Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807041311/gk2094sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807041311/gk2094Isup2.hkl |
CCDC reference: 660369
Key indicators
- Single-crystal X-ray study
- T = 291 K
- Mean (C-C) = 0.004 Å
- Disorder in main residue
- R factor = 0.045
- wR factor = 0.132
- Data-to-parameter ratio = 11.5
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.74 Ratio PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C1 PLAT301_ALERT_3_C Main Residue Disorder ......................... 9.00 Perc. PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 6
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 28.69 From the CIF: _reflns_number_total 1234 Count of symmetry unique reflns 1239 Completeness (_total/calc) 99.60% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . S PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 17
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 3 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
checkCIF publication errors
Alert level A PUBL024_ALERT_1_A The number of authors is greater than 5. Please specify the role of each of the co-authors for your paper.
Author Response: The role of each author is listed below: Grant A. Boyle- supervised student in laboratory and contributed to writing of the paper. Thavendran Govender- Co-supervisor of project. Hendrik G. Kruger- Supervisor of project. Glenn E.M. Maguire- Co-supervisor of project. Tyrone K. Negus- Student involved in synthesis of crystal. Melanie Rademeyer- Collected X-ray diffraction data and contributed to writing of the paper. |
1 ALERT level A = Data missing that is essential or data in wrong format 0 ALERT level G = General alerts. Data that may be required is missing
Acetic anhydride (30 mol equivalents) was added dropwise to a stirred solution of (S)-(+)-valine (1 mol equivalent) in formic acid (approximately 30 ml per 1.0 g of amino acid) at 0°C. After addition of the acetic anhydride, the external ice bath was removed and the solution stirred at room temperature during 24 h. The solution was treated with water (60 ml) and stirred for 1 hr. The solvent was removed under reduced pressure to yield a white residue. This residue was recrystallized from water to yield the pure product (Muramatsu, 1965). Yield 72%. Colourless crystals suitable for X-ray diffraction were obtained by evaporation of water at room temperature in a fume hood over a period of 2 days.
Friedel pairs were merged before the final refinement. Hydrogen atoms H1 and H6 were placed as observed in the Fourier map and refined. All other hydrogen atoms were placed in calculated positions, with methyl C—H distances of 0.96 Å and methine C—H distances of 0.98 Å, and were refined using a riding model, with Uiso(H)=1.2Ueq of the parent atom. The iso-propyl group is disordered over two positions, with site occupancy factors of 0.784 (5) and 0.216 (5) for atoms C4A and C4B respectively.
The title compound (I) was used as a source of chirality for various pentacycloundecane ligands (Boyle et al., 2004a) and macrocycles (Boyle et al., 2004b) that were synthesized for applications in asymmetric catalysis. Here we report the crystal stucture of the title compound, (I). The compound was derived from commercially available (S)-(+)-valine and exists as a single enantiomer since the stereochemistry of the amino acid is unchanged during the reaction. The geometry and labelling scheme employed for the molecule is illustrated in Fig. 1.
In the molecule the iso-propyl moiety is disordered over two positions, with site occupancy factors of 0.82 and 0.18 for atoms C4A and C4B respectively. Atoms C1, C2, C3 and C5 are co-planar.
The molecules are involved in intermolecular O—H···O and N—H···O hydrogen bonding. The hydrogen bonding geometry is listed in Table 1. The molecular packing and hydrogen bonding interactions are illustrated in Fig. 2. The O2—H2A···O3i ((i) -x + 3/2, -y + 1, z - 1/2) interaction links molecules in a head to tail fashion to form a corrugated, one-dimensional hydrogen bonded chain that extends along the a-direction. Neighbouring chains are connected via the N1—H1O···O1ii ((ii)-x + 2, y - 1/2, -z + 1/2) interaction. It is interesting to note that each chain interacts with four other chains, two above it and two below it, when viewed down the a axis. In the interaction with the chains above, one of the neighbouring chains act as N—H···O hydrogen bond donor to the chain considered, while the second chain above acts as hydrogen bond acceptor to the chain under discussion. The same is true for the interactions to the hydrogen bonded chains below the chain. A three-dimensional hydrogen bonding network results, with the smallest hydrogen bonded ring described by the graph set notation R66(34).
For related literature, see: Boyle et al. (2004a,b, 2007); Muramatsu (1965).
Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Mercury (Bruno et al., 2002); software used to prepare material for publication: PLATON (Spek, 2003) and WinGX (Farrugia, 1999).
C6H11NO3 | F(000) = 312 |
Mr = 145.16 | Dx = 1.174 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2582 reflections |
a = 7.0760 (6) Å | θ = 4.0–32.0° |
b = 9.5221 (8) Å | µ = 0.09 mm−1 |
c = 12.1934 (12) Å | T = 291 K |
V = 821.57 (13) Å3 | Plate, colourless |
Z = 4 | 0.20 × 0.20 × 0.05 mm |
Oxford Diffraction Xcalibur2 diffractometer | 1234 independent reflections |
Radiation source: fine-focus sealed tube | 780 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
ω scans | θmax = 28.7°, θmin = 4.0° |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006) | h = −9→9 |
Tmin = 0.962, Tmax = 0.995 | k = −12→9 |
7394 measured reflections | l = −16→16 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.132 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | w = 1/[σ2(Fo2) + (0.1363P)2] where P = (Fo2 + 2Fc2)/3 |
1234 reflections | (Δ/σ)max < 0.001 |
107 parameters | Δρmax = 0.16 e Å−3 |
17 restraints | Δρmin = −0.19 e Å−3 |
C6H11NO3 | V = 821.57 (13) Å3 |
Mr = 145.16 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.0760 (6) Å | µ = 0.09 mm−1 |
b = 9.5221 (8) Å | T = 291 K |
c = 12.1934 (12) Å | 0.20 × 0.20 × 0.05 mm |
Oxford Diffraction Xcalibur2 diffractometer | 1234 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006) | 780 reflections with I > 2σ(I) |
Tmin = 0.962, Tmax = 0.995 | Rint = 0.023 |
7394 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 17 restraints |
wR(F2) = 0.132 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | Δρmax = 0.16 e Å−3 |
1234 reflections | Δρmin = −0.19 e Å−3 |
107 parameters |
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 | Occ. (<1) | |
O3 | 0.8283 (3) | 0.57349 (19) | 0.48653 (15) | 0.0656 (6) | |
O2 | 0.8665 (3) | 0.42040 (17) | 0.16325 (16) | 0.0678 (6) | |
H2A | 0.8101 | 0.4268 | 0.1047 | 0.081* | |
O1 | 0.9249 (3) | 0.64337 (18) | 0.13073 (16) | 0.0779 (7) | |
C6 | 0.8854 (4) | 0.4570 (3) | 0.45614 (19) | 0.0528 (6) | |
C2 | 1.0487 (3) | 0.5464 (2) | 0.29479 (19) | 0.0494 (6) | |
H2 | 1.0202 | 0.6363 | 0.3303 | 0.059* | |
C3 | 1.2604 (4) | 0.5434 (4) | 0.2727 (3) | 0.0826 (9) | |
H3B | 1.2864 | 0.6233 | 0.2242 | 0.099* | 0.819 (6) |
H3A | 1.2872 | 0.4475 | 0.2541 | 0.099* | 0.181 (6) |
C5 | 1.3680 (6) | 0.5682 (6) | 0.3806 (4) | 0.1294 (16) | |
H5A | 1.3225 | 0.5044 | 0.4355 | 0.155* | |
H5B | 1.3482 | 0.6631 | 0.4046 | 0.155* | |
H5C | 1.5006 | 0.5526 | 0.3689 | 0.155* | |
C4A | 1.3294 (6) | 0.4166 (5) | 0.2145 (4) | 0.1077 (18) | 0.819 (6) |
H4A3 | 1.4634 | 0.4237 | 0.2036 | 0.129* | 0.819 (6) |
H4A1 | 1.2676 | 0.4092 | 0.1446 | 0.129* | 0.819 (6) |
H4A2 | 1.3018 | 0.3346 | 0.2575 | 0.129* | 0.819 (6) |
C4B | 1.334 (3) | 0.6303 (19) | 0.1810 (11) | 0.087 (6) | 0.181 (6) |
H4B1 | 1.4683 | 0.6182 | 0.1755 | 0.104* | 0.181 (6) |
H4B2 | 1.3058 | 0.7273 | 0.1947 | 0.104* | 0.181 (6) |
H4B3 | 1.2754 | 0.6015 | 0.1137 | 0.104* | 0.181 (6) |
H6 | 0.855 (6) | 0.366 (4) | 0.492 (3) | 0.104* | |
H1 | 1.013 (6) | 0.354 (4) | 0.357 (3) | 0.104* | |
N1 | 0.9895 (3) | 0.4357 (2) | 0.36939 (16) | 0.0505 (5) | |
C1 | 0.9393 (3) | 0.5421 (2) | 0.18868 (18) | 0.0473 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O3 | 0.0753 (12) | 0.0554 (10) | 0.0662 (11) | 0.0019 (9) | 0.0235 (10) | −0.0055 (8) |
O2 | 0.0863 (13) | 0.0493 (10) | 0.0677 (11) | −0.0118 (10) | −0.0304 (10) | 0.0097 (8) |
O1 | 0.1141 (17) | 0.0465 (10) | 0.0730 (12) | −0.0149 (11) | −0.0281 (13) | 0.0134 (10) |
C6 | 0.0603 (14) | 0.0536 (15) | 0.0443 (11) | −0.0022 (13) | 0.0000 (11) | 0.0018 (11) |
C2 | 0.0581 (14) | 0.0455 (12) | 0.0445 (11) | −0.0007 (11) | 0.0020 (11) | 0.0003 (11) |
C3 | 0.0542 (16) | 0.116 (3) | 0.0779 (18) | −0.011 (2) | −0.0072 (15) | 0.015 (2) |
C5 | 0.090 (3) | 0.171 (4) | 0.128 (3) | −0.027 (3) | −0.050 (3) | 0.015 (3) |
C4A | 0.061 (2) | 0.157 (4) | 0.106 (3) | 0.024 (3) | 0.019 (2) | 0.001 (3) |
C4B | 0.078 (11) | 0.098 (13) | 0.083 (12) | −0.037 (10) | 0.017 (10) | 0.003 (11) |
N1 | 0.0673 (12) | 0.0412 (10) | 0.0431 (9) | 0.0048 (10) | 0.0042 (10) | −0.0006 (9) |
C1 | 0.0544 (13) | 0.0406 (11) | 0.0468 (12) | −0.0028 (10) | 0.0004 (11) | 0.0017 (11) |
O3—C6 | 1.238 (3) | C3—H3B | 0.98 |
O2—C1 | 1.305 (3) | C3—H3A | 0.96 |
O2—H2A | 0.8200 | C5—H5A | 0.96 |
O1—C1 | 1.200 (3) | C5—H5B | 0.96 |
C6—N1 | 1.305 (3) | C5—H5C | 0.96 |
C6—H6 | 0.99 (4) | C4A—H4A3 | 0.96 |
C2—N1 | 1.454 (3) | C4A—H4A1 | 0.96 |
C2—C1 | 1.508 (3) | C4A—H4A2 | 0.96 |
C2—C3 | 1.522 (4) | C4B—H4B1 | 0.96 |
C2—H2 | 0.98 | C4B—H4B2 | 0.96 |
C3—C4A | 1.484 (4) | C4B—H4B3 | 0.96 |
C3—C4B | 1.484 (5) | N1—H1 | 0.81 (4) |
C3—C5 | 1.539 (5) | ||
C1—O2—H2A | 109.5 | H5A—C5—H5B | 109.5 |
O3—C6—N1 | 124.5 (2) | C3—C5—H5C | 109.5 |
O3—C6—H6 | 126 (2) | H5A—C5—H5C | 109.5 |
N1—C6—H6 | 110 (2) | H5B—C5—H5C | 109.5 |
N1—C2—C1 | 111.65 (18) | C3—C4A—H4A3 | 109.5 |
N1—C2—C3 | 112.4 (2) | C3—C4A—H4A1 | 109.5 |
C1—C2—C3 | 110.6 (2) | H4A3—C4A—H4A1 | 109.5 |
N1—C2—H2 | 107.3 | C3—C4A—H4A2 | 109.5 |
C1—C2—H2 | 107.3 | H4A3—C4A—H4A2 | 109.5 |
C3—C2—H2 | 107.3 | H4A1—C4A—H4A2 | 109.5 |
C4A—C3—C2 | 115.1 (3) | C3—C4B—H4B1 | 109.5 |
C4B—C3—C2 | 117.9 (9) | C3—C4B—H4B2 | 109.5 |
C4A—C3—C5 | 111.8 (4) | H4B1—C4B—H4B2 | 109.5 |
C4B—C3—C5 | 112.6 (8) | C3—C4B—H4B3 | 109.5 |
C2—C3—C5 | 109.4 (3) | H4B1—C4B—H4B3 | 109.5 |
C4A—C3—H3B | 106.4 | H4B2—C4B—H4B3 | 109.5 |
C2—C3—H3B | 106.1 | C6—N1—C2 | 123.9 (2) |
C5—C3—H3B | 107.7 | C6—N1—H1 | 115 (3) |
C4B—C3—H3A | 106.5 | C2—N1—H1 | 121 (3) |
C2—C3—H3A | 104.7 | O1—C1—O2 | 122.7 (2) |
C5—C3—H3A | 104.5 | O1—C1—C2 | 121.8 (2) |
C3—C5—H5A | 109.5 | O2—C1—C2 | 115.51 (18) |
C3—C5—H5B | 109.5 | ||
N1—C2—C3—C4A | 64.7 (4) | C1—C2—N1—C6 | −105.3 (3) |
C1—C2—C3—C4A | −60.8 (4) | C3—C2—N1—C6 | 129.6 (3) |
N1—C2—C3—C4B | 167.5 (9) | N1—C2—C1—O1 | 157.9 (2) |
C1—C2—C3—C4B | 41.9 (9) | C3—C2—C1—O1 | −76.1 (3) |
N1—C2—C3—C5 | −62.1 (3) | N1—C2—C1—O2 | −23.8 (3) |
C1—C2—C3—C5 | 172.3 (3) | C3—C2—C1—O2 | 102.2 (3) |
O3—C6—N1—C2 | −1.6 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2A···O3i | 0.82 | 1.74 | 2.559 (2) | 173 |
N1—H1···O1ii | 0.81 (4) | 2.06 (4) | 2.849 (3) | 165 (4) |
Symmetry codes: (i) −x+3/2, −y+1, z−1/2; (ii) −x+2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C6H11NO3 |
Mr | 145.16 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 291 |
a, b, c (Å) | 7.0760 (6), 9.5221 (8), 12.1934 (12) |
V (Å3) | 821.57 (13) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.20 × 0.20 × 0.05 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur2 |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2006) |
Tmin, Tmax | 0.962, 0.995 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7394, 1234, 780 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.675 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.132, 0.98 |
No. of reflections | 1234 |
No. of parameters | 107 |
No. of restraints | 17 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.19 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), Mercury (Bruno et al., 2002), PLATON (Spek, 2003) and WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2A···O3i | 0.82 | 1.74 | 2.559 (2) | 173.4 |
N1—H1···O1ii | 0.81 (4) | 2.06 (4) | 2.849 (3) | 165 (4) |
Symmetry codes: (i) −x+3/2, −y+1, z−1/2; (ii) −x+2, y−1/2, −z+1/2. |
The title compound (I) was used as a source of chirality for various pentacycloundecane ligands (Boyle et al., 2004a) and macrocycles (Boyle et al., 2004b) that were synthesized for applications in asymmetric catalysis. Here we report the crystal stucture of the title compound, (I). The compound was derived from commercially available (S)-(+)-valine and exists as a single enantiomer since the stereochemistry of the amino acid is unchanged during the reaction. The geometry and labelling scheme employed for the molecule is illustrated in Fig. 1.
In the molecule the iso-propyl moiety is disordered over two positions, with site occupancy factors of 0.82 and 0.18 for atoms C4A and C4B respectively. Atoms C1, C2, C3 and C5 are co-planar.
The molecules are involved in intermolecular O—H···O and N—H···O hydrogen bonding. The hydrogen bonding geometry is listed in Table 1. The molecular packing and hydrogen bonding interactions are illustrated in Fig. 2. The O2—H2A···O3i ((i) -x + 3/2, -y + 1, z - 1/2) interaction links molecules in a head to tail fashion to form a corrugated, one-dimensional hydrogen bonded chain that extends along the a-direction. Neighbouring chains are connected via the N1—H1O···O1ii ((ii)-x + 2, y - 1/2, -z + 1/2) interaction. It is interesting to note that each chain interacts with four other chains, two above it and two below it, when viewed down the a axis. In the interaction with the chains above, one of the neighbouring chains act as N—H···O hydrogen bond donor to the chain considered, while the second chain above acts as hydrogen bond acceptor to the chain under discussion. The same is true for the interactions to the hydrogen bonded chains below the chain. A three-dimensional hydrogen bonding network results, with the smallest hydrogen bonded ring described by the graph set notation R66(34).