| 193 |
|
being applied by the charge at each atom. For the potential, the |
| 194 |
|
origin of the box was used as a point of reference. This allows for a |
| 195 |
|
potential value to be added to each atom as the molecule move in space |
| 196 |
< |
within the box. |
| 196 |
> |
within the box. Fields values were applied in a manner representing |
| 197 |
> |
those that would be applable in an experimental set-up. The assumed |
| 198 |
> |
electrode seperation was 5 nm and the field was input as |
| 199 |
> |
$\frac{V}{\text{\AA}}$. The three field environments were, 1) no field |
| 200 |
> |
applied, 2) 0.01 $\frac{V}{\text{\AA}}$ (0.5 V) and 3) 0.024 |
| 201 |
> |
$\frac{V}{\text{\AA}}$ (1.2 V). Each field was applied in the |
| 202 |
> |
Z-axis of the simulation box. |
| 203 |
|
|
| 204 |
|
For quantum calculation of the nitrile bond frequency, Gaussian 09 was |
| 205 |
|
used. A single 5CB molecule was selected for the center of the |
| 206 |
|
cluster. For effects from molecules located near the chosen nitrile |
| 207 |
|
group, parts of molecules nearest to the nitrile group were |
| 208 |
< |
included. For the body not including the tail, any atom within 6~\AA\ |
| 208 |
> |
included. For the body not including the tail, any atom within 6~\AA |
| 209 |
|
of the midpoint of the nitrile group was included. For the tail |
| 210 |
< |
structure, the whole tail was included if a tail atom was within 4~\AA\ |
| 210 |
> |
structure, the whole tail was included if a tail atom was within 4~\AA |
| 211 |
|
of the midpoint. If the tail did not include any atoms from the ring |
| 212 |
|
structure, it was considered a propane molecule and included as |
| 213 |
|
such. Once the clusters were generated, input files were created that |
| 214 |
< |
stretched the nitrile bond along its axis from 0.87 to 1.52~\AA\ at |
| 214 |
> |
stretched the nitrile bond along its axis from 0.87 to 1.52~\AA at |
| 215 |
|
increments of 0.05~\AA. This generated 13 single point energies to be |
| 216 |
|
calculated. The Gaussian files were run with B3LYP/6-311++G(d,p) with |
| 217 |
< |
no other keywords. Once completed, the central nitrile bond frequency |
| 217 |
> |
no other keywords for the zero field simulation. Simulations with |
| 218 |
> |
fields applied included the keyword ''Field=Z+5'' to match the |
| 219 |
> |
external field applied in molecular dynamic runs. Once completed, the central nitrile bond frequency |
| 220 |
|
was calculated with a Morse fit. Using this fit and the solved energy |
| 221 |
|
levels for a Morse oscillator, the frequency was found. |
| 222 |
|
|
| 223 |
|
Classical nitrile bond frequencies were found by replacing the rigid |
| 224 |
< |
cyanide bond with a flexible Morse oscillator bond. Once replaced, the |
| 224 |
> |
cyanide bond with a flexible Morse oscillator bond |
| 225 |
> |
($r_0= 1.157437$ \AA , $D_0 = 212.95$ and |
| 226 |
> |
$\beta = 2.67566$) . Once replaced, the |
| 227 |
|
systems were allowed to re-equilibrate in NVT for 100 ps. After |
| 228 |
|
re-equilibration, the system was run in NVE for 20 ps with a snapshot |
| 229 |
|
spacing of 1 fs. These snapshot were then used in bond correlation |
