For a typical network breaking dissolution reaction, a single water molecule was introduced by removing the bridging oxygen between two silicon ions (or an Si and P), and placing an OH group on each of the two network formers. The simulation was then run for 80,000 timesteps ( t = 2 fs) with temperature scaling for the first 60,000 timesteps. Configurational energies were then calculated as averages over the
final 20,000 timesteps. Similar to Chapter 5, a discussion of the evolution of procedural parameters for the network hydrolysis reactions follows.
At first, six bond-breaking experiments were performed for each of the three compositions (three involving a P-O-Si linkage and three involving a Si-O-Si linkage). In each case, this was attempted by first removing the oxygen ion in the linkage and then placing an oxygen ion 1.62 Å above (in the z-direction) each network former, and a hydrogen ion 1.00 Å above each of those two oxygen ions.
These distances are approximately the equilibrium separations expected for their respective bonds. Placing all OH groups directly above the network formers was chosen for simplicity and led to some problems, which are addressed later.
This approach led to OH groups becoming detached from their network former in over half of the cases. This detachment of OH groups during simulation was a recurring problem throughout this research and demanded attention particularly for the hydrolysis reactions, but also for some multiple ion-exchange experiments (see Chapter 5).
The first attempt in solving this problem was to look more closely at the starting configuration in each case, primarily through the SGI visualization program CERIUS2. It was noticed that by “blindly” placing an OH group directly in the z- direction could easily cause some interference with another oxygen ion on the same network former. For example, the original Si-O-Si linkage may be nearly in the xy- plane of the simulation with another oxygen ion not involved in the linkage pointing nearly directly in the z-direction. Once the bond is broken and the OH group is placed, there now exists an oxygen and OH group very close to one another, such that, on restarting the simulation, the two species repulse each other with a force such that the OH group is released from the network former. In most cases, an NBO from a nearby network former would attach itself to the (now) three-coordinated network former, creating a BO.
In the cases of these troublesome simulations, the starting configurations of the OH groups were manually manipulated to fill the empty space between the network formers involved in the reaction without interfering with one another. In a few cases, this worked, but many of the simulations still had the problem of detaching
OH groups. A number of additional reactions for other linkages were attempted to see if the problem was related to local structure, and thus perhaps less of a problem elsewhere on the surfaces. However, it was still found that about half of all attempts failed to result in two OH groups fully attached to network former ions.
The next attempt to solve this problem was based on the observation that it appeared that OH groups were preferentially released from Si ions, rather than P ions.
One of the differences between the simulated P-OH and Si-OH linkages is that there exists a three-body term for Si-OH linkages, which imposes an extra “constraint” on the interaction of OH groups with the network former. So, the Si-O-H three-body term was eliminated for a number of simulations. This was also based on some initial results of using the same potential on an SiO2 surface, where it was found that for some bond-breaking simulations, an improvement of retaining a hydrogen ion with its associated oxygen by eliminating the Si-O-H three-body potential. This lead to values of Si-O-H angles that were much higher as compared to quantum mechanical calculations.279 However, no improvement in the ability of Si ions to retain an OH group resulted for the bioactive glass surface.
The next attempt at solving the problem addressed the issue of timestep length. It was noticed that when the OH groups detached, it was almost exclusively within the first 1000 timesteps of the simulation. It was hypothesized that the timestep was too large, such that the forces (which no doubt changed quite significantly due to the introduction of the OH groups) caused the ions to move “too much” during the initial timesteps as the local environment accommodated them. To
“slow down” the dynamics of the reaction and allow a more moderate initial response by the local environment, the timestep was decreased from 2 fs to 1 fs. This resulted in some improvement in the number of simulations that “worked,” though there were still some problems, even for those simulations in which the updated timestep as well as manual manipulation solutions were employed. This smaller timestep was used for all subsequent surface simulations cited in this work. Attempts at 0.5 fs timesteps showed no improvement, so the timestep was kept at 1 fs.
These two fixes had greatly improved the efficiency of “good” bond-breaking simulations, but an additional approach proved to be even more helpful. Built into
the DL_POLY code is a simulation control directive named ‘zero,’ a 0 K MD simulation (essentially, an energy minimization). This feature acts to minimize the local forces on ions, which was essentially the problem these simulations seemed to face. Simulations using the ‘zero’ directive were tested, and it was found that the 300 K simulations reached approximately 0 K (below 1 K) within a few hundred timesteps. It was determined that an 800-timestep ‘zero’ simulation run was sufficient to remove the problematic forces in most cases (except for some of those for which “overlapping” oxygen ions existed in the original configuration, as mentioned above) as there was an increased efficiency of “good” bond-breaking simulations when the 800-timestep ‘zero’ run was performed prior to the nominal 80,000 timestep 300 K run. The “shock” of returning to 300 K from 0 K did not seem to disrupt the simulation. The 800-timestep ‘zero’ run was tested on simulations which were previously “good” (without implementation of any of these additional solutions), and similar results followed with differences in reaction energies on the order of 0.2-0.3 eV, within the root-mean-squared (r.m.s.) fluctuations of configurational energy observed in the simulations over the last 20,000 timesteps.
Another attempt to increase the number of “good” simulations included placing the oxygen of each OH group 1 Å above the cation, and the hydrogen 0.5 Å above the oxygen. The bond distances were shortened to keep the OH group initially closer to the network former and hopefully reduce the tendency for it to be pulled away from the network former (a similar technique was implemented for the ion- exchange reactions discussed in Chapter 5). Little improvement was found.
Finally, to reduce some of the inconsistency and problems associated with placing the OH groups in the z-direction relative to the network former ions, it was decided that the OH groups should be placed in the direction of the original BO. To do this without overlapping H ions, the two bond distances were reduced to 0.5 Å.
An example of a problematic initial configuration is given in Figure 6.1. An example of the optimized initial configuration used in the simulations is shown in Figure 6.2.
Figure 6.1. Example of “bad” OH group placement for a hydrolysis reaction on ion- exchanged surface; a) original configuration, b) BO removed and 2 OH groups placed, and c) one OH group leaves while nearby NBO become BO to preserve 4- coordination of P ion.
Figure 6.2. Example of “good” OH group placement for a hydrolysis reaction; a) before hydroxylation and b) after OH-placement.