Formation energies and NMR chemical shifts calculated for putative serine-silicate complexes in silica biomineralization

We have used ab initio Hartree-Fock (HF) theory to determine the thermodynamic feasibility for the formation of H-bonded and covalently bonded serine-silicic acid complexes, with Si in quadra- and penta-coordination (Si-Q and Si-P, respectively). Such complexes have been suggested previously to play a role in silica biomineralization, a process that controls silicon fluxes in the oceans, and thus, global silicon cycling. Geometries and energies were obtained at the HF/6-31G* level, where solvation was represented by a spherical cavity in a dielectric continuum. Si-29,C-13, acid O-17 NMR shifts at the HF/6-311+G(2d,p) level, and O-17 nuclear quadrapole coupling constants (NQCC) at the HF/6 to 31G* level are also reported to aid in experimental identification of the complexes. Our results show that if H-bonded and/or covalently bonded serine-Si-Q complexes did exist in biogenic silicification, they would not be detected by Si-29-NMR because their predicted isotropic shifts are similar to inorganic Si-Q. The penta-coordinated complex, [serO(P)Si(OH)(4)](1-), would be detectable because of large Si-29 isotropic (-121 to -142.1 ppm) and anisotropic shifts (110-142 ppm) and diagnostically long Si-P-O bond lengths (1.7-1.9 Angstrom). C-13 shifts are found to be insensitive to the type of bonding. O-17 shifts are the most sensitive to bond type and Si coordination number, because it is the most directly involved nucleus in the C-O-Si bonding. The formation of the covalent quadra-coordinated complex, serO(Q)Si(OH)(3) is 10 kcal mol(-1) more exothermic than the H-bonded complex, serOH...Si-Q(OH)(4). The penta-coordinated complex, is thermodynamically unfavorable at the acidic pH of the silica deposition vesicle within diatoms. Silicic acid is energetically favored over organic silicon complexes as the form of dissolved silicon tak;en up by the organism at the basic pH of seawater. Copyright (C) 2001 Elsevier Sciene Ltd.