Herein, we report on Car-Parrinello [1] simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. We show some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlight the importance of accessing subtle details of ion-water interactions from first principles.Calcium plays a vital role in many biological systems, including signal transduction, blood clotting, and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). [2,3] The ability of calcium to coordinate multiple ligands (from six to eight oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water.Experimental studies have used a variety of techniques, including X-ray diffraction (XRD), [4][5][6] extended X-ray absorption fine structure (EXAFS) spectroscopy, [7,8] and neutron diffraction [9,10] to elucidate the coordination of Ca 2 + ions in water. The range of coordination numbers (n C ) inferred by X-ray diffraction studies varies from six to eight, and is consistent with that reported in EXAFS experiments (8 [7] and 7.2 [8] ). A wider range of values (6 to 10) was found in early neutron diffraction studies, [9] depending on concentration, while a more recent measurement by Badyal et al. reports a value close to seven. [10] In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca 2 + ions in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) [4,7,11] and quantum molecular (QM)/MM simulations [12,13] report n C values in the range of eight to ten; in general, n C appears to be highly sensitive to the choice of the ion-water potential used in the calculations.[11] Even ab initio MD simulations have so far obtained conflicting values for n C . For the structure of the first solvation shell Naor et al. found n C = 7 to 8 and a Ca 2 + -oxygen average distance (r Ca-O ) of 2.64 , [14] while Bakó et al. found n C = 6 and r Ca-O = 2.45 . [15] In view of the existing controversies, we have carried out extensive Car-Parrinello [1,16] simulations of Ca 2 + solvation in water, using both a rigid and a flexible water model, up to time scales of 40 ps. Our simulations show variations of coordination numbers from 6, 7 and 8 occurring over intervals of % 0.3 to 0.4 exchanges per picosecond, and yielding average coordination numbers of 6.2 and 7 for flexible and rigid water models, respectively. These results are consistent with ...
We present the results of Car-Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require timescales substantially longer than presently feasible (e.g. simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed.
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