Crystal structure of 5-(β-D-gluco­pyran­osyl­thio)-N-(4-methyl­phen­yl)-1,3,4-thia­diazol-2-amine

In the title compound, the angle between the tolyl and thia­diazole rings is 9.2 (1)°. The hydrogen bonding is a combination of a ribbon involving hydrogen bonds of the sugar residues, and a layer based on N—H...O and O—H...N hydrogen bonds.

Key indicators

Structure: I

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.019
• wR factor = 0.050
• Data-to-parameter ratio = 14.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT031_ALERT_4_C Refined Extinction Parameter Within Range of ...      3.000 Sigma
PLAT414_ALERT_2_C Short Intra D-H..H-X       H05      ..H16B     .       1.97 Ang.
                                                      x,y,z  =      1_555 Check

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          8 Note
PLAT143_ALERT_4_G s.u. on c - Axis Small or Missing ..............    0.00017 Ang.
PLAT176_ALERT_4_G The CIF-Embedded .res File Contains SADI Records          1 Report
PLAT480_ALERT_4_G Long H...A H-Bond Reported H15      ..O2       .       2.66 Ang.
PLAT480_ALERT_4_G Long H...A H-Bond Reported H11      ..O3       .       2.68 Ang.
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          5 Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          7 Note
PLAT899_ALERT_4_G SHELXL2018 is Deprecated and Succeeded by SHELXL     2019/3 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          9 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 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
   1 ALERT type 3 Indicator that the structure quality may be low
   8 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: CrysAlis PRO (Rigaku OD, 2021); cell refinement: CrysAlis PRO (Rigaku OD, 2021); data reduction: CrysAlis PRO (Rigaku OD, 2021); program(s) used to solve structure: SHELXT (Sheldrick, 2015b); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015a); molecular graphics: XP (Siemens, 1994); software used to prepare material for publication: SHELXL2018/3 (Sheldrick, 2015a).

5-[(β-D-Glucopyranosyl)sulfanyl]-N-(4-methylphenyl)-1,3,4-thiadiazol-2-amine

Crystal data

C15H19N3O5S2	F(000) = 404
Mr = 385.45	Dx = 1.507 Mg m^−3
Monoclinic, P21	Cu Kα radiation, λ = 1.54184 Å
a = 6.23840 (6) Å	Cell parameters from 61296 reflections
b = 7.4355 (1) Å	θ = 2.4–77.5°
c = 18.32032 (17) Å	µ = 3.14 mm^−1
β = 91.4183 (8)°	T = 100 K
V = 849.54 (2) Å^3	Plate, colourless
Z = 2	0.10 × 0.08 × 0.02 mm

Data collection

XtaLAB Synergy diffractometer	3520 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source	3502 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.030
Detector resolution: 10.0000 pixels mm^-1	θmax = 77.3°, θmin = 2.4°
ω scans	h = −7→7
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021)	k = −9→8
Tmin = 0.851, Tmax = 1.000	l = −23→23
70354 measured reflections

Refinement

Refinement on F^2	H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full	w = 1/[σ^2(Fo^2) + (0.0289P)^2 + 0.2573P] where P = (Fo^2 + 2Fc^2)/3
R[F^2 > 2σ(F^2)] = 0.019	(Δ/σ)max < 0.001
wR(F^2) = 0.050	Δρmax = 0.30 e Å^−3
S = 1.03	Δρmin = −0.21 e Å^−3
3520 reflections	Extinction correction: SHELXL-2018/3 (Sheldrick, 2015a), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
248 parameters	Extinction coefficient: 0.0009 (3)
7 restraints	Absolute structure: Flack x determined using 1554 quotients [(I^+)-(I^-)]/[(I^+)+(I^-)] (Parsons et al., 2013)
Primary atom site location: dual	Absolute structure parameter: −0.006 (5)
Hydrogen site location: mixed

Special details

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.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

3.7080 (0.0039) x + 2.0545 (0.0042) y + 13.5622 (0.0105) z = 13.7691 (0.0045)

* 0.0205 (0.0007) S1 * -0.0130 (0.0010) C2 * -0.0030 (0.0011) N3 * 0.0244 (0.0010) N4 * -0.0289 (0.0010) C5 -0.1014 (0.0026) N1 0.0173 (0.0026) S2

Rms deviation of fitted atoms = 0.0201

3.4518 (0.0038) x + 1.0131 (0.0062) y + 14.7993 (0.0080) z = 13.9365 (0.0076)

Angle to previous plane (with approximate esd) = 9.200 ( 0.107 )

* 0.0048 (0.0012) C21 * -0.0074 (0.0013) C22 * 0.0034 (0.0013) C23 * 0.0035 (0.0014) C24 * -0.0062 (0.0014) C25 * 0.0020 (0.0013) C26 0.0546 (0.0026) N1 0.0234 (0.0033) C27

Rms deviation of fitted atoms = 0.0049

3.6049 (0.0167) x + 0.8656 (0.1231) y + 14.5324 (0.0137) z = 13.6402 (0.0694)

Angle to previous plane (with approximate esd) = 1.978 ( 0.397 )

* 0.0000 (0.0000) H01 * 0.0000 (0.0000) C5 * 0.0000 (0.0000) C21 0.0965 (0.0103) N1

Rms deviation of fitted atoms = 0.0000

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

	x	y	z	Uiso*/Ueq
S1	0.68679 (6)	0.56520 (6)	0.74337 (2)	0.01368 (10)
C2	0.7401 (3)	0.7619 (2)	0.69652 (9)	0.0141 (4)
N3	0.6138 (2)	0.8948 (2)	0.71166 (8)	0.0164 (3)
N4	0.4594 (2)	0.8505 (2)	0.76262 (8)	0.0164 (3)
C5	0.4713 (3)	0.6807 (3)	0.78116 (9)	0.0141 (3)
C11	1.0267 (2)	0.5674 (3)	0.61331 (9)	0.0129 (3)
H11	0.908249	0.505970	0.585259	0.015*
C12	1.2263 (3)	0.5825 (3)	0.56692 (9)	0.0125 (3)
H12	1.336334	0.656908	0.593626	0.015*
C13	1.3196 (3)	0.3958 (3)	0.55237 (9)	0.0132 (3)
H13	1.225617	0.331025	0.516019	0.016*
C14	1.3421 (3)	0.2844 (3)	0.62159 (9)	0.0129 (3)
H14	1.457744	0.336867	0.653816	0.015*
C15	1.1297 (3)	0.2862 (3)	0.66200 (9)	0.0135 (3)
H15	1.014260	0.235018	0.629328	0.016*
C16	1.1351 (3)	0.1833 (3)	0.73351 (10)	0.0159 (3)
H16A	1.005890	0.214160	0.761185	0.019*
H16B	1.129897	0.052814	0.722861	0.019*
O1	1.07795 (19)	0.47115 (17)	0.67845 (7)	0.0135 (3)
O2	1.1689 (2)	0.66863 (19)	0.50027 (7)	0.0153 (3)
H02	1.264 (4)	0.740 (4)	0.4908 (15)	0.038 (8)*
O3	1.52906 (19)	0.41758 (19)	0.52349 (7)	0.0168 (3)
H03	1.522 (4)	0.482 (4)	0.4857 (13)	0.029 (7)*
O4	1.3989 (2)	0.10451 (18)	0.60228 (7)	0.0162 (3)
H04	1.471 (4)	0.067 (4)	0.6365 (12)	0.030 (7)*
O5	1.3225 (2)	0.22073 (19)	0.77822 (7)	0.0178 (3)
H05	1.382 (4)	0.122 (3)	0.7831 (14)	0.032 (8)*
N1	0.3417 (2)	0.5861 (2)	0.82558 (8)	0.0156 (3)
H01	0.353 (4)	0.473 (4)	0.8230 (13)	0.020 (6)*
C21	0.1567 (3)	0.6454 (3)	0.86130 (9)	0.0154 (3)
C22	0.0393 (3)	0.5129 (3)	0.89691 (10)	0.0191 (4)
H22	0.082328	0.390608	0.894194	0.023*
C23	−0.1396 (3)	0.5595 (3)	0.93618 (10)	0.0221 (4)
H23	−0.216466	0.468512	0.960842	0.027*
C24	−0.2085 (3)	0.7375 (3)	0.94008 (11)	0.0220 (4)
C25	−0.0925 (3)	0.8667 (3)	0.90351 (11)	0.0230 (4)
H25	−0.138366	0.988413	0.905038	0.028*
C26	0.0901 (3)	0.8234 (3)	0.86446 (10)	0.0195 (4)
H26	0.167780	0.914713	0.840330	0.023*
S2	0.94984 (6)	0.79473 (6)	0.63645 (2)	0.01473 (10)
C27	−0.4029 (3)	0.7886 (4)	0.98327 (13)	0.0322 (5)
H27A	−0.533285	0.765916	0.953762	0.048*
H27B	−0.395250	0.916469	0.996023	0.048*
H27C	−0.406140	0.716487	1.028010	0.048*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.01271 (18)	0.0111 (2)	0.01736 (19)	0.00212 (16)	0.00360 (13)	0.00076 (16)
C2	0.0134 (8)	0.0129 (10)	0.0161 (8)	0.0005 (6)	0.0007 (6)	−0.0002 (7)
N3	0.0159 (7)	0.0146 (8)	0.0188 (7)	0.0029 (6)	0.0043 (6)	0.0020 (6)
N4	0.0147 (7)	0.0164 (8)	0.0183 (7)	0.0024 (6)	0.0050 (6)	0.0016 (6)
C5	0.0127 (8)	0.0155 (9)	0.0140 (8)	0.0021 (7)	0.0004 (6)	−0.0013 (7)
C11	0.0123 (7)	0.0115 (8)	0.0149 (7)	0.0006 (7)	0.0020 (6)	0.0008 (7)
C12	0.0122 (7)	0.0120 (8)	0.0133 (7)	0.0005 (7)	0.0016 (5)	0.0015 (7)
C13	0.0114 (8)	0.0139 (9)	0.0145 (8)	0.0002 (6)	0.0031 (6)	−0.0006 (7)
C14	0.0141 (7)	0.0103 (8)	0.0145 (7)	0.0010 (7)	0.0031 (6)	0.0000 (7)
C15	0.0140 (7)	0.0103 (8)	0.0163 (7)	0.0011 (7)	0.0034 (6)	−0.0013 (7)
C16	0.0154 (8)	0.0153 (9)	0.0174 (8)	0.0007 (7)	0.0033 (6)	0.0017 (7)
O1	0.0160 (6)	0.0102 (6)	0.0144 (6)	0.0027 (5)	0.0040 (4)	0.0010 (5)
O2	0.0146 (6)	0.0151 (7)	0.0162 (6)	−0.0009 (5)	0.0017 (4)	0.0053 (5)
O3	0.0147 (6)	0.0166 (7)	0.0194 (6)	0.0030 (5)	0.0074 (5)	0.0049 (5)
O4	0.0202 (6)	0.0122 (7)	0.0163 (6)	0.0046 (5)	0.0039 (5)	0.0000 (5)
O5	0.0211 (7)	0.0135 (7)	0.0188 (6)	0.0027 (5)	−0.0010 (5)	0.0006 (5)
N1	0.0149 (7)	0.0127 (9)	0.0193 (7)	0.0012 (6)	0.0035 (5)	0.0009 (6)
C21	0.0120 (8)	0.0208 (10)	0.0136 (7)	0.0020 (7)	0.0007 (6)	−0.0009 (7)
C22	0.0177 (8)	0.0202 (10)	0.0195 (8)	0.0008 (7)	0.0013 (7)	0.0005 (7)
C23	0.0157 (8)	0.0301 (11)	0.0207 (8)	−0.0037 (9)	0.0038 (6)	0.0027 (9)
C24	0.0141 (8)	0.0309 (12)	0.0211 (9)	0.0000 (7)	0.0035 (7)	−0.0081 (8)
C25	0.0197 (9)	0.0225 (11)	0.0271 (10)	0.0042 (8)	0.0049 (8)	−0.0046 (8)
C26	0.0177 (8)	0.0194 (11)	0.0217 (8)	0.0012 (7)	0.0046 (7)	0.0001 (8)
S2	0.01492 (19)	0.0101 (2)	0.01939 (19)	0.00117 (15)	0.00557 (14)	0.00078 (16)
C27	0.0195 (9)	0.0386 (13)	0.0389 (11)	−0.0030 (10)	0.0112 (8)	−0.0133 (11)

Geometric parameters (Å, º)

S1—C2	1.7322 (19)	C16—O5	1.438 (2)
S1—C5	1.7525 (18)	C16—H16A	0.9900
C2—N3	1.298 (2)	C16—H16B	0.9900
C2—S2	1.7473 (17)	O2—H02	0.82 (2)
N3—N4	1.397 (2)	O3—H03	0.84 (2)
N4—C5	1.309 (3)	O4—H04	0.81 (2)
C5—N1	1.358 (2)	O5—H05	0.83 (2)
C11—O1	1.421 (2)	N1—C21	1.411 (2)
C11—C12	1.529 (2)	N1—H01	0.84 (3)
C11—S2	1.811 (2)	C21—C26	1.389 (3)
C11—H11	1.0000	C21—C22	1.398 (3)
C12—O2	1.417 (2)	C22—C23	1.387 (3)
C12—C13	1.531 (3)	C22—H22	0.9500
C12—H12	1.0000	C23—C24	1.394 (3)
C13—O3	1.4311 (19)	C23—H23	0.9500
C13—C14	1.518 (2)	C24—C25	1.386 (3)
C13—H13	1.0000	C24—C27	1.513 (2)
C14—O4	1.431 (2)	C25—C26	1.397 (2)
C14—C15	1.534 (2)	C25—H25	0.9500
C14—H14	1.0000	C26—H26	0.9500
C15—O1	1.446 (2)	C27—H27A	0.9800
C15—C16	1.517 (2)	C27—H27B	0.9800
C15—H15	1.0000	C27—H27C	0.9800
C2—S1—C5	86.59 (9)	O5—C16—C15	113.27 (15)
N3—C2—S1	114.31 (13)	O5—C16—H16A	108.9
N3—C2—S2	119.74 (14)	C15—C16—H16A	108.9
S1—C2—S2	125.88 (10)	O5—C16—H16B	108.9
C2—N3—N4	113.29 (16)	C15—C16—H16B	108.9
C5—N4—N3	111.44 (15)	H16A—C16—H16B	107.7
N4—C5—N1	128.67 (17)	C11—O1—C15	110.51 (13)
N4—C5—S1	114.15 (14)	C12—O2—H02	108 (2)
N1—C5—S1	117.17 (15)	C13—O3—H03	109.9 (19)
O1—C11—C12	109.56 (13)	C14—O4—H04	106 (2)
O1—C11—S2	109.19 (11)	C16—O5—H05	104 (2)
C12—C11—S2	106.59 (13)	C5—N1—C21	128.45 (18)
O1—C11—H11	110.5	C5—N1—H01	115.6 (16)
C12—C11—H11	110.5	C21—N1—H01	113.9 (17)
S2—C11—H11	110.5	C26—C21—C22	119.40 (17)
O2—C12—C11	108.70 (13)	C26—C21—N1	124.47 (17)
O2—C12—C13	110.40 (13)	C22—C21—N1	116.11 (17)
C11—C12—C13	110.38 (15)	C23—C22—C21	120.26 (19)
O2—C12—H12	109.1	C23—C22—H22	119.9
C11—C12—H12	109.1	C21—C22—H22	119.9
C13—C12—H12	109.1	C22—C23—C24	121.12 (19)
O3—C13—C14	107.70 (13)	C22—C23—H23	119.4
O3—C13—C12	108.45 (14)	C24—C23—H23	119.4
C14—C13—C12	112.14 (14)	C25—C24—C23	117.89 (17)
O3—C13—H13	109.5	C25—C24—C27	120.9 (2)
C14—C13—H13	109.5	C23—C24—C27	121.2 (2)
C12—C13—H13	109.5	C24—C25—C26	122.0 (2)
O4—C14—C13	108.79 (13)	C24—C25—H25	119.0
O4—C14—C15	110.46 (15)	C26—C25—H25	119.0
C13—C14—C15	109.59 (13)	C21—C26—C25	119.31 (18)
O4—C14—H14	109.3	C21—C26—H26	120.3
C13—C14—H14	109.3	C25—C26—H26	120.3
C15—C14—H14	109.3	C2—S2—C11	102.94 (8)
O1—C15—C16	107.46 (13)	C24—C27—H27A	109.5
O1—C15—C14	107.97 (14)	C24—C27—H27B	109.5
C16—C15—C14	114.29 (14)	H27A—C27—H27B	109.5
O1—C15—H15	109.0	C24—C27—H27C	109.5
C16—C15—H15	109.0	H27A—C27—H27C	109.5
C14—C15—H15	109.0	H27B—C27—H27C	109.5
C5—S1—C2—N3	2.54 (14)	O1—C15—C16—O5	−74.18 (17)
C5—S1—C2—S2	179.52 (13)	C14—C15—C16—O5	45.6 (2)
S1—C2—N3—N4	−0.4 (2)	C12—C11—O1—C15	−66.50 (18)
S2—C2—N3—N4	−177.57 (12)	S2—C11—O1—C15	177.11 (10)
C2—N3—N4—C5	−3.0 (2)	C16—C15—O1—C11	−168.02 (13)
N3—N4—C5—N1	−175.82 (17)	C14—C15—O1—C11	68.24 (16)
N3—N4—C5—S1	4.95 (19)	N4—C5—N1—C21	2.2 (3)
C2—S1—C5—N4	−4.30 (14)	S1—C5—N1—C21	−178.54 (14)
C2—S1—C5—N1	176.37 (14)	C5—N1—C21—C26	−9.0 (3)
O1—C11—C12—O2	176.33 (14)	C5—N1—C21—C22	172.65 (16)
S2—C11—C12—O2	−65.64 (15)	C26—C21—C22—C23	−1.2 (3)
O1—C11—C12—C13	55.11 (18)	N1—C21—C22—C23	177.18 (16)
S2—C11—C12—C13	173.14 (11)	C21—C22—C23—C24	1.1 (3)
O2—C12—C13—O3	72.56 (16)	C22—C23—C24—C25	−0.1 (3)
C11—C12—C13—O3	−167.24 (13)	C22—C23—C24—C27	−179.64 (18)
O2—C12—C13—C14	−168.64 (13)	C23—C24—C25—C26	−0.9 (3)
C11—C12—C13—C14	−48.44 (18)	C27—C24—C25—C26	178.71 (19)
O3—C13—C14—O4	−69.37 (17)	C22—C21—C26—C25	0.3 (3)
C12—C13—C14—O4	171.39 (13)	N1—C21—C26—C25	−177.94 (17)
O3—C13—C14—C15	169.77 (14)	C24—C25—C26—C21	0.7 (3)
C12—C13—C14—C15	50.53 (19)	N3—C2—S2—C11	−164.51 (14)
O4—C14—C15—O1	−178.61 (13)	S1—C2—S2—C11	18.65 (13)
C13—C14—C15—O1	−58.76 (17)	O1—C11—S2—C2	−55.86 (12)
O4—C14—C15—C16	61.89 (19)	C12—C11—S2—C2	−174.12 (11)
C13—C14—C15—C16	−178.26 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H02···O3^i	0.82 (2)	1.87 (2)	2.6846 (19)	174 (3)
O3—H03···O4^i	0.84 (2)	1.93 (2)	2.7375 (18)	161 (3)
O4—H04···N3^ii	0.81 (2)	2.06 (2)	2.848 (2)	162 (3)
O5—H05···N4^ii	0.83 (2)	2.11 (2)	2.899 (2)	159 (3)
O5—H05···N3^ii	0.83 (2)	2.60 (2)	3.282 (2)	141 (2)
N1—H01···O5^iii	0.84 (3)	2.05 (3)	2.853 (2)	158 (2)
C14—H14···S1^iv	1.00	2.74	3.7044 (18)	163
C15—H15···O2^v	1.00	2.66	3.577 (2)	153
C11—H11···O3^iii	1.00	2.68	3.652 (2)	164
C16—H16B···S2^vi	0.99	2.71	3.570 (2)	145

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