Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101004590/av1074sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270101004590/av1074Isup2.hkl |
CCDC reference: 166993
%T A solution of {ιt meso}-{ιt N},{ιt N'}-oxalyl-bis(valine methyl ester) (221 mg, 0.698 mmol) in MeOH (5 ml) and LiOH (1 M, 4.3 ml) was stirred for 2 d at room temperature. The most of the solvent was evaporated under reduced pressure, H$_2$O (5 ml) was added and solution was acidified with HCl (1 M) to pH 2. Resulting aqueous solution was partitioned with EtOAc ($2τimes15$ ml), organic phase was dried (Na$_2$SO$_4$) and evaporated to give the title compound (I) (191 mg, 89.9°); m.p. 512-514 K (from MeOH-EtOAc-light petroleum). The single crystals suitable for X-ray analysis were obtained by vapour diffusion of pentane into the solution of (I) in MeOH/AtOAc (1:7 v/v) $1$H NMR (DMSO-d$_6$, 300 MHz, $δelta$, p.p.m.): 12.99 (m, 2H, COOH), 8.42 (d, {ιt J} = 8.6, 2H, NH), 4.14 (dd, {ιt J} = 8.6, {ιt J'} = 6.0 Hz, 2H, CH$_{αlpha}$), 2.23-2.16 (m, 2H, CH$_{βeta}$), 0.90 and 0.88 (2d, {ιt J} = 6.6 and 6.5 Hz, 12H, CH$_{3(γamma)}$);${13}$C NMR (DMSO-d$_6$, 75 MHz $δelta$, p.p.m.): 172.1 (COOH), 159.5 (CONH), 58.0 (CH$_{αlpha}$), 29.8 (CH$_{βeta}$), 19.2 and 18.3 (CH$_{3(γamma)}$); IR (KBr, $νu_{max}$, cm${-1}$): 3280 and 3130 br (NH) 1715 (COOH), 1652 (amide I), 1508 (amide II). Analysis calculated for C$_{12}$H$_{20}$N$_{2}$O$_{6}$: C 49.99, H 6.99, N 9.72°; found C 50.07, H 7.20, N 9.84°.
{ιt meso}-{ιt N},{ιt N'}-oxalyl-bis(valine methyl ester) was preparated from {σmall L},{σmall D}-valine methyl ester hydrochloride according to the procedure described by Talma {ιt et al.}. (1985) and was separated from the reaction mixture by crystallization from CH$_2$Cl$_2$-light petroleum.
H atoms were placed in calculated positions and restrained to ride on the atom to which they are bonded. Exceptions are H atoms involved in hydrogen bonds (H1 and H3) which are refined without restraints.
Data collection: CAD-4 EXPRESS (Enraf Nonius, 1992); cell refinement: CAD-4 EXPRESS; data reduction: HELENA (Spek, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1999); software used to prepare material for publication: PLATON.
C12H20N2O6 | F(000) = 308 |
Mr = 288.30 | Dx = 1.305 Mg m−3 |
Monoclinic, P21/c | Melting point: 513 K |
Hall symbol: -P 2ybc | Cu Kα radiation, λ = 1.54178 Å |
a = 7.6058 (8) Å | Cell parameters from 25 reflections |
b = 10.3780 (2) Å | θ = 40.0–46.0° |
c = 10.695 (1) Å | µ = 0.89 mm−1 |
β = 119.635 (7)° | T = 293 K |
V = 733.76 (10) Å3 | Prism, colourless |
Z = 2 | 0.27 × 0.20 × 0.07 mm |
Enraf-Nonius CAD4 diffractometer | 1132 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.025 |
Graphite monochromator | θmax = 74.0°, θmin = 6.4° |
ω/2θ scans | h = 0→9 |
Absorption correction: analytical PLATON (Spek, 1999) | k = −12→0 |
Tmin = 0.819, Tmax = 0.941 | l = −13→11 |
1597 measured reflections | 3 standard reflections every 120 min |
1485 independent reflections | intensity decay: none |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.063 | w = 1/[σ2(Fo2) + (0.1404P)2 + 0.0375P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.194 | (Δ/σ)max < 0.001 |
S = 1.06 | Δρmax = 0.36 e Å−3 |
1485 reflections | Δρmin = −0.34 e Å−3 |
101 parameters |
C12H20N2O6 | V = 733.76 (10) Å3 |
Mr = 288.30 | Z = 2 |
Monoclinic, P21/c | Cu Kα radiation |
a = 7.6058 (8) Å | µ = 0.89 mm−1 |
b = 10.3780 (2) Å | T = 293 K |
c = 10.695 (1) Å | 0.27 × 0.20 × 0.07 mm |
β = 119.635 (7)° |
Enraf-Nonius CAD4 diffractometer | 1132 reflections with I > 2σ(I) |
Absorption correction: analytical PLATON (Spek, 1999) | Rint = 0.025 |
Tmin = 0.819, Tmax = 0.941 | 3 standard reflections every 120 min |
1597 measured reflections | intensity decay: none |
1485 independent reflections |
R[F2 > 2σ(F2)] = 0.063 | 0 restraints |
wR(F2) = 0.194 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.36 e Å−3 |
1485 reflections | Δρmin = −0.34 e Å−3 |
101 parameters |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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 | ||
O1 | 0.4589 (3) | −0.06329 (19) | 0.33627 (16) | 0.0578 (6) | |
O2 | 0.1925 (3) | 0.1954 (2) | 0.03707 (18) | 0.0688 (7) | |
O3 | 0.3670 (3) | 0.27478 (19) | 0.25763 (17) | 0.0591 (6) | |
N1 | 0.2775 (2) | 0.08487 (17) | 0.37605 (16) | 0.0373 (5) | |
C1 | 0.4294 (3) | 0.0030 (2) | 0.41814 (17) | 0.0358 (5) | |
C2 | 0.1379 (3) | 0.10772 (19) | 0.22368 (18) | 0.0356 (5) | |
C3 | 0.2342 (3) | 0.1964 (2) | 0.1613 (2) | 0.0401 (6) | |
C4 | −0.0629 (3) | 0.1622 (2) | 0.2032 (2) | 0.0432 (6) | |
C5 | −0.2113 (4) | 0.1921 (4) | 0.0466 (3) | 0.0726 (12) | |
C6 | −0.1577 (4) | 0.0672 (3) | 0.2607 (4) | 0.0752 (11) | |
H1 | 0.278 (4) | 0.140 (3) | 0.441 (3) | 0.059 (8)* | |
H2 | 0.10968 | 0.02490 | 0.17334 | 0.0427* | |
H3 | 0.412 (5) | 0.328 (3) | 0.212 (3) | 0.075 (9)* | |
H4 | −0.03400 | 0.24227 | 0.25855 | 0.0518* | |
H51 | −0.22966 | 0.11685 | −0.01087 | 0.1089* | |
H52 | −0.15932 | 0.26111 | 0.01450 | 0.1089* | |
H53 | −0.33889 | 0.21714 | 0.03706 | 0.1089* | |
H61 | −0.19161 | −0.01078 | 0.20523 | 0.1133* | |
H62 | −0.27803 | 0.10413 | 0.25358 | 0.1133* | |
H63 | −0.06337 | 0.04815 | 0.35956 | 0.1133* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0543 (10) | 0.0770 (12) | 0.0347 (8) | 0.0273 (9) | 0.0164 (7) | 0.0001 (7) |
O2 | 0.0744 (12) | 0.0943 (15) | 0.0319 (8) | −0.0222 (11) | 0.0218 (8) | 0.0029 (8) |
O3 | 0.0590 (10) | 0.0759 (12) | 0.0370 (9) | −0.0252 (9) | 0.0196 (8) | −0.0012 (8) |
N1 | 0.0356 (8) | 0.0462 (9) | 0.0264 (8) | 0.0094 (7) | 0.0126 (7) | 0.0061 (7) |
C1 | 0.0319 (9) | 0.0437 (10) | 0.0292 (9) | 0.0052 (7) | 0.0132 (8) | 0.0070 (7) |
C2 | 0.0317 (9) | 0.0426 (10) | 0.0252 (9) | 0.0033 (7) | 0.0086 (7) | 0.0014 (7) |
C3 | 0.0331 (9) | 0.0528 (12) | 0.0273 (9) | 0.0041 (8) | 0.0094 (7) | 0.0060 (8) |
C4 | 0.0306 (9) | 0.0545 (12) | 0.0370 (10) | 0.0052 (8) | 0.0109 (8) | −0.0020 (8) |
C5 | 0.0415 (12) | 0.111 (3) | 0.0447 (13) | 0.0240 (15) | 0.0056 (11) | 0.0047 (14) |
C6 | 0.0486 (14) | 0.096 (2) | 0.085 (2) | −0.0044 (14) | 0.0360 (15) | 0.0106 (17) |
O1—C1 | 1.218 (3) | C4—C6 | 1.519 (4) |
O2—C3 | 1.204 (3) | C4—C5 | 1.518 (3) |
O3—C3 | 1.309 (3) | C2—H2 | 0.9800 |
O3—H3 | 0.91 (4) | C4—H4 | 0.9801 |
N1—C2 | 1.459 (2) | C5—H51 | 0.9604 |
N1—C1 | 1.321 (3) | C5—H52 | 0.9598 |
N1—H1 | 0.90 (3) | C5—H53 | 0.9601 |
C1—C1i | 1.537 (2) | C6—H61 | 0.9602 |
C2—C3 | 1.520 (3) | C6—H62 | 0.9599 |
C2—C4 | 1.539 (3) | C6—H63 | 0.9600 |
C3—O3—H3 | 107.7 (18) | C3—C2—H2 | 108.18 |
C1—N1—C2 | 121.07 (16) | C4—C2—H2 | 108.16 |
C2—N1—H1 | 118.9 (19) | C2—C4—H4 | 108.36 |
C1—N1—H1 | 119 (2) | C5—C4—H4 | 108.38 |
O1—C1—C1i | 121.5 (2) | C6—C4—H4 | 108.38 |
O1—C1—N1 | 123.99 (17) | C4—C5—H51 | 109.47 |
N1—C1—C1i | 114.53 (17) | C4—C5—H52 | 109.51 |
N1—C2—C3 | 110.25 (17) | C4—C5—H53 | 109.48 |
N1—C2—C4 | 109.97 (16) | H51—C5—H52 | 109.46 |
C3—C2—C4 | 112.00 (17) | H51—C5—H53 | 109.43 |
O3—C3—C2 | 112.48 (17) | H52—C5—H53 | 109.48 |
O2—C3—O3 | 123.6 (2) | C4—C6—H61 | 109.45 |
O2—C3—C2 | 123.9 (2) | C4—C6—H62 | 109.48 |
C2—C4—C5 | 112.1 (2) | C4—C6—H63 | 109.49 |
C2—C4—C6 | 109.9 (2) | H61—C6—H62 | 109.46 |
C5—C4—C6 | 109.7 (2) | H61—C6—H63 | 109.45 |
N1—C2—H2 | 108.17 | H62—C6—H63 | 109.49 |
C2—N1—C1—O1 | −3.9 (3) | N1—C2—C3—O3 | −28.4 (3) |
C1i—C1—N1—C2 | 175.99 (18) | C4—C2—C3—O2 | −85.2 (3) |
C1—N1—C2—C3 | −77.8 (2) | N1—C2—C3—O2 | 152.0 (2) |
C1—N1—C2—C4 | 158.21 (19) | N1—C2—C4—C5 | 178.0 (2) |
O1—C1—C1i—O1i | −180.0 (2) | N1—C2—C4—C6 | −59.8 (2) |
N1—C1—C1i—N1i | 180.0 (4) | C4—C2—C3—O3 | 94.4 (2) |
O1—C1—C1i—N1i | −0.2 (3) | C3—C2—C4—C5 | 55.1 (3) |
N1—C1—C1i—O1i | 0.2 (3) | C3—C2—C4—C6 | 177.3 (2) |
Symmetry code: (i) −x+1, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.90 (3) | 2.37 (3) | 2.727 (2) | 104 (2) |
N1—H1···O2ii | 0.90 (3) | 2.25 (3) | 3.112 (3) | 161 (3) |
O3—H3···O1iii | 0.91 (4) | 1.73 (4) | 2.627 (3) | 167 (3) |
C6—H63···N1 | 0.96 | 2.54 | 2.911 (4) | 103 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y+1/2, z+1/2; (iii) −x+1, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C12H20N2O6 |
Mr | 288.30 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 7.6058 (8), 10.3780 (2), 10.695 (1) |
β (°) | 119.635 (7) |
V (Å3) | 733.76 (10) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 0.89 |
Crystal size (mm) | 0.27 × 0.20 × 0.07 |
Data collection | |
Diffractometer | Enraf-Nonius CAD4 diffractometer |
Absorption correction | Analytical PLATON (Spek, 1999) |
Tmin, Tmax | 0.819, 0.941 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1597, 1485, 1132 |
Rint | 0.025 |
(sin θ/λ)max (Å−1) | 0.624 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.063, 0.194, 1.06 |
No. of reflections | 1485 |
No. of parameters | 101 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.36, −0.34 |
Computer programs: CAD-4 EXPRESS (Enraf Nonius, 1992), CAD-4 EXPRESS, HELENA (Spek, 1997), SIR97 (Altomare et al., 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 1999), PLATON.
C1i—C1—N1—C2 | 175.99 (18) | N1—C2—C3—O3 | −28.4 (3) |
C1—N1—C2—C3 | −77.8 (2) | N1—C2—C4—C5 | 178.0 (2) |
Symmetry code: (i) −x+1, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.90 (3) | 2.37 (3) | 2.727 (2) | 104 (2) |
N1—H1···O2ii | 0.90 (3) | 2.25 (3) | 3.112 (3) | 161 (3) |
O3—H3···O1iii | 0.91 (4) | 1.73 (4) | 2.627 (3) | 167 (3) |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y+1/2, z+1/2; (iii) −x+1, y+1/2, −z+1/2. |
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%T The molecule of the title compound, (I), belongs to the specific class of retro-bipeptides that have an oxalamide (–NH–CO–CO–NH–) unit (Karle {ιt et al.}., 1994). It is reported that compounds of this class are good gelators of water and organic solvents; their gelling properties depend on stereochemistry of substituents at the oxalamide unit (Joki\'{c} {ιt et al.}., 1995). On the other hand, the oxalamide moiety was chosen as a good structural unit in design of molecular solids (Coe {ιt et al.}., 1997; Nguyen {ιt et al.}., 1998). Coe {ιt et al.}. (1997) investigated centrosymmetric oxalamides with terminal substituted carboxyl groups. The authors have found two modes of connection of molecules into infinite two-dimensional hydrogen-bonding patterns. The first mode involves intermolecular hydrogen bonds N—H$χdots$O between the oxalamide units and simultaneously intermolecular hydrogen bonds between carboxyl groups, O—H$χdots$O. The second mode includes intermolecular hydrogen bonds between oxalamide unit and carboxyl group. Coe {ιt et al.}. (1997) reported also a polymorphism of the retro-bipeptide of glycine with oxalamide unit (HO–Gly–CO–CO–Gly–OH). These two polymorphs represent two described modes of hydrogen-bonding patterns: the first mode appears in the triclinic polymorph whereas the second one is characteristic of the monoclinic $P2_1/c$ form. The second mode is also observed in the crystal packing of retro-bipeptide of the isobutyric amino acid with the oxalamide unit, HO–Aib–CO–CO–Aib–OH (Karle \& Ranganathan, 1995). Coe {ιt et al.}. (1997) argued that the second mode is favoured for retro-bipeptides containing amino acids with larger substituents attached at the oxalamide unit. Hydrogen bonds between oxalamide and carboxyl groups are not disturbed by sterical hindrances of side chains which are significant in interactions of two oxalamide groups. This argument is also valid for the structure reported in this paper. \sch
The molecular structure of (I) is given in Fig. 1. The crystal structure with hydrogen-bond pattern is shown in Fig 2. The structural parameters of (I) are compared with those of HO–Gly–CO–CO–Gly–OH and HO–Aib–CO–CO–Aib–OH. The conformations of these retropeptides are defined by the set of torsion angles $οmega$, $πhi$, $πsi$ and $χhi$ as proposed in the literature (Karle {ιt et al.}., 1994). The $πsi$ angle in (I) defines (-){ιt synperiplanar} conformation (Klyne \& Prelog, 1960; Table 1) whereas in Gly and Aib analogues $(πm)$-{ιt antiperiplanar} was observed. The only retro-bipeptide of this kind with {ιt synperiplanar} conformation found in the Cambridge Structural Database (CSD, Version of October 2000; Allen \& Kennard, 1993) is methyl ester of Aib analogue (YIDGEX; Karle {ιt et al.}., 1994). However, characteristics of the crystal packing of HO–Gly–CO–CO–Gly–OH, HO–Aib–CO–CO–Aib–OH and (I) are similar. They all crystallize in $P2_1/c$ space group. Molecules are connected by hydrogen bonds between oxalamide and carboxyl groups (second mode described above), with characteristic $R_22(9)$ graph-set descriptor (Bernstein {ιt et al.}., 1995). According to arguments given by Coe {ιt et al.}. (1997) we can conclude that retro-bipeptides with the oxalamide unit having achiral amino acids larger than glycine, or those having amino acids of oposite chirality substituted at the oxalamide unit, tend to crystallize in $P2_1/c$ space group with $R_22(9)$ hydrogen-bonding pattern including oxalamide and carboxyl groups.