Literature DB >> 21200918

A cocrystal of pyridine-2,4-dicarboxylic acid and serine.

Abstract

The title compound, pyridine-2,4-dicarboxylic acid-S-serine (1/1), C(7)H(5)NO(4)·C(3)H(7)NO(3), has serine in its zwitterionic form. The crystal structure is stabilized by an extensive series of inter-molecular O-H⋯O, N-H⋯N and N-H⋯O hydrogen bonds, forming a three-dimensional network.

Entities: Chemical Disease Gene

Year: 2007 PMID： 21200918 PMCID： PMC2915001 DOI： 10.1107/S160053680706240X

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For related structures of organic acids and amino acids, see: Coupar et al. (1997 ▶); Pandiarajan et al. (2001 ▶); Sobczyk et al. (2000 ▶); Srinivasan et al. (2002 ▶).

Experimental

Crystal data

C7H5NO4·C3H7NO3 M = 272.22 Triclinic, a = 4.4941 (13) Å b = 6.4512 (18) Å c = 10.123 (3) Å α = 81.273 (3)° β = 87.060 (3)° γ = 86.247 (3)° V = 289.22 (14) Å3 Z = 1 Mo Kα radiation μ = 0.14 mm−1 T = 298 (2) K 0.37 × 0.33 × 0.30 mm

Data collection

Bruker SMART CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.952, T max = 0.961 2493 measured reflections 1287 independent reflections 1202 reflections with I > 2σ(I) R int = 0.021

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.090 S = 1.05 1287 reflections 184 parameters 9 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.24 e Å−3 Δρmin = −0.25 e Å−3 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: SHELXTL (Bruker, 1998 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680706240X/sj2422sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053680706240X/sj2422Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₇H₅NO₄·C₃H₇NO₃	Z = 1
M_r = 272.22	F₀₀₀ = 142
Triclinic, P1	D_x = 1.563 Mg m⁻³
Hall symbol: P 1	Mo Kα radiation λ = 0.71073 Å
a = 4.4941 (13) Å	Cell parameters from 1233 reflections
b = 6.4512 (18) Å	θ = 2.7–27.8º
c = 10.123 (3) Å	µ = 0.14 mm⁻¹
α = 81.273 (3)º	T = 298 (2) K
β = 87.060 (3)º	Block, colorless
γ = 86.247 (3)º	0.37 × 0.33 × 0.30 mm
V = 289.22 (14) Å³

Bruker SMART CCD area-detector diffractometer	1287 independent reflections
Radiation source: fine-focus sealed tube	1202 reflections with I > 2σ(I)
Monochromator: graphite	R_int = 0.021
T = 298(2) K	θ_max = 27.5º
ω scans	θ_min = 2.0º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)	h = −5→5
T_min = 0.952, T_max = 0.961	k = −8→8
2493 measured reflections	l = −13→13

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.036	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.090	w = 1/[σ²(F_o²) + (0.0577P)² + 0.006P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
1287 reflections	Δρ_max = 0.24 e Å⁻³
184 parameters	Δρ_min = −0.25 e Å⁻³
9 restraints	Extinction correction: none
Primary atom site location: structure-invariant direct methods

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.

	x	y	z	U_iso*/U_eq
O1	1.0517 (4)	0.0560 (3)	0.0626 (2)	0.0334 (5)
H1	1.1822	−0.0201	0.0317	0.050*
O2	0.9510 (4)	−0.2405 (3)	0.1977 (2)	0.0356 (5)
O3	0.1493 (6)	−0.2074 (3)	0.5583 (2)	0.0516 (7)
O4	−0.0519 (5)	0.1089 (3)	0.5859 (2)	0.0434 (6)
H4	−0.1431	0.0430	0.6491	0.065*
O5	0.4623 (4)	0.7963 (3)	0.9831 (2)	0.0337 (5)
O6	0.5883 (5)	0.9761 (3)	0.7854 (2)	0.0359 (5)
O7	0.4881 (4)	0.3780 (3)	0.8451 (2)	0.0377 (5)
H7	0.4986	0.2569	0.8290	0.057*
N1	0.6382 (5)	0.2780 (3)	0.1903 (2)	0.0293 (5)
N2	0.9518 (5)	0.5231 (3)	0.9729 (2)	0.0269 (5)
C1	0.6767 (6)	0.0717 (4)	0.2350 (3)	0.0249 (5)
C2	0.5179 (6)	−0.0277 (4)	0.3443 (3)	0.0271 (5)
H2	0.5490	−0.1714	0.3717	0.033*
C3	0.3112 (6)	0.0908 (4)	0.4122 (3)	0.0270 (5)
C4	0.2762 (6)	0.3039 (4)	0.3694 (3)	0.0327 (6)
H4A	0.1446	0.3884	0.4148	0.039*
C5	0.4416 (6)	0.3894 (4)	0.2573 (3)	0.0333 (6)
H5	0.4132	0.5326	0.2274	0.040*
C6	0.9072 (6)	−0.0535 (4)	0.1629 (3)	0.0261 (5)
C7	0.1307 (6)	−0.0215 (4)	0.5278 (3)	0.0320 (6)
C8	0.6098 (5)	0.8204 (4)	0.8753 (3)	0.0236 (5)
C9	0.8388 (5)	0.6435 (4)	0.8475 (3)	0.0253 (5)
H9	1.0081	0.7073	0.7955	0.030*
C10	0.7075 (6)	0.4937 (4)	0.7658 (3)	0.0329 (6)
H10A	0.6184	0.5730	0.6870	0.039*
H10B	0.8645	0.3982	0.7367	0.039*
H2A	0.826 (7)	0.433 (5)	1.017 (4)	0.080*
H2B	1.120 (5)	0.448 (5)	0.955 (4)	0.080*
H2C	0.998 (9)	0.607 (6)	1.031 (4)	0.080*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0327 (10)	0.0268 (10)	0.0373 (11)	0.0043 (8)	0.0169 (8)	−0.0029 (8)
O2	0.0397 (11)	0.0250 (10)	0.0390 (11)	0.0046 (8)	0.0125 (8)	−0.0022 (8)
O3	0.0690 (16)	0.0327 (12)	0.0461 (14)	0.0018 (10)	0.0271 (12)	0.0043 (10)
O4	0.0507 (13)	0.0357 (12)	0.0398 (12)	0.0011 (9)	0.0226 (10)	−0.0022 (10)
O5	0.0320 (10)	0.0297 (10)	0.0364 (11)	0.0046 (7)	0.0156 (8)	−0.0036 (8)
O6	0.0460 (11)	0.0237 (10)	0.0335 (10)	0.0063 (8)	0.0135 (8)	0.0015 (8)
O7	0.0352 (11)	0.0269 (10)	0.0526 (13)	−0.0027 (8)	0.0124 (9)	−0.0153 (9)
N1	0.0300 (12)	0.0222 (11)	0.0337 (12)	0.0017 (9)	0.0082 (9)	−0.0023 (9)
N2	0.0275 (11)	0.0197 (11)	0.0317 (11)	0.0013 (8)	0.0099 (9)	−0.0024 (8)
C1	0.0227 (11)	0.0253 (12)	0.0262 (12)	0.0008 (9)	0.0023 (10)	−0.0043 (10)
C2	0.0315 (13)	0.0224 (12)	0.0259 (12)	0.0014 (9)	0.0043 (10)	−0.0015 (10)
C3	0.0272 (13)	0.0301 (13)	0.0234 (12)	−0.0022 (10)	0.0034 (10)	−0.0041 (10)
C4	0.0319 (14)	0.0282 (14)	0.0359 (14)	0.0054 (11)	0.0112 (12)	−0.0056 (12)
C5	0.0363 (15)	0.0224 (13)	0.0390 (15)	0.0027 (11)	0.0090 (12)	−0.0031 (11)
C6	0.0255 (12)	0.0243 (13)	0.0282 (14)	0.0005 (10)	0.0053 (10)	−0.0058 (10)
C7	0.0346 (15)	0.0335 (16)	0.0254 (14)	0.0007 (12)	0.0087 (11)	−0.0014 (11)
C8	0.0239 (11)	0.0189 (11)	0.0280 (12)	−0.0015 (8)	0.0049 (10)	−0.0050 (9)
C9	0.0243 (12)	0.0229 (12)	0.0261 (12)	0.0019 (9)	0.0122 (10)	−0.0009 (9)
C10	0.0372 (14)	0.0279 (14)	0.0341 (14)	0.0000 (11)	0.0089 (11)	−0.0104 (11)

O1—C6	1.315 (3)	N2—H2C	0.90 (4)
O1—H1	0.8200	C1—C2	1.381 (3)
O2—C6	1.211 (3)	C1—C6	1.500 (3)
O3—C7	1.191 (4)	C2—C3	1.386 (3)
O4—C7	1.318 (4)	C2—H2	0.9300
O4—H4	0.8200	C3—C4	1.378 (4)
O5—C8	1.242 (3)	C3—C7	1.508 (4)
O6—C8	1.251 (3)	C4—C5	1.386 (4)
O7—C10	1.417 (3)	C4—H4A	0.9300
O7—H7	0.8200	C5—H5	0.9300
N1—C5	1.327 (4)	C8—C9	1.535 (3)
N1—C1	1.342 (3)	C9—C10	1.528 (4)
N2—C9	1.479 (3)	C9—H9	0.9800
N2—H2A	0.89 (3)	C10—H10A	0.9700
N2—H2B	0.90 (3)	C10—H10B	0.9700

C6—O1—H1	109.5	N1—C5—H5	118.2
C7—O4—H4	109.5	C4—C5—H5	118.2
C10—O7—H7	109.5	O2—C6—O1	124.4 (2)
C5—N1—C1	117.4 (2)	O2—C6—C1	120.9 (2)
C9—N2—H2A	115 (3)	O1—C6—C1	114.7 (2)
C9—N2—H2B	110 (3)	O3—C7—O4	125.2 (3)
H2A—N2—H2B	107 (2)	O3—C7—C3	122.6 (3)
C9—N2—H2C	112 (3)	O4—C7—C3	112.2 (2)
H2A—N2—H2C	106 (2)	O5—C8—O6	126.1 (2)
H2B—N2—H2C	107 (2)	O5—C8—C9	117.8 (2)
N1—C1—C2	123.1 (2)	O6—C8—C9	116.2 (2)
N1—C1—C6	117.7 (2)	N2—C9—C10	109.4 (2)
C2—C1—C6	119.3 (2)	N2—C9—C8	111.60 (19)
C1—C2—C3	118.7 (2)	C10—C9—C8	111.4 (2)
C1—C2—H2	120.6	N2—C9—H9	108.1
C3—C2—H2	120.6	C10—C9—H9	108.1
C4—C3—C2	118.7 (2)	C8—C9—H9	108.1
C4—C3—C7	123.3 (2)	O7—C10—C9	109.5 (2)
C2—C3—C7	118.1 (2)	O7—C10—H10A	109.8
C3—C4—C5	118.6 (2)	C9—C10—H10A	109.8
C3—C4—H4A	120.7	O7—C10—H10B	109.8
C5—C4—H4A	120.7	C9—C10—H10B	109.8
N1—C5—C4	123.6 (2)	H10A—C10—H10B	108.2

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O5ⁱ	0.82	1.77	2.590 (3)	173
O4—H4···O6ⁱⁱ	0.82	1.81	2.598 (3)	162
O7—H7···O6ⁱⁱⁱ	0.82	1.94	2.754 (3)	171
N2—H2A···N1^iv	0.89 (3)	2.05 (2)	2.872 (3)	152 (4)
N2—H2A···O1^iv	0.89 (3)	2.55 (4)	3.023 (3)	113 (3)
N2—H2B···O7^v	0.90 (3)	2.01 (2)	2.848 (3)	155 (4)
N2—H2C···O2^vi	0.90 (4)	2.07 (4)	2.925 (3)	158 (4)
N2—H2C···O5^v	0.90 (4)	2.48 (4)	2.998 (3)	117 (3)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O5ⁱ	0.82	1.77	2.590 (3)	173
O4—H4⋯O6ⁱⁱ	0.82	1.81	2.598 (3)	162
O7—H7⋯O6ⁱⁱⁱ	0.82	1.94	2.754 (3)	171
N2—H2A⋯N1^iv	0.89 (3)	2.05 (2)	2.872 (3)	152 (4)
N2—H2A⋯O1^iv	0.89 (3)	2.55 (4)	3.023 (3)	113 (3)
N2—H2B⋯O7^v	0.90 (3)	2.01 (2)	2.848 (3)	155 (4)
N2—H2C⋯O2^vi	0.90 (4)	2.07 (4)	2.925 (3)	158 (4)
N2—H2C⋯O5^v	0.90 (4)	2.48 (4)	2.998 (3)	117 (3)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

1 in total

1. Poly[μ(2)-aqua-aqua-μ(4)-pyridine-2,4-dicarboxyl-ato-strontium].

Authors: Janet Soleimannejad; Yaghoub Mohammadzadeh; Hossein Aghabozorg; Zohreh Derikvand
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2009-07-15

1 in total