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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2014 Nov 29;70(Pt 12):596–598. doi: 10.1107/S1600536814025677

Crystal structure of N-(tert-but­oxy­carbon­yl)glycyl-(Z)-β-bromo­dehydro­alanine methyl ester [Boc–Gly–(β-Br)(Z)ΔAla–OMe]

Paweł Lenartowicz a, Maciej Makowski a, Bartosz Zarychta a,*, Krzysztof Ejsmont a
PMCID: PMC4257433  PMID: 25553002

In a de­hydro­amino acid with a C=C bond between the α- and β-C atoms, the amino acid residues are linked trans to each other and there are no strong intra­molecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the mol­ecule.

Keywords: crystal structure, β-bromo­dehydro­alanine, de­hydro­amino acid, non-helical conformation, hydrogen bonding

Abstract

The title compound, C11H17BrN2O5, is a de­hydro­amino acid with a C=C bond between the α- and β-C atoms. The amino acid residues are linked trans to each other and there are no strong intra­molecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the mol­ecule. The dipeptide folding is influenced by an inter­molecular N—H⋯O hydrogen bond and also minimizes steric repulsion. In the crystal, mol­ecules are linked by strong N—H⋯O hydrogen bonds, generating (001) sheets. The sheets are linked by weak C—H⋯O and C—H⋯Br bonds and short Br⋯Br [3.4149 (3) Å] inter­actions.

Chemical context  

De­hydro­amino acids are analogues of amino acids characterized by the presence of an unsaturated doubled bound between the α- and β-carbon atoms in their structure. These compounds were found to be components of natural products (Bonauer et al., 2006), with lanti­biotics being especially important since they are an important class of natural bacteriocins produced by Gram-positive bacteria (Willey & van der Donk, 2007). The development of synthetic methods for the preparation of de­hydro­peptides allows researchers to search for their practical applications and to use them as substrates for the production of peptidomimetics. One of the inter­esting classes of such mimetics are β-bromo-de­hydro­amino acids and their derivatives, which are usually obtained by radical halogenation of de­hydro­amino acids using N-bromo­succinimide (NBS). This reaction proceeds in two steps, namely by halogenation of de­hydro­amino acids, which gives α-bromo-imines, followed by tautomerization to the desired products upon treatment with an amine (Coleman & Carpenter, 1993; Zhang et al., 2002). β-Bromo-de­hydro­amino acid derivatives are useful substrates in coupling reactions with alkynes (Singh et al., 2003) or organoboranes (Collier et al. 2002; Zhang et al., 2002). Further asymmetric hydrogenation of their double bound allows non-proteinogenic α-amino acids and their derivatives to be obtained. Another important reaction of β-bromo-α,β-de­hydro­amino acid derivatives in drug research is their coupling cyclization in which oxazole derivatives are produced (Liu et al., 2014).graphic file with name e-70-00596-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound, (I), is shown in Fig. 1. The amino acids in the compound are linked trans to each other. The ω2 angle (C9—C10—N12—C13) is 175.79 (16)°, while ω3 (O5—C6—N8—C9) is 176.12 (15)°. There are no strong intra­molecular hydrogen bonds. The values of the ϕ2,3 and ψ2,3 angles corresponds to a non-helical conformation (Venkatachalam, 1968). The dipeptide folds accordingly to the inter­molecular N—H⋯O-type hydrogen bonds. The β-bromo-de­hydro­alanine moiety shows typical geometrical tendencies. The C10—N12 bond is longer [1.366 (2) Å] than a typical bond in alanine, while the N12—C13 bond is shorter [1.406 (2) Å]. This effect is common for other de­hydro-residues (Ajó et al., 1979; Pieroni et al. 1975; Rzeszotarska et al., 2002; Jain & Chauhan, 1996). This indicates conjugation between the side chain of de­hydro­alanine and the peptide bond. The torsion angles around the Br(H)C=C grouping are −0.9 (3) and −174.28 (13)° (N12—C13—C14—Br15 and C16—C13—C14—Br15, respectively), meaning the stereochemistry about the bond is especially planar. This is consistent with the nature of an sp 2-hybridized carbon on C13. The valance angles around the de­hydro­alanine group show some unusual values, especially N12—C13—C14 [124.27 (18)°], which may correspond to the presence of the bromine atom in the structure. The other angles are normal, as the backbone of the mol­ecule is folded to minimize steric repulsion. The Boc group features two short intra­molecular C—H⋯O contacts

Figure 1.

Figure 1

The mol­ecular structure of Boc–Gly–(β-Br)(Z)ΔAla–OMe along with selected intra­molecular hydrogen bonds (dashed lines), drawn with 50% displacement ellipsoids.

Supra­molecular features  

In the crystal, mol­ecules form two strong twin N—H⋯O (N8—H8A⋯O17i and N12—H12A⋯O7ii) and one weak accompanying C9—H9A⋯O11i hydrogen bonds (Fig. 1 and Table 1), forming infinite sheets in the (001) plane [symmetry codes: (i) −x + 2, −y, −z + 1 and (ii) −x + 3, −y, −z + 1]. The sheets are connected to each other by weak C14—H14A⋯O11iii and C19—H19B⋯Br15iii hydrogen bonds and one Br⋯Briv [3.4149 (3) Å] halogen bond (Fig. 2) of type I (Mukherjee & Desiraju, 2014) [symmetry codes: (iii) −x + 2, −y + 1, −z + 1; (iv) −x + 3, −y + 1, −z + 1].

Table 1. Hydrogen-bond geometry (, ).

DHA DH HA D A DHA
C2H2AO7 0.96 2.51 3.058(2) 116
C3H3AO7 0.96 2.44 3.007(3) 117
N8H8AO17i 0.86 2.19 3.018(2) 162
C9H9AO11i 0.97 2.61 3.255(2) 124
N12H12AO7ii 0.86 2.04 2.901(2) 174
C14H14AO11iii 0.93 2.43 3.095(2) 129
C19H19BBr15iii 0.96 3.14 3.668(3) 117

Symmetry codes: (i) Inline graphic; (ii) Inline graphic; (iii) Inline graphic.

Figure 2.

Figure 2

A packing diagram of (I), viewed along the b axis, showing the inter­molecular hydrogen-bonding scheme (dashed lines).

Synthesis and crystallization  

Boc–Gly–ΔAla and its methyl ester were prepared according to the methodology described by Makowski et al. (1985) and Cossec et al. (2008). The β-bromo-vinyl derivative was obtained based on a procedure described previously (Bull et al., 2007). For this purpose 0.129 g (0.5 mM) of Boc–Gly–ΔAla–OMe was dissolved in 2.5 ml of di­chloro­methane and cooled to 193 K. Then, bromine 0.027 ml (0.5 mM) was added. The solution was stirred over 10 minutes followed by addition of tri­ethyl­amine 0.210 ml (1.5 mM). After 15 minutes, the mixture was quenched with 20 ml of saturated aqueous NaHCO3 and warmed to room temperature. The product was extracted by di­chloro­methane (3 × 15 ml). The organic layer was washed with brine (3 × 10 ml) and dried over anhydrous Na2SO4. Evaporation of the solvent at reduced pressure gave 0.119 g (0.35 mM) of crude product (70% yield). Recrystal­lization was performed from mixtures of diethyl ether/ethyl acetate­(2:1)/hexane solvents, yielding irregular colourless crystals. It is worth noting that in the case of our study, the formation of only the Z isomer was observed while in the preceding paper, the bromination of de­hydro­alanine-containing compound gave the E isomer. 1H NMR (400 MHz, DMSO) δ 1.38 (s, (s, 9H, C—H3 t-Boc), 3.67 (s, 3H, O—CH3), 3.69 (d, J = 6.2 Hz, 2H, C—H2 Gly), 7.05 (t, J = 6.2 Hz, 1H, N—HGly), 7.30 (s, 1H, C=CHBr), 9.63 (s, 1H, N—Hβ-Br–ΔAla). 13C NMR (101 MHz, DMSO) δ 28.21, 42.79, 52.54, 78.12, 113.26, 132.88, 155.80, 162.63, 168.80. Melting point = 386–388 K.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were positioned geometrically and treated as riding on their parent C or N atoms: for methyl groups, C—H = 0.96 Å and U iso (H) = 1.5U eq(C); for N atoms, N—H = 0.86 Å and U iso (H) = 1.2U eq(C); for secondary C atoms, C—H = 0.97 Å and U iso (H) = 1.2U eq(C), with no refinement of their parameters.

Table 2. Experimental details.

Crystal data
Chemical formula C11H17BrN2O5
M r 337.17
Crystal system, space group Triclinic, P Inline graphic
Temperature (K) 100
a, b, c () 9.0431(4), 9.3160(4), 9.7540(4)
, , () 83.381(3), 75.420(4), 64.863(4)
V (3) 719.92(6)
Z 2
Radiation type Mo K
(mm1) 2.87
Crystal size (mm) 0.30 0.25 0.20
 
Data collection
Diffractometer Oxford Diffraction Xcalibur
Absorption correction Multi-scan (CrysAlis RED; Oxford Diffraction, 2010)
T min, T max 0.655, 1.000
No. of measured, independent and observed [I > 2(I)] reflections 4860, 2780, 2490
R int 0.016
(sin /)max (1) 0.617
 
Refinement
R[F 2 > 2(F 2)], wR(F 2), S 0.024, 0.066, 1.06
No. of reflections 2780
No. of parameters 172
H-atom treatment H-atom parameters constrained
max, min (e 3) 0.53, 0.43

Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2010), SHELXS2014 and SHELXL2014 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814025677/hb7312sup1.cif

e-70-00596-sup1.cif (186.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814025677/hb7312Isup2.hkl

e-70-00596-Isup2.hkl (152.7KB, hkl)

CCDC reference: 1035539

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

Acknowledgments

This study was supported by the Wrocław Research Centre EIT+ under the project Biotechnologies and advanced medical technologies – BioMed (POIG.01.01.02–02-003/08) financed from the European Regional Development Fund (Operational Programme Innovative Economy, 1.1.2). PL is the recipient of a PhD fellowships from a project funded by the European Social Fund.

supplementary crystallographic information

Crystal data

C11H17BrN2O5 Z = 2
Mr = 337.17 F(000) = 344
Triclinic, P1 Dx = 1.555 Mg m3
a = 9.0431 (4) Å Mo Kα radiation, λ = 0.71073 Å
b = 9.3160 (4) Å Cell parameters from 4860 reflections
c = 9.7540 (4) Å θ = 3.2–26.0°
α = 83.381 (3)° µ = 2.87 mm1
β = 75.420 (4)° T = 100 K
γ = 64.863 (4)° Irregular, colourless
V = 719.92 (6) Å3 0.30 × 0.25 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur diffractometer 2780 independent reflections
Radiation source: fine-focus sealed tube 2490 reflections with I > 2σ(I)
Graphite monochromator Rint = 0.016
Detector resolution: 1024 pixels mm-1 θmax = 26.0°, θmin = 3.2°
ω scan h = −8→11
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010) k = −10→11
Tmin = 0.655, Tmax = 1.000 l = −12→12
4860 measured reflections

Refinement

Refinement on F2 0 restraints
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.024 H-atom parameters constrained
wR(F2) = 0.066 w = 1/[σ2(Fo2) + (0.0444P)2] where P = (Fo2 + 2Fc2)/3
S = 1.06 (Δ/σ)max = 0.001
2780 reflections Δρmax = 0.53 e Å3
172 parameters Δρmin = −0.43 e Å3

Special details

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.33.57 (release 26-01-2010 CrysAlis171 .NET) (compiled Jan 26 2010,14:36:55) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.
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.

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

x y z Uiso*/Ueq
C1 1.2957 (3) −0.1495 (2) 0.9892 (2) 0.0186 (4)
C2 1.4783 (3) −0.2662 (3) 0.9655 (2) 0.0248 (5)
H2A 1.5455 −0.2243 0.8952 0.037*
H2B 1.4904 −0.3651 0.9336 0.037*
H2C 1.5146 −0.2830 1.0527 0.037*
C3 1.2675 (3) 0.0136 (3) 1.0284 (2) 0.0291 (5)
H3A 1.3374 0.0518 0.9572 0.044*
H3B 1.2952 0.0083 1.1182 0.044*
H3C 1.1520 0.0844 1.0348 0.044*
C4 1.1870 (3) −0.2140 (3) 1.1000 (2) 0.0313 (5)
H4A 1.0720 −0.1387 1.1146 0.047*
H4B 1.2228 −0.2316 1.1875 0.047*
H4C 1.1975 −0.3122 1.0679 0.047*
O5 1.23184 (17) −0.14194 (16) 0.86239 (14) 0.0186 (3)
C6 1.2959 (2) −0.0915 (2) 0.7363 (2) 0.0144 (4)
O7 1.40332 (16) −0.03851 (15) 0.71486 (14) 0.0161 (3)
N8 1.2267 (2) −0.10813 (19) 0.63638 (17) 0.0155 (3)
H8A 1.1573 −0.1522 0.6578 0.019*
C9 1.2670 (2) −0.0531 (2) 0.49289 (19) 0.0149 (4)
H9A 1.2529 −0.1157 0.4283 0.018*
H9B 1.3835 −0.0685 0.4688 0.018*
C10 1.1567 (2) 0.1209 (2) 0.47430 (19) 0.0143 (4)
O11 1.00831 (16) 0.18140 (15) 0.53245 (14) 0.0179 (3)
N12 1.23628 (19) 0.20273 (18) 0.38410 (17) 0.0146 (3)
H12A 1.3421 0.1556 0.3484 0.017*
C13 1.1490 (2) 0.3623 (2) 0.34831 (19) 0.0136 (4)
C14 1.1990 (2) 0.4770 (2) 0.3536 (2) 0.0164 (4)
H14A 1.1341 0.5792 0.3266 0.020*
Br15 1.39326 (2) 0.44202 (2) 0.41252 (2) 0.02292 (9)
C16 1.0010 (2) 0.4006 (2) 0.2866 (2) 0.0163 (4)
O17 0.97138 (18) 0.30286 (17) 0.24167 (15) 0.0210 (3)
O18 0.90913 (18) 0.55685 (16) 0.28281 (16) 0.0239 (3)
C19 0.7741 (3) 0.6065 (3) 0.2098 (3) 0.0324 (5)
H19A 0.7155 0.7199 0.2129 0.049*
H19B 0.6979 0.5594 0.2552 0.049*
H19C 0.8193 0.5731 0.1130 0.049*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
C1 0.0226 (10) 0.0227 (10) 0.0121 (9) −0.0104 (9) −0.0065 (8) 0.0034 (8)
C2 0.0266 (11) 0.0256 (11) 0.0202 (11) −0.0075 (9) −0.0108 (9) 0.0066 (9)
C3 0.0397 (14) 0.0268 (12) 0.0204 (11) −0.0129 (10) −0.0070 (10) −0.0014 (9)
C4 0.0369 (13) 0.0432 (14) 0.0172 (11) −0.0222 (11) −0.0058 (9) 0.0088 (10)
O5 0.0202 (7) 0.0248 (7) 0.0141 (7) −0.0133 (6) −0.0061 (6) 0.0077 (6)
C6 0.0131 (9) 0.0102 (9) 0.0158 (10) −0.0021 (7) −0.0029 (7) 0.0040 (7)
O7 0.0173 (7) 0.0166 (7) 0.0174 (7) −0.0100 (6) −0.0049 (5) 0.0028 (5)
N8 0.0169 (8) 0.0164 (8) 0.0167 (8) −0.0105 (7) −0.0063 (7) 0.0074 (7)
C9 0.0175 (9) 0.0136 (9) 0.0136 (9) −0.0069 (8) −0.0042 (7) 0.0038 (7)
C10 0.0187 (10) 0.0152 (9) 0.0126 (9) −0.0091 (8) −0.0065 (8) 0.0017 (7)
O11 0.0153 (7) 0.0149 (7) 0.0198 (7) −0.0054 (6) −0.0009 (6) 0.0035 (5)
N12 0.0120 (8) 0.0130 (8) 0.0169 (8) −0.0050 (6) −0.0019 (6) 0.0034 (6)
C13 0.0147 (9) 0.0143 (9) 0.0115 (9) −0.0069 (8) −0.0019 (7) 0.0031 (7)
C14 0.0137 (9) 0.0164 (9) 0.0191 (10) −0.0061 (8) −0.0049 (8) 0.0021 (8)
Br15 0.01942 (12) 0.02164 (12) 0.03230 (14) −0.01022 (9) −0.00996 (9) −0.00138 (8)
C16 0.0181 (10) 0.0171 (10) 0.0130 (9) −0.0083 (8) −0.0032 (8) 0.0060 (8)
O17 0.0250 (8) 0.0209 (7) 0.0224 (8) −0.0129 (6) −0.0093 (6) 0.0028 (6)
O18 0.0222 (7) 0.0168 (7) 0.0346 (9) −0.0061 (6) −0.0164 (6) 0.0071 (6)
C19 0.0287 (12) 0.0290 (12) 0.0417 (14) −0.0095 (10) −0.0229 (11) 0.0157 (10)

Geometric parameters (Å, º)

C1—O5 1.474 (2) C9—C10 1.518 (2)
C1—C3 1.508 (3) C9—H9A 0.9700
C1—C2 1.517 (3) C9—H9B 0.9700
C1—C4 1.521 (3) C10—O11 1.220 (2)
C2—H2A 0.9600 C10—N12 1.366 (2)
C2—H2B 0.9600 N12—C13 1.406 (2)
C2—H2C 0.9600 N12—H12A 0.8600
C3—H3A 0.9600 C13—C14 1.335 (3)
C3—H3B 0.9600 C13—C16 1.494 (3)
C3—H3C 0.9600 C14—Br15 1.8715 (19)
C4—H4A 0.9600 C14—H14A 0.9300
C4—H4B 0.9600 C16—O17 1.204 (2)
C4—H4C 0.9600 C16—O18 1.337 (2)
O5—C6 1.345 (2) O18—C19 1.447 (2)
C6—O7 1.229 (2) C19—H19A 0.9600
C6—N8 1.338 (2) C19—H19B 0.9600
N8—C9 1.446 (2) C19—H19C 0.9600
N8—H8A 0.8600
O5—C1—C3 110.80 (16) C9—N8—H8A 119.5
O5—C1—C2 109.75 (16) N8—C9—C10 111.87 (15)
C3—C1—C2 112.96 (18) N8—C9—H9A 109.2
O5—C1—C4 101.56 (15) C10—C9—H9A 109.2
C3—C1—C4 110.90 (18) N8—C9—H9B 109.2
C2—C1—C4 110.29 (18) C10—C9—H9B 109.2
C1—C2—H2A 109.5 H9A—C9—H9B 107.9
C1—C2—H2B 109.5 O11—C10—N12 122.87 (17)
H2A—C2—H2B 109.5 O11—C10—C9 122.69 (16)
C1—C2—H2C 109.5 N12—C10—C9 114.41 (16)
H2A—C2—H2C 109.5 C10—N12—C13 121.43 (16)
H2B—C2—H2C 109.5 C10—N12—H12A 119.3
C1—C3—H3A 109.5 C13—N12—H12A 119.3
C1—C3—H3B 109.5 C14—C13—N12 124.27 (18)
H3A—C3—H3B 109.5 C14—C13—C16 118.50 (17)
C1—C3—H3C 109.5 N12—C13—C16 116.92 (16)
H3A—C3—H3C 109.5 C13—C14—Br15 123.17 (15)
H3B—C3—H3C 109.5 C13—C14—H14A 118.4
C1—C4—H4A 109.5 Br15—C14—H14A 118.4
C1—C4—H4B 109.5 O17—C16—O18 124.26 (18)
H4A—C4—H4B 109.5 O17—C16—C13 124.08 (18)
C1—C4—H4C 109.5 O18—C16—C13 111.61 (16)
H4A—C4—H4C 109.5 C16—O18—C19 115.57 (16)
H4B—C4—H4C 109.5 O18—C19—H19A 109.5
C6—O5—C1 121.71 (14) O18—C19—H19B 109.5
O7—C6—N8 124.52 (17) H19A—C19—H19B 109.5
O7—C6—O5 125.30 (17) O18—C19—H19C 109.5
N8—C6—O5 110.18 (16) H19A—C19—H19C 109.5
C6—N8—C9 120.96 (15) H19B—C19—H19C 109.5
C6—N8—H8A 119.5
C3—C1—O5—C6 62.8 (2) C9—C10—N12—C13 175.79 (16)
C2—C1—O5—C6 −62.6 (2) C10—N12—C13—C14 130.6 (2)
C4—C1—O5—C6 −179.35 (17) C10—N12—C13—C16 −55.9 (2)
C1—O5—C6—O7 −4.7 (3) N12—C13—C14—Br15 −0.9 (3)
C1—O5—C6—N8 174.87 (15) C16—C13—C14—Br15 −174.28 (13)
O7—C6—N8—C9 −4.3 (3) C14—C13—C16—O17 159.29 (19)
O5—C6—N8—C9 176.12 (15) N12—C13—C16—O17 −14.6 (3)
C6—N8—C9—C10 −86.1 (2) C14—C13—C16—O18 −18.4 (2)
N8—C9—C10—O11 −38.0 (3) N12—C13—C16—O18 167.72 (16)
N8—C9—C10—N12 143.70 (16) O17—C16—O18—C19 −4.6 (3)
O11—C10—N12—C13 −2.5 (3) C13—C16—O18—C19 173.12 (17)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C2—H2A···O7 0.96 2.51 3.058 (2) 116
C3—H3A···O7 0.96 2.44 3.007 (3) 117
N8—H8A···O17i 0.86 2.19 3.018 (2) 162
C9—H9A···O11i 0.97 2.61 3.255 (2) 124
N12—H12A···O7ii 0.86 2.04 2.901 (2) 174
C14—H14A···O11iii 0.93 2.43 3.095 (2) 129
C19—H19B···Br15iii 0.96 3.14 3.668 (3) 117

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

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814025677/hb7312sup1.cif

e-70-00596-sup1.cif (186.6KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814025677/hb7312Isup2.hkl

e-70-00596-Isup2.hkl (152.7KB, hkl)

CCDC reference: 1035539

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


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