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Acta Cryst. (2008). E64, o704    [ doi:10.1107/S160053680800528X ]

H-D-Phe-D-Pro-Gly methyl ester hydrochloride monohydrate

M. Doi, Y. Ichimiya and A. Asano

Abstract top

The conformation of the title tripeptide methyl ester hydrochloride monohydrate, 1-[2-(methoxycarbonylmethylaminocarbonyl)pyrrolidin-1-ylcarbonyl]-2-phenylethanaminium chloride monohydrate, C17H24N3O4+·Cl-·H2O, is extended, but the structure cannot be classified as any typical secondary structure. Interactions through water molecules and chloride ions were formed, in addition to peptide-peptide hydrogen bonds, stabilizing the molecular packing. In comparison with the previous [beta]-turn structure of the Phe-D-Pro-Gly analogue [Doi, Ichimiya & Asano (2007). Acta Cryst. E63, o4691], it was suggested that the difference between the chiralities of Phe and Pro residues of the title compound is important to induce the [beta]-turn structure.

Comment top

The β-turn structures were formed at D-Pro residue in a Gramicidin S and its analogue (Doi et al., 2001; Yamada et al., 2002; Llamas-Saiz, et al., 2007), and a motif including D-Pro promoted β-hairpin in the protein GB1 analogue (Espinosa & Gellman, 2000). A tripeptide motif of Boc–Phe–D-Pro–Gly–OMe (Boc = t-butyloxycarbonyl; OMe = methylester) was designed from these peptides, and the β-turn structure was elucidated (Doi et al., 2007). Moreover, the CD spectra of Gramicidin S analogues suggested that the chiral combination of Phe and Pro residues contributes to the β-turn formation (Tamaki et al., 1985). Title peptide (I) was designed to highlight the chirality of the Phe residue in this tripeptide β-turn motif.

The molecular structure of (I) is shown in Fig. 1. The peptide is a chloride salt and its N-terminal (N10 atom) is protonated. The peptide molecule is somewhat extended, but the structure is not classified to any typical secondary structures from torsion angles. The Pro residue shows a ring puckering with amplitude of Q2 = 0.361 (2) Å and phase of φ2 = 293.1 (2) ° (Cremer & Pople, 1975), which is slightly different from those of the β-turn structure of Boc–Phe–D-Pro–Gly–OMe (Doi et al., 2007).

A peptide-peptide hydrogen bond is formed between N10 and O18 atoms. This interaction makes the molecular arrangement propagated along the b axis, but no sheet structure is created (Fig. 2). Molecular packing is stabilized by the interactions with chloride ion (Cl) and water molecule (O1).

CD spectra of (I) showed no clear proof of special structures existed in acetonitril solution (data not shown), and the structure of (I) was somewhat extended. In contrast to the β-turn structure of the diastereomeric tripeptide (Boc–Phe–D-Pro–Gly–OMe), these results indicate that the chirality of Phe different from that of Pro is important for folding of this tripeptide motif.

Related literature top

For related literature, see: Cremer & Pople (1975); Doi, Fujita et al. (2001); Doi, Ichimiya et al. (2007); Espinosa & Gellman (2000); Llamas-Saiz et al. (2007); Tamaki et al. (1985); Yamada et al. (2002).

Experimental top

The title compound was synthesized by a conventional liquid-phase method and the protected peptide, Boc–D-Phe–D-Pro–Gly–OMe (Boc = t-Butyloxycarboxy; OMe = methylester), was obtained. Boc group was removed by using HCl/dioxane, and the hydrocloride salt was obtained. Crystals were grown from aqueous acetonitrile solutions by vapor diffusion method.

Refinement top

The non-H atoms were refined anisotropically. H atoms were treated as riding atoms with distances C—H = 0.95–1.00 Å, N—H (–NH3+) = 0.91 Å and N—H (CONH) = 0.88 Å; Uiso(H) = 1.2Uiso(C), Uiso(H) = 1.5Ueq(Cmethyl), Uiso(H) = 1.2Ueq(NCONH) and Uiso(H) = 1.5Ueq(NNH3). H atoms of the water molecule were found in a difference Fourier map considering hydrogen-bond networks and fixed during refinements with Uiso(H) = 1.2Ueq(O). The absolute structure was based on the starting materials and was established by Flack parameter.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SMART (Bruker, 1998); data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of (I) with displacement ellipsoids drawn at the 50% probability level with the aid of PLATON (Spek, 2003). Dotted lines represent hydrogen bonds.
[Figure 2] Fig. 2. Packing diagram of (I). Side chains of amino acids are omitted for clarity. Dotted lines represent hydrogen bonds. Circles and filled-circles represent chloride ion (Cl) and water (O1) molecules.
1-[2-(methoxycarbonylmethylaminocarbonyl)pyrrolidin-1-ylcarbonyl]-2- phenylethanaminium chloride monohydrate top
Crystal data top
C17H24N3O4+·Cl–·H2OF000 = 824
Mr = 387.86Dx = 1.334 Mg m−3
Orthorhombic, P212121Mo Kα radiation
λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 8392 reflections
a = 7.3707 (5) Åθ = 2.3–28.3º
b = 9.6667 (7) ŵ = 0.23 mm−1
c = 27.099 (2) ÅT = 90 (2) K
V = 1930.8 (2) Å3Cubic, colourless
Z = 40.40 × 0.35 × 0.35 mm
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		4553 independent reflections
Radiation source: MacScience, M18XCE rotating anode4540 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.020
Detector resolution: 8.366 pixels mm-1θmax = 27.9º
T = 90(2) Kθmin = 2.6º
ω–scanh = −9→9
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		k = −12→12
Tmin = 0.874, Tmax = 0.923l = −35→35
23047 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.032  w = 1/[σ2(Fo2) + (0.0703P)2 + 0.8632P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.088(Δ/σ)max = 0.001
S = 0.85Δρmax = 0.46 e Å−3
4553 reflectionsΔρmin = −0.21 e Å−3
237 parametersExtinction correction: none
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 1920 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.03 (4)
Crystal data top
C17H24N3O4+·Cl–·H2OV = 1930.8 (2) Å3
Mr = 387.86Z = 4
Orthorhombic, P212121Mo Kα
a = 7.3707 (5) ŵ = 0.23 mm−1
b = 9.6667 (7) ÅT = 90 (2) K
c = 27.099 (2) Å0.40 × 0.35 × 0.35 mm
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		4553 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		4540 reflections with I > 2σ(I)
Tmin = 0.874, Tmax = 0.923Rint = 0.020
23047 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.088Δρmax = 0.46 e Å−3
S = 0.85Δρmin = −0.21 e Å−3
4553 reflectionsAbsolute structure: Flack (1983), 1920 Friedel pairs
237 parametersFlack parameter: 0.03 (4)
Special details top

Geometry. Cremer & Pople Puckering Parameters [D. Cremer & J.A. Pople, J.Amer.Chem.Soc., 97, (1975), 1354–1358] ——————————————————————- Q(2) = 0.3608 (15) A ng., Phi(2) = 293.1 (2) Deg

The equation of the plane is of the form: P * x + Q * y + R * z - S = 0 where P, Q, R, S are constants and x, y, z are fractional coordinates.

P = 5.153 (2), Q = 1.935 (5), R = -18.602 (8), S = -9.378 (8) Atom Distance x y z X Y Z * O(18): -0.0397 (9) 0.4138 0.9441 0.7191 3.0500 9.1267 19.4869 * N(20): 0.0350 (11) 0.2674 0.8185 0.6615 1.9711 7.9123 17.9252 * C(10): 0.0337 (12) 0.4982 0.7074 0.7139 3.6722 6.8378 19.3462 * C(18): -0.0103 (12) 0.3858 0.8324 0.6981 2.8434 8.0464 18.9186 * C(20): 0.0268 (13) 0.1632 0.9399 0.6457 1.2030 9.0862 17.4973 * C(23): -0.0454 (14) 0.2080 0.6914 0.6361 1.5330 6.6837 17.2377

P = 4.443 (3), Q = 0.711 (4), R = 21.531 (8), S = 15.452 (5) Atom Distance x y z X Y Z * O(24): 0.1064 (11) 0.4222 1.0289 0.6015 3.1119 9.9466 16.2998 * N(30): 0.0315 (11) 0.2213 1.1812 0.6344 1.6313 11.4182 17.1924 * C(20): -0.1560 (13) 0.1632 0.9399 0.6457 1.2030 9.0862 17.4973 * C(24): 0.0232 (13) 0.2849 1.0527 0.6252 2.1002 10.1765 16.9412 * C(30): -0.1661 (14) 0.2878 1.2994 0.6076 2.1213 12.5607 16.4662 * H(30): 0.16108 0.1378 1.1928 0.6573 1.0157 11.5304 17.8122

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
Cl0.11272 (5)0.69212 (3)0.784634 (14)0.02274 (9)
N100.52851 (16)0.72346 (11)0.76814 (4)0.0135 (2)
H10A0.60340.79670.77370.020*
H10B0.58020.64510.78030.020*
H10C0.42030.73840.78340.020*
C100.49822 (17)0.70736 (13)0.71391 (4)0.0131 (2)
H100.43070.61980.70700.016*
C110.68581 (19)0.70458 (16)0.68855 (5)0.0175 (3)
H11A0.73010.80080.68510.021*
H11B0.77200.65450.71010.021*
C120.68628 (19)0.63705 (14)0.63820 (5)0.0165 (3)
C130.6299 (2)0.70899 (16)0.59619 (5)0.0199 (3)
H130.58990.80210.59900.024*
C140.6322 (2)0.6449 (2)0.55034 (6)0.0310 (4)
H140.59240.69390.52190.037*
C150.6927 (3)0.5092 (2)0.54597 (7)0.0399 (5)
H150.69510.46580.51450.048*
C160.7488 (3)0.43792 (18)0.58701 (8)0.0391 (5)
H160.79010.34520.58390.047*
C170.7457 (2)0.50079 (16)0.63329 (7)0.0261 (3)
H170.78410.45070.66160.031*
C180.38577 (18)0.83238 (13)0.69813 (4)0.0132 (2)
O180.41380 (14)0.94414 (10)0.71910 (3)0.0177 (2)
N200.26742 (16)0.81851 (11)0.66147 (4)0.0138 (2)
C200.16322 (18)0.93995 (13)0.64568 (5)0.0140 (3)
H200.08870.97640.67360.017*
C220.1285 (2)0.74806 (14)0.58840 (5)0.0187 (3)
H22A0.03790.68350.57440.022*
H22B0.22480.76460.56360.022*
C210.0392 (2)0.88425 (14)0.60427 (5)0.0183 (3)
H21A−0.08520.86790.61670.022*
H21B0.03350.95010.57630.022*
C230.20798 (19)0.69142 (14)0.63610 (5)0.0160 (3)
H23A0.11530.64130.65560.019*
H23B0.31150.62890.62950.019*
C240.28494 (18)1.05274 (13)0.62516 (5)0.0143 (2)
O240.42220 (15)1.02895 (11)0.60149 (4)0.0226 (2)
N300.22132 (17)1.18119 (12)0.63443 (4)0.0175 (2)
H300.13781.19280.65730.021*
C300.2878 (2)1.29938 (15)0.60763 (5)0.0206 (3)
H30A0.42061.29030.60310.025*
H30B0.26501.38410.62720.025*
C310.1982 (2)1.31382 (14)0.55761 (5)0.0183 (3)
O310.09911 (18)1.22970 (12)0.53927 (4)0.0269 (2)
O320.24639 (17)1.43362 (11)0.53707 (4)0.0248 (2)
C320.1767 (3)1.4570 (2)0.48750 (6)0.0367 (4)
H32A0.22701.38750.46500.055*
H32B0.21211.54960.47630.055*
H32C0.04411.44980.48780.055*
O10.81122 (14)0.92109 (10)0.78001 (4)0.0195 (2)
H10.90290.87220.77870.023*
H20.83240.98510.76380.023*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl0.01806 (16)0.01737 (15)0.03278 (18)−0.00004 (13)0.00761 (14)−0.00212 (13)
N100.0160 (5)0.0120 (5)0.0123 (5)0.0004 (4)−0.0018 (4)0.0010 (4)
C100.0151 (5)0.0122 (5)0.0119 (5)0.0002 (5)−0.0010 (5)0.0010 (5)
C110.0148 (6)0.0220 (7)0.0157 (6)−0.0005 (5)0.0005 (5)−0.0006 (5)
C120.0135 (5)0.0168 (6)0.0191 (6)−0.0028 (5)0.0032 (5)−0.0043 (5)
C130.0174 (6)0.0246 (7)0.0178 (6)−0.0043 (6)0.0012 (5)−0.0029 (5)
C140.0218 (7)0.0511 (10)0.0202 (7)−0.0096 (8)0.0021 (6)−0.0081 (7)
C150.0281 (8)0.0539 (12)0.0375 (9)−0.0133 (9)0.0105 (7)−0.0320 (9)
C160.0241 (8)0.0245 (8)0.0686 (13)−0.0067 (7)0.0142 (9)−0.0251 (9)
C170.0175 (6)0.0179 (7)0.0429 (9)−0.0013 (6)0.0049 (7)−0.0024 (6)
C180.0145 (5)0.0123 (5)0.0127 (5)−0.0018 (5)0.0024 (5)0.0026 (4)
O180.0226 (5)0.0122 (4)0.0182 (4)−0.0010 (4)−0.0045 (4)0.0000 (4)
N200.0166 (5)0.0092 (5)0.0157 (5)−0.0006 (4)−0.0014 (4)0.0010 (4)
C200.0162 (6)0.0119 (6)0.0140 (5)0.0011 (5)0.0000 (5)0.0023 (4)
C220.0217 (7)0.0187 (6)0.0157 (6)−0.0025 (5)−0.0052 (5)−0.0013 (5)
C210.0182 (6)0.0174 (6)0.0194 (6)−0.0035 (5)−0.0053 (5)0.0025 (5)
C230.0174 (6)0.0124 (6)0.0183 (6)−0.0031 (5)−0.0027 (5)−0.0003 (5)
C240.0170 (6)0.0130 (6)0.0130 (5)−0.0010 (5)−0.0026 (5)0.0017 (5)
O240.0220 (5)0.0192 (5)0.0266 (5)−0.0012 (4)0.0077 (4)0.0041 (4)
N300.0227 (6)0.0128 (5)0.0169 (5)−0.0005 (5)0.0011 (4)0.0021 (4)
C300.0268 (7)0.0137 (6)0.0214 (6)−0.0047 (6)−0.0040 (5)0.0038 (5)
C310.0215 (6)0.0153 (6)0.0181 (6)0.0031 (6)0.0039 (5)0.0006 (5)
O310.0353 (6)0.0221 (5)0.0233 (5)−0.0015 (5)−0.0060 (5)−0.0025 (4)
O320.0299 (6)0.0211 (5)0.0233 (5)0.0000 (5)−0.0007 (5)0.0089 (4)
C320.0483 (11)0.0399 (9)0.0218 (7)0.0074 (9)0.0005 (7)0.0101 (7)
O10.0186 (5)0.0172 (4)0.0227 (5)0.0001 (4)0.0005 (4)0.0003 (4)
Geometric parameters (Å, °) top
N10—C101.4947 (16)C20—C211.5441 (18)
N10—H10A0.9100C20—H201.0000
N10—H10B0.9100C22—C231.5209 (18)
N10—H10C0.9100C22—C211.533 (2)
C10—C181.5265 (17)C22—H22A0.9900
C10—C111.5442 (18)C22—H22B0.9900
C10—H101.0000C21—H21A0.9900
C11—C121.5125 (18)C21—H21B0.9900
C11—H11A0.9900C23—H23A0.9900
C11—H11B0.9900C23—H23B0.9900
C12—C171.394 (2)C24—O241.2197 (17)
C12—C131.397 (2)C24—N301.3509 (17)
C13—C141.388 (2)N30—C301.4397 (17)
C13—H130.9500N30—H300.8800
C14—C151.391 (3)C30—C311.5144 (19)
C14—H140.9500C30—H30A0.9900
C15—C161.372 (3)C30—H30B0.9900
C15—H150.9500C31—O311.2006 (19)
C16—C171.394 (3)C31—O321.3329 (17)
C16—H160.9500O32—C321.456 (2)
C17—H170.9500C32—H32A0.9800
C18—O181.2381 (16)C32—H32B0.9800
C18—N201.3289 (17)C32—H32C0.9800
N20—C201.4666 (16)O1—H10.825
N20—C231.4745 (17)O1—H20.775
C20—C241.5176 (18)
C10—N10—H10A109.5N20—C20—H20110.4
C10—N10—H10B109.5C24—C20—H20110.4
H10A—N10—H10B109.5C21—C20—H20110.4
C10—N10—H10C109.5C23—C22—C21103.65 (11)
H10A—N10—H10C109.5C23—C22—H22A111.0
H10B—N10—H10C109.5C21—C22—H22A111.0
N10—C10—C18105.90 (10)C23—C22—H22B111.0
N10—C10—C11107.80 (10)C21—C22—H22B111.0
C18—C10—C11112.04 (10)H22A—C22—H22B109.0
N10—C10—H10110.3C22—C21—C20104.43 (11)
C18—C10—H10110.3C22—C21—H21A110.9
C11—C10—H10110.3C20—C21—H21A110.9
C12—C11—C10114.26 (11)C22—C21—H21B110.9
C12—C11—H11A108.7C20—C21—H21B110.9
C10—C11—H11A108.7H21A—C21—H21B108.9
C12—C11—H11B108.7N20—C23—C22102.16 (10)
C10—C11—H11B108.7N20—C23—H23A111.3
H11A—C11—H11B107.6C22—C23—H23A111.3
C17—C12—C13119.06 (14)N20—C23—H23B111.3
C17—C12—C11119.64 (14)C22—C23—H23B111.3
C13—C12—C11121.30 (13)H23A—C23—H23B109.2
C14—C13—C12120.25 (15)O24—C24—N30123.99 (13)
C14—C13—H13119.9O24—C24—C20123.20 (12)
C12—C13—H13119.9N30—C24—C20112.77 (12)
C13—C14—C15120.05 (18)C24—N30—C30121.16 (12)
C13—C14—H14120.0C24—N30—H30119.4
C15—C14—H14120.0C30—N30—H30119.4
C16—C15—C14120.10 (16)N30—C30—C31112.10 (12)
C16—C15—H15120.0N30—C30—H30A109.2
C14—C15—H15120.0C31—C30—H30A109.2
C15—C16—C17120.34 (17)N30—C30—H30B109.2
C15—C16—H16119.8C31—C30—H30B109.2
C17—C16—H16119.8H30A—C30—H30B107.9
C16—C17—C12120.20 (17)O31—C31—O32125.29 (13)
C16—C17—H17119.9O31—C31—C30124.98 (13)
C12—C17—H17119.9O32—C31—C30109.73 (12)
O18—C18—N20122.73 (12)C31—O32—C32115.22 (13)
O18—C18—C10118.15 (11)O32—C32—H32A109.5
N20—C18—C10119.07 (11)O32—C32—H32B109.5
C18—N20—C20118.75 (11)H32A—C32—H32B109.5
C18—N20—C23128.88 (11)O32—C32—H32C109.5
C20—N20—C23112.05 (10)H32A—C32—H32C109.5
N20—C20—C24111.86 (11)H32B—C32—H32C109.5
N20—C20—C21104.05 (10)H1—O1—H2105.56
C24—C20—C21109.51 (11)
N10—C10—C11—C12158.2 (1)C23—N20—C20—C24−122.61 (12)
C18—C10—C11—C12−85.66 (14)C18—N20—C20—C21−178.58 (11)
C10—C11—C12—C17−99.94 (15)C23—N20—C20—C21−4.49 (14)
C10—C11—C12—C1380.71 (17)C23—C22—C21—C2034.16 (14)
C17—C12—C13—C140.4 (2)N20—C20—C21—C22−18.6 (1)
C11—C12—C13—C14179.76 (13)C24—C20—C21—C22101.18 (12)
C12—C13—C14—C15−0.8 (2)C18—N20—C23—C22−160.99 (13)
C13—C14—C15—C160.5 (3)C20—N20—C23—C2225.66 (14)
C14—C15—C16—C170.0 (3)C21—C22—C23—N20−36.02 (13)
C15—C16—C17—C12−0.4 (3)N20—C20—C24—O2435.04 (17)
C13—C12—C17—C160.1 (2)C21—C20—C24—O24−79.78 (16)
C11—C12—C17—C16−179.22 (14)N20—C20—C24—N30−147.2 (1)
N10—C10—C18—O1834.80 (15)C21—C20—C24—N3098.00 (13)
C11—C10—C18—O18−82.47 (14)O24—C24—N30—C3014.4 (2)
N10—C10—C18—N20−147.7 (1)C20—C24—N30—C30−163.4 (1)
C11—C10—C18—N2095.02 (14)C24—N30—C30—C3180.9 (2)
O18—C18—N20—C20−1.09 (19)N30—C30—C31—O31−8.2 (2)
C10—C18—N20—C20−178.5 (1)N30—C30—C31—O32172.0 (1)
O18—C18—N20—C23−174.05 (12)O31—C31—O32—C32−3.0 (2)
C10—C18—N20—C238.58 (19)C30—C31—O32—C32176.89 (14)
C18—N20—C20—C2463.3 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N10—H10A···O10.911.962.845 (2)166
N10—H10C···Cl0.912.313.112 (1)147
N10—H10B···O18i0.911.942.755 (1)148
O1—H2···Clii0.772.433.201 (1)177
N30—H30···Cliii0.882.433.299 (1)171
O1—H1···Cliv0.822.333.139 (1)165
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, y+1/2, −z+3/2; (iii) −x, y+1/2, −z+3/2; (iv) x+1, y, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N10—H10A···O10.911.962.845 (2)166
N10—H10C···Cl0.912.313.112 (1)147
N10—H10B···O18i0.911.942.755 (1)148
O1—H2···Clii0.772.433.201 (1)177
N30—H30···Cliii0.882.433.299 (1)171
O1—H1···Cliv0.822.333.139 (1)165
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, y+1/2, −z+3/2; (iii) −x, y+1/2, −z+3/2; (iv) x+1, y, z.
references
References top

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