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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): o3243–o3244.
Published online 2010 November 20. doi:  10.1107/S1600536810047604
PMCID: PMC3011776

Trimethyl 2,2′,2′′-[1,3,5-triazine-2,4,6-tri­yltris­(aza­nedi­yl)]triacetate

Abstract

The title compound, C12H18N6O6, was synthesized via nucleophilic substitution by reacting 2,4,6-trichloro-1,3,5-triazine with glycine methyl ester hydro­chloride in reflux (dried toluene) under anhydrous atmosphere. Individual mol­ecules self-assemble via strong N—H(...)O hydrogen bonds into supra­molecular double tapes running parallel to the [010] crystallographic direction. The close packing of supra­molecular tapes is mediated by geometrical reasons in tandem with a number of weaker N—H(...)O and C—H(...)N hydrogen-bonding inter­actions.

Related literature

For background to nucleophilic reactions of 1,3,5-triazine, see: Blotny (2006 [triangle]); Giacomelli et al. (2004 [triangle]). For coordination polymers based on N,N′,N′′-1,3,5-triazine-2,4,6-triyltrisglycine, see: Wang et al. (2007a [triangle],b [triangle],c [triangle]). For previous work from our research group on the synthesis of derivatives of 2,4,6-trichloro-1,3,5-triazine from reactions with glycine methyl ester hydro­chloride, see: Vilela et al. (2009a [triangle],b [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o3243-scheme1.jpg

Experimental

Crystal data

  • C12H18N6O6
  • M r = 342.32
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3243-efi1.jpg
  • a = 24.0808 (11) Å
  • b = 9.4111 (4) Å
  • c = 15.5791 (7) Å
  • β = 116.018 (3)°
  • V = 3172.8 (3) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 150 K
  • 0.19 × 0.16 × 0.06 mm

Data collection

  • Bruker X8 Kappa CCD APEXII diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1998) [triangle] T min = 0.978, T max = 0.993
  • 27764 measured reflections
  • 4182 independent reflections
  • 2794 reflections with I > 2σ(I)
  • R int = 0.043

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.112
  • S = 1.03
  • 4182 reflections
  • 229 parameters
  • 3 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.24 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: APEX2 (Bruker, 2006 [triangle]); cell refinement: SAINT-Plus (Bruker, 2005 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: DIAMOND (Brandenburg, 2009 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810047604/gk2317sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810047604/gk2317Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We are grateful to the Fundação para a Ciência e a Tecnologia (FCT, Portugal) for their financial support through the R&D project PTDC/QUI-QUI/098098/2008 (FCOMP-01–0124-FEDER-010785), and also for specific funding toward the purchase of the single-crystal diffractometer. SMFV acknowledges the Associated Laboratory CICECO for a research grant and the FCT for PhD scholarship No. SFRH/BD/66371/2009.

supplementary crystallographic information

Comment

2,4,6-Trichloro-1,3,5-triazine is a versatile organic molecule which can be used for the design and construction of larger entities because the three chlorine atoms are prone to nucleophilic substitution by several functional groups to form amides, nitriles and carboxylic acids, among several others (Blotny, 2006; Giacomelli et al., 2004). Resulting compounds exhibit specific physico-chemical properties which render them of potential academic and industrial interest (e. g., in the textile and pharmaceutical industries). Following our interest on crystal engineering of functional solids we have been using 2,4,6-trichloro-1,3,5-triazine as a molecular canvas for the design and synthesis of novel multipodal organic ligands. For instance, we have recently reported the synthesis and structural characterization of the monosubstituted form of the title compound: methyl 2-(4,6-dichloro-1,3,5-triazin-2-ylamino)acetate (Vilela et al., 2009a). Following the same reaction procedure we were able to isolate the title compound (the trisubstituted derivative) as a pure phase. Noteworthy, the title molecule can be a precursor of N,N',N''-1,3,5-triazine-2,4,6-triyltrisglycine which has been used in the construction of a number of transition metal coordination polymers (Wang et al., 2007a,b,c).

The complete nucleophilic substitution of the chlorine atoms of the chlorotriazine ring by methyl glycinate (Vilela et al., 2009b) led to the isolation in the solid state of the title compound (see Scheme). This novel compound crystallizes in the monoclinic centrosymmetric C2/c space group with one whole molecular unit composing the asymmetric unit as represented in Figure 1. The presence of three pendant substituent groups imposes significant steric impediment around the aromatic ring, ultimately preventing the existence of onset π-π stacking interactions as reported in the crystal packing of the monosubstituted analogue compound (Vilela et al., 2009a). In addition, the spatial arrangement of the pendant groups promotes a minimization of the overall steric repulsion: adjacent pendant moieties are either pointing toward different sides of the ring or, when located on the same side, the N—C bond rotates so the groups are as far away as possible from each other (Figure 1).

The N—H groups are hydrogen-bonded to two carbonyl groups from adjacent molecular units. O4 acts as a double acceptor of two strong (dD···A in the 2.91–2.99 Å range) and highly directional [<(DHA) angle in the 168–172° range] N—H···O hydrogen bonding interactions (Figure 2 and Table 1). These interactions lead to the formation of a double tape of molecular units running along the [010] crystallographic direction. As represented in Figure 3, the pendant groups point outwards of the double tape, thus allowing for an effective close packing of tapes in the crystal structure. Besides these pure geometrical reasons, the N6—H6 moieties located in the periphery establish physical connections between adjacent supramolecular tapes via a weaker N—H···O hydrogen bond (not shown; see Table 1 for geometrical details). It is also worth to mention that the presence of several crystallographically independent —CH2— and terminal —CH3 groups in close proximity with nitrogen and oxygen atoms promotes the existence of several weak C—H···(N,O) contacts which further strengthen the connections between adjacent molecular units (not shown). This structural feature is particularly important in the parallel close packing of tapes along the [100] direction (Figure 4).

Experimental

Glycine methyl ester hydrochloride (193 mg, 2.17 mmol; Sigma-Adrich, 99%) and potassium carbonate (200 mg, 1.45 mmol; Sigma-Aldrich, >99.0%) were added at 273 K to a solution of 2,4,6-trichloro-1,3,5-triazine (100 mg, 0.542 mmol; Sigma-Aldrich, >98,0%) in dried toluene (ca 5 ml). The reaction mixture was kept under magnetic stirring and slowly heated to reflux under anhydrous atmosphere. The progress of the reaction was monitored by TLC and stopped after 24 h. The reaction mixture was then separated by flash column chromatography using as eluent a gradient (from 0 to 5%) of methanol in dichloromethane. The third isolated fraction was identified as the title compound (27% yield). Single crystals suitable for X-ray analysis were isolated from recrystallization of the crude product from a solution of dichloromethane: methanol (ca 1: 1). All employed solvents were of analytical grade and purchased from commercial sources.

1H NMR (300.13 MHz, CDCl3/DMSO-d6) δ: 3.45 (s, 9H, OCH3), 3.74–3.86 (m, 6H, CH2), 5.64–5.81 (m, 3H, NH). 13C NMR (75.47 MHz, CDCl3/DMSO-d6) δ: 41.9 (CH2), 51.4 (OCH3), 165.3 (CNH), 170.7 (CO2Me). MS (TOF MS ES+)m/z: 343.1 (M+H)+. Selected FT—IR data (ATR, in cm-1): ν(N—H) = 3347m; νasym(—CH3) = 2957m; ν(C=O) = 1725vs; νin-plane(ring) = 1493s and 1515s; δ(—CH3) = 1407m; ν(C=N) = 1370m; νasym(C—O—C) = 1206s; νsym(C—O—C) = 1165s; γ(ring) = 841s.

Refinement

Hydrogen atoms bound to carbon were located at their idealized positions and were included in the final structural model in riding-motion approximation with C—H distances of 0.99 Å (—CH2— groups) or 0.98 Å (terminal —CH3 groups). The isotropic thermal displacement parameters for these atoms were fixed at 1.2 (—CH2—) or 1.5 (—CH3 moieties) times Ueq of the carbon atom to which they are attached.

All hydrogen atoms associated with the NH moieties were directly located from difference Fourier maps and included in the structure with the N—H distances restrained to 0.95 (1) Å and with Uiso fixed at 1.5 times Ueq of the N atom to which they are attached.

Figures

Fig. 1.
Schematic representation of the molecular unit of the title compound. Non-hydrogen atoms are represented as thermal ellipsoids drawn at the 50% probability level and hydrogen atoms as small spheres with arbitrary radii. The atomic labeling scheme is provided ...
Fig. 2.
Fragment of the crystal structure emphasizing the contacts interconnecting adjacent chemical entities. The C=O4 carbonyl groups act as double acceptors in strong and highly directional N—H···O hydrogen bonds promoting the ...
Fig. 3.
Supramolecular double tape formed by strong and highly directional N—H···O hydrogen bonding interactions viewed in perspective along the [010] direction of the unit cell.
Fig. 4.
Crystal packing viewed in perspective along the [010] direction of the unit cell. N—H···O hydrogen bonds are represented as purple (intra-tape) or green (inter-tape) dashed lines. For hydrogen bonding geometric details ...

Crystal data

C12H18N6O6F(000) = 1440
Mr = 342.32Dx = 1.433 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 5859 reflections
a = 24.0808 (11) Åθ = 2.4–27.5°
b = 9.4111 (4) ŵ = 0.12 mm1
c = 15.5791 (7) ÅT = 150 K
β = 116.018 (3)°Plate, colourless
V = 3172.8 (3) Å30.19 × 0.16 × 0.06 mm
Z = 8

Data collection

Bruker X8 Kappa CCD APEXII diffractometer4182 independent reflections
Radiation source: fine-focus sealed tube2794 reflections with I > 2σ(I)
graphiteRint = 0.043
ω and [var phi] scansθmax = 29.1°, θmin = 3.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1998)h = −32→32
Tmin = 0.978, Tmax = 0.993k = −12→12
27764 measured reflectionsl = −21→21

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0517P)2 + 1.3693P] where P = (Fo2 + 2Fc2)/3
4182 reflections(Δ/σ)max < 0.001
229 parametersΔρmax = 0.24 e Å3
3 restraintsΔρmin = −0.23 e Å3

Special details

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)

xyzUiso*/Ueq
N1−0.02089 (6)0.95185 (13)0.62956 (8)0.0207 (3)
N20.05790 (6)0.82777 (12)0.60540 (8)0.0205 (3)
N3−0.02269 (6)0.69671 (12)0.62052 (8)0.0215 (3)
N40.05746 (6)1.07016 (13)0.61287 (9)0.0230 (3)
H40.0395 (8)1.1562 (13)0.6156 (13)0.034*
N50.05373 (6)0.58500 (13)0.59451 (9)0.0232 (3)
H50.0322 (7)0.4997 (13)0.5904 (13)0.035*
N6−0.09379 (6)0.82321 (14)0.65212 (9)0.0247 (3)
H6−0.1074 (8)0.9110 (13)0.6648 (13)0.037*
C10.03017 (7)0.94590 (15)0.61581 (9)0.0193 (3)
C20.02848 (7)0.70791 (15)0.60707 (9)0.0198 (3)
C3−0.04387 (7)0.82330 (15)0.63353 (9)0.0198 (3)
C40.11497 (7)1.06968 (16)0.60499 (10)0.0243 (3)
H4A0.12661.16850.59810.029*
H4B0.10971.01610.54720.029*
C50.16599 (7)1.00236 (16)0.69218 (11)0.0249 (3)
C60.26088 (9)0.8795 (3)0.74867 (15)0.0550 (6)
H6A0.28370.95270.79560.083*
H6B0.28810.83560.72430.083*
H6C0.24630.80670.77900.083*
C70.09765 (7)0.58905 (16)0.55491 (11)0.0255 (3)
H7A0.11190.49120.55220.031*
H7B0.13400.64560.59740.031*
C80.07052 (7)0.65318 (15)0.45528 (11)0.0243 (3)
C90.09384 (10)0.7424 (2)0.33368 (14)0.0436 (5)
H9A0.07060.66810.28800.065*
H9B0.12970.77010.32330.065*
H9C0.06720.82530.32460.065*
C10−0.12386 (7)0.69593 (17)0.66106 (10)0.0257 (3)
H10A−0.14320.71490.70440.031*
H10B−0.09230.62100.69070.031*
C11−0.17285 (7)0.64147 (16)0.56692 (10)0.0234 (3)
C12−0.25262 (8)0.47226 (18)0.49934 (12)0.0335 (4)
H12A−0.28350.54420.46320.050*
H12B−0.27240.39610.51880.050*
H12C−0.23450.43270.45910.050*
O10.20846 (5)0.94345 (14)0.67039 (8)0.0397 (3)
O20.16898 (5)1.00247 (12)0.77126 (8)0.0325 (3)
O30.11481 (5)0.68883 (13)0.43052 (8)0.0362 (3)
O40.01591 (5)0.66684 (10)0.40391 (7)0.0255 (2)
O5−0.20447 (5)0.53693 (12)0.58329 (7)0.0282 (3)
O6−0.18196 (6)0.68287 (12)0.48864 (8)0.0336 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0204 (7)0.0224 (6)0.0187 (6)0.0007 (5)0.0080 (5)−0.0003 (5)
N20.0225 (7)0.0194 (6)0.0188 (6)0.0006 (5)0.0085 (5)0.0002 (5)
N30.0245 (7)0.0217 (7)0.0190 (6)−0.0017 (5)0.0103 (5)−0.0005 (5)
N40.0217 (7)0.0186 (7)0.0272 (7)0.0015 (5)0.0094 (6)0.0020 (5)
N50.0293 (7)0.0189 (7)0.0236 (6)0.0018 (5)0.0137 (6)0.0004 (5)
N60.0241 (7)0.0270 (7)0.0255 (6)−0.0025 (6)0.0132 (6)−0.0051 (5)
C10.0205 (8)0.0209 (7)0.0126 (6)−0.0002 (6)0.0037 (6)0.0005 (5)
C20.0238 (8)0.0206 (7)0.0129 (6)0.0004 (6)0.0061 (6)0.0003 (5)
C30.0201 (7)0.0242 (8)0.0127 (6)−0.0006 (6)0.0051 (6)−0.0018 (5)
C40.0245 (8)0.0252 (8)0.0229 (7)−0.0024 (6)0.0099 (7)0.0042 (6)
C50.0227 (8)0.0286 (8)0.0226 (7)−0.0042 (6)0.0093 (7)−0.0005 (6)
C60.0332 (11)0.0885 (17)0.0407 (11)0.0262 (11)0.0137 (9)0.0179 (11)
C70.0275 (8)0.0248 (8)0.0269 (8)0.0048 (7)0.0145 (7)0.0000 (6)
C80.0315 (9)0.0175 (8)0.0285 (8)0.0028 (6)0.0174 (7)−0.0018 (6)
C90.0574 (12)0.0458 (11)0.0437 (11)0.0095 (10)0.0371 (10)0.0135 (9)
C100.0265 (8)0.0320 (9)0.0215 (7)−0.0045 (7)0.0130 (7)−0.0016 (6)
C110.0243 (8)0.0257 (8)0.0235 (7)0.0007 (6)0.0135 (7)−0.0013 (6)
C120.0309 (9)0.0375 (10)0.0277 (8)−0.0100 (8)0.0089 (7)−0.0075 (7)
O10.0268 (6)0.0666 (9)0.0275 (6)0.0153 (6)0.0137 (5)0.0104 (6)
O20.0323 (7)0.0442 (7)0.0191 (5)0.0018 (5)0.0095 (5)0.0001 (5)
O30.0351 (7)0.0434 (7)0.0386 (7)0.0067 (6)0.0241 (6)0.0092 (5)
O40.0300 (6)0.0202 (6)0.0261 (6)0.0024 (5)0.0122 (5)0.0008 (4)
O50.0279 (6)0.0334 (6)0.0229 (5)−0.0075 (5)0.0109 (5)−0.0018 (4)
O60.0390 (7)0.0393 (7)0.0218 (5)−0.0073 (5)0.0128 (5)0.0007 (5)

Geometric parameters (Å, °)

N1—C11.3387 (18)C6—H6A0.9800
N1—C31.3430 (18)C6—H6B0.9800
N2—C21.3383 (18)C6—H6C0.9800
N2—C11.3428 (18)C7—C81.520 (2)
N3—C21.3417 (18)C7—H7A0.9900
N3—C31.3458 (18)C7—H7B0.9900
N4—C11.3519 (19)C8—O41.2096 (19)
N4—C41.4430 (18)C8—O31.3266 (18)
N4—H40.927 (9)C9—O31.455 (2)
N5—C21.3603 (18)C9—H9A0.9800
N5—C71.4399 (17)C9—H9B0.9800
N5—H50.943 (9)C9—H9C0.9800
N6—C31.3545 (18)C10—C111.512 (2)
N6—C101.4377 (19)C10—H10A0.9900
N6—H60.941 (9)C10—H10B0.9900
C4—C51.514 (2)C11—O61.2052 (18)
C4—H4A0.9900C11—O51.3355 (18)
C4—H4B0.9900C12—O51.447 (2)
C5—O21.2021 (18)C12—H12A0.9800
C5—O11.3316 (19)C12—H12B0.9800
C6—O11.447 (2)C12—H12C0.9800
C1—N1—C3113.31 (12)H6B—C6—H6C109.5
C2—N2—C1113.58 (12)N5—C7—C8112.37 (13)
C2—N3—C3112.87 (12)N5—C7—H7A109.1
C1—N4—C4119.93 (12)C8—C7—H7A109.1
C1—N4—H4120.7 (11)N5—C7—H7B109.1
C4—N4—H4119.4 (11)C8—C7—H7B109.1
C2—N5—C7119.85 (12)H7A—C7—H7B107.9
C2—N5—H5117.8 (11)O4—C8—O3124.06 (14)
C7—N5—H5118.6 (11)O4—C8—C7124.99 (13)
C3—N6—C10123.59 (12)O3—C8—C7110.92 (13)
C3—N6—H6117.9 (11)O3—C9—H9A109.5
C10—N6—H6118.3 (11)O3—C9—H9B109.5
N1—C1—N2126.46 (13)H9A—C9—H9B109.5
N1—C1—N4117.61 (13)O3—C9—H9C109.5
N2—C1—N4115.93 (12)H9A—C9—H9C109.5
N2—C2—N3126.84 (13)H9B—C9—H9C109.5
N2—C2—N5116.12 (12)N6—C10—C11113.58 (12)
N3—C2—N5117.05 (13)N6—C10—H10A108.8
N1—C3—N3126.83 (12)C11—C10—H10A108.8
N1—C3—N6115.64 (12)N6—C10—H10B108.8
N3—C3—N6117.53 (12)C11—C10—H10B108.8
N4—C4—C5110.88 (11)H10A—C10—H10B107.7
N4—C4—H4A109.5O6—C11—O5124.43 (14)
C5—C4—H4A109.5O6—C11—C10126.17 (14)
N4—C4—H4B109.5O5—C11—C10109.39 (12)
C5—C4—H4B109.5O5—C12—H12A109.5
H4A—C4—H4B108.1O5—C12—H12B109.5
O2—C5—O1123.66 (15)H12A—C12—H12B109.5
O2—C5—C4125.40 (14)O5—C12—H12C109.5
O1—C5—C4110.93 (12)H12A—C12—H12C109.5
O1—C6—H6A109.5H12B—C12—H12C109.5
O1—C6—H6B109.5C5—O1—C6116.24 (13)
H6A—C6—H6B109.5C8—O3—C9115.57 (14)
O1—C6—H6C109.5C11—O5—C12115.80 (12)
H6A—C6—H6C109.5
C3—N1—C1—N20.7 (2)C10—N6—C3—N31.7 (2)
C3—N1—C1—N4−178.61 (12)C1—N4—C4—C5−63.99 (17)
C2—N2—C1—N11.9 (2)N4—C4—C5—O2−29.1 (2)
C2—N2—C1—N4−178.83 (12)N4—C4—C5—O1151.76 (13)
C4—N4—C1—N1175.63 (12)C2—N5—C7—C8−60.15 (18)
C4—N4—C1—N2−3.74 (19)N5—C7—C8—O4−17.7 (2)
C1—N2—C2—N3−2.1 (2)N5—C7—C8—O3164.11 (12)
C1—N2—C2—N5178.47 (12)C3—N6—C10—C11−86.95 (18)
C3—N3—C2—N2−0.3 (2)N6—C10—C11—O610.5 (2)
C3—N3—C2—N5179.17 (12)N6—C10—C11—O5−170.70 (12)
C7—N5—C2—N2−17.1 (2)O2—C5—O1—C6−1.1 (2)
C7—N5—C2—N3163.40 (13)C4—C5—O1—C6178.03 (16)
C1—N1—C3—N3−3.6 (2)O4—C8—O3—C9−2.2 (2)
C1—N1—C3—N6176.83 (12)C7—C8—O3—C9175.96 (13)
C2—N3—C3—N13.4 (2)O6—C11—O5—C12−0.2 (2)
C2—N3—C3—N6−177.03 (12)C10—C11—O5—C12−179.05 (13)
C10—N6—C3—N1−178.64 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N4—H4···O4i0.93 (1)2.07 (1)2.9851 (16)168 (2)
N5—H5···O4ii0.94 (1)1.97 (1)2.9097 (16)172 (2)
N6—H6···O2iii0.94 (1)2.29 (1)3.0733 (17)141 (1)
C9—H9C···N1i0.982.623.546 (3)158

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GK2317).

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