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1 gezelter 4007 \documentclass[journal = jpccck, manuscript = article]{achemso}
2     \setkeys{acs}{usetitle = true}
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23 gezelter 4007 \usepackage[colorinlistoftodos]{todonotes}
24     \usepackage[version=3]{mhchem} % this is a great package for formatting chemical reactions
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40    
41    
42     \title{Nitrile vibrations as reporters of field-induced phase
43     transitions in liquid crystals}
44     \author{James M. Marr}
45     \author{J. Daniel Gezelter}
46     \email{gezelter@nd.edu}
47     \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
48     Department of Chemistry and Biochemistry\\
49     University of Notre Dame\\
50     Notre Dame, Indiana 46556}
51    
52     \date{\today}
53    
54     \begin{document}
55    
56     \maketitle
57    
58     \begin{doublespace}
59    
60     \begin{abstract}
61     The behavior of the spectral lineshape of the nitrile group in
62     4-Cyano-4'-pentylbiphenyl (5CB) in response to an applied electric
63     field has been simulated using both classical molecular dynamics
64     simulations and {\it ab initio} quantum mechanical calculations of
65     liquid-like clusters. This nitrile group is a well-known reporter
66     of local field effects in other condensed phase settings, and our
67     simulations suggest that there is a significant response when 5CB
68     liquids are exposed to a relatively large external field. However,
69     this response is due largely to the field-induced phase transition.
70     We observe a peak shift to the red of nearly 40
71     cm\textsuperscript{-1}. These results indicate that applied fields
72     can play a role in the observed peak shape and position even if
73     those fields are significantly weaker than the local electric fields
74     that are normally felt within polar liquids.
75     \end{abstract}
76    
77     \newpage
78    
79     \section{Introduction}
80    
81     The fundamental characteristic of liquid crystal mesophases is that
82     they maintain some degree of orientational order while translational
83     order is limited or absent. This orientational order produces a
84     complex direction-dependent response to external perturbations like
85     electric fields and mechanical distortions. The anisotropy of the
86     macroscopic phases originates in the anisotropy of the constituent
87     molecules, which typically have highly non-spherical structures with a
88     significant degree of internal rigidity. In nematic phases, rod-like
89     molecules are orientationally ordered with isotropic distributions of
90     molecular centers of mass, while in smectic phases, the molecules
91     arrange themselves into layers with their long (symmetry) axis normal
92     ($S_{A}$) or tilted ($S_{C}$) with respect to the layer planes.
93    
94     The behavior of the $S_{A}$ phase can be partially explained with
95     models mainly based on geometric factors and van der Waals
96     interactions. However, these simple models are insufficient to
97     describe liquid crystal phases which exhibit more complex polymorphic
98     nature. X-ray diffraction studies have shown that the ratio between
99     lamellar spacing ($s$) and molecular length ($l$) can take on a wide
100     range of values.\cite{Gray:1984hc,Leadbetter:1976vf,Hardouin:1980yq}
101     Typical $S_{A}$ phases have $s/l$ ratios on the order of $0.8$, while
102     for some compounds, e.g. the 4-alkyl-4'-cyanobiphenyls, the $s/l$
103     ratio is on the order of $1.4$. Molecules which form $S_{A}$ phases
104     can exhibit a wide variety of subphases like monolayers ($S_{A1}$),
105     uniform bilayers ($S_{A2}$), partial bilayers ($S_{\tilde A}$) as well
106     as interdigitated bilayers ($S_{A_{d}}$), and often have a terminal
107     cyano or nitro group. In particular lyotropic liquid crystals (those
108     exhibiting liquid crystal phase transition as a function of water
109     concentration) often have polar head groups or zwitterionic charge
110     separated groups that result in strong dipolar
111     interactions.\cite{Collings97} Because of their versatile polymorphic
112     nature, polar liquid crystalline materials have important
113     technological applications in addition to their immense relevance to
114     biological systems.\cite{Collings97}
115    
116     Experimental studies by Levelut {\it et al.}~\cite{Levelut:1981eu}
117     revealed that terminal cyano or nitro groups usually induce permanent
118     longitudinal dipole moments on the molecules.
119    
120     Liquid crystalline materials with dipole moments located at the ends
121     of the molecules have important applications in display technologies
122     in addition to their relevance in biological systems.\cite{LCapp}
123    
124     Many of the technological applications of the lyotropic mesogens
125     manipulate the orientation and structuring of the liquid crystal
126     through application of local electric fields.\cite{?}
127     Macroscopically, this restructuring is visible in the interactions the
128     bulk phase has with scattered or transmitted light.\cite{?}
129    
130     4-Cyano-4'-pentylbiphenyl (5CB), has been a model for field-induced
131     phase changes due to the known electric field response of the liquid
132     crystal\cite{Hatta:1991ee}. It was discovered (along with three
133     similar compounds) in 1973 in an effort to find a LC that had a
134     melting point near room temperature.\cite{Gray:1973ca} It's known to
135     have a crystalline to nematic phase transition at 18 C and a nematic
136     to isotropic transition at 35 C.\cite{Gray:1973ca}
137    
138     Nitrile groups can serve as very precise electric field reporters via
139     their distinctive Raman and IR signatures.\cite{Boxer:2009xw} The
140     triple bond between the nitrogen and the carbon atom is very sensitive
141     to local field changes and is observed to have a direct impact on the
142     peak position within the spectrum. The Stark shift in the spectrum
143     can be quantified and mapped into a field value that is impinging upon
144     the nitrile bond. This has been used extensively in biological systems
145     like proteins and enzymes.\cite{Tucker:2004qq,Webb:2008kn}
146    
147     To date, the nitrile electric field response of
148     4-Cyano-4'-n-alkylbiphenyl liquid crystals has not been investigated.
149     While macroscopic electric fields applied across macro electrodes show
150     the phase change of the molecule as a function of electric
151     field,\cite{Lim:2006xq} the effect of a microscopic field application
152     has not been probed. These previous studies have shown the nitrile
153     group serves as an excellent indicator of the molecular orientation
154     within the field applied. Blank showed the 180 degree change in field
155     direction could be probed with the nitrile peak intensity as it
156     decreased and increased with molecule alignment in the
157     field.\cite{Lee:2006qd,Leyte:97}
158    
159     While these macroscopic fields worked well at showing the bulk
160     response, the atomic scale response has not been studied. With the
161     advent of nano-electrodes and coupling them with atomic force
162     microscopy, control of electric fields applied across nanometer
163     distances is now possible\cite{citation1}. This application of
164     nanometer length is interesting in the case of a nitrile group on the
165     molecule. While macroscopic fields are insufficient to cause a Stark
166     effect, small fields across nanometer-sized gaps are of sufficient
167     strength. If one were to assume a gap of 5 nm between a lower
168     electrode having a nanoelectrode placed near it via an atomic force
169     microscope, a field of 1 V applied across the electrodes would
170     translate into a field of 2x10\textsuperscript{8} $\frac{V}{M}$. This
171     field is theoretically strong enough to cause a phase change from
172     isotropic to nematic, as well as Stark tuning of the nitrile
173     bond. This should be readily visible experimentally through Raman or
174     IR spectroscopy.
175    
176     Herein, we show the computational investigation of these electric field effects through atomistic simulations. These are then coupled with ab intio and classical spectrum calculations to predict changes experiments should be able to replicate.
177    
178     \section{Computational Details}
179     The force field was mainly taken from Guo et al.\cite{Zhang:2011hh} A
180     deviation from this force field was made to create a rigid body from
181     the phenyl rings. Bond distances within the rigid body were taken from
182     equilibrium bond distances. While the phenyl rings were held rigid,
183     bonds, bends, torsions and inversion centers still included the rings.
184    
185     Simulations were with boxes of 270 molecules locked at experimental
186     densities with periodic boundaries. The molecules were thermalized
187     from 0 kelvin to 300 kelvin. To equilibrate, each was first run in NVT
188     for 1 ns. This was followed by NVE for simulations used in the data
189     collection.
190    
191     External electric fields were applied in a simplistic charge-field
192     interaction. Forces were calculated by multiplying the electric field
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 jmarr 4008 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 gezelter 4007
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 jmarr 4008 included. For the body not including the tail, any atom within 6~\AA
209 gezelter 4007 of the midpoint of the nitrile group was included. For the tail
210 jmarr 4008 structure, the whole tail was included if a tail atom was within 4~\AA
211 gezelter 4007 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 jmarr 4008 stretched the nitrile bond along its axis from 0.87 to 1.52~\AA at
215 gezelter 4007 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 jmarr 4008 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 gezelter 4007 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 jmarr 4008 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 gezelter 4007 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
230     calculation to find the decay structure of the bond in time using the
231     average bond displacement in time,
232     \begin{equation}
233     C(t) = \langle \left(r(t) - r_0 \right) \cdot \left(r(0) - r_0 \right) \rangle
234     \end{equation}
235     %
236     where $r_0$ is the equilibrium bond distance and $r(t)$ is the
237     instantaneous bond displacement at time $t$. Once calculated,
238     smoothing was applied by adding an exponential decay on top of the
239     decay with a $\tau$ of 3000 (have to check this). Further smoothing
240     was applied by padding 20,000 zeros on each side of the symmetric
241     data. This was done five times by allowing the systems to run 1 ns
242     with a rigid bond followed by an equilibrium run with the bond
243     switched back on and the short production run.
244    
245     \section{Results}
246    
247     In order to characterize the orientational ordering of the system, the
248     primary quantity of interest is the nematic (orientational) order
249     parameter. This is determined using the tensor
250     \begin{equation}
251     Q_{\alpha \beta} = \frac{1}{2N} \sum_{i=1}^{N} \left(3 \hat{e}_{i
252     \alpha} \hat{e}_{i \beta} - \delta_{\alpha \beta} \right)
253     \end{equation}
254     where $\alpha, \beta = x, y, z$, and $\hat{e}_i$ is the molecular
255     end-to-end unit vector for molecule $i$. The nematic order parameter
256     $S$ is the largest eigenvalue of $Q_{\alpha \beta}$, and the
257     corresponding eigenvector defines the director axis for the phase.
258     $S$ takes on values close to 1 in highly ordered phases, but falls to
259     zero for isotropic fluids.
260    
261 jmarr 4013 \begin{figure}
262     \includegraphics[trim = 5mm 10mm 3mm 10mm, clip, width=3.25in]{P2}
263     \caption{Order Parameter}
264     \label{fig:orderParameter}
265     \end{figure}
266 gezelter 4007
267 jmarr 4013 \begin{figure}
268     \includegraphics[width=3.25in]{2Spectra}
269     \caption{The classically calculated nitrile bond spetrum from }
270     \label{fig:twoSpectra}
271     \end{figure}
272 jmarr 4012
273    
274 jmarr 4013 \begin{figure}
275     \centering
276     \begin{subfigure}[b]{0.3\textwidth}
277     \includegraphics[trim = 100mm 20mm 50mm 20mm, clip, width=2in]{0x00V_Elip-1}
278     \label{fig:zeroField}
279     \end{subfigure}
280     \begin{subfigure}[b]{0.3\textwidth}
281     \includegraphics[trim = 100mm 20mm 50mm 20mm, clip, width=2in]{0x50V_Elip-1}
282     \label{fig:partialField}
283     \end{subfigure}
284     \begin{subfigure}[b]{0.3\textwidth}
285     \includegraphics[trim = 100mm 20mm 50mm 20mm, clip, width=2in]{1x20V_Elip-1}
286     \label{fig:fullField}
287     \end{subfigure}
288     \caption{Ellipsoid reprsentation of 5CB at three different
289     field strengths, Zero Field (Left), Partial Field (Middle), and Full
290     Field (Right)}\label{fig:Cigars}
291     \end{figure}
292    
293 gezelter 4007 \section{Discussion}
294    
295     \section{Conclusions}
296     \newpage
297    
298     \bibliography{5CB}
299    
300     \end{doublespace}
301     \end{document}