2005 ) report on previously studied boronic acid Ugi compounds. Miyaura & Suzuki (1995 ) give an excellent review on the Suzuki–Miyaura cross-coupling reaction of aryl halides with organoboron derivatives. Vogels et al. (2006 ) describe the synthesis and characterization of aryl boronate esters derived from aniline. Yang et al. (2003 ) highlight recent advances of boron chemistry in medicinal research.

Experimental

Crystal data

C₁₈H₂₅BN₂O₄S₂
M_r = 408.33
Triclinic, $[P \overline 1]$
a = 11.9274 (17) Å
b = 13.5021 (19) Å
c = 15.225 (2) Å
α = 112.172 (2)°
β = 93.531 (2)°
γ = 109.706 (2)°
V = 2086.9 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.28 mm⁻¹
T = 173 (1) K
0.6 × 0.6 × 0.4 mm

Data collection

Bruker SMART1000/P4 diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1997 ) T_min = 0.850, T_max = 0.896
14611 measured reflections
9077 independent reflections
7758 reflections with I > 2σ(I)
R_int = 0.017

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.113
S = 1.03
9077 reflections
499 parameters
H-atom parameters constrained
Δρ_max = 0.51 e Å⁻³
Δρ_min = −0.41 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N8—H8⋯S3	0.88	2.91	3.7702 (15)	167
N6—H6⋯O49ⁱ	0.88	2.06	2.8666 (17)	152
N36—H36⋯O19ⁱⁱ	0.88	2.14	2.9670 (17)	155
N38—H38⋯S2ⁱⁱⁱ	0.88	2.61	3.4817 (14)	170
Symmetry codes: (i) x, y-1, z; (ii) x-1, y, z; (iii) -x, -y+1, -z.

Data collection: SMART (Bruker, 1999 ); cell refinement: SMART; data reduction: SAINT (Bruker, 2006 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808005965/gk2133sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808005965/gk2133Isup2.hkl

checkCIF report

Comment top

Compounds containing boronic acids [RB(OH)₂] or boronate esters [RB(OR')₂] have found remarkable synthetic utility in Suzuki-Miyaura cross coupling reactions (Miyaura and Suzuki, 1995) over the past decade. Interest in these compounds also arises from their diverse and potent biological activities (Yang et al., 2003). Indeed, we have recently shown that dihydropyrimidinones (Biginelli products) containing boronic acids show significant promise for their ability to inhibit the MCF7 breast cancer cell line (Blacquiere et al., 2005). Biginelli compounds containing thiophenes showed the most promise in this study. Some of the biological properties of boron compounds have been attributed to the ability of the three-coordinate boron atom to form bonds with biomolecules, as well as form hydrogen bonds with the adjacent O atoms of the boronic acid or boronate ester group. We are preparing a family of boron-containing Biginelli products in order to understand the mechanism of action of these compounds in an effort to design more potent candidates.

The title compound crystallizes with two independent molecules per asymmetric unit. In one of the independent molecules the ester group is coplanar with the pyrimidine ring [torsion angles: C40—C48—O50—C51 = 177.11 (13)° and C48—O50—C51—C52 = 179.83 (16)°], the second independent molecule shows rotation of the ethyl group of the ester moiety that displaces the methyl group from the pyrimidine ring plane [torsion angles: C10—C18—O20—C21 = -179.33 (13)° and C18—O20—C21—C22 = -81.2 (2)°]. Conversely, the latter molecule displays coplanar dioxaborolane and thiophene rings [torsion angles: C2—C1—B1—O2 = 6.2 (3)° and S1—C1—B1—O1 = 3.4 (2)°], while the former shows rotation about the inter-ring linkage [torsion angles: C32—C31—B31—O32 = 20.9 (2)° and S3—C31—B31—O31 = 24.7 (3)°]. However, these torsion angles allow for orbital overlap between the boron p_z orbital and the aryl π-electron system. The Bpin skeleton displays similar bond lengths and angles as found in related aniline derivatives (Vogels et al., 2006). Although steric crowding at the boron center is not present, the title compound shows no appreciable intra- or intermolecular Lewis acid-base interactions. However, hydrogen bonding is observed for all N—H groups of the 3,4-dihydropyrimidine-2(1H)-thione fragment. Two NH···O bonds are present for H6 and H36 (H6···O49ⁱ= 2.06 Å, (i): x, y - 1, z and H36···O19ⁱⁱ = 2.14 Å. (ii): x - 1, y, z) while two very long NH···S bonds are found for H8 and H38 (H8···S3 = 2.91 Å and H38···S2ⁱⁱⁱ = 2.61 Å, (iii): -x, -y + 1, -z).

Related literature top

Blacquiere et al. (2005) report on previously studied boronic acid Ugi compounds. Miyaura & Suzuki (1995) give an excellent review on the Suzuki–Miyaura cross-coupling reaction of aryl halides with organoboron derivatives. Vogels et al. (2006) describe the synthesis and characterization of aryl boronate esters derived from aniline. Yang et al. (2003) highlight recent advances of boron chemistry in medicinal research.

Experimental top

2-(4,4,5,5-Tetramethyl-1,3,2,-dioxaborolan-3-yl)thiophenecarboxaldehyde (548 mg, 2.30 mmol), ethyl acetoacetate (456 mg, 3.50 mmol) and thiourea (266 mg, 3.49 mmol) were added together with CH₃CN (15 ml) and a catalytic amount of lithium bromide (40 mg, 0.46 mmol). The reaction was heated at reflux for 60 h. The solvent was reduced to 5 ml and allowed to stand at room temperature. The title compound precipitated as colourless crystals. Yield: 740 mg (79%); m.p. 469 – 471 K.

Computing details top

Data collection: SMART (Bruker, 1999); cell refinement: SMART (Bruker, 1999); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. H atoms have been omitted.

Ethyl 6-methyl-4-[2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)thiophen-3-yl]- 2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate top

Crystal data top

C₁₈H₂₅BN₂O₄S₂	Z = 4
M_r = 408.33	F(000) = 864
Triclinic, P1	D_x = 1.300 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 11.9274 (17) Å	Cell parameters from 5490 reflections
b = 13.5021 (19) Å	θ = 2.7–28.5°
c = 15.225 (2) Å	µ = 0.28 mm⁻¹
α = 112.172 (2)°	T = 173 K
β = 93.531 (2)°	Irregular, colourless
γ = 109.706 (2)°	0.6 × 0.6 × 0.4 mm
V = 2086.9 (5) Å³

Data collection top

Bruker SMART1000/P4 diffractometer	9077 independent reflections
Radiation source: fine-focus sealed tube	7758 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.017
ϕ and ω scans	θ_max = 27.5°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	h = −15→15
T_min = 0.850, T_max = 0.896	k = −16→17
14611 measured reflections	l = −19→19

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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.113	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.061P)² + 0.8428P] where P = (F_o² + 2F_c²)/3
9077 reflections	(Δ/σ)_max = 0.001
499 parameters	Δρ_max = 0.51 e Å⁻³
0 restraints	Δρ_min = −0.41 e Å⁻³

Crystal data top

C₁₈H₂₅BN₂O₄S₂	γ = 109.706 (2)°
M_r = 408.33	V = 2086.9 (5) Å³
Triclinic, P1	Z = 4
a = 11.9274 (17) Å	Mo Kα radiation
b = 13.5021 (19) Å	µ = 0.28 mm⁻¹
c = 15.225 (2) Å	T = 173 K
α = 112.172 (2)°	0.6 × 0.6 × 0.4 mm
β = 93.531 (2)°

Data collection top

Bruker SMART1000/P4 diffractometer	9077 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	7758 reflections with I > 2σ(I)
T_min = 0.850, T_max = 0.896	R_int = 0.017
14611 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	0 restraints
wR(F²) = 0.113	H-atom parameters constrained
S = 1.04	Δρ_max = 0.51 e Å⁻³
9077 reflections	Δρ_min = −0.41 e Å⁻³
499 parameters

Special details top

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. 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 (Å²) top

	x	y	z	U_iso*/U_eq
B1	0.58518 (16)	0.09209 (15)	0.27239 (12)	0.0268 (3)
O1	0.61743 (12)	0.02062 (10)	0.30254 (8)	0.0377 (3)
O2	0.55784 (13)	0.05290 (10)	0.17436 (8)	0.0392 (3)
C1	0.57648 (13)	0.20455 (12)	0.34609 (10)	0.0241 (3)
C2	0.53195 (13)	0.27993 (12)	0.33090 (10)	0.0230 (3)
C3	0.52890 (16)	0.36718 (14)	0.41845 (11)	0.0324 (3)
H3	0.5002	0.4255	0.4207	0.039*
C4	0.57164 (17)	0.35812 (14)	0.49885 (11)	0.0346 (4)
H4	0.5762	0.4091	0.5635	0.042*
C5	0.48905 (13)	0.27052 (12)	0.23100 (10)	0.0232 (3)
H5	0.5127	0.2116	0.1819	0.028*
N6	0.35516 (12)	0.23074 (11)	0.20829 (9)	0.0274 (3)
H6	0.3125	0.1567	0.1918	0.033*
C7	0.29331 (14)	0.29623 (13)	0.21037 (10)	0.0271 (3)
N8	0.36068 (13)	0.40921 (12)	0.22901 (10)	0.0324 (3)
H8	0.3244	0.4585	0.2442	0.039*
C9	0.48338 (15)	0.45081 (13)	0.22532 (11)	0.0296 (3)
C10	0.54748 (14)	0.38534 (13)	0.22401 (10)	0.0262 (3)
C11	0.59061 (18)	−0.08779 (14)	0.21602 (12)	0.0366 (4)
C12	0.5912 (2)	−0.04760 (16)	0.13318 (13)	0.0435 (5)
C13	0.4647 (2)	−0.17160 (18)	0.21154 (18)	0.0577 (6)
H13A	0.4638	−0.1794	0.2729	0.086*
H13B	0.4460	−0.2477	0.1580	0.086*
H13C	0.4035	−0.1415	0.2008	0.086*
C14	0.6837 (2)	−0.13695 (18)	0.22800 (16)	0.0526 (5)
H14A	0.7657	−0.0798	0.2377	0.079*
H14B	0.6682	−0.2079	0.1696	0.079*
H14C	0.6778	−0.1551	0.2845	0.079*
C15	0.5030 (3)	−0.1337 (2)	0.03940 (16)	0.0806 (10)
H15A	0.4195	−0.1507	0.0496	0.121*
H15B	0.5180	−0.2053	0.0159	0.121*
H15C	0.5136	−0.1013	−0.0088	0.121*
C16	0.7206 (3)	−0.0007 (2)	0.1157 (2)	0.0859 (10)
H16A	0.7208	0.0386	0.0732	0.129*
H16B	0.7460	−0.0654	0.0850	0.129*
H16C	0.7775	0.0545	0.1780	0.129*
C17	0.52927 (18)	0.56795 (15)	0.22327 (14)	0.0409 (4)
H17A	0.5924	0.6242	0.2819	0.061*
H17B	0.4616	0.5932	0.2209	0.061*
H17C	0.5637	0.5629	0.1657	0.061*
C18	0.67612 (15)	0.42200 (14)	0.21689 (11)	0.0305 (3)
O19	0.74306 (12)	0.51853 (11)	0.22815 (9)	0.0418 (3)
O20	0.71312 (11)	0.33367 (11)	0.19778 (9)	0.0371 (3)
C21	0.83969 (17)	0.35731 (19)	0.18969 (14)	0.0436 (4)
H21A	0.8652	0.3001	0.2015	0.052*
H21B	0.8925	0.4356	0.2398	0.052*
C22	0.8558 (2)	0.3510 (2)	0.09137 (15)	0.0562 (5)
H22A	0.8012	0.2745	0.0415	0.084*
H22B	0.9405	0.3628	0.0867	0.084*
H22C	0.8362	0.4114	0.0814	0.084*
S1	0.61592 (4)	0.24412 (3)	0.46920 (3)	0.02971 (10)
S2	0.14012 (4)	0.24790 (4)	0.19037 (3)	0.03629 (11)
B31	0.02234 (17)	0.68959 (16)	0.39397 (12)	0.0284 (3)
O31	0.00329 (13)	0.61897 (11)	0.43996 (9)	0.0414 (3)
O32	−0.01311 (12)	0.77979 (11)	0.43404 (9)	0.0381 (3)
C31	0.07500 (14)	0.66371 (13)	0.30092 (11)	0.0258 (3)
C32	0.06028 (13)	0.69246 (12)	0.22483 (10)	0.0238 (3)
C33	0.11366 (16)	0.64187 (15)	0.14773 (12)	0.0328 (3)
H33	0.1109	0.6525	0.0895	0.039*
C34	0.16881 (17)	0.57679 (17)	0.16648 (13)	0.0391 (4)
H34	0.2099	0.5374	0.1236	0.047*
C35	−0.00662 (13)	0.76922 (13)	0.22187 (10)	0.0241 (3)
H35	−0.0143	0.8128	0.2893	0.029*
N36	−0.13008 (12)	0.69678 (11)	0.15964 (9)	0.0280 (3)
H36	−0.1828	0.6552	0.1828	0.034*
C37	−0.17010 (14)	0.68757 (13)	0.07252 (11)	0.0274 (3)
N38	−0.09181 (13)	0.76047 (12)	0.04064 (9)	0.0315 (3)
H38	−0.1143	0.7523	−0.0187	0.038*
C39	0.02087 (15)	0.84658 (14)	0.09561 (11)	0.0287 (3)
C40	0.06281 (14)	0.85601 (13)	0.18401 (11)	0.0263 (3)
C41	−0.03602 (17)	0.67207 (16)	0.52899 (12)	0.0356 (4)
C42	−0.07393 (17)	0.76491 (15)	0.51102 (12)	0.0355 (4)
C43	−0.1385 (2)	0.5765 (2)	0.53879 (17)	0.0565 (5)
H43A	−0.2023	0.5341	0.4791	0.085*
H43B	−0.1728	0.6105	0.5939	0.085*
H43C	−0.1068	0.5229	0.5497	0.085*
C44	0.0726 (2)	0.7245 (2)	0.61186 (15)	0.0584 (6)
H44A	0.1004	0.6640	0.6119	0.088*
H44B	0.0492	0.7581	0.6735	0.088*
H44C	0.1386	0.7854	0.6040	0.088*
C45	−0.2104 (2)	0.7200 (2)	0.46867 (17)	0.0579 (6)
H45A	−0.2260	0.7746	0.4468	0.087*
H45B	−0.2564	0.7127	0.5186	0.087*
H45C	−0.2362	0.6439	0.4134	0.087*
C46	−0.0335 (2)	0.88144 (19)	0.59638 (15)	0.0570 (6)
H46A	0.0552	0.9131	0.6192	0.086*
H46B	−0.0734	0.8726	0.6489	0.086*
H46C	−0.0561	0.9346	0.5766	0.086*
C47	0.08465 (18)	0.92231 (16)	0.04776 (13)	0.0403 (4)
H47A	0.0885	1.0012	0.0839	0.060*
H47B	0.0395	0.8907	−0.0192	0.060*
H47C	0.1676	0.9244	0.0474	0.060*
C48	0.18103 (15)	0.94540 (13)	0.24476 (11)	0.0280 (3)
O49	0.25664 (11)	1.01361 (11)	0.22269 (9)	0.0409 (3)
O50	0.19949 (10)	0.94226 (10)	0.33108 (8)	0.0307 (2)
C51	0.31590 (15)	1.02263 (15)	0.39685 (12)	0.0339 (3)
H51A	0.3266	1.1037	0.4118	0.041*
H51B	0.3836	1.0078	0.3673	0.041*
C52	0.3146 (2)	1.0030 (2)	0.48767 (15)	0.0570 (6)
H52A	0.2462	1.0165	0.5153	0.085*
H52B	0.3914	1.0568	0.5350	0.085*
H52C	0.3054	0.9229	0.4719	0.085*
S3	0.15505 (4)	0.57455 (4)	0.27683 (3)	0.03606 (11)
S4	−0.31028 (4)	0.59544 (4)	0.00464 (3)	0.03619 (11)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
B1	0.0314 (9)	0.0225 (8)	0.0266 (8)	0.0111 (7)	0.0046 (7)	0.0102 (7)
O1	0.0608 (8)	0.0294 (6)	0.0272 (6)	0.0273 (6)	0.0044 (5)	0.0087 (5)
O2	0.0701 (9)	0.0296 (6)	0.0245 (5)	0.0290 (6)	0.0087 (5)	0.0101 (5)
C1	0.0282 (7)	0.0220 (7)	0.0214 (6)	0.0092 (6)	0.0049 (5)	0.0093 (5)
C2	0.0270 (7)	0.0199 (6)	0.0228 (6)	0.0093 (6)	0.0060 (5)	0.0096 (5)
C3	0.0467 (10)	0.0283 (8)	0.0271 (7)	0.0214 (7)	0.0099 (7)	0.0103 (6)
C4	0.0493 (10)	0.0309 (8)	0.0242 (7)	0.0202 (8)	0.0089 (7)	0.0081 (6)
C5	0.0275 (7)	0.0197 (7)	0.0233 (6)	0.0089 (6)	0.0055 (5)	0.0101 (5)
N6	0.0289 (7)	0.0222 (6)	0.0308 (6)	0.0072 (5)	0.0038 (5)	0.0140 (5)
C7	0.0319 (8)	0.0298 (8)	0.0201 (6)	0.0125 (6)	0.0045 (6)	0.0106 (6)
N8	0.0352 (7)	0.0268 (7)	0.0376 (7)	0.0163 (6)	0.0044 (6)	0.0129 (6)
C9	0.0371 (8)	0.0226 (7)	0.0262 (7)	0.0084 (6)	0.0005 (6)	0.0112 (6)
C10	0.0330 (8)	0.0219 (7)	0.0232 (7)	0.0081 (6)	0.0055 (6)	0.0115 (6)
C11	0.0522 (11)	0.0266 (8)	0.0310 (8)	0.0208 (8)	0.0056 (7)	0.0078 (7)
C12	0.0767 (14)	0.0308 (9)	0.0301 (8)	0.0310 (9)	0.0170 (9)	0.0105 (7)
C13	0.0665 (14)	0.0335 (10)	0.0689 (14)	0.0158 (10)	0.0229 (12)	0.0195 (10)
C14	0.0705 (14)	0.0420 (11)	0.0486 (11)	0.0375 (11)	0.0057 (10)	0.0101 (9)
C15	0.151 (3)	0.0480 (13)	0.0311 (10)	0.0518 (16)	−0.0135 (13)	−0.0019 (9)
C16	0.119 (3)	0.0636 (16)	0.101 (2)	0.0466 (17)	0.083 (2)	0.0432 (16)
C17	0.0500 (11)	0.0251 (8)	0.0476 (10)	0.0113 (8)	−0.0009 (8)	0.0201 (8)
C18	0.0352 (8)	0.0289 (8)	0.0247 (7)	0.0077 (7)	0.0063 (6)	0.0130 (6)
O19	0.0404 (7)	0.0334 (6)	0.0465 (7)	0.0030 (5)	0.0085 (6)	0.0219 (6)
O20	0.0338 (6)	0.0349 (6)	0.0438 (7)	0.0133 (5)	0.0150 (5)	0.0170 (5)
C21	0.0352 (9)	0.0517 (11)	0.0443 (10)	0.0170 (8)	0.0140 (8)	0.0198 (9)
C22	0.0513 (12)	0.0645 (14)	0.0458 (11)	0.0183 (11)	0.0217 (9)	0.0184 (10)
S1	0.0382 (2)	0.0288 (2)	0.02272 (18)	0.01457 (17)	0.00229 (15)	0.01086 (15)
S2	0.0301 (2)	0.0475 (3)	0.0326 (2)	0.01577 (18)	0.00692 (16)	0.01790 (19)
B31	0.0318 (9)	0.0316 (9)	0.0264 (8)	0.0150 (7)	0.0083 (7)	0.0144 (7)
O31	0.0678 (9)	0.0464 (7)	0.0334 (6)	0.0363 (7)	0.0252 (6)	0.0262 (6)
O32	0.0580 (8)	0.0422 (7)	0.0335 (6)	0.0314 (6)	0.0248 (6)	0.0231 (5)
C31	0.0286 (7)	0.0256 (7)	0.0268 (7)	0.0135 (6)	0.0075 (6)	0.0120 (6)
C32	0.0241 (7)	0.0231 (7)	0.0255 (7)	0.0089 (6)	0.0084 (5)	0.0113 (6)
C33	0.0382 (9)	0.0375 (9)	0.0287 (7)	0.0191 (7)	0.0146 (7)	0.0153 (7)
C34	0.0428 (10)	0.0458 (10)	0.0356 (9)	0.0274 (8)	0.0172 (7)	0.0141 (8)
C35	0.0249 (7)	0.0250 (7)	0.0252 (7)	0.0097 (6)	0.0075 (5)	0.0132 (6)
N36	0.0244 (6)	0.0313 (7)	0.0314 (6)	0.0087 (5)	0.0084 (5)	0.0178 (6)
C37	0.0276 (7)	0.0283 (7)	0.0275 (7)	0.0140 (6)	0.0091 (6)	0.0099 (6)
N38	0.0335 (7)	0.0358 (7)	0.0234 (6)	0.0089 (6)	0.0046 (5)	0.0149 (6)
C39	0.0328 (8)	0.0278 (8)	0.0283 (7)	0.0112 (6)	0.0084 (6)	0.0149 (6)
C40	0.0291 (8)	0.0245 (7)	0.0282 (7)	0.0098 (6)	0.0080 (6)	0.0145 (6)
C41	0.0440 (10)	0.0445 (10)	0.0257 (7)	0.0211 (8)	0.0138 (7)	0.0182 (7)
C42	0.0457 (10)	0.0397 (9)	0.0286 (8)	0.0225 (8)	0.0172 (7)	0.0157 (7)
C43	0.0691 (15)	0.0523 (12)	0.0567 (12)	0.0208 (11)	0.0256 (11)	0.0325 (11)
C44	0.0548 (13)	0.0888 (17)	0.0381 (10)	0.0383 (13)	0.0068 (9)	0.0250 (11)
C45	0.0492 (12)	0.0742 (16)	0.0594 (13)	0.0369 (12)	0.0166 (10)	0.0256 (12)
C46	0.0811 (16)	0.0480 (12)	0.0403 (10)	0.0300 (12)	0.0205 (10)	0.0116 (9)
C47	0.0455 (10)	0.0405 (10)	0.0341 (8)	0.0059 (8)	0.0041 (7)	0.0252 (8)
C48	0.0320 (8)	0.0249 (7)	0.0308 (7)	0.0112 (6)	0.0062 (6)	0.0156 (6)
O49	0.0372 (7)	0.0382 (7)	0.0454 (7)	0.0009 (5)	0.0016 (5)	0.0290 (6)
O50	0.0304 (6)	0.0308 (6)	0.0272 (5)	0.0060 (5)	0.0029 (4)	0.0143 (5)
C51	0.0315 (8)	0.0316 (8)	0.0325 (8)	0.0084 (7)	0.0003 (6)	0.0117 (7)
C52	0.0549 (13)	0.0628 (14)	0.0447 (11)	0.0078 (11)	−0.0086 (9)	0.0302 (10)
S3	0.0420 (2)	0.0420 (2)	0.0362 (2)	0.0287 (2)	0.01057 (18)	0.01775 (18)
S4	0.0273 (2)	0.0421 (2)	0.0285 (2)	0.00897 (17)	0.00539 (15)	0.00812 (17)

Geometric parameters (Å, º) top

B1—O2	1.357 (2)	B31—O31	1.352 (2)
B1—O1	1.361 (2)	B31—O32	1.361 (2)
B1—C1	1.553 (2)	B31—C31	1.552 (2)
O1—C11	1.4688 (19)	O31—C41	1.4639 (19)
O2—C12	1.465 (2)	O32—C42	1.4575 (19)
C1—C2	1.378 (2)	C31—C32	1.373 (2)
C1—S1	1.7280 (14)	C31—S3	1.7265 (15)
C2—C3	1.420 (2)	C32—C33	1.425 (2)
C2—C5	1.5185 (19)	C32—C35	1.517 (2)
C3—C4	1.361 (2)	C33—C34	1.357 (2)
C3—H3	0.9500	C33—H33	0.9500
C4—S1	1.7045 (17)	C34—S3	1.7088 (18)
C4—H4	0.9500	C34—H34	0.9500
C5—N6	1.4737 (19)	C35—N36	1.4766 (19)
C5—C10	1.5184 (19)	C35—C40	1.5184 (19)
C5—H5	1.0000	C35—H35	1.0000
N6—C7	1.322 (2)	N36—C37	1.327 (2)
N6—H6	0.8800	N36—H36	0.8800
C7—N8	1.368 (2)	C37—N38	1.369 (2)
C7—S2	1.6836 (16)	C37—S4	1.6808 (16)
N8—C9	1.393 (2)	N38—C39	1.390 (2)
N8—H8	0.8800	N38—H38	0.8800
C9—C10	1.346 (2)	C39—C40	1.350 (2)
C9—C17	1.503 (2)	C39—C47	1.504 (2)
C10—C18	1.470 (2)	C40—C48	1.466 (2)
C11—C14	1.507 (3)	C41—C44	1.509 (3)
C11—C13	1.524 (3)	C41—C43	1.512 (3)
C11—C12	1.549 (2)	C41—C42	1.574 (2)
C12—C15	1.495 (3)	C42—C46	1.505 (3)
C12—C16	1.540 (3)	C42—C45	1.531 (3)
C13—H13A	0.9800	C43—H43A	0.9800
C13—H13B	0.9800	C43—H43B	0.9800
C13—H13C	0.9800	C43—H43C	0.9800
C14—H14A	0.9800	C44—H44A	0.9800
C14—H14B	0.9800	C44—H44B	0.9800
C14—H14C	0.9800	C44—H44C	0.9800
C15—H15A	0.9800	C45—H45A	0.9800
C15—H15B	0.9800	C45—H45B	0.9800
C15—H15C	0.9800	C45—H45C	0.9800
C16—H16A	0.9800	C46—H46A	0.9800
C16—H16B	0.9800	C46—H46B	0.9800
C16—H16C	0.9800	C46—H46C	0.9800
C17—H17A	0.9800	C47—H47A	0.9800
C17—H17B	0.9800	C47—H47B	0.9800
C17—H17C	0.9800	C47—H47C	0.9800
C18—O19	1.216 (2)	C48—O49	1.2187 (19)
C18—O20	1.346 (2)	C48—O50	1.3379 (18)
O20—C21	1.457 (2)	O50—C51	1.4494 (19)
C21—C22	1.495 (3)	C51—C52	1.503 (3)
C21—H21A	0.9900	C51—H51A	0.9900
C21—H21B	0.9900	C51—H51B	0.9900
C22—H22A	0.9800	C52—H52A	0.9800
C22—H22B	0.9800	C52—H52B	0.9800
C22—H22C	0.9800	C52—H52C	0.9800

O2—B1—O1	113.78 (14)	O31—B31—O32	114.26 (14)
O2—B1—C1	124.84 (14)	O31—B31—C31	121.32 (15)
O1—B1—C1	121.33 (14)	O32—B31—C31	124.37 (14)
B1—O1—C11	107.00 (12)	B31—O31—C41	108.06 (13)
B1—O2—C12	106.97 (12)	B31—O32—C42	107.96 (12)
C2—C1—B1	130.36 (13)	C32—C31—B31	130.28 (14)
C2—C1—S1	109.91 (11)	C32—C31—S3	110.11 (11)
B1—C1—S1	119.54 (11)	B31—C31—S3	119.35 (11)
C1—C2—C3	113.10 (13)	C31—C32—C33	113.05 (14)
C1—C2—C5	123.78 (12)	C31—C32—C35	123.94 (13)
C3—C2—C5	123.12 (13)	C33—C32—C35	123.01 (13)
C4—C3—C2	112.63 (14)	C34—C33—C32	112.64 (14)
C4—C3—H3	123.7	C34—C33—H33	123.7
C2—C3—H3	123.7	C32—C33—H33	123.7
C3—C4—S1	111.65 (12)	C33—C34—S3	111.55 (12)
C3—C4—H4	124.2	C33—C34—H34	124.2
S1—C4—H4	124.2	S3—C34—H34	124.2
N6—C5—C10	109.92 (12)	N36—C35—C32	109.80 (12)
N6—C5—C2	109.99 (11)	N36—C35—C40	109.87 (12)
C10—C5—C2	111.69 (12)	C32—C35—C40	110.98 (12)
N6—C5—H5	108.4	N36—C35—H35	108.7
C10—C5—H5	108.4	C32—C35—H35	108.7
C2—C5—H5	108.4	C40—C35—H35	108.7
C7—N6—C5	125.95 (13)	C37—N36—C35	127.04 (13)
C7—N6—H6	117.0	C37—N36—H36	116.5
C5—N6—H6	117.0	C35—N36—H36	116.5
N6—C7—N8	116.36 (14)	N36—C37—N38	116.33 (14)
N6—C7—S2	123.93 (12)	N36—C37—S4	123.02 (12)
N8—C7—S2	119.70 (12)	N38—C37—S4	120.63 (12)
C7—N8—C9	123.85 (14)	C37—N38—C39	124.42 (13)
C7—N8—H8	118.1	C37—N38—H38	117.8
C9—N8—H8	118.1	C39—N38—H38	117.8
C10—C9—N8	118.87 (14)	C40—C39—N38	119.54 (14)
C10—C9—C17	127.11 (16)	C40—C39—C47	126.23 (15)
N8—C9—C17	114.02 (15)	N38—C39—C47	114.23 (14)
C9—C10—C18	121.80 (14)	C39—C40—C48	121.59 (14)
C9—C10—C5	120.77 (14)	C39—C40—C35	121.27 (14)
C18—C10—C5	117.42 (13)	C48—C40—C35	117.01 (13)
O1—C11—C14	108.90 (14)	O31—C41—C44	106.68 (15)
O1—C11—C13	106.61 (15)	O31—C41—C43	107.56 (16)
C14—C11—C13	109.29 (17)	C44—C41—C43	110.40 (17)
O1—C11—C12	102.07 (13)	O31—C41—C42	102.79 (12)
C14—C11—C12	116.75 (17)	C44—C41—C42	113.58 (17)
C13—C11—C12	112.48 (17)	C43—C41—C42	115.03 (16)
O2—C12—C15	109.08 (17)	O32—C42—C46	108.64 (16)
O2—C12—C16	106.04 (17)	O32—C42—C45	105.51 (15)
C15—C12—C16	110.6 (2)	C46—C42—C45	109.92 (17)
O2—C12—C11	102.69 (13)	O32—C42—C41	103.19 (12)
C15—C12—C11	116.02 (18)	C46—C42—C41	115.69 (16)
C16—C12—C11	111.7 (2)	C45—C42—C41	113.09 (17)
C11—C13—H13A	109.5	C41—C43—H43A	109.5
C11—C13—H13B	109.5	C41—C43—H43B	109.5
H13A—C13—H13B	109.5	H43A—C43—H43B	109.5
C11—C13—H13C	109.5	C41—C43—H43C	109.5
H13A—C13—H13C	109.5	H43A—C43—H43C	109.5
H13B—C13—H13C	109.5	H43B—C43—H43C	109.5
C11—C14—H14A	109.5	C41—C44—H44A	109.5
C11—C14—H14B	109.5	C41—C44—H44B	109.5
H14A—C14—H14B	109.5	H44A—C44—H44B	109.5
C11—C14—H14C	109.5	C41—C44—H44C	109.5
H14A—C14—H14C	109.5	H44A—C44—H44C	109.5
H14B—C14—H14C	109.5	H44B—C44—H44C	109.5
C12—C15—H15A	109.5	C42—C45—H45A	109.5
C12—C15—H15B	109.5	C42—C45—H45B	109.5
H15A—C15—H15B	109.5	H45A—C45—H45B	109.5
C12—C15—H15C	109.5	C42—C45—H45C	109.5
H15A—C15—H15C	109.5	H45A—C45—H45C	109.5
H15B—C15—H15C	109.5	H45B—C45—H45C	109.5
C12—C16—H16A	109.5	C42—C46—H46A	109.5
C12—C16—H16B	109.5	C42—C46—H46B	109.5
H16A—C16—H16B	109.5	H46A—C46—H46B	109.5
C12—C16—H16C	109.5	C42—C46—H46C	109.5
H16A—C16—H16C	109.5	H46A—C46—H46C	109.5
H16B—C16—H16C	109.5	H46B—C46—H46C	109.5
C9—C17—H17A	109.5	C39—C47—H47A	109.5
C9—C17—H17B	109.5	C39—C47—H47B	109.5
H17A—C17—H17B	109.5	H47A—C47—H47B	109.5
C9—C17—H17C	109.5	C39—C47—H47C	109.5
H17A—C17—H17C	109.5	H47A—C47—H47C	109.5
H17B—C17—H17C	109.5	H47B—C47—H47C	109.5
O19—C18—O20	123.16 (16)	O49—C48—O50	122.17 (14)
O19—C18—C10	126.16 (16)	O49—C48—C40	127.06 (14)
O20—C18—C10	110.66 (13)	O50—C48—C40	110.75 (13)
C18—O20—C21	117.03 (14)	C48—O50—C51	116.55 (12)
O20—C21—C22	111.17 (16)	O50—C51—C52	106.59 (14)
O20—C21—H21A	109.4	O50—C51—H51A	110.4
C22—C21—H21A	109.4	C52—C51—H51A	110.4
O20—C21—H21B	109.4	O50—C51—H51B	110.4
C22—C21—H21B	109.4	C52—C51—H51B	110.4
H21A—C21—H21B	108.0	H51A—C51—H51B	108.6
C21—C22—H22A	109.5	C51—C52—H52A	109.5
C21—C22—H22B	109.5	C51—C52—H52B	109.5
H22A—C22—H22B	109.5	H52A—C52—H52B	109.5
C21—C22—H22C	109.5	C51—C52—H52C	109.5
H22A—C22—H22C	109.5	H52A—C52—H52C	109.5
H22B—C22—H22C	109.5	H52B—C52—H52C	109.5
C4—S1—C1	92.71 (7)	C34—S3—C31	92.65 (8)

C2—C1—B1—O2	6.2 (3)	C18—O20—C21—C22	−81.2 (2)
S1—C1—B1—O1	3.4 (2)	C48—O50—C51—C52	179.83 (16)
C32—C31—B31—O32	−24.7 (3)	C10—C18—O20—C21	−179.33 (13)
S3—C31—B31—O31	−20.9 (2)	C40—C48—O50—C51	177.11 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N8—H8···S3	0.88	2.91	3.7702 (15)	167
N6—H6···O49ⁱ	0.88	2.06	2.8666 (17)	152
N36—H36···O19ⁱⁱ	0.88	2.14	2.9670 (17)	155
N38—H38···S2ⁱⁱⁱ	0.88	2.61	3.4817 (14)	170

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

Experimental details

Crystal data
Chemical formula	C₁₈H₂₅BN₂O₄S₂
M_r	408.33
Crystal system, space group	Triclinic, P1
Temperature (K)	173
a, b, c (Å)	11.9274 (17), 13.5021 (19), 15.225 (2)
α, β, γ (°)	112.172 (2), 93.531 (2), 109.706 (2)
V (Å³)	2086.9 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.28
Crystal size (mm)	0.6 × 0.6 × 0.4

Data collection
Diffractometer	Bruker SMART1000/P4 diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1997)
T_min, T_max	0.850, 0.896
No. of measured, independent and observed [I > 2σ(I)] reflections	14611, 9077, 7758
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.113, 1.04
No. of reflections	9077
No. of parameters	499
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.51, −0.41

Computer programs: SMART (Bruker, 1999), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N8—H8···S3	0.88	2.91	3.7702 (15)	167
N6—H6···O49ⁱ	0.88	2.06	2.8666 (17)	152
N36—H36···O19ⁱⁱ	0.88	2.14	2.9670 (17)	155
N38—H38···S2ⁱⁱⁱ	0.88	2.61	3.4817 (14)	170

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

Acknowledgements

This work was funded by the Natural Science and Engineering Research Council and AIF/ACOA (Canada).

References

Blacquiere, J. M., Sicora, O., Vogels, C. M., Čuperlović-Culf, M., Decken, A., Ouellette, R. J. & Westcott, S. A. (2005). Can. J. Chem. 83, 2052–2059. Web of Science CSD CrossRef CAS Google Scholar
Bruker (1999). SMART. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2006). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Miyaura, N. & Suzuki, A. (1995). Chem. Rev. 95, 2457–2483. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (1997). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Vogels, C. M., Decken, A. & Westcott, S. A. (2006). Tetrahedron Lett. 47, 2419–2422. Web of Science CSD CrossRef CAS Google Scholar
Yang, W., Gao, X. & Wang, B. (2003). Med. Res. Rev. 23, 346–368. Web of Science CrossRef PubMed CAS Google Scholar

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Ethyl 6-methyl-4-[2-(4,4,5,5-tetra­methyl-1,3,2-dioxaborolan-2-yl)thio­phen-3-yl]-2-thioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

Ethyl 6-methyl-4-[2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)thiophen-3-yl]-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate