(3S,4S)-4-Amino-5-phenyl­pentane-1,3-diol

The title compound, C₁₁H₁₇NO₂, was obtained by hydrogeno­lysis of (3S,4S)-4-(dibenzyl­amino)-5-phenyl­pentane-1,3-diol. In the crystal structure, inter­molecular O—H...O, O—H...N and N—H...O hydrogen bonds link the mol­ecules into a sheet parallel to the ab plane.

Key indicators

• Single-crystal X-ray study
• T = 273 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.034
• wR factor = 0.100
• Data-to-parameter ratio = 7.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       7.44
PLAT420_ALERT_2_C D-H Without Acceptor       N1     -   H2N    ...          ?
PLAT731_ALERT_1_C Bond    Calc     0.87(3), Rep   0.871(10) ......       3.00 su-Rat
              N1   -H2N     1.555   1.555
PLAT735_ALERT_1_C D-H     Calc     0.87(3), Rep   0.870(10) ......       3.00 su-Rat
              N1   -H2N     1.555   1.555

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           25.00
           From the CIF: _reflns_number_total               1019
           Count of symmetry unique reflns         1037
           Completeness (_total/calc)             98.26%
           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

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

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

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Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

(3S,4S)-4-Amino-5-phenylpentane-1,3-diol

Crystal data

C11H17NO2	F(000) = 212
Mr = 195.26	Dx = 1.236 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 2218 reflections
a = 7.960 (3) Å	θ = 2.6–28.5°
b = 5.4531 (17) Å	µ = 0.09 mm^−1
c = 12.142 (4) Å	T = 273 K
β = 95.379 (6)°	Block, colourless
V = 524.7 (3) Å^3	0.56 × 0.28 × 0.18 mm
Z = 2

Data collection

Bruker APEX area-detector diffractometer	1019 independent reflections
Radiation source: fine-focus sealed tube	1006 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
φ and ω scans	θmax = 25.0°, θmin = 2.6°
Absorption correction: multi-scan SADABS (Bruker, 2001)	h = −9→8
Tmin = 0.959, Tmax = 0.987	k = −6→6
2647 measured reflections	l = −14→13

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.100	All H-atom parameters refined
S = 0.98	w = 1/[σ^2(Fo^2) + (0.0762P)^2 + 0.0605P] where P = (Fo^2 + 2Fc^2)/3
1019 reflections	(Δ/σ)max = 0.001
137 parameters	Δρmax = 0.11 e Å^−3
3 restraints	Δρmin = −0.15 e Å^−3

Special details

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
N1	0.6183 (2)	0.3623 (5)	0.08653 (15)	0.0414 (5)
O1	1.27047 (17)	0.3814 (5)	0.05291 (13)	0.0560 (6)
H1	1.3715	0.3730	0.0731	0.084*
O2	0.8704 (2)	−0.0277 (3)	0.16370 (12)	0.0402 (4)
H2	0.8340	−0.0422	0.0986	0.060*
C1	1.1776 (2)	0.2766 (5)	0.13395 (16)	0.0387 (6)
H1A	1.2247	0.3282	0.2069	0.046*
H1B	1.1844	0.0993	0.1303	0.046*
C2	0.9971 (2)	0.3558 (5)	0.11535 (16)	0.0321 (5)
H2A	0.9556	0.3238	0.0390	0.039*
H2B	0.9902	0.5310	0.1278	0.039*
C3	0.8867 (2)	0.2244 (4)	0.19073 (15)	0.0294 (5)
H3	0.9444	0.2336	0.2656	0.035*
C4	0.7157 (2)	0.3473 (5)	0.19484 (15)	0.0321 (5)
H4	0.7358	0.5151	0.2218	0.039*
C5	0.6085 (2)	0.2179 (5)	0.27469 (16)	0.0403 (6)
H5A	0.4984	0.2954	0.2703	0.048*
H5B	0.5923	0.0489	0.2512	0.048*
C6	0.6826 (2)	0.2207 (5)	0.39287 (16)	0.0334 (5)
C7	0.7870 (3)	0.0374 (5)	0.43539 (19)	0.0405 (6)
H7	0.8105	−0.0947	0.3909	0.049*
C8	0.8575 (3)	0.0465 (5)	0.5431 (2)	0.0499 (7)
H8	0.9299	−0.0775	0.5706	0.060*
C9	0.8211 (3)	0.2381 (6)	0.60966 (18)	0.0519 (7)
H9	0.8682	0.2441	0.6826	0.062*
C10	0.7156 (3)	0.4197 (6)	0.5689 (2)	0.0518 (7)
H10	0.6901	0.5495	0.6142	0.062*
C11	0.6469 (3)	0.4115 (5)	0.46099 (19)	0.0420 (6)
H11	0.5753	0.5365	0.4336	0.050*
H1N	0.632 (4)	0.229 (4)	0.050 (2)	0.061 (10)*
H2N	0.661 (4)	0.479 (4)	0.049 (2)	0.058 (9)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0249 (8)	0.0644 (14)	0.0346 (9)	0.0041 (10)	0.0014 (7)	0.0082 (10)
O1	0.0222 (7)	0.1030 (18)	0.0428 (8)	0.0039 (9)	0.0030 (6)	0.0270 (10)
O2	0.0459 (9)	0.0363 (9)	0.0380 (8)	0.0032 (7)	0.0021 (6)	−0.0013 (7)
C1	0.0244 (9)	0.0578 (16)	0.0342 (10)	0.0036 (10)	0.0042 (7)	0.0096 (11)
C2	0.0232 (9)	0.0426 (11)	0.0303 (9)	0.0021 (9)	0.0019 (7)	0.0007 (9)
C3	0.0237 (9)	0.0387 (12)	0.0253 (8)	0.0028 (9)	−0.0005 (7)	−0.0011 (9)
C4	0.0240 (9)	0.0425 (12)	0.0298 (9)	0.0019 (9)	0.0025 (7)	0.0009 (9)
C5	0.0234 (9)	0.0617 (16)	0.0358 (10)	−0.0051 (11)	0.0036 (7)	0.0045 (12)
C6	0.0254 (9)	0.0443 (13)	0.0317 (10)	−0.0039 (9)	0.0091 (7)	0.0036 (10)
C7	0.0418 (12)	0.0394 (14)	0.0412 (11)	0.0020 (10)	0.0074 (9)	0.0004 (10)
C8	0.0491 (14)	0.0546 (17)	0.0452 (12)	0.0058 (13)	0.0006 (11)	0.0152 (12)
C9	0.0511 (13)	0.0719 (19)	0.0321 (10)	−0.0091 (15)	0.0016 (9)	0.0032 (13)
C10	0.0547 (14)	0.0588 (19)	0.0437 (12)	−0.0046 (13)	0.0144 (11)	−0.0133 (12)
C11	0.0343 (11)	0.0468 (15)	0.0460 (12)	0.0060 (11)	0.0085 (9)	0.0029 (11)

Geometric parameters (Å, º)

N1—C4	1.465 (3)	C4—H4	0.98
N1—H1N	0.868 (10)	C5—C6	1.500 (3)
N1—H2N	0.871 (10)	C5—H5A	0.97
O1—C1	1.406 (3)	C5—H5B	0.97
O1—H1	0.82	C6—C7	1.370 (3)
O2—C3	1.416 (3)	C6—C11	1.375 (3)
O2—H2	0.82	C7—C8	1.374 (4)
C1—C2	1.496 (3)	C7—H7	0.93
C1—H1A	0.97	C8—C9	1.369 (4)
C1—H1B	0.97	C8—H8	0.93
C2—C3	1.508 (3)	C9—C10	1.361 (4)
C2—H2A	0.97	C9—H9	0.93
C2—H2B	0.97	C10—C11	1.372 (3)
C3—C4	1.523 (3)	C10—H10	0.93
C3—H3	0.98	C11—H11	0.93
C4—C5	1.523 (3)
C4—N1—H1N	110 (2)	C3—C4—H4	107.7
C4—N1—H2N	108 (2)	C5—C4—H4	107.7
H1N—N1—H2N	106 (3)	C6—C5—C4	114.26 (17)
C1—O1—H1	109.5	C6—C5—H5A	108.7
C3—O2—H2	109.5	C4—C5—H5A	108.7
O1—C1—C2	109.73 (17)	C6—C5—H5B	108.7
O1—C1—H1A	109.7	C4—C5—H5B	108.7
C2—C1—H1A	109.7	H5A—C5—H5B	107.6
O1—C1—H1B	109.7	C7—C6—C11	118.5 (2)
C2—C1—H1B	109.7	C7—C6—C5	121.6 (2)
H1A—C1—H1B	108.2	C11—C6—C5	119.9 (2)
C1—C2—C3	112.16 (19)	C6—C7—C8	120.8 (2)
C1—C2—H2A	109.2	C6—C7—H7	119.6
C3—C2—H2A	109.2	C8—C7—H7	119.6
C1—C2—H2B	109.2	C9—C8—C7	119.9 (2)
C3—C2—H2B	109.2	C9—C8—H8	120.0
H2A—C2—H2B	107.9	C7—C8—H8	120.0
O2—C3—C2	111.51 (18)	C10—C9—C8	119.9 (2)
O2—C3—C4	111.82 (18)	C10—C9—H9	120.1
C2—C3—C4	112.62 (19)	C8—C9—H9	120.1
O2—C3—H3	106.8	C9—C10—C11	120.0 (2)
C2—C3—H3	106.8	C9—C10—H10	120.0
C4—C3—H3	106.8	C11—C10—H10	120.0
N1—C4—C3	113.26 (16)	C10—C11—C6	120.8 (2)
N1—C4—C5	108.44 (16)	C10—C11—H11	119.6
C3—C4—C5	111.89 (19)	C6—C11—H11	119.6
N1—C4—H4	107.7
O1—C1—C2—C3	172.8 (2)	C4—C5—C6—C11	89.1 (2)
C1—C2—C3—O2	−68.4 (2)	C11—C6—C7—C8	−1.4 (3)
C1—C2—C3—C4	164.94 (18)	C5—C6—C7—C8	178.2 (2)
O2—C3—C4—N1	−67.2 (2)	C6—C7—C8—C9	1.2 (4)
C2—C3—C4—N1	59.3 (3)	C7—C8—C9—C10	−0.3 (4)
O2—C3—C4—C5	55.7 (2)	C8—C9—C10—C11	−0.4 (4)
C2—C3—C4—C5	−177.81 (18)	C9—C10—C11—C6	0.2 (4)
N1—C4—C5—C6	−171.8 (2)	C7—C6—C11—C10	0.7 (3)
C3—C4—C5—C6	62.5 (3)	C5—C6—C11—C10	−178.9 (2)
C4—C5—C6—C7	−90.5 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1^i	0.82	1.96	2.763 (2)	167
O2—H2···O1^ii	0.82	1.99	2.805 (2)	172
N1—H1N···O1^ii	0.87 (1)	2.43 (1)	3.288 (3)	168 (3)
N1—H2N···O1^iii	0.87 (1)	2.60 (1)	3.456 (3)	167 (3)

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