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Acta Cryst. (2009). E65, o2308-o2309    [ doi:10.1107/S1600536809034291 ]

N-{1-[(3-Bromopropyl)aminocarbonyl]ethyl}-2-(2-nitrobenzenesulfonamido)propionamide

R. Thirupathi, D. N. Reddy, S. Brinda and E. N. Prabhakaran

Abstract top

In the title compound, C15H21BrN4O6S, all three NH groups are involved in intermolecular N-H...O interactions which, together with two intermolecular C-H...O contacts, lead to a continuous antiparallel [beta]-sheet structure. There are no [pi]-[pi] interactions between molecules, and two C-H...[pi] interactions primarily govern the linkage between sheets.

Comment top

The title compound is a precursor for making conformationally restricted dipeptide analogues, which are essential for many molecular recognition events including interactions between antigens and antibodies, peptide hormones and their receptors, and enzymes and their corresponding substrates (Ripka et al., 1993; Belvisi et al., 2000). The dipeptide sequence Ala-Ala has a low frequency of appearance in the conformationally ordered regions of polypeptides (Wilmot & Thornton, 1988; Venkatraman et al., 2001). The sulfonamide group is known to render conformational ordering in peptides and many sulfonamides are crystalline in nature. The title compound was synthesized to investigate the ordering rendered to Ala-Ala dipeptide by the N-nosyl (2-nitro-benzenesulfonylamino) protecting group. In the crystal structure all the three NH groups of the molecule are involved in intermolecular N—H···O interactions.

The two adjacent amide N-H bonds, N3—H3 and N4—H4, that flank the C- terminal alanine in the title compound are antiperiplanar to each other. The phi, psi angles for the C-terminal alanine are phi = -151.9 (5)°, psi = 130.4 (2)°. These angles and the H3-N3-N4-H4 dihedral angle (166.1 (3)°) are within the limits of those found in b-strand structures (Loughlin et al., 2004). On the other hand, the two adjacent N-H bonds N2—H2 and N3—H3 that flank the N-terminal alanine are slightly distorted away from ideal antiperiplanarity (H2-N2-N3-H3 dihedral angle = 150.2 (5)°). The phi, psi angles for the N-terminal alanine are phi = 95.6 (2)°, psi = 137.8 (7)°. The distortion from the ideal phi value for a beta-strand near N2 is probably due to the fact that N2 is bonded to a sulfonyl group rather than an acyl group.

The strands are arranged in a head-to-tail fashion, with three intermolecular N—H···O interactions and two intermolecular C—H···O interactions (Table 1). These interactions are between adjacent strands and assist in forming a continuous beta-sheet structure. The C1—S1—N2—C7 torsion angle is 62.9 (3)°. This orients the phenyl ring at a dihedral angle of 73.9 (1)° from the mean plane of the rest of the molecule. The crystal structure is stabilized by two C—H···π interactions. One is intermolecular (C11—Cg = 3.85 A°, Cg: the centroid of the phenyl ring) and the other is intramolecular (C11—Cg = 3.92 A°). There are no π–π interactions between the phenyl rings and the interactions between the sheets are solely governed by the C—H···π interactions.

Related literature top

For conformationally restricted peptide analogues, see: Belvisi et al. (2000); Ripka et al. (1993). For C-H···π interactions in crystals and peptides, see: Ciunik et al. (1998); Görbitz (1989); Nishio (2004); Nishio & Hirota (1989). For the correlation between peptide sequences and folds, see: Venkatraman et al. (2001); Wilmot & Thornton (1988). For bond angles in β-strand structures, see: Loughlin et al. (2004).

Experimental top

To a stirring solution of 2-[2'-(2-nitrosulfonylamido)-propionamido]-propanoic acid (650 mg, 1.88 mmol) in THF (10 ml) at 258 K was added N-methyl morpholene (0.31 ml, 2.82 mmol) followed by ethylchloroformate (0.18 ml,1.93 mmol) under N2 atmosphere. After two minutes a solution of 3-bromopropan-1-ammonium bromide (536 mg, 2.44 mmol) and N-Methyl morpholene (0.51 ml, 4.7 mmol) in a mixture of DMF/THF (1.5/3 ml) were added to the mixture and stirred for 10 min. The reaction mixture was warmed to room temperature and stirred for further 8 h. THF was removed under reduced pressure and the resulting residue was diluted with EtOAc (10 ml) and washed with saturated aqueous citric acid solution (5 ml), saturated aqueous NaHCO3 (5 ml) solution and dried (anhydrous Na2SO4). The solvent was removed under reduced pressure and the resulting residue was purified by silica gel flash column chromatography (EtOAc/Hexane:1/2) to obtain the title compound as a colorless solid 392 mg (0.84 mmol, 45%) (m.p. 404 K). Needle like crystals were obtained for the isolated compound by slow evaporation at room temperature from a solution in 2-propanol (2.1 mM).

Refinement top

All the H atoms were positioned geometrically with C—H bond lengths of 0.93 (3)–0.97 (3) Å, and refined using a riding model approximation with Uiso(H) = 1.2 Ueq(C) or 1.5 Ueq(C) for methyl H atoms.

Computing details top

Data collection: SMART (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); 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, 1999) and CAMERON (Watkin et al., 1993); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. View of the title compound with the atom numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level. H atoms have been omitted for clarity.
[Figure 2] Fig. 2. Packing diagram of (I). The dotted lines indicate intermolecular C—H···O and N—H···O interactions.
N-{1-[(3-Bromopropyl)aminocarbonyl]ethyl}-2-(2- nitrobenzenesulfonamido)propionamide top
Crystal data top
C15H21BrN4O6SDx = 1.479 Mg m−3
Mr = 465.33Melting point: 404 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3007 reflections
a = 9.4467 (4) Åθ = 2.0–26.0°
b = 12.7438 (5) ŵ = 2.11 mm−1
c = 17.3257 (7) ÅT = 292 K
V = 2085.79 (15) Å3Needle, colourless
Z = 40.30 × 0.20 × 0.10 mm
F(000) = 948
Data collection top
Bruker SMART CCD area-detector
diffractometer		4107 independent reflections
Radiation source: fine-focus sealed tube3007 reflections with I > 2σ(I)
graphiteRint = 0.054
φ and ω scansθmax = 26.0°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)		h = −11→11
Tmin = 0.571, Tmax = 0.817k = −15→15
33853 measured reflectionsl = −21→21
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.138 w = 1/[σ2(Fo2) + (0.08P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
4107 reflectionsΔρmax = 0.50 e Å−3
247 parametersΔρmin = −0.51 e Å−3
0 restraintsAbsolute structure: Flack (1983), 1763 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.011 (13)
Crystal data top
C15H21BrN4O6SV = 2085.79 (15) Å3
Mr = 465.33Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.4467 (4) ŵ = 2.11 mm−1
b = 12.7438 (5) ÅT = 292 K
c = 17.3257 (7) Å0.30 × 0.20 × 0.10 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		4107 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)		3007 reflections with I > 2σ(I)
Tmin = 0.571, Tmax = 0.817Rint = 0.054
33853 measured reflectionsθmax = 26.0°
Refinement top
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.138Δρmax = 0.50 e Å−3
S = 1.10Δρmin = −0.51 e Å−3
4107 reflectionsAbsolute structure: Flack (1983), 1763 Friedel pairs
247 parametersFlack parameter: −0.011 (13)
0 restraints
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
xyzUiso*/Ueq
Br10.53403 (7)−0.37246 (5)1.22175 (4)0.0837 (3)
S10.50247 (10)0.51539 (8)0.93158 (6)0.0381 (3)
C10.4914 (5)0.4329 (3)0.8477 (2)0.0399 (9)
C40.4882 (8)0.3109 (5)0.7161 (3)0.0774 (18)
H40.48820.26970.67190.093*
C20.6041 (5)0.3690 (4)0.8313 (3)0.0553 (12)
H20.68260.36810.86370.066*
C60.3764 (5)0.4355 (4)0.7986 (3)0.0436 (11)
C50.3759 (6)0.3765 (4)0.7309 (3)0.0633 (14)
H50.30090.38150.69630.076*
C30.6009 (6)0.3060 (4)0.7667 (4)0.0692 (16)
H30.67510.25990.75710.083*
O30.4231 (3)0.6086 (2)0.91578 (19)0.0506 (8)
O40.6505 (3)0.5244 (3)0.9481 (2)0.0550 (9)
O10.1799 (4)0.4744 (3)0.8693 (2)0.0690 (10)
O20.2243 (5)0.5726 (3)0.7713 (3)0.0828 (12)
N10.2509 (4)0.5005 (4)0.8145 (3)0.0526 (10)
N20.4295 (3)0.4562 (2)1.0023 (2)0.0345 (8)
H2A0.35570.48351.02330.041*
C90.4065 (4)0.2648 (3)0.9969 (3)0.0363 (9)
C70.4847 (4)0.3563 (3)1.0325 (2)0.0335 (8)
H70.58560.35071.01990.040*
C80.4666 (7)0.3526 (4)1.1197 (3)0.0709 (16)
H8A0.52110.40781.14300.106*
H8B0.49880.28601.13880.106*
H8C0.36850.36171.13250.106*
O50.2778 (3)0.2645 (3)0.9909 (2)0.0607 (10)
N30.4858 (3)0.1824 (2)0.9757 (2)0.0362 (8)
H3A0.57650.18670.97890.043*
C120.5198 (4)−0.0043 (3)0.9661 (2)0.0383 (9)
C100.4212 (4)0.0847 (3)0.9472 (3)0.0432 (11)
H100.33070.07350.97350.052*
C110.3953 (6)0.0907 (4)0.8584 (3)0.0611 (14)
H11A0.33420.14890.84710.092*
H11B0.35180.02680.84110.092*
H11C0.48410.10010.83230.092*
O60.6452 (3)−0.0016 (2)0.94723 (19)0.0473 (8)
N40.4607 (4)−0.0872 (3)1.0009 (2)0.0497 (9)
H4A0.3710−0.08651.00920.060*
C130.5414 (6)−0.1783 (4)1.0252 (3)0.0582 (13)
H13A0.6400−0.15821.03070.070*
H13B0.5362−0.23120.98510.070*
C140.4926 (6)−0.2250 (4)1.0989 (3)0.0663 (14)
H14A0.3973−0.25211.09240.080*
H14B0.4901−0.17121.13850.080*
C150.5908 (7)−0.3138 (5)1.1244 (3)0.0698 (15)
H15A0.6866−0.28721.12870.084*
H15B0.5905−0.36861.08550.084*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0935 (5)0.0790 (5)0.0787 (4)−0.0189 (3)−0.0056 (3)0.0102 (4)
S10.0347 (5)0.0326 (5)0.0469 (6)−0.0058 (4)−0.0054 (4)0.0037 (4)
C10.042 (2)0.037 (2)0.041 (2)0.0002 (19)0.0050 (19)0.0055 (18)
C40.111 (5)0.065 (3)0.056 (3)−0.004 (4)0.031 (4)−0.018 (3)
C20.049 (3)0.053 (3)0.064 (3)0.003 (2)0.013 (2)0.002 (3)
C60.048 (3)0.043 (3)0.039 (3)−0.006 (2)0.0000 (18)−0.004 (2)
C50.075 (4)0.066 (3)0.049 (3)−0.011 (3)0.003 (2)−0.003 (3)
C30.071 (3)0.054 (3)0.083 (4)0.011 (3)0.026 (3)−0.006 (3)
O30.060 (2)0.0286 (15)0.063 (2)0.0015 (14)−0.0122 (15)0.0029 (15)
O40.0340 (15)0.062 (2)0.069 (2)−0.0152 (15)−0.0057 (14)0.0093 (18)
O10.058 (2)0.087 (3)0.062 (2)0.013 (2)0.0060 (19)−0.007 (2)
O20.097 (3)0.073 (3)0.078 (3)0.020 (2)−0.024 (2)0.021 (3)
N10.052 (2)0.059 (3)0.047 (2)0.0065 (19)−0.0159 (19)−0.008 (2)
N20.0293 (17)0.0308 (17)0.043 (2)−0.0017 (13)0.0021 (14)−0.0028 (15)
C90.029 (2)0.030 (2)0.050 (3)−0.0036 (16)0.0025 (18)0.0012 (19)
C70.0304 (19)0.0297 (19)0.040 (2)0.0039 (16)−0.0006 (17)−0.0001 (17)
C80.106 (5)0.059 (3)0.047 (3)0.002 (3)−0.004 (3)0.000 (2)
O50.0262 (15)0.0428 (19)0.113 (3)0.0017 (13)0.0000 (17)−0.021 (2)
N30.0216 (15)0.0293 (16)0.058 (2)−0.0037 (14)−0.0016 (15)−0.0067 (15)
C120.034 (2)0.032 (2)0.050 (2)−0.0031 (17)−0.0015 (17)−0.0110 (18)
C100.030 (2)0.029 (2)0.070 (3)−0.0064 (16)0.003 (2)−0.006 (2)
C110.075 (4)0.049 (3)0.059 (3)0.000 (2)−0.023 (3)−0.011 (3)
O60.0345 (15)0.0413 (17)0.066 (2)−0.0021 (13)0.0056 (13)−0.0032 (16)
N40.041 (2)0.040 (2)0.068 (2)−0.0050 (16)0.0005 (17)0.0037 (18)
C130.063 (3)0.038 (2)0.074 (4)0.001 (2)0.003 (3)−0.001 (2)
C140.062 (3)0.052 (3)0.086 (4)−0.009 (3)0.001 (3)0.001 (3)
C150.089 (4)0.068 (4)0.053 (3)−0.002 (3)−0.004 (3)−0.002 (3)
Geometric parameters (Å, °) top
Br1—C151.921 (6)C7—H70.9800
S1—O31.431 (3)C8—H8A0.9600
S1—O41.431 (3)C8—H8B0.9600
S1—N21.595 (3)C8—H8C0.9600
S1—C11.797 (4)N3—C101.471 (5)
C1—C21.370 (7)N3—H3A0.8600
C1—C61.380 (6)C12—O61.229 (5)
C4—C51.375 (8)C12—N41.338 (5)
C4—C31.381 (9)C12—C101.503 (6)
C4—H40.9300C10—C111.560 (6)
C2—C31.377 (7)C10—H100.9800
C2—H20.9300C11—H11A0.9600
C6—C51.393 (7)C11—H11B0.9600
C6—N11.473 (6)C11—H11C0.9600
C5—H50.9300N4—C131.452 (6)
C3—H30.9300N4—H4A0.8600
O1—N11.209 (6)C13—C141.482 (8)
O2—N11.211 (6)C13—H13A0.9700
N2—C71.472 (5)C13—H13B0.9700
N2—H2A0.8600C14—C151.529 (8)
C9—O51.220 (5)C14—H14A0.9700
C9—N31.342 (5)C14—H14B0.9700
C9—C71.513 (5)C15—H15A0.9700
C7—C81.521 (6)C15—H15B0.9700
O3—S1—O4118.90 (19)C7—C8—H8C109.5
O3—S1—N2108.22 (19)H8A—C8—H8C109.5
O4—S1—N2107.87 (19)H8B—C8—H8C109.5
O3—S1—C1107.47 (19)C9—N3—C10121.5 (3)
O4—S1—C1105.4 (2)C9—N3—H3A119.3
N2—S1—C1108.64 (18)C10—N3—H3A119.3
C2—C1—C6119.8 (4)O6—C12—N4122.9 (4)
C2—C1—S1118.1 (4)O6—C12—C10121.2 (4)
C6—C1—S1122.0 (3)N4—C12—C10115.8 (3)
C5—C4—C3120.3 (5)N3—C10—C12108.0 (3)
C5—C4—H4119.8N3—C10—C11110.8 (4)
C3—C4—H4119.8C12—C10—C11110.4 (4)
C1—C2—C3119.9 (5)N3—C10—H10109.2
C1—C2—H2120.1C12—C10—H10109.2
C3—C2—H2120.1C11—C10—H10109.2
C1—C6—C5120.6 (5)C10—C11—H11A109.5
C1—C6—N1122.1 (4)C10—C11—H11B109.5
C5—C6—N1117.3 (4)H11A—C11—H11B109.5
C4—C5—C6118.8 (5)C10—C11—H11C109.5
C4—C5—H5120.6H11A—C11—H11C109.5
C6—C5—H5120.6H11B—C11—H11C109.5
C2—C3—C4120.4 (5)C12—N4—C13122.9 (4)
C2—C3—H3119.8C12—N4—H4A118.6
C4—C3—H3119.8C13—N4—H4A118.6
O1—N1—O2125.4 (5)N4—C13—C14114.1 (5)
O1—N1—C6116.0 (4)N4—C13—H13A108.7
O2—N1—C6118.6 (4)C14—C13—H13A108.7
C7—N2—S1122.0 (3)N4—C13—H13B108.7
C7—N2—H2A119.0C14—C13—H13B108.7
S1—N2—H2A119.0H13A—C13—H13B107.6
O5—C9—N3122.1 (4)C13—C14—C15111.0 (5)
O5—C9—C7121.6 (4)C13—C14—H14A109.4
N3—C9—C7116.3 (3)C15—C14—H14A109.4
N2—C7—C9110.4 (3)C13—C14—H14B109.4
N2—C7—C8109.9 (4)C15—C14—H14B109.4
C9—C7—C8109.0 (4)H14A—C14—H14B108.0
N2—C7—H7109.2C14—C15—Br1111.9 (4)
C9—C7—H7109.2C14—C15—H15A109.2
C8—C7—H7109.2Br1—C15—H15A109.2
C7—C8—H8A109.5C14—C15—H15B109.2
C7—C8—H8B109.5Br1—C15—H15B109.2
H8A—C8—H8B109.5H15A—C15—H15B107.9
O3—S1—C1—C2148.8 (4)O4—S1—N2—C7−50.8 (3)
O4—S1—C1—C221.1 (4)C1—S1—N2—C762.9 (3)
N2—S1—C1—C2−94.3 (4)S1—N2—C7—C9−95.6 (4)
O3—S1—C1—C6−28.7 (4)S1—N2—C7—C8144.0 (4)
O4—S1—C1—C6−156.4 (4)O5—C9—C7—N2−45.2 (5)
N2—S1—C1—C688.2 (4)N3—C9—C7—N2137.9 (4)
C6—C1—C2—C3−1.3 (7)O5—C9—C7—C875.7 (6)
S1—C1—C2—C3−178.8 (4)N3—C9—C7—C8−101.3 (5)
C2—C1—C6—C5−2.4 (7)O5—C9—N3—C10−2.8 (7)
S1—C1—C6—C5175.0 (4)C7—C9—N3—C10174.1 (4)
C2—C1—C6—N1178.3 (4)C9—N3—C10—C12−152.0 (4)
S1—C1—C6—N1−4.3 (6)C9—N3—C10—C1187.0 (5)
C3—C4—C5—C6−1.7 (8)O6—C12—C10—N3−52.6 (5)
C1—C6—C5—C43.9 (7)N4—C12—C10—N3130.4 (4)
N1—C6—C5—C4−176.8 (5)O6—C12—C10—C1168.6 (5)
C1—C2—C3—C43.5 (8)N4—C12—C10—C11−108.4 (4)
C5—C4—C3—C2−1.9 (9)O6—C12—N4—C135.1 (7)
C1—C6—N1—O1−67.9 (6)C10—C12—N4—C13−178.0 (4)
C5—C6—N1—O1112.8 (5)C12—N4—C13—C14143.2 (5)
C1—C6—N1—O2114.4 (5)N4—C13—C14—C15−174.7 (4)
C5—C6—N1—O2−64.9 (6)C13—C14—C15—Br1177.8 (4)
O3—S1—N2—C7179.3 (3)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···O6i0.862.072.884 (4)158
N3—H3A···O60.862.542.829 (4)100
N3—H3A···O5ii0.862.072.899 (4)162
N4—H4A···O4i0.862.353.165 (5)159
C2—H2···O40.932.492.867 (6)104
C7—H7···O5ii0.982.343.193 (5)145
C10—H10···O4i0.982.513.431 (5)156
C13—H13A···O60.972.462.802 (6)100
C13—H13B···O3iii0.972.603.496 (6)154
C11—H11A···Cg3.390.963.922 (6)117
C11—H11B···Cgi3.270.963.857 (6)121
Symmetry codes: (i) x−1/2, −y+1/2, −z+2; (ii) x+1/2, −y+1/2, −z+2; (iii) x, y−1, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···O6i0.862.072.884 (4)158
N3—H3A···O60.862.542.829 (4)100
N3—H3A···O5ii0.862.072.899 (4)162
N4—H4A···O4i0.862.353.165 (5)159
C2—H2···O40.932.492.867 (6)104
C7—H7···O5ii0.982.343.193 (5)145
C10—H10···O4i0.982.513.431 (5)156
C13—H13A···O60.972.462.802 (6)100
C13—H13B···O3iii0.972.603.496 (6)154
C11—H11A···Cg3.390.963.922 (6)117
C11—H11B···Cgi3.270.963.857 (6)121
Symmetry codes: (i) x−1/2, −y+1/2, −z+2; (ii) x+1/2, −y+1/2, −z+2; (iii) x, y−1, z.
Acknowledgements top

The authors are grateful to Professor T. N. Guru Row for valuable discussions and for allowing access to the CCD facility, IISc, Bangalore. RT and DNR thank the CSIR for their Junior Research Fellowships.

references
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