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Crystal structure and X-ray absorption spectroscopy of trimethylarsine oxide dihydrate, (CH3)3AsO⋅2H2O

Published online by Cambridge University Press:  13 July 2020

Joel W. Reid*
Affiliation:
Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada
James A. Kaduk
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, Illinois 60616, USA
Peter E. R. Blanchard
Affiliation:
Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada
*
a)Author to whom correspondence should be addressed. Electronic mail: [email protected]

Abstract

The crystal structure of trimethylarsine oxide dihydrate, (CH3)3AsO⋅2H2O, (TMAO dihydrate) has been solved using parallel tempering with the FOX software package and refined using synchrotron powder diffraction data obtained from beamline 08B1-1 at the Canadian Light Source. Rietveld refinement, performed with the software package GSASII, yielded orthorhombic lattice parameters of a = 13.3937(4) Å, b = 9.53025(30) Å, and c = 11.5951(3) Å (Z = 8, space group Pbca). The Rietveld refined structure was compared with density functional theory calculations performed with VASP and shows reasonable agreement. Arsenic K-edge X-ray absorption spectroscopy analysis also revealed additional information on the electronic structure of the arsenic atom within the TMAO dihydrate structure.

Type
Technical Article
Copyright
Copyright © 2020 International Centre for Diffraction Data

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References

Agency for Toxic Substances and Disease Registry, ATSDR (2020). Priority list of hazardous substances. Available at: http://www.atsdr.cdc.gov/SPL/index.html.Google Scholar
Boultif, A. and Louer, D. (2004). “Powder pattern indexing with the dichotomy method,” J. Appl. Crystallogr. 37, 724731.CrossRefGoogle Scholar
Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E., and Orpen, A. G. (2004). “Retrieval of crystallographically-derived molecular geometry information,” J. Chem. Inf. Comput. Sci. 44, 21332144.CrossRefGoogle ScholarPubMed
Bunker, G. (2010). Introduction to XAFS: A Practical Guide to X-ray Absorption Fine Structure Spectroscopy (Cambridge Press, New York).CrossRefGoogle Scholar
Capitani, E. M. D. (2011). “Arsenic toxicology – a review,” in Arsenic: Natural and Anthropogenic, edited by Deschamps, F. and Matschullat, J. (CRC Press, London), pp. 2737.CrossRefGoogle Scholar
Chen, W. Q., Shi, Y. L., Wu, S. L., and Zhu, Y. G. (2016). “Anthropogenic arsenic cycles: a research framework and features,” J. Cleaner Production 139, 328336.CrossRefGoogle Scholar
Cullen, W. R. and Reimer, K. J. (1989). “Arsenic speciation in the environment,” Chem. Rev. 89, 713764.CrossRefGoogle Scholar
Cullen, W. R., Liu, Q., Lu, X., McKnight-Whitford, A., Peng, H., Popowich, A., Yan, X., Zhang, Q., Fricke, M., Sun, H., and Le, X. C. (2016). “Methylated and thiolated arsenic species for environmental and health research – a review on synthesis and characterization,” J. Environ. Sci. 49, 727.CrossRefGoogle ScholarPubMed
Dovesi, R., Orlando, R., Erba, A., Zicovich-Wilson, C. M., Civalleri, B., Casassa, S., Maschio, L., Ferrabone, M., De La Pierre, M., D'Arco, P., Noel, Y., Causa, M., Rerat, M., and Kirtman, B. (2014). “CRYSTAL14: a program for the ab initio investigation of crystalline solids,” Int. J. Quant. Chem. 114, 12871313.CrossRefGoogle Scholar
Favre-Nicolin, V., and Černý, R. (2002). “FOX, ‘Free objects for crystallography’: a modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. 35, 734743.CrossRefGoogle Scholar
Fodje, M., Grochulski, P., Janzen, K., Labiuk, S., Gorin, J., and Berg, R. (2014). “08B1-1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source,” J. Synchrotron Rad. 21, 633637.CrossRefGoogle ScholarPubMed
Foust, R. D. Jr., Bauer, A. M., Costanza-Robinson, M., Blinn, D. W., Prince, R. C., Pickering, I. J., and George, G. N. (2016). “Arsenic transfer and biotransformation in a fully characterized freshwater food web,” Coord. Chem. Rev. 306, 558565.CrossRefGoogle Scholar
Gatti, C., Saunders, V. R., and Roetti, C. (1994). “Crystal-field effects on the topological properties of the electron-density in molecular crystals – the case of urea,” J. Chem. Phys. 101, 1068610696.CrossRefGoogle Scholar
George, G. R., Prince, R. C., Singh, S. P., and Pickering, I. J. (2009). “Arsenic K-edge X-ray absorption spectroscopy of arsenic in seafood,” Mol. Nutr. Food Res. 53, 552557.CrossRefGoogle ScholarPubMed
Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., and Hutchison, G. R. (2012). “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform,” J. Cheminform. 4, 17.CrossRefGoogle ScholarPubMed
Hunter, D. A., Goessler, W., and Francesconi, K. A. (1998). “Uptake of arsenate, trimethylarsine oxide, and arsenobetaine by the shrimp Crangon crangon,” Mar. Biol. 131, 543552.CrossRefGoogle Scholar
Jiang, D. T., Chen, N., Zhang, L., Malgorzata, G., Wright, G., Igarashi, R., Beauregard, D., Kirkham, M., and McKibben, M. (2007). “XAFS at canadian light source,” AIP Conf. Proc. 882, 893895.CrossRefGoogle Scholar
Koch, I., McPherson, K., Smith, P., Easton, L., Doe, K. G., and Reimer, K. J. (2007). “Arsenic bioaccessibility and speciation in clams and seaweed from a contaminated marine environment,” Mar. Pollut. Bull. 54, 586594.CrossRefGoogle ScholarPubMed
Kresse, G. and Furthmüller, J. (1996). “Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set,” Phys. Rev. B 54, 11169.CrossRefGoogle ScholarPubMed
Laugier, J. and Bochu, B. (2000). “LMGP-Suite Suite of Programs for the interpretation of X-ray Experiments,” ENSP/Laboratoire des Matériaux et du Génie Physique, BP 46. 38042 Saint Martin d'Hères, France. Available at: http://www.inpg.fr/LMGP and http://www.ccp14.ac.uk/tutorial/lmgp/.Google Scholar
Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriquez-Monge, L., Taylor, R., van de Streek, J., and Wood, P. A. (2008). “Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures,” J. Appl. Crystallogr. 41, 466470.CrossRefGoogle Scholar
Materials Design (2016). MedeA 2.20.4 (Materials Design Inc., Angel Fire, NM).Google Scholar
Matschullat, J. (2011). “The global arsenic cycle revisited,” in Arsenic: Natural and Anthropogenic, edited by Deschamps, F. and Matschullat, J. (CRC Press, London), pp. 326.CrossRefGoogle Scholar
Momma, K. and Izumi, F. (2011). “VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data,” J. Appl. Crystallogr. 44, 12721276.CrossRefGoogle Scholar
Newville, M. (2004). Fundamentals of XAFS (University of Chicago, Chicago), 1.7 ed.Google Scholar
Ng, Y. S., Rodley, G. A., and Robinson, W. T. (1977). “Tri-μ-(trimethylarsine oxide)-hexakis(trimethylarsine oxide)dicalcium(II) tetraperchlorate – a dinuclear calcium complex,” Acta Crystallogr. B 33, 931934.CrossRefGoogle Scholar
O'Boyle, N., Banck, M., James, C. A., Morley, C., Vandermeersch, T., and Hutchison, G. R. (2011). “Open Babel: an open chemical toolbox,” J. Cheminform. 3, 33.CrossRefGoogle ScholarPubMed
Peintinger, M. F., Vilela Oliveira, D., and Bredow, T. (2013). “Consistent Gaussian basis sets of triple-zeta valence with polarization quality for solid-state calculations,” J. Comput. Chem. 34, 451459.CrossRefGoogle ScholarPubMed
Pickett, A. W., McBride, B. C., and Cullen, W. C. (1988). “Metabolism of trimethylarsine,” Appl. Organomet. Chem. 2, 479482.CrossRefGoogle Scholar
Rammohan, A. and Kaduk, J. A. (2018). “Crystal structures of alkali metal (Group 1) citrate salts,” Acta Crystallogr. B 74, 239252.CrossRefGoogle ScholarPubMed
Ravel, B. and Newville, M. (2005). “ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT,” J. Synchrotron Rad. 12, 537541.CrossRefGoogle ScholarPubMed
Rehy, L. and Albers, R. (1990). “Scattering-matrix formulation of curved-wave multiple-scattering theory: application to X-ray-absorption fine structure,” Phys. Rev. B 41, 81398149.Google Scholar
Savage, L., Carey, M., Hossain, M., Rafiqul Islam, M., Mangala, P., de Silva, C. S., Williams, P. N., and Meharg, A. A. (2017). “Elevated trimethylarsine oxide and inorganic arsenic in northern hemisphere summer monsoonal wet deposition,” Environ. Sci. Technol. 51, 1221012218.CrossRefGoogle ScholarPubMed
Smith, P. G., Kock, I., Gordon, R. A., Mandoli, D. F., Chapman, B. D., and Reimer, K. J. (2005). “X-ray absorption near-edge structure analysis of arsenic species for application to biological environmental samples,” Environ. Sci. Technol. 39, 248254.CrossRefGoogle ScholarPubMed
Thompson, P., Cox, D. E., and Hastings, J. B. (1987). “Rietveld refinement of Debye–Scherrer synchrotron X-ray data from A1203,”,” J. Appl. Crystallogr. 20, 7983.CrossRefGoogle Scholar
Toby, B. H. and Von Dreele, R. B. (2013). “GSAS II: the genesis of a modern open-source all-purpose crystallography software package,” J. Appl. Crystallogr. 46, 544549.CrossRefGoogle Scholar
Van de Streek, J. and Neumann, M. A. (2014). “Validation of molecular crystal structures from powder diffraction data with dispersion corrected density functional theory (DFT-D),” Acta Crystallogr. B 70, 10201032.CrossRefGoogle Scholar