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 thermodyna mic 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 solvati on 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 q uadrapole coupling constants (NQCC) at the HF/6 to 31G* level are also repo rted to aid in experimental identification of the complexes. Our results show that if H-bonded and/or covalently bonded serine-Si-Q comp lexes did exist in biogenic silicification, they would not be detected by S i-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 detec table 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. Th e 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 th e acidic pH of the silica deposition vesicle within diatoms. Silicic acid i s energetically favored over organic silicon complexes as the form of disso lved silicon tak;en up by the organism at the basic pH of seawater. Copyrig ht (C) 2001 Elsevier Sciene Ltd.