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The valine side chains in the crystal structure of the title compound [systematic name: 2-(2-ammonio-3-methyl­butan­amido)-3-hydroxy­propano­ate tri­hydrate], C8H16N2O4·3H2O, stack along an a axis of 4.77 Å to form hydro­phobic columns surrounded by remarkable water/hydroxyl shells. The peptide main chains are connected by hydrogen bonds in two-dimensional layers. The peptide mol­ecules in each layer are related only by translation, and generate a very rare pattern. This is rendered possible through the formation of the shortest C[alpha]-H...O(carboxyl­ate) inter­action ever recorded.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270105003732/sx1167sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270105003732/sx1167Isup2.hkl
Contains datablock I

CCDC reference: 269027

Comment top

As part of a systematic survey of dipeptides with one hydrophobic and one hydrophilic residue (Netland et al., 2004), the structure of L-valyl-L-serine trihydrate, (I), has been determined.

The asymmetric unit of (I), with one peptide molecule and three water molecules, is shown in Fig. 1. The peptide main chain is quite extended, as reflected by the torsion angles given in Table 1. The valine side chain has a common trans/gauche- orientation for N1—C1—C2—C3/N1—C1—C2—C4, while a search in the Cambridge Structural Database (CSD, Version 5.25, November 2003; Allen, 2002) shows that gauche+ for N2—C6—C7—O2 represents the most frequently observed serine conformation.

Fig. 2 illustrates the crystal packing pattern of (I). The peptide main chains generate layers, seen edge-on in Fig. 2, through hydrogen bonding. The most notable structural feature is the fact that the molecules in a layer are, in an unusual manner, lined up perpendicular to the unique axis, rather than along it, as one might expect. Consequently, all valine side chains point in the same direction. Under these circumstances, the hydrophobic groups cannot form separate layers, as they normally do in peptide crystals with a tight two-dimensional association of peptide main chains. Rather, the valine side chains are stacked into hydrophobic columns along the very short a axis [4.77 Å]; we find fewer than 20 other peptides with a shorter crystallographic axis in the CSD. Each column is surrounded by a hydrophilic shell of water molecules and serine hydroxyl groups in a quite unusual manner. Numerous C—H···O contacts are involved, including C4—H42···O3(x + 1, y, z + 1) (Fig. 2), with an H···O distance of 2.59 Å (Table 2). The rest of the contacts have H···O distances greater than 2.80 Å. The construction of a related water cage around a valine side chain was observed for L-phenylalanyl-L-valine (Görbitz, 2002), with comparable H···O and C···O distances.

Out of about 100 distinctly different dipeptide structures with a zwitterionic peptide main chain in the CSD, 37 contain hydrogen-bonded layers in which each amino group donates H atoms to two independent carboxylate groups which are related by a simple unit-cell translation, or in some cases with Z' > 1 by pseudotranslational symmetry. Consecutive molecules in the resulting head-to-tail chains (Suresh & Vijayan, 1985) are usually related by a twofold screw operation in space group P21 or P212121. In (I), the layers generated by hydrogen bonding between the peptide main chains involve molecules related by translation only (Fig. 3), a phenomenon observed for only eight other dipeptide structures. Only the structure of L-glutamyl-L-aspartic acid hydrate, (II) (Eggleston & Hodgson, 1985), in space group P1, contains a fairly similar pattern (Fig. 3). The main differences between (I) and (II) concern a long N—H···O hydrogen bond in (II) (labelled 1 in Fig. 3; H···O 2.50 Å and N—H···O 143°) that has normal dimensions for this type of interaction in (I) (1.93 Å and 170°; Table 2), and a weak secondary interaction in (II) (2 in Fig. 3; 2.60 Å and 120°) that is missing in (I) (3.18 Å and 94°). A comparison of the main-chain conformations showns significant differences; the values for ψ1, ω1, ϕ2 and ψT [N1—C1—C5—N2, C1—C5—N2—C6, C5—N2—C6—C8 and N2—C6—C8—O3 in (I)] are 148.0, 161.3, −118.2 and −31.9°, respectively, in (II), compared with 134.16 (7), 174.68 (7), −160.24 (8) and 0.38 (10)°, respectively, in (I) (Table 1).

The classic paper by Suresh & Vijayan (1985) on head-to-tail chains lists a series of theoretical layered aggregation patterns for dipeptides, but does not include the pattern illustrated in Fig. 3. The reason is probably that, at the time, the importance of C—H···O interactions had not yet been realised. As is evident from Fig. 3, CαH···O(carboxylate) interactions play a key role in completing the hydrogen-bond network of (I). Thus, the tapes with carbonyl acceptors, familiar from about 12 other dipeptide structures, have C1α—H as well as >N—H donors. More uncommon is the C2αH···O(carboxylate) interaction (labelled 3 in Fig. 3). A total number of about 250 peptide structures in the CSD have an unprotected negatively charged C-terminal carboxylate group. Within this subset, there are 33 CαH···O(carboxylate) interactions (in 25 structures) with H···O distance < 2.60 Å, but only eight (in six structures) with H···O < 2.40 Å. In (I), H61···O3(x + 1, y, z) is 2.28 Å, the smallest value ever recorded for this type of contact. The corresponding distance in (II) is 2.51 Å.

Apart from the presence of two amino···carboxylate hydrogen bonds, there are few similarities between the structure of (I) and the structures of L-alanyl-L-serine (Jones et al., 1978) and the retroanalogue L-seryl-L-valine, studied previously as part of our ongoing investigation (Moen et al., 2004). This is not unexpected, since (I) was crystallized as a trihydrate, while the other two structures are devoid of solvent water moleules.

Experimental top

The title compound was obtained from Bachem. Crystals were grown by diffusion of acetonitrile into 30µl of an aqueous solution containing about 1 mg of the peptide.

Refinement top

Positional parameters were refined for H atoms bonded to N and O atoms. Other H atoms were positioned with idealized geometry and fixed C—H distances in the range 0.98–1.00 Å Please check added text. Uiso(H) values were 1.2Ueq of the carrier atom, or 1.5Ueq for amino and methyl groups and for water molecules. In the absence of significant anomalous scattering effects, 1916 Friedel pairs were merged. The absolute configuration was known for the purchased material.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The molecular structure of (I). Displacement ellipsoids are shown at the 50% probability level and H atoms are shown as spheres of arbitrary size.
[Figure 2] Fig. 2. The molecular packing and unit cell of (I), viewed along the a axis. Hydrogen bonding is indicated by dashed lines.
[Figure 3] Fig. 3. The hydrogen bonding between the peptide main chains in the structures of (I) and (II). For a description of 1, 2 and 3, see text.
2-(2-ammonio-3-methylbutanamido)-3-hydroxypropanoate trihydrate top
Crystal data top
C8H16N2O4·3H2OF(000) = 280
Mr = 258.28Dx = 1.322 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 4.7695 (2) ÅCell parameters from 6036 reflections
b = 16.1323 (5) Åθ = 2.4–37.8°
c = 8.6789 (3) ŵ = 0.12 mm1
β = 103.636 (1)°T = 105 K
V = 648.96 (4) Å3Needle, colourless
Z = 20.90 × 0.30 × 0.05 mm
Data collection top
Siemens SMART CCD area-detector
diffractometer
3564 independent reflections
Radiation source: fine-focus sealed tube3309 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.026
Detector resolution: 8.3 pixels mm-1θmax = 37.8°, θmin = 2.4°
Sets of exposures each taken over 0.3° ω rotation scansh = 88
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
k = 2327
Tmin = 0.738, Tmax = 0.994l = 1414
9845 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.0542P)2]
where P = (Fo2 + 2Fc2)/3
3564 reflections(Δ/σ)max < 0.001
189 parametersΔρmax = 0.38 e Å3
1 restraintΔρmin = 0.23 e Å3
Crystal data top
C8H16N2O4·3H2OV = 648.96 (4) Å3
Mr = 258.28Z = 2
Monoclinic, P21Mo Kα radiation
a = 4.7695 (2) ŵ = 0.12 mm1
b = 16.1323 (5) ÅT = 105 K
c = 8.6789 (3) Å0.90 × 0.30 × 0.05 mm
β = 103.636 (1)°
Data collection top
Siemens SMART CCD area-detector
diffractometer
3564 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
3309 reflections with I > 2σ(I)
Tmin = 0.738, Tmax = 0.994Rint = 0.026
9845 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0311 restraint
wR(F2) = 0.083H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.38 e Å3
3564 reflectionsΔρmin = 0.23 e Å3
189 parameters
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. Data were collected by measuring two sets of exposures with the detector set at 2θ = 29° and three sets of exposures with the detector set at 2θ = 55°, crystal-to-detector distance 5.08 cm. Refinement of F2 against ALL reflections.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.71552 (13)0.19696 (5)0.50129 (8)0.01886 (12)
O20.04617 (17)0.06576 (5)0.20935 (9)0.02353 (14)
H50.054 (4)0.0645 (14)0.305 (2)0.035*
O30.13086 (14)0.27850 (5)0.11828 (8)0.01977 (13)
O40.06301 (14)0.21670 (5)0.06325 (7)0.01951 (12)
N10.49006 (15)0.19819 (5)0.77628 (8)0.01454 (11)
H10.480 (4)0.1508 (12)0.7475 (18)0.022*
H20.379 (4)0.2004 (12)0.8444 (19)0.022*
H30.669 (4)0.2072 (12)0.8160 (19)0.022*
N20.25663 (14)0.22248 (5)0.36224 (8)0.01360 (11)
H40.098 (4)0.2359 (10)0.3655 (17)0.016*
C10.38448 (16)0.25649 (5)0.64082 (8)0.01250 (12)
H110.16980.26130.62020.015*
C20.52085 (19)0.34294 (5)0.67957 (10)0.01736 (14)
H210.73500.33590.71230.021*
C30.4511 (4)0.39910 (7)0.53299 (14)0.0361 (3)
H310.52950.45460.56180.054*
H320.24140.40260.49280.054*
H330.53780.37590.45070.054*
C40.4216 (2)0.38332 (6)0.81706 (12)0.02363 (17)
H410.53330.43400.84970.035*
H420.45170.34470.90660.035*
H430.21630.39720.78300.035*
C50.46537 (15)0.22119 (5)0.49473 (9)0.01278 (11)
C60.30036 (16)0.19788 (5)0.20816 (8)0.01292 (12)
H610.48880.22090.19620.016*
C70.30820 (19)0.10319 (5)0.19349 (10)0.01737 (14)
H710.34350.08840.08900.021*
H720.47010.08110.27640.021*
C80.05691 (16)0.23510 (5)0.07835 (9)0.01386 (12)
O1W0.16044 (19)0.44775 (5)0.20405 (10)0.02603 (15)
H11W0.156 (5)0.3959 (15)0.175 (3)0.039*
H12W0.321 (5)0.4627 (15)0.162 (3)0.039*
O2W1.11366 (19)0.06715 (5)0.54931 (10)0.02642 (15)
H21W0.987 (5)0.0947 (16)0.552 (2)0.040*
H22W1.091 (5)0.0294 (17)0.606 (2)0.040*
O3W0.30128 (18)0.02436 (6)0.10050 (10)0.02693 (15)
H31W0.180 (5)0.0002 (15)0.129 (2)0.040*
H32W0.229 (4)0.0332 (16)0.015 (2)0.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0116 (2)0.0275 (3)0.0168 (3)0.0032 (2)0.00218 (18)0.0014 (2)
O20.0271 (3)0.0212 (3)0.0214 (3)0.0076 (3)0.0040 (2)0.0021 (2)
O30.0172 (3)0.0222 (3)0.0196 (3)0.0060 (2)0.0035 (2)0.0023 (2)
O40.0167 (2)0.0302 (3)0.0107 (2)0.0010 (2)0.00156 (18)0.0012 (2)
N10.0158 (3)0.0157 (3)0.0118 (2)0.0011 (2)0.0027 (2)0.0005 (2)
N20.0110 (2)0.0183 (3)0.0106 (2)0.0015 (2)0.00077 (18)0.0013 (2)
C10.0116 (3)0.0146 (3)0.0106 (3)0.0000 (2)0.0011 (2)0.0006 (2)
C20.0190 (3)0.0146 (3)0.0174 (3)0.0026 (3)0.0023 (2)0.0018 (3)
C30.0671 (9)0.0176 (4)0.0225 (5)0.0071 (5)0.0082 (5)0.0029 (3)
C40.0325 (5)0.0171 (4)0.0204 (4)0.0002 (3)0.0045 (3)0.0055 (3)
C50.0117 (2)0.0147 (3)0.0113 (3)0.0007 (2)0.00136 (19)0.0008 (2)
C60.0121 (3)0.0158 (3)0.0102 (3)0.0002 (2)0.0014 (2)0.0005 (2)
C70.0196 (3)0.0160 (3)0.0163 (3)0.0025 (3)0.0036 (3)0.0015 (3)
C80.0122 (3)0.0165 (3)0.0122 (3)0.0007 (2)0.0015 (2)0.0024 (2)
O1W0.0246 (3)0.0243 (3)0.0270 (3)0.0023 (3)0.0016 (3)0.0054 (3)
O2W0.0292 (4)0.0216 (3)0.0305 (4)0.0039 (3)0.0111 (3)0.0077 (3)
O3W0.0220 (3)0.0285 (4)0.0282 (4)0.0014 (3)0.0019 (3)0.0010 (3)
Geometric parameters (Å, º) top
O1—C51.2439 (9)C3—H310.9800
O2—C71.4235 (11)C3—H320.9800
O2—H50.82 (2)C3—H330.9800
O3—C81.2486 (11)C4—H410.9800
O4—C81.2712 (10)C4—H420.9800
N1—C11.4970 (10)C4—H430.9800
N1—H10.803 (19)C6—C71.5340 (12)
N1—H20.883 (17)C6—C81.5366 (11)
N1—H30.852 (17)C6—H611.0000
N2—C51.3319 (10)C7—H710.9900
N2—C61.4563 (10)C7—H720.9900
N2—H40.794 (17)O1W—H11W0.88 (2)
C1—C51.5204 (11)O1W—H12W0.80 (2)
C1—C21.5420 (11)O2W—H21W0.76 (2)
C1—H111.0000O2W—H22W0.81 (3)
C2—C41.5292 (13)O3W—H31W0.79 (2)
C2—C31.5331 (14)O3W—H32W0.99 (2)
C2—H211.0000
C7—O2—H5106.0 (15)C2—C4—H41109.5
C1—N1—H1111.7 (12)C2—C4—H42109.5
C1—N1—H2110.9 (12)H41—C4—H42109.5
H1—N1—H2104.2 (17)C2—C4—H43109.5
C1—N1—H3109.2 (12)H41—C4—H43109.5
H1—N1—H3105.6 (18)H42—C4—H43109.5
H2—N1—H3115.0 (15)O1—C5—N2123.93 (7)
C5—N2—C6123.28 (6)O1—C5—C1120.58 (7)
C5—N2—H4119.9 (10)N2—C5—C1115.41 (6)
C6—N2—H4116.8 (11)N2—C6—C7111.05 (7)
N1—C1—C5108.37 (6)N2—C6—C8108.64 (6)
N1—C1—C2110.51 (6)C7—C6—C8110.93 (7)
C5—C1—C2110.11 (6)N2—C6—H61108.7
N1—C1—H11109.3C7—C6—H61108.7
C5—C1—H11109.3C8—C6—H61108.7
C2—C1—H11109.3O2—C7—C6112.04 (7)
C4—C2—C3110.44 (9)O2—C7—H71109.2
C4—C2—C1111.30 (7)C6—C7—H71109.2
C3—C2—C1110.83 (8)O2—C7—H72109.2
C4—C2—H21108.0C6—C7—H72109.2
C3—C2—H21108.0H71—C7—H72107.9
C1—C2—H21108.0O3—C8—O4125.50 (8)
C2—C3—H31109.5O3—C8—C6118.89 (7)
C2—C3—H32109.5O4—C8—C6115.60 (7)
H31—C3—H32109.5H11W—O1W—H12W104 (2)
C2—C3—H33109.5H21W—O2W—H22W102 (2)
H31—C3—H33109.5H31W—O3W—H32W106.7 (19)
H32—C3—H33109.5
N1—C1—C5—N2134.16 (7)C6—N2—C5—O11.94 (13)
C1—C5—N2—C6174.68 (7)N1—C1—C5—O149.10 (10)
C5—N2—C6—C8160.24 (8)C2—C1—C5—O171.88 (10)
N2—C6—C8—O30.38 (10)C2—C1—C5—N2104.87 (8)
N1—C1—C2—C3171.31 (9)C5—N2—C6—C777.50 (9)
N1—C1—C2—C465.36 (9)C8—C6—C7—O260.50 (9)
N2—C6—C7—O260.42 (9)C7—C6—C8—O3122.72 (8)
C6—C7—O2—H579.3 (16)N2—C6—C8—O4178.13 (7)
C5—C1—C2—C4174.95 (7)C7—C6—C8—O455.79 (10)
C5—C1—C2—C351.63 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2Wi0.803 (19)2.533 (18)3.1472 (12)134.4 (16)
N1—H1···O3Wii0.803 (19)2.518 (18)3.0816 (12)128.4 (14)
N1—H2···O4iii0.883 (17)1.885 (17)2.7413 (10)163.1 (16)
N1—H3···O4ii0.852 (17)1.932 (17)2.7752 (9)170.1 (17)
N2—H4···O1i0.794 (17)2.475 (16)3.1233 (9)139.7 (15)
O2—H5···O2Wi0.82 (2)2.07 (2)2.8917 (12)174 (2)
C1—H11···O1i1.002.413.2783 (10)146
C4—H42···O3ii0.982.593.4086 (12)140
C6—H61···O3iv1.002.283.2645 (11)169
O1W—H11W···O30.88 (2)1.97 (2)2.8423 (11)177 (2)
O1W—H12W···O3Wv0.80 (2)2.02 (2)2.7997 (12)165 (2)
O2W—H21W···O10.76 (2)2.08 (3)2.7915 (11)157 (2)
O2W—H22W···O1Wvi0.81 (3)2.07 (2)2.8490 (11)161 (2)
O3W—H31W···O1Wvii0.79 (2)2.06 (2)2.8492 (13)174 (2)
O3W—H32W···O20.99 (2)1.95 (2)2.8849 (11)156.6 (18)
Symmetry codes: (i) x1, y, z; (ii) x+1, y, z+1; (iii) x, y, z+1; (iv) x+1, y, z; (v) x1, y+1/2, z; (vi) x+1, y1/2, z+1; (vii) x, y1/2, z.

Experimental details

Crystal data
Chemical formulaC8H16N2O4·3H2O
Mr258.28
Crystal system, space groupMonoclinic, P21
Temperature (K)105
a, b, c (Å)4.7695 (2), 16.1323 (5), 8.6789 (3)
β (°) 103.636 (1)
V3)648.96 (4)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.90 × 0.30 × 0.05
Data collection
DiffractometerSiemens SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.738, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections
9845, 3564, 3309
Rint0.026
(sin θ/λ)max1)0.862
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.031, 0.083, 1.07
No. of reflections3564
No. of parameters189
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.38, 0.23

Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 2001), SAINT, SHELXTL (Bruker, 2000), SHELXTL.

Selected torsion angles (º) top
N1—C1—C5—N2134.16 (7)N1—C1—C2—C3171.31 (9)
C1—C5—N2—C6174.68 (7)N1—C1—C2—C465.36 (9)
C5—N2—C6—C8160.24 (8)N2—C6—C7—O260.42 (9)
N2—C6—C8—O30.38 (10)C6—C7—O2—H579.3 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2Wi0.803 (19)2.533 (18)3.1472 (12)134.4 (16)
N1—H1···O3Wii0.803 (19)2.518 (18)3.0816 (12)128.4 (14)
N1—H2···O4iii0.883 (17)1.885 (17)2.7413 (10)163.1 (16)
N1—H3···O4ii0.852 (17)1.932 (17)2.7752 (9)170.1 (17)
N2—H4···O1i0.794 (17)2.475 (16)3.1233 (9)139.7 (15)
O2—H5···O2Wi0.82 (2)2.07 (2)2.8917 (12)174 (2)
C1—H11···O1i1.00002.413.2783 (10)146
C4—H42···O3ii0.98002.593.4086 (12)140
C6—H61···O3iv1.00002.283.2645 (11)169
O1W—H11W···O30.88 (2)1.97 (2)2.8423 (11)177 (2)
O1W—H12W···O3Wv0.80 (2)2.02 (2)2.7997 (12)165 (2)
O2W—H21W···O10.76 (2)2.08 (3)2.7915 (11)157 (2)
O2W—H22W···O1Wvi0.81 (3)2.07 (2)2.8490 (11)161 (2)
O3W—H31W···O1Wvii0.79 (2)2.06 (2)2.8492 (13)174 (2)
O3W—H32W···O20.99 (2)1.95 (2)2.8849 (11)156.6 (18)
Symmetry codes: (i) x1, y, z; (ii) x+1, y, z+1; (iii) x, y, z+1; (iv) x+1, y, z; (v) x1, y+1/2, z; (vi) x+1, y1/2, z+1; (vii) x, y1/2, z.
 

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