trunk/5cb/5CB.bib

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@article{FILLER:1964yg,
        Abstract = {An interpolation formula is derived which gives an apodized spectrum as the convolution of the unapodized spectrum (sampled at suitable points) with the apodized apparatus function. This allows many apodizations to be applied to a single interferogram with the performance of only a single Fourier transformation. A further saving in computation effort is possible if the apodized apparatus function decays rapidly away from its center. Examples of such cases are presented, where the interferogram is weighted by a function which is a cosine series of only a few terms.},
        Author = {A. S. FILLER},
        Date-Added = {2014-02-20 18:13:39 +0000},
        Date-Modified = {2014-02-20 18:13:39 +0000},
        Doi = {10.1364/JOSA.54.000762},
        Journal = {J. Opt. Soc. Am.},
        Month = {Jun},
        Number = {6},
        Pages = {762--764},
        Publisher = {OSA},
        Title = {Apodization and Interpolation in Fourier-Transform Spectroscopy},
        Url = {http://www.opticsinfobase.org/abstract.cfm?URI=josa-54-6-762},
        Volume = {54},
        Year = {1964},
        Bdsk-Url-1 = {http://www.opticsinfobase.org/abstract.cfm?URI=josa-54-6-762},
        Bdsk-Url-2 = {http://dx.doi.org/10.1364/JOSA.54.000762}}

@article{Naylor:2007rm,
        Abstract = {Apodizing functions are used in Fourier transform spectroscopy (FTS) to reduce the magnitude of the sidelobes in the instrumental line shape (ILS), which are a direct result of the finite maximum optical path difference in the measured interferogram. Three apodizing functions, which are considered optimal in the sense of producing the smallest loss in spectral resolution for a given reduction in the magnitude of the largest sidelobe, find frequent use in FTS \[J. Opt. Soc. Am.66, 259 (1976)\]. We extend this series to include optimal apodizing functions corresponding to increases in the width of the ILS ranging from factors of 1.1 to 2.0 compared with its unapodized value, and we compare the results with other commonly used apodizing functions.},
        Author = {David A. Naylor and Margaret K. Tahic},
        Date-Added = {2014-02-20 16:45:24 +0000},
        Date-Modified = {2014-02-20 16:45:24 +0000},
        Doi = {10.1364/JOSAA.24.003644},
        Journal = {J. Opt. Soc. Am. A},
        Keywords = {Linewidth; Spectroscopy, Fourier transforms},
        Month = {Nov},
        Number = {11},
        Pages = {3644--3648},
        Publisher = {OSA},
        Title = {Apodizing functions for Fourier transform spectroscopy},
        Url = {http://josaa.osa.org/abstract.cfm?URI=josaa-24-11-3644},
        Volume = {24},
        Year = {2007},
        Bdsk-Url-1 = {http://josaa.osa.org/abstract.cfm?URI=josaa-24-11-3644},
        Bdsk-Url-2 = {http://dx.doi.org/10.1364/JOSAA.24.003644}}

@article{Morse:1929xy,
        Author = {Morse, Philip M.},
        Date-Added = {2014-02-19 21:18:41 +0000},
        Date-Modified = {2014-02-19 21:18:43 +0000},
        Doi = {10.1103/PhysRev.34.57},
        Issue = {1},
        Journal = {Phys. Rev.},
        Month = {Jul},
        Numpages = {0},
        Pages = {57--64},
        Publisher = {American Physical Society},
        Title = {Diatomic Molecules According to the Wave Mechanics. II. Vibrational Levels},
        Url = {http://link.aps.org/doi/10.1103/PhysRev.34.57},
        Volume = {34},
        Year = {1929},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRev.34.57},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRev.34.57}}

@article{Lee:1988qf,
        Author = {Lee, Chengteh and Yang, Weitao and Parr, Robert G.},
        Date-Added = {2014-02-19 21:03:16 +0000},
        Date-Modified = {2014-02-19 21:03:19 +0000},
        Doi = {10.1103/PhysRevB.37.785},
        Issue = {2},
        Journal = {Phys. Rev. B},
        Month = {Jan},
        Numpages = {0},
        Pages = {785--789},
        Publisher = {American Physical Society},
        Title = {Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density},
        Url = {http://link.aps.org/doi/10.1103/PhysRevB.37.785},
        Volume = {37},
        Year = {1988},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevB.37.785},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevB.37.785}}

@article{Becke:1993kq,
        Author = {Becke, Axel D.},
        Date-Added = {2014-02-19 21:02:30 +0000},
        Date-Modified = {2014-02-19 21:02:30 +0000},
        Doi = {http://dx.doi.org/10.1063/1.464913},
        Journal = {The Journal of Chemical Physics},
        Number = {7},
        Pages = {5648-5652},
        Title = {Density‐functional thermochemistry. III. The role of exact exchange},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/98/7/10.1063/1.464913},
        Volume = {98},
        Year = {1993},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/98/7/10.1063/1.464913},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.464913}}

@book{Collings:1997rz,
        Author = {Collings, P.J. and Hird, M.},
        Date-Added = {2014-02-18 21:05:20 +0000},
        Date-Modified = {2014-02-18 21:05:20 +0000},
        Isbn = {9780203211199},
        Publisher = {Taylor \& Francis},
        Series = {Liquid Crystals Book Series},
        Title = {Introduction to Liquid Crystals: Chemistry and Physics},
        Url = {http://books.google.com/books?id=GBeDkKpZ5VQC},
        Year = {1997},
        Bdsk-Url-1 = {http://books.google.com/books?id=GBeDkKpZ5VQC}}

@article{Cleaver:1996rt,
        Author = {Cleaver, Douglas J. and Care, Christopher M. and Allen, Michael P. and Neal, Maureen P.},
        Date-Added = {2014-02-18 21:01:40 +0000},
        Date-Modified = {2014-02-18 21:01:42 +0000},
        Doi = {10.1103/PhysRevE.54.559},
        Issue = {1},
        Journal = {Phys. Rev. E},
        Month = {Jul},
        Numpages = {0},
        Pages = {559--567},
        Publisher = {American Physical Society},
        Title = {Extension and generalization of the Gay-Berne potential},
        Url = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
        Volume = {54},
        Year = {1996},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.54.559}}

@article{Kushick:1976xy,
        Author = {Kushick, J. and Berne, Bruce J.},
        Date-Added = {2014-02-18 21:00:21 +0000},
        Date-Modified = {2014-02-18 21:00:21 +0000},
        Doi = {http://dx.doi.org/10.1063/1.432403},
        Journal = {The Journal of Chemical Physics},
        Number = {4},
        Pages = {1362-1367},
        Title = {Computer simulation of anisotropic molecular fluids},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
        Volume = {64},
        Year = {1976},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.432403}}

@article{Gay:1981yu,
        Author = {Gay, J. G. and Berne, B. J.},
        Date-Added = {2014-02-18 20:57:16 +0000},
        Date-Modified = {2014-02-18 20:57:16 +0000},
        Doi = {http://dx.doi.org/10.1063/1.441483},
        Journal = {The Journal of Chemical Physics},
        Number = {6},
        Pages = {3316-3319},
        Title = {Modification of the overlap potential to mimic a linear site--site potential},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
        Volume = {74},
        Year = {1981},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.441483}}

@article{Luckhurst90,
        Author = {Luckhurst, G.~R. and Stephens, R.~A. and Phippen, R.~W.},
        Date = OCT,
        Date-Added = {2014-02-18 20:38:33 +0000},
        Date-Modified = {2014-02-18 20:38:33 +0000},
        Journal = lc,
        Number = 4,
        Pages = {451 - 464},
        Title = {COMPUTER-SIMULATION STUDIES OF ANISOTROPIC SYSTEMS .19. MESOPHASES FORMED BY THE GAY-BERNE MODEL MESOGEN},
        Volume = 8,
        Year = 1990}

@article{Berne72,
        Author = {Berne, B.~J. and Pechukas, P},
        Date-Added = {2014-02-18 20:38:09 +0000},
        Date-Modified = {2014-02-18 20:38:09 +0000},
        Journal = {Journal of Chemical Physics},
        Number = 8,
        Pages = {4213-4216},
        Title = {Gaussian Model Potentials for Molecular Interactions},
        Volume = 56,
        Year = 1972}

@article{Choi:2008cr,
        Author = {Choi, Jun-Ho and Oh, Kwang-Im and Lee, Hochan and Lee, Chewook and Cho, Minhaeng},
        Date-Added = {2014-02-18 18:20:28 +0000},
        Date-Modified = {2014-02-18 18:20:28 +0000},
        Doi = {http://dx.doi.org/10.1063/1.2844787},
        Eid = 134506,
        Journal = {The Journal of Chemical Physics},
        Number = {13},
        Pages = {-},
        Title = {Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/128/13/10.1063/1.2844787},
        Volume = {128},
        Year = {2008},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/128/13/10.1063/1.2844787},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2844787}}

@article{Fafarman:2010dq,
        Author = {Fafarman, Aaron T. and Sigala, Paul A. and Herschlag, Daniel and Boxer, Steven G.},
        Date-Added = {2014-02-18 18:13:20 +0000},
        Date-Modified = {2014-02-18 18:13:20 +0000},
        Doi = {10.1021/ja104573b},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja104573b},
        Journal = {Journal of the American Chemical Society},
        Number = {37},
        Pages = {12811-12813},
        Title = {Decomposition of Vibrational Shifts of Nitriles into Electrostatic and Hydrogen-Bonding Effects},
        Url = {http://pubs.acs.org/doi/abs/10.1021/ja104573b},
        Volume = {132},
        Year = {2010},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja104573b},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja104573b}}

@article{Lindquist:2008bh,
        Author = {Lindquist, Beth A. and Haws, Ryan T. and Corcelli, Steven A.},
        Date-Added = {2014-02-18 16:27:15 +0000},
        Date-Modified = {2014-02-18 16:27:15 +0000},
        Doi = {10.1021/jp804900u},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp804900u},
        Journal = {The Journal of Physical Chemistry B},
        Note = {PMID: 18855431},
        Number = {44},
        Pages = {13991-14001},
        Title = {Optimized Quantum Mechanics/Molecular Mechanics Strategies for Nitrile Vibrational Probes: Acetonitrile and para-Tolunitrile in Water and Tetrahydrofuran},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp804900u},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp804900u},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp804900u}}

@article{Lindquist:2008qf,
        Author = {Lindquist, Beth A. and Corcelli, Steven A.},
        Date-Added = {2014-02-18 16:26:29 +0000},
        Date-Modified = {2014-02-18 16:26:29 +0000},
        Doi = {10.1021/jp802039e},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp802039e},
        Journal = {The Journal of Physical Chemistry B},
        Note = {PMID: 18438998},
        Number = {20},
        Pages = {6301-6303},
        Title = {Nitrile Groups as Vibrational Probes: Calculations of the CN Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp802039e},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp802039e},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp802039e}}

@article{Waegele:2010ve,
        Author = {Waegele, Matthias M. and Gai, Feng},
        Date-Added = {2014-02-18 16:24:37 +0000},
        Date-Modified = {2014-02-18 16:24:37 +0000},
        Doi = {10.1021/jz900429z},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jz900429z},
        Journal = {The Journal of Physical Chemistry Letters},
        Number = {4},
        Pages = {781-786},
        Title = {Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jz900429z},
        Volume = {1},
        Year = {2010},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jz900429z},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jz900429z}}

@article{Leyte:1997zl,
        Abstract = {Time-resolved (TR) spectra of 5CB in the millisecond domain were obtained during excitation with electric fields of different time dependence: ac, dc, and ac $+$ dc. The response to ac excitation occurs mainly at twice the modulating frequency. The effect of the addition of dc to an ac field is the induction of an additional response at the ac frequency. The additional 'single frequency' response persists indefinitely, even though the response to the application of only a permanent dc field relaxes within roughly 200 ms. The amplitude of the oscillating responses diminishes with increasing ac frequency. This result is in accordance with the expected response to the torque exerted by the ac field. Different functional group absorptions respond without a significant phase difference in this time scale.},
        Author = {J. C. Leyte and P. C. M. Van Woerkom},
        Date-Added = {2014-02-18 16:19:03 +0000},
        Date-Modified = {2014-02-18 16:19:03 +0000},
        Journal = {Appl. Spectrosc.},
        Month = {Nov},
        Number = {11},
        Pages = {1711--1714},
        Publisher = {OSA},
        Title = {FT-IR TRS of Liquid Crystalline 5CB in ac, dc, and ac $+$ dc Electric Fields},
        Url = {http://as.osa.org/abstract.cfm?URI=as-51-11-1711},
        Volume = {51},
        Year = {1997},
        Bdsk-Url-1 = {http://as.osa.org/abstract.cfm?URI=as-51-11-1711}}

@article{Moreno-Razo:2012rz,
        Annote = {10.1038/nature11084},
        Author = {Moreno-Razo, J. A. and Sambriski, E. J. and Abbott, N. L. and Hernandez-Ortiz, J. P. and de Pablo, J. J.},
        Date = {2012/05/03/print},
        Date-Added = {2014-02-18 16:07:15 +0000},
        Date-Modified = {2014-02-18 16:07:15 +0000},
        Day = {03},
        Isbn = {0028-0836},
        Journal = {Nature},
        L3 = {http://www.nature.com/nature/journal/v485/n7396/abs/nature11084.html#supplementary-information},
        M3 = {10.1038/nature11084},
        Month = {05},
        Number = {7396},
        Pages = {86--89},
        Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
        Title = {Liquid-crystal-mediated self-assembly at nanodroplet interfaces},
        Ty = {JOUR},
        Url = {http://dx.doi.org/10.1038/nature11084},
        Volume = {485},
        Year = {2012},
        Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature11084}}

@article{Schkolnik:2012ty,
        Author = {Schkolnik, Gal and Salewski, Johannes and Millo, Diego and Zebger, Ingo and Franzen, Stefan and Hildebrandt, Peter},
        Date-Added = {2014-02-18 15:43:30 +0000},
        Date-Modified = {2014-02-18 15:43:30 +0000},
        Doi = {10.3390/ijms13067466},
        Issn = {1422-0067},
        Journal = {International Journal of Molecular Sciences},
        Number = {6},
        Pages = {7466--7482},
        Pubmedid = {22837705},
        Title = {Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces},
        Url = {http://www.mdpi.com/1422-0067/13/6/7466},
        Volume = {13},
        Year = {2012},
        Bdsk-Url-1 = {http://www.mdpi.com/1422-0067/13/6/7466},
        Bdsk-Url-2 = {http://dx.doi.org/10.3390/ijms13067466}}

@article{Andrews:2000qv,
        Author = {Andrews, Steven S. and Boxer, Steven G.},
        Date-Added = {2014-02-18 15:39:01 +0000},
        Date-Modified = {2014-02-18 15:39:01 +0000},
        Doi = {10.1021/jp002242r},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp002242r},
        Journal = {The Journal of Physical Chemistry A},
        Number = {51},
        Pages = {11853-11863},
        Title = {Vibrational Stark Effects of Nitriles I. Methods and Experimental Results},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp002242r},
        Volume = {104},
        Year = {2000},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp002242r},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp002242r}}

@article{Oklejas:2002uq,
        Author = {Oklejas, Vanessa and Sjostrom, Chris and Harris, Joel M.},
        Date-Added = {2014-02-18 15:24:01 +0000},
        Date-Modified = {2014-02-18 15:24:01 +0000},
        Doi = {10.1021/ja017656s},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja017656s},
        Journal = {Journal of the American Chemical Society},
        Number = {11},
        Pages = {2408-2409},
        Title = {SERS Detection of the Vibrational Stark Effect from Nitrile-Terminated SAMs to Probe Electric Fields in the Diffuse Double-Layer},
        Url = {http://pubs.acs.org/doi/abs/10.1021/ja017656s},
        Volume = {124},
        Year = {2002},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja017656s},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja017656s}}

@article{Lindquist:2009fk,
        Abstract = {This paper presents an overview of recent experiments and theoretical developments aimed at using vibrational spectroscopy to understand the structure and dynamics of nitrile-labeled biomolecules. Nitrile groups are excellent vibrational probes of proteins and DNA because they absorb in a region of the spectrum that is relatively free of absorption due to the biomolecule{,} and they have high extinction coefficients. The vibrational frequency of nitrile groups is also extraordinarily sensitive to its local environment{,} and thus C[triple bond{,} length as m-dash]N bonds have been employed in both linear and 2-D infrared (IR) spectroscopy experiments and also as vibrational Stark probes of electric fields in proteins. The interpretation and design of these experiments would be enhanced by accurate calculations of IR spectra from molecular dynamics simulations. Recently{,} theoretical developments towards computing the vibrational spectrum of nitrile groups in the condensed-phase have been highly successful. A strong synergy between experiment and theory will further promote the use of vibrational spectroscopy of nitrile-labeled biomolecules to address fundamental questions of structure and dynamics that are elusive to other techniques.},
        Author = {Lindquist, Beth A. and Furse, Kristina E. and Corcelli, Steven A.},
        Date-Added = {2014-02-18 15:16:38 +0000},
        Date-Modified = {2014-02-18 15:16:38 +0000},
        Doi = {10.1039/B908588B},
        Issue = {37},
        Journal = {Phys. Chem. Chem. Phys.},
        Pages = {8119-8132},
        Publisher = {The Royal Society of Chemistry},
        Title = {Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview},
        Url = {http://dx.doi.org/10.1039/B908588B},
        Volume = {11},
        Year = {2009},
        Bdsk-Url-1 = {http://dx.doi.org/10.1039/B908588B}}

@article{Meineke05,
        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
        Date-Added = {2014-02-14 19:21:43 +0000},
        Date-Modified = {2014-02-14 19:21:43 +0000},
        Journal = {J. Comp. Chem.},
        Pages = {252-271},
        Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
        Volume = 26,
        Year = 2005}

@article{Fennell:2006zl,
        Abstract = {We investigate pairwise electrostatic interaction methods and show that there are viable computationally efficient (O(N)) alternatives to the Ewald summation for typical modern molecular simulations. These methods are extended from the damped and cutoff-neutralized Coulombic sum originally proposed by Wolf [J. Chem. Phys. 110, 8255 (1999)]. One of these, the damped shifted force method, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. Comparisons were performed with this and other pairwise methods against the smooth particle-mesh Ewald summation to see how well they reproduce the energetics and dynamics of a variety of molecular simulations. (c) 2006 American Institute of Physics.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Fennell, Christopher~J. and Gezelter, J.~Daniel},
        Date = {JUN 21 2006},
        Date-Added = {2014-02-14 19:21:36 +0000},
        Date-Modified = {2014-02-14 19:21:36 +0000},
        Doi = {ARTN 234104},
        Journal = jcp,
        Publisher = {AMER INST PHYSICS},
        Timescited = {15},
        Title = {Is the {E}wald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/234104}}

@article{PhysRevLett.111.227801,
        Author = {Whitmer, Jonathan K. and Wang, Xiaoguang and Mondiot, Frederic and Miller, Daniel S. and Abbott, Nicholas L. and de Pablo, Juan J.},
        Date-Added = {2014-02-06 20:01:25 +0000},
        Date-Modified = {2014-02-06 20:01:25 +0000},
        Doi = {10.1103/PhysRevLett.111.227801},
        Issue = {22},
        Journal = {Phys. Rev. Lett.},
        Month = {Nov},
        Numpages = {5},
        Pages = {227801},
        Publisher = {American Physical Society},
        Title = {Nematic-Field-Driven Positioning of Particles in Liquid Crystal Droplets},
        Url = {http://link.aps.org/doi/10.1103/PhysRevLett.111.227801},
        Volume = {111},
        Year = {2013},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.111.227801},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.111.227801}}

@article{Oh:2008fk,
        Abstract = {Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.},
        Author = {Oh, Kwang-Im and Choi, Jun-Ho and Lee, Joo-Hyun and Han, Jae-Beom and Lee, Hochan and Cho, Minhaeng},
        Date-Added = {2014-02-06 18:11:52 +0000},
        Date-Modified = {2014-02-06 18:11:52 +0000},
        Doi = {10.1063/1.2904558},
        Journal = {J Chem Phys},
        Journal-Full = {The Journal of chemical physics},
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        Volume = {128},
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        Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUGJCVYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3ASAAGGoKgHCBMUFRYaIVUkbnVsbNMJCgsMDxJXTlMua2V5c1pOUy5vYmplY3RzViRjbGFzc6INDoACgAOiEBGABIAFgAdccmVsYXRpdmVQYXRoWWFsaWFzRGF0YV8QGi4uLy4uL0Ryb3Bib3gvMzE3NzI5NzQucGRm0hcLGBlXTlMuZGF0YU8RAW4AAAAAAW4AAgAADE1hY2ludG9zaCBIRAAAAAAAAAAAAAAAAAAAAMcrh89IKwAAAF4d6gwzMTc3Mjk3NC5wZGYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADiyANzkzZRwAAAAAAAAAAAAIAAgAACSAAAAAAAAAAAAAAAAAAAAAHRHJvcGJveAAAEAAIAADHK84fAAAAEQAIAADOTRGHAAAAAQAMAF4d6gAOa74AAJGNAAIAME1hY2ludG9zaCBIRDpVc2VyczoAam1hcnI6AERyb3Bib3g6ADMxNzcyOTc0LnBkZgAOABoADAAzADEANwA3ADIAOQA3ADQALgBwAGQAZgAPABoADABNAGEAYwBpAG4AdABvAHMAaAAgAEgARAASACBVc2Vycy9qbWFyci9Ecm9wYm94LzMxNzcyOTc0LnBkZgATAAEvAAAVAAIADP//AACABtIbHB0eWiRjbGFzc25hbWVYJGNsYXNzZXNdTlNNdXRhYmxlRGF0YaMdHyBWTlNEYXRhWE5TT2JqZWN00hscIiNcTlNEaWN0aW9uYXJ5oiIgXxAPTlNLZXllZEFyY2hpdmVy0SYnVHJvb3SAAQAIABEAGgAjAC0AMgA3AEAARgBNAFUAYABnAGoAbABuAHEAcwB1AHcAhACOAKsAsAC4AioCLAIxAjwCRQJTAlcCXgJnAmwCeQJ8Ao4CkQKWAAAAAAAAAgEAAAAAAAAAKAAAAAAAAAAAAAAAAAAAApg=}}

@article{Gray:1973ca,
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        Date-Added = {2014-01-20 19:18:33 +0000},
        Date-Modified = {2014-01-20 19:18:35 +0000},
        Doi = {10.1049/el:19730096},
        Issn = {0013-5194},
        Journal = {Electronics Letters},
        Keywords = {display systems;electro-optical effects;liquid crystals;displays;nematic liquid crystals;positive dielectric anisotropy},
        Number = {6},
        Pages = {130-131},
        Title = {New family of nematic liquid crystals for displays},
        Volume = {9},
        Year = {1973},
        Bdsk-Url-1 = {http://dx.doi.org/10.1049/el:19730096}}

@article{Lee:2006qd,
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        Date-Added = {2014-01-20 19:14:33 +0000},
        Date-Modified = {2014-01-20 19:39:28 +0000},
        Doi = {http://dx.doi.org/10.1063/1.2210930},
        Eid = 024705,
        Journal = {The Journal of Chemical Physics},
        Number = {2},
        Pages = {024705},
        Title = {Anchoring and electro-optical dynamics of thin liquid crystalline films in a polyimide cell: Experiment and theory},
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        Volume = {125},
        Year = {2006},
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        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2210930}}

@article{Zhang:2011hh,
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        Date-Added = {2014-01-20 19:13:11 +0000},
        Date-Modified = {2014-01-20 19:39:44 +0000},
        Doi = {10.1021/jp111408n},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp111408n},
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        Number = {10},
        Pages = {2214-2227},
        Title = {An Atomistic Simulation for 4-Cyano-4$^\prime$-pentylbiphenyl and Its Homologue with a Reoptimized Force Field},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp111408n},
        Volume = {115},
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        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp111408n},
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@article{Lim:2006xq,
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        Date-Added = {2014-01-20 19:11:44 +0000},
        Date-Modified = {2014-01-20 19:38:40 +0000},
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        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Number = {1--3},
        Pages = {178 - 182},
        Title = {Raman spectroscopy study and density functional theory calculations of the nematic liquid crystal 4-n-pentyl-4$^\prime$-cyanobiphenyl under an electric field},
        Url = {http://www.sciencedirect.com/science/article/pii/S0009261406003873},
        Volume = {423},
        Year = {2006},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0009261406003873},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.cplett.2006.03.055}}

@article{Tucker:2004qq,
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        Date-Added = {2014-01-20 19:10:42 +0000},
        Date-Modified = {2014-01-20 19:10:45 +0000},
        Doi = {10.1021/ja032015d},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja032015d},
        Journal = {Journal of the American Chemical Society},
        Number = {16},
        Pages = {5078-5079},
        Title = {A New Method for Determining the Local Environment and Orientation of Individual Side Chains of Membrane-Binding Peptides},
        Url = {http://pubs.acs.org/doi/abs/10.1021/ja032015d},
        Volume = {126},
        Year = {2004},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja032015d},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja032015d}}

@article{Webb:2008kn,
        Author = {Webb, Lauren J. and Boxer, Steven G.},
        Date-Added = {2014-01-20 19:09:37 +0000},
        Date-Modified = {2014-01-20 19:38:19 +0000},
        Doi = {10.1021/bi701708u},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi701708u},
        Journal = {Biochemistry},
        Note = {PMID: 18205401},
        Number = {6},
        Pages = {1588-1598},
        Title = {Electrostatic Fields Near the Active Site of Human Aldose Reductase: 1. New Inhibitors and Vibrational Stark Effect Measurements},
        Url = {http://pubs.acs.org/doi/abs/10.1021/bi701708u},
        Volume = {47},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/bi701708u},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/bi701708u}}

@article{Boxer:2009xw,
        Author = {Boxer, Steven G.},
        Date-Added = {2014-01-20 19:07:47 +0000},
        Date-Modified = {2014-01-20 19:37:48 +0000},
        Doi = {10.1021/jp8067393},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp8067393},
        Journal = {The Journal of Physical Chemistry B},
        Number = {10},
        Pages = {2972-2983},
        Title = {Stark Realities},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp8067393},
        Volume = {113},
        Year = {2009},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp8067393},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp8067393}}

@article{Hatta:1991ee,
        Author = {A. Hatta and H. Amano and W. Su{\"e}taka},
        Date-Added = {2014-01-20 19:05:00 +0000},
        Date-Modified = {2014-01-20 19:05:03 +0000},
        Doi = {http://dx.doi.org/10.1016/0924-2031(91)80006-A},
        Issn = {0924-2031},
        Journal = {Vibrational Spectroscopy},
        Keywords = {Liquid crystals},
        Number = {4},
        Pages = {371 - 376},
        Title = {Electric field response of 5CB liquid crystal molecules in the electrode boundary region as probed by modulation infrared \{ATR\} spectroscopy},
        Url = {http://www.sciencedirect.com/science/article/pii/092420319180006A},
        Volume = {1},
        Year = {1991},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/092420319180006A},
        Bdsk-Url-2 = {http://dx.doi.org/10.1016/0924-2031(91)80006-A}}

@incollection{Prost:1980wt,
        Author = {Prost, J.},
        Booktitle = {Liquid Crystals of One- and Two-Dimensional Order},
        Date-Added = {2014-01-20 19:01:37 +0000},
        Date-Modified = {2014-01-20 19:01:41 +0000},
        Doi = {10.1007/978-3-642-67848-6_29},
        Editor = {Helfrich, W. and Heppke, G.},
        Isbn = {978-3-642-67850-9},
        Language = {English},
        Pages = {125-145},
        Publisher = {Springer Berlin Heidelberg},
        Series = {Springer Series in Chemical Physics},
        Title = {Reflections on the Reentrant Nematic and the SA-SA Phase Transitions},
        Url = {http://dx.doi.org/10.1007/978-3-642-67848-6_29},
        Volume = {11},
        Year = {1980},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-67848-6_29}}

@article{HARDOUIN:1983qf,
        Author = {HARDOUIN, F and LEVELUT, AM and ACHARD, MF and SIGAUD, G},
        Date-Added = {2014-01-20 18:56:21 +0000},
        Date-Modified = {2014-01-20 18:56:21 +0000},
        Issn = {{0021-7689}},
        Journal = {{JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE}},
        Number = {{1}},
        Pages = {{53-64}},
        Title = {{POLYMORPHISM IN POLAR MESOGENS .1. PHYSICO-CHEMISTRY AND STRUCTURAL ASPECTS}},
        Unique-Id = {{ISI:A1983QJ60700008}},
        Volume = {{80}},
        Year = {{1983}}}

@article{Leadbetter:1976vf,
        Author = {Leadbetter, A. J. and Durrant, J. L. A. and Rugman, M.},
        Date-Added = {2014-01-20 18:54:50 +0000},
        Date-Modified = {2014-01-20 18:54:54 +0000},
        Doi = {10.1080/15421407708083712},
        Eprint = {http://www.tandfonline.com/doi/pdf/10.1080/15421407708083712},
        Journal = {Molecular Crystals and Liquid Crystals},
        Number = {10},
        Pages = {231-235},
        Title = {The Density Of 4 n-Octyl-4-Cyano-Biphenyl (8CB)},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/15421407708083712},
        Volume = {34},
        Year = {1976},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/15421407708083712},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/15421407708083712}}

@book{Gray:1984hc,
        Author = {Gray, G.W. and Goodby, J.W.G.},
        Date-Added = {2014-01-20 18:39:08 +0000},
        Date-Modified = {2014-01-20 18:39:08 +0000},
        Isbn = {9780249441680},
        Lccn = {lc84164554},
        Publisher = {L. Hill},
        Title = {Smectic liquid crystals: textures and structures},
        Url = {http://books.google.com/books?id=WgTwAAAAMAAJ},
        Year = {1984},
        Bdsk-Url-1 = {http://books.google.com/books?id=WgTwAAAAMAAJ}}

@article{Vanakaras:1998it,
        Author = {Vanakaras, Alexandros G. and Photinos, Demetri J. and Samulski, Edward T.},
        Date-Added = {2014-01-20 18:37:13 +0000},
        Date-Modified = {2014-01-20 18:37:15 +0000},
        Doi = {10.1103/PhysRevE.57.R4875},
        Issue = {5},
        Journal = {Phys. Rev. E},
        Month = {May},
        Numpages = {0},
        Pages = {R4875--R4878},
        Publisher = {American Physical Society},
        Title = {Tilt, polarity, and spontaneous symmetry breaking in liquid crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRevE.57.R4875},
        Volume = {57},
        Year = {1998},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.57.R4875},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.57.R4875}}

@article{Prost:1984qe,
        Author = {Prost, J.},
        Date-Added = {2014-01-20 18:36:25 +0000},
        Date-Modified = {2014-01-20 18:36:29 +0000},
        Doi = {10.1080/00018738400101631},
        Eprint = {http://www.tandfonline.com/doi/pdf/10.1080/00018738400101631},
        Journal = {Advances in Physics},
        Number = {1},
        Pages = {1-46},
        Title = {The smectic state},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/00018738400101631},
        Volume = {33},
        Year = {1984},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/00018738400101631},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/00018738400101631}}

@article{Photinos:1976xe,
        Author = {Photinos, Panagoitis J. and Saupe, Alfred},
        Date-Added = {2014-01-20 18:34:10 +0000},
        Date-Modified = {2014-01-20 18:34:14 +0000},
        Doi = {10.1103/PhysRevA.13.1926},
        Issue = {5},
        Journal = {Phys. Rev. A},
        Month = {May},
        Numpages = {0},
        Pages = {1926--1930},
        Publisher = {American Physical Society},
        Title = {Mean-field study of uniaxial smectic liquid crystals with polarized layers},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.13.1926},
        Volume = {13},
        Year = {1976},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.13.1926},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.13.1926}}

@article{Netz:1992cr,
        Author = {Netz, Roland R. and Berker, A. Nihat},
        Date-Added = {2014-01-20 18:33:40 +0000},
        Date-Modified = {2014-01-20 18:33:43 +0000},
        Doi = {10.1103/PhysRevLett.68.333},
        Issue = {3},
        Journal = {Phys. Rev. Lett.},
        Month = {Jan},
        Numpages = {0},
        Pages = {333--336},
        Publisher = {American Physical Society},
        Title = {Smectic-<i>C</i> order, in-plane domains, and nematic reentrance in a microscopic model of liquid crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRevLett.68.333},
        Volume = {68},
        Year = {1992},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevLett.68.333},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevLett.68.333}}

@article{Meyer:1976qd,
        Author = {Meyer, Robert B. and Lubensky, T. C.},
        Date-Added = {2014-01-20 18:33:13 +0000},
        Date-Modified = {2014-01-20 19:12:04 +0000},
        Doi = {10.1103/PhysRevA.14.2307},
        Issue = {6},
        Journal = {Phys. Rev. A},
        Month = {Dec},
        Numpages = {0},
        Pages = {2307--2320},
        Publisher = {American Physical Society},
        Title = {Mean-field theory of the nematic-smectic-A phase change in liquid crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.14.2307},
        Volume = {14},
        Year = {1976},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.14.2307},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.14.2307}}

@article{Levesque:1993pd,
        Author = {Levesque, D. and Weis, J. J. and Zarragoicoechea, G. J.},
        Date-Added = {2014-01-20 18:32:43 +0000},
        Date-Modified = {2014-01-20 18:32:45 +0000},
        Doi = {10.1103/PhysRevE.47.496},
        Issue = {1},
        Journal = {Phys. Rev. E},
        Month = {Jan},
        Numpages = {0},
        Pages = {496--505},
        Publisher = {American Physical Society},
        Title = {Monte Carlo simulation study of mesophase formation in dipolar spherocylinders},
        Url = {http://link.aps.org/doi/10.1103/PhysRevE.47.496},
        Volume = {47},
        Year = {1993},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.47.496},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.47.496}}

@article{Levelut:1981eu,
        Author = {Levelut, A. M. and Tarento, R. J. and Hardouin, F. and Achard, M. F. and Sigaud, G.},
        Date-Added = {2014-01-20 18:32:07 +0000},
        Date-Modified = {2014-01-20 18:49:25 +0000},
        Doi = {10.1103/PhysRevA.24.2180},
        Issue = {4},
        Journal = {Phys. Rev. A},
        Month = {Oct},
        Numpages = {0},
        Pages = {2180--2186},
        Publisher = {American Physical Society},
        Title = {Number of SA phases},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.24.2180},
        Volume = {24},
        Year = {1981},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.24.2180},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.24.2180}}

@article{Jeu:1983ly,
        Abstract = {The physical properties and the phase behaviour of some nematic liquid crystals are discussed, with emphasis on the influence of short-range antiparallel dipole correlation that occurs in mesogenic compounds with a strong terminal dipole moment. Evidence for this effect, which stems especially from dielectric studies, is summarized. Variations of the dipole correlation with molecular structure can explain the sometimes unexpected phase behaviour and physical properties of these substances. A qualitative model is given in terms of a monomer--dimer equilibrium.},
        Author = {Jeu, W. H. De and Raynes, E. P. and Price, A. H. and Clark, M. G.},
        Date-Added = {2014-01-20 18:30:36 +0000},
        Date-Modified = {2014-01-20 18:30:39 +0000},
        Doi = {10.1098/rsta.1983.0035},
        Eprint = {http://rsta.royalsocietypublishing.org/content/309/1507/217.full.pdf+html},
        Journal = {Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences},
        Number = {1507},
        Pages = {217-229},
        Title = {Liquid Crystalline Materials: Physical Properties and Intermolecular Interactions [and Discussion]},
        Url = {http://rsta.royalsocietypublishing.org/content/309/1507/217.abstract},
        Volume = {309},
        Year = {1983},
        Bdsk-Url-1 = {http://rsta.royalsocietypublishing.org/content/309/1507/217.abstract},
        Bdsk-Url-2 = {http://dx.doi.org/10.1098/rsta.1983.0035}}

@article{Indekeu:1986ty,
        Author = {Indekeu, J. O. and Berker, A. Nihat},
        Date-Added = {2014-01-20 18:27:51 +0000},
        Date-Modified = {2014-01-20 18:50:31 +0000},
        Doi = {10.1103/PhysRevA.33.1158},
        Issue = {2},
        Journal = {Phys. Rev. A},
        Month = {Feb},
        Numpages = {0},
        Pages = {1158--1162},
        Publisher = {American Physical Society},
        Title = {Quadruple reentrance (nematic-smectic-Ad-nematic-smectic-Ad-nematic-smectic-A1) from the frustrated spin-gas model of liquid crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.33.1158},
        Volume = {33},
        Year = {1986},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.33.1158},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.33.1158}}

@incollection{Hardouin:1980yq,
        Author = {Hardouin, F. and Levelut, A.M. and Benattar, J.J. and Sigaud, G.},
        Booktitle = {Liquid Crystals of One- and Two-Dimensional Order},
        Date-Added = {2014-01-20 18:26:57 +0000},
        Date-Modified = {2014-01-20 18:26:59 +0000},
        Doi = {10.1007/978-3-642-67848-6_31},
        Editor = {Helfrich, W. and Heppke, G.},
        Isbn = {978-3-642-67850-9},
        Language = {English},
        Pages = {147-147},
        Publisher = {Springer Berlin Heidelberg},
        Series = {Springer Series in Chemical Physics},
        Title = {X-Ray Investigations of the Smectic A1 --- Smectic A2 Transition},
        Url = {http://dx.doi.org/10.1007/978-3-642-67848-6_31},
        Volume = {11},
        Year = {1980},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-67848-6_31}}

@article{Dowell:1985qf,
        Author = {Dowell, F.},
        Date-Added = {2014-01-20 18:25:24 +0000},
        Date-Modified = {2014-01-20 18:25:26 +0000},
        Doi = {10.1103/PhysRevA.31.3214},
        Issue = {5},
        Journal = {Phys. Rev. A},
        Month = {May},
        Numpages = {0},
        Pages = {3214--3219},
        Publisher = {American Physical Society},
        Title = {Effect of longitudinal dipoles in liquid crystals},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.31.3214},
        Volume = {31},
        Year = {1985},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.31.3214},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.31.3214}}

@article{Baus:1989fk,
        Author = {Baus, Marc and Colot, Jean-Louis},
        Date-Added = {2014-01-20 18:24:36 +0000},
        Date-Modified = {2014-01-20 18:24:39 +0000},
        Doi = {10.1103/PhysRevA.40.5444},
        Issue = {9},
        Journal = {Phys. Rev. A},
        Month = {Nov},
        Numpages = {0},
        Pages = {5444--5446},
        Publisher = {American Physical Society},
        Title = {Ferroelectric nematic liquid-crystal phases of dipolar hard ellipsoids},
        Url = {http://link.aps.org/doi/10.1103/PhysRevA.40.5444},
        Volume = {40},
        Year = {1989},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.40.5444},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.40.5444}}
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