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4  
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9  
10  
11  
12 + @book{Collings:1997rz,
13 +        Author = {Collings, P.J. and Hird, M.},
14 +        Date-Added = {2014-02-18 21:05:20 +0000},
15 +        Date-Modified = {2014-02-18 21:05:20 +0000},
16 +        Isbn = {9780203211199},
17 +        Publisher = {Taylor \& Francis},
18 +        Series = {Liquid Crystals Book Series},
19 +        Title = {Introduction to Liquid Crystals: Chemistry and Physics},
20 +        Url = {http://books.google.com/books?id=GBeDkKpZ5VQC},
21 +        Year = {1997},
22 +        Bdsk-Url-1 = {http://books.google.com/books?id=GBeDkKpZ5VQC}}
23 +
24 + @article{Cleaver:1996rt,
25 +        Author = {Cleaver, Douglas J. and Care, Christopher M. and Allen, Michael P. and Neal, Maureen P.},
26 +        Date-Added = {2014-02-18 21:01:40 +0000},
27 +        Date-Modified = {2014-02-18 21:01:42 +0000},
28 +        Doi = {10.1103/PhysRevE.54.559},
29 +        Issue = {1},
30 +        Journal = {Phys. Rev. E},
31 +        Month = {Jul},
32 +        Numpages = {0},
33 +        Pages = {559--567},
34 +        Publisher = {American Physical Society},
35 +        Title = {Extension and generalization of the Gay-Berne potential},
36 +        Url = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
37 +        Volume = {54},
38 +        Year = {1996},
39 +        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
40 +        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.54.559}}
41 +
42 + @article{Kushick:1976xy,
43 +        Author = {Kushick, J. and Berne, Bruce J.},
44 +        Date-Added = {2014-02-18 21:00:21 +0000},
45 +        Date-Modified = {2014-02-18 21:00:21 +0000},
46 +        Doi = {http://dx.doi.org/10.1063/1.432403},
47 +        Journal = {The Journal of Chemical Physics},
48 +        Number = {4},
49 +        Pages = {1362-1367},
50 +        Title = {Computer simulation of anisotropic molecular fluids},
51 +        Url = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
52 +        Volume = {64},
53 +        Year = {1976},
54 +        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
55 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.432403}}
56 +
57 + @article{Gay:1981yu,
58 +        Author = {Gay, J. G. and Berne, B. J.},
59 +        Date-Added = {2014-02-18 20:57:16 +0000},
60 +        Date-Modified = {2014-02-18 20:57:16 +0000},
61 +        Doi = {http://dx.doi.org/10.1063/1.441483},
62 +        Journal = {The Journal of Chemical Physics},
63 +        Number = {6},
64 +        Pages = {3316-3319},
65 +        Title = {Modification of the overlap potential to mimic a linear site--site potential},
66 +        Url = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
67 +        Volume = {74},
68 +        Year = {1981},
69 +        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
70 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.441483}}
71 +
72 + @article{Luckhurst90,
73 +        Author = {Luckhurst, G.~R. and Stephens, R.~A. and Phippen, R.~W.},
74 +        Date = OCT,
75 +        Date-Added = {2014-02-18 20:38:33 +0000},
76 +        Date-Modified = {2014-02-18 20:38:33 +0000},
77 +        Journal = lc,
78 +        Number = 4,
79 +        Pages = {451 - 464},
80 +        Title = {COMPUTER-SIMULATION STUDIES OF ANISOTROPIC SYSTEMS .19. MESOPHASES FORMED BY THE GAY-BERNE MODEL MESOGEN},
81 +        Volume = 8,
82 +        Year = 1990}
83 +
84 + @article{Berne72,
85 +        Author = {Berne, B.~J. and Pechukas, P},
86 +        Date-Added = {2014-02-18 20:38:09 +0000},
87 +        Date-Modified = {2014-02-18 20:38:09 +0000},
88 +        Journal = {Journal of Chemical Physics},
89 +        Number = 8,
90 +        Pages = {4213-4216},
91 +        Title = {Gaussian Model Potentials for Molecular Interactions},
92 +        Volume = 56,
93 +        Year = 1972}
94 +
95 + @article{Choi:2008cr,
96 +        Author = {Choi, Jun-Ho and Oh, Kwang-Im and Lee, Hochan and Lee, Chewook and Cho, Minhaeng},
97 +        Date-Added = {2014-02-18 18:20:28 +0000},
98 +        Date-Modified = {2014-02-18 18:20:28 +0000},
99 +        Doi = {http://dx.doi.org/10.1063/1.2844787},
100 +        Eid = 134506,
101 +        Journal = {The Journal of Chemical Physics},
102 +        Number = {13},
103 +        Pages = {-},
104 +        Title = {Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis},
105 +        Url = {http://scitation.aip.org/content/aip/journal/jcp/128/13/10.1063/1.2844787},
106 +        Volume = {128},
107 +        Year = {2008},
108 +        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/128/13/10.1063/1.2844787},
109 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.2844787}}
110 +
111 + @article{Fafarman:2010dq,
112 +        Author = {Fafarman, Aaron T. and Sigala, Paul A. and Herschlag, Daniel and Boxer, Steven G.},
113 +        Date-Added = {2014-02-18 18:13:20 +0000},
114 +        Date-Modified = {2014-02-18 18:13:20 +0000},
115 +        Doi = {10.1021/ja104573b},
116 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja104573b},
117 +        Journal = {Journal of the American Chemical Society},
118 +        Number = {37},
119 +        Pages = {12811-12813},
120 +        Title = {Decomposition of Vibrational Shifts of Nitriles into Electrostatic and Hydrogen-Bonding Effects},
121 +        Url = {http://pubs.acs.org/doi/abs/10.1021/ja104573b},
122 +        Volume = {132},
123 +        Year = {2010},
124 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja104573b},
125 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja104573b}}
126 +
127 + @article{Lindquist:2008bh,
128 +        Author = {Lindquist, Beth A. and Haws, Ryan T. and Corcelli, Steven A.},
129 +        Date-Added = {2014-02-18 16:27:15 +0000},
130 +        Date-Modified = {2014-02-18 16:27:15 +0000},
131 +        Doi = {10.1021/jp804900u},
132 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp804900u},
133 +        Journal = {The Journal of Physical Chemistry B},
134 +        Note = {PMID: 18855431},
135 +        Number = {44},
136 +        Pages = {13991-14001},
137 +        Title = {Optimized Quantum Mechanics/Molecular Mechanics Strategies for Nitrile Vibrational Probes: Acetonitrile and para-Tolunitrile in Water and Tetrahydrofuran},
138 +        Url = {http://pubs.acs.org/doi/abs/10.1021/jp804900u},
139 +        Volume = {112},
140 +        Year = {2008},
141 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp804900u},
142 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp804900u}}
143 +
144 + @article{Lindquist:2008qf,
145 +        Author = {Lindquist, Beth A. and Corcelli, Steven A.},
146 +        Date-Added = {2014-02-18 16:26:29 +0000},
147 +        Date-Modified = {2014-02-18 16:26:29 +0000},
148 +        Doi = {10.1021/jp802039e},
149 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp802039e},
150 +        Journal = {The Journal of Physical Chemistry B},
151 +        Note = {PMID: 18438998},
152 +        Number = {20},
153 +        Pages = {6301-6303},
154 +        Title = {Nitrile Groups as Vibrational Probes: Calculations of the CN Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran},
155 +        Url = {http://pubs.acs.org/doi/abs/10.1021/jp802039e},
156 +        Volume = {112},
157 +        Year = {2008},
158 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp802039e},
159 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp802039e}}
160 +
161 + @article{Waegele:2010ve,
162 +        Author = {Waegele, Matthias M. and Gai, Feng},
163 +        Date-Added = {2014-02-18 16:24:37 +0000},
164 +        Date-Modified = {2014-02-18 16:24:37 +0000},
165 +        Doi = {10.1021/jz900429z},
166 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jz900429z},
167 +        Journal = {The Journal of Physical Chemistry Letters},
168 +        Number = {4},
169 +        Pages = {781-786},
170 +        Title = {Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water},
171 +        Url = {http://pubs.acs.org/doi/abs/10.1021/jz900429z},
172 +        Volume = {1},
173 +        Year = {2010},
174 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jz900429z},
175 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jz900429z}}
176 +
177 + @article{Leyte:1997zl,
178 +        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.},
179 +        Author = {J. C. Leyte and P. C. M. Van Woerkom},
180 +        Date-Added = {2014-02-18 16:19:03 +0000},
181 +        Date-Modified = {2014-02-18 16:19:03 +0000},
182 +        Journal = {Appl. Spectrosc.},
183 +        Month = {Nov},
184 +        Number = {11},
185 +        Pages = {1711--1714},
186 +        Publisher = {OSA},
187 +        Title = {FT-IR TRS of Liquid Crystalline 5CB in ac, dc, and ac $+$ dc Electric Fields},
188 +        Url = {http://as.osa.org/abstract.cfm?URI=as-51-11-1711},
189 +        Volume = {51},
190 +        Year = {1997},
191 +        Bdsk-Url-1 = {http://as.osa.org/abstract.cfm?URI=as-51-11-1711}}
192 +
193 + @article{Moreno-Razo:2012rz,
194 +        Annote = {10.1038/nature11084},
195 +        Author = {Moreno-Razo, J. A. and Sambriski, E. J. and Abbott, N. L. and Hernandez-Ortiz, J. P. and de Pablo, J. J.},
196 +        Date = {2012/05/03/print},
197 +        Date-Added = {2014-02-18 16:07:15 +0000},
198 +        Date-Modified = {2014-02-18 16:07:15 +0000},
199 +        Day = {03},
200 +        Isbn = {0028-0836},
201 +        Journal = {Nature},
202 +        L3 = {http://www.nature.com/nature/journal/v485/n7396/abs/nature11084.html#supplementary-information},
203 +        M3 = {10.1038/nature11084},
204 +        Month = {05},
205 +        Number = {7396},
206 +        Pages = {86--89},
207 +        Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
208 +        Title = {Liquid-crystal-mediated self-assembly at nanodroplet interfaces},
209 +        Ty = {JOUR},
210 +        Url = {http://dx.doi.org/10.1038/nature11084},
211 +        Volume = {485},
212 +        Year = {2012},
213 +        Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature11084}}
214 +
215 + @article{Schkolnik:2012ty,
216 +        Author = {Schkolnik, Gal and Salewski, Johannes and Millo, Diego and Zebger, Ingo and Franzen, Stefan and Hildebrandt, Peter},
217 +        Date-Added = {2014-02-18 15:43:30 +0000},
218 +        Date-Modified = {2014-02-18 15:43:30 +0000},
219 +        Doi = {10.3390/ijms13067466},
220 +        Issn = {1422-0067},
221 +        Journal = {International Journal of Molecular Sciences},
222 +        Number = {6},
223 +        Pages = {7466--7482},
224 +        Pubmedid = {22837705},
225 +        Title = {Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces},
226 +        Url = {http://www.mdpi.com/1422-0067/13/6/7466},
227 +        Volume = {13},
228 +        Year = {2012},
229 +        Bdsk-Url-1 = {http://www.mdpi.com/1422-0067/13/6/7466},
230 +        Bdsk-Url-2 = {http://dx.doi.org/10.3390/ijms13067466}}
231 +
232 + @article{Andrews:2000qv,
233 +        Author = {Andrews, Steven S. and Boxer, Steven G.},
234 +        Date-Added = {2014-02-18 15:39:01 +0000},
235 +        Date-Modified = {2014-02-18 15:39:01 +0000},
236 +        Doi = {10.1021/jp002242r},
237 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp002242r},
238 +        Journal = {The Journal of Physical Chemistry A},
239 +        Number = {51},
240 +        Pages = {11853-11863},
241 +        Title = {Vibrational Stark Effects of Nitriles I. Methods and Experimental Results},
242 +        Url = {http://pubs.acs.org/doi/abs/10.1021/jp002242r},
243 +        Volume = {104},
244 +        Year = {2000},
245 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp002242r},
246 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp002242r}}
247 +
248 + @article{Oklejas:2002uq,
249 +        Author = {Oklejas, Vanessa and Sjostrom, Chris and Harris, Joel M.},
250 +        Date-Added = {2014-02-18 15:24:01 +0000},
251 +        Date-Modified = {2014-02-18 15:24:01 +0000},
252 +        Doi = {10.1021/ja017656s},
253 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja017656s},
254 +        Journal = {Journal of the American Chemical Society},
255 +        Number = {11},
256 +        Pages = {2408-2409},
257 +        Title = {SERS Detection of the Vibrational Stark Effect from Nitrile-Terminated SAMs to Probe Electric Fields in the Diffuse Double-Layer},
258 +        Url = {http://pubs.acs.org/doi/abs/10.1021/ja017656s},
259 +        Volume = {124},
260 +        Year = {2002},
261 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ja017656s},
262 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/ja017656s}}
263 +
264 + @article{Lindquist:2009fk,
265 +        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.},
266 +        Author = {Lindquist, Beth A. and Furse, Kristina E. and Corcelli, Steven A.},
267 +        Date-Added = {2014-02-18 15:16:38 +0000},
268 +        Date-Modified = {2014-02-18 15:16:38 +0000},
269 +        Doi = {10.1039/B908588B},
270 +        Issue = {37},
271 +        Journal = {Phys. Chem. Chem. Phys.},
272 +        Pages = {8119-8132},
273 +        Publisher = {The Royal Society of Chemistry},
274 +        Title = {Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview},
275 +        Url = {http://dx.doi.org/10.1039/B908588B},
276 +        Volume = {11},
277 +        Year = {2009},
278 +        Bdsk-Url-1 = {http://dx.doi.org/10.1039/B908588B}}
279 +
280 + @article{Meineke05,
281 +        Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
282 +        Date-Added = {2014-02-14 19:21:43 +0000},
283 +        Date-Modified = {2014-02-14 19:21:43 +0000},
284 +        Journal = {J. Comp. Chem.},
285 +        Pages = {252-271},
286 +        Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
287 +        Volume = 26,
288 +        Year = 2005}
289 +
290 + @article{Fennell:2006zl,
291 +        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.},
292 +        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
293 +        Author = {Fennell, Christopher~J. and Gezelter, J.~Daniel},
294 +        Date = {JUN 21 2006},
295 +        Date-Added = {2014-02-14 19:21:36 +0000},
296 +        Date-Modified = {2014-02-14 19:21:36 +0000},
297 +        Doi = {ARTN 234104},
298 +        Journal = jcp,
299 +        Publisher = {AMER INST PHYSICS},
300 +        Timescited = {15},
301 +        Title = {Is the {E}wald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
302 +        Volume = {124},
303 +        Year = {2006},
304 +        Bdsk-Url-1 = {http://dx.doi.org/234104}}
305 +
306   @article{PhysRevLett.111.227801,
307          Author = {Whitmer, Jonathan K. and Wang, Xiaoguang and Mondiot, Frederic and Miller, Daniel S. and Abbott, Nicholas L. and de Pablo, Juan J.},
308          Date-Added = {2014-02-06 20:01:25 +0000},
# Line 60 | Line 354
354          Year = {1973},
355          Bdsk-Url-1 = {http://dx.doi.org/10.1049/el:19730096}}
356  
63 – @article{Leyte:97,
64 –        Abstract = {{\textless}abstract/{\textgreater}},
65 –        Author = {J. C. Leyte and P. C. M. Van Woerkom},
66 –        Date-Added = {2014-01-20 19:15:28 +0000},
67 –        Date-Modified = {2014-01-20 19:15:28 +0000},
68 –        Journal = {Appl. Spectrosc.},
69 –        Month = {Feb},
70 –        Number = {2},
71 –        Pages = {283--284},
72 –        Publisher = {OSA},
73 –        Title = {Electric Field Dependence of the Response of 5CB Observed by FT-IR},
74 –        Url = {http://as.osa.org/abstract.cfm?URI=as-51-2-283},
75 –        Volume = {51},
76 –        Year = {1997},
77 –        Bdsk-Url-1 = {http://as.osa.org/abstract.cfm?URI=as-51-2-283}}
78 –
357   @article{Lee:2006qd,
358          Author = {Lee, Lay Min and Kwon, Hye J. and Kang, Joo H. and Nuzzo, Ralph G. and Schweizer, Kenneth S.},
359          Date-Added = {2014-01-20 19:14:33 +0000},
# Line 461 | Line 739
739          Year = {1989},
740          Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevA.40.5444},
741          Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevA.40.5444}}
464 –
465 – @book{Collings97,
466 –        Address = {London},
467 –        Author = {Collings, P.~J. and Hird, M},
468 –        Date-Added = {2014-01-20 18:19:49 +0000},
469 –        Date-Modified = {2014-01-20 18:19:49 +0000},
470 –        Publisher = {Taylor and Francis},
471 –        Title = {Introduction to Liquid Crystals: Chemistry and Physics},
472 –        Year = 1997}

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