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Crystal structure of [VOCl2(H2O)(C6H9O2)2] from powder diffraction data
Journal of Molecular Structure 641 (2002) 153–157 www.elsevier.com/locate/molstruc
Crystal structure of [VOCl2(H2O)(C6H8O2)2] from powder diffraction data Wiesław Łasocha*, Ryszard Grybos´ Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland Received 28 January 2002; revised 26 March 2002; accepted 26 March 2002
Abstract Crystal structure of aquadichlorobis(2-hydroxy-3-methyl-2-cyclopenten-1-one) oxovanadium(IV)—VO6Cl2C12H18 was 94.28(2)8, V ¼ solved by powder diffraction method. Space group C2=cð15Þ; a; b; c; b ¼ 19:777ð5Þ; 9:570ð2Þ; 8:442ð2Þ A; 3 1591:62ð4Þ A : RF and Rwp are 10.0 and 12.1%, respectively. Even though investigated compound seems to be of interest in biochemistry, its crystal structure has not been solved up till now. Presented structure is the first example of complex compound of 2-hydroxy-3-methyl-2-cyclopenten-1-one ligand with a transition metal. q 2002 Elsevier Science B.V. All rights reserved. Keywords: Powder diffraction; Rietveld method; Vanadium (IV) complexes
1. Introduction
2. Experimental
Vanadyl complexes have been widely investigated due to their potent biological activities including insulin mimetic effects in animal in vitro and in vivo, as well as in humans [1 –4]. Vanadyl compounds with O,O-donor ligands are very effective insulin-like agents. Majority of them have a square pyramidal or a distorted octahedral co-ordination geometry with two bidentate ligands trans arranged around the vanadium ion. In this work, we studied [VOCl2(H2O)(Hmcp)2], where Hmcp denotes: 2-hydroxy-3methyl-2-cyclopenten-1-one. To the best of our knowledge, none of X-ray crystal structure of vanadyl, or any metal complexes with Hmcp have been reported, though the crystal structure of hydrated Hmcp was established [5].
[VOCl2(H2O)(Hmcp)2] was prepared by redox reaction of VOCl 3 with an excess of Hmcp (V/Hmcp ¼ 1:3) in benzene [6]. Details of data collection are presented in Table 1. Diffraction pattern was indexed in the monoclinic system by program written by Visser [7]. After refinement of the lattice constants with use of the PROSZKI system [8], the space group C2/c (or Cc ) was found by systematic absences analysis. List of powder diffraction lines was sent to ICDD to be included in PDF-2 file.
* Corresponding author. Tel.: þ48-12-633-6377; fax: þ 48-12634-0515. E-mail address: [email protected] (W. Łasocha).
3. Crystal structure solution and refinement Initial structure model was built by EXPO [9] program. Unfortunately, only vanadium atom and ˚ from it four additional atoms in a distance about 2 A were found. It was not possible to find a bigger part of
0022-2860/02/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved. PII: S 0 0 2 2 - 2 8 6 0 ( 0 2 ) 0 0 1 6 7 - 9
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
154
Table 1 Details of data collection, crystal structure solution and refinement for [VOCl2(H2O)(Hmcp)2] Diffractometer Radiation 2u range Step scan increment, count time (8, s) Standard peak: hkl, 2ua R for standard peak (%) Space group ˚) a (A ˚) b (A ˚) c (A b (8) ˚) V (A Pattern decomposition Program used for structure solution Number of atoms initially found Structure refinement Number of observations Number of reflections Total number of atoms Number of structural parameters refined Number of profile parameters refined Number of constraints RF Rwp Maximum shift/error Texture correction formula Preferred orientation vector and factor G
PW3710 Philips X’pert Cu Ka, graphite monochromator 8–80 0.02, 16 110, 11.96 1.5% C2=cð15Þ 19.777 (5) 9.570 (2) 8.442 (2) 94.28 (2) 1591.62 (4) EXTRA (in EXPO) [9] EXPO [9] 5 (V, 4O) XRS82 [10,11] 3359 304 12b 39 10 12 distances, 16 angles 10.0 12.1 0.05 expðG cos 2aÞ [100], 20.09(3)
a
In XRS82 so-called ‘learned’ peak shape is used. Selected by user standard peak is decomposed into set of base functions. These functions in tabulated form are used next by profile fitting procedure. b Structure was solved and refined initially in Cc space group, in such a case number of independent atoms was 21.
Table 2 Atomic co-ordinates and isotropic temperature factors Atom
x
y
z
U
V Cl O1 O3 O4 C1 C2 C3 C4 C5 C6 O2
0 0.076(1) 0.078(1) 0 0 0.103(2) 0.158(3) 0.183(3) 0.147(4) 0.100(3) 0.243(3) 0.182(3)
0.198(1) 0.198(1) 0.198(2) 0.369(4) 20.010(4) 0.247(2) 0.179(3) 0.276(5) 0.412(5) 0.391(4) 0.255(6) 0.050(5)
0.2500 0.483(2) 0.115(3) 0.2500 0.2500 0.002(5) 20.085(7) 20.186(6) 20.16(1) 20.04(1) 20.287(8) 20.060(7)
0.04(1) 0.07(1) 0.07(2) 0.02(6) 0.02 0.08(1) 0.08 0.08 0.08 0.08 0.05 0.05(2)
The e.s.d of the last significant digit is given in parentheses. The e.s.d’s were calculated according to Scott [12]. The U value without e.s.d were constrained to be equal to proceeding one.
the molecule using this known fragment as initial information in the Le Bail procedure. The structure was completed by the Rietveld method using XRS-82 [10,11] program. Actually, the structure was solved in Ccð9Þ space group, however, when all atoms were found it became obvious that the structure can be described by C2=c space group without increasing the R factors. Since the temperature factor for the O3 atom was refined to negative value, all the atoms were divided into six groups and their B factors were constrained to be equal to each other within the group during the refinement, which allowed to refine all the B factors to positive values without a change in R factors. The difference pattern is not flat in some regions, but it is not caused by existence of any known vanadate phase listed in PDF-2. It is probably due to errors in description of a peak shape (Fig. 1).
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
155
Fig. 1. Calculated (upper), observed (middle), and difference (lower) Rietveld profiles.
4. Structure description and discussion
Table 3 ˚) Selected bond lengths (A Atom 1
Atom 2
Bond
e.s.d
V
O3 O1, O1_3a O4 Cl, Cl_3 O2_1b O1, O1_3 O1 C5 C2 O2 C3 C4 C6 C5
1.64 1.99 2.00 2.39 3.20 3.11 1.20 1.43 1.50 1.33 1.38 1.50 1.53 1.44
(4) (4) (4) (2) (5) (5) (6) (5) (7) (6) (7) (7) (8) (11)
Cl C1
C2 C3 C4 a b
Symmetry codes: _1 ¼ x; 2y; z þ 1=2; _3 ¼ 2x; y; 2z þ 1=2: Intermolecular hydrogen bond.
The molecule with numbering scheme is presented in Fig. 2(a). Fig. 2(b) shows molecular packing. Lists of atomic co-ordinations and bond distances are given in Tables 2 and 3. Co-ordination polyhedron of vanadium atom, which actually is a distorted octahedron with C2 symmetry, consists of two oxygen atoms belonging to ˚ ), two two Hmcp groups (V–O1 distance 1.99(4) A ˚ ), one water chlorine atoms (V–Cl distance 2.39(2) A ˚ ) and one oxygen molecule (V–O4 distance 2.00(4) A ˚ ) (see Fig. 2(a) and atom (V–O3 distance 1.64(4) A Table 3). Each VO(Hmcp)2Cl2·H2O molecule is connected with two analogous molecules by intermolecular hydrogen bonds, forming infinite strips parallel to z axis (see Fig. 2(b)). The Hmcp rings are essentially planar, the angle between two Hmcp rings connected to the same V atom is ,268. According to the literature [5], Hmcp can exist either in dicarbonyl or enol form; in the solid state Hmcp hydrate exists as the enol form. In our studies, both forms were tested in Rietveld refinement. Slightly better results were obtained for the enol
156
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
Fig. 2. (a) Molecular structure with numbering scheme. (b) Drawing of the molecular packing along [010] (an a axis is oriented upwards). Dashed lines indicate intermolecular H-bonds.
form. Since the differences between R factors for both forms were not large, some kind of equilibrium between both forms (with the enol form as dominating one) can be assumed. Unexpectedly large e.s.d of C4 – C5 bond distance can be attributed to equilibrium between tautomeric forms and dynamic disorder in non-planar Hmcp rings in dicarbonyl form. It can be expected that each vanadium atom is coordinated by two Hmcp molecules, and chelate compound is formed. However, the arrangement of atoms found by the Fourier method clearly shows that the vanadium atom is co-ordinated by two Hmcp groups, and each of these groups is connected to vanadium by only one oxygen atom. This observation is in agreement with the spectroscopic data indicating the presence of OH group in the structure. If the V and Hmcp molecule had formed chelate compound, OH group would have not been observed. Described structure was solved by conventional powder diffraction methods. The powerful crystal structure solution package EXPO [9] was used to decompose powder diffraction pattern into intensities, next by the direct methods the structure model was built. Subsequently, by the Rietveld method the missing atoms were found. In the presented work, initial model consisted of five atoms and represented 41% of electrons of the whole molecule. To sum up, it is evident from the presented
research that with structure complexity about 20 atoms in the asymmetric unit it is possible to solve crystal structure ‘ab initio’ using laboratory powder diffraction data, even in the case of wrong assumption concerning symmetry centre and without exact knowledge of the molecular structure.
Acknowledgments The support of Polish Committee of Science Research (KBN, 0312/T09/98/15) is kindly acknowledged.
References [1] V. Badmaev, A. Prakash, M. Majeed, J. Altern. Complement Med. 5 (1999) 273–279. [2] B.A. Reul, S.S. Amin, J.P. Buchet, L.N. Ongemba, D.C. Crans, S.M. Brichard, Br. J. Pharmacol. 126 (1999) 467 –477. [3] P. Poucheret, S. Verma, M.D. Grynaps, J.H. McNeill, Mol. Cell. Biochem. 188 (1998) 73 –80. [4] A.M. Kordowiak, R. Trzos, R. Grybos´, Horm. Metab. Res. 29 (1997) 101 –105. [5] S.E. Fayle, J.A. Gerrard, H.E. Nursten, P.J. Steel, Acta Crystallogr. C54 (1998) 404–405. [6] R. Grybos´, A. Samotus, Submitted for publication. [7] J.W. Visser, J. Appl. Crystallogr. 2 (1969) 89–95. [8] W. Łasocha, K. Lewinski, Proszki—a system of programs for
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157 powder diffraction data analysis, J. Appl. Crystallogr. 27 (1994) 437–438. [9] A. Altomare, M.C. Burla, G. Cascarano, C. Giacovazzo, A. Guagliardi, A.G.G. Moliterni, G. Polidori, EXPO: a program for full pattern decomposition and crystal structure solution, J. Appl. Crystallogr. 32 (1999) 339 –340. [10] Ch. Baerlocher, XRS-82, The X-ray Rietveld System,
157
Institut f.Kristallographie, ETH, Zurich, Switzerland, 1992. [11] D. Mucha, W. Łasocha, XRS-82 runs on PC 386/486 computers, J. Appl. Crystallogr. 27 (1994) 201 –202. PC version of XRS. [12] H.G.J. Scott, Appl. Crystallogr. 16 (1983) 159–163.
Crystal structure of [VOCl2(H2O)(C6H8O2)2] from powder diffraction data Wiesław Łasocha*, Ryszard Grybos´ Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland Received 28 January 2002; revised 26 March 2002; accepted 26 March 2002
Abstract Crystal structure of aquadichlorobis(2-hydroxy-3-methyl-2-cyclopenten-1-one) oxovanadium(IV)—VO6Cl2C12H18 was 94.28(2)8, V ¼ solved by powder diffraction method. Space group C2=cð15Þ; a; b; c; b ¼ 19:777ð5Þ; 9:570ð2Þ; 8:442ð2Þ A; 3 1591:62ð4Þ A : RF and Rwp are 10.0 and 12.1%, respectively. Even though investigated compound seems to be of interest in biochemistry, its crystal structure has not been solved up till now. Presented structure is the first example of complex compound of 2-hydroxy-3-methyl-2-cyclopenten-1-one ligand with a transition metal. q 2002 Elsevier Science B.V. All rights reserved. Keywords: Powder diffraction; Rietveld method; Vanadium (IV) complexes
1. Introduction
2. Experimental
Vanadyl complexes have been widely investigated due to their potent biological activities including insulin mimetic effects in animal in vitro and in vivo, as well as in humans [1 –4]. Vanadyl compounds with O,O-donor ligands are very effective insulin-like agents. Majority of them have a square pyramidal or a distorted octahedral co-ordination geometry with two bidentate ligands trans arranged around the vanadium ion. In this work, we studied [VOCl2(H2O)(Hmcp)2], where Hmcp denotes: 2-hydroxy-3methyl-2-cyclopenten-1-one. To the best of our knowledge, none of X-ray crystal structure of vanadyl, or any metal complexes with Hmcp have been reported, though the crystal structure of hydrated Hmcp was established [5].
[VOCl2(H2O)(Hmcp)2] was prepared by redox reaction of VOCl 3 with an excess of Hmcp (V/Hmcp ¼ 1:3) in benzene [6]. Details of data collection are presented in Table 1. Diffraction pattern was indexed in the monoclinic system by program written by Visser [7]. After refinement of the lattice constants with use of the PROSZKI system [8], the space group C2/c (or Cc ) was found by systematic absences analysis. List of powder diffraction lines was sent to ICDD to be included in PDF-2 file.
* Corresponding author. Tel.: þ48-12-633-6377; fax: þ 48-12634-0515. E-mail address: [email protected] (W. Łasocha).
3. Crystal structure solution and refinement Initial structure model was built by EXPO [9] program. Unfortunately, only vanadium atom and ˚ from it four additional atoms in a distance about 2 A were found. It was not possible to find a bigger part of
0022-2860/02/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved. PII: S 0 0 2 2 - 2 8 6 0 ( 0 2 ) 0 0 1 6 7 - 9
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
154
Table 1 Details of data collection, crystal structure solution and refinement for [VOCl2(H2O)(Hmcp)2] Diffractometer Radiation 2u range Step scan increment, count time (8, s) Standard peak: hkl, 2ua R for standard peak (%) Space group ˚) a (A ˚) b (A ˚) c (A b (8) ˚) V (A Pattern decomposition Program used for structure solution Number of atoms initially found Structure refinement Number of observations Number of reflections Total number of atoms Number of structural parameters refined Number of profile parameters refined Number of constraints RF Rwp Maximum shift/error Texture correction formula Preferred orientation vector and factor G
PW3710 Philips X’pert Cu Ka, graphite monochromator 8–80 0.02, 16 110, 11.96 1.5% C2=cð15Þ 19.777 (5) 9.570 (2) 8.442 (2) 94.28 (2) 1591.62 (4) EXTRA (in EXPO) [9] EXPO [9] 5 (V, 4O) XRS82 [10,11] 3359 304 12b 39 10 12 distances, 16 angles 10.0 12.1 0.05 expðG cos 2aÞ [100], 20.09(3)
a
In XRS82 so-called ‘learned’ peak shape is used. Selected by user standard peak is decomposed into set of base functions. These functions in tabulated form are used next by profile fitting procedure. b Structure was solved and refined initially in Cc space group, in such a case number of independent atoms was 21.
Table 2 Atomic co-ordinates and isotropic temperature factors Atom
x
y
z
U
V Cl O1 O3 O4 C1 C2 C3 C4 C5 C6 O2
0 0.076(1) 0.078(1) 0 0 0.103(2) 0.158(3) 0.183(3) 0.147(4) 0.100(3) 0.243(3) 0.182(3)
0.198(1) 0.198(1) 0.198(2) 0.369(4) 20.010(4) 0.247(2) 0.179(3) 0.276(5) 0.412(5) 0.391(4) 0.255(6) 0.050(5)
0.2500 0.483(2) 0.115(3) 0.2500 0.2500 0.002(5) 20.085(7) 20.186(6) 20.16(1) 20.04(1) 20.287(8) 20.060(7)
0.04(1) 0.07(1) 0.07(2) 0.02(6) 0.02 0.08(1) 0.08 0.08 0.08 0.08 0.05 0.05(2)
The e.s.d of the last significant digit is given in parentheses. The e.s.d’s were calculated according to Scott [12]. The U value without e.s.d were constrained to be equal to proceeding one.
the molecule using this known fragment as initial information in the Le Bail procedure. The structure was completed by the Rietveld method using XRS-82 [10,11] program. Actually, the structure was solved in Ccð9Þ space group, however, when all atoms were found it became obvious that the structure can be described by C2=c space group without increasing the R factors. Since the temperature factor for the O3 atom was refined to negative value, all the atoms were divided into six groups and their B factors were constrained to be equal to each other within the group during the refinement, which allowed to refine all the B factors to positive values without a change in R factors. The difference pattern is not flat in some regions, but it is not caused by existence of any known vanadate phase listed in PDF-2. It is probably due to errors in description of a peak shape (Fig. 1).
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
155
Fig. 1. Calculated (upper), observed (middle), and difference (lower) Rietveld profiles.
4. Structure description and discussion
Table 3 ˚) Selected bond lengths (A Atom 1
Atom 2
Bond
e.s.d
V
O3 O1, O1_3a O4 Cl, Cl_3 O2_1b O1, O1_3 O1 C5 C2 O2 C3 C4 C6 C5
1.64 1.99 2.00 2.39 3.20 3.11 1.20 1.43 1.50 1.33 1.38 1.50 1.53 1.44
(4) (4) (4) (2) (5) (5) (6) (5) (7) (6) (7) (7) (8) (11)
Cl C1
C2 C3 C4 a b
Symmetry codes: _1 ¼ x; 2y; z þ 1=2; _3 ¼ 2x; y; 2z þ 1=2: Intermolecular hydrogen bond.
The molecule with numbering scheme is presented in Fig. 2(a). Fig. 2(b) shows molecular packing. Lists of atomic co-ordinations and bond distances are given in Tables 2 and 3. Co-ordination polyhedron of vanadium atom, which actually is a distorted octahedron with C2 symmetry, consists of two oxygen atoms belonging to ˚ ), two two Hmcp groups (V–O1 distance 1.99(4) A ˚ ), one water chlorine atoms (V–Cl distance 2.39(2) A ˚ ) and one oxygen molecule (V–O4 distance 2.00(4) A ˚ ) (see Fig. 2(a) and atom (V–O3 distance 1.64(4) A Table 3). Each VO(Hmcp)2Cl2·H2O molecule is connected with two analogous molecules by intermolecular hydrogen bonds, forming infinite strips parallel to z axis (see Fig. 2(b)). The Hmcp rings are essentially planar, the angle between two Hmcp rings connected to the same V atom is ,268. According to the literature [5], Hmcp can exist either in dicarbonyl or enol form; in the solid state Hmcp hydrate exists as the enol form. In our studies, both forms were tested in Rietveld refinement. Slightly better results were obtained for the enol
156
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157
Fig. 2. (a) Molecular structure with numbering scheme. (b) Drawing of the molecular packing along [010] (an a axis is oriented upwards). Dashed lines indicate intermolecular H-bonds.
form. Since the differences between R factors for both forms were not large, some kind of equilibrium between both forms (with the enol form as dominating one) can be assumed. Unexpectedly large e.s.d of C4 – C5 bond distance can be attributed to equilibrium between tautomeric forms and dynamic disorder in non-planar Hmcp rings in dicarbonyl form. It can be expected that each vanadium atom is coordinated by two Hmcp molecules, and chelate compound is formed. However, the arrangement of atoms found by the Fourier method clearly shows that the vanadium atom is co-ordinated by two Hmcp groups, and each of these groups is connected to vanadium by only one oxygen atom. This observation is in agreement with the spectroscopic data indicating the presence of OH group in the structure. If the V and Hmcp molecule had formed chelate compound, OH group would have not been observed. Described structure was solved by conventional powder diffraction methods. The powerful crystal structure solution package EXPO [9] was used to decompose powder diffraction pattern into intensities, next by the direct methods the structure model was built. Subsequently, by the Rietveld method the missing atoms were found. In the presented work, initial model consisted of five atoms and represented 41% of electrons of the whole molecule. To sum up, it is evident from the presented
research that with structure complexity about 20 atoms in the asymmetric unit it is possible to solve crystal structure ‘ab initio’ using laboratory powder diffraction data, even in the case of wrong assumption concerning symmetry centre and without exact knowledge of the molecular structure.
Acknowledgments The support of Polish Committee of Science Research (KBN, 0312/T09/98/15) is kindly acknowledged.
References [1] V. Badmaev, A. Prakash, M. Majeed, J. Altern. Complement Med. 5 (1999) 273–279. [2] B.A. Reul, S.S. Amin, J.P. Buchet, L.N. Ongemba, D.C. Crans, S.M. Brichard, Br. J. Pharmacol. 126 (1999) 467 –477. [3] P. Poucheret, S. Verma, M.D. Grynaps, J.H. McNeill, Mol. Cell. Biochem. 188 (1998) 73 –80. [4] A.M. Kordowiak, R. Trzos, R. Grybos´, Horm. Metab. Res. 29 (1997) 101 –105. [5] S.E. Fayle, J.A. Gerrard, H.E. Nursten, P.J. Steel, Acta Crystallogr. C54 (1998) 404–405. [6] R. Grybos´, A. Samotus, Submitted for publication. [7] J.W. Visser, J. Appl. Crystallogr. 2 (1969) 89–95. [8] W. Łasocha, K. Lewinski, Proszki—a system of programs for
W. Łasocha, R. Grybos´ / Journal of Molecular Structure 641 (2002) 153–157 powder diffraction data analysis, J. Appl. Crystallogr. 27 (1994) 437–438. [9] A. Altomare, M.C. Burla, G. Cascarano, C. Giacovazzo, A. Guagliardi, A.G.G. Moliterni, G. Polidori, EXPO: a program for full pattern decomposition and crystal structure solution, J. Appl. Crystallogr. 32 (1999) 339 –340. [10] Ch. Baerlocher, XRS-82, The X-ray Rietveld System,
157
Institut f.Kristallographie, ETH, Zurich, Switzerland, 1992. [11] D. Mucha, W. Łasocha, XRS-82 runs on PC 386/486 computers, J. Appl. Crystallogr. 27 (1994) 201 –202. PC version of XRS. [12] H.G.J. Scott, Appl. Crystallogr. 16 (1983) 159–163.