organic compounds
Redetermined N-(β-carboxyethyl)-α-isoleucine
ofaDepartment of Physics, Thiagarajar College, Madurai 625 009, Tamil Nadu, India
*Correspondence e-mail: mailtorvkk@yahoo.com
Redetermination of the N-(β-carboxyethyl)-α-isoleucine, C9H18N2O3, reported earlier by Nehls et al. [Acta Cryst. (2013), E69, o172–o173], was undertaken in which the ionization state assigned to the molecule as unionized has been modified as zwitterionic in the present work. Single-crystal data obtained from freshly grown crystals and freely refining the amino H atoms provide enhanced and structural parameters, particularly the hydrogen-bonding scheme. N—H⋯O hydrogen bonds dominate the intermolecular interactions along with a C—H⋯O hydrogen bond. The intermolecular interaction pattern is a three-dimensional network. The structure was refined as a two-component perfect inversion twin.
ofKeywords: crystal structure; amino acids; ionization state; hydrogen bonding; isoleucine.
CCDC reference: 1416394
1. Related literature
For earlier work on the N-(β-carboxyethyl)-α-isoleucine, see: Nehls et al. (2013). For the of L-isoleucine and its indolylacetyl derivative, respectively, see Görbitz & Dalhus (1996); Kojić-Prodić et al. (1991). For the importance of freely refining the positions of amino-group H atoms, see: Görbitz (2014). For and structure parameters, see Flack (1983); Flack & Bernardinelli (2000); Hooft et al. (2008); Spek (2009); Parsons et al. (2013). For chiral and achiral crystal structures, see Flack (2003).
of2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014.
Supporting information
CCDC reference: 1416394
https://doi.org/10.1107/S2056989015014498/bg2563sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015014498/bg2563Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989015014498/bg2563Isup3.cml
Amino acids in their free form exist as
in their crystals with a deprotonated carboxyl group (COO–) and a protonated NH3+ group (NH2+ in proline). Any deviation from this general preferences of amino acids is worth careful considerations. The motivation for the present work is the unionized state reported by Nehls et al., 2013, for the title compound in contrast to the usually preferred 'zwitterionic' state. In this context, redetermination of the of the title compouned was undertaken.Coordinates were refined for amino H atoms; other H atoms were positioned with idealized geometry, with fixed C— H = 0.98 (methyl), 0.99 (methylene) or 1.00 Å (methine). Uiso(H) values were set at 1.2Ueq of the
or at 1.5Ueq for methyl and amino groups. The could not be determined by anomalous-dispersion effects in the X-ray diffraction measurements of the crystal, but assigned as L- based on an unchanged chiral centre in the synthetic procedure. The absoulte structure was refined as a perfect inversion twin.Nehls et al., (2013) seem to have presumed an unionized state for the title compound with an undissociated carboxyl (COOH) and a deprotonated amino (NH) group. A scrutiny of the work by Nehls et al. revealed that all the H-atoms, including the donor group H atoms were assigned an idealized geometry and refined as riding on their respective non-H atoms to which they are attached. Redetermination of the
carried out by measuring data from freshly grown crystals and freely refining the amino-H atoms clearly indicate that the title compound indeed exist as a zwitterion. The correct assignment of the ionized state provided enhanced and structural parameters. Thus, the present redtermination demonstrates the importance of freely refining donor group hydrogens. The S,S (equivalently L-) is deduced from the synthetic pathway as the starting material involved L-isoleucine. The absoulte structure was refined as a perfect in order that the Flack x (Flack, 1983; Flack & Bernardinelli, 2000; Parsons et al., 2013) and Hooft y parameters (Spek, 2009) showed good agreement.The correct assignment of the ionization state to the title compound as 'zwitterion' presents an acceptable description of the intermolecular interaction patterns with all the amino-H atoms participating in them. The carboxylate O1 atom of the amino acid derivative participates in a strong head-to-tail N—H···O hydrogen bond characteristic of amino acids, in addition to a C—H···O hydrogen-bond as acceptor. This has consequently resulted in the lengthening of the C6—O1[1.253 (2)Å] bond compared to its counterpart C6—O2[1.234 (2)Å]. The carbamoyl group N2 and O3 form N—H···O hydrogen-bonds within themselves leading to C32(8) chains linking screw related molecules along the shortest a-axis. The respective amino and carboxylate group N and O atoms form characteristic head-to-tail hydrogen-bonds leading to a layers parallel to the ab-plane. The intermolecular interaction pattern is a three-dimensional network dominated by N—H···O hydrogen bonds, in addition to a C—H···O hydrogen-bond involving the α-carbon atom (C2) as donor and the carboxylate O1 as acceptor.
Amino acids in their free form exist as
in their crystals with a deprotonated carboxyl group (COO–) and a protonated NH3+ group (NH2+ in proline). Any deviation from this general preferences of amino acids is worth careful considerations. The motivation for the present work is the unionized state reported by Nehls et al., 2013, for the title compound in contrast to the usually preferred 'zwitterionic' state. In this context, redetermination of the of the title compouned was undertaken.Nehls et al., (2013) seem to have presumed an unionized state for the title compound with an undissociated carboxyl (COOH) and a deprotonated amino (NH) group. A scrutiny of the work by Nehls et al. revealed that all the H-atoms, including the donor group H atoms were assigned an idealized geometry and refined as riding on their respective non-H atoms to which they are attached. Redetermination of the
carried out by measuring data from freshly grown crystals and freely refining the amino-H atoms clearly indicate that the title compound indeed exist as a zwitterion. The correct assignment of the ionized state provided enhanced and structural parameters. Thus, the present redtermination demonstrates the importance of freely refining donor group hydrogens. The S,S (equivalently L-) is deduced from the synthetic pathway as the starting material involved L-isoleucine. The absoulte structure was refined as a perfect in order that the Flack x (Flack, 1983; Flack & Bernardinelli, 2000; Parsons et al., 2013) and Hooft y parameters (Spek, 2009) showed good agreement.The correct assignment of the ionization state to the title compound as 'zwitterion' presents an acceptable description of the intermolecular interaction patterns with all the amino-H atoms participating in them. The carboxylate O1 atom of the amino acid derivative participates in a strong head-to-tail N—H···O hydrogen bond characteristic of amino acids, in addition to a C—H···O hydrogen-bond as acceptor. This has consequently resulted in the lengthening of the C6—O1[1.253 (2)Å] bond compared to its counterpart C6—O2[1.234 (2)Å]. The carbamoyl group N2 and O3 form N—H···O hydrogen-bonds within themselves leading to C32(8) chains linking screw related molecules along the shortest a-axis. The respective amino and carboxylate group N and O atoms form characteristic head-to-tail hydrogen-bonds leading to a layers parallel to the ab-plane. The intermolecular interaction pattern is a three-dimensional network dominated by N—H···O hydrogen bonds, in addition to a C—H···O hydrogen-bond involving the α-carbon atom (C2) as donor and the carboxylate O1 as acceptor.
For earlier work on the β-carboxyethyl)-α-isoleucine, see: Nehls et al. (2013). For the of L-isoleucine and its indolylacetyl derivative, respectively, see Görbitz & Dalhus (1996); Kojić-Prodić et al. (1991). For the importance of freely refining the positions of amino-group H atoms, see: Görbitz (2014). For and structure parameters, see Flack (1983); Flack & Bernardinelli (2000); Hooft et al. (2008); Spek (2009); Parsons et al. (2013). For chiral and achiral crystal structures, see Flack (2003).
of N-(For crystallization details, see Nehls et al. (2013).
detailsCoordinates were refined for amino H atoms; other H atoms were positioned with idealized geometry, with fixed C— H = 0.98 (methyl), 0.99 (methylene) or 1.00 Å (methine). Uiso(H) values were set at 1.2Ueq of the
or at 1.5Ueq for methyl and amino groups. The could not be determined by anomalous-dispersion effects in the X-ray diffraction measurements of the crystal, but assigned as L- based on an unchanged chiral centre in the synthetic procedure. The absoulte structure was refined as a perfect inversion twin.Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).Fig. 1. Thermal ellipsoid plot of the title compound, showing the atom numbering scheme. | |
Fig. 2. The characteristic head-to-tail N—H···O hydrogen bonds involving the carboxylate and the amino groups. Non pariticipating N-carboxyethl group atoms have been omitted for clarity. | |
Fig. 3. Carbamoyl group N2 and O3 forming N—H···O hydrogen-bonds within themselves leading to C32(8) chains linking screw related molecules along the a axis. |
C9H18N2O3 | F(000) = 440 |
Mr = 202.25 | Dx = 1.213 Mg m−3 Dm = 1.21 Mg m−3 Dm measured by floatation method |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.2996 (5) Å | µ = 0.09 mm−1 |
b = 9.0053 (7) Å | T = 293 K |
c = 23.211 (2) Å | Needle, colourless |
V = 1107.75 (17) Å3 | 0.26 × 0.18 × 0.10 mm |
Z = 4 |
Bruker APEXII CCD diffractometer | 2538 reflections with I > 2σ(I) |
ω and φ scans | Rint = 0.036 |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | θmax = 29.9°, θmin = 2.4° |
Tmin = 0.97, Tmax = 0.99 | h = −7→7 |
22904 measured reflections | k = −12→11 |
3127 independent reflections | l = −31→32 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.042 | w = 1/[σ2(Fo2) + (0.0479P)2 + 0.1014P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.102 | (Δ/σ)max < 0.001 |
S = 1.08 | Δρmax = 0.30 e Å−3 |
3127 reflections | Δρmin = −0.19 e Å−3 |
146 parameters | Absolute structure: Refined as a perfect inversion twin. |
0 restraints | Absolute structure parameter: 0.5 |
C9H18N2O3 | V = 1107.75 (17) Å3 |
Mr = 202.25 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.2996 (5) Å | µ = 0.09 mm−1 |
b = 9.0053 (7) Å | T = 293 K |
c = 23.211 (2) Å | 0.26 × 0.18 × 0.10 mm |
Bruker APEXII CCD diffractometer | 3127 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2538 reflections with I > 2σ(I) |
Tmin = 0.97, Tmax = 0.99 | Rint = 0.036 |
22904 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.102 | Δρmax = 0.30 e Å−3 |
S = 1.08 | Δρmin = −0.19 e Å−3 |
3127 reflections | Absolute structure: Refined as a perfect inversion twin. |
146 parameters | Absolute structure parameter: 0.5 |
0 restraints |
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. Refined as a 2-component perfect inversion twin. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.2868 (2) | 0.54162 (13) | 0.74549 (7) | 0.0379 (4) | |
O2 | 0.2473 (3) | 0.77532 (13) | 0.71778 (7) | 0.0383 (4) | |
O3 | 0.6665 (3) | 0.6614 (2) | 0.94137 (7) | 0.0550 (5) | |
N1 | 0.7861 (3) | 0.57896 (16) | 0.76272 (6) | 0.0213 (3) | |
N2 | 1.0857 (4) | 0.6555 (3) | 0.95384 (9) | 0.0475 (5) | |
C5 | 0.7705 (8) | 0.7167 (5) | 0.55526 (12) | 0.0942 (12) | |
H5A | 0.9472 | 0.7357 | 0.5606 | 0.141* | |
H5B | 0.7017 | 0.7884 | 0.5290 | 0.141* | |
H5C | 0.7479 | 0.6188 | 0.5398 | 0.141* | |
C4 | 0.6370 (5) | 0.7281 (3) | 0.61215 (10) | 0.0506 (6) | |
H4A | 0.4584 | 0.7101 | 0.6062 | 0.061* | |
H4B | 0.6555 | 0.8285 | 0.6267 | 0.061* | |
C3 | 0.7352 (4) | 0.6194 (2) | 0.65736 (8) | 0.0329 (4) | |
H3 | 0.9199 | 0.6235 | 0.6558 | 0.040* | |
C6 | 0.6603 (6) | 0.4612 (3) | 0.64363 (10) | 0.0571 (7) | |
H6A | 0.7232 | 0.3961 | 0.6731 | 0.086* | |
H6B | 0.7304 | 0.4330 | 0.6071 | 0.086* | |
H6C | 0.4797 | 0.4540 | 0.6420 | 0.086* | |
C2 | 0.6583 (3) | 0.66957 (19) | 0.71782 (7) | 0.0224 (4) | |
H2 | 0.7123 | 0.7729 | 0.7227 | 0.027* | |
C1 | 0.3732 (3) | 0.66295 (19) | 0.72788 (8) | 0.0244 (4) | |
C7 | 0.7684 (4) | 0.6481 (2) | 0.82050 (8) | 0.0297 (4) | |
H7A | 0.5926 | 0.6536 | 0.8319 | 0.036* | |
H7B | 0.8340 | 0.7485 | 0.8187 | 0.036* | |
C8 | 0.9134 (4) | 0.5614 (2) | 0.86493 (8) | 0.0354 (5) | |
H8A | 1.0912 | 0.5611 | 0.8551 | 0.042* | |
H8B | 0.8547 | 0.4594 | 0.8655 | 0.042* | |
C9 | 0.8776 (4) | 0.6301 (2) | 0.92372 (8) | 0.0348 (4) | |
H1N1 | 0.723 (4) | 0.488 (2) | 0.7648 (9) | 0.029 (5)* | |
H2N1 | 0.947 (4) | 0.568 (2) | 0.7544 (9) | 0.027 (5)* | |
H2N2 | 1.228 (6) | 0.631 (3) | 0.9411 (11) | 0.051 (7)* | |
H1N2 | 1.082 (6) | 0.697 (3) | 0.9890 (13) | 0.064 (9)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0150 (6) | 0.0337 (7) | 0.0651 (10) | −0.0005 (5) | 0.0039 (6) | 0.0146 (6) |
O2 | 0.0213 (7) | 0.0261 (6) | 0.0675 (10) | 0.0044 (6) | −0.0089 (7) | −0.0012 (6) |
O3 | 0.0324 (8) | 0.0925 (14) | 0.0400 (9) | 0.0071 (9) | 0.0034 (7) | −0.0200 (8) |
N1 | 0.0129 (6) | 0.0224 (7) | 0.0287 (8) | −0.0001 (5) | 0.0007 (5) | −0.0012 (6) |
N2 | 0.0339 (11) | 0.0737 (15) | 0.0348 (10) | −0.0011 (10) | −0.0030 (8) | −0.0149 (10) |
C5 | 0.101 (3) | 0.142 (3) | 0.0405 (15) | −0.019 (3) | 0.0009 (16) | 0.0249 (17) |
C4 | 0.0549 (15) | 0.0597 (14) | 0.0371 (11) | −0.0110 (12) | −0.0076 (11) | 0.0114 (11) |
C3 | 0.0225 (9) | 0.0464 (11) | 0.0299 (9) | −0.0034 (9) | 0.0010 (8) | −0.0003 (8) |
C6 | 0.080 (2) | 0.0488 (14) | 0.0423 (13) | 0.0016 (14) | 0.0050 (13) | −0.0135 (11) |
C2 | 0.0141 (7) | 0.0235 (8) | 0.0296 (8) | −0.0012 (6) | −0.0007 (6) | 0.0019 (7) |
C1 | 0.0142 (7) | 0.0270 (8) | 0.0319 (9) | −0.0006 (7) | −0.0014 (7) | −0.0027 (7) |
C7 | 0.0266 (9) | 0.0320 (9) | 0.0305 (9) | 0.0073 (8) | −0.0013 (7) | −0.0079 (7) |
C8 | 0.0320 (11) | 0.0428 (11) | 0.0313 (10) | 0.0088 (9) | −0.0057 (8) | −0.0070 (9) |
C9 | 0.0319 (10) | 0.0430 (11) | 0.0295 (9) | 0.0018 (9) | −0.0019 (9) | −0.0027 (8) |
O1—C1 | 1.253 (2) | C4—H4B | 0.9700 |
O2—C1 | 1.234 (2) | C3—C6 | 1.513 (3) |
O3—C9 | 1.224 (3) | C3—C2 | 1.530 (2) |
N1—C7 | 1.481 (2) | C3—H3 | 0.9800 |
N1—C2 | 1.487 (2) | C6—H6A | 0.9600 |
N1—H1N1 | 0.89 (2) | C6—H6B | 0.9600 |
N1—H2N1 | 0.88 (2) | C6—H6C | 0.9600 |
N2—C9 | 1.326 (3) | C2—C1 | 1.530 (2) |
N2—H2N2 | 0.84 (3) | C2—H2 | 0.9800 |
N2—H1N2 | 0.90 (3) | C7—C8 | 1.504 (3) |
C5—C4 | 1.502 (4) | C7—H7A | 0.9700 |
C5—H5A | 0.9600 | C7—H7B | 0.9700 |
C5—H5B | 0.9600 | C8—C9 | 1.510 (3) |
C5—H5C | 0.9600 | C8—H8A | 0.9700 |
C4—C3 | 1.527 (3) | C8—H8B | 0.9700 |
C4—H4A | 0.9700 | ||
C7—N1—C2 | 112.03 (13) | H6A—C6—H6B | 109.5 |
C7—N1—H1N1 | 108.3 (13) | C3—C6—H6C | 109.5 |
C2—N1—H1N1 | 111.9 (14) | H6A—C6—H6C | 109.5 |
C7—N1—H2N1 | 107.9 (14) | H6B—C6—H6C | 109.5 |
C2—N1—H2N1 | 110.4 (14) | N1—C2—C3 | 111.07 (14) |
H1N1—N1—H2N1 | 106.1 (19) | N1—C2—C1 | 108.74 (14) |
C9—N2—H2N2 | 121.0 (18) | C3—C2—C1 | 113.06 (15) |
C9—N2—H1N2 | 122 (2) | N1—C2—H2 | 107.9 |
H2N2—N2—H1N2 | 117 (3) | C3—C2—H2 | 107.9 |
C4—C5—H5A | 109.5 | C1—C2—H2 | 107.9 |
C4—C5—H5B | 109.5 | O2—C1—O1 | 125.42 (16) |
H5A—C5—H5B | 109.5 | O2—C1—C2 | 118.20 (15) |
C4—C5—H5C | 109.5 | O1—C1—C2 | 116.38 (15) |
H5A—C5—H5C | 109.5 | N1—C7—C8 | 111.73 (14) |
H5B—C5—H5C | 109.5 | N1—C7—H7A | 109.3 |
C5—C4—C3 | 113.6 (2) | C8—C7—H7A | 109.3 |
C5—C4—H4A | 108.9 | N1—C7—H7B | 109.3 |
C3—C4—H4A | 108.9 | C8—C7—H7B | 109.3 |
C5—C4—H4B | 108.9 | H7A—C7—H7B | 107.9 |
C3—C4—H4B | 108.9 | C7—C8—C9 | 110.04 (16) |
H4A—C4—H4B | 107.7 | C7—C8—H8A | 109.7 |
C6—C3—C4 | 111.70 (19) | C9—C8—H8A | 109.7 |
C6—C3—C2 | 113.68 (17) | C7—C8—H8B | 109.7 |
C4—C3—C2 | 110.48 (17) | C9—C8—H8B | 109.7 |
C6—C3—H3 | 106.9 | H8A—C8—H8B | 108.2 |
C4—C3—H3 | 106.9 | O3—C9—N2 | 122.98 (19) |
C2—C3—H3 | 106.9 | O3—C9—C8 | 120.75 (18) |
C3—C6—H6A | 109.5 | N2—C9—C8 | 116.27 (19) |
C3—C6—H6B | 109.5 | ||
C5—C4—C3—C6 | −71.2 (3) | N1—C2—C1—O2 | 144.24 (16) |
C5—C4—C3—C2 | 161.2 (2) | C3—C2—C1—O2 | −91.9 (2) |
C7—N1—C2—C3 | 165.30 (14) | N1—C2—C1—O1 | −36.3 (2) |
C7—N1—C2—C1 | −69.67 (18) | C3—C2—C1—O1 | 87.5 (2) |
C6—C3—C2—N1 | 62.6 (2) | C2—N1—C7—C8 | −176.01 (15) |
C4—C3—C2—N1 | −170.95 (17) | N1—C7—C8—C9 | −176.58 (17) |
C6—C3—C2—C1 | −60.0 (2) | C7—C8—C9—O3 | 48.8 (3) |
C4—C3—C2—C1 | 66.5 (2) | C7—C8—C9—N2 | −130.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2i | 0.89 (2) | 1.96 (2) | 2.7772 (19) | 152 (2) |
N1—H2N1···O1ii | 0.88 (2) | 1.83 (2) | 2.7047 (19) | 174 (2) |
N2—H1N2···O3iii | 0.90 (3) | 2.11 (3) | 2.970 (3) | 161 (3) |
N2—H2N2···O3ii | 0.84 (3) | 2.34 (3) | 3.092 (3) | 149 (2) |
C2—H2···O1iv | 0.98 | 2.53 | 3.469 (2) | 160 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) x+1, y, z; (iii) x+1/2, −y+3/2, −z+2; (iv) −x+1, y+1/2, −z+3/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2i | 0.89 (2) | 1.96 (2) | 2.7772 (19) | 152 (2) |
N1—H2N1···O1ii | 0.88 (2) | 1.83 (2) | 2.7047 (19) | 174 (2) |
N2—H1N2···O3iii | 0.90 (3) | 2.11 (3) | 2.970 (3) | 161 (3) |
N2—H2N2···O3ii | 0.84 (3) | 2.34 (3) | 3.092 (3) | 149 (2) |
C2—H2···O1iv | 0.98 | 2.53 | 3.469 (2) | 160.4 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) x+1, y, z; (iii) x+1/2, −y+3/2, −z+2; (iv) −x+1, y+1/2, −z+3/2. |
Acknowledgements
The authors thank the Sophisticated Analytical Instrumentation Facility (SAIF), Indian Institue of Technology, Chennai, for the data collection.
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