Hydro­phobic dipeptides: the final piece in the puzzle

Görbitz, C.H.

doi:10.1107/S2052520618007151

Hydrophobic dipeptides: the final piece in the puzzle

The crystal structure of L-valyl-L-leucine acetonitrile solvate presented here adds to 24 previously reported structures of dipeptides constructed from the five nonpolar amino acids L-alanine, L-valine, L-isoleucine, L-leucine and L-phenylalanine. It thus constitutes the final piece in the 5 × 5 puzzle of hydrophobic dipeptide structures. This opportunity is taken to review the crystal packing arrangements and hydrogen-bonding preferences of a rather unique group of substances, with updated information on the various hydrogen-bonding patterns and the associated peptide conformations.

Keywords: dipeptides; hydrogen bonding; crystal packing; conformations.

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Supporting information

	Portable Document Format (PDF) file https://doi.org/10.1107/S2052520618007151/aw5008sup3.pdf Additional tables and figures.
	Crystallographic Information File (CIF) https://doi.org/10.1107/S2052520618007151/aw5008sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S2052520618007151/aw5008Isup2.hkl Contains datablock I

CCDC reference: 1825080

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: APEX2 (Bruker, 2014); data reduction: APEX2 (Bruker, 2014); program(s) used to solve structure: APEX2 (Bruker, 2014); program(s) used to refine structure: SHELXT (Sheldrick, 2015a); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b).

(S)-2-((S)-2-Amino-3-methyl-butyrylamino)-4-methyl-pentanoic acid acetonitrile solvate top

Crystal data top

C₁₁H₂₂N₂O₃·C₂H₃N	D_x = 1.165 Mg m⁻³
M_r = 271.36	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 858 reflections
a = 5.341 (3) Å	θ = 2.5–20.7°
b = 13.536 (6) Å	µ = 0.08 mm⁻¹
c = 21.406 (8) Å	T = 100 K
V = 1547.6 (12) Å³	Plate, colorless
Z = 4	0.42 × 0.15 × 0.01 mm
F(000) = 592

Data collection top

Bruker D8 Venture with Photon 100 CMOS detector diffractometer	1572 independent reflections
Radiation source: fine-focus sealed tube	903 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.190
Detector resolution: 8.3 pixels mm^-1	θ_max = 20.8°, θ_min = 2.4°
Sets of exposures each taken over 0.5° ω rotation scans	h = −5→4
Absorption correction: multi-scan SADABS (Bruker, 2014)	k = −13→12
T_min = 0.612, T_max = 1.000	l = −21→19
6287 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.082	w = 1/[σ²(F_o²) + (0.0807P)²] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.184	(Δ/σ)_max < 0.001
S = 1.01	Δρ_max = 0.26 e Å⁻³
1572 reflections	Δρ_min = −0.28 e Å⁻³
140 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
72 restraints	Extinction coefficient: 0.093 (13)

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Non-terminal C-atoms refined isotropically due to poor reflection-to-parameter ratio. All H atoms in theoretical positions.

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

	x	y	z	U_iso*/U_eq
O1	0.0880 (14)	0.6221 (6)	0.2086 (3)	0.029 (2)
O2	0.0294 (16)	0.3336 (5)	0.2523 (3)	0.028 (2)
O3	−0.3193 (14)	0.3338 (5)	0.1909 (3)	0.023 (2)
N1	0.5574 (18)	0.7039 (6)	0.2281 (4)	0.025 (3)
H1	0.5398	0.7151	0.1864	0.037*
H2	0.7148	0.7210	0.2402	0.037*
H3	0.4436	0.7408	0.2495	0.037*
N2	0.2677 (18)	0.4746 (6)	0.1816 (3)	0.018 (3)
H4	0.4091	0.4414	0.1792	0.022*
C1	0.513 (2)	0.5941 (7)	0.2418 (5)	0.022 (3)*
H11	0.6553	0.5547	0.2242	0.026*
C2	0.503 (2)	0.5788 (7)	0.3127 (5)	0.024 (3)*
H2A	0.3637	0.6196	0.3303	0.029*
C3	0.455 (2)	0.4695 (8)	0.3284 (5)	0.031 (4)
H31	0.4490	0.4611	0.3738	0.046*
H32	0.2953	0.4487	0.3101	0.046*
H33	0.5907	0.4290	0.3111	0.046*
C4	0.756 (2)	0.6102 (8)	0.3446 (5)	0.034 (4)
H41	0.7440	0.5997	0.3898	0.051*
H42	0.8932	0.5703	0.3277	0.051*
H43	0.7884	0.6802	0.3362	0.051*
C5	0.270 (3)	0.5645 (9)	0.2086 (5)	0.026 (3)*
C6	0.037 (2)	0.4292 (7)	0.1560 (5)	0.024 (3)*
H61	−0.0846	0.4834	0.1469	0.028*
C7	0.094 (2)	0.3760 (8)	0.0945 (4)	0.020 (3)*
H71	−0.0575	0.3399	0.0811	0.025*
H72	0.2274	0.3266	0.1022	0.025*
C8	0.180 (2)	0.4454 (8)	0.0401 (5)	0.022 (3)*
H81	0.3251	0.4851	0.0555	0.026*
C9	−0.030 (2)	0.5183 (8)	0.0217 (5)	0.037 (4)
H91	−0.0821	0.5560	0.0586	0.056*
H92	0.0322	0.5637	−0.0104	0.056*
H93	−0.1734	0.4813	0.0052	0.056*
C10	0.269 (2)	0.3846 (8)	−0.0147 (4)	0.032 (4)
H101	0.4019	0.3396	−0.0009	0.048*
H102	0.1292	0.3463	−0.0315	0.048*
H103	0.3348	0.4286	−0.0472	0.048*
C11	−0.087 (3)	0.3579 (8)	0.2046 (5)	0.024 (3)*
C13	0.032 (2)	0.8103 (9)	0.0897 (5)	0.047 (4)
H131	0.0379	0.8689	0.0629	0.070*
H132	0.0140	0.8308	0.1334	0.070*
H133	−0.1104	0.7689	0.0778	0.070*
C12	0.265 (3)	0.7538 (10)	0.0825 (6)	0.038 (4)
N3	0.450 (2)	0.7083 (8)	0.0788 (5)	0.043 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.012 (5)	0.038 (5)	0.038 (5)	0.001 (4)	0.000 (4)	−0.007 (4)
O2	0.021 (6)	0.040 (5)	0.022 (4)	0.003 (5)	−0.004 (4)	0.008 (4)
O3	0.007 (5)	0.029 (5)	0.033 (5)	0.001 (4)	0.003 (4)	−0.001 (4)
N1	0.015 (7)	0.040 (6)	0.019 (5)	−0.005 (6)	0.003 (5)	0.000 (5)
N2	0.010 (5)	0.026 (4)	0.019 (4)	0.005 (4)	−0.002 (4)	−0.002 (4)
C3	0.026 (9)	0.048 (8)	0.019 (7)	0.006 (8)	−0.003 (7)	0.000 (6)
C4	0.027 (9)	0.049 (8)	0.025 (7)	0.008 (9)	−0.010 (7)	−0.003 (6)
C9	0.041 (10)	0.041 (7)	0.030 (7)	−0.010 (8)	−0.001 (7)	0.001 (6)
C10	0.027 (9)	0.047 (8)	0.022 (7)	0.004 (8)	0.004 (7)	−0.001 (6)
C13	0.015 (9)	0.064 (9)	0.062 (9)	0.008 (8)	−0.001 (8)	−0.004 (7)
C12	0.031 (8)	0.051 (8)	0.032 (7)	−0.004 (7)	0.001 (7)	−0.003 (6)
N3	0.037 (9)	0.048 (7)	0.045 (7)	−0.005 (7)	−0.003 (7)	0.002 (6)

Geometric parameters (Å, º) top

O1—C5	1.246 (13)	C4—H43	0.9800
O2—C11	1.238 (12)	C6—C7	1.530 (13)
O3—C11	1.317 (13)	C6—C11	1.566 (14)
N1—C1	1.534 (12)	C6—H61	1.0000
N1—H1	0.9100	C7—C8	1.565 (13)
N1—H2	0.9100	C7—H71	0.9900
N1—H3	0.9100	C7—H72	0.9900
N2—C5	1.347 (12)	C8—C10	1.509 (13)
N2—C6	1.482 (14)	C8—C9	1.544 (14)
N2—H4	0.8800	C8—H81	1.0000
C1—C2	1.533 (14)	C9—H91	0.9800
C1—C5	1.535 (17)	C9—H92	0.9800
C1—H11	1.0000	C9—H93	0.9800
C2—C3	1.538 (13)	C10—H101	0.9800
C2—C4	1.573 (16)	C10—H102	0.9800
C2—H2A	1.0000	C10—H103	0.9800
C3—H31	0.9800	C13—C12	1.468 (18)
C3—H32	0.9800	C13—H131	0.9800
C3—H33	0.9800	C13—H132	0.9800
C4—H41	0.9800	C13—H133	0.9800
C4—H42	0.9800	C12—N3	1.165 (15)

C1—N1—H1	109.5	C7—C6—C11	111.5 (8)
C1—N1—H2	109.5	N2—C6—H61	107.9
H1—N1—H2	109.5	C7—C6—H61	107.9
C1—N1—H3	109.5	C11—C6—H61	107.9
H1—N1—H3	109.5	C6—C7—C8	114.7 (8)
H2—N1—H3	109.5	C6—C7—H71	108.6
C5—N2—C6	122.8 (11)	C8—C7—H71	108.6
C5—N2—H4	118.6	C6—C7—H72	108.6
C6—N2—H4	118.6	C8—C7—H72	108.6
C2—C1—N1	109.0 (8)	H71—C7—H72	107.6
C2—C1—C5	113.1 (10)	C10—C8—C9	112.3 (9)
N1—C1—C5	107.1 (9)	C10—C8—C7	110.1 (9)
C2—C1—H11	109.2	C9—C8—C7	111.2 (10)
N1—C1—H11	109.2	C10—C8—H81	107.7
C5—C1—H11	109.2	C9—C8—H81	107.7
C1—C2—C3	110.6 (8)	C7—C8—H81	107.7
C1—C2—C4	111.2 (10)	C8—C9—H91	109.5
C3—C2—C4	107.9 (10)	C8—C9—H92	109.5
C1—C2—H2A	109.0	H91—C9—H92	109.5
C3—C2—H2A	109.0	C8—C9—H93	109.5
C4—C2—H2A	109.0	H91—C9—H93	109.5
C2—C3—H31	109.5	H92—C9—H93	109.5
C2—C3—H32	109.5	C8—C10—H101	109.5
H31—C3—H32	109.5	C8—C10—H102	109.5
C2—C3—H33	109.5	H101—C10—H102	109.5
H31—C3—H33	109.5	C8—C10—H103	109.5
H32—C3—H33	109.5	H101—C10—H103	109.5
C2—C4—H41	109.5	H102—C10—H103	109.5
C2—C4—H42	109.5	O2—C11—O3	126.2 (11)
H41—C4—H42	109.5	O2—C11—C6	120.0 (12)
C2—C4—H43	109.5	O3—C11—C6	113.7 (11)
H41—C4—H43	109.5	C12—C13—H131	109.5
H42—C4—H43	109.5	C12—C13—H132	109.5
O1—C5—N2	123.9 (12)	H131—C13—H132	109.5
O1—C5—C1	119.8 (11)	C12—C13—H133	109.5
N2—C5—C1	116.2 (12)	H131—C13—H133	109.5
N2—C6—C7	110.3 (10)	H132—C13—H133	109.5
N2—C6—C11	111.1 (9)	N3—C12—C13	177.7 (15)

N1—C1—C2—C3	179.2 (9)	C5—N2—C6—C7	139.9 (9)
C5—C1—C2—C3	60.2 (14)	C5—N2—C6—C11	−95.9 (11)
N1—C1—C2—C4	−60.9 (13)	N2—C6—C7—C8	−65.0 (12)
C5—C1—C2—C4	−179.9 (9)	C11—C6—C7—C8	171.0 (10)
C6—N2—C5—O1	−8.0 (17)	C6—C7—C8—C10	171.2 (10)
C6—N2—C5—C1	170.7 (9)	C6—C7—C8—C9	−63.6 (13)
C2—C1—C5—O1	79.9 (13)	N2—C6—C11—O2	−11.7 (14)
N1—C1—C5—O1	−40.2 (14)	C7—C6—C11—O2	111.9 (12)
C2—C1—C5—N2	−98.9 (12)	N2—C6—C11—O3	164.8 (9)
N1—C1—C5—N2	140.9 (9)	C7—C6—C11—O3	−71.7 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3	0.91	2.35	3.247 (12)	167
N1—H2···O2ⁱ	0.91	2.05	2.851 (13)	146
N1—H2···O1ⁱⁱ	0.91	2.50	3.071 (12)	122
N1—H3···O3ⁱⁱⁱ	0.91	1.91	2.778 (11)	158
N2—H4···O3ⁱⁱ	0.88	2.07	2.922 (11)	162
C1—H11···O1ⁱⁱ	1.00	2.51	3.173 (15)	124
C3—H32···O2	0.98	2.45	3.348 (14)	153
C13—H132···O2ⁱⁱⁱ	0.98	2.46	3.413 (14)	164
C13—H133···N3^iv	0.98	2.49	3.412 (17)	157

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

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Hydro­phobic dipeptides: the final piece in the puzzle

Supporting information

Hydrophobic dipeptides: the final piece in the puzzle