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\begin{document} |
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\LARGE |
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Supplemental Material |
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\normalsize |
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\vspace{1cm} |
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|
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Canonical ensemble (NVT) molecular dynamics calculations were |
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performed using the OOPSE molecular mechanics package.\cite{Meineke05} |
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All molecules were treated as rigid bodies, with orientational motion |
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propagated using the symplectic DLM integration method. Details about |
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the implementation of this technique can be found in a recent |
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publication.\cite{Dullweber1997} |
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|
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Thermodynamic integration is an established technique for |
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determination of free energies of condensed phases of |
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materials.\cite{Frenkel84,Hermens88,Meijer90,Baez95a,Vlot99}. This |
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method, implemented in the same manner illustrated by B\`{a}ez and |
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Clancy, was utilized to calculate the free energy of several ice |
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crystals at 200 K using the TIP3P, TIP4P, TIP5P, SPC/E, SSD/RF, and |
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SSD/E water models.\cite{Baez95a} Liquid state free energies at 300 |
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and 400 K for all of these water models were also determined using |
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this same technique, in order to determine melting points and to |
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generate phase diagrams. System sizes were 648 or 1728 molecules for |
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ice B, 1024 or 1280 molecules for ice $I_h$, 1000 molecules for ice |
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$I_c$, and 1024 molecules for Ice-{\it i} and the liquid state |
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simulations. The larger crystal sizes were necessary for simulations |
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involving larger cutoff values. All simulations were carried out at |
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densities which correspond to a pressure of approximately 1 atm at |
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their respective temperatures. |
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|
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Thermodynamic integration involves a sequence of simulations during |
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which the system of interest is converted into a reference system for |
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which the free energy is known analytically. This transformation path |
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is then integrated in order to determine the free energy difference |
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between the two states: |
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\begin{equation} |
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\Delta A = \int_0^1\left\langle\frac{\partial V(\lambda |
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)}{\partial\lambda}\right\rangle_\lambda d\lambda, |
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\end{equation} |
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where $V$ is the interaction potential and $\lambda$ is the |
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transformation parameter that scales the overall potential. |
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Simulations are distributed strategically along this path in order to |
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sufficiently sample the regions of greatest change in the potential. |
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Typical integrations in this study consisted of $\sim$25 simulations |
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ranging from 300 ps (for the unaltered system) to 75 ps (near the |
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reference state) in length. |
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|
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For the thermodynamic integration of molecular crystals, the Einstein |
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crystal was chosen as the reference system. In an Einstein crystal, |
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the molecules are restrained at their ideal lattice locations and |
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orientations. Using harmonic restraints, as applied by B\`{a}ez and |
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Clancy, the total potential for this reference crystal |
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($V_\mathrm{EC}$) is the sum of all the harmonic restraints, |
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\begin{equation} |
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V_\mathrm{EC} = \frac{K_\mathrm{v}r^2}{2} + \frac{K_\theta\theta^2}{2} + |
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\frac{K_\omega\omega^2}{2}, |
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\end{equation} |
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where $K_\mathrm{v}$, $K_\mathrm{\theta}$, and $K_\mathrm{\omega}$ are |
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the spring constants restraining translational motion and deflection |
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of and rotation around the principle axis of the molecule |
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respectively. These spring constants are typically calculated from |
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the mean-square displacements of water molecules in an unrestrained |
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ice crystal at 200 K. For these studies, $K_\mathrm{r} = 4.29$ kcal |
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mol$^{-1}$, $K_\theta\ = 13.88$ kcal mol$^{-1}$, and $K_\omega\ = |
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17.75$ kcal mol$^{-1}$. It is clear from Fig. \ref{waterSpring} that |
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the values of $\theta$ range from $0$ to $\pi$, while $\omega$ ranges |
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from $-\pi$ to $\pi$. The partition function for a molecular crystal |
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restrained in this fashion can be evaluated analytically, and the |
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Helmholtz Free Energy ({\it A}) is given by |
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\begin{eqnarray} |
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A = E_m\ -\ kT\ln \left (\frac{kT}{h\nu}\right )^3&-&kT\ln \left |
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[\pi^\frac{1}{2}\left (\frac{8\pi^2I_\mathrm{A}kT}{h^2}\right |
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)^\frac{1}{2}\left (\frac{8\pi^2I_\mathrm{B}kT}{h^2}\right |
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)^\frac{1}{2}\left (\frac{8\pi^2I_\mathrm{C}kT}{h^2}\right |
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)^\frac{1}{2}\right ] \nonumber \\ &-& kT\ln \left [\frac{kT}{2(\pi |
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K_\omega K_\theta)^{\frac{1}{2}}}\exp\left |
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(-\frac{kT}{2K_\theta}\right)\int_0^{\left (\frac{kT}{2K_\theta}\right |
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)^\frac{1}{2}}\exp(t^2)\mathrm{d}t\right ], |
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\label{ecFreeEnergy} |
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\end{eqnarray} |
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where $2\pi\nu = (K_\mathrm{v}/m)^{1/2}$, and $E_m$ is the minimum |
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potential energy of the ideal crystal.\cite{Baez95a} |
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|
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\begin{figure} |
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\begin{center} |
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\includegraphics[width=3in]{rotSpring.eps} |
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\caption{Possible orientational motions for a restrained molecule. |
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$\theta$ angles correspond to displacement from the body-frame {\it |
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z}-axis, while $\omega$ angles correspond to rotation about the |
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body-frame {\it z}-axis. $K_\theta$ and $K_\omega$ are spring |
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constants for the harmonic springs restraining motion in the $\theta$ |
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and $\omega$ directions.} |
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\label{waterSpring} |
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\end{center} |
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\end{figure} |
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|
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In the case of molecular liquids, the ideal vapor is chosen as the |
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target reference state. There are several examples of liquid state |
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free energy calculations of water models present in the |
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literature.\cite{Hermens88,Quintana92,Mezei92,Baez95b} These methods |
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typically differ in regard to the path taken for switching off the |
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interaction potential to convert the system to an ideal gas of water |
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molecules. In this study, we applied one of the most convenient |
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methods and integrated over the $\lambda^4$ path, where all |
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interaction parameters are scaled equally by this transformation |
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parameter. This method has been shown to be reversible and provide |
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results in excellent agreement with other established |
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methods.\cite{Baez95b} |
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|
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Charge, dipole, and Lennard-Jones interactions were modified by a |
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cubic switching between 100\% and 85\% of the cutoff value (9 \AA). |
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By applying this function, these interactions are smoothly truncated, |
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thereby avoiding the poor energy conservation which results from |
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harsher truncation schemes. The effect of a long-range correction was |
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also investigated on select model systems in a variety of manners. |
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For the SSD/RF model, a reaction field with a fixed dielectric |
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constant of 80 was applied in all simulations.\cite{Onsager36} For a |
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series of the least computationally expensive models (SSD/E, SSD/RF, |
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TIP3P, and SPC/E), simulations were performed with longer cutoffs of |
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10.5, 12, 13.5, and 15 \AA\ to compare with the 9 \AA\ cutoff results. |
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Finally, the effects provided by an Ewald summation were estimated for |
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TIP3P and SPC/E by performing single configuration calculations with |
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Particle-Mesh Ewald (PME) in the TINKER molecular mechanics software |
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package.\cite{Tinker} The calculated energy difference in the presence |
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and absence of PME was applied to the previous results in order to |
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predict changes to the free energy landscape. |
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|
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Additionally, $g_{OO}(r)$ and $S(\vec{q})$ plots were generated for |
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the two Ice-{\it i} variants (along with example ice $I_h$ and $I_c$ |
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plots) at 77K, and they are shown in figures \ref{fig:gofr} and |
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\ref{fig:sofq}. The $S(\vec{q})$ is related to a three dimensional |
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Fourier transform of the radial distribution function, which |
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simplifies to the following expression: |
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|
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\begin{equation} |
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S(q) = 1 + 4\pi\rho\int_{0}^{\infty} r^2 \frac{\sin kr}{kr}g_{OO}(r)dr, |
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\label{sofqEq} |
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\end{equation} |
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|
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where $\rho$ is the number density. To obtain a good estimation of |
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$S(\vec{q})$, $g_{OO}(r)$ needs to extend to large $r$ values. Thus, |
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simulations to obtain these plots were run on crystals eight times the |
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size of those used in the thermodynamic integrations. |
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|
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\begin{figure} |
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\begin{center} |
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\includegraphics[width=4in]{iceGofr.eps} |
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\caption{Radial distribution functions of ice $I_h$, $I_c$, and |
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Ice-{\it i} calculated from from simulations of the SSD/RF water model |
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at 77 K. The Ice-{\it i} distribution function was obtained from |
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simulations composed of TIP4P water.} |
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\label{fig:gofr} |
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\end{center} |
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\end{figure} |
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|
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\begin{figure} |
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\begin{center} |
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\includegraphics[width=4in]{sofq.eps} |
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\caption{Predicted structure factors for ice $I_h$, $I_c$, Ice-{\it i}, |
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and Ice-{\it i}$^\prime$ at 77 K. The raw structure factors have |
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been convoluted with a gaussian instrument function (0.075 \AA$^{-1}$ |
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width) to compensate for the trunction effects in our finite size |
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simulations.} |
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\label{fig:sofq} |
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\end{center} |
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\end{figure} |
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|
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|
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\newpage |
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|
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\bibliographystyle{jcp} |
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\bibliography{iceiSupplemental} |
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\end{document} |
