N-(L-2-Amino­penta­noyl)-L-phenyl­alanine dihydrate, a hydro­phobic dipeptide with a nonproteinogenic residue

The title dipeptide, better known as L-norvalyl-L-phenyl­alanine {systematic name: (S)-2-[(S)-2-amino­penta­namido]-3-phenyl­propanoic acid dihydrate}, C₁₄H₂₀N₂O₃·2H₂O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a mol­ecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydro­phobic N-terminal residue and a C-terminal L-phenyl­alanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydro­phobic and hydro­philic layers, the latter encompassing cocrystallized water mol­ecules connecting the charged N- and C-terminal groups.

S1. Introduction

Among dipeptides with two hydro­phobic residues, seven compounds rich in Leu, Phe and Trp residues constitute the Phe—Phe class of nanoporous structures (Görbitz, 2007) characterized by hydro­philic channels (all amino acids discussed here are of the L configuration and stereochemical indicators are thus not included). In order to see if this family could be expanded by including dipeptides with nonproteinogenic, nonpolar residues, the title dipeptide, N-(L-2-amino­penta­noyl)-L-phenyl­alanine dihydrate, Nva–Phe.2H₂O (Nva = norvaline), (I), was synthesized and its structure examined with single-crystal X-ray diffraction methods.

S2. Experimental

S2.1. Synthesis and crystallization

The title compound was prepared by a three-step solution-phase reaction process (described in the Supplementary materials). Slow evaporation of water from the product obtained in the final step (0.060 g) over a period of three weeks afforded colorless crystals of (I).

S2.2. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. The positional parameters of water H atoms, which had been located in a difference map, were refined with their respective O—H distances restrained to 0.85 (2) Å. N—H and C—H distances were fixed at 0.91 (NH₃⁺), 0.88 (>N—H), 0.99 (methyl­ene), 1.00 (methine) or 0.95 Å (aromatic), with free rotation for the amino group. U_iso(H) values were set at 1.5U_eq of the carrier atom for water, methyl and amino H atoms, and at 1.2U_eq for the other H atoms. In the absence of significant anomalous scattering effects, Friedel pairs were merged.

S3. Results and discussion

The vast majority of dipeptides, such as Ala–Phe 2-propanol solvate [Cambridge Structural Database (CSD, Version 5.34; Allen 2002) refcode COCGEG (Görbitz, 1999)] included in the overview of torsion angles in Table 2, take on conformations in the solid state that bring side chains on opposite sides of the peptide plane. The molecular geometry of (I) (Fig. 1) is clearly different in that both side chains are positioned on the same side of the peptide plane. This relatively rare folded conformation is normally associated with members of the Phe–Phe class (Görbitz, 2007) such as Leu–Phe and Phe–Phe (IDUZUC and IFABEW; Görbitz, 2001) (Table 2). In this case, however, it is clear from Fig. 2(a) that the crystal packing arrangement is not nanoporous, but rather is divided into layers, thus making (I) isostructural to Val–Phe (MOBYAD; Görbitz, 2002) in Fig. 2(b). Cocrystallized water molecules here serve as bridges between the charged N- and C-terminal groups, the list of hydrogen bonds in Table 3 notably have entries for neither direct amino–carboxyl­ate nor water–water inter­actions. Ile–Phe in Fig. 2(c) (ETONIK; Görbitz, 2004a) also has the same type of hydration and hydrogen-bonding pattern, but it crystallizes in the monoclinic space group P2₁ rather than the orthorhombic space group P2₁2₁2₁, giving a different type of inter­face at the centre of the hydro­phobic layer in Fig. 2(c) compared to Figs. 2(a) and 2(b). Differences between (I) and Val–Phe (and also Ile–Phe) in Table 2 are particularly evident for the N1—C1—C5—N2 torsion angle (ψ₁), but also for C6—C7—C8—C9 (χ₂^2,1), which in (I) displays a large deviation from the broad rotational energy minimum at ±90° (Scouras & Daggett, 2010). It appears that this is associated with a slightly shorter a axis for (I) than for Val–Phe [5.6223 (9) versus 5.6592 (4) Å], which is rendered possible by the more slender side chain while forcing a tighter contact between aromatic groups. The shortest aromatic C—H···C contact in (I) is C10—H10···C10(x-1/2, -y+3/2, -z+1) of 2.81 Å, while the corresponding contact in Val–Phe is 2.85 Å (after normalization of the C—H bond length to 0.95 Å). The extreme value for χ₂^2,1 in Table 2 [-18.1 (6)°] represents an unusual conformation resulting from an intra­molecular inter­action between the two aromatic moieties in Phe–Phe.

For comparison, Fig. 2(d) shows the monoclinic P2₁ structure of Leu–Phe (IDUZUC; Görbitz, 2001), which has Z' = 2 and water-filled channels surrounded by four dipeptide molecules participating in a one-dimensional hydrogen-bonding network. This structure has two regular head-to-tail hydrogen-bonded chains and constitutes a tubular analogue to one of the four basic two-dimensional hydrogen-bonding patterns regularly observed in dipeptide structures (Görbitz, 2010). It appears that Leu residues are particularly strong drivers towards formation of Phe–Phe class nanotubular structures, if fact even more so than Phe since, for example, Ile–Leu is nanotubular (ETITUW; Görbitz, 2004b), while Ile–Phe (ETONIK; Görbitz, 2004a) is not. This is evidently due to the inverse trapesoid shape of the Leu side chain, which fits well into tubular structures and less well in layered structures (Fig. 2).

Related literature

For related literature, see: Allen (2002); Görbitz (1999, 2001, 2002, 2004a, 2004b, 2007, 2010); Scouras & Daggett (2010).

Computing details

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures

The asymmetric unit of (I), with displacement ellipsoids drawn at the 50% probability level.

The crystal packing of (a) (I), (b) Val–Phe dihydrate (CSD refcode MOBYAD; Görbitz, 2002), (c) Ile–Phe dihydrate (ETONIK; Görbitz, 2004a) and (d) Leu–Phe 0.96-hydrate (IDUZUC; Görbitz, 2001). H atoms not involved in hydrogen bonds have been omitted for clarity. [In the electronic version of the paper, red (Phe) and blue shades (other residues) highlight the different shapes of the amino acid side chains.]

(S)-2-[(S)-2-Aminopentanamido]-3-phenylpropanoic acid dihydrate

Crystal data

C14H20N2O3·2H2O	F(000) = 648
Mr = 300.25	Dx = 1.289 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 668 reflections
a = 5.6223 (9) Å	θ = 2.6–15.3°
b = 8.2012 (12) Å	µ = 0.10 mm^−1
c = 33.573 (5) Å	T = 105 K
V = 1548.0 (4) Å^3	Blocks, colourless
Z = 4	0.22 × 0.07 × 0.03 mm

Data collection

Bruker APEXII CCD diffractometer	1896 independent reflections
Radiation source: fine-focus sealed tube	1542 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.121
Detector resolution: 8.3 pixels mm^-1	θmax = 26.4°, θmin = 2.4°
Sets of exposures each taken over 0.5° ω rotation scans	h = −7→7
Absorption correction: multi-scan (SADABS; Bruker, 2007)	k = −9→10
Tmin = 0.992, Tmax = 0.997	l = −42→42
12815 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.070	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.125	H atoms treated by a mixture of independent and constrained refinement
S = 1.11	w = 1/[σ^2(Fo^2) + (0.0302P)^2 + 1.1996P] where P = (Fo^2 + 2Fc^2)/3
1896 reflections	(Δ/σ)max < 0.001
204 parameters	Δρmax = 0.26 e Å^−3
6 restraints	Δρmin = −0.32 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.4407 (5)	0.5037 (4)	0.31846 (9)	0.0223 (7)
O2	0.4630 (5)	0.8756 (4)	0.30223 (8)	0.0212 (7)
O3	0.7497 (5)	0.8556 (4)	0.34789 (9)	0.0218 (7)
N1	0.1140 (7)	0.3184 (5)	0.28315 (10)	0.0208 (9)
H1	0.0417	0.2197	0.2857	0.031*
H2	0.2741	0.3060	0.2858	0.031*
H3	0.0807	0.3611	0.2588	0.031*
N2	0.1761 (6)	0.6709 (4)	0.34880 (10)	0.0180 (8)
H4	0.0251	0.6954	0.3522	0.022*
C1	0.0242 (8)	0.4314 (5)	0.31495 (13)	0.0178 (10)
H11	−0.1070	0.5004	0.3039	0.021*
C2	−0.0672 (8)	0.3358 (6)	0.35103 (13)	0.0224 (10)
H21	−0.1414	0.4134	0.3699	0.027*
H22	−0.1928	0.2598	0.3419	0.027*
C3	0.1223 (9)	0.2381 (6)	0.37331 (13)	0.0273 (12)
H31	0.2530	0.3116	0.3816	0.033*
H32	0.1895	0.1538	0.3555	0.033*
C4	0.0132 (10)	0.1570 (6)	0.41001 (13)	0.0344 (13)
H41	0.1358	0.0944	0.4241	0.052*
H42	−0.1151	0.0835	0.4017	0.052*
H43	−0.0511	0.2408	0.4278	0.052*
C5	0.2327 (8)	0.5400 (6)	0.32695 (13)	0.0191 (10)
C6	0.3566 (8)	0.7744 (6)	0.36719 (13)	0.0187 (10)
H61	0.2719	0.8718	0.3781	0.022*
C7	0.4768 (8)	0.6897 (6)	0.40252 (12)	0.0224 (10)
H71	0.5723	0.5977	0.3921	0.027*
H72	0.5886	0.7680	0.4149	0.027*
C8	0.3146 (8)	0.6253 (6)	0.43452 (13)	0.0203 (10)
C9	0.0967 (8)	0.6980 (6)	0.44423 (13)	0.0225 (11)
H91	0.0414	0.7881	0.4291	0.027*
C10	−0.0394 (8)	0.6404 (6)	0.47562 (13)	0.0251 (11)
H101	−0.1861	0.6920	0.4818	0.030*
C11	0.0355 (9)	0.5094 (6)	0.49792 (13)	0.0268 (11)
H111	−0.0579	0.4713	0.5196	0.032*
C12	0.2491 (9)	0.4332 (6)	0.48848 (14)	0.0279 (12)
H121	0.3017	0.3421	0.5035	0.033*
C13	0.3851 (8)	0.4908 (6)	0.45697 (12)	0.0228 (11)
H131	0.5298	0.4371	0.4505	0.027*
C14	0.5378 (8)	0.8382 (5)	0.33643 (12)	0.0186 (10)
O1W	1.0180 (5)	0.9733 (4)	0.28669 (9)	0.0205 (7)
H11W	1.145 (5)	0.924 (6)	0.2946 (13)	0.031*
H12W	0.922 (6)	0.957 (6)	0.3058 (10)	0.031*
O2W	0.4174 (6)	0.6854 (4)	0.23115 (10)	0.0271 (8)
H21W	0.457 (10)	0.586 (3)	0.2264 (13)	0.041*
H22W	0.440 (10)	0.693 (6)	0.2562 (6)	0.041*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0157 (16)	0.0246 (18)	0.0267 (17)	0.0028 (16)	0.0000 (14)	−0.0030 (15)
O2	0.0193 (16)	0.0228 (18)	0.0216 (16)	0.0000 (16)	−0.0008 (14)	0.0016 (13)
O3	0.0177 (15)	0.0242 (19)	0.0236 (16)	−0.0024 (15)	−0.0002 (14)	0.0044 (14)
N1	0.022 (2)	0.022 (2)	0.0181 (18)	−0.0031 (19)	−0.0003 (16)	−0.0006 (17)
N2	0.0130 (17)	0.020 (2)	0.0213 (19)	0.0001 (17)	0.0000 (16)	−0.0003 (17)
C1	0.016 (2)	0.013 (2)	0.024 (2)	−0.003 (2)	0.000 (2)	−0.0019 (18)
C2	0.023 (2)	0.022 (3)	0.022 (2)	−0.001 (2)	0.006 (2)	0.002 (2)
C3	0.038 (3)	0.022 (3)	0.022 (3)	−0.002 (2)	−0.004 (2)	−0.001 (2)
C4	0.054 (4)	0.025 (3)	0.024 (2)	−0.005 (3)	−0.004 (3)	0.003 (2)
C5	0.019 (2)	0.019 (3)	0.019 (2)	−0.006 (2)	−0.0028 (19)	0.0052 (19)
C6	0.019 (2)	0.019 (2)	0.018 (2)	−0.001 (2)	0.0006 (19)	−0.0026 (19)
C7	0.016 (2)	0.032 (3)	0.018 (2)	−0.004 (2)	−0.0006 (19)	−0.002 (2)
C8	0.020 (2)	0.022 (3)	0.019 (2)	0.000 (2)	−0.004 (2)	0.001 (2)
C9	0.022 (2)	0.025 (3)	0.021 (2)	−0.002 (2)	−0.006 (2)	−0.002 (2)
C10	0.017 (2)	0.035 (3)	0.024 (2)	−0.002 (2)	0.005 (2)	−0.001 (2)
C11	0.030 (3)	0.029 (3)	0.021 (2)	−0.006 (3)	0.005 (2)	−0.003 (2)
C12	0.033 (3)	0.026 (3)	0.025 (2)	−0.003 (3)	−0.004 (2)	0.001 (2)
C13	0.022 (2)	0.027 (3)	0.020 (2)	0.001 (2)	−0.0024 (19)	−0.004 (2)
C14	0.017 (2)	0.017 (2)	0.022 (2)	0.005 (2)	0.0011 (19)	−0.0030 (19)
O1W	0.0168 (16)	0.0251 (18)	0.0196 (15)	0.0023 (15)	0.0001 (14)	0.0012 (14)
O2W	0.033 (2)	0.0240 (18)	0.0247 (17)	0.0018 (17)	−0.0006 (16)	−0.0034 (15)

Geometric parameters (Å, º)

O1—C5	1.240 (5)	C6—C7	1.532 (6)
O2—C14	1.261 (5)	C6—C14	1.542 (6)
O3—C14	1.260 (5)	C6—H61	1.0000
N1—C1	1.501 (5)	C7—C8	1.505 (6)
N1—H1	0.9100	C7—H71	0.9900
N1—H2	0.9100	C7—H72	0.9900
N1—H3	0.9100	C8—C13	1.393 (6)
N2—C5	1.339 (6)	C8—C9	1.401 (6)
N2—C6	1.459 (6)	C9—C10	1.385 (6)
N2—H4	0.8800	C9—H91	0.9500
C1—C5	1.527 (6)	C10—C11	1.376 (7)
C1—C2	1.532 (6)	C10—H101	0.9500
C1—H11	1.0000	C11—C12	1.390 (7)
C2—C3	1.528 (6)	C11—H111	0.9500
C2—H21	0.9900	C12—C13	1.388 (6)
C2—H22	0.9900	C12—H121	0.9500
C3—C4	1.529 (6)	C13—H131	0.9500
C3—H31	0.9900	O1W—H11W	0.862 (19)
C3—H32	0.9900	O1W—H12W	0.848 (19)
C4—H41	0.9800	O2W—H21W	0.862 (19)
C4—H42	0.9800	O2W—H22W	0.852 (19)
C4—H43	0.9800
C1—N1—H1	109.5	N2—C6—C7	111.8 (4)
C1—N1—H2	109.5	N2—C6—C14	111.9 (3)
H1—N1—H2	109.5	C7—C6—C14	112.4 (4)
C1—N1—H3	109.5	N2—C6—H61	106.8
H1—N1—H3	109.5	C7—C6—H61	106.8
H2—N1—H3	109.5	C14—C6—H61	106.8
C5—N2—C6	122.2 (4)	C8—C7—C6	116.4 (4)
C5—N2—H4	118.9	C8—C7—H71	108.2
C6—N2—H4	118.9	C6—C7—H71	108.2
N1—C1—C5	106.8 (4)	C8—C7—H72	108.2
N1—C1—C2	111.0 (4)	C6—C7—H72	108.2
C5—C1—C2	110.3 (4)	H71—C7—H72	107.3
N1—C1—H11	109.5	C13—C8—C9	117.4 (4)
C5—C1—H11	109.5	C13—C8—C7	119.5 (4)
C2—C1—H11	109.5	C9—C8—C7	123.1 (4)
C3—C2—C1	114.9 (4)	C10—C9—C8	121.0 (5)
C3—C2—H21	108.5	C10—C9—H91	119.5
C1—C2—H21	108.5	C8—C9—H91	119.5
C3—C2—H22	108.5	C11—C10—C9	120.7 (5)
C1—C2—H22	108.5	C11—C10—H101	119.6
H21—C2—H22	107.5	C9—C10—H101	119.6
C2—C3—C4	110.1 (4)	C10—C11—C12	119.4 (5)
C2—C3—H31	109.6	C10—C11—H111	120.3
C4—C3—H31	109.6	C12—C11—H111	120.3
C2—C3—H32	109.6	C13—C12—C11	119.8 (5)
C4—C3—H32	109.6	C13—C12—H121	120.1
H31—C3—H32	108.2	C11—C12—H121	120.1
C3—C4—H41	109.5	C12—C13—C8	121.6 (5)
C3—C4—H42	109.5	C12—C13—H131	119.2
H41—C4—H42	109.5	C8—C13—H131	119.2
C3—C4—H43	109.5	O3—C14—O2	124.5 (4)
H41—C4—H43	109.5	O3—C14—C6	117.3 (4)
H42—C4—H43	109.5	O2—C14—C6	118.1 (4)
O1—C5—N2	122.9 (4)	H11W—O1W—H12W	103 (3)
O1—C5—C1	121.6 (4)	H21W—O2W—H22W	102 (3)
N2—C5—C1	115.5 (4)
N1—C1—C5—N2	166.5 (4)	C14—C6—C7—C8	179.1 (4)
C1—C5—N2—C6	171.5 (4)	C6—C7—C8—C13	151.3 (4)
C5—N2—C6—C14	55.0 (5)	C13—C8—C9—C10	1.7 (7)
N2—C6—C14—O2	37.2 (6)	C7—C8—C9—C10	−175.8 (4)
N1—C1—C2—C3	64.7 (5)	C8—C9—C10—C11	−0.5 (7)
C1—C2—C3—C4	176.5 (4)	C9—C10—C11—C12	−0.7 (7)
N2—C6—C7—C8	−54.0 (5)	C10—C11—C12—C13	0.5 (7)
C6—C7—C8—C9	−31.2 (6)	C11—C12—C13—C8	0.7 (7)
C5—C1—C2—C3	−53.5 (5)	C9—C8—C13—C12	−1.8 (7)
C6—N2—C5—O1	−5.1 (7)	C7—C8—C13—C12	175.8 (4)
N1—C1—C5—O1	−16.8 (6)	N2—C6—C14—O3	−145.7 (4)
C2—C1—C5—O1	104.0 (5)	C7—C6—C14—O3	−19.0 (6)
C2—C1—C5—N2	−72.7 (5)	C7—C6—C14—O2	163.9 (4)
C5—N2—C6—C7	−72.1 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1W^i	0.91	2.03	2.884 (5)	157
N1—H2···O2W^ii	0.91	2.08	2.892 (5)	149
N1—H3···O1W^ii	0.91	1.87	2.768 (5)	171
N2—H4···O3^iii	0.88	2.04	2.836 (5)	151
C1—H11···O1^iii	1.00	2.59	3.336 (5)	131
O1W—H11W···O2^iv	0.86 (2)	1.85 (2)	2.678 (4)	160 (5)
O1W—H12W···O3	0.85 (2)	1.91 (2)	2.726 (4)	162 (5)
O2W—H21W···O2^ii	0.86 (2)	2.02 (2)	2.857 (5)	162 (4)
O2W—H22W···O2	0.85 (2)	2.15 (3)	2.862 (5)	140 (4)

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