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Berardi R, Lintuvuori JS, Wilson MR, Zannoni C. Phase diagram of the uniaxial and biaxial soft–core Gay–Berne model. J Chem Phys 2011; 135:134119. [DOI: 10.1063/1.3646310] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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52
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Losasso V, Pietropaolo A, Zannoni C, Gustincich S, Carloni P. Structural role of compensatory amino acid replacements in the α-synuclein protein. Biochemistry 2011; 50:6994-7001. [PMID: 21736378 DOI: 10.1021/bi2007564] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A subset of familial Parkinson's disease (PD) cases is associated with the presence of disease-causing point mutations in human α-synuclein [huAS(wt)], including A53T. Surprisingly, the human neurotoxic amino acid 53T is present in non-primate, wild-type sequences of α-synucleins, including that expressed by mice [mAS(wt)]. Because huAS(A53T) causes neurodegeneration when expressed in rodents, the amino acid changes between the wild-type human protein [huAS(wt)] and mAS(wt) might act as intramolecular suppressors of A53T toxicity in the mouse protein, restoring its physiological structure and function. The lack of structural information for mAS(wt) in aqueous solution has prompted us to conduct a comparative molecular dynamics study of huAS(wt), huAS(A53T), and mAS(wt) in water at 300 K. The calculations are based on an ensemble of nuclear magnetic resonance-derived huAS(wt) structures. huAS(A53T) turns out to be more flexible and less compact than huAS(wt). Its central (NAC) region, involved in fibril formation by the protein, is more solvent-exposed than that of the wild-type protein, in agreement with nuclear magnetic resonance data. The compactness of mAS(wt) is similar to that of the human protein. In addition, its NAC region is less solvent-exposed and more rigid than that of huAS(A53T). All of these features may be caused by an increase in the level of intramolecular interactions on passing from huAS(A53T) to mAS(wt). We conclude that the presence of "compensatory replacements" in the mouse protein causes a significant change in the protein relative to huAS(A53T), restoring features not too dissimilar to those of the human protein.
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Gonidec M, Biagi R, Corradini V, Moro F, De Renzi V, del Pennino U, Summa D, Muccioli L, Zannoni C, Amabilino DB, Veciana J. Surface Supramolecular Organization of a Terbium(III) Double-Decker Complex on Graphite and its Single Molecule Magnet Behavior. J Am Chem Soc 2011; 133:6603-12. [DOI: 10.1021/ja109296c] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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54
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Papadopoulos TA, Muccioli L, Athanasopoulos S, Walker AB, Zannoni C, Beljonne D. Does supramolecular ordering influence exciton transport in conjugated systems? Insight from atomistic simulations. Chem Sci 2011. [DOI: 10.1039/c0sc00467g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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55
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Pizzirusso A, Savini M, Muccioli L, Zannoni C. An atomistic simulation of the liquid-crystalline phases of sexithiophene. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm01284j] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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56
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Sukul PK, Asthana D, Mukhopadhyay P, Summa D, Muccioli L, Zannoni C, Beljonne D, Rowan AE, Malik S. Assemblies of perylene diimide derivatives with melamine into luminescent hydrogels. Chem Commun (Camb) 2011; 47:11858-60. [DOI: 10.1039/c1cc14189a] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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57
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Tiberio G, Muccioli L, Berardi R, Zannoni C. How Does the Trans-Cis Photoisomerization of Azobenzene Take Place in Organic Solvents? Chemphyschem 2010; 11:1018-28. [DOI: 10.1002/cphc.200900652] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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58
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Berardi R, Zannoni C, Lintuvuori JS, Wilson MR. A soft-core Gay-Berne model for the simulation of liquid crystals by Hamiltonian replica exchange. J Chem Phys 2010; 131:174107. [PMID: 19894998 DOI: 10.1063/1.3254019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Gay-Berne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>10(5)) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits both liquid crystal phase behavior and rapid equilibration. We show that the Hamiltonian replica exchange method, coupled with the newly introduced soft-core GB model, can effectively speed up the equilibration of a GB liquid crystal phase by frequent exchange of configurations between replicas, while still recovering the mesogenic properties of the standard GB potential.
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Olivier Y, Muccioli L, Lemaur V, Geerts YH, Zannoni C, Cornil J. Theoretical characterization of the structural and hole transport dynamics in liquid-crystalline phthalocyanine stacks. J Phys Chem B 2010; 113:14102-11. [PMID: 19799445 DOI: 10.1021/jp9061169] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a joint molecular dynamics (MD)/kinetic Monte Carlo (KMC) study aimed at the atomistic description of charge transport in stacks of liquid-crystalline tetraalkoxy-substituted, metal-free phthalocyanines. The molecular dynamics simulations reproduce the major structural features of the mesophases, in particular, a phase transition around 340 K between the rectangular and hexagonal phases. Charge transport simulations based on a Monte Carlo algorithm show an increase by 2 orders of magnitude in the hole mobility when accounting for the rotational and translational dynamics. The results point to the formation of dynamical structural defects along the columns.
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60
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Ricci M, Mazzeo M, Berardi R, Pasini P, Zannoni C. A molecular level simulation of a twisted nematic cell. Faraday Discuss 2010; 144:171-85; discussion 203-22, 467-81. [DOI: 10.1039/b901784d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Pietropaolo A, Muccioli L, Zannoni C, Rizzarelli E. Conformational Preferences of the Full Chicken Prion Protein in Solution and Its Differences with Respect to Mammals. Chemphyschem 2009; 10:1500-10. [DOI: 10.1002/cphc.200900078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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62
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Bacchiocchi C, Miglioli I, Arcioni A, Vecchi I, Rai K, Fontecchio A, Zannoni C. Order and Dynamics Inside H-PDLC Nanodroplets: An ESR Spin Probe Study. J Phys Chem B 2009; 113:5391-402. [DOI: 10.1021/jp8105887] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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63
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Tiberio G, Muccioli L, Berardi R, Zannoni C. Towardsin SilicoLiquid Crystals. Realistic Transition Temperatures and Physical Properties forn-Cyanobiphenyls via Molecular Dynamics Simulations. Chemphyschem 2009; 10:125-36. [DOI: 10.1002/cphc.200800231] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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64
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Mendola D, Pietropaolo A, Pappalardo G, Zannoni C, Rizzarelli E. Prion Proteins Leading to Neurodegeneration. Curr Alzheimer Res 2008; 5:579-90. [DOI: 10.2174/156720508786898415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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65
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Berardi R, Muccioli L, Orlandi S, Ricci M, Zannoni C. Computer simulations of biaxial nematics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:463101. [PMID: 21693834 DOI: 10.1088/0953-8984/20/46/463101] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biaxial nematic (N(b)) liquid crystals are a fascinating condensed matter phase that has baffled, for more than thirty years, scientists engaged in the challenge of demonstrating its actual existence, and which has only recently been experimentally found. During this period computer simulations of model N(b) have played an important role, both in providing the basic physical properties to be expected from these systems, and in giving clues about the molecular features essential for the thermodynamic stability of N(b) phases. However, simulation studies are expected to be even more crucial in the future for unravelling the structural features of biaxial mesogens at the molecular level, and for helping in the design and optimization of devices towards the technological deployment of N(b) materials. This review article gives an overview of the simulation work performed so far, and relying on the recent experimental findings, focuses on the still unanswered questions which will determine the future challenges in the field.
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66
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Skacej G, Zannoni C. Controlling surface defect valence in colloids. PHYSICAL REVIEW LETTERS 2008; 100:197802. [PMID: 18518488 DOI: 10.1103/physrevlett.100.197802] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Indexed: 05/26/2023]
Abstract
We perform large-scale Monte Carlo simulations of orientational ordering in nematic shells and study the type and position of topological defects when an external electric field (homogeneous or quadrupolar) is applied. The field-induced variation of the defect number (and strength) can be used to change the valence of colloidal particles coated with a nematic layer.
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Pietropaolo A, Muccioli L, Zannoni C, La Mendola D, Maccarrone G, Pappalardo G, Rizzarelli E. Unveiling the role of histidine and tyrosine residues on the conformation of the avian prion hexarepeat domain. J Phys Chem B 2008; 112:5182-8. [PMID: 18386869 DOI: 10.1021/jp710702q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prion protein (PrPC) is a glycoprotein that in mammals, differently from avians, can lead to prion diseases, by misfolding into a beta-sheet-rich pathogenic isoform (PrPSc). Mammal and avian proteins show different N-terminal tandem repeats: PHGGGWGQ and PHNPGY, both containing histidine, whereas tyrosine is included only in the primary sequence of the avian protein. Here, by means of potentiometric, circular dichroism (CD), and molecular dynamics (MD) studies at different pH values, we have investigated the conformation of the avian tetrahexarepeat (PHNPGY)4 (TetraHexaPY) with both N- and C-termini blocked by acetylation and amidation, respectively. We have found, also with the help of a recently proposed protein chirality indicator (Pietropaolo, A.; Muccioli, L.; Berardi, R.; Zannoni, C. Proteins 2008, 70, 667-677), a conformational dependence on the protonation states of histidine and tyrosine residues: the turn formation is pH driven, and at physiological pH a pivotal role is played by the tyrosine OH groups which give rise to a very compact bent structure of backbone upon forming a hydrogen-bond network.
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68
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Lee J, Sokolovskii R, Berardi R, Zannoni C, Burnell E. Orientational order of solutes in liquid crystals: The effect of distributed electric quadrupoles. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.01.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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69
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Skacej G, Zannoni C. Biaxial liquid-crystal elastomers: a lattice model. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2008; 25:181-186. [PMID: 18357411 DOI: 10.1140/epje/i2007-10280-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 01/28/2008] [Indexed: 05/26/2023]
Abstract
We present a simple coarse-grained lattice model for monodomain biaxial liquid-crystal elastomers and perform large-scale Monte Carlo simulations in the proposed model system. Orientational ordering--uniaxial or biaxial--reflects in sample deformations on cooling the system. The simulation output is used to predict calorimetry data and deuterium magnetic resonance spectra.
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70
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Bacchiocchi C, Hennebicq E, Orlandi S, Muccioli L, Beljonne D, Zannoni C. "Reduced" Distributed Monopole Model for the Efficient Prediction of Energy Transfer in Condensed Phases. J Phys Chem B 2008; 112:1752-60. [DOI: 10.1021/jp076732w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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71
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Berardi R, Muccioli L, Zannoni C. Field response and switching times in biaxial nematics. J Chem Phys 2008; 128:024905. [DOI: 10.1063/1.2815804] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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72
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Pietropaolo A, Muccioli L, Berardi R, Zannoni C. A chirality index for investigating protein secondary structures and their time evolution. Proteins 2008; 70:667-77. [PMID: 17879347 DOI: 10.1002/prot.21578] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly-L-proline II left-handed helices, often not detected by secondary structure assignment algorithms. Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory.
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73
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Olivier Y, Muccioli L, Zannoni C, Cornil J, Simos TE, Maroulis G, Psihoyios G, Tsitouras C. Charge Transport in Conjugated Materials: From Theoretical Models to Experimental Systems. ACTA ACUST UNITED AC 2008. [DOI: 10.1063/1.2997306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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74
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Orlandi S, Muccioli L, Ricci M, Berardi R, Zannoni C. Core charge distribution and self assembly of columnar phases: the case of triphenylenes and azatriphenylenes. Chem Cent J 2007; 1:15. [PMID: 17880748 PMCID: PMC1994060 DOI: 10.1186/1752-153x-1-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relation between the structure of discotic molecules and columnar properties, a crucial point for the realization of new advanced materials, is still largely unknown. A paradigmatic case is that hexa-alkyl-thio substituted triphenylenes present mesogenic behavior while the corresponding azatriphenylenes, similar in shape and chemical structure, but with a different core charge distribution, do not form any liquid crystalline mesophase. This study is aimed at investigating, with the help of computer simulations techniques, the effects on phase behaviour of changes of the charge distribution in the discotic core. RESULTS We described the shape and the pair, dispersive and electrostatic, interactions of hexa alkyl triphenylenes by uniaxial Gay-Berne discs with embedded point charges. Gay-Berne parameters were deduced by fitting the dispersive energies obtained from an atomistic molecular dynamics simulation of a small sample of hexa-octyl-thio triphenylene molecules in columnar phase, while a genetic algorithm was used to get a minimal set of point charges that properly reproduces the ab anitio electrostatic potential. We performed Monte Carlo simulations of three molecular models: the pure Gay-Berne disc, used as a reference, the Gay-Berne disc with hexa-thio triphenylene point charges, the Gay-Berne disc with hexa-thio azatriphenylene point charges. The phase diagram of the pure model evidences a rich polymorphism, with isotropic, columnar and crystalline phases at low pressure, and the appearance of nematic phase at higher pressure. CONCLUSION We found that the intermolecular electrostatic potential among the cores is fundamental in sta-bilizing/destabilizing columnar phases; in particular the triphenylene charge distribution stabilizes the columnar structure, while the azatriphenylene distribution suppresses its formation in favor of the nematic phase. We believe the present model could be successfully employed as the basis for coarse-grained level simulations of a wider class of triphenylene derivatives.
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Vecchi I, Arcioni A, Bacchiocchi C, Tiberio G, Zanirato P, Zannoni C. Expected and Unexpected Behavior of the Orientational Order and Dynamics Induced by Azobenzene Solutes in a Nematic. J Phys Chem B 2007; 111:3355-62. [PMID: 17388493 DOI: 10.1021/jp0651788] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have explored the changes in the phase stability, orientational order, and dynamics of the nematic 4-cyano-4'-n-pentylbiphenyl (5CB) doped with either the trans or the cis form of different p-azobenzene derivatives using the ESR spin-probe technique. In particular, we have studied the effects induced by each of the seven nonmesogenic 4-R-phenylazobenzenes (R = H, F, Br, CH3, CF3, On-Bu, Ot-Bu) at 1% and 7% mole fraction on the order parameter <P2> and on the shift of the nematic-isotropic transition temperature (TNI), as reported by a nitroxide spin probe, and we have tried to relate them to the solute shape and charge distribution. In all the cases the presence of the azo-derivative causes a depression of T(NI), more pronounced for the cis isomers. The dependence of <P2> on the reduced temperature T* = T/T(NI) remains the same as that of pure 5CB in all trans-doped samples at 1% and 7% and decreases only slightly in the cis at 1%. However, we observe different and in some cases large variations (up to 25%) in <P2> for the cis at 7%, showing solute effects that go beyond the shift in T(NI). Surprisingly enough, even at the highest concentration, the probe dynamics appears to be essentially independent of the nature, the configuration, and the concentration of the different solutes and very similar to that observed in the pure 5CB.
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