L-Citrullinium perchlorate

In the title compound, C₆H₁₄N₃O₃⁺·ClO₄⁻, the citrullinium residue forms a strong O—H...O hydrogen bonds with the terminal O atom of a symmetry-related residue. This residue has a gauche I-trans-trans-trans conformation. The crystal structure is stabilized by an N—H...O hydrogen-bonding network. The perchlorate anion is linked to the cation, forming chains along the a axis.

Key indicators

• Single-crystal X-ray study
• T = 105 K
• Mean [sigma](C-C) = 0.001 Å
• R factor = 0.023
• wR factor = 0.068
• Data-to-parameter ratio = 32.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_354  Alert C Short   O-H Bond (0.82A)   O(1B)  -   H(1)   =       0.70 Ang.

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           37.49
         From the CIF: _reflns_number_total               5866
         Count of symmetry unique reflns         3382
         Completeness (_total/calc)            173.45%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured      2484
         Fraction of Friedel pairs measured     0.734
         Are heavy atom types Z>Si present          yes
          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.


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

Citrulline amino acid is found in the urea cycle. The crystal structures of L-citrulline hydrochloride (Naganathan & Ventatesan, 1971), L-citrulline hydrochloride and L-homocitrulline hydrochloride (Ashida et al., 1972), and L-citrulline (Toffoli et al., 1987) have been reported. In the present study, the crystal structure determination of L-citrullinium perchlorate, (I), was undertaken.

The asymmetric part of the unit cell of (I) contains a citrullinium residue and a perchlorate anion (Fig. 1). The unsymmetrical C—O bond distances [1.2189 (8) and 1.3151 (8) Å] and the O—C—C bond angles [122.81 (6) and 111.63 (5)°], clearly confirm the protonation of the carboxyl group. Generally, the citrulline residue has three planar groups, viz. the carboxyl group, the aliphatic group and the carbamylamino group or urea fraction (Naganathan & Venkatesan, 1971). The backbone conformation angle ψ¹ (O1A—C1—C2—N1) is in a cis conformation [7.52 (8)°]. The deviation of the α-amino N atom from the mean carboxyl plane is 0.149 (1) Å. This tendency of twisting about the C—N bond is found in various amino acids (Lakshminarayanana et al., 1967). The straight-chain conformation angle χ¹ (N1—C2—C3—C4) is gauche I [68.99 (7)°], while χ² (C2—C3—C4—C5) is trans [−177.39 (6)°]. The other two conformation angles χ³ (C3—C4—C5—N2) and χ⁴ (C4—C5—N2—C6) are also both trans [−179.47 (6) and 162.71 (7)°]. The conformation angles χ⁵¹ (C5—N2—C6—O1C) and χ⁵² (C5—N2—C6—N3) are 174.51 (6) and −4.72 (11)°, respectively. The aliphatic chain has a fully extended planar conformation (Table 1).

The average Cl—O bond distances and O—Cl—O bond angles are 1.4450 (6) and 109.47 (4)°, respectively, confirming a nearly tetrahedral symmetry. The perchlorate anion plays a vital role in hydrogen bonding and stabilize the crystal structure. The carboxyl O atom of the citrulline residue forms a strong O—H···O hydrogen bond with its symmetry-related terminal O atom (Table 2). The α-, ε- and η-N atoms (N1, N2 and N3) of the citrullinium residue form N—H···O hydrogen bonds with the O atoms of the perchlorate anion. In addition, the α-N atom forms an intermolecular N—H···O hydrogen bond with the terminal O atoms (Fig. 3). A class-I hydrogen-bonding pattern is observed in the present structure, having three two-centered hydrogen bonding (Jeffrey & Saenger, 1991). Atom O4 of the perchlorate anion links the citrullinium residues through N^α—H···O hydrogen bonds in a chain running along the a axis [O4ⁱ···H1A—N1—H1B···O4ⁱⁱ; symmetry codes: (i) −x + 2, y + 1/2, −z + 1/2; (ii) (-x + 1, y + 1/2, −z + 1/2]. The citrullinium residues are packed as corrugated sheets in the ab plane, interconnected by O—H···O hydrogen bonding (Fig. 3).

S2. Experimental

The title compound was crystallized by slow evaporation from an aqueous solution of citrulline and perchloric acid in a stoichiometric ratio of 1:1.

S3. Refinement

All H atoms were located from a difference Fourier map. Those on the N and O atoms were refined freely but the remainder were placed in idealized positions and were refined as riding on their parent atoms. 2484 Fridel pairs were observed.

Computing details

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; 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 title compound, showing the atom-numbering scheme and 50% probability displacement ellipsoids (Johnson, 1976).
	Fig. 2. Packing diagram of (I), viewed down the a axis.
	Fig. 3. Packing diagran of (I), viewed down the c axis. H atoms have been omitted for clarity.

L-citrullinium perchlorate

Crystal data

C6H14N3O3^+·ClO4^−	Dx = 1.628 Mg m^−3 Dm = 1.615 Mg m^−3 Dm measured by flotation in a mixture of carbon tetrachloride and xylene
Mr = 275.65	Mo Kα radiation, λ = 0.71074 Å
Orthorhombic, P212121	Cell parameters from 7473 reflections
a = 5.1113 (1) Å	θ = 2.1–37.5°
b = 11.3497 (2) Å	µ = 0.37 mm^−1
c = 19.3853 (3) Å	T = 105 K
V = 1124.57 (3) Å^3	Block, colorless
Z = 4	0.70 × 0.45 × 0.30 mm
F(000) = 576

Data collection

Bruker SMART CCD diffractometer	5866 independent reflections
Radiation source: fine-focus sealed tube	5757 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.017
Detector resolution: 8.33 pixels mm^-1	θmax = 37.5°, θmin = 2.8°
ω scans	h = −8→8
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −19→18
Tmin = 0.77, Tmax = 0.89	l = −32→33
25355 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.023	w = 1/[σ^2(Fo^2) + (0.047P)^2 + 0.1185P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.068	(Δ/σ)max = 0.001
S = 1.03	Δρmax = 0.44 e Å^−3
5866 reflections	Δρmin = −0.48 e Å^−3
183 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0217 (18)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.02 (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
Cl	0.52869 (3)	0.658716 (14)	0.364590 (9)	0.01423 (4)
O1	0.43020 (14)	0.76304 (6)	0.39710 (4)	0.02633 (13)
O2	0.43595 (17)	0.65146 (7)	0.29480 (3)	0.02981 (15)
O3	0.81046 (11)	0.65797 (6)	0.36648 (4)	0.02524 (12)
O4	0.43557 (12)	0.55514 (5)	0.40299 (3)	0.01674 (9)
O1A	0.62548 (10)	0.80024 (5)	0.04814 (3)	0.01436 (9)
O1B	0.76258 (12)	0.66178 (5)	0.12320 (3)	0.01739 (9)
H1	0.650 (4)	0.6314 (17)	0.1129 (10)	0.045 (5)*
C1	0.78834 (12)	0.75951 (5)	0.08739 (3)	0.01095 (9)
C2	1.05443 (12)	0.81549 (5)	0.09844 (3)	0.01099 (9)
H2	1.1853	0.7645	0.0767	0.013*
N1	1.05839 (13)	0.93125 (5)	0.06170 (3)	0.01426 (9)
H1A	1.217 (3)	0.9531 (15)	0.0610 (8)	0.030 (4)*
H1B	0.956 (3)	0.9867 (13)	0.0841 (7)	0.023 (3)*
H1C	0.984 (3)	0.9255 (13)	0.0187 (7)	0.025 (3)*
C3	1.13069 (12)	0.83020 (6)	0.17432 (3)	0.01208 (10)
H3A	1.1576	0.7529	0.1944	0.014*
H3B	1.2953	0.8725	0.1769	0.014*
C4	0.92603 (14)	0.89619 (7)	0.21684 (3)	0.01550 (11)
H4A	0.8931	0.9724	0.1959	0.019*
H4B	0.7634	0.8521	0.2164	0.019*
C5	1.01385 (14)	0.91384 (6)	0.29068 (3)	0.01429 (10)
H5A	1.0471	0.8381	0.3121	0.017*
H5B	1.1747	0.9592	0.2916	0.017*
N2	0.80997 (13)	0.97608 (5)	0.32860 (3)	0.01255 (9)
H2A	0.704 (3)	1.0176 (12)	0.3064 (7)	0.020 (3)*
C6	0.79013 (13)	0.98153 (5)	0.39767 (3)	0.01096 (9)
O1C	0.61697 (11)	1.04561 (5)	0.42560 (3)	0.01511 (9)
N3	0.95763 (13)	0.91948 (5)	0.43683 (3)	0.01455 (9)
H3C	0.928 (3)	0.9158 (11)	0.4782 (7)	0.015 (3)*
H3D	1.061 (3)	0.8712 (12)	0.4194 (7)	0.017 (3)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl	0.01302 (6)	0.01252 (6)	0.01715 (6)	−0.00012 (4)	−0.00106 (5)	0.00302 (5)
O1	0.0203 (3)	0.0156 (2)	0.0431 (4)	0.0045 (2)	−0.0010 (3)	−0.0050 (2)
O2	0.0398 (4)	0.0334 (3)	0.0162 (2)	−0.0069 (3)	−0.0066 (2)	0.0089 (2)
O3	0.0118 (2)	0.0219 (2)	0.0421 (3)	0.00055 (18)	0.0028 (2)	0.0052 (3)
O4	0.0177 (2)	0.01562 (19)	0.0169 (2)	−0.00234 (17)	−0.00082 (17)	0.00517 (16)
O1A	0.01091 (19)	0.0185 (2)	0.01366 (19)	−0.00150 (15)	−0.00222 (14)	0.00144 (16)
O1B	0.0187 (2)	0.01492 (19)	0.0186 (2)	−0.00439 (18)	−0.00520 (16)	0.00358 (17)
C1	0.0104 (2)	0.0129 (2)	0.00953 (19)	−0.00050 (17)	0.00038 (16)	−0.00213 (17)
C2	0.0096 (2)	0.0141 (2)	0.00929 (19)	−0.00007 (17)	−0.00008 (16)	−0.00218 (16)
N1	0.0143 (2)	0.0173 (2)	0.01111 (19)	−0.00463 (18)	−0.00152 (17)	0.00068 (16)
C3	0.0110 (2)	0.0154 (2)	0.0099 (2)	0.00152 (18)	−0.00155 (16)	−0.00241 (17)
C4	0.0144 (3)	0.0229 (3)	0.0092 (2)	0.0058 (2)	−0.00150 (18)	−0.00383 (19)
C5	0.0130 (3)	0.0203 (3)	0.0095 (2)	0.0038 (2)	−0.00060 (17)	−0.00397 (18)
N2	0.0146 (2)	0.0148 (2)	0.00829 (18)	0.00438 (18)	0.00008 (16)	−0.00087 (15)
C6	0.0119 (2)	0.0115 (2)	0.0095 (2)	0.00113 (17)	0.00010 (16)	−0.00131 (16)
O1C	0.0169 (2)	0.0173 (2)	0.01119 (19)	0.00716 (16)	0.00089 (15)	−0.00252 (15)
N3	0.0167 (2)	0.0169 (2)	0.01003 (19)	0.00580 (19)	−0.00088 (18)	−0.00009 (16)

Geometric parameters (Å, º)

Cl—O1	1.4327 (7)	C3—H3A	0.9700
Cl—O2	1.4360 (7)	C3—H3B	0.9700
Cl—O3	1.4407 (6)	C4—C5	1.5135 (9)
Cl—O4	1.4706 (5)	C4—H4A	0.9700
O1A—C1	1.2189 (8)	C4—H4B	0.9700
O1B—C1	1.3151 (8)	C5—N2	1.4578 (9)
O1B—H1	0.70 (2)	C5—H5A	0.9700
C1—C2	1.5164 (9)	C5—H5B	0.9700
C2—N1	1.4946 (9)	N2—C6	1.3443 (8)
C2—C3	1.5308 (8)	N2—H2A	0.837 (15)
C2—H2	0.9800	C6—O1C	1.2670 (8)
N1—H1A	0.846 (17)	C6—N3	1.3436 (9)
N1—H1B	0.926 (15)	N3—H3C	0.818 (13)
N1—H1C	0.918 (15)	N3—H3D	0.833 (15)
C3—C4	1.5279 (9)
O1—Cl—O2	110.24 (5)	C4—C3—H3B	108.9
O1—Cl—O3	110.18 (4)	C2—C3—H3B	108.9
O2—Cl—O3	110.71 (5)	H3A—C3—H3B	107.7
O1—Cl—O4	108.92 (4)	C5—C4—C3	111.84 (5)
O2—Cl—O4	108.92 (4)	C5—C4—H4A	109.2
O3—Cl—O4	107.82 (4)	C3—C4—H4A	109.2
C1—O1B—H1	110.3 (17)	C5—C4—H4B	109.2
O1A—C1—O1B	125.52 (6)	C3—C4—H4B	109.2
O1A—C1—C2	122.81 (6)	H4A—C4—H4B	107.9
O1B—C1—C2	111.63 (5)	N2—C5—C4	109.21 (5)
N1—C2—C1	108.25 (5)	N2—C5—H5A	109.8
N1—C2—C3	111.02 (5)	C4—C5—H5A	109.8
C1—C2—C3	114.19 (5)	N2—C5—H5B	109.8
N1—C2—H2	107.7	C4—C5—H5B	109.8
C1—C2—H2	107.7	H5A—C5—H5B	108.3
C3—C2—H2	107.7	C6—N2—C5	125.34 (6)
C2—N1—H1A	106.2 (12)	C6—N2—H2A	116.0 (10)
C2—N1—H1B	111.5 (9)	C5—N2—H2A	118.4 (10)
H1A—N1—H1B	110.4 (15)	O1C—C6—N3	120.30 (6)
C2—N1—H1C	111.4 (9)	O1C—C6—N2	120.32 (6)
H1A—N1—H1C	113.7 (15)	N3—C6—N2	119.38 (6)
H1B—N1—H1C	103.9 (13)	C6—N3—H3C	117.6 (10)
C4—C3—C2	113.42 (5)	C6—N3—H3D	121.3 (9)
C4—C3—H3A	108.9	H3C—N3—H3D	118.8 (13)
C2—C3—H3A	108.9
O1A—C1—C2—N1	7.52 (8)	C2—C3—C4—C5	−177.39 (6)
O1B—C1—C2—N1	−174.58 (5)	C3—C4—C5—N2	−179.47 (6)
O1A—C1—C2—C3	131.73 (6)	C4—C5—N2—C6	162.71 (7)
O1B—C1—C2—C3	−50.37 (7)	C5—N2—C6—O1C	174.51 (6)
N1—C2—C3—C4	68.99 (7)	C5—N2—C6—N3	−4.72 (11)
C1—C2—C3—C4	−53.72 (8)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1B—H1···O1C^i	0.70 (2)	1.84 (2)	2.5292 (8)	171 (2)
N1—H1A···O4^ii	0.846 (17)	2.234 (17)	3.0226 (9)	155 (2)
N1—H1B···O4^iii	0.926 (15)	2.162 (16)	2.9699 (9)	145 (1)
N1—H1C···O1C^iv	0.918 (15)	1.906 (15)	2.7986 (8)	164 (1)
N2—H2A···O2^iii	0.837 (15)	2.583 (14)	3.3562 (10)	154 (1)
N3—H3C···O4^v	0.818 (13)	2.326 (13)	3.1205 (8)	164 (1)
N3—H3D···O1^vi	0.833 (15)	2.292 (15)	3.0952 (9)	162 (1)

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