L-Serine III at 8.0 GPa

The structure of a new high-pressure polymorph of L-serine (form III), C₃H₇NO₃, was solved and refined at 8 GPa by single-crystal X-ray diffraction in a diamond anvil cell in situ. The existence of this form was supposed from Raman spectroscopy [Kolesnik et al. (2005). Dokl. Phys. Chem. 404, 61-64 (in Russian), 169-172 (in English)], but its structure remained unknown. Form III preserves the space group P2₁2₁2₁ of the two other forms of L-serine; the conformation of the zwitterion and the inter­molecular hydrogen bonding in form III differ from those in forms I and II.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.016 Å
• R factor = 0.045
• wR factor = 0.087
• Data-to-parameter ratio = 7.2

checkCIF/PLATON results

No syntax errors found



Alert level A
ATOM007_ALERT_1_A  _atom_site_aniso_label is missing
            Unique label identifying the atom site.

Author Response: Non-hydrogen atoms were refined isotropically, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ.

GOODF01_ALERT_2_A  The least squares goodness of fit parameter lies
            outside the range 0.40 <> 6.00
            Goodness of fit given =      0.388

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. This has affected goodness of fit parameter.

THETM01_ALERT_3_A  The value of sine(theta_max)/wavelength is less than 0.550
            Calculated sin(theta_max)/wavelength =    0.4808

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. No measurable reflections could be collected at higher theta angles.

PLAT023_ALERT_3_A Resolution (too) Low [sin(th)/Lambda < 0.6].....      19.98 Deg.

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. No measurable reflections could be collected at higher theta angles.

PLAT026_ALERT_3_A Ratio Observed / Unique Reflections too Low ....         24 Perc.

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. No measurable reflections could be collected at higher theta angles.

PLAT027_ALERT_3_A _diffrn_reflns_theta_full (too) Low ............      19.98 Deg.

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. No measurable reflections could be collected at higher theta angles.

PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low .......       0.67

Author Response: Only stronger reflections in a restricted part of the reciprocal space could be collected, what is unavoidable for data sets collected from poorly diffracting organic crystals at high pressures in a diamond anvil cell in situ. No measurable reflections could be collected at higher theta angles.

Alert level B
PLAT086_ALERT_2_B Unsatisfactory S Value (Too Low or Not Given) ..       0.39
PLAT201_ALERT_2_B Isotropic non-H Atoms in Main Residue(s) .......          7
PLAT210_ALERT_3_B No Anisotropic ADP's Found in CIF ..............          ?
PLAT340_ALERT_3_B Low Bond Precision on C-C bonds (x 1000) Ang ...         17
PLAT415_ALERT_2_B Short Inter D-H..H-X       H4     ..  H5      ..       2.00 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact  O1     ..  C3      ..       2.90 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact  O1     ..  C2      ..       2.91 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact  O2     ..  C3      ..       2.91 Ang.

Alert level C
REFNR01_ALERT_3_C  Ratio of reflections to parameters is < 8 for a
            non-centrosymmetric structure, where ZMAX < 18
            sine(theta)/lambda                0.4808
            Proportion of unique data used    1.0000
            Ratio reflections to parameters   7.2333
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       7.23
PLAT415_ALERT_2_C Short Inter D-H..H-X       H6     ..  H7      ..       2.10 Ang.
PLAT432_ALERT_2_C Short Inter X...Y Contact  O3     ..  C1      ..       2.95 Ang.
PLAT432_ALERT_2_C Short Inter X...Y Contact  C1     ..  C2      ..       3.12 Ang.

Alert level G
REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values
           From the CIF: _diffrn_reflns_theta_max           19.98
           From the CIF: _reflns_number_total                217
           From the CIF: _diffrn_reflns_limit_ max hkl    5.    4.    8.
           From the CIF: _diffrn_reflns_limit_ min hkl   -5.   -4.   -8.
           TEST1: Expected hkl limits for theta max
           Calculated maximum hkl    5.    6.    9.
           Calculated minimum hkl   -5.   -6.   -9.
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           19.98
           From the CIF: _reflns_number_total                217
           Count of symmetry unique reflns          218
           Completeness (_total/calc)             99.54%
           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

   7 ALERT level A = In general: serious problem
   8 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  10 ALERT type 2 Indicator that the structure model may be wrong or deficient
   9 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: in house program, fixed φ mode (Finger & King, 1978); cell refinement: in-home program, reflections in 8 positions (King & Finger, 1979); data reduction: in-home program, profile analysis; program(s) used to solve structure: starting model for L-serine II (Moggach et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PowderCell (Kraus & Nolze, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999) and SHELXL97.

L-serine

Crystal data

C3H7NO3	F(000) = 224
Mr = 105.10	Dx = 1.991 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 16 reflections
a = 5.6117 (9) Å	θ = 8–22°
b = 6.556 (2) Å	µ = 0.18 mm^−1
c = 9.5321 (12) Å	T = 295 K
V = 350.69 (13) Å^3	Block, colourless
Z = 4	0.16 × 0.08 × 0.05 mm

Data collection

Stoe four-circle diffractometer	Rint = 0.071
Radiation source: fine-focus sealed tube	θmax = 20.0°, θmin = 3.8°
Graphite monochromator	h = −5→5
fixed–φ mode, ω scans	k = −4→4
426 measured reflections	l = −8→8
217 independent reflections	2 standard reflections every 20 reflections
53 reflections with I > 2σ(I)	intensity decay: none

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.087	H-atom parameters constrained
S = 0.39	w = 1/[σ^2(Fo^2)
217 reflections	(Δ/σ)max < 0.001
30 parameters	Δρmax = 0.17 e Å^−3
0 restraints	Δρmin = −0.20 e Å^−3

Special details

Experimental. Hydrostatic pressure 8 GPa was created in the DAC without Be-supports (Ahsbahs, 2004). Gasket material: Thyrodur-2709, starting thickness 0.220 mm, preindented to 0.100 mm and then hardened by heating/cooling (Ahsbahs, 1996), hole diameter 0.300 mm. Absolute methanol to ethanol of 4:1 volume ratio was used as pressure-transmitting liquid (Fujishiro et al., 1981).

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	−0.015 (2)	0.225 (3)	0.2179 (12)	0.005 (3)*
C2	0.233 (2)	0.160 (3)	0.2521 (11)	0.007 (3)*
H1	0.2514	0.0147	0.2298	0.009*
C3	0.297 (2)	0.193 (3)	0.4005 (12)	0.019 (4)*
H6	0.1797	0.1310	0.4616	0.023*
H5	0.4516	0.1333	0.4206	0.023*
N1	0.4054 (14)	0.278 (3)	0.1691 (10)	0.008 (3)*
H3	0.5528	0.2397	0.1915	0.012*
H4	0.3874	0.4102	0.1875	0.012*
H2	0.3804	0.2556	0.0782	0.012*
O1	−0.0521 (12)	0.303 (3)	0.1009 (8)	0.015 (3)*
O2	−0.1719 (15)	0.1822 (19)	0.3068 (6)	0.011 (3)*
O3	0.3045 (18)	0.4089 (18)	0.4226 (11)	0.005 (2)*
H7	0.3169	0.4326	0.5068	0.008*

Geometric parameters (Å, º)

C1—O1	1.244 (12)	C3—H6	0.9700
C1—O2	1.254 (11)	C3—H5	0.9700
C1—C2	1.492 (16)	N1—H3	0.8900
C2—N1	1.469 (16)	N1—H4	0.8900
C2—C3	1.476 (13)	N1—H2	0.8900
C2—H1	0.9800	O3—H7	0.8200
C3—O3	1.430 (19)
O1—C1—O2	125.4 (11)	C2—C3—H6	110.3
O1—C1—C2	118.0 (10)	O3—C3—H5	110.3
O2—C1—C2	116.4 (9)	C2—C3—H5	110.3
N1—C2—C3	106.1 (11)	H6—C3—H5	108.5
N1—C2—C1	110.2 (11)	C2—N1—H3	109.5
C3—C2—C1	113.2 (10)	C2—N1—H4	109.5
N1—C2—H1	109.1	H3—N1—H4	109.5
C3—C2—H1	109.1	C2—N1—H2	109.5
C1—C2—H1	109.1	H3—N1—H2	109.5
O3—C3—C2	107.2 (11)	H4—N1—H2	109.5
O3—C3—H6	110.3	C3—O3—H7	109.5
O1—C1—C2—N1	25 (2)	O2—C1—C2—C3	−41 (2)
O2—C1—C2—N1	−159.9 (13)	N1—C2—C3—O3	53.8 (14)
O1—C1—C2—C3	143.7 (15)	C1—C2—C3—O3	−67.2 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H3···O2^i	0.89	1.93	2.782 (11)	159
N1—H3···O1^i	0.89	2.41	3.117 (11)	136
N1—H4···O2^ii	0.89	2.16	2.966 (19)	151
N1—H2···O1^iii	0.89	1.79	2.639 (12)	159
O3—H7···O2^iv	0.82	1.93	2.651 (13)	146
O3—H7···O1^v	0.82	2.36	2.898 (15)	124
N1—H3···O3^vi	0.89	2.55	3.04 (2)	115

Symmetry codes: (i) x+1, y, z; (ii) −x, y+1/2, −z+1/2; (iii) x+1/2, −y+1/2, −z; (iv) x+1/2, −y+1/2, −z+1; (v) −x+1/2, −y+1, z+1/2; (vi) −x+1, y−1/2, −z+1/2.