D-Serinium D-serine nitrate

In the title compound, C₃H₈O₃N⁺·NO₃⁻·C₃H₇O₃N, the serinium and the serine as zwitterion are held together by a strong O—H...O hydrogen bond. The serinium cation has a gauche I conformation and the serine mol­ecule has a gauche II conformation for the hydroxyl O atom. The nitrate anion links the amino N atom of mol­ecule 1 extending in a chain running along the a axis.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.026
• wR factor = 0.074
• Data-to-parameter ratio = 6.2

checkCIF results

No syntax errors found



ADDSYM reports no extra symmetry

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           24.98
         From the CIF: _reflns_number_total               1030
         Count of symmetry unique reflns         1038
         Completeness (_total/calc)             99.23%
         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
          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.

---

S1. Comment

The crystal structures of L-serine (Benedetti et al., 1972), DL-serine (Shoemaker et al., 1953; Frey et al., 1973; Kistenmacher et al., 1974) and L-serine monohydrate (Frey et al., 1973) have been reported previously. In the present study, the structure determination of D-serine with nitric acid was undertaken.

The geometry of the two crystallographically independent serine and serinium constituents are similar and agree well with earlier X-ray studies of DL-serine (Shoemaker et al., 1953) and L-serine (Benedetti et al., 1972). The conformation angle ψ₁ is -1.5 (3) and -3.9 (3)° for serinium and serine, respectively. This tendency of the C—N bond to twist is found in various amino acids (Lakshminarayanan et al., 1967). The straight side-chain conformation angle χ₁ for the serinium cation is in a gauche I conformation [63.8 (3)°] and for the serine molecule is in a gauche II conformation [-66.4 (3)°].

The nitrate anion plays a vital role in the hydrogen bonding with both ions and in stabilizing the structure. Serine and serinium are connected by a strong O—H···O hydrogen bond O1B—H1B···O2A^iv. The nitrate anion, as acceptor, hydrogen bonds with the amino N and hydroxyl O atom of both molecules in a three-dimensional network. The nitrate anion links the amino N atom of the serinium cation resulting in a chain running along the a axis. The hydroxyl O atom of serinium, as acceptor, links the amino N atom of serinium.

The serine molecule is engaged in a straight (S1) head-to-tail sequence, since the N21—H21C···O2B^iv hydrogen bond connects two amino acids separated by a period along the a axis, and a zigzag (Z2) head-to-tail sequence, since N21—H21B···O2B^v connects two 2₁-related amino acids (Vijayan, 1988).

S2. Experimental

The title compound was crystallized in aqueous solution from 2:1 stoichiometric ratio of D-serine and nitric acid. Colorless needle-shaped crystals were obtained.

S3. Refinement

The reflection/parameter ratio is 6.20 in spite of the fact that data for 1030 of the possible 1038 reflections have been collected which has resulted with a reasonable final R factor of 0.0263. A l l H atoms were fixed by geometric restraints using HFIX and allowed to ride on the preceding atom.

Computing details

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1999); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. The molecular structures of the two independent serinium and serine cations showing the atomic numbering scheme and 50% probability displacement ellipsoids (Johnson, 1976).
	Fig. 2. Packing diagram of the molecule viewed down the a axis.

D-serinium D-serine nitrate

Crystal data

C3H8NO3^+·NO3^−·C3H7NO3	F(000) = 288
Mr = 273.21	Dx = 1.649 Mg m^−3 Dm = 1.63 Mg m^−3 Dm measured by flotation in bromoform and xylene
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
a = 5.929 (1) Å	Cell parameters from 25 reflections
b = 8.195 (7) Å	θ = 10.0–13.9°
c = 11.503 (2) Å	µ = 0.16 mm^−1
β = 100.06 (1)°	T = 293 K
V = 550.3 (5) Å^3	Needles, colorless
Z = 2	0.5 × 0.2 × 0.07 mm

Data collection

Enraf-Nonius sealed tube diffractometer	908 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.019
Graphite monochromator	θmax = 25.0°, θmin = 1.8°
ω–2θ scans	h = −1→7
Absorption correction: ψ scan (North et al., 1968)	k = −1→9
Tmin = 0.962, Tmax = 0.988	l = −13→13
1533 measured reflections	25 standard reflections every 3 reflections
1030 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.026	H-atom parameters not refined
wR(F^2) = 0.074	w = 1/[σ^2(Fo^2) + (0.0554P)^2 + 0.0361P] where P = (Fo^2 + 2Fc^2)/3
S = 0.95	(Δ/σ)max < 0.001
1030 reflections	Δρmax = 0.16 e Å^−3
166 parameters	Δρmin = −0.15 e Å^−3
1 restraint	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: none

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	0.2112 (4)	0.6693 (3)	0.2735 (2)	0.0291 (6)
O1	0.1846 (3)	0.7597 (3)	0.35930 (18)	0.0349 (5)
O2	0.3677 (3)	0.5658 (3)	0.28774 (18)	0.0320 (5)
O3	0.0807 (4)	0.6802 (4)	0.1785 (2)	0.0516 (7)
O1A	−0.0492 (4)	0.4171 (3)	0.40845 (17)	0.0342 (5)
O1B	0.0050 (3)	0.2719 (3)	0.25099 (16)	0.0298 (5)
H1B	−0.1147	0.3147	0.2187	0.045*
C11	0.0427 (4)	0.3090 (3)	0.3623 (2)	0.0219 (6)
C12	0.2213 (5)	0.1976 (3)	0.4321 (2)	0.0238 (6)
H12	0.1604	0.0861	0.4269	0.029*
N11	0.2616 (4)	0.2479 (3)	0.55848 (18)	0.0253 (5)
H11A	0.3664	0.1830	0.5998	0.038*
H11B	0.1313	0.2403	0.5866	0.038*
H11C	0.3111	0.3506	0.5646	0.038*
C13	0.4435 (5)	0.1979 (4)	0.3831 (3)	0.0333 (7)
H13A	0.4099	0.1742	0.2993	0.040*
H13B	0.5113	0.3059	0.3928	0.040*
O1C	0.6033 (4)	0.0821 (3)	0.43978 (19)	0.0361 (5)
H1C	0.6771	0.1225	0.4998	0.054*
O2B	0.7608 (3)	0.5252 (3)	−0.01191 (19)	0.0351 (5)
O2A	0.6496 (4)	0.3634 (3)	0.12392 (18)	0.0350 (5)
C21	0.6142 (4)	0.4583 (3)	0.0366 (2)	0.0231 (6)
C22	0.3617 (4)	0.4921 (4)	−0.0140 (2)	0.0225 (6)
H22	0.3314	0.6073	0.0003	0.027*
N21	0.2126 (4)	0.3924 (3)	0.04927 (19)	0.0245 (5)
H21A	0.2486	0.4114	0.1265	0.037*
H21B	0.2332	0.2871	0.0353	0.037*
H21C	0.0667	0.4188	0.0240	0.037*
C23	0.3054 (5)	0.4630 (4)	−0.1455 (2)	0.0293 (7)
H23A	0.1434	0.4823	−0.1728	0.035*
H23B	0.3904	0.5396	−0.1856	0.035*
O2C	0.3601 (4)	0.3023 (3)	−0.17467 (19)	0.0373 (6)
H2C	0.2485	0.2431	−0.1747	0.056*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0256 (12)	0.0321 (14)	0.0294 (12)	−0.0027 (12)	0.0037 (10)	−0.0031 (12)
O1	0.0355 (12)	0.0329 (12)	0.0365 (11)	0.0026 (11)	0.0067 (9)	−0.0116 (10)
O2	0.0291 (11)	0.0269 (11)	0.0394 (11)	0.0063 (10)	0.0043 (9)	−0.0013 (10)
O3	0.0456 (13)	0.0640 (18)	0.0378 (13)	0.0203 (13)	−0.0133 (11)	−0.0139 (12)
O1A	0.0348 (11)	0.0352 (12)	0.0326 (10)	0.0112 (10)	0.0064 (9)	−0.0028 (10)
O1B	0.0252 (10)	0.0370 (12)	0.0254 (9)	0.0058 (9)	−0.0010 (7)	−0.0021 (9)
C11	0.0194 (12)	0.0213 (15)	0.0258 (13)	−0.0034 (12)	0.0061 (10)	−0.0010 (12)
C12	0.0269 (13)	0.0203 (15)	0.0240 (13)	−0.0004 (12)	0.0033 (11)	0.0007 (12)
N11	0.0235 (11)	0.0277 (13)	0.0246 (11)	0.0004 (11)	0.0042 (9)	0.0029 (11)
C13	0.0306 (15)	0.0407 (19)	0.0305 (14)	0.0139 (14)	0.0110 (12)	0.0071 (14)
O1C	0.0354 (12)	0.0348 (12)	0.0344 (11)	0.0150 (11)	−0.0038 (9)	−0.0028 (10)
O2B	0.0217 (10)	0.0382 (14)	0.0456 (12)	−0.0026 (9)	0.0066 (9)	−0.0011 (11)
O2A	0.0285 (11)	0.0378 (12)	0.0343 (11)	0.0021 (10)	−0.0064 (9)	0.0076 (10)
C21	0.0210 (14)	0.0193 (14)	0.0288 (13)	−0.0002 (12)	0.0035 (11)	−0.0078 (12)
C22	0.0205 (14)	0.0179 (14)	0.0289 (13)	0.0003 (12)	0.0034 (11)	0.0017 (12)
N21	0.0224 (12)	0.0249 (13)	0.0273 (11)	0.0029 (10)	0.0080 (9)	0.0014 (11)
C23	0.0276 (15)	0.0316 (16)	0.0284 (14)	−0.0019 (14)	0.0045 (12)	0.0061 (13)
O2C	0.0392 (12)	0.0383 (13)	0.0352 (11)	−0.0006 (11)	0.0084 (10)	−0.0094 (10)

Geometric parameters (Å, º)

N1—O3	1.227 (3)	C13—H13B	0.9700
N1—O2	1.247 (3)	O1C—H1C	0.8200
N1—O1	1.266 (3)	O2B—C21	1.240 (4)
O1A—C11	1.210 (3)	O2A—C21	1.259 (4)
O1B—C11	1.297 (3)	C21—C22	1.534 (3)
O1B—H1B	0.8200	C22—N21	1.485 (3)
C11—C12	1.518 (4)	C22—C23	1.510 (4)
C12—N11	1.490 (3)	C22—H22	0.9800
C12—C13	1.520 (4)	N21—H21A	0.8900
C12—H12	0.9800	N21—H21B	0.8900
N11—H11A	0.8900	N21—H21C	0.8900
N11—H11B	0.8900	C23—O2C	1.411 (4)
N11—H11C	0.8900	C23—H23A	0.9700
C13—O1C	1.417 (4)	C23—H23B	0.9700
C13—H13A	0.9700	O2C—H2C	0.8200
O3—N1—O2	120.4 (2)	H13A—C13—H13B	107.9
O3—N1—O1	120.4 (2)	C13—O1C—H1C	109.5
O2—N1—O1	119.2 (2)	O2B—C21—O2A	126.9 (2)
C11—O1B—H1B	109.5	O2B—C21—C22	117.6 (2)
O1A—C11—O1B	126.3 (3)	O2A—C21—C22	115.5 (2)
O1A—C11—C12	122.3 (2)	N21—C22—C23	111.0 (2)
O1B—C11—C12	111.4 (2)	N21—C22—C21	109.8 (2)
N11—C12—C11	109.1 (2)	C23—C22—C21	112.5 (2)
N11—C12—C13	111.1 (2)	N21—C22—H22	107.8
C11—C12—C13	111.9 (2)	C23—C22—H22	107.8
N11—C12—H12	108.2	C21—C22—H22	107.8
C11—C12—H12	108.2	C22—N21—H21A	109.5
C13—C12—H12	108.2	C22—N21—H21B	109.5
C12—N11—H11A	109.5	H21A—N21—H21B	109.5
C12—N11—H11B	109.5	C22—N21—H21C	109.5
H11A—N11—H11B	109.5	H21A—N21—H21C	109.5
C12—N11—H11C	109.5	H21B—N21—H21C	109.5
H11A—N11—H11C	109.5	O2C—C23—C22	111.5 (2)
H11B—N11—H11C	109.5	O2C—C23—H23A	109.3
O1C—C13—C12	112.4 (2)	C22—C23—H23A	109.3
O1C—C13—H13A	109.1	O2C—C23—H23B	109.3
C12—C13—H13A	109.1	C22—C23—H23B	109.3
O1C—C13—H13B	109.1	H23A—C23—H23B	108.0
C12—C13—H13B	109.1	C23—O2C—H2C	109.5
O1A—C11—C12—N11	−1.5 (3)	O2B—C21—C22—N21	175.7 (2)
O1B—C11—C12—N11	178.7 (2)	O2A—C21—C22—N21	−3.9 (3)
O1A—C11—C12—C13	−124.8 (3)	O2B—C21—C22—C23	51.6 (3)
O1B—C11—C12—C13	55.4 (3)	O2A—C21—C22—C23	−128.0 (3)
N11—C12—C13—O1C	63.8 (3)	N21—C22—C23—O2C	−66.4 (3)
C11—C12—C13—O1C	−174.0 (2)	C21—C22—C23—O2C	57.0 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N11—H11A···O2^i	0.89	2.09	2.972 (3)	170
N11—H11B···O1^ii	0.89	2.08	2.963 (3)	171
N11—H11C···O1C^iii	0.89	1.97	2.853 (4)	173
O1C—H1C···O1^i	0.82	2.02	2.833 (3)	168
O1C—H1C···O2^i	0.82	2.55	3.112 (3)	127
O1B—H1B···O2A^iv	0.82	1.66	2.462 (3)	164
N21—H21A···O2	0.89	2.25	3.084 (3)	155
N21—H21A···O1B	0.89	2.48	2.979 (3)	116
N21—H21A···O3	0.89	2.53	2.965 (4)	111
N21—H21B···O2B^v	0.89	2.16	3.048 (4)	172
N21—H21C···O2B^iv	0.89	1.99	2.863 (3)	167
O2C—H2C···O3^vi	0.82	2.01	2.792 (3)	159

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