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Interaction models of the Si(OH)2 functionality with Zn2+ cation in simplified biological environments: a DFT study

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Abstract

We report a DFT study (M06L/cc-pVDZ) of the interactions between the Si(OH)2 group in three simplified gem-silanediols [i.e., N-[dihydroxy(methyl)silyl] methyl}formamide (DHSF), 3-[dihydroxy (methyl) silyl] propanamide (DHSP), and 3,3′-(dihydroxysilanediyl)dipropanamide (DHSDP)], which have a similar structure to silanediol-based inhibitors of metalloproteases, and simplified active site models: [Zn(Imdz)3–OH2]2+ and [Zn(Imdz)2R–OH2]2+, where R can be a formaldehyde, an acetone, or an acetic acid molecule. These models partly resemble the structure of the first coordination sphere of some metalloproteases (e.g., angiotensin I converting enzyme and thermolysin). Different types of bonding patterns were found for the systems into study. The three related silanediols may coordinate with the zinc dication in monodentate, pseudo-bidentate, and pseudo-tridentate way. Pseudo-bidentate interaction was reported to be that corresponding to the silanediol transition-state-analog of the thermolysin enzyme as confirmed by the X-ray structural study (Juers et al., Biochemistry 44:16524–16528, 2005). The binding ability of the mentioned silanediols was determined as the energy of the water displacement reaction for the mentioned active sites models in gas phase and in water solution (PCM model). The calculated binding energies point out to the higher strength of the pseudo-bidentate Zn2+–MBG interaction. Moreover, DHSDP ligand is calculated to be the strongest MBG for Zn2+ in both active sites models. NBO population analysis and the AIM methodology were implemented as a tool for evaluating electronic structure of the complexes. The results obtained may point out to the fact that the higher the electronic delocalization around the metal center is, the stronger the interaction between the MBG and the active site, bringing about a higher binding energy.

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Acknowledgments

The authors thank Andalusian government for funding (FQM173). P.G.R.O. thanks Spanish Ministerio de Educación for a Ph.D. studentship (AP2009-3949) supporting this work.

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Authors and Affiliations

  1. Department of Physical and Analytical Chemistry, Experimental Sciences Faculty, University of Jaén, Campus Las Lagunillas, 23071, Jaén, Spain

    M. P. G. Rodríguez Ortega, M. Montejo & J. J. López González

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  1. M. P. G. Rodríguez Ortega
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  2. M. Montejo
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  3. J. J. López González
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Correspondence to J. J. López González.

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Rodríguez Ortega, M.P.G., Montejo, M. & López González, J.J. Interaction models of the Si(OH)2 functionality with Zn2+ cation in simplified biological environments: a DFT study. Struct Chem 25, 127–138 (2014). https://doi.org/10.1007/s11224-013-0258-5

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