A high-pressure polymorph of l-α-leucine

Yamashita, M.; Inomata, S.; Ishikawa, K.; Kashiwagi, T.; Matsuo, H.; Sawamura, S.; Kato, M.

doi:10.1107/S1600536807018764

A high-pressure polymorph of L-α-leucine

M. Yamashita, S. Inomata, K. Ishikawa, T. Kashiwagi, H. Matsuo, S. Sawamura and M. Kato

A new high-pressure phase of the title amino acid (systematic name: 2-ammonio-4-methylpentanoate), C₆H₁₃NO₂, is reported, with one molecule per asymmetric unit, in contrast to the atmospheric pressure phase, (I), reported by Harding & Howieson [Acta Cryst. (1976). B32, 633–634], which has two molecules in the asymmetric unit. The packing consists of a double layer structure, similar to those of (I) and other amino acids with non-polar side chains.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807018764/bg2041sup1.cif Contains datablocks global, III
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807018764/bg2041IIIsup2.hkl Contains datablock III

CCDC reference: 646718

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Key indicators

Single-crystal X-ray study
T = 296 K
Mean (C-C) = 0.009 Å
R factor = 0.033
wR factor = 0.104
Data-to-parameter ratio = 10.0

checkCIF/PLATON results

No syntax errors found





Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.95

Alert level C
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ....       0.94
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.42 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.34 Ratio
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C4
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          9
PLAT432_ALERT_2_C Short Inter X...Y Contact  C2     ..  C2      ..       3.17 Ang.

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           79.47
           From the CIF: _reflns_number_total                834
           Count of symmetry unique reflns          889
           Completeness (_total/calc)             93.81%
           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 C1     = .          S

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   6 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 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


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: Specially-designed pressure vessels were needed for high pressure crystallization. Sawamura and Kato designed the pressure vessels, and prepared the budget for this work. Yamashita, Inomata, and Matsuo took charge of building the high-pressure crystallization system, sample preparation, pressure control, density measurement and infrared spectra measurement. Ishikawa and Kashiwagi performed X-ray diffraction experiments and refinement.


   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

Computing details top

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1988); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: TEXSAN; molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: TEXSAN.

2-ammonio-4-methylpentanoate top

Crystal data top

C₆H₁₃NO₂	F(000) = 288.00
M_r = 131.17	D_x = 1.173 Mg m⁻³ D_m = 1.168 Mg m⁻³ D_m measured by not measured
Monoclinic, C2	Cu Kα radiation, λ = 1.5418 Å
Hall symbol: C 2y	Cell parameters from 25 reflections
a = 8.807 (3) Å	θ = 28.4–29.6°
b = 5.975 (1) Å	µ = 0.72 mm⁻¹
c = 14.193 (3) Å	T = 296 K
β = 96.17 (2)°	Prism, colourless
V = 742.5 (3) Å³	0.40 × 0.40 × 0.20 mm
Z = 4

Data collection top

Rigaku AFC-5S diffractometer	756 reflections with F² > 2σ(F²)
Radiation source: sealed X-ray tube	R_int = 0.024
Graphite monochromator	θ_max = 79.5°
ω–2θ scans	h = −10→0
Absorption correction: ψ scan (North et al., 1968)	k = −7→7
T_min = 0.738, T_max = 0.868	l = −17→18
1570 measured reflections	3 standard reflections every 150 reflections
834 independent reflections	intensity decay: 2.9%

Refinement top

Refinement on F²	0 constraints
Least-squares matrix: full	H-atom parameters not refined
R[F² > 2σ(F²)] = 0.033	w = 1/[σ²(F_o²) + (0.05(Max(F_o²,0) + 2F_c²)/3)²]
wR(F²) = 0.104	(Δ/σ)_max = 0.017
S = 1.50	Δρ_max = 0.17 e Å⁻³
834 reflections	Δρ_min = −0.15 e Å⁻³
83 parameters	Extinction correction: Zachariasen (1967) type 2, Gaussian isotropic
0 restraints	Extinction coefficient: 0.11 (2)

Special details top

Experimental. A value of '_diffrn_measured_fraction_theta_full' is slightly low. The reason is the blind region caused by the chi circle of the four-circle diffractometer.

Geometry. Some bad geometries such as a relatively high U_eq value of C4 atom and a relatively short contact between C2 atoms were observed. The crystal was crystallized under a high pressure (400 MPa) and the data collection was carried out at a normal pressure condition. Actually, the peak profile of the diffraction was not so good. The stress brought by the change of the pressure may cause the bad effect to the crystal quality and the resulting structure.

Refinement. Refinement was carried out using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt). Because of the small anomalous dispersion effects, the Flack parameter resulted in the meaningless value (-0.31 (21)). Therefore, in order to improve data quality, the final cycles of refinement were performed using the reflection data in which Friedl pairs were merged and averaged, and the Flack parameter was not refined.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.4071 (1)	0.592 (2)	0.60053 (9)	0.0373 (3)
O2	0.5502 (2)	0.900 (2)	0.6072 (1)	0.0421 (4)
N1	0.7934 (2)	0.640 (2)	0.5727 (1)	0.0308 (3)
C1	0.6790 (2)	0.559 (2)	0.6351 (1)	0.0300 (4)
C2	0.5317 (2)	0.693 (2)	0.6121 (1)	0.0300 (4)
C3	0.7453 (2)	0.591 (2)	0.7382 (1)	0.0395 (5)
C4	0.6481 (3)	0.493 (2)	0.8107 (2)	0.0534 (6)
C5	0.6636 (4)	0.239 (2)	0.8159 (2)	0.0750 (9)
C6	0.6968 (6)	0.595 (2)	0.9079 (2)	0.103 (1)
H1	0.6594	0.4026	0.6233	0.0365*
H2	0.7558	0.7455	0.7499	0.0486*
H3	0.8430	0.5206	0.7466	0.0486*
H4	0.5441	0.5268	0.7925	0.0657*
H5	0.7669	0.1987	0.8356	0.0911*
H6	0.6341	0.1747	0.7551	0.0911*
H7	0.5998	0.1798	0.8600	0.0911*
H8	0.8005	0.5607	0.9265	0.1220*
H9	0.6353	0.5318	0.9531	0.1220*
H10	0.6818	0.7507	0.9049	0.1220*
H11	0.8854	0.5561	0.5855	0.0376*
H12	0.7542	0.6195	0.5083	0.0376*
H13	0.8133	0.7930	0.5849	0.0376*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0243 (6)	0.0374 (7)	0.0493 (7)	−0.0031 (5)	−0.0006 (5)	0.0008 (6)
O2	0.0252 (7)	0.0277 (6)	0.0723 (10)	0.0064 (5)	0.0009 (6)	−0.0016 (6)
N1	0.0237 (7)	0.0275 (7)	0.0408 (7)	0.0045 (6)	0.0018 (5)	−0.0002 (5)
C1	0.0248 (8)	0.0271 (8)	0.0377 (7)	0.0034 (6)	0.0014 (6)	−0.0002 (6)
C2	0.0251 (8)	0.0283 (7)	0.0360 (8)	0.0038 (6)	0.0006 (6)	−0.0023 (6)
C3	0.037 (1)	0.040 (1)	0.0393 (8)	0.0054 (8)	−0.0062 (6)	−0.0007 (7)
C4	0.051 (1)	0.067 (1)	0.043 (1)	0.014 (1)	0.0085 (9)	0.0078 (9)
C5	0.093 (2)	0.065 (1)	0.066 (2)	−0.019 (2)	0.000 (2)	0.012 (1)
C6	0.184 (4)	0.083 (2)	0.041 (1)	0.007 (3)	0.012 (2)	−0.004 (1)

Geometric parameters (Å, º) top

O1—C2	1.248 (8)	C3—H3	0.954
O2—C2	1.250 (17)	C4—C5	1.525 (17)
N1—C1	1.493 (3)	C4—C6	1.526 (5)
N1—H11	0.955	C4—H4	0.947
N1—H12	0.951	C5—H5	0.954
N1—H13	0.941	C5—H6	0.954
C1—C2	1.530 (9)	C5—H7	0.954
C1—C3	1.528 (3)	C6—H8	0.946
C1—H1	0.960	C6—H9	0.960
C3—C4	1.526 (4)	C6—H10	0.941
C3—H2	0.942

O1···N1ⁱ	2.884 (2)	O1···O2ⁱ	3.530 (9)
O1···N1ⁱⁱ	2.893 (16)	O2···N1ⁱⁱⁱ	2.678 (9)
O1···C2ⁱ	3.179 (3)	O2···O2ⁱ	3.078 (4)
O1···C1ⁱ	3.355 (2)	O2···N1^iv	3.351 (8)
O1···O2ⁱⁱ	3.357 (6)	O2···C2ⁱ	3.355 (7)
O1···N1ⁱⁱⁱ	3.434 (16)	O2···C1ⁱⁱⁱ	3.467 (3)
O1···O1ⁱ	3.439 (3)	N1···C2^v	3.406 (13)
O1···C1ⁱⁱⁱ	3.503 (14)	C2···C2ⁱ	3.170 (4)

C1—N1—H11	109.1	H2—C3—H3	109.9
C1—N1—H12	109.2	C3—C4—C5	111.2 (3)
C1—N1—H13	109.4	C3—C4—C6	109.4 (3)
H11—N1—H12	109.0	C3—C4—H4	109.2
H11—N1—H13	109.9	C5—C4—C6	109.9 (3)
H12—N1—H13	110.3	C5—C4—H4	107.9
N1—C1—C2	108.4 (7)	C6—C4—H4	109.2
N1—C1—C3	108.3 (2)	C4—C5—H5	110.1
N1—C1—H1	109.6	C4—C5—H6	110.1
C2—C1—C3	111.5 (5)	C4—C5—H7	110.2
C2—C1—H1	109.9	H5—C5—H6	108.8
C3—C1—H1	109.4	H5—C5—H7	108.9
O1—C2—O2	126.1 (7)	H6—C5—H7	108.8
O1—C2—C1	119.3 (11)	C4—C6—H8	109.6
O2—C2—C1	114.7 (5)	C4—C6—H9	108.9
C1—C3—C4	114.5 (5)	C4—C6—H10	109.3
C1—C3—H2	108.2	H8—C6—H9	108.9
C1—C3—H3	108.1	H8—C6—H10	110.6
C4—C3—H2	108.1	H9—C6—H10	109.4
C4—C3—H3	108.1

O1—C2—C1—N1	133.1 (5)	N1—C1—C3—C4	−173.9 (9)
O1—C2—C1—C3	−107.8 (7)	C1—C3—C4—C5	76.1 (8)
O2—C2—C1—N1	−47.3 (6)	C1—C3—C4—C6	−162.5 (8)
O2—C2—C1—C3	71.9 (7)	C2—C1—C3—C4	67.0 (12)

Symmetry codes: (i) −x+1, y, −z+1; (ii) x−1/2, y−1/2, z; (iii) x−1/2, y+1/2, z; (iv) −x+3/2, y+1/2, −z+1; (v) x+1/2, y−1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H13···O1^vi	0.940	1.972	2.890 (10)	165.100
N1—H12···O1ⁱ	0.951	1.990	2.884 (2)	155.910
N1—H11···O2^v	0.955	1.725	2.680 (8)	178.977

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

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