L-Argininium dinitrate

In the title compound, C₆H₁₆N₄O₂²⁺·2NO₃ ⁻, the diprotonated argininium mol­ecule is linked by a strong O—H...O [2.653 (7) Å] hydrogen bond to the nitrate anion. The single-bonded O atom of the carboxyl group exhibits a very unusual cis conformation with respect to the α-amino N atom. Chelated three-centered hydrogen bonds are observed in the case of the N^α and N^[epsilon] atoms with the nitrate anions. The argininium mol­ecules are connected by type A, B and D interactions through nitrate anions.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.010 Å
• R factor = 0.070
• wR factor = 0.218
• Data-to-parameter ratio = 7.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           68.00
         From the CIF: _reflns_number_total               1284
         Count of symmetry unique reflns         1302
         Completeness (_total/calc)             98.62%
         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

L-Arginine is one of the essential amino acids widely distributed in biological substances. L-Arginine phosphate monohydrate is found to exhibit interesting non-linear optical properties (Jiang et al., 1983). The strong basicity of the guanidyl group are responsible for the functions in living matter (Aoki et al., 1971). The crystal structures of L-arginine dihydrate (Karle & Karle, 1964), L-arginine hydrochloride monohydrate (Dow et al., 1970), L-arginine phosphate monohydrate (Aoki et al., 1971), L-arginine perchlorate (Monaco et al., 1987; Srinivasan & Rajaram, 1997) and L-arginine diarsenate (Zalkin et al., 1989) have been reported. In the present study, the crystal structure of L-arginine dinitrate, (I), was undertaken to study conformational aspects.

The conformation of the arginine molecule may be characterized by three planar groups: (i) the carboxyl group, (ii) the side chain C atoms consisting of the α-, β-, γ- and δ-carbon (C12, C13, C14 and C15) and (iii) the guanidyl group including the δ-carbon atom (C15, N4, C16, N5 and N6) (Aoki et al., 1971). The conformation of the single-bonded carboxyl O atom is cis with respect to the amino N atom [-29.7 (10)°] for the diprotonated argininium molecule. In general, this conformation is found to be trans, whereas the present structure is different from earlier studies, viz. L-valine hydrochloride (Koetzle et al., 1974), DL-valine hydrochloride (Di Blasio et al., 1977), L-arginine diarsenate (Zalkin et al., 1989), bis(DL-methioninium) sulfate (Srinivasan et al., 2001), tri(L-isoleucinium) sulfate bisulfate (Sridhar et al., 2001) and L-valine L-valinium perchlorate monohydrate (Pandiarajan et al., 2001).

The side-chain conformation angle χ¹ has a gauche II form [-62.5 (8)°], while χ² and χ³ are in the trans form [-168.6 (6) and 178.0 (6)°] for the argininium molecule (Fig. 1). The other conformation angle, which has guanidyl group at the end of the residue, χ⁴ is [-92.9 (10)°] as expected and χ⁵¹ and χ⁵² are 6.6 (14) and -172.6 (8)°, respectively. These conformational angles are very similar to L-arginine diarsenate, except for χ⁴ which is 148.8°. The argininium molecule, in the present study, is in a slightly folded conformation.

The guanidyl group is protonated and exists as a guanidinium ion. The three C—N bonds in this group are nearly equal in length with an average value of 1.313 (9) Å. The three N—C—N angles are very close to 120°, confirming the planarity of the guanidyl group. Like other arginine molecules, the C15 atom is only slightly displaced [0.15 (2) Å] from the plane of the guanidyl group. The two crystallographically independent nitrate anions have similar geometries.

The carboxyl O atom of the diprotonated argininium cation is linked through a strong O—H···O hydrogen bond [2.653 (7) Å] with the nitrate anion (Fig. 2 and Table 2), while the amino-N and the N atoms of guanidyl group are linked through normal hydrogen bonds with the two nitrate anions. Chelated three-centered hydrogen bonds are observed in the case of the N^α and N^ε atoms (N3—H3C···O5ⁱⁱ and N3—H3C···O4ⁱⁱ, and N4—H4···O3ⁱⁱⁱ and N4—H4···O2ⁱⁱⁱ; Jeffrey & Saenger, 1991). The O atom (O2) of nitrate anion links the carboxyl O atom (O1B), N^ε and N^η1 (N5) through a chain along the z axis. The O atoms of the second nitrate anion (O5 and O4) links the α-amino N atom and N^η2 (N6) through a chain along the x axis. The intermolecular guanidyl–nitrate interactions are observed as (i) type D between N atoms ε, η1 with O2; (ii) type A between N atoms η1, η2 with O3 and O1 and (iii) type B between N atoms ε, η1 with O3 and O2 of the nitrate anions (Salunke & Vijayan, 1981). An intermolecular short contact of 2.903 (12) Å is observed between O4 and the carboxyl C11(1 - x, 1/2 + y, 1 - z) atom.

S2. Experimental

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

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, 1997); 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 structure of the diprotonated argininium cation showing the atomic numbering scheme and 50% probability displacement ellipsoids (Spek, 1999).

L-Argininium dinitrate

Crystal data

C6H16N4O2^2+·2NO3^−	F(000) = 316
Mr = 300.25	Dx = 1.519 Mg m^−3 Dm = 1.519 Mg m^−3 Dm measured by flotation in a mixture of carbon tetrachloride and xylene
Monoclinic, P21	Cu Kα radiation, λ = 1.54180 Å
a = 7.744 (5) Å	Cell parameters from 25 reflections
b = 7.284 (5) Å	θ = 14.9–26.9°
c = 11.653 (5) Å	µ = 1.22 mm^−1
β = 92.600 (5)°	T = 293 K
V = 656.6 (7) Å^3	Needles, colorless
Z = 2	0.03 × 0.02 × 0.01 mm

Data collection

Enraf-Nonius sealed tube diffractometer	1213 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.000
Graphite monochromator	θmax = 68.0°, θmin = 3.8°
ω–2θ scans	h = −9→9
Absorption correction: ψ scan (North et al., 1968)	k = 0→8
Tmin = 0.967, Tmax = 0.984	l = 0→14
1284 measured reflections	3 standard reflections every 60 min
1284 independent reflections	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)] = 0.070	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.218	H-atom parameters constrained
S = 1.08	w = 1/[σ^2(Fo^2) + (0.2P)^2] where P = (Fo^2 + 2Fc^2)/3
1284 reflections	(Δ/σ)max < 0.001
181 parameters	Δρmax = 0.35 e Å^−3
1 restraint	Δρmin = −0.44 e Å^−3

Special details

Experimental. Intensity measurement was not carried out for the Friedel pairs.

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	0.4833 (7)	0.1038 (9)	0.8694 (5)	0.0397 (14)
O1	0.3517 (6)	0.1002 (8)	0.8013 (4)	0.0445 (13)
O2	0.6214 (6)	0.0334 (10)	0.8405 (4)	0.0531 (16)
O3	0.4728 (7)	0.1721 (12)	0.9646 (5)	0.065 (2)
N2	0.7063 (8)	0.4811 (11)	0.6596 (6)	0.0480 (16)
O4	0.8176 (8)	0.6055 (11)	0.6715 (5)	0.0661 (19)
O5	0.6552 (8)	0.4366 (9)	0.5605 (5)	0.0555 (16)
O6	0.6464 (11)	0.4076 (14)	0.7431 (6)	0.090 (3)
O1A	0.0856 (7)	0.5379 (11)	0.3654 (4)	0.0589 (17)
O1B	0.3654 (6)	0.4622 (11)	0.3822 (4)	0.0531 (17)
H1B	0.3669	0.5026	0.3166	0.080*
C11	0.2076 (9)	0.4760 (13)	0.4196 (6)	0.0420 (18)
C12	0.1966 (10)	0.4121 (11)	0.5432 (6)	0.0393 (16)
H12	0.0814	0.3603	0.5531	0.047*
N3	0.3284 (8)	0.2670 (9)	0.5704 (5)	0.0398 (14)
H3A	0.3205	0.2312	0.6430	0.060*
H3B	0.4336	0.3119	0.5605	0.060*
H3C	0.3096	0.1715	0.5239	0.060*
C13	0.2213 (9)	0.5750 (11)	0.6234 (6)	0.0386 (16)
H13A	0.1391	0.6701	0.6005	0.046*
H13B	0.3366	0.6244	0.6160	0.046*
C14	0.1973 (10)	0.5257 (11)	0.7482 (6)	0.0382 (16)
H14A	0.0919	0.4551	0.7543	0.046*
H14B	0.2934	0.4505	0.7766	0.046*
C15	0.1877 (10)	0.6979 (11)	0.8201 (6)	0.0415 (17)
H15A	0.2947	0.7658	0.8145	0.050*
H15B	0.0947	0.7745	0.7886	0.050*
N4	0.1587 (7)	0.6630 (11)	0.9416 (5)	0.0410 (15)
H4	0.2482	0.6442	0.9864	0.049*
C16	0.0089 (9)	0.6584 (11)	0.9869 (6)	0.0339 (15)
N5	0.0006 (8)	0.6455 (12)	1.1008 (5)	0.0504 (18)
H5A	0.0941	0.6403	1.1435	0.061*
H5B	−0.0983	0.6423	1.1316	0.061*
N6	−0.1363 (8)	0.6680 (12)	0.9253 (5)	0.0496 (17)
H6A	−0.1347	0.6778	0.8518	0.060*
H6B	−0.2333	0.6645	0.9583	0.060*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.041 (3)	0.042 (3)	0.036 (3)	−0.001 (3)	−0.001 (2)	0.004 (3)
O1	0.038 (3)	0.054 (3)	0.042 (3)	−0.007 (3)	0.004 (2)	0.006 (3)
O2	0.038 (3)	0.080 (4)	0.041 (3)	0.019 (3)	0.005 (2)	−0.006 (3)
O3	0.043 (3)	0.101 (6)	0.052 (3)	0.009 (4)	0.003 (2)	−0.032 (4)
N2	0.046 (4)	0.052 (4)	0.046 (4)	−0.001 (3)	−0.004 (3)	0.010 (3)
O4	0.065 (4)	0.076 (5)	0.056 (4)	−0.026 (4)	−0.010 (3)	0.015 (4)
O5	0.068 (4)	0.057 (4)	0.041 (3)	−0.005 (3)	−0.007 (3)	0.005 (3)
O6	0.111 (6)	0.113 (7)	0.047 (3)	−0.054 (5)	0.006 (3)	0.024 (4)
O1A	0.053 (3)	0.085 (5)	0.039 (3)	0.009 (3)	0.000 (2)	0.007 (3)
O1B	0.036 (3)	0.089 (5)	0.034 (2)	−0.006 (3)	0.003 (2)	0.015 (3)
C11	0.033 (3)	0.058 (5)	0.034 (3)	−0.005 (4)	−0.006 (3)	−0.001 (4)
C12	0.046 (4)	0.037 (4)	0.034 (3)	0.002 (3)	0.005 (3)	0.007 (3)
N3	0.052 (3)	0.035 (3)	0.033 (3)	0.000 (3)	0.005 (2)	−0.001 (3)
C13	0.037 (3)	0.041 (4)	0.038 (4)	0.001 (3)	0.009 (3)	0.008 (3)
C14	0.049 (4)	0.038 (4)	0.028 (3)	−0.001 (3)	0.008 (3)	0.003 (3)
C15	0.047 (4)	0.038 (4)	0.040 (4)	−0.005 (3)	0.012 (3)	−0.005 (3)
N4	0.030 (3)	0.060 (4)	0.034 (3)	0.010 (3)	−0.001 (2)	−0.008 (3)
C16	0.025 (3)	0.043 (4)	0.035 (3)	0.011 (3)	0.004 (2)	−0.006 (3)
N5	0.040 (3)	0.070 (5)	0.042 (3)	0.005 (4)	0.007 (2)	−0.006 (4)
N6	0.039 (3)	0.069 (5)	0.041 (3)	0.011 (4)	0.009 (2)	−0.001 (4)

Geometric parameters (Å, º)

N1—O3	1.222 (8)	C13—H13A	0.97
N1—O2	1.246 (8)	C13—H13B	0.97
N1—O1	1.262 (7)	C14—C15	1.512 (11)
N2—O6	1.221 (9)	C14—H14A	0.97
N2—O5	1.246 (8)	C14—H14B	0.97
N2—O4	1.254 (10)	C15—N4	1.465 (9)
O1A—C11	1.201 (9)	C15—H15A	0.97
O1B—C11	1.320 (8)	C15—H15B	0.97
O1B—H1B	0.8200	N4—C16	1.296 (9)
C11—C12	1.520 (10)	N4—H4	0.86
C12—N3	1.493 (10)	C16—N6	1.308 (9)
C12—C13	1.517 (11)	C16—N5	1.336 (9)
C12—H12	0.98	N5—H5A	0.86
N3—H3A	0.89	N5—H5B	0.86
N3—H3B	0.89	N6—H6A	0.86
N3—H3C	0.89	N6—H6B	0.86
C13—C14	1.518 (9)
O3—N1—O2	120.4 (6)	C14—C13—H13B	109.0
O3—N1—O1	119.6 (6)	H13A—C13—H13B	107.8
O2—N1—O1	120.0 (6)	C15—C14—C13	110.2 (6)
O6—N2—O5	120.5 (8)	C15—C14—H14A	109.6
O6—N2—O4	120.8 (7)	C13—C14—H14A	109.6
O5—N2—O4	118.6 (7)	C15—C14—H14B	109.6
C11—O1B—H1B	109.5	C13—C14—H14B	109.6
O1A—C11—O1B	124.9 (7)	H14A—C14—H14B	108.1
O1A—C11—C12	122.5 (6)	N4—C15—C14	113.9 (7)
O1B—C11—C12	112.5 (6)	N4—C15—H15A	108.8
N3—C12—C13	110.9 (6)	C14—C15—H15A	108.8
N3—C12—C11	110.5 (6)	N4—C15—H15B	108.8
C13—C12—C11	109.5 (7)	C14—C15—H15B	108.8
N3—C12—H12	108.6	H15A—C15—H15B	107.7
C13—C12—H12	108.6	C16—N4—C15	125.3 (6)
C11—C12—H12	108.6	C16—N4—H4	117.4
C12—N3—H3A	109.5	C15—N4—H4	117.4
C12—N3—H3B	109.5	N4—C16—N6	122.5 (6)
H3A—N3—H3B	109.5	N4—C16—N5	119.4 (6)
C12—N3—H3C	109.5	N6—C16—N5	118.0 (6)
H3A—N3—H3C	109.5	C16—N5—H5A	120.0
H3B—N3—H3C	109.5	C16—N5—H5B	120.0
C12—C13—C14	112.8 (6)	H5A—N5—H5B	120.0
C12—C13—H13A	109.0	C16—N6—H6A	120.0
C14—C13—H13A	109.0	C16—N6—H6B	120.0
C12—C13—H13B	109.0	H6A—N6—H6B	120.0
O1A—C11—C12—N3	152.9 (9)	C12—C13—C14—C15	−168.6 (6)
O1B—C11—C12—N3	−29.7 (10)	C13—C14—C15—N4	178.0 (6)
O1A—C11—C12—C13	−84.6 (10)	C14—C15—N4—C16	−92.9 (10)
O1B—C11—C12—C13	92.8 (9)	C15—N4—C16—N6	6.6 (14)
N3—C12—C13—C14	−62.5 (8)	C15—N4—C16—N5	−172.6 (8)
C11—C12—C13—C14	175.3 (6)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1B—H1B···O2^i	0.82	1.85	2.653 (7)	166
N3—H3A···O1	0.89	2.08	2.950 (8)	165
N3—H3B···O5	0.89	1.94	2.823 (9)	170
N3—H3C···O5^ii	0.89	2.00	2.855 (9)	161
N3—H3C···O4^ii	0.89	2.49	3.212 (9)	139
N4—H4···O3^iii	0.86	2.22	3.010 (8)	153
N4—H4···O2^iii	0.86	2.36	3.138 (8)	151
N5—H5A···O2^iii	0.86	2.34	3.086 (9)	146
N5—H5B···O1^iv	0.86	2.17	3.022 (8)	173
N6—H6A···O4^v	0.86	2.18	2.998 (9)	158
N6—H6B···O3^iv	0.86	2.10	2.957 (9)	177

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