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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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\begin{document} |
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\begin{tocentry} |
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%\includegraphics[width=9cm]{Elip_3} |
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\includegraphics[width=9cm]{cluster.pdf} |
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\end{tocentry} |
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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 Stark shift of the terminal nitrile group. A field-induced |
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isotropic-nematic phase transition was observed in the simulations, |
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and the effects of this transition on the distribution of nitrile |
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frequencies were computed. Classical bond displacement correlation |
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functions exhibit a $\sim~3~\mathrm{cm}^{-1}$ red shift of a portion |
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of the main nitrile peak, and this shift was observed only when the |
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fields were large enough to induce orientational ordering of the |
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bulk phase. Distributions of frequencies obtained via cluster-based |
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fits to quantum mechanical energies of nitrile bond deformations |
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exhibit a similar $\sim~2.7~\mathrm{cm}^{-1}$ red shift. Joint |
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spatial-angular distribution functions indicate that phase-induced |
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anti-caging of the nitrile bond is contributing to the change in the |
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nitrile spectrum. |
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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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Because the triple bond between nitrogen and carbon is sensitive to |
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local electric fields, nitrile groups can report on field strengths |
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via their distinctive Raman and IR signatures.\cite{Boxer:2009xw} The |
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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{Tucker:2004qq,Webb:2008kn,Lindquist:2009fk,Fafarman:2010dq} |
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The vibrational Stark effect has also been used to study the effects |
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of electric fields on nitrile-containing self-assembled monolayers at |
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metallic 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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possibility that the field-induced changes in the local environment |
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could have dramatic effects on the vibrations of this particular nitrile |
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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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explained with models based solely on geometric factors and van der |
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Waals interactions. The Gay-Berne potential, in particular, has been |
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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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sub-phases 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 response at a molecular scale has not been studied. With |
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the advent of nano-electrodes and the ability to couple these |
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electrodes to atomic force microscopy, control of electric fields |
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applied across nanometer distances is now possible.\cite{C3AN01651J} |
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In special cases where the macroscopic fields are insufficient to |
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cause an observable Stark effect without dielectric breakdown of the |
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material, small potentials across nanometer-sized gaps may have |
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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 $2 \times 10^8~\mathrm{V/m}$. This field is certainly strong |
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enough to cause the isotropic-nematic phase change and an observable |
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Stark tuning of the nitrile bond. We expect that this would be readily |
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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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(united atom) classical molecular dynamics simulations of 5CB that |
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were done in the presence of static electric fields. These simulations |
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were then coupled with both {\it ab intio} calculations of |
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CN-deformations and classical bond-length correlation functions to |
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predict spectral shifts. These predictions should be verifiable via |
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scanning electrochemical microscopy. |
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\section{Computational Details} |
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The force-field used to model 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, both of the phenyl rings and the nitrile bond were |
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treated as rigid bodies to allow for larger time steps and longer |
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simulation times. The geometries of the rigid bodies were taken from |
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equilibrium bond distances and angles. Although the individual phenyl |
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rings were held rigid, bonds, bends, torsions and inversion centers |
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that involved atoms in these substructures (but with connectivity to |
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the rest of the molecule) were still included in the potential and |
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force calculations. |
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|
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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 60~ns 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 separation 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 introduced 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 (separated in |
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time by 10 ns) were sampled from the last 110 ns of the induced-field |
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runs. These configurations were then equilibrated with the flexible |
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nitrile moiety for 100 ps, and time correlation functions were |
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computed using data sampled from an additional 20 ps of run time |
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carried out in the microcanonical ensemble. |
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|
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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 ($0 \rightarrow 0.3$) for isotropic |
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fluids. Note that the nitrogen and the terminal chain atom were used |
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to define the vectors for each molecule, so the typical order |
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parameters are lower than if one defined a vector using only the rigid |
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core of the molecule. In nematic phases, typical values for $S$ are |
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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 the 60 ns simulation. Ellipsoidal renderings of |
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the final configurations of the runs show 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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|
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\begin{figure}[H] |
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\includegraphics[width=\linewidth]{orderParameter.pdf} |
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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 line shapes 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 comparatively |
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primitive) methods for mapping classical simulations onto vibrational |
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spectra were brought to bear on the simulations in this work: |
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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 |
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Morse-oscillator fits for the local vibrational motion along that |
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bond. |
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\item A static-field extension of the empirical frequency correlation |
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maps developed by Choi {\it et al.}~\cite{Oh:2008fk} for nitrile |
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moieties in water was attempted. |
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\item Classical bond-length autocorrelation functions were Fourier |
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transformed to directly obtain the vibrational spectrum from |
303 |
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molecular dynamics simulations. |
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\end{enumerate} |
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|
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\subsection{CN frequencies from isolated clusters} |
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The size of the condensed phase liquid crystal system prevented direct |
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computation of the complete library of nitrile bond frequencies using |
309 |
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{\it ab initio} methods. In order to sample the nitrile frequencies |
310 |
|
|
present in the condensed-phase, individual molecules were selected |
311 |
|
|
randomly to serve as the center of a local (gas phase) cluster. To |
312 |
|
|
include steric, electrostatic, and other effects from molecules |
313 |
|
|
located near the targeted nitrile group, portions of other molecules |
314 |
|
|
nearest to the nitrile group were included in the quantum mechanical |
315 |
|
|
calculations. The surrounding solvent molecules were divided into |
316 |
|
|
``body'' (the two phenyl rings and the nitrile bond) and ``tail'' (the |
317 |
gezelter |
4039 |
alkyl chain). Any molecule which had a body atom within 6~\AA\ of the |
318 |
gezelter |
4033 |
midpoint of the target nitrile bond had its own molecular body (the |
319 |
gezelter |
4039 |
4-cyano-biphenyl moiety) included in the configuration. Likewise, the |
320 |
|
|
entire alkyl tail was included if any tail atom was within 4~\AA\ of |
321 |
|
|
the target nitrile bond. If tail atoms (but no body atoms) were |
322 |
gezelter |
4035 |
included within these distances, only the tail was included as a |
323 |
|
|
capped propane molecule. |
324 |
gezelter |
4029 |
|
325 |
gezelter |
4033 |
\begin{figure}[H] |
326 |
gezelter |
4097 |
\includegraphics[width=\linewidth]{cluster.pdf} |
327 |
gezelter |
4033 |
\caption{Cluster calculations were performed on randomly sampled 5CB |
328 |
gezelter |
4095 |
molecules (shown in red) from the full-field and no-field |
329 |
|
|
simulations. Surrounding molecular bodies were included if any |
330 |
|
|
body atoms were within 6 \AA\ of the target nitrile bond, and |
331 |
|
|
tails were included if they were within 4 \AA. Included portions |
332 |
|
|
of these molecules are shown in green. The CN bond on the target |
333 |
|
|
molecule was stretched and compressed, and the resulting single |
334 |
|
|
point energies were fit to Morse oscillators to obtain a |
335 |
|
|
distribution of frequencies.} |
336 |
gezelter |
4033 |
\label{fig:cluster} |
337 |
|
|
\end{figure} |
338 |
gezelter |
4032 |
|
339 |
gezelter |
4035 |
Inferred hydrogen atom locations were added to the cluster geometries, |
340 |
|
|
and the nitrile bond was stretched from 0.87 to 1.52~\AA\ at |
341 |
|
|
increments of 0.05~\AA. This generated 13 configurations per gas phase |
342 |
|
|
cluster. Single-point energies were computed using the B3LYP |
343 |
|
|
functional~\cite{Becke:1993kq,Lee:1988qf} and the 6-311++G(d,p) basis |
344 |
|
|
set. For the cluster configurations that had been generated from |
345 |
|
|
molecular dynamics running under applied fields, the density |
346 |
|
|
functional calculations had a field of $5 \times 10^{-4}$ atomic units |
347 |
|
|
($E_h / (e a_0)$) applied in the $+z$ direction in order to match the |
348 |
|
|
molecular dynamics simulations. |
349 |
gezelter |
4007 |
|
350 |
gezelter |
4035 |
The energies for the stretched / compressed nitrile bond in each of |
351 |
gezelter |
4039 |
the clusters were used to fit Morse potentials, and the frequencies |
352 |
gezelter |
4035 |
were obtained from the $0 \rightarrow 1$ transition for the energy |
353 |
|
|
levels for this potential.\cite{Morse:1929xy} To obtain a spectrum, |
354 |
gezelter |
4096 |
each of the frequencies was convoluted with a Lorentzian line shape |
355 |
gezelter |
4035 |
with a width of 1.5 $\mathrm{cm}^{-1}$. Available computing resources |
356 |
gezelter |
4097 |
limited the sampling to 100 clusters for both the no-field and |
357 |
|
|
full-field spectra. Comparisons of the quantum mechanical spectrum to |
358 |
|
|
the classical are shown in figure \ref{fig:spectra}. The mean |
359 |
|
|
frequencies obtained from the distributions give a field-induced red |
360 |
|
|
shift of $2.68~\mathrm{cm}^{-1}$. |
361 |
gezelter |
4033 |
|
362 |
gezelter |
4029 |
\subsection{CN frequencies from potential-frequency maps} |
363 |
gezelter |
4039 |
|
364 |
gezelter |
4035 |
One approach which has been used to successfully analyze the spectrum |
365 |
|
|
of nitrile and thiocyanate probes in aqueous environments was |
366 |
|
|
developed by Choi {\it et al.}~\cite{Choi:2008cr,Oh:2008fk} This |
367 |
|
|
method involves finding a multi-parameter fit that maps between the |
368 |
|
|
local electrostatic potential at selected sites surrounding the |
369 |
|
|
nitrile bond and the vibrational frequency of that bond obtained from |
370 |
|
|
more expensive {\it ab initio} methods. This approach is similar in |
371 |
gezelter |
4042 |
character to the field-frequency maps developed by the Skinner group |
372 |
|
|
for OH stretches in liquid water.\cite{Corcelli:2004ai,Auer:2007dp} |
373 |
gezelter |
4035 |
|
374 |
|
|
To use the potential-frequency maps, the local electrostatic |
375 |
gezelter |
4039 |
potential, $\phi_a$, is computed at 20 sites ($a = 1 \rightarrow 20$) |
376 |
gezelter |
4035 |
that surround the nitrile bond, |
377 |
gezelter |
4029 |
\begin{equation} |
378 |
gezelter |
4035 |
\phi_{a} = \frac{1}{4\pi \epsilon_{0}} \sum_{j} |
379 |
|
|
\frac{q_j}{\left|r_{aj}\right|}. |
380 |
gezelter |
4029 |
\end{equation} |
381 |
gezelter |
4097 |
Here $q_j$ is the partial charge on atom $j$ (residing on a different |
382 |
gezelter |
4036 |
molecule) and $r_{aj}$ is the distance between site $a$ and atom $j$. |
383 |
|
|
The original map was parameterized in liquid water and comprises a set |
384 |
|
|
of parameters, $l_a$, that predict the shift in nitrile peak |
385 |
|
|
frequency, |
386 |
gezelter |
4029 |
\begin{equation} |
387 |
gezelter |
4036 |
\delta\tilde{\nu} =\sum^{20}_{a=1} l_{a}\phi_{a}. |
388 |
gezelter |
4029 |
\end{equation} |
389 |
gezelter |
4035 |
|
390 |
gezelter |
4039 |
The simulations of 5CB were carried out in the presence of |
391 |
gezelter |
4036 |
externally-applied uniform electric fields. Although uniform fields |
392 |
|
|
exert forces on charge sites, they only contribute to the potential if |
393 |
|
|
one defines a reference point that can serve as an origin. One simple |
394 |
gezelter |
4039 |
modification to the potential at each of the probe sites is to use the |
395 |
gezelter |
4036 |
centroid of the \ce{CN} bond as the origin for that site, |
396 |
gezelter |
4029 |
\begin{equation} |
397 |
gezelter |
4036 |
\phi_a^\prime = \phi_a + \frac{1}{4\pi\epsilon_{0}} \vec{E} \cdot |
398 |
|
|
\left(\vec{r}_a - \vec{r}_\ce{CN} \right) |
399 |
gezelter |
4029 |
\end{equation} |
400 |
gezelter |
4036 |
where $\vec{E}$ is the uniform electric field, $\left( \vec{r}_{a} - |
401 |
|
|
\vec{r}_\ce{CN} \right)$ is the displacement between the |
402 |
gezelter |
4096 |
coordinates described by Choi {\it et |
403 |
gezelter |
4036 |
al.}~\cite{Choi:2008cr,Oh:2008fk} and the \ce{CN} bond centroid. |
404 |
|
|
$\phi_a^\prime$ then contains an effective potential contributed by |
405 |
|
|
the uniform field in addition to the local potential contributions |
406 |
|
|
from other molecules. |
407 |
gezelter |
4029 |
|
408 |
gezelter |
4039 |
The sites $\{\vec{r}_a\}$ and weights $\left\{l_a \right\}$ |
409 |
|
|
developed by Choi {\it et al.}~\cite{Choi:2008cr,Oh:2008fk} are quite |
410 |
|
|
symmetric around the \ce{CN} centroid, and even at large uniform field |
411 |
gezelter |
4096 |
values we observed nearly-complete cancellation of the potential |
412 |
gezelter |
4039 |
contributions from the uniform field. In order to utilize the |
413 |
|
|
potential-frequency maps for this problem, one would therefore need |
414 |
|
|
extensive reparameterization of the maps to include explicit |
415 |
|
|
contributions from the external field. This reparameterization is |
416 |
|
|
outside the scope of the current work, but would make a useful |
417 |
|
|
addition to the potential-frequency map approach. |
418 |
gezelter |
4029 |
|
419 |
gezelter |
4094 |
We note that in 5CB there does not appear to be a particularly strong |
420 |
gezelter |
4097 |
correlation between the electric field strengths observed at the |
421 |
|
|
nitrile centroid and the calculated vibrational frequencies. In |
422 |
gezelter |
4094 |
Fig. \ref{fig:fieldMap} we show the calculated frequencies plotted |
423 |
gezelter |
4097 |
against the field magnitude as well as the parallel and perpendicular |
424 |
|
|
components of that field. |
425 |
gezelter |
4094 |
|
426 |
|
|
\begin{figure} |
427 |
gezelter |
4097 |
\includegraphics[width=\linewidth]{fieldMap.pdf} |
428 |
gezelter |
4094 |
\caption{The observed cluster frequencies have no apparent |
429 |
|
|
correlation with the electric field felt at the centroid of the |
430 |
gezelter |
4095 |
nitrile bond. Upper panel: vibrational frequencies plotted |
431 |
|
|
against the component of the field parallel to the CN bond. |
432 |
gezelter |
4097 |
Middle panel: plotted against the magnitude of the field |
433 |
|
|
components perpendicular to the CN bond. Lower panel: plotted |
434 |
|
|
against the total field magnitude.} |
435 |
gezelter |
4094 |
\label{fig:fieldMap} |
436 |
|
|
\end{figure} |
437 |
|
|
|
438 |
|
|
|
439 |
gezelter |
4029 |
\subsection{CN frequencies from bond length autocorrelation functions} |
440 |
|
|
|
441 |
gezelter |
4039 |
The distribution of nitrile vibrational frequencies can also be found |
442 |
gezelter |
4036 |
using classical time correlation functions. This was done by |
443 |
|
|
replacing the rigid \ce{CN} bond with a flexible Morse oscillator |
444 |
|
|
described in Eq. \ref{eq:morse}. Since the systems were perturbed by |
445 |
|
|
the addition of a flexible high-frequency bond, they were allowed to |
446 |
|
|
re-equilibrate in the canonical (NVT) ensemble for 100 ps with 1 fs |
447 |
gezelter |
4096 |
time steps. After equilibration, each configuration was run in the |
448 |
gezelter |
4036 |
microcanonical (NVE) ensemble for 20 ps. Configurations sampled every |
449 |
|
|
fs were then used to compute bond-length autocorrelation functions, |
450 |
gezelter |
4007 |
\begin{equation} |
451 |
gezelter |
4036 |
C(t) = \langle \delta r(t) \cdot \delta r(0) ) \rangle |
452 |
gezelter |
4007 |
\end{equation} |
453 |
|
|
% |
454 |
gezelter |
4036 |
where $\delta r(t) = r(t) - r_0$ is the deviation from the equilibrium |
455 |
gezelter |
4048 |
bond distance at time $t$. Because the other atomic sites have very |
456 |
|
|
small partial charges, this correlation function is an approximation |
457 |
|
|
to the dipole autocorrelation function for the molecule, which would |
458 |
gezelter |
4097 |
be particularly relevant to computing the IR spectrum. Eleven |
459 |
gezelter |
4048 |
statistically-independent correlation functions were obtained by |
460 |
|
|
allowing the systems to run 10 ns with rigid \ce{CN} bonds followed by |
461 |
|
|
120 ps equilibration and data collection using the flexible \ce{CN} |
462 |
gezelter |
4097 |
bonds. This process was repeated 11 times, and the total sampling |
463 |
|
|
time, from sample preparation to final configurations, exceeded 160 ns |
464 |
gezelter |
4048 |
for each of the field strengths investigated. |
465 |
gezelter |
4007 |
|
466 |
gezelter |
4036 |
The correlation functions were filtered using exponential apodization |
467 |
gezelter |
4042 |
functions,\cite{FILLER:1964yg} $f(t) = e^{-|t|/c}$, with a time |
468 |
gezelter |
4048 |
constant, $c =$ 3.5 ps, and were Fourier transformed to yield a |
469 |
gezelter |
4039 |
spectrum, |
470 |
gezelter |
4036 |
\begin{equation} |
471 |
|
|
I(\omega) = \int_{-\infty}^{\infty} C(t) f(t) e^{-i \omega t} dt. |
472 |
|
|
\end{equation} |
473 |
|
|
The sample-averaged classical nitrile spectrum can be seen in Figure |
474 |
|
|
\ref{fig:spectra}. Note that the Morse oscillator parameters listed |
475 |
gezelter |
4039 |
above yield a natural frequency of 2358 $\mathrm{cm}^{-1}$, somewhat |
476 |
|
|
higher than the experimental peak near 2226 $\mathrm{cm}^{-1}$. This |
477 |
|
|
shift does not effect the ability to qualitatively compare peaks from |
478 |
|
|
the classical and quantum mechanical approaches, so the classical |
479 |
|
|
spectra are shown as a shift relative to the natural oscillation of |
480 |
gezelter |
4097 |
the Morse bond. The quantum cluster values are referenced to the |
481 |
|
|
actual experimental vibrational frequency. |
482 |
gezelter |
4007 |
|
483 |
gezelter |
4095 |
\begin{figure} |
484 |
gezelter |
4097 |
\includegraphics[width=\linewidth]{spectra.pdf} |
485 |
gezelter |
4095 |
\caption{Spectrum of nitrile frequency shifts for the no-field |
486 |
|
|
(black) and the full-field (red) simulations. Upper panel: |
487 |
|
|
frequency shifts obtained from {\it ab initio} cluster |
488 |
|
|
calculations. Lower panel: classical bond-length autocorrelation |
489 |
|
|
spectrum for the flexible nitrile measured relative to the natural |
490 |
|
|
frequency for the flexible bond. The dashed lines indicate the |
491 |
|
|
mean frequencies for each of the distributions. The cluster |
492 |
|
|
calculations exhibit a $2.68~\mathrm{cm}^{-1}$ field-induced red |
493 |
|
|
shift, while the classical correlation functions predict a red |
494 |
|
|
shift of $3.05~\mathrm{cm}^{-1}$.} |
495 |
|
|
\label{fig:spectra} |
496 |
|
|
\end{figure} |
497 |
jmarr |
4020 |
|
498 |
gezelter |
4091 |
The classical approach includes both intramolecular and electrostatic |
499 |
|
|
interactions, and so it implicitly couples \ce{CN} vibrations to other |
500 |
|
|
vibrations within the molecule as well as to nitrile vibrations on |
501 |
|
|
other nearby molecules. The classical frequency spectrum is |
502 |
gezelter |
4095 |
significantly broader because of this coupling. The {\it ab initio} |
503 |
|
|
cluster approach exercises only the targeted nitrile bond, with no |
504 |
|
|
additional coupling to other degrees of freedom. As a result the |
505 |
|
|
quantum calculations are quite narrowly peaked around the experimental |
506 |
|
|
nitrile frequency. Although the spectra are quite noisy, the main |
507 |
|
|
effect seen in both distributions is a moderate shift to the red |
508 |
|
|
($3.05~\mathrm{cm}^{-1}$ classical and $2.68~\mathrm{cm}^{-1}$ |
509 |
gezelter |
4097 |
quantum) after the electrostatic field had induced the nematic phase |
510 |
|
|
transition. |
511 |
jmarr |
4020 |
|
512 |
gezelter |
4036 |
\section{Discussion} |
513 |
gezelter |
4048 |
Our simulations show that the united-atom model can reproduce the |
514 |
gezelter |
4042 |
field-induced nematic ordering of the 4-cyano-4'-pentylbiphenyl. |
515 |
gezelter |
4052 |
Because we are simulating a very small electrode separation (5~nm), a |
516 |
|
|
voltage drop as low as 1.2~V was sufficient to induce the phase |
517 |
gezelter |
4091 |
change. This potential is significantly smaller than 100~V that was |
518 |
|
|
used with a 5~$\mu$m gap to study the electrochemiluminescence of |
519 |
|
|
rubrene in neat 5CB,\cite{Kojima19881789} and suggests that by using |
520 |
|
|
electrodes separated by a nanometer-scale gap, it will be relatively |
521 |
gezelter |
4052 |
straightforward to observe the nitrile Stark shift in 5CB. |
522 |
jmarr |
4023 |
|
523 |
gezelter |
4043 |
Both the classical correlation function and the isolated cluster |
524 |
gezelter |
4091 |
approaches to estimating the IR spectrum show that a population of |
525 |
gezelter |
4094 |
nitrile stretches shift by $\sim~3~\mathrm{cm}^{-1}$ to the red of |
526 |
gezelter |
4091 |
the unperturbed vibrational line. To understand the origin of this |
527 |
gezelter |
4052 |
shift, a more complete picture of the spatial ordering around the |
528 |
gezelter |
4091 |
nitrile bonds is required. We have computed the angle-dependent pair |
529 |
|
|
distribution functions, |
530 |
gezelter |
4040 |
\begin{align} |
531 |
gezelter |
4091 |
g(r, \cos \omega) = & \frac{1}{\rho N} \left< \sum_{i} \sum_{j} |
532 |
|
|
\delta \left(r - r_{ij}\right) \delta\left(\cos \omega_{ij} - |
533 |
gezelter |
4040 |
\cos \omega\right) \right> \\ \nonumber \\ |
534 |
|
|
g(r, \cos \theta) = & \frac{1}{\rho N} \left< \sum_{i} |
535 |
|
|
\sum_{j} \delta \left(r - r_{ij}\right) \delta\left(\cos \theta_{i} - |
536 |
|
|
\cos \theta \right) \right> |
537 |
|
|
\end{align} |
538 |
gezelter |
4052 |
which provide information about the joint spatial and angular |
539 |
|
|
correlations present in the system. The angles $\omega$ and $\theta$ |
540 |
|
|
are defined by vectors along the CN axis of each nitrile bond (see |
541 |
gezelter |
4097 |
figure \ref{fig:definition}). |
542 |
gezelter |
4039 |
\begin{figure} |
543 |
gezelter |
4097 |
\includegraphics[width=4in]{definition.pdf} |
544 |
gezelter |
4040 |
\caption{Definitions of the angles between two nitrile bonds.} |
545 |
gezelter |
4039 |
\label{fig:definition} |
546 |
|
|
\end{figure} |
547 |
|
|
|
548 |
gezelter |
4052 |
The primary structural effect of the field-induced phase transition is |
549 |
|
|
apparent in figure \ref{fig:gofromega}. The nematic ordering transfers |
550 |
|
|
population from the perpendicular ($\cos\omega\approx 0$) and |
551 |
gezelter |
4096 |
anti-aligned ($\cos\omega\approx -1$) to the nitrile-aligned peak |
552 |
gezelter |
4052 |
near $\cos\omega\approx 1$, leaving most other features undisturbed. This |
553 |
|
|
change is visible in the simulations as an increased population of |
554 |
|
|
aligned nitrile bonds in the first solvation shell. |
555 |
gezelter |
4091 |
|
556 |
gezelter |
4039 |
\begin{figure} |
557 |
gezelter |
4097 |
\includegraphics[width=\linewidth]{gofrOmega.pdf} |
558 |
gezelter |
4039 |
\caption{Contours of the angle-dependent pair distribution functions |
559 |
gezelter |
4052 |
for nitrile bonds on 5CB in the no field (upper panel) and full |
560 |
gezelter |
4039 |
field (lower panel) simulations. Dark areas signify regions of |
561 |
|
|
enhanced density, while light areas signify depletion relative to |
562 |
|
|
the bulk density.} |
563 |
gezelter |
4091 |
\label{fig:gofromega} |
564 |
|
|
\end{figure} |
565 |
|
|
|
566 |
gezelter |
4052 |
Although it is certainly possible that the coupling between |
567 |
|
|
closely-spaced nitrile pairs is responsible for some of the red-shift, |
568 |
gezelter |
4091 |
that is not the only structural change that is taking place. The |
569 |
gezelter |
4052 |
second two-dimensional pair distribution function, $g(r,\cos\theta)$, |
570 |
|
|
shows that nematic ordering also transfers population that is directly |
571 |
|
|
in line with the nitrile bond (see figure \ref{fig:gofrtheta}) to the |
572 |
gezelter |
4097 |
sides of the molecule, thereby freeing steric blockage which can |
573 |
|
|
directly influence the nitrile vibration. This is confirmed by |
574 |
|
|
observing the one-dimensional $g(z)$ obtained by following the \ce{C |
575 |
|
|
-> N} vector for each nitrile bond and observing the local density |
576 |
|
|
($\rho(z)/\rho$) of other atoms at a distance $z$ along this |
577 |
|
|
direction. The full-field simulation shows a significant drop in the |
578 |
|
|
first peak of $g(z)$, indicating that the nematic ordering has moved |
579 |
|
|
density away from the region that is directly in line with the |
580 |
|
|
nitrogen side of the CN bond. |
581 |
gezelter |
4091 |
|
582 |
gezelter |
4048 |
\begin{figure} |
583 |
gezelter |
4097 |
\includegraphics[width=\linewidth]{gofrTheta.pdf} |
584 |
gezelter |
4048 |
\caption{Contours of the angle-dependent pair distribution function, |
585 |
gezelter |
4052 |
$g(r,\cos \theta)$, for finding any other atom at a distance and |
586 |
|
|
angular deviation from the center of a nitrile bond. The top edge |
587 |
|
|
of each contour plot corresponds to local density along the |
588 |
|
|
direction of the nitrogen in the CN bond, while the bottom is in |
589 |
|
|
the direction of the carbon atom. Bottom panel: $g(z)$ data taken |
590 |
|
|
by following the \ce{C -> N} vector for each nitrile bond shows |
591 |
|
|
that the field-induced phase transition reduces the population of |
592 |
|
|
atoms that are directly in line with the nitrogen motion.} |
593 |
gezelter |
4051 |
\label{fig:gofrtheta} |
594 |
gezelter |
4048 |
\end{figure} |
595 |
|
|
|
596 |
gezelter |
4091 |
We are suggesting an anti-caging mechanism here -- the nematic |
597 |
|
|
ordering provides additional space directly inline with the nitrile |
598 |
|
|
vibration, and since the oscillator is fairly anharmonic, this freedom |
599 |
|
|
provides a fraction of the nitrile bonds with a significant red-shift. |
600 |
|
|
|
601 |
gezelter |
4052 |
The cause of this shift does not appear to be related to the alignment |
602 |
|
|
of those nitrile bonds with the field, but rather to the change in |
603 |
gezelter |
4091 |
local steric environment that is brought about by the |
604 |
|
|
isotropic-nematic transition. We have compared configurations for many |
605 |
|
|
of the cluster that exhibited the lowest frequencies (between 2190 and |
606 |
|
|
2215 $\mathrm{cm}^{-1}$) and have observed some similar structural |
607 |
|
|
features. The lowest frequencies appear to come from configurations |
608 |
|
|
which have nearly-empty pockets directly opposite the nitrogen atom |
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gezelter |
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from the nitrile carbon. However, because we do not have a |
610 |
|
|
particularly large cluster population to interrogate, this is |
611 |
|
|
certainly not quantitative confirmation of this effect. |
612 |
gezelter |
4048 |
|
613 |
gezelter |
4091 |
The prediction of a small red-shift of the nitrile peak in 5CB in |
614 |
|
|
response to a field-induced nematic ordering is the primary result of |
615 |
|
|
this work, and although the proposed anti-caging mechanism is somewhat |
616 |
|
|
speculative, this work provides some impetus for further theory and |
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|
|
experiments. |
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gezelter |
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|
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gezelter |
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\section{Acknowledgements} |
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gezelter |
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The authors thank Steven Corcelli and Zac Schultz for helpful comments |
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|
|
and suggestions. Support for this project was provided by the National |
622 |
gezelter |
4036 |
Science Foundation under grant CHE-0848243. Computational time was |
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|
|
provided by the Center for Research Computing (CRC) at the University |
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|
|
of Notre Dame. |
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|
|
|
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gezelter |
4007 |
\newpage |
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|
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\bibliography{5CB} |
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|
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\end{document} |