Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100016164/gg1024sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270100016164/gg1024Isup2.hkl |
CCDC reference: 159998
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.
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.
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.
C9H18N2O4 | F(000) = 236 |
Mr = 218.25 | Dx = 1.184 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54178 Å |
a = 5.3288 (3) Å | Cell parameters from 72 reflections |
b = 6.3696 (6) Å | θ = 8.4–43.1° |
c = 18.1263 (9) Å | µ = 0.78 mm−1 |
β = 95.811 (4)° | T = 293 K |
V = 612.09 (7) Å3 | Plate, colourless |
Z = 2 | 0.7 × 0.7 × 0.05 mm |
KM4 (KUMA Diffraction) diffractometer | 1325 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.023 |
Graphite monochromator | θmax = 77.2°, θmin = 2.5° |
ω–2θ scans | h = −6→6 |
Absorption correction: numerical (Sheldrick, 1990b) | k = 0→7 |
Tmin = 0.625, Tmax = 0.962 | l = −22→22 |
2765 measured reflections | 3 standard reflections every 100 reflections |
1405 independent reflections | intensity decay: none |
Refinement on F2 | H 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) = 0.077 | Δρmax = 0.16 e Å−3 |
S = 1.02 | Δρmin = −0.14 e Å−3 |
1405 reflections | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/(sin(2θ)]-1/4 |
166 parameters | Extinction coefficient: 0.027 (2) |
1 restraint | Absolute structure: Flack (1983) |
C9H18N2O4 | V = 612.09 (7) Å3 |
Mr = 218.25 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 5.3288 (3) Å | µ = 0.78 mm−1 |
b = 6.3696 (6) Å | T = 293 K |
c = 18.1263 (9) Å | 0.7 × 0.7 × 0.05 mm |
β = 95.811 (4)° |
KM4 (KUMA Diffraction) diffractometer | 1325 reflections with I > 2σ(I) |
Absorption correction: numerical (Sheldrick, 1990b) | Rint = 0.023 |
Tmin = 0.625, Tmax = 0.962 | 3 standard reflections every 100 reflections |
2765 measured reflections | intensity decay: none |
1405 independent reflections |
R[F2 > 2σ(F2)] = 0.029 | 1 restraint |
wR(F2) = 0.077 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.16 e Å−3 |
1405 reflections | Δρmin = −0.14 e Å−3 |
166 parameters | Absolute structure: Flack (1983) |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.3053 (2) | 0.4795 (2) | 0.10759 (7) | 0.0337 (3) | |
N2 | 0.1723 (2) | 0.9356 (2) | 0.21610 (6) | 0.0330 (3) | |
O1 | 0.42114 (19) | 0.7565 (2) | −0.00187 (5) | 0.0408 (3) | |
O2 | −0.07307 (19) | 0.6642 (2) | 0.17178 (7) | 0.0455 (3) | |
O3 | −0.11401 (19) | 1.1844 (2) | 0.12175 (5) | 0.0425 (3) | |
O4 | −0.41706 (18) | 1.20961 (19) | 0.19775 (6) | 0.0416 (3) | |
C1 | 0.3235 (2) | 0.7070 (2) | 0.12340 (7) | 0.0302 (3) | |
H1 | 0.4923 | 0.7430 | 0.1465 | 0.032 (4)* | |
C2 | 0.2634 (3) | 0.8287 (3) | 0.05110 (8) | 0.0389 (3) | |
H2A | 0.0879 | 0.8081 | 0.0326 | 0.043 (5)* | |
H2B | 0.2909 | 0.9775 | 0.0599 | 0.084 (9)* | |
C3 | 0.1231 (2) | 0.7656 (2) | 0.17449 (7) | 0.0308 (3) | |
C4 | −0.0331 (2) | 1.0485 (2) | 0.24562 (7) | 0.0345 (3) | |
H4 | −0.1353 | 0.9480 | 0.2705 | 0.050 (6)* | |
C5 | 0.0703 (3) | 1.2134 (4) | 0.30190 (9) | 0.0517 (5) | |
H5A | −0.0703 | 1.2898 | 0.3190 | 0.066 (7)* | |
H5B | 0.1713 | 1.3128 | 0.2772 | 0.074 (8)* | |
C6 | 0.2314 (5) | 1.1240 (7) | 0.36947 (13) | 0.0911 (11) | |
H6 | 0.3693 | 1.0421 | 0.3519 | 0.092 (10)* | |
C7 | 0.3440 (8) | 1.3034 (12) | 0.4162 (2) | 0.158 (3) | |
H7A | 0.2112 | 1.3833 | 0.4348 | 0.237* | |
H7B | 0.4388 | 1.3923 | 0.3864 | 0.237* | |
H7C | 0.4534 | 1.2487 | 0.4570 | 0.237* | |
C8 | 0.0822 (11) | 0.9840 (13) | 0.4140 (2) | 0.163 (3) | |
H8A | 0.1860 | 0.9378 | 0.4574 | 0.245* | |
H8B | 0.0250 | 0.8644 | 0.3848 | 0.245* | |
H8C | −0.0606 | 1.0593 | 0.4287 | 0.245* | |
C9 | −0.2014 (2) | 1.1553 (2) | 0.18281 (7) | 0.0318 (3) | |
H1NA | 0.142 (4) | 0.441 (4) | 0.1083 (10) | 0.038 (4)* | |
H1NB | 0.369 (4) | 0.452 (5) | 0.0644 (13) | 0.052 (6)* | |
H1NC | 0.412 (4) | 0.403 (4) | 0.1408 (12) | 0.045 (5)* | |
H2N | 0.317 (4) | 0.999 (4) | 0.2126 (10) | 0.040 (5)* | |
H1O | 0.323 (5) | 0.729 (6) | −0.0415 (15) | 0.066 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0313 (5) | 0.0318 (6) | 0.0392 (6) | 0.0038 (5) | 0.0099 (4) | 0.0020 (5) |
N2 | 0.0274 (5) | 0.0364 (6) | 0.0359 (5) | 0.0031 (5) | 0.0070 (4) | −0.0017 (5) |
O1 | 0.0454 (5) | 0.0443 (7) | 0.0342 (4) | 0.0003 (5) | 0.0118 (4) | −0.0001 (5) |
O2 | 0.0311 (5) | 0.0446 (7) | 0.0630 (7) | −0.0053 (5) | 0.0153 (4) | −0.0084 (5) |
O3 | 0.0417 (5) | 0.0491 (7) | 0.0376 (5) | 0.0027 (5) | 0.0091 (4) | 0.0067 (5) |
O4 | 0.0310 (4) | 0.0411 (6) | 0.0539 (6) | 0.0043 (4) | 0.0095 (4) | 0.0073 (5) |
C1 | 0.0261 (5) | 0.0317 (7) | 0.0333 (6) | 0.0009 (5) | 0.0055 (4) | −0.0004 (5) |
C2 | 0.0473 (7) | 0.0345 (8) | 0.0368 (7) | 0.0073 (6) | 0.0132 (5) | 0.0054 (6) |
C3 | 0.0251 (5) | 0.0343 (7) | 0.0332 (6) | 0.0034 (5) | 0.0048 (4) | 0.0038 (5) |
C4 | 0.0320 (6) | 0.0377 (8) | 0.0350 (6) | 0.0065 (6) | 0.0093 (5) | 0.0012 (6) |
C5 | 0.0498 (8) | 0.0634 (12) | 0.0414 (7) | 0.0122 (8) | 0.0020 (6) | −0.0164 (8) |
C6 | 0.0844 (15) | 0.132 (3) | 0.0518 (11) | 0.0365 (19) | −0.0167 (10) | −0.0274 (15) |
C7 | 0.135 (3) | 0.226 (7) | 0.100 (2) | 0.042 (4) | −0.053 (2) | −0.093 (4) |
C8 | 0.189 (5) | 0.225 (8) | 0.072 (2) | 0.018 (5) | −0.006 (2) | 0.067 (3) |
C9 | 0.0302 (6) | 0.0286 (7) | 0.0373 (6) | −0.0014 (5) | 0.0059 (5) | −0.0001 (5) |
N1—C1 | 1.479 (2) | C4—C9 | 1.5353 (18) |
N2—C3 | 1.3305 (19) | C5—C6 | 1.532 (3) |
N2—C4 | 1.4559 (17) | C6—C8 | 1.487 (7) |
O1—C2 | 1.4155 (17) | C6—C7 | 1.510 (6) |
O2—C3 | 1.2254 (18) | N1—H1NA | 0.91 (2) |
O3—C9 | 1.2572 (15) | N1—H1NB | 0.91 (2) |
O4—C9 | 1.2558 (17) | N1—H1NC | 0.92 (2) |
C1—C2 | 1.5282 (18) | N2—H2N | 0.88 (2) |
C1—C3 | 1.5290 (17) | O1—H1O | 0.86 (3) |
C4—C5 | 1.527 (2) | ||
C1—N1—H1NA | 107.7 (15) | O2—C3—N2 | 124.74 (12) |
C1—N1—H1NB | 109.6 (19) | O2—C3—C1 | 119.51 (13) |
H1NA—N1—H1NB | 114 (2) | N2—C3—C1 | 115.61 (12) |
C1—N1—H1NC | 111.6 (16) | N2—C4—C5 | 110.58 (11) |
H1NA—N1—H1NC | 112.2 (18) | N2—C4—C9 | 110.53 (11) |
H1NB—N1—H1NC | 102 (2) | C5—C4—C9 | 109.54 (13) |
C3—N2—C4 | 119.88 (11) | C4—C5—C6 | 114.4 (2) |
C3—N2—H2N | 117.1 (14) | C8—C6—C7 | 110.7 (4) |
C4—N2—H2N | 119.9 (15) | C8—C6—C5 | 111.7 (3) |
C2—O1—H1O | 106.3 (17) | C7—C6—C5 | 109.0 (4) |
N1—C1—C2 | 109.08 (11) | O4—C9—O3 | 125.31 (13) |
N1—C1—C3 | 108.67 (12) | O4—C9—C4 | 116.16 (11) |
C3—C1—C2 | 107.28 (11) | O3—C9—C4 | 118.53 (11) |
O1—C2—C1 | 109.24 (12) | ||
N1—C1—C2—O1 | −53.90 (15) | C3—N2—C4—C9 | −68.23 (16) |
C3—C1—C2—O1 | −171.44 (12) | N2—C4—C5—C6 | −60.8 (2) |
C4—N2—C3—O2 | −17.7 (2) | C9—C4—C5—C6 | 177.15 (17) |
C4—N2—C3—C1 | 157.99 (12) | C4—C5—C6—C7 | 174.0 (2) |
N1—C1—C3—O2 | −29.01 (18) | C4—C5—C6—C8 | −63.4 (4) |
C2—C1—C3—O2 | 88.79 (17) | N2—C4—C9—O4 | 161.92 (13) |
N1—C1—C3—N2 | 155.04 (11) | C5—C4—C9—O4 | −75.99 (16) |
C2—C1—C3—N2 | −87.15 (14) | N2—C4—C9—O3 | −19.08 (19) |
C3—N2—C4—C5 | 170.29 (13) | C5—C4—C9—O3 | 103.01 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O2 | 0.91 (2) | 2.22 (2) | 2.6978 (16) | 112 (2) |
N1—H1NA···O3i | 0.91 (2) | 2.16 (2) | 2.9509 (17) | 146 (2) |
N1—H1NB···O1ii | 0.90 (2) | 2.08 (3) | 2.8951 (16) | 149 (2) |
N1—H1NC···O4iii | 0.92 (2) | 1.80 (2) | 2.7066 (17) | 168 (2) |
N2—H2N···O4iv | 0.88 (2) | 1.99 (2) | 2.8449 (16) | 164 (2) |
O1—H1O···O3v | 0.86 (3) | 1.76 (3) | 2.6250 (15) | 177 (3) |
C1—H1···O2iv | 0.98 | 2.37 | 3.2575 (16) | 150 |
C2—H2B···O1vi | 0.97 | 2.64 | 3.369 (2) | 133 |
C5—H5B···O4iv | 0.97 | 2.82 | 3.474 (2) | 125 |
Symmetry codes: (i) x, y−1, z; (ii) −x+1, y−1/2, −z; (iii) x+1, y−1, z; (iv) x+1, y, z; (v) −x, y−1/2, −z; (vi) −x+1, y+1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C9H18N2O4 |
Mr | 218.25 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 5.3288 (3), 6.3696 (6), 18.1263 (9) |
β (°) | 95.811 (4) |
V (Å3) | 612.09 (7) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 0.78 |
Crystal size (mm) | 0.7 × 0.7 × 0.05 |
Data collection | |
Diffractometer | KM4 (KUMA Diffraction) diffractometer |
Absorption correction | Numerical (Sheldrick, 1990b) |
Tmin, Tmax | 0.625, 0.962 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2765, 1405, 1325 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.632 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.029, 0.077, 1.02 |
No. of reflections | 1405 |
No. of parameters | 166 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.14 |
Absolute structure | Flack (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.
N1—C1 | 1.479 (2) | O4—C9 | 1.2558 (17) |
N2—C3 | 1.3305 (19) | C1—C2 | 1.5282 (18) |
N2—C4 | 1.4559 (17) | C1—C3 | 1.5290 (17) |
O1—C2 | 1.4155 (17) | C4—C5 | 1.527 (2) |
O2—C3 | 1.2254 (18) | C4—C9 | 1.5353 (18) |
O3—C9 | 1.2572 (15) | ||
C3—N2—C4 | 119.88 (11) | N2—C3—C1 | 115.61 (12) |
N1—C1—C2 | 109.08 (11) | N2—C4—C5 | 110.58 (11) |
N1—C1—C3 | 108.67 (12) | N2—C4—C9 | 110.53 (11) |
C3—C1—C2 | 107.28 (11) | C5—C4—C9 | 109.54 (13) |
O1—C2—C1 | 109.24 (12) | O4—C9—O3 | 125.31 (13) |
O2—C3—N2 | 124.74 (12) | O4—C9—C4 | 116.16 (11) |
O2—C3—C1 | 119.51 (13) | O3—C9—C4 | 118.53 (11) |
C4—N2—C3—O2 | −17.7 (2) | C3—N2—C4—C9 | −68.23 (16) |
C4—N2—C3—C1 | 157.99 (12) | C4—C5—C6—C7 | 174.0 (2) |
N1—C1—C3—N2 | 155.04 (11) | C4—C5—C6—C8 | −63.4 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O2 | 0.91 (2) | 2.22 (2) | 2.6978 (16) | 112 (2) |
N1—H1NA···O3i | 0.91 (2) | 2.16 (2) | 2.9509 (17) | 146 (2) |
N1—H1NB···O1ii | 0.90 (2) | 2.08 (3) | 2.8951 (16) | 149 (2) |
N1—H1NC···O4iii | 0.92 (2) | 1.80 (2) | 2.7066 (17) | 168 (2) |
N2—H2N···O4iv | 0.88 (2) | 1.99 (2) | 2.8449 (16) | 164 (2) |
O1—H1O···O3v | 0.86 (3) | 1.76 (3) | 2.6250 (15) | 177 (3) |
C1—H1···O2iv | 0.98 | 2.37 | 3.2575 (16) | 150 |
C2—H2B···O1vi | 0.97 | 2.64 | 3.369 (2) | 133 |
C5—H5B···O4iv | 0.97 | 2.82 | 3.474 (2) | 125 |
Symmetry codes: (i) x, y−1, z; (ii) −x+1, y−1/2, −z; (iii) x+1, y−1, z; (iv) x+1, y, z; (v) −x, y−1/2, −z; (vi) −x+1, y+1/2, −z. |
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 C═O 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—C3═O2 - 29.01 (18)°; N2—C4—C9═O3 - 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).