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The structure of L-seryl-L-leucine, C9H18N2O4, has been determined and analysed in relation to the geometries of its amino acid constituents. The most important feature is the different conformational behaviour of the side chains at the Cβ atoms; a less pronounced discrepancy concerns the orientation of the C=O bond with respect to the Cα—N bond. The conformational preferences of these torsion angles are also established for related structures stored in the Cambridge Structural Database [Allen & Kennard (1993). Chem. Des. Autom. News, 8, 1, 31–37]; the title structure compares well with these data. The mol­ecules are organized in double layers, with the hydro­philic faces linked by an extensive hydrogen-bonding network, as in L-leucine.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100016164/gg1024sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270100016164/gg1024Isup2.hkl
Contains datablock I

CCDC reference: 159998

Comment top

The α-amino acids constitute one of the most extensively studied classes of organic compounds crucial for all living organisms. Yet the relationship between the sequence of amino acids in the polypeptide chain and the resulting spatial architecture still remains a challenging issue for both theoreticians and bio-organic chemists. For certain structural fragments non-bonded interaction patterns in small molecules resemble those in macromolecular systems. Therefore, it is important to study structural relationships in small polypeptide systems such as, e.g. L-seryl-L-leucine, (I). \sch

The title molecule is zwitterionic with a trans configuration of the peptide linkage [Δω = -17.7 (2)°] (Fig.1). The comparison of its geometrical parameters (Table 1) with the most accurate structure determinations of its amino acid components in the literature (LSERIN01; Kistenmacher et al., 1974; LSERIN10; Benedetti et al., 1973; LEUCIN02, Görbitz & Dalhus, 1996) does not reveal any systematic differences, although a few deviations exist depending on the data source and may be attributed, at least partially, to the underestimation of the standard deviations in the given papers. The discrepancy in the isopropyl side-chain geometry is clearly due to the large displacement parameters of the terminal carbon atoms. The only noticeable shortening, obviously resulting from the peptide linkage formation, is observed for N2—C4 (0.04 Å).

The most striking differences occur at the Cβ atoms, the side-chains adopting gauche- conformations towards the Cα—N bonds [N1—C1—C2—O1 - 53.90 (15)° and N2—C4—C5—C6 - 60.8 (2)°] compared to gauche+ (61.5°) in L-serine (Kistenmacher et al., 1974) and trans (-176.81° and -170.01°) in L-leucine (Görbitz & Dalhus, 1996) (Fig. 2). The conformational preferences of seryl and leucyl fragments were further studied based on the data retrieved from the Cambridge Structural Database (Allen & Kennard, 1993).

The conformational analysis of the available data (164 serine/seryl fragments and 121 leucine/leucyl fragments) demonstrates the apparent tendency of the torsion angles to cluster around selected values, i.e. ±60° for N—Cα—Cβ—OH in serine/seryl and -60° as well as ±180° for N—Cα—Cβ—Cg in leucine/leucyl fragments, indicating that in the latter trans and gauche- conformations are strongly favoured, while in the former one both gauche locations are preferred. The CO and the N—Cα bonds are not strictly co-planar in leucine/leucyl fragments (preferred ~±30°). This departure is less pronounced in seryl subunits, where the dihedral N—Cα—C'O angle is close to 0° with an additional maximum at about 30°. The structure of (I) conforms closely to the above distribution [N1—C1—C3O2 - 29.01 (18)°; N2—C4—C9O3 - 19.08 (19)°]. The flexibility of the molecular shape is presumably associated with both the prospective intermolecular hydrogen-bonding pattern in the crystal and the compulsion for most efficient close packing (Harding & Howieson, 1976).

The wafer-like molecular packing with typical double layers formed alternatively by hydrophilic and hydrophobic sheets (Fig. 3) resembles that of parent L-leucine, and also other amino acids containing non-polar groups as reported by Harding & Howieson (1976). On the hydrophilic side the molecules are held together by an extensive hydrogen bonding network, the two shortest H···O contacts are 1.76 (3) and 1.79 (3) Å. The hydrogen bonds in Table 2 were selected based on the hydrogen bonding criteria developed by Pedireddi & Desiraju (1992).

Related literature top

For related literature, see: Allen & Kennard (1993); Benedetti et al. (1973); Görbitz & Dalhus (1996); Harding & Howieson (1976); Kistenmacher et al. (1974); Pedireddi & Desiraju (1992).

Experimental top

A sample of L-seryl-L-leucine was purchased from Sigma and crystallized from an aqueous solution at room temperature. Single crystals were obtained after 24 days and like L-leucine, the crystals grew as filmy, slightly bent transparent flakes (Görbitz & Dalhus, 1996), the shape corresponding closely to their internal layered structure.

Refinement top

Only H atoms involved in hydrogen bonding and bonded to N or O atoms were refined as isotropic. Those bonded to C atoms were treated by the riding model refinement (C—H = 0.96–0.98 Å), H atoms in the CH3 groups had their isotropic displacement parameters set equal to 1.5 times Ueq of their parent C atom.

Computing details top

Data collection: KM4B8 (Gałdecki, Kowalski, Kucharczyk & Uszyński et al., 1997); cell refinement: KM4B8; data reduction: DATAPROC (Gałdecki, Kowalski & Uszyński et al., 1997); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick,1990b); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. The structure of (I) showing 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. Superposition of L-seryl-L-leucine (dashed line) and a) L-serine (full line) (LSERIN01; Kistenmacher et al., 1974), b) L-leucine (full line) (LEUCIN02, molecule A, Görbitz & Dalhus, 1996). Fitting was performed on Cα and its three non-hydrogen neighbouring atoms (Cβ, C'and N).
[Figure 3] Fig. 3. View of the crystal packing along the a axis showing the layered molecular architecture. Hydrogen atoms omitted for clarity.
L-Seryl-L-leucine top
Crystal data top
C9H18N2O4F(000) = 236
Mr = 218.25Dx = 1.184 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
a = 5.3288 (3) ÅCell parameters from 72 reflections
b = 6.3696 (6) Åθ = 8.4–43.1°
c = 18.1263 (9) ŵ = 0.78 mm1
β = 95.811 (4)°T = 293 K
V = 612.09 (7) Å3Plate, colourless
Z = 20.7 × 0.7 × 0.05 mm
Data collection top
KM4 (KUMA Diffraction)
diffractometer
1325 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.023
Graphite monochromatorθmax = 77.2°, θmin = 2.5°
ω–2θ scansh = 66
Absorption correction: numerical
(Sheldrick, 1990b)
k = 07
Tmin = 0.625, Tmax = 0.962l = 2222
2765 measured reflections3 standard reflections every 100 reflections
1405 independent reflections intensity decay: none
Refinement top
Refinement on F2H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0569P)2 + 0.0176P]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.029(Δ/σ)max < 0.001
wR(F2) = 0.077Δρmax = 0.16 e Å3
S = 1.02Δρmin = 0.14 e Å3
1405 reflectionsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/(sin(2θ)]-1/4
166 parametersExtinction coefficient: 0.027 (2)
1 restraintAbsolute structure: Flack (1983)
Crystal data top
C9H18N2O4V = 612.09 (7) Å3
Mr = 218.25Z = 2
Monoclinic, P21Cu Kα radiation
a = 5.3288 (3) ŵ = 0.78 mm1
b = 6.3696 (6) ÅT = 293 K
c = 18.1263 (9) Å0.7 × 0.7 × 0.05 mm
β = 95.811 (4)°
Data collection top
KM4 (KUMA Diffraction)
diffractometer
1325 reflections with I > 2σ(I)
Absorption correction: numerical
(Sheldrick, 1990b)
Rint = 0.023
Tmin = 0.625, Tmax = 0.9623 standard reflections every 100 reflections
2765 measured reflections intensity decay: none
1405 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0291 restraint
wR(F2) = 0.077H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.16 e Å3
1405 reflectionsΔρmin = 0.14 e Å3
166 parametersAbsolute structure: Flack (1983)
Special details top

Experimental. Only H atoms involved in hydrogen bonding and bonded to N or O atoms were refined as isotropic. Those bonded to C atoms were treated by the riding model refinement (C—H = 0.96–0.98 Å), H atoms in the CH3 groups had their isotropic displacement parameters set equal to 1.5 times Ueq of their parent C atom.

Friedel pairs have not been measured (except for the 240 h0l/-h0 - l pairs).

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
N10.3053 (2)0.4795 (2)0.10759 (7)0.0337 (3)
N20.1723 (2)0.9356 (2)0.21610 (6)0.0330 (3)
O10.42114 (19)0.7565 (2)0.00187 (5)0.0408 (3)
O20.07307 (19)0.6642 (2)0.17178 (7)0.0455 (3)
O30.11401 (19)1.1844 (2)0.12175 (5)0.0425 (3)
O40.41706 (18)1.20961 (19)0.19775 (6)0.0416 (3)
C10.3235 (2)0.7070 (2)0.12340 (7)0.0302 (3)
H10.49230.74300.14650.032 (4)*
C20.2634 (3)0.8287 (3)0.05110 (8)0.0389 (3)
H2A0.08790.80810.03260.043 (5)*
H2B0.29090.97750.05990.084 (9)*
C30.1231 (2)0.7656 (2)0.17449 (7)0.0308 (3)
C40.0331 (2)1.0485 (2)0.24562 (7)0.0345 (3)
H40.13530.94800.27050.050 (6)*
C50.0703 (3)1.2134 (4)0.30190 (9)0.0517 (5)
H5A0.07031.28980.31900.066 (7)*
H5B0.17131.31280.27720.074 (8)*
C60.2314 (5)1.1240 (7)0.36947 (13)0.0911 (11)
H60.36931.04210.35190.092 (10)*
C70.3440 (8)1.3034 (12)0.4162 (2)0.158 (3)
H7A0.21121.38330.43480.237*
H7B0.43881.39230.38640.237*
H7C0.45341.24870.45700.237*
C80.0822 (11)0.9840 (13)0.4140 (2)0.163 (3)
H8A0.18600.93780.45740.245*
H8B0.02500.86440.38480.245*
H8C0.06061.05930.42870.245*
C90.2014 (2)1.1553 (2)0.18281 (7)0.0318 (3)
H1NA0.142 (4)0.441 (4)0.1083 (10)0.038 (4)*
H1NB0.369 (4)0.452 (5)0.0644 (13)0.052 (6)*
H1NC0.412 (4)0.403 (4)0.1408 (12)0.045 (5)*
H2N0.317 (4)0.999 (4)0.2126 (10)0.040 (5)*
H1O0.323 (5)0.729 (6)0.0415 (15)0.066 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0313 (5)0.0318 (6)0.0392 (6)0.0038 (5)0.0099 (4)0.0020 (5)
N20.0274 (5)0.0364 (6)0.0359 (5)0.0031 (5)0.0070 (4)0.0017 (5)
O10.0454 (5)0.0443 (7)0.0342 (4)0.0003 (5)0.0118 (4)0.0001 (5)
O20.0311 (5)0.0446 (7)0.0630 (7)0.0053 (5)0.0153 (4)0.0084 (5)
O30.0417 (5)0.0491 (7)0.0376 (5)0.0027 (5)0.0091 (4)0.0067 (5)
O40.0310 (4)0.0411 (6)0.0539 (6)0.0043 (4)0.0095 (4)0.0073 (5)
C10.0261 (5)0.0317 (7)0.0333 (6)0.0009 (5)0.0055 (4)0.0004 (5)
C20.0473 (7)0.0345 (8)0.0368 (7)0.0073 (6)0.0132 (5)0.0054 (6)
C30.0251 (5)0.0343 (7)0.0332 (6)0.0034 (5)0.0048 (4)0.0038 (5)
C40.0320 (6)0.0377 (8)0.0350 (6)0.0065 (6)0.0093 (5)0.0012 (6)
C50.0498 (8)0.0634 (12)0.0414 (7)0.0122 (8)0.0020 (6)0.0164 (8)
C60.0844 (15)0.132 (3)0.0518 (11)0.0365 (19)0.0167 (10)0.0274 (15)
C70.135 (3)0.226 (7)0.100 (2)0.042 (4)0.053 (2)0.093 (4)
C80.189 (5)0.225 (8)0.072 (2)0.018 (5)0.006 (2)0.067 (3)
C90.0302 (6)0.0286 (7)0.0373 (6)0.0014 (5)0.0059 (5)0.0001 (5)
Geometric parameters (Å, º) top
N1—C11.479 (2)C4—C91.5353 (18)
N2—C31.3305 (19)C5—C61.532 (3)
N2—C41.4559 (17)C6—C81.487 (7)
O1—C21.4155 (17)C6—C71.510 (6)
O2—C31.2254 (18)N1—H1NA0.91 (2)
O3—C91.2572 (15)N1—H1NB0.91 (2)
O4—C91.2558 (17)N1—H1NC0.92 (2)
C1—C21.5282 (18)N2—H2N0.88 (2)
C1—C31.5290 (17)O1—H1O0.86 (3)
C4—C51.527 (2)
C1—N1—H1NA107.7 (15)O2—C3—N2124.74 (12)
C1—N1—H1NB109.6 (19)O2—C3—C1119.51 (13)
H1NA—N1—H1NB114 (2)N2—C3—C1115.61 (12)
C1—N1—H1NC111.6 (16)N2—C4—C5110.58 (11)
H1NA—N1—H1NC112.2 (18)N2—C4—C9110.53 (11)
H1NB—N1—H1NC102 (2)C5—C4—C9109.54 (13)
C3—N2—C4119.88 (11)C4—C5—C6114.4 (2)
C3—N2—H2N117.1 (14)C8—C6—C7110.7 (4)
C4—N2—H2N119.9 (15)C8—C6—C5111.7 (3)
C2—O1—H1O106.3 (17)C7—C6—C5109.0 (4)
N1—C1—C2109.08 (11)O4—C9—O3125.31 (13)
N1—C1—C3108.67 (12)O4—C9—C4116.16 (11)
C3—C1—C2107.28 (11)O3—C9—C4118.53 (11)
O1—C2—C1109.24 (12)
N1—C1—C2—O153.90 (15)C3—N2—C4—C968.23 (16)
C3—C1—C2—O1171.44 (12)N2—C4—C5—C660.8 (2)
C4—N2—C3—O217.7 (2)C9—C4—C5—C6177.15 (17)
C4—N2—C3—C1157.99 (12)C4—C5—C6—C7174.0 (2)
N1—C1—C3—O229.01 (18)C4—C5—C6—C863.4 (4)
C2—C1—C3—O288.79 (17)N2—C4—C9—O4161.92 (13)
N1—C1—C3—N2155.04 (11)C5—C4—C9—O475.99 (16)
C2—C1—C3—N287.15 (14)N2—C4—C9—O319.08 (19)
C3—N2—C4—C5170.29 (13)C5—C4—C9—O3103.01 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1NA···O20.91 (2)2.22 (2)2.6978 (16)112 (2)
N1—H1NA···O3i0.91 (2)2.16 (2)2.9509 (17)146 (2)
N1—H1NB···O1ii0.90 (2)2.08 (3)2.8951 (16)149 (2)
N1—H1NC···O4iii0.92 (2)1.80 (2)2.7066 (17)168 (2)
N2—H2N···O4iv0.88 (2)1.99 (2)2.8449 (16)164 (2)
O1—H1O···O3v0.86 (3)1.76 (3)2.6250 (15)177 (3)
C1—H1···O2iv0.982.373.2575 (16)150
C2—H2B···O1vi0.972.643.369 (2)133
C5—H5B···O4iv0.972.823.474 (2)125
Symmetry codes: (i) x, y1, z; (ii) x+1, y1/2, z; (iii) x+1, y1, z; (iv) x+1, y, z; (v) x, y1/2, z; (vi) x+1, y+1/2, z.

Experimental details

Crystal data
Chemical formulaC9H18N2O4
Mr218.25
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)5.3288 (3), 6.3696 (6), 18.1263 (9)
β (°) 95.811 (4)
V3)612.09 (7)
Z2
Radiation typeCu Kα
µ (mm1)0.78
Crystal size (mm)0.7 × 0.7 × 0.05
Data collection
DiffractometerKM4 (KUMA Diffraction)
diffractometer
Absorption correctionNumerical
(Sheldrick, 1990b)
Tmin, Tmax0.625, 0.962
No. of measured, independent and
observed [I > 2σ(I)] reflections
2765, 1405, 1325
Rint0.023
(sin θ/λ)max1)0.632
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.029, 0.077, 1.02
No. of reflections1405
No. of parameters166
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.16, 0.14
Absolute structureFlack (1983)

Computer programs: KM4B8 (Gałdecki, Kowalski, Kucharczyk & Uszyński et al., 1997), KM4B8, DATAPROC (Gałdecki, Kowalski & Uszyński et al., 1997), SHELXS86 (Sheldrick, 1990a), SHELXL97 (Sheldrick, 1997), SHELXTL/PC (Sheldrick,1990b), SHELXL97.

Selected geometric parameters (Å, º) top
N1—C11.479 (2)O4—C91.2558 (17)
N2—C31.3305 (19)C1—C21.5282 (18)
N2—C41.4559 (17)C1—C31.5290 (17)
O1—C21.4155 (17)C4—C51.527 (2)
O2—C31.2254 (18)C4—C91.5353 (18)
O3—C91.2572 (15)
C3—N2—C4119.88 (11)N2—C3—C1115.61 (12)
N1—C1—C2109.08 (11)N2—C4—C5110.58 (11)
N1—C1—C3108.67 (12)N2—C4—C9110.53 (11)
C3—C1—C2107.28 (11)C5—C4—C9109.54 (13)
O1—C2—C1109.24 (12)O4—C9—O3125.31 (13)
O2—C3—N2124.74 (12)O4—C9—C4116.16 (11)
O2—C3—C1119.51 (13)O3—C9—C4118.53 (11)
C4—N2—C3—O217.7 (2)C3—N2—C4—C968.23 (16)
C4—N2—C3—C1157.99 (12)C4—C5—C6—C7174.0 (2)
N1—C1—C3—N2155.04 (11)C4—C5—C6—C863.4 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1NA···O20.91 (2)2.22 (2)2.6978 (16)112 (2)
N1—H1NA···O3i0.91 (2)2.16 (2)2.9509 (17)146 (2)
N1—H1NB···O1ii0.90 (2)2.08 (3)2.8951 (16)149 (2)
N1—H1NC···O4iii0.92 (2)1.80 (2)2.7066 (17)168 (2)
N2—H2N···O4iv0.88 (2)1.99 (2)2.8449 (16)164 (2)
O1—H1O···O3v0.86 (3)1.76 (3)2.6250 (15)177 (3)
C1—H1···O2iv0.982.373.2575 (16)150
C2—H2B···O1vi0.972.643.369 (2)133
C5—H5B···O4iv0.972.823.474 (2)125
Symmetry codes: (i) x, y1, z; (ii) x+1, y1/2, z; (iii) x+1, y1, z; (iv) x+1, y, z; (v) x, y1/2, z; (vi) x+1, y+1/2, z.
 

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