Ampicillin trihydrate from synchrotron powder diffraction data

# 2006 International Union of Crystallography All rights reserved The crystal structure of ampicillin trihydrate {systematic name: 6-[d( )-aminophenylacetamido]penicillanic acid trihydrate}, C16H19N3O4S 3H2O, a broad-spectrum -lactam antibiotic of the aminopenicillin type, has been determined from synchrotron X-ray powder diffraction data. The three water molecules form an infinite hydrogen-bonded chain through the crystal structure, with hydrogen bonds to the NH3 , COO , C O and NH groups of the ampicillin molecules.

The crystal structure of ampicillin trihydrate {systematic name: 6-[d(À)--aminophenylacetamido]penicillanic acid trihydrate}, C 16 H 19 N 3 O 4 SÁ3H 2 O, a broad-spectrum -lactam antibiotic of the aminopenicillin type, has been determined from synchrotron X-ray powder diffraction data. The three water molecules form an infinite hydrogen-bonded chain through the crystal structure, with hydrogen bonds to the NH 3 + , COO À , C O and NH groups of the ampicillin molecules.

Comment
The title compound, (I), has been used as a broad-spectrum antibiotic since 1961. The crystal structure was reported in 1968 (James et al., 1968), but no atomic coordinates were given in the paper or deposited. Boles et al. (1978) published the crystal structure of a related compound, amoxycillin trihydrate. They apparently had access to the atomic coordinates of the crystal structure of compound (I), because in their paper they show that the two crystal structures are isostructural. However, the atomic coordinates of the title compound have not been published to date. We report the crystal structure here, determined from synchrotron X-ray powder diffraction.
The structural model of compound (I) obtained in the present work (Fig. 1a) is both chemically reasonable and in accord with the figures given by James et al. (1968). Selected geometric parameters are given in Table 1. We note, however, that the hydrogen bond O26 000 Á Á ÁO25 000 in their Fig. 1, which appears to link four water molecules together into a closed tetramer, is spurious, and instead should have formed a chain (Fig. 1b). Both the pattern of hydrogen bonding, and the positions of the H atoms of the water molecules in the structure, are chemically sensible and compare well with those from the crystal structure of the isostructural amoxycillin trihydrate (Boles et al., 1978). Details of the O-HÁ Á ÁO and N-HÁ Á ÁO hydrogen bonds are given in Table 2 and Fig. 1.

Table 2
Hydrogen-bond geometry (Å , ).    Table 2 for details). (b) A view along the b axis of the hydrogenbonded (dashed lines) water network in the crystal structure of compound (I).

Figure 2
Observed, calculated and difference X-ray powder diffraction profiles for compound (I). The region 25-42 in 2 has been magnified 10 times.
The starting model for Rietveld refinement was obtained by solving the crystal structure from the powder diffraction pattern. This also provided an independent check that the published crystal structure is correct. However, with the crystal structure being known, its determination from the powder pattern is mainly academic. The crystal structure was determined with the program DASH (David et al., 2004). For the structure solution, the data were truncated at 22.855 in 2, corresponding to a real-space resolution of 1.767 Å . The background was subtracted with a Bayesian high-pass filter (David & Sivia, 2001). Peak positions for indexing were obtained by fitting with an asymmetry-corrected Voigt function, followed by indexing with the program DICVOL (Boultif & Louer, 1991). An orthorhombic and several monoclinic unit cells were obtained. However, all the monoclinic unit cells were pseudo-orthorhombic with nearly the same parameters as the orthorhombic cell, indicating that the orthorhombic unit cell is the correct one. The figures of merit given by DICVOL were M(20) = 62.1 and F(20) = 337.1 (0.0014, 42). The space group reported for the single-crystal structure, P2 1 2 1 2 1 , gave an excellent Pawley fit.
Simulated annealing was used to solve the crystal structure of compound (I) from the powder pattern in direct space. The starting molecular geometry was taken from the anhydrate (Boles & Girven, 1976), entry AMCILL in the Cambridge Structural Database (Allen, 2002). The molecule is a zwitterion, in agreement with the singlecrystal study. Because H atoms do not contribute significantly to the powder diffraction pattern, due to their low X-ray scattering power, they were ignored during the structure solution process. Hence, the water molecule can be reduced to an O atom, which reduces its number of degrees of freedom from six to three. The molecule has five flexible torsion angles, which, when combined with the three water molecules, give a total of 20 degrees of freedom. In ten simulated annealing runs, the correct crystal structure was found twice, with a profile 2 = 81.7, 11 times the Pawley 2 . The next-best crystal structure had a profile 2 = 240. The low success rate and high profile 2 are caused by the high R factor of 10.6% of the crystal structure of AMCILL from which the starting model was taken; when the structure solution was repeated with a better starting model (obtained from Rietveld refinement against the powder data), the correct structure was found four times in ten runs, with a profile 2 = 20, less than three times the Pawley 2 . The background subtraction, peak fitting, indexing, Pawley refinement and simulated-annealing algorithms used are as implemented in the program DASH.
For the Rietveld refinement (Fig. 2), H atoms were included in the initial model in calculated positions. Bond lengths, bond angles and planar groupings were subjected to suitable constraints, including bonds to H atoms. Data were included to 41.42 in 2, corresponding to a real-space resolution of 0.99 Å . The refinement was not particularly sensitive to the position of the water H atoms and these were included in calculated positions, with the water molecules being fixed in position for the final refinement cycles. The refinement proceeded smoothly to reach a minimum characterized by an excellent fit to the diffraction profile ( 2 = 5.637, R p = 0.0296, R wp = 0.0296 and R Bragg = 0.0295).