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\title{Nitrile vibrations as reporters of field-induced phase |
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transitions in 4-cyano-4'-pentylbiphenyl (5CB)} |
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\author{James M. Marr} |
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\author{J. Daniel Gezelter} |
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\email{gezelter@nd.edu} |
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\affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\ |
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Department of Chemistry and Biochemistry\\ |
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University of Notre Dame\\ |
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Notre Dame, Indiana 46556} |
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\date{\today} |
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\begin{document} |
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\maketitle |
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\begin{doublespace} |
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\begin{abstract} |
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4-cyano-4'-pentylbiphenyl (5CB) is a liquid-crystal-forming compound |
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with a terminal nitrile group aligned with the long axis of the |
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molecule. Simulations of condensed-phase 5CB were carried out both |
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with and without applied electric fields to provide an understanding |
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of the the Stark shift of the terminal nitrile group. A |
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field-induced isotropic-nematic phase transition was observed in the |
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simulations, and the effects of this transition on the distribution |
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of nitrile frequencies were computed. Classical bond displacement |
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correlation functions exhibit a $\sim 40 \mathrm{~cm}^{-1}$ red |
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shift of a portion of the main nitrile peak, and this shift was |
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observed only when the fields were large enough to induce |
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orientational ordering of the bulk phase. Our simulations appear to |
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indicate that phase-induced changes to the local surroundings are a |
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larger contribution to the change in the nitrile spectrum than |
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direct field contributions. |
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\end{abstract} |
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\newpage |
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\section{Introduction} |
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|
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Nitrile groups can serve as very precise electric field reporters via |
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their distinctive Raman and IR signatures.\cite{Boxer:2009xw} The |
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triple bond between the nitrogen and the carbon atom is very sensitive |
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to local field changes and has been observed to have a direct impact |
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on the peak position within the spectrum. The Stark shift in the |
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spectrum can be quantified and mapped onto a field that is impinging |
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upon the nitrile bond. This has been used extensively in biological |
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systems like proteins and enzymes.\cite{Tucker:2004qq,Webb:2008kn} |
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|
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The response of nitrile groups to electric fields has now been |
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investigated for a number of small molecules,\cite{Andrews:2000qv} as |
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well as in biochemical settings, where nitrile groups can act as |
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minimally invasive probes of structure and |
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dynamics.\cite{Lindquist:2009fk,Fafarman:2010dq} The vibrational Stark |
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effect has also been used to study the effects of electric fields on |
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nitrile-containing self-assembled monolayers at metallic |
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interfaces.\cite{Oklejas:2002uq,Schkolnik:2012ty} |
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|
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Recently 4-cyano-4'-pentylbiphenyl (5CB), a liquid crystalline |
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molecule with a terminal nitrile group, has seen renewed interest as |
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one way to impart order on the surfactant interfaces of |
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nanodroplets,\cite{Moreno-Razo:2012rz} or to drive surface-ordering |
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that can be used to promote particular kinds of |
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self-assembly.\cite{PhysRevLett.111.227801} The nitrile group in 5CB |
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is a particularly interesting case for studying electric field |
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effects, as 5CB exhibits an isotropic to nematic phase transition that |
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can be triggered by the application of an external field near room |
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temperature.\cite{Gray:1973ca,Hatta:1991ee} This presents the |
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possiblity that the field-induced changes in the local environment |
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could have dramatic effects on the vibrations of this particular CN |
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bond. Although the infrared spectroscopy of 5CB has been |
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well-investigated, particularly as a measure of the kinetics of the |
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phase transition,\cite{Leyte:1997zl} the 5CB nitrile group has not yet |
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seen the detailed theoretical treatment that biologically-relevant |
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small molecules have |
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received.\cite{Lindquist:2008bh,Lindquist:2008qf,Oh:2008fk,Choi:2008cr,Morales:2009fp,Waegele:2010ve} |
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|
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The fundamental characteristic of liquid crystal mesophases is that |
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they maintain some degree of orientational order while translational |
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order is limited or absent. This orientational order produces a |
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complex direction-dependent response to external perturbations like |
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electric fields and mechanical distortions. The anisotropy of the |
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macroscopic phases originates in the anisotropy of the constituent |
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molecules, which typically have highly non-spherical structures with a |
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significant degree of internal rigidity. In nematic phases, rod-like |
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molecules are orientationally ordered with isotropic distributions of |
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molecular centers of mass. For example, 5CB has a solid to nematic |
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phase transition at 18C and a nematic to isotropic transition at |
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35C.\cite{Gray:1973ca} |
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|
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In smectic phases, the molecules arrange themselves into layers with |
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their long (symmetry) axis normal ($S_{A}$) or tilted ($S_{C}$) with |
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respect to the layer planes. The behavior of the $S_{A}$ phase can be |
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partially explained with models mainly based on geometric factors and |
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van der Waals interactions. The Gay-Berne potential, in particular, |
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has been widely used in the liquid crystal community to describe this |
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anisotropic phase |
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behavior.~\cite{Gay:1981yu,Berne:1972pb,Kushick:1976xy,Luckhurst:1990fy,Cleaver:1996rt} |
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However, these simple models are insufficient to describe liquid |
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crystal phases which exhibit more complex polymorphic nature. |
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Molecules which form $S_{A}$ phases can exhibit a wide variety of |
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subphases like monolayers ($S_{A1}$), uniform bilayers ($S_{A2}$), |
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partial bilayers ($S_{\tilde A}$) as well as interdigitated bilayers |
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($S_{A_{d}}$), and often have a terminal cyano or nitro group. In |
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particular, lyotropic liquid crystals (those exhibiting liquid crystal |
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phase transitions as a function of water concentration), often have |
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polar head groups or zwitterionic charge separated groups that result |
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in strong dipolar interactions,\cite{Collings:1997rz} and terminal |
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cyano groups (like the one in 5CB) can induce permanent longitudinal |
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dipoles.\cite{Levelut:1981eu} Modeling of the phase behavior of these |
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molecules either requires additional dipolar |
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interactions,\cite{Bose:2012eu} or a unified-atom approach utilizing |
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point charges on the sites that contribute to the dipole |
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moment.\cite{Zhang:2011hh} |
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|
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Macroscopic electric fields applied using electrodes on opposing sides |
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of a sample of 5CB have demonstrated the phase change of the molecule |
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as a function of electric field.\cite{Lim:2006xq} These previous |
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studies have shown the nitrile group serves as an excellent indicator |
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of the molecular orientation within the applied field. Lee {\it et |
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al.}~showed a 180 degree change in field direction could be probed |
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with the nitrile peak intensity as it changed along with molecular |
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alignment in the field.\cite{Lee:2006qd,Leyte:1997zl} |
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|
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While these macroscopic fields work well at indicating the bulk |
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response, the atomic scale response has not been studied. With the |
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advent of nano-electrodes and coupling them with atomic force |
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microscopy, control of electric fields applied across nanometer |
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distances is now possible.\cite{citation1} While macroscopic fields |
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are insufficient to cause a Stark effect without dielectric breakdown |
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of the material, small fields across nanometer-sized gaps may be of |
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sufficient strength. For a gap of 5 nm between a lower electrode |
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having a nanoelectrode placed near it via an atomic force microscope, |
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a potential of 1 V applied across the electrodes is equivalent to a |
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field of 2x10\textsuperscript{8} $\frac{V}{M}$. This field is |
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certainly strong enough to cause the isotropic-nematic phase change |
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and as well as Stark tuning of the nitrile bond. This should be |
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readily visible experimentally through Raman or IR spectroscopy. |
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|
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In the sections that follow, we outline a series of coarse-grained |
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classical molecular dynamics simulations of 5CB that were done in the |
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presence of static electric fields. These simulations were then |
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coupled with both {\it ab intio} calculations of CN-deformations and |
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classical bond-length correlation functions to predict spectral |
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shifts. These predictions made should be easily varifiable with |
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scanning electrochemical microscopy experiments. |
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\section{Computational Details} |
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The force field used for 5CB was a united-atom model that was |
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parameterized by Guo {\it et al.}\cite{Zhang:2011hh} However, for most |
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of the simulations, each of the phenyl rings was treated as a rigid |
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body to allow for larger time steps and very long simulation times. |
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The geometries of the rigid bodies were taken from equilibrium bond |
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distances and angles. Although the phenyl rings were held rigid, |
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bonds, bends, torsions and inversion centers that involved atoms in |
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these substructures (but with connectivity to the rest of the |
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molecule) were still included in the potential and force calculations. |
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Periodic simulations cells containing 270 molecules in random |
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orientations were constructed and were locked at experimental |
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densities. Electrostatic interactions were computed using damped |
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shifted force (DSF) electrostatics.\cite{Fennell:2006zl} The molecules |
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were equilibrated for 1~ns at a temperature of 300K. Simulations with |
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applied fields were carried out in the microcanonical (NVE) ensemble |
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with an energy corresponding to the average energy from the canonical |
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(NVT) equilibration runs. Typical applied-field equilibration runs |
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were more than 60ns in length. |
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|
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Static electric fields with magnitudes similar to what would be |
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available in an experimental setup were applied to the different |
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simulations. With an assumed electrode seperation of 5 nm and an |
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electrostatic potential that is limited by the voltage required to |
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split water (1.23V), the maximum realistic field that could be applied |
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is $\sim 0.024$ V/\AA. Three field environments were investigated: |
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(1) no field applied, (2) partial field = 0.01 V/\AA\ , and (3) full |
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field = 0.024 V/\AA\ . |
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|
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After the systems had come to equilibrium under the applied fields, |
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additional simulations were carried out with a flexible (Morse) |
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nitrile bond, |
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\begin{displaymath} |
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V(r_\ce{CN}) = D_e \left(1 - e^{-\beta (r_\ce{CN}-r_e)}\right)^2 |
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\label{eq:morse} |
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\end{displaymath} |
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where $r_e= 1.157437$ \AA , $D_e = 212.95 \mathrm{~kcal~} / |
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\mathrm{mol}^{-1}$ and $\beta = 2.67566 $\AA~$^{-1}$. These |
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parameters correspond to a vibrational frequency of $2358 |
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\mathrm{~cm}^{-1}$, somewhat higher than the experimental |
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frequency. The flexible nitrile moiety required simulation time steps |
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of 1~fs, so the additional flexibility was introducuced only after the |
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rigid systems had come to equilibrium under the applied fields. |
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Whenever time correlation functions were computed from the flexible |
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simulations, statistically-independent configurations were sampled |
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from the last ns of the induced-field runs. These configurations were |
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then equilibrated with the flexible nitrile moiety for 100 ps, and |
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time correlation functions were computed using data sampled from an |
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additional 200 ps of run time carried out in the microcanonical |
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ensemble. |
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\section{Field-induced Nematic Ordering} |
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In order to characterize the orientational ordering of the system, the |
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primary quantity of interest is the nematic (orientational) order |
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parameter. This was determined using the tensor |
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\begin{equation} |
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Q_{\alpha \beta} = \frac{1}{2N} \sum_{i=1}^{N} \left(3 \hat{u}_{i |
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\alpha} \hat{u}_{i \beta} - \delta_{\alpha \beta} \right) |
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\end{equation} |
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where $\alpha, \beta = x, y, z$, and $\hat{u}_i$ is the molecular |
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end-to-end unit vector for molecule $i$. The nematic order parameter |
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$S$ is the largest eigenvalue of $Q_{\alpha \beta}$, and the |
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corresponding eigenvector defines the director axis for the phase. |
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$S$ takes on values close to 1 in highly ordered (smectic A) phases, |
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but falls to much smaller values ($\sim 0-0.2$) for isotropic fluids. |
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Note that the nitrogen and the terminal chain atom were used to define |
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the vectors for each molecule, so the typical order parameters are |
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lower than if one defined a vector using only the rigid core of the |
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molecule. In nematic phases, typical values for $S$ are close to 0.5. |
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|
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The field-induced phase transition can be clearly seen over the course |
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of a 60 ns equilibration runs in figure \ref{fig:orderParameter}. All |
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three of the systems started in a random (isotropic) packing, with |
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order parameters near 0.2. Over the course 10 ns, the full field |
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causes an alignment of the molecules (due primarily to the interaction |
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of the nitrile group dipole with the electric field). Once this |
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system began exhibiting nematic ordering, the orientational order |
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parameter became stable for the remaining 150 ns of simulation time. |
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It is possible that the partial-field simulation is meta-stable and |
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given enough time, it would eventually find a nematic-ordered phase, |
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but the partial-field simulation was stable as an isotropic phase for |
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the full duration of a 60 ns simulation. Ellipsoidal renderings of the |
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final configurations of the runs shows that the full-field (0.024 |
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V/\AA\ ) experienced a isotropic-nematic phase transition and has |
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ordered with a director axis that is parallel to the direction of the |
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applied field. |
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\begin{figure}[H] |
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\includegraphics[width=\linewidth]{Figure1} |
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\caption{Evolution of the orientational order parameters for the |
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no-field, partial field, and full field simulations over the |
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course of 60 ns. Each simulation was started from a |
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statistically-independent isotropic configuration. On the right |
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are ellipsoids representing the final configurations at three |
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different field strengths: zero field (bottom), partial field |
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(middle), and full field (top)} |
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\label{fig:orderParameter} |
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\end{figure} |
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|
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\section{Sampling the CN bond frequency} |
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|
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The vibrational frequency of the nitrile bond in 5CB depends on |
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features of the local solvent environment of the individual molecules |
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as well as the bond's orientation relative to the applied field. The |
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primary quantity of interest for interpreting the condensed phase |
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spectrum of this vibration is the distribution of frequencies |
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exhibited by the 5CB nitrile bond under the different electric fields. |
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There have been a number of elegant techniques for obtaining |
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vibrational lineshapes from classical simulations, including a |
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perturbation theory approach,\cite{Morales:2009fp} the use of an |
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optimized QM/MM approach coupled with the fluctuating frequency |
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approximation,\cite{Lindquist:2008qf} and empirical frequency |
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correlation maps.\cite{Oh:2008fk} Three distinct (and somewhat |
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primitive) methods for mapping classical simulations onto vibrational |
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spectra were brought to bear on the simulations here: |
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\begin{enumerate} |
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\item Isolated 5CB molecules and their immediate surroundings were |
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extracted from the simulations. These nitrile bonds were stretched |
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and single-point {\em ab initio} calculations were used to obtain |
311 |
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Morse-oscillator fits for the local vibrational motion along that |
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bond. |
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\item The empirical frequency correlation maps developed by Cho {\it |
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et al.}~\cite{Oh:2008fk} for nitrile moieties in water were |
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investigated. This method involves mapping the electrostatic |
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potential around the bond to the vibrational frequency, and is |
317 |
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similar in approach to field-frequency maps for OH stretches that |
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were pioneered by the Skinner |
319 |
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group.\cite{Corcelli:2004ai,Auer:2007dp} |
320 |
gezelter |
4029 |
\item Classical bond-length autocorrelation functions were Fourier |
321 |
|
|
transformed to directly obtain the vibrational spectrum from |
322 |
|
|
molecular dynamics simulations. |
323 |
|
|
\end{enumerate} |
324 |
|
|
|
325 |
|
|
\subsection{CN frequencies from isolated clusters} |
326 |
gezelter |
4033 |
The size of the periodic condensed phase system prevented direct |
327 |
|
|
computation of the complete library of nitrile bond frequencies using |
328 |
|
|
{\it ab initio} methods. In order to sample the nitrile frequencies |
329 |
|
|
present in the condensed-phase, individual molecules were selected |
330 |
|
|
randomly to serve as the center of a local (gas phase) cluster. To |
331 |
|
|
include steric, electrostatic, and other effects from molecules |
332 |
|
|
located near the targeted nitrile group, portions of other molecules |
333 |
|
|
nearest to the nitrile group were included in the quantum mechanical |
334 |
|
|
calculations. The surrounding solvent molecules were divided into |
335 |
|
|
``body'' (the two phenyl rings and the nitrile bond) and ``tail'' (the |
336 |
gezelter |
4039 |
alkyl chain). Any molecule which had a body atom within 6~\AA\ of the |
337 |
gezelter |
4033 |
midpoint of the target nitrile bond had its own molecular body (the |
338 |
gezelter |
4039 |
4-cyano-biphenyl moiety) included in the configuration. Likewise, the |
339 |
|
|
entire alkyl tail was included if any tail atom was within 4~\AA\ of |
340 |
|
|
the target nitrile bond. If tail atoms (but no body atoms) were |
341 |
gezelter |
4035 |
included within these distances, only the tail was included as a |
342 |
|
|
capped propane molecule. |
343 |
gezelter |
4029 |
|
344 |
gezelter |
4033 |
\begin{figure}[H] |
345 |
|
|
\includegraphics[width=\linewidth]{Figure2} |
346 |
|
|
\caption{Cluster calculations were performed on randomly sampled 5CB |
347 |
gezelter |
4035 |
molecules (shown in red) from each of the simulations. Surrounding |
348 |
|
|
molecular bodies were included if any body atoms were within 6 |
349 |
|
|
\AA\ of the target nitrile bond, and tails were included if they |
350 |
|
|
were within 4 \AA. Included portions of these molecules are shown |
351 |
|
|
in green. The CN bond on the target molecule was stretched and |
352 |
|
|
compressed, and the resulting single point energies were fit to |
353 |
gezelter |
4039 |
Morse oscillators to obtain a distribution of frequencies.} |
354 |
gezelter |
4033 |
\label{fig:cluster} |
355 |
|
|
\end{figure} |
356 |
gezelter |
4032 |
|
357 |
gezelter |
4035 |
Inferred hydrogen atom locations were added to the cluster geometries, |
358 |
|
|
and the nitrile bond was stretched from 0.87 to 1.52~\AA\ at |
359 |
|
|
increments of 0.05~\AA. This generated 13 configurations per gas phase |
360 |
|
|
cluster. Single-point energies were computed using the B3LYP |
361 |
|
|
functional~\cite{Becke:1993kq,Lee:1988qf} and the 6-311++G(d,p) basis |
362 |
|
|
set. For the cluster configurations that had been generated from |
363 |
|
|
molecular dynamics running under applied fields, the density |
364 |
|
|
functional calculations had a field of $5 \times 10^{-4}$ atomic units |
365 |
|
|
($E_h / (e a_0)$) applied in the $+z$ direction in order to match the |
366 |
|
|
molecular dynamics simulations. |
367 |
gezelter |
4007 |
|
368 |
gezelter |
4035 |
The energies for the stretched / compressed nitrile bond in each of |
369 |
gezelter |
4039 |
the clusters were used to fit Morse potentials, and the frequencies |
370 |
gezelter |
4035 |
were obtained from the $0 \rightarrow 1$ transition for the energy |
371 |
|
|
levels for this potential.\cite{Morse:1929xy} To obtain a spectrum, |
372 |
|
|
each of the frequencies was convoluted with a Lorentzian lineshape |
373 |
|
|
with a width of 1.5 $\mathrm{cm}^{-1}$. Available computing resources |
374 |
|
|
limited the sampling to 67 clusters for the zero-field spectrum, and |
375 |
|
|
59 for the full field. Comparisons of the quantum mechanical spectrum |
376 |
|
|
to the classical are shown in figure \ref{fig:spectrum}. |
377 |
gezelter |
4033 |
|
378 |
gezelter |
4029 |
\subsection{CN frequencies from potential-frequency maps} |
379 |
gezelter |
4039 |
|
380 |
gezelter |
4035 |
One approach which has been used to successfully analyze the spectrum |
381 |
|
|
of nitrile and thiocyanate probes in aqueous environments was |
382 |
|
|
developed by Choi {\it et al.}~\cite{Choi:2008cr,Oh:2008fk} This |
383 |
|
|
method involves finding a multi-parameter fit that maps between the |
384 |
|
|
local electrostatic potential at selected sites surrounding the |
385 |
|
|
nitrile bond and the vibrational frequency of that bond obtained from |
386 |
|
|
more expensive {\it ab initio} methods. This approach is similar in |
387 |
gezelter |
4042 |
character to the field-frequency maps developed by the Skinner group |
388 |
|
|
for OH stretches in liquid water.\cite{Corcelli:2004ai,Auer:2007dp} |
389 |
gezelter |
4035 |
|
390 |
|
|
To use the potential-frequency maps, the local electrostatic |
391 |
gezelter |
4039 |
potential, $\phi_a$, is computed at 20 sites ($a = 1 \rightarrow 20$) |
392 |
gezelter |
4035 |
that surround the nitrile bond, |
393 |
gezelter |
4029 |
\begin{equation} |
394 |
gezelter |
4035 |
\phi_{a} = \frac{1}{4\pi \epsilon_{0}} \sum_{j} |
395 |
|
|
\frac{q_j}{\left|r_{aj}\right|}. |
396 |
gezelter |
4029 |
\end{equation} |
397 |
gezelter |
4036 |
Here $q_j$ is the partial site on atom $j$ (residing on a different |
398 |
|
|
molecule) and $r_{aj}$ is the distance between site $a$ and atom $j$. |
399 |
|
|
The original map was parameterized in liquid water and comprises a set |
400 |
|
|
of parameters, $l_a$, that predict the shift in nitrile peak |
401 |
|
|
frequency, |
402 |
gezelter |
4029 |
\begin{equation} |
403 |
gezelter |
4036 |
\delta\tilde{\nu} =\sum^{20}_{a=1} l_{a}\phi_{a}. |
404 |
gezelter |
4029 |
\end{equation} |
405 |
gezelter |
4035 |
|
406 |
gezelter |
4039 |
The simulations of 5CB were carried out in the presence of |
407 |
gezelter |
4036 |
externally-applied uniform electric fields. Although uniform fields |
408 |
|
|
exert forces on charge sites, they only contribute to the potential if |
409 |
|
|
one defines a reference point that can serve as an origin. One simple |
410 |
gezelter |
4039 |
modification to the potential at each of the probe sites is to use the |
411 |
gezelter |
4036 |
centroid of the \ce{CN} bond as the origin for that site, |
412 |
gezelter |
4029 |
\begin{equation} |
413 |
gezelter |
4036 |
\phi_a^\prime = \phi_a + \frac{1}{4\pi\epsilon_{0}} \vec{E} \cdot |
414 |
|
|
\left(\vec{r}_a - \vec{r}_\ce{CN} \right) |
415 |
gezelter |
4029 |
\end{equation} |
416 |
gezelter |
4036 |
where $\vec{E}$ is the uniform electric field, $\left( \vec{r}_{a} - |
417 |
|
|
\vec{r}_\ce{CN} \right)$ is the displacement between the |
418 |
|
|
cooridinates described by Choi {\it et |
419 |
|
|
al.}~\cite{Choi:2008cr,Oh:2008fk} and the \ce{CN} bond centroid. |
420 |
|
|
$\phi_a^\prime$ then contains an effective potential contributed by |
421 |
|
|
the uniform field in addition to the local potential contributions |
422 |
|
|
from other molecules. |
423 |
gezelter |
4029 |
|
424 |
gezelter |
4039 |
The sites $\{\vec{r}_a\}$ and weights $\left\{l_a \right\}$ |
425 |
|
|
developed by Choi {\it et al.}~\cite{Choi:2008cr,Oh:2008fk} are quite |
426 |
|
|
symmetric around the \ce{CN} centroid, and even at large uniform field |
427 |
|
|
values we observed nearly-complete cancellation of the potenial |
428 |
|
|
contributions from the uniform field. In order to utilize the |
429 |
|
|
potential-frequency maps for this problem, one would therefore need |
430 |
|
|
extensive reparameterization of the maps to include explicit |
431 |
|
|
contributions from the external field. This reparameterization is |
432 |
|
|
outside the scope of the current work, but would make a useful |
433 |
|
|
addition to the potential-frequency map approach. |
434 |
gezelter |
4029 |
|
435 |
|
|
\subsection{CN frequencies from bond length autocorrelation functions} |
436 |
|
|
|
437 |
gezelter |
4039 |
The distribution of nitrile vibrational frequencies can also be found |
438 |
gezelter |
4036 |
using classical time correlation functions. This was done by |
439 |
|
|
replacing the rigid \ce{CN} bond with a flexible Morse oscillator |
440 |
|
|
described in Eq. \ref{eq:morse}. Since the systems were perturbed by |
441 |
|
|
the addition of a flexible high-frequency bond, they were allowed to |
442 |
|
|
re-equilibrate in the canonical (NVT) ensemble for 100 ps with 1 fs |
443 |
|
|
timesteps. After equilibration, each configuration was run in the |
444 |
|
|
microcanonical (NVE) ensemble for 20 ps. Configurations sampled every |
445 |
|
|
fs were then used to compute bond-length autocorrelation functions, |
446 |
gezelter |
4007 |
\begin{equation} |
447 |
gezelter |
4036 |
C(t) = \langle \delta r(t) \cdot \delta r(0) ) \rangle |
448 |
gezelter |
4007 |
\end{equation} |
449 |
|
|
% |
450 |
gezelter |
4036 |
where $\delta r(t) = r(t) - r_0$ is the deviation from the equilibrium |
451 |
|
|
bond distance at time $t$. Ten statistically-independent correlation |
452 |
|
|
functions were obtained by allowing the systems to run 10 ns with |
453 |
|
|
rigid \ce{CN} bonds followed by 120 ps equilibration and data |
454 |
gezelter |
4039 |
collection using the flexible \ce{CN} bonds, and repeating this |
455 |
|
|
process. The total sampling time, from sample preparation to final |
456 |
|
|
configurations, exceeded 150 ns for each of the field strengths |
457 |
|
|
investigated. |
458 |
gezelter |
4007 |
|
459 |
gezelter |
4036 |
The correlation functions were filtered using exponential apodization |
460 |
gezelter |
4042 |
functions,\cite{FILLER:1964yg} $f(t) = e^{-|t|/c}$, with a time |
461 |
gezelter |
4039 |
constant, $c =$ 6 ps, and were Fourier transformed to yield a |
462 |
|
|
spectrum, |
463 |
gezelter |
4036 |
\begin{equation} |
464 |
|
|
I(\omega) = \int_{-\infty}^{\infty} C(t) f(t) e^{-i \omega t} dt. |
465 |
|
|
\end{equation} |
466 |
|
|
The sample-averaged classical nitrile spectrum can be seen in Figure |
467 |
|
|
\ref{fig:spectra}. Note that the Morse oscillator parameters listed |
468 |
gezelter |
4039 |
above yield a natural frequency of 2358 $\mathrm{cm}^{-1}$, somewhat |
469 |
|
|
higher than the experimental peak near 2226 $\mathrm{cm}^{-1}$. This |
470 |
|
|
shift does not effect the ability to qualitatively compare peaks from |
471 |
|
|
the classical and quantum mechanical approaches, so the classical |
472 |
|
|
spectra are shown as a shift relative to the natural oscillation of |
473 |
|
|
the Morse bond. |
474 |
gezelter |
4007 |
|
475 |
jmarr |
4013 |
\begin{figure} |
476 |
gezelter |
4036 |
\includegraphics[width=3.25in]{Convolved} |
477 |
jmarr |
4013 |
\includegraphics[width=3.25in]{2Spectra} |
478 |
gezelter |
4039 |
\caption{Quantum mechanical nitrile spectrum for the no-field simulation |
479 |
|
|
(black) and the full field simulation (red). The lower panel |
480 |
|
|
shows the corresponding classical bond-length autocorrelation |
481 |
|
|
spectrum for the flexible nitrile measured relative to the natural |
482 |
|
|
frequency for the flexible bond.} |
483 |
gezelter |
4036 |
\label{fig:spectra} |
484 |
jmarr |
4013 |
\end{figure} |
485 |
jmarr |
4020 |
|
486 |
gezelter |
4036 |
Note that due to electrostatic interactions, the classical approach |
487 |
|
|
implicitly couples \ce{CN} vibrations to the same vibrational mode on |
488 |
|
|
other nearby molecules. This coupling is not handled in the {\it ab |
489 |
|
|
initio} cluster approach. |
490 |
jmarr |
4020 |
|
491 |
gezelter |
4036 |
\section{Discussion} |
492 |
|
|
|
493 |
gezelter |
4042 |
It is clear that united-atom simulations can reproduce the |
494 |
|
|
field-induced nematic ordering of the 4-cyano-4'-pentylbiphenyl. |
495 |
|
|
Because we are simulating a small electrode separation (5nm), a |
496 |
|
|
voltage drop as low as 1.2 V was sufficient to induce the phase |
497 |
|
|
change. This potential is significantly lower than the 500V that is |
498 |
|
|
known to cause dielectric breakdown in 5CB.\cite{XXX} |
499 |
jmarr |
4023 |
|
500 |
gezelter |
4042 |
|
501 |
|
|
|
502 |
gezelter |
4039 |
Ordering corresponds to shift of a portion of the nitrile spectrum to |
503 |
|
|
the red. |
504 |
|
|
At the same time, the system exhibits an increase in aligned and anti-a |
505 |
|
|
|
506 |
|
|
|
507 |
|
|
|
508 |
jmarr |
4020 |
Since no explicit dependence was observed between the calculated |
509 |
|
|
frequency and the electric field, it was not a viable route for the |
510 |
|
|
calculation of a nitrile spectrum. Instead, the frequencies were taken |
511 |
jmarr |
4024 |
and convolved together with a lorentzian line shape applied around the |
512 |
gezelter |
4036 |
frequency value. These spectra are seen below in Figure 4. While the |
513 |
|
|
spectrum without a field is lower in intensity and is almost bimodel |
514 |
|
|
in distrobution, the external field spectrum is much more |
515 |
|
|
unimodel. This tighter clustering has the affect of increasing the |
516 |
jmarr |
4020 |
intensity around 2226 cm\textsuperscript{-1} where the peak is |
517 |
jmarr |
4023 |
centered. The external field also has fewer frequencies of higher |
518 |
gezelter |
4036 |
energy in the spectrum. Unlike the the zero field, where some |
519 |
|
|
frequencies reach as high as 2280 cm\textsuperscript{-1}. |
520 |
|
|
|
521 |
jmarr |
4024 |
Interestingly, the field that is needed to switch the phase of 5CB |
522 |
|
|
macroscopically is larger than 1 V. However, in this case, only a |
523 |
|
|
voltage of 1.2 V was need to induce a phase change. This is impart due |
524 |
gezelter |
4036 |
to the short distance of 5 nm the field is being applied across. At |
525 |
|
|
such a small distance, the field is much larger than the macroscopic |
526 |
|
|
and thus easily induces a field dependent phase change. However, this |
527 |
|
|
field will not cause a breakdown of the 5CB since electrochemistry |
528 |
|
|
studies have shown that it can be used in the presence of fields as |
529 |
|
|
high as 500 V macroscopically. This large of a field near the surface |
530 |
|
|
of the elctrode would cause breakdown of 5CB if it could happen. |
531 |
jmarr |
4024 |
|
532 |
jmarr |
4020 |
The absence of any electric field dependency of the freuquency with |
533 |
jmarr |
4025 |
the Gaussian simulations is interesting. A large base of research has been |
534 |
jmarr |
4024 |
built upon the known tuning of the nitrile bond as the local field |
535 |
|
|
changes. This difference may be due to the absence of water or a |
536 |
|
|
molecule that induces a large internal field. Liquid water is known to have a very high internal field which |
537 |
jmarr |
4020 |
is much larger than the internal fields of neat 5CB. Even though the |
538 |
jmarr |
4024 |
application of Gaussian simulations followed by mapping it to |
539 |
jmarr |
4020 |
some classical parameter is easy and straight forward, this system |
540 |
|
|
illistrates how that 'go to' method can break down. |
541 |
gezelter |
4007 |
|
542 |
jmarr |
4020 |
While this makes the application of nitrile Stark effects in |
543 |
jmarr |
4024 |
simulations without water harder, these data show |
544 |
jmarr |
4021 |
that it is not a deal breaker. The classically calculated nitrile |
545 |
|
|
spectrum shows changes in the spectra that will be easily seen through |
546 |
|
|
experimental routes. It indicates a shifted peak lower in energy |
547 |
jmarr |
4024 |
should arise. This peak is a few wavenumbers from the leading edge of |
548 |
|
|
the larger peak and almost 75 wavenumbers from the center. This |
549 |
|
|
seperation between the two peaks means experimental results will show |
550 |
|
|
an easily resolved peak. |
551 |
jmarr |
4021 |
|
552 |
jmarr |
4024 |
The Gaussian derived spectra do indicate an applied field |
553 |
jmarr |
4023 |
and subsiquent phase change does cause a narrowing of freuency |
554 |
jmarr |
4025 |
distrobution. With narrowing, it would indicate an increased |
555 |
|
|
homogeneous distrobution of the local field near the nitrile. |
556 |
gezelter |
4039 |
|
557 |
gezelter |
4040 |
The angle-dependent pair distribution functions, |
558 |
|
|
\begin{align} |
559 |
|
|
g(r, \cos \omega) = & \frac{1}{\rho N} \left< \sum_{i} |
560 |
|
|
\sum_{j} \delta \left(r - r_{ij}\right) \delta\left(\cos \omega_{ij} - |
561 |
|
|
\cos \omega\right) \right> \\ \nonumber \\ |
562 |
|
|
g(r, \cos \theta) = & \frac{1}{\rho N} \left< \sum_{i} |
563 |
|
|
\sum_{j} \delta \left(r - r_{ij}\right) \delta\left(\cos \theta_{i} - |
564 |
|
|
\cos \theta \right) \right> |
565 |
|
|
\end{align} |
566 |
|
|
provide information about the joint spatial and angular correlations |
567 |
|
|
in the system. The angles $\omega$ and $\theta$ are defined by vectors |
568 |
|
|
along the CN axis of each nitrile bond (see figure |
569 |
|
|
\ref{fig:definition}). |
570 |
gezelter |
4039 |
|
571 |
|
|
\begin{figure} |
572 |
|
|
\includegraphics[width=\linewidth]{definition} |
573 |
gezelter |
4040 |
\caption{Definitions of the angles between two nitrile bonds.} |
574 |
gezelter |
4039 |
\label{fig:definition} |
575 |
|
|
\end{figure} |
576 |
|
|
|
577 |
|
|
In figure \ref{fig:gofromega} the effects of the field-induced phase |
578 |
|
|
transition are clear. The nematic ordering transfers population from |
579 |
|
|
the perpendicular or unaligned region in the center of the plot to the |
580 |
|
|
nitrile-alinged peak near $\cos\omega = 1$. Most other features are |
581 |
|
|
undisturbed. This increased population of aligned nitrile bonds in |
582 |
|
|
the close solvation shells is also the population that contributes |
583 |
|
|
most heavily to the low-frequency peaks in the vibrational spectrum. |
584 |
|
|
|
585 |
|
|
\begin{figure} |
586 |
|
|
\includegraphics[width=\linewidth]{Figure4} |
587 |
|
|
\caption{Contours of the angle-dependent pair distribution functions |
588 |
|
|
for nitrile bonds on 5CB in the zero-field (upper panel) and full |
589 |
|
|
field (lower panel) simulations. Dark areas signify regions of |
590 |
|
|
enhanced density, while light areas signify depletion relative to |
591 |
|
|
the bulk density.} |
592 |
|
|
\label{fig:gofromega} |
593 |
|
|
\end{figure} |
594 |
|
|
|
595 |
|
|
|
596 |
gezelter |
4007 |
\section{Conclusions} |
597 |
jmarr |
4024 |
Field dependent changes |
598 |
gezelter |
4036 |
|
599 |
|
|
\section{Acknowledgements} |
600 |
|
|
The authors thank Steven Corcelli for helpful comments and |
601 |
|
|
suggestions. Support for this project was provided by the National |
602 |
|
|
Science Foundation under grant CHE-0848243. Computational time was |
603 |
|
|
provided by the Center for Research Computing (CRC) at the University |
604 |
|
|
of Notre Dame. |
605 |
|
|
|
606 |
gezelter |
4007 |
\newpage |
607 |
|
|
|
608 |
|
|
\bibliography{5CB} |
609 |
|
|
|
610 |
|
|
\end{doublespace} |
611 |
|
|
\end{document} |