L Ornithine nitrate

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organic papers

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S. Ramaswamyet al. C₅H₁₃N₂O₂+NO₃ÿ DOI: 10.1107/S1600536802008358 Acta Cryst.(2002). E58, o646±o648 Acta Crystallographica Section E

Structure Reports Online

ISSN 1600-5368

L

-Ornithine nitrate

S. Ramaswamy,a_{B. Sridhar,}b

V. Ramakrishnana_and

R. K. Rajaramb_*

a_{Laser Laboratory, School of Physics, Madurai}

Kamaraj University, Madurai 625 021, India, andb_{Department of Physics, Madurai Kamaraj}

University, Madurai 625 021, India

Correspondence e-mail: [email protected]

Key indicators Single-crystal X-ray study

T= 293 K

Mean(C±C) = 0.004 AÊ

Rfactor = 0.037

wRfactor = 0.090 Data-to-parameter ratio = 7.0

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

In the title compound, C5H13N2O2+NO3ÿ, both the- and

-amino N atoms form strong NÐH O hydrogen bonds with the carboxyl group and nitrate anions. The straight side-chain conformation shows an alltransform.

Comment

Ornithine is an important amino acid, which induces the release of growth hormones and thus encourages the mechanism of muscle building. The crystal structure of l -ornithine hydrochloride (Chibaet al., 1967) has been solved. In the present study, the crystal stucture ofl-ornithine nitrate, (I), has been determined.

The asymmetric part of the asymmetric unit contains one ornithine cation and one nitrate anion. The ornithine residue contains two planar groups,viz. the carboxyl group and the aliphatic side chain. The CÐO bond distances [1.238 (3) and 1.258 (3) AÊ] and OÐCÐC angles [117.0 (2) and 116.1 (2)_{] of}

the carboxyl group indicate the resonance form shown above. The backbone conformation angle 1_[_ÿ_{39.2 (3)}_{] indicates a}

cis form. The -amino N atom deviates from the carboxyl plane by 0.854 (4) AÊ. This tendency for the CÐN bond to twist is found in various amino acids (Lakshiminarayanan et al., 1967). The side-chain conformation angles 1_, 2 _and 3

[ÿ173.5 (2), ÿ169.4 (2) and 172.2 (2)_{, respectively]}

corre-spond to transforms having a fully extended con®guration. The maximum deviation from the mean plane of the side-chain atoms is 0.151 (2) AÊ for C_{. The side-chain plane forms a}

dihedral angle of 78_{with the carboxyl plane.}

The amino atom N1 of the ornithine forms strong NÐ H O hydrogen bonds with the carboxyl and nitrate groups (Table 2). The ornithine residue is involved in both zigzag (Z2) and straight (S2) head-to-tail sequences. The-amino atom N2 forms strong NÐH O hydrogen bonds with nitrate atoms O2 and O3, and also with the carboxyl O1aatom (Fig. 2).

Experimental

The title compound was crystallized by slow evaporation from an aqueous solution ofl-ornithine and nitric acid (1:1).

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Crystal data C5H13N2O2+_NO3ÿ Mr= 195.18

Monoclinic,P21 a= 5.1944 (6) AÊ b= 7.803 (1) AÊ c= 11.050 (1) AÊ = 98.75 (1) V= 442.66 (9) AÊ3 Z= 2

Dx= 1.464 Mg mÿ3

Dm= 1.438 Mg mÿ3

Dmmeasured by ¯otation in a

mixture of carbon tetrachloride and xylene

MoKradiation Cell parameters from 24

re¯ections = 9.8±14.4 = 0.13 mmÿ1 T= 293 (2) K Needle, colorless 0.60.30.3 mm

Data collection Enraf±Nonius CAD-4

diffractometer !-2scans

Absorption correction: scan (Northet al., 1968) Tmin= 0.887,Tmax= 0.956 1295 measured re¯ections 963 independent re¯ections 919 re¯ections withI> 2(I)

Rint= 0.0316 max= 25.0 h=ÿ1!6 k=ÿ1!9 l=ÿ13!13 3 standard re¯ections

frequency: 60 min intensity decay: none

Re®nement Re®nement onF2 R[F2_{> 2}_(F2_{)] = 0.037} wR(F2_{) = 0.090} S= 1.16 838 re¯ections 119 parameters

H-atom parameters constrained

w= 1/[2_(F

o2) + (0.06P)2

+ 0.0457P]

whereP= (Fo2+ 2Fc2)/3

(/)max< 0.001 max= 0.22 e AÊÿ3 min=ÿ0.24 e AÊÿ3

Extinction correction:SHELXL97 Extinction coef®cient: 0.64 (5)

Table 1

Selected geometric parameters (AÊ,_).

O1AÐC1 1.238 (3) O1BÐC1 1.258 (3)

O1AÐC1ÐO1B 126.8 (2)

O1AÐC1ÐC2 117.02 (18) O1BÐC1ÐC2 116.14 (19)

O1AÐC1ÐC2ÐN1 ÿ39.2 (3)

N1ÐC2ÐC3ÐC4 ÿ173.54 (19) C2ÐC3ÐC4ÐC5C3ÐC4ÐC5ÐN2 ÿ169.4 (2)172.15 (18)

Table 2

Hydrogen-bonding geometry (AÊ,_).

DÐH A DÐH H A D A DÐH A

N1ÐH1A O1Bi _0.89 _1.93 _{2.813 (3)} ₁₆₉

N1ÐH1B O1ii _0.89 _1.93 _{2.818 (3)} ₁₇₂

N1ÐH1C O1Biii _0.89 _2.06 _{2.911 (3)} ₁₆₁

N2ÐH2A O2iv _0.89 _2.01 _{2.899 (4)} ₁₇₃

N2ÐH2B O3v _0.89 _2.02 _{2.911 (4)} ₁₇₉

N2ÐH2C O1Aii _0.89 _2.03 _{2.900 (3)} ₁₆₅

Symmetry codes: (i) 1ÿx;1

2y;1ÿz; (ii) 1ÿx;yÿ12;1ÿz; (iii) xÿ1;y;z; (iv)

1ÿx;yÿ3_2;₁_ÿ_z_{; (v)}_x_;_y_ÿ₁_;₁_z_.

All H atoms were placed in geometrically calculated positions and included in the re®nement in the riding-model approximation, with

Uiso equal to 1.2Ueq of the carrier atom. The Friedel pairs were

merged during the ®nal cycles of re®nement.

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

BS and RKR thank the Department of Science and Tech-nology (DST), Government of India, for ®nancial support.

References

Chiba, A., Ueki, T., Ashida, T., Sasada, Y. & Kakudo, M. (1967).Acta Cryst.22, 863±870.

Enraf±Nonius (1989).CAD-4Software. Version 5.0. Enraf±Nonius, Delft, The Netherlands.

Acta Cryst.(2002). E58, o646±o648 S. Ramaswamyet al. C₅H₁₃N₂O₂+NO₃ÿ

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organic papers

Figure 2

The packing of the title molecules, viewed down theaaxis.

Figure 1

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organic papers

o648

S. Ramaswamyet al. C₅H₁₃N₂O₂+NO₃ÿ Acta Cryst.(2002). E58, o646±o648

Johnson, C. K. (1976).ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.

Lakshiminarayanan, A. V., Sashisekharan, V. & Ramachandran, G. N. (1967). InConformation of Biopolymers, edited by G. N. Ramachandran.London: Academic Press.

North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968).Acta Cryst.A24, 351± 359.

Sheldrick, G. M. (1997). SHELXL97 and SHELXS97. University of GoÈttingen, Germany.

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Acta Cryst. (2002). E58, o646–o648

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Acta Cryst. (2002). E58, o646–o648 [https://doi.org/10.1107/S1600536802008358]

L

-Ornithine nitrate

S. Ramaswamy, B. Sridhar, V. Ramakrishnan and R. K. Rajaram

L-ornithine nitrate

Crystal data

C5H13N2O2+·NO3−

Mr = 195.18

Monoclinic, P21

a = 5.1944 (6) Å b = 7.803 (1) Å c = 11.050 (1) Å β = 98.75 (1)° V = 442.66 (9) Å3

Z = 2 F(000) = 208

Dx = 1.464 Mg m−3

Dm = 1.438 Mg m−3

Dm measured by flotation in a mixture of carbon

tetrachloride and xylene Mo Kα radiation, λ = 0.71073 Å Cell parameters from 24 reflections θ = 9.8–14.4°

µ = 0.13 mm−1

T = 293 K Needle, colorless 0.6 × 0.3 × 0.3 mm

Data collection

Enraf-Nonius CAD-4 diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

ω–2/q scans

Absorption correction: ψ scan (North et al., 1968)

Tmin = 0.887, Tmax = 0.956

1295 measured reflections

963 independent reflections 919 reflections with I > 2σ(I) Rint = 0.032

θmax = 25.0°, θmin = 1.9°

h = −1→6 k = −1→9 l = −13→13

3 standard reflections every 60 min intensity decay: none

Refinement

Refinement on F2

Least-squares matrix: full R[F2_{> 2}_σ₍_F2_{)] = 0.037}

wR(F2_{) = 0.090}

S = 1.16 838 reflections 119 parameters 1 restraint

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H-atom parameters constrained w = 1/[σ2₍_F

o2) + (0.06P)2 + 0.0457P]

where P = (Fo2 + 2Fc2)/3

(Δ/σ)max < 0.001

Δρmax = 0.22 e Å−3

Δρmin = −0.24 e Å−3

Extinction correction: SHELXL97, Fc*_{=3DkFc[1+0.001xFc}2_λ3_/sin(2_θ_)]-1/4

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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 (Å2₎

x y z Uiso*/Ueq

O1A 0.2581 (3) 0.1101 (3) 0.41866 (14) 0.0382 (5) O1B 0.6749 (3) 0.1187 (3) 0.50548 (16) 0.0352 (5) C1 0.4346 (4) 0.1404 (3) 0.5045 (2) 0.0256 (5) C2 0.3529 (4) 0.2038 (3) 0.62462 (19) 0.0256 (5) H2 0.5000 0.2617 0.6742 0.031* N1 0.1297 (4) 0.3251 (3) 0.59711 (17) 0.0273 (5) H1A 0.1774 0.4146 0.5557 0.041* H1B 0.0821 0.3611 0.6669 0.041* H1C −0.0037 0.2721 0.5523 0.041* C3 0.2634 (5) 0.0528 (3) 0.6963 (2) 0.0310 (6) H3A 0.1892 0.0968 0.7656 0.037* H3B 0.1273 −0.0088 0.6440 0.037* N2 0.5796 (4) −0.3618 (3) 0.82032 (19) 0.0369 (5) H2A 0.5132 −0.4560 0.8490 0.055* H2B 0.7047 −0.3203 0.8766 0.055* H2C 0.6458 −0.3874 0.7528 0.055* C4 0.4809 (5) −0.0708 (4) 0.7427 (2) 0.0341 (6) H4A 0.5762 −0.1000 0.6766 0.041* H4B 0.6010 −0.0168 0.8073 0.041* C5 0.3714 (5) −0.2318 (4) 0.7912 (2) 0.0339 (6) H5A 0.2971 −0.2050 0.8643 0.041* H5B 0.2340 −0.2772 0.7304 0.041* N11 0.8877 (5) 0.8459 (3) 0.0809 (2) 0.0454 (6) O1 1.0196 (5) 0.9042 (4) 0.17461 (18) 0.0695 (9) O2 0.6487 (5) 0.8499 (4) 0.0688 (3) 0.0658 (7) O3 0.9906 (7) 0.7785 (8) 0.0018 (4) 0.1055 (15)

Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

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Acta Cryst. (2002). E58, o646–o648

N2 0.0432 (12) 0.0340 (11) 0.0337 (10) 0.0055 (10) 0.0066 (8) 0.0048 (9) C4 0.0345 (12) 0.0318 (13) 0.0356 (11) 0.0038 (12) 0.0045 (10) 0.0039 (11) C5 0.0383 (13) 0.0322 (13) 0.0326 (12) 0.0038 (11) 0.0104 (10) 0.0029 (10) N11 0.0526 (14) 0.0534 (15) 0.0331 (11) −0.0146 (12) 0.0156 (11) −0.0062 (11) O1 0.0846 (16) 0.090 (2) 0.0349 (10) −0.0521 (17) 0.0108 (10) −0.0085 (13) O2 0.0509 (13) 0.0727 (17) 0.0745 (16) 0.0021 (12) 0.0116 (11) −0.0244 (13) O3 0.0603 (13) 0.194 (4) 0.0663 (14) −0.012 (2) 0.0237 (11) −0.060 (2)

Geometric parameters (Å, º)

O1A—C1 1.238 (3) N2—C5 1.482 (3) O1B—C1 1.258 (3) N2—H2A 0.89 C1—C2 1.535 (3) N2—H2B 0.89 C2—N1 1.492 (3) N2—H2C 0.89 C2—C3 1.531 (3) C4—C5 1.510 (4) C2—H2 0.98 C4—H4A 0.97 N1—H1A 0.89 C4—H4B 0.97 N1—H1B 0.89 C5—H5A 0.97 N1—H1C 0.89 C5—H5B 0.97 C3—C4 1.514 (3) N11—O3 1.212 (4) C3—H3A 0.97 N11—O2 1.229 (3) C3—H3B 0.97 N11—O1 1.238 (3)

O1A—C1—O1B 126.8 (2) C5—N2—H2A 109.5 O1A—C1—C2 117.02 (18) C5—N2—H2B 109.5 O1B—C1—C2 116.14 (19) H2A—N2—H2B 109.5 N1—C2—C3 107.80 (18) C5—N2—H2C 109.5 N1—C2—C1 109.69 (17) H2A—N2—H2C 109.5 C3—C2—C1 110.17 (19) H2B—N2—H2C 109.5 N1—C2—H2 109.7 C5—C4—C3 110.4 (2) C3—C2—H2 109.7 C5—C4—H4A 109.6 C1—C2—H2 109.7 C3—C4—H4A 109.6 C2—N1—H1A 109.5 C5—C4—H4B 109.6 C2—N1—H1B 109.5 C3—C4—H4B 109.6 H1A—N1—H1B 109.5 H4A—C4—H4B 108.1 C2—N1—H1C 109.5 N2—C5—C4 110.2 (2) H1A—N1—H1C 109.5 N2—C5—H5A 109.6 H1B—N1—H1C 109.5 C4—C5—H5A 109.6 C4—C3—C2 113.29 (19) N2—C5—H5B 109.6 C4—C3—H3A 108.9 C4—C5—H5B 109.6 C2—C3—H3A 108.9 H5A—C5—H5B 108.1 C4—C3—H3B 108.9 O3—N11—O2 118.8 (3) C2—C3—H3B 108.9 O3—N11—O1 120.9 (3) H3A—C3—H3B 107.7 O2—N11—O1 120.2 (3)

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O1B—C1—C2—C3 −98.2 (2) C3—C4—C5—N2 172.15 (18)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A

N1—H1A···O1Bi _0.89 _1.93 _{2.813 (3)} ₁₆₉

N1—H1B···O1ii _0.89 _1.93 _{2.818 (3)} ₁₇₂

N1—H1C···O1Biii _0.89 _2.06 _{2.911 (3)} ₁₆₁

N2—H2A···O2iv _0.89 _2.01 _{2.899 (4)} ₁₇₃

N2—H2B···O3v _0.89 _2.02 _{2.911 (4)} ₁₇₉

N2—H2C···O1Aii _0.89 _2.03 _{2.900 (3)} ₁₆₅