2008 |
Banerjee, Anirban ; Fromme, Christopher J; Jiralerspong, Sao ; Radom, Christopher T; Bruner, Steven D; Chung, Sang Jeon ; Yang, Wei ; Karplus, Martin ; Verdine, Gregory L Interrogation, Recognition, and Repair of Damaged Bases in DNA Article de journal Dans: CHEMICAL RESEARCH IN TOXICOLOGY, 21 (12), p. 2433, 2008, ISSN: 0893-228X. @article{banerjee_interrogation_2008, title = {Interrogation, Recognition, and Repair of Damaged Bases in DNA}, author = {Banerjee, Anirban and Fromme, J. Christopher and Jiralerspong, Sao and Radom, Christopher T. and Bruner, Steven D. and Chung, Sang Jeon and Yang, Wei and Karplus, Martin and Verdine, Gregory L.}, issn = {0893-228X}, year = {2008}, date = {2008-12-01}, journal = {CHEMICAL RESEARCH IN TOXICOLOGY}, volume = {21}, number = {12}, pages = {2433}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Finlayson, Chris E; Friend, Richard H; Otten, Matthijs B J; Schwartz, Erik ; Cornelissen, Jeroen. J L M; Nolte, Roeland. L M; Rowan, Alan E; Samori, Paolo ; Palermo, Vicenzo ; Liscio, Andrea ; Peneva, Kalina ; Muellen, Klaus ; Trapani, Sara ; Beljonne, David Electronic Transport Properties or Ensembles of Perylene-Substituted Poly-isocyanopeptide Arrays Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (24), p. 3947–3955, 2008, ISSN: 1616-301X. @article{finlayson_electronic_2008, title = {Electronic Transport Properties or Ensembles of Perylene-Substituted Poly-isocyanopeptide Arrays}, author = {Finlayson, Chris E. and Friend, Richard H. and Otten, Matthijs B. J. and Schwartz, Erik and Cornelissen, Jeroen. J. L. M. and Nolte, Roeland. L. M. and Rowan, Alan E. and Samori, Paolo and Palermo, Vicenzo and Liscio, Andrea and Peneva, Kalina and Muellen, Klaus and Trapani, Sara and Beljonne, David}, doi = {10.1002/adfm.200800943}, issn = {1616-301X}, year = {2008}, date = {2008-12-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {18}, number = {24}, pages = {3947--3955}, abstract = {The electronic transport properties of stacks of perylene-bis(dicarboximide) (PDI) chromophores, covalently fixed to the side arms of rigid, helical polyisocyanopeptides, are studied using thin-film transistors. In device architectures where the transistor channel lengths are somewhat greater than the average polymer chain length, carrier mobilities of order 10(-3) cm(2) V(-1) s(-1) at 350K are found, which are limited by inter-chain transport processes. The influence of pi-pi interactions on the material properties is studied by using PDIs with and without bulky substituents in the bay area. In order to attain a deeper understanding of both the electronic and the electronic-transport Properties of these systems, studies of self-assembly on surfaces are combined with electronic characterization using Kelvin probe force microscopy, and also a theoretical study of electronic coupling. The use of a rigid polymer backbone as a scaffold to achieve a full control Over the position and orientation of functional groups is of general applicability and interest in the design of building blocks for technologically important functional materials, as well as in more fundamental studies of chromophoric interactions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The electronic transport properties of stacks of perylene-bis(dicarboximide) (PDI) chromophores, covalently fixed to the side arms of rigid, helical polyisocyanopeptides, are studied using thin-film transistors. In device architectures where the transistor channel lengths are somewhat greater than the average polymer chain length, carrier mobilities of order 10(-3) cm(2) V(-1) s(-1) at 350K are found, which are limited by inter-chain transport processes. The influence of pi-pi interactions on the material properties is studied by using PDIs with and without bulky substituents in the bay area. In order to attain a deeper understanding of both the electronic and the electronic-transport Properties of these systems, studies of self-assembly on surfaces are combined with electronic characterization using Kelvin probe force microscopy, and also a theoretical study of electronic coupling. The use of a rigid polymer backbone as a scaffold to achieve a full control Over the position and orientation of functional groups is of general applicability and interest in the design of building blocks for technologically important functional materials, as well as in more fundamental studies of chromophoric interactions. |
Puntoriero, Fausto ; Campagna, Sebastiano ; Stadler, Adrian-Mihail ; Lehn, Jean-Marie Luminescence properties and redox behavior of Ru(II) molecular racks Article de journal Dans: COORDINATION CHEMISTRY REVIEWS, 252 (23-24, SI), p. 2480–2492, 2008, ISSN: 0010-8545. @article{puntoriero_luminescence_2008, title = {Luminescence properties and redox behavior of Ru(II) molecular racks}, author = {Puntoriero, Fausto and Campagna, Sebastiano and Stadler, Adrian-Mihail and Lehn, Jean-Marie}, doi = {10.1016/j.ccr.2007.12.009}, issn = {0010-8545}, year = {2008}, date = {2008-12-01}, journal = {COORDINATION CHEMISTRY REVIEWS}, volume = {252}, number = {23-24, SI}, pages = {2480--2492}, abstract = {The absorption spectra, luminescence properties, and redox behavior of Ru(II) molecular racks are reviewed, together with the same properties of closely related systems, including homo- (Fe(II)) and hetero-metallic (Fe(II)[Ru(II) and Fe(II)/Os(II)) molecular gtids and their mononuclear Ru(II) and Os(II) precursors, and bis-dirhodiurn(II, II) molecular racks. The systems discussed are based on polytopic molecular strands made of poly(pyridine-pyrimidine), poly(naphthyridine-pyrimidine), and poly(hydrazone-pyrimidine/pyrazine) subunits. Linearly-arranged systems based on tris-terpyridine molecular strands are also reported for completeness. The results indicate that the title species are quite promising multicomponent systems for the development of functional supramolecular systems, with particular regards towards the design of nano-organized species featuring information storage functions, molecular wire-type behavior, and light-harvesting antennae properties. (C) 2007 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The absorption spectra, luminescence properties, and redox behavior of Ru(II) molecular racks are reviewed, together with the same properties of closely related systems, including homo- (Fe(II)) and hetero-metallic (Fe(II)[Ru(II) and Fe(II)/Os(II)) molecular gtids and their mononuclear Ru(II) and Os(II) precursors, and bis-dirhodiurn(II, II) molecular racks. The systems discussed are based on polytopic molecular strands made of poly(pyridine-pyrimidine), poly(naphthyridine-pyrimidine), and poly(hydrazone-pyrimidine/pyrazine) subunits. Linearly-arranged systems based on tris-terpyridine molecular strands are also reported for completeness. The results indicate that the title species are quite promising multicomponent systems for the development of functional supramolecular systems, with particular regards towards the design of nano-organized species featuring information storage functions, molecular wire-type behavior, and light-harvesting antennae properties. (C) 2007 Elsevier B.V. All rights reserved. |
Barluenga, Sofia ; Dakas, Pierre-Yves ; Boulifa, Mehdi ; Moulin, Emilie ; Winssinger, Nicolas Resorcylic acid lactones: A pluripotent scaffold with therapeutic potential Article de journal Dans: COMPTES RENDUS CHIMIE, 11 (11-12), p. 1306–1317, 2008, ISSN: 1631-0748. @article{barluenga_resorcylic_2008, title = {Resorcylic acid lactones: A pluripotent scaffold with therapeutic potential}, author = {Barluenga, Sofia and Dakas, Pierre-Yves and Boulifa, Mehdi and Moulin, Emilie and Winssinger, Nicolas}, doi = {10.1016/j.crci.2008.01.020}, issn = {1631-0748}, year = {2008}, date = {2008-12-01}, journal = {COMPTES RENDUS CHIMIE}, volume = {11}, number = {11-12}, pages = {1306--1317}, abstract = {The recent discoveries of potent HSP90 and MAP kinase inhibitors amongst the resorcylic acid lactones (RALs) have revived interest in this family of natural products. Both HSP90 and MAP kinase inhibition hold tremendous therapeutic potential, particularly in the treatment of cancer. Our synthetic efforts towards the RALs and, in particular, selective inhibitors of HSP90 and kinases are reviewed. To cite this article: S. Barluenga et al., C R. Chimie 11 (2008). (C) 2008 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The recent discoveries of potent HSP90 and MAP kinase inhibitors amongst the resorcylic acid lactones (RALs) have revived interest in this family of natural products. Both HSP90 and MAP kinase inhibition hold tremendous therapeutic potential, particularly in the treatment of cancer. Our synthetic efforts towards the RALs and, in particular, selective inhibitors of HSP90 and kinases are reviewed. To cite this article: S. Barluenga et al., C R. Chimie 11 (2008). (C) 2008 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved. |
Huc, Vincent ; Bendiab, Nedjma ; Rosman, Noel ; Ebbesen, Thomas ; Delacour, Cecile ; Bouchiat, Vincent Large and flat graphene flakes produced by epoxy bonding and reverse exfoliation of highly oriented pyrolytic graphite Article de journal Dans: NANOTECHNOLOGY, 19 (45), 2008, ISSN: 0957-4484. @article{huc_large_2008, title = {Large and flat graphene flakes produced by epoxy bonding and reverse exfoliation of highly oriented pyrolytic graphite}, author = {Huc, Vincent and Bendiab, Nedjma and Rosman, Noel and Ebbesen, Thomas and Delacour, Cecile and Bouchiat, Vincent}, doi = {10.1088/0957-4484/19/45/455601}, issn = {0957-4484}, year = {2008}, date = {2008-11-01}, journal = {NANOTECHNOLOGY}, volume = {19}, number = {45}, abstract = {We present a fabrication method producing large and flat graphene flakes that have a few layers down to a single layer based on substrate bonding of a thick sample of highly oriented pyrolytic graphite (HOPG), followed by its controlled exfoliation down to the few to single graphene atomic layers. As the graphite underlayer is intimately bonded to the substrate during the exfoliation process, the obtained graphene flakes are remarkably large and flat and present very few folds and pleats. The high occurrence of single-layered graphene sheets being tens of microns wide in lateral dimensions is assessed by complementary probes including spatially resolved micro-Raman spectroscopy, atomic force microscopy and electrostatic force microscopy. This versatile method opens the way for deposition of graphene on any substrates, including flexible ones.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present a fabrication method producing large and flat graphene flakes that have a few layers down to a single layer based on substrate bonding of a thick sample of highly oriented pyrolytic graphite (HOPG), followed by its controlled exfoliation down to the few to single graphene atomic layers. As the graphite underlayer is intimately bonded to the substrate during the exfoliation process, the obtained graphene flakes are remarkably large and flat and present very few folds and pleats. The high occurrence of single-layered graphene sheets being tens of microns wide in lateral dimensions is assessed by complementary probes including spatially resolved micro-Raman spectroscopy, atomic force microscopy and electrostatic force microscopy. This versatile method opens the way for deposition of graphene on any substrates, including flexible ones. |
Liscio, Andrea ; Palermo, Vincenzo ; Muellen, Klaus ; Samori, Paolo Tip-Sample Interactions in Kelvin Probe Force Microscopy: Quantitative Measurement of the Local Surface Potential Article de journal Dans: JOURNAL OF PHYSICAL CHEMISTRY C, 112 (44), p. 17368–17377, 2008, ISSN: 1932-7447. @article{liscio_tip-sample_2008, title = {Tip-Sample Interactions in Kelvin Probe Force Microscopy: Quantitative Measurement of the Local Surface Potential}, author = {Liscio, Andrea and Palermo, Vincenzo and Muellen, Klaus and Samori, Paolo}, doi = {10.1021/jp806657k}, issn = {1932-7447}, year = {2008}, date = {2008-11-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY C}, volume = {112}, number = {44}, pages = {17368--17377}, abstract = {We study the influence of different experimental parameters on the interaction between the probe and the sample in Kelvin probe force microscopy (KPFM) measurements. We provide a precise and reproducible determination of the local surface potential (SP) of clean macroscopic highly oriented pyrolytic graphite (HOPG) samples and of organic semiconducting nanostructures of an alkyl-substituted perylene-bis(dicarboximide) (PDI) self-assembled at surfaces. We distinguish two different terms in the measured SP, intrinsic and extrinsic, containing the electrical properties of the studied object and the experimental artifacts, respectively. We investigate the effect of the most relevant experimental parameters including tip-sample distance, relative humidity (RH), and potential applied to the tip, which govern the extrinsic term of the measured SP. Moreover, we devise a theoretical description of the tip-sample interaction taking into account the extra modulation of the probe due to the applied ac potential during the KPFM scan. A deep understanding of all the terms which contribute to the measured SP in air environment made it possible to devise a new protocol to quantify the electrical properties of nano-objects leading to an improvement of the achieved lateral resolution, as demonstrated by the good agreement between the proposed model and the experimental results.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We study the influence of different experimental parameters on the interaction between the probe and the sample in Kelvin probe force microscopy (KPFM) measurements. We provide a precise and reproducible determination of the local surface potential (SP) of clean macroscopic highly oriented pyrolytic graphite (HOPG) samples and of organic semiconducting nanostructures of an alkyl-substituted perylene-bis(dicarboximide) (PDI) self-assembled at surfaces. We distinguish two different terms in the measured SP, intrinsic and extrinsic, containing the electrical properties of the studied object and the experimental artifacts, respectively. We investigate the effect of the most relevant experimental parameters including tip-sample distance, relative humidity (RH), and potential applied to the tip, which govern the extrinsic term of the measured SP. Moreover, we devise a theoretical description of the tip-sample interaction taking into account the extra modulation of the probe due to the applied ac potential during the KPFM scan. A deep understanding of all the terms which contribute to the measured SP in air environment made it possible to devise a new protocol to quantify the electrical properties of nano-objects leading to an improvement of the achieved lateral resolution, as demonstrated by the good agreement between the proposed model and the experimental results. |
Palermo, Vincenzo ; Otten, Matthijs B J; Liscio, Andrea ; Schwartz, Erik ; de Witte, Pieter A J; Castriciano, Maria Angela ; Wienk, Martijn M; Nolde, Fabian ; De Luca, Giovanna ; Cornelissen, Jeroen J L M; Janssen, Rene A J; Muellen, Klaus ; Rowan, Alan E; Nolte, Roeland J M; Samori, Paolo The Relationship between Nanoscale Architecture and Function in Photovoltaic Multichromophoric Arrays as Visualized by Kelvin Probe Force Microscopy Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (44), p. 14605–14614, 2008, ISSN: 0002-7863. @article{palermo_relationship_2008, title = {The Relationship between Nanoscale Architecture and Function in Photovoltaic Multichromophoric Arrays as Visualized by Kelvin Probe Force Microscopy}, author = {Palermo, Vincenzo and Otten, Matthijs B. J. and Liscio, Andrea and Schwartz, Erik and de Witte, Pieter A. J. and Castriciano, Maria Angela and Wienk, Martijn M. and Nolde, Fabian and De Luca, Giovanna and Cornelissen, Jeroen J. L. M. and Janssen, Rene A. J. and Muellen, Klaus and Rowan, Alan E. and Nolte, Roeland J. M. and Samori, Paolo}, doi = {10.1021/ja804069n}, issn = {0002-7863}, year = {2008}, date = {2008-11-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, number = {44}, pages = {14605--14614}, abstract = {The physicochemical properties of organic (multi)component films for optoelectronic applications depend on both the mesoscopic and nanoscale architectures within the semiconducting material. Two main classes of semiconducting materials are commonly used: polymers and (liquid) crystals of small aromatic molecules. Whereas polymers (e.g., polyphenylenevinylenes and polythiophenes) are easy to process in solution in thin and uniform layers, small molecules can form highly defined (liquid) crystals featuring high charge mobilities. Herein, we combine the two material types by employing structurally well-defined polyisocyanopeptide polymers as scaffolds to precisely arrange thousands of electron-accepting molecules, namely, perylenebis(dicarboximides) (PDIs), in defined chromophoric wires with lengths of hundreds of nanometers. The polymer backbone enforces high control over the spatial location of PDI dyes, favoring both enhanced exciton and charge transfer. When blended with an electron-donor system such as regioregular poly(3-hexylthiophene), this polymeric PDI shows a relative improvement in charge generation and diffusion with respect to monomeric, aggregated PDI. In order to correlate this enhanced behavior with respect to the architecture, atomic force microscopy investigations on the mixtures were carried out. These studies revealed that the two polymers form interpenetrated bundles having a nanophase-segregated character and featuring a high density of contact points between the two different phases. In order to visualize the relationship between the architecture and the photovoltaic efficiency, Kelvin probe force microscopy measurements were carried out on submonolayer-thick films. This technique allowed for the first time the direct visualization of the photovoltaic activity occurring in such a nanoscale phase-segregated ultrathin film with true nanoscale spatial resolution, thus making possible a study of the correlation between function and architecture with nanoscale resolution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The physicochemical properties of organic (multi)component films for optoelectronic applications depend on both the mesoscopic and nanoscale architectures within the semiconducting material. Two main classes of semiconducting materials are commonly used: polymers and (liquid) crystals of small aromatic molecules. Whereas polymers (e.g., polyphenylenevinylenes and polythiophenes) are easy to process in solution in thin and uniform layers, small molecules can form highly defined (liquid) crystals featuring high charge mobilities. Herein, we combine the two material types by employing structurally well-defined polyisocyanopeptide polymers as scaffolds to precisely arrange thousands of electron-accepting molecules, namely, perylenebis(dicarboximides) (PDIs), in defined chromophoric wires with lengths of hundreds of nanometers. The polymer backbone enforces high control over the spatial location of PDI dyes, favoring both enhanced exciton and charge transfer. When blended with an electron-donor system such as regioregular poly(3-hexylthiophene), this polymeric PDI shows a relative improvement in charge generation and diffusion with respect to monomeric, aggregated PDI. In order to correlate this enhanced behavior with respect to the architecture, atomic force microscopy investigations on the mixtures were carried out. These studies revealed that the two polymers form interpenetrated bundles having a nanophase-segregated character and featuring a high density of contact points between the two different phases. In order to visualize the relationship between the architecture and the photovoltaic efficiency, Kelvin probe force microscopy measurements were carried out on submonolayer-thick films. This technique allowed for the first time the direct visualization of the photovoltaic activity occurring in such a nanoscale phase-segregated ultrathin film with true nanoscale spatial resolution, thus making possible a study of the correlation between function and architecture with nanoscale resolution. |
Laluet, J-Y; Drezet, A; Genet, C; Ebbesen, T W Generation of surface plasmons at single subwavelength slits: from slit to ridge plasmon Article de journal Dans: NEW JOURNAL OF PHYSICS, 10 , 2008, ISSN: 1367-2630. @article{laluet_generation_2008, title = {Generation of surface plasmons at single subwavelength slits: from slit to ridge plasmon}, author = {Laluet, J-Y and Drezet, A. and Genet, C. and Ebbesen, T. W.}, doi = {10.1088/1367-2630/10/10/105014}, issn = {1367-2630}, year = {2008}, date = {2008-10-01}, journal = {NEW JOURNAL OF PHYSICS}, volume = {10}, abstract = {Understanding how surface plasmons can be launched by single subwavelength structures is crucial for the development of surface plasmon-based devices within highly integrated photonic circuits. In this paper, we study the coupling efficiency of light to surface plasmons for single slits milled in a thin metal film by analyzing the far-field optical images recorded in the Fourier plane of a leakage microscopy setup. A simple model based on a Fano-type interference allows us to give a clear physical interpretation of the plasmonic generation efficiency with an optimum value separating two regimes depending on the size of the system. This is an issue of practical interest in the context of plasmonic features with size close to or smaller than optical diffraction limit.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding how surface plasmons can be launched by single subwavelength structures is crucial for the development of surface plasmon-based devices within highly integrated photonic circuits. In this paper, we study the coupling efficiency of light to surface plasmons for single slits milled in a thin metal film by analyzing the far-field optical images recorded in the Fourier plane of a leakage microscopy setup. A simple model based on a Fano-type interference allows us to give a clear physical interpretation of the plasmonic generation efficiency with an optimum value separating two regimes depending on the size of the system. This is an issue of practical interest in the context of plasmonic features with size close to or smaller than optical diffraction limit. |
Anikeyev, V; Temnov, V V; Woggon, U; Devaux, E; Ebbesen, T W Propagation oscillations in the near-field response of traveling surface waves launched by metallic nanoapertures Article de journal Dans: APPLIED PHYSICS B-LASERS AND OPTICS, 93 (1, SI), p. 171–176, 2008, ISSN: 0946-2171. @article{anikeyev_propagation_2008, title = {Propagation oscillations in the near-field response of traveling surface waves launched by metallic nanoapertures}, author = {Anikeyev, V. and Temnov, V. V. and Woggon, U. and Devaux, E. and Ebbesen, T. W.}, doi = {10.1007/s00340-008-3175-3}, issn = {0946-2171}, year = {2008}, date = {2008-10-01}, journal = {APPLIED PHYSICS B-LASERS AND OPTICS}, volume = {93}, number = {1, SI}, pages = {171--176}, abstract = {We discuss the implications of a frequency-dependent complex dielectric function epsilon(omega) of a metal for the interpretation of scanning near-field optical microscopy (SNOM) measurements in the vicinity of metallic nanoapertures. For subwavelength slits in gold films we observe distinct spatial intensity oscillations in the near-field signal for specific wavelengths in the visible spectrum. These oscillations of the SNOM signal far away from the nanoslit are ascribed to a constructive interference between the propagating surface plasmon (SP) with light scattered parallel to the gold-air interface. In these spatial SNOM-signal oscillations information about the surface plasmon dielectric function is encoded which can be extracted, for example, in surface plasmon interferometry for applications as sensors or waveguides.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We discuss the implications of a frequency-dependent complex dielectric function epsilon(omega) of a metal for the interpretation of scanning near-field optical microscopy (SNOM) measurements in the vicinity of metallic nanoapertures. For subwavelength slits in gold films we observe distinct spatial intensity oscillations in the near-field signal for specific wavelengths in the visible spectrum. These oscillations of the SNOM signal far away from the nanoslit are ascribed to a constructive interference between the propagating surface plasmon (SP) with light scattered parallel to the gold-air interface. In these spatial SNOM-signal oscillations information about the surface plasmon dielectric function is encoded which can be extracted, for example, in surface plasmon interferometry for applications as sensors or waveguides. |
Elbing, Mark ; Blaszczyk, Alfred ; von Haenisch, Carsten ; Mayor, Marcel ; Ferri, Violetta ; Grave, Christian ; Rampi, Maria Anita ; Pace, Giuseppina ; Samori, Paolo ; Shaporenko, Andrei ; Zharnikov, Michael Single Component Self-Assembled Monolayers of Aromatic Azo-Biphenyl: Influence of the Packing Tightness on the SAM Structure and Light-Induced Molecular Movements Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (19), p. 2972–2983, 2008, ISSN: 1616-301X. @article{elbing_single_2008, title = {Single Component Self-Assembled Monolayers of Aromatic Azo-Biphenyl: Influence of the Packing Tightness on the SAM Structure and Light-Induced Molecular Movements}, author = {Elbing, Mark and Blaszczyk, Alfred and von Haenisch, Carsten and Mayor, Marcel and Ferri, Violetta and Grave, Christian and Rampi, Maria Anita and Pace, Giuseppina and Samori, Paolo and Shaporenko, Andrei and Zharnikov, Michael}, doi = {10.1002/adfm.200800652}, issn = {1616-301X}, year = {2008}, date = {2008-10-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {18}, number = {19}, pages = {2972--2983}, abstract = {Aiming at modulating the packing density within functional self-assembled monolayers (SAMs), two azo-biphenyl derivatives AZO1 and AZO2 comprising a terminal sulfur anchor group have been designed and synthesized. While AZO1 allows for a coplanar arrangement of both biphenyl subunits, additional steric repulsion due to two methyl side groups attached to the footing biphenyl of AZO2 results in an increased intermolecular distance within the SAM, providing additional free volume. SAMs of both derivatives on gold and platinum substrates have been formed and thoroughly investigated by photoelectron (XPS) and near-edge absorption fine structure (NEXAFS) spectroscopy as well as cyclic voltammetry and scanning tunneling microscopy. These measurements confirmed the formation of tightly packed SAMs for AZO1, while AZO2 formed SAMs consisting of less organized and more loosely packed molecules. Optical investigations of both azo derivatives in solution as well as their SAMs displayed efficient photoisomerization in solution and in SAMs. Comparable maximal cis/trans ratios of ca. 0.9 have been observed in all cases upon irradiation at lambda = 370 and 360 nm for AZO1 and AZO2, respectively. The thermally induced cis -textbackslashtextbackslashtextgreater trans back reaction on AZO1 was found to be slower by a factor of 3 in SAMs as compared to solution, while AZO2 displayed comparable rates of the back reaction in both environments. This behavior can be explained by the different nature of molecular isomerization in the two SAM systems: whereas the isomerization in AZO1 SAMs takes place in a highly coordinated, collective way and involves many adjacent molecules, AZO2 species behave rather individually even packed in SAMs, such that their isomerization process is similar in SAMs and in solutions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aiming at modulating the packing density within functional self-assembled monolayers (SAMs), two azo-biphenyl derivatives AZO1 and AZO2 comprising a terminal sulfur anchor group have been designed and synthesized. While AZO1 allows for a coplanar arrangement of both biphenyl subunits, additional steric repulsion due to two methyl side groups attached to the footing biphenyl of AZO2 results in an increased intermolecular distance within the SAM, providing additional free volume. SAMs of both derivatives on gold and platinum substrates have been formed and thoroughly investigated by photoelectron (XPS) and near-edge absorption fine structure (NEXAFS) spectroscopy as well as cyclic voltammetry and scanning tunneling microscopy. These measurements confirmed the formation of tightly packed SAMs for AZO1, while AZO2 formed SAMs consisting of less organized and more loosely packed molecules. Optical investigations of both azo derivatives in solution as well as their SAMs displayed efficient photoisomerization in solution and in SAMs. Comparable maximal cis/trans ratios of ca. 0.9 have been observed in all cases upon irradiation at lambda = 370 and 360 nm for AZO1 and AZO2, respectively. The thermally induced cis -textbackslashtextbackslashtextgreater trans back reaction on AZO1 was found to be slower by a factor of 3 in SAMs as compared to solution, while AZO2 displayed comparable rates of the back reaction in both environments. This behavior can be explained by the different nature of molecular isomerization in the two SAM systems: whereas the isomerization in AZO1 SAMs takes place in a highly coordinated, collective way and involves many adjacent molecules, AZO2 species behave rather individually even packed in SAMs, such that their isomerization process is similar in SAMs and in solutions. |
Krivov, Sergei V; Karplus, Martin Diffusive reaction dynamics on invariant free energy profiles Article de journal Dans: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (37), p. 13841–13846, 2008, ISSN: 0027-8424. @article{krivov_diffusive_2008, title = {Diffusive reaction dynamics on invariant free energy profiles}, author = {Krivov, Sergei V. and Karplus, Martin}, doi = {10.1073/pnas.0800228105}, issn = {0027-8424}, year = {2008}, date = {2008-09-01}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {105}, number = {37}, pages = {13841--13846}, abstract = {A fundamental problem in the analysis of protein folding and other complex reactions in which the entropy plays an important role is the determination of the activation free energy from experimental measurements or computer simulations. This article shows how to combine minimum-cut-based free energy profiles (F-C), obtained from equilibrium molecular dynamics simulations, with conventional histogram-based free energy profiles (F-H) to extract the coordinate-dependent diffusion coefficient on the F-C (i.e., the method determines free energies and a diffusive preexponential factor along an appropriate reaction coordinate). The F-C, in contrast to the F-H, is shown to be invariant with respect to arbitrary transformations of the reaction coordinate, which makes possible partition of configuration space into basins in an invariant way. A “natural coordinate,” for which F-H and F-C differ by a multiplicative constant (constant diffusion coefficient), is introduced. The approach is illustrated by a model one-dimensional system, the alanine dipeptide, and the folding reaction of a double beta-hairpin miniprotein. It is shown how the results can be used to test whether the putative reaction coordinate is a good reaction coordinate.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A fundamental problem in the analysis of protein folding and other complex reactions in which the entropy plays an important role is the determination of the activation free energy from experimental measurements or computer simulations. This article shows how to combine minimum-cut-based free energy profiles (F-C), obtained from equilibrium molecular dynamics simulations, with conventional histogram-based free energy profiles (F-H) to extract the coordinate-dependent diffusion coefficient on the F-C (i.e., the method determines free energies and a diffusive preexponential factor along an appropriate reaction coordinate). The F-C, in contrast to the F-H, is shown to be invariant with respect to arbitrary transformations of the reaction coordinate, which makes possible partition of configuration space into basins in an invariant way. A “natural coordinate,” for which F-H and F-C differ by a multiplicative constant (constant diffusion coefficient), is introduced. The approach is illustrated by a model one-dimensional system, the alanine dipeptide, and the folding reaction of a double beta-hairpin miniprotein. It is shown how the results can be used to test whether the putative reaction coordinate is a good reaction coordinate. |
Osorio, E A; Bjornholm, T; Lehn, J-M; Ruben, M; van der Zant, H S J Single-molecule transport in three-terminal devices Article de journal Dans: JOURNAL OF PHYSICS-CONDENSED MATTER, 20 (37), 2008, ISSN: 0953-8984. @article{osorio_single-molecule_2008, title = {Single-molecule transport in three-terminal devices}, author = {Osorio, E. A. and Bjornholm, T. and Lehn, J-M and Ruben, M. and van der Zant, H. S. J.}, doi = {10.1088/0953-8984/20/37/374121}, issn = {0953-8984}, year = {2008}, date = {2008-09-01}, journal = {JOURNAL OF PHYSICS-CONDENSED MATTER}, volume = {20}, number = {37}, abstract = {Transport through single molecules has been studied using different test beds. In this paper we focus on three-terminal devices in which a molecule bridges the gap between two gold electrodes and a third electrode-the gate-is able to modulate the conduction properties of the junction. Depending on the electronic coupling, Gamma, between the molecule and the gold electrodes, different transport regimes can be distinguished. We show measurements on junctions incorporating different single-molecule systems which demonstrate the distinction between these regimes, as well as the experimental limitations in controlling the exact value of Gamma.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transport through single molecules has been studied using different test beds. In this paper we focus on three-terminal devices in which a molecule bridges the gap between two gold electrodes and a third electrode-the gate-is able to modulate the conduction properties of the junction. Depending on the electronic coupling, Gamma, between the molecule and the gold electrodes, different transport regimes can be distinguished. We show measurements on junctions incorporating different single-molecule systems which demonstrate the distinction between these regimes, as well as the experimental limitations in controlling the exact value of Gamma. |
Castano, Sabine ; Delord, Brigitte ; Fevrier, Annie ; Lehn, Jean-Marie ; Lehn, Pierre ; Desbat, Bernard Brewster angle microscopy and PMIRRAS study of DNA interactions with BGTC, a cationic lipid used for gene transfer Article de journal Dans: LANGMUIR, 24 (17), p. 9598–9606, 2008, ISSN: 0743-7463. @article{castano_brewster_2008, title = {Brewster angle microscopy and PMIRRAS study of DNA interactions with BGTC, a cationic lipid used for gene transfer}, author = {Castano, Sabine and Delord, Brigitte and Fevrier, Annie and Lehn, Jean-Marie and Lehn, Pierre and Desbat, Bernard}, doi = {10.1021/la703491r}, issn = {0743-7463}, year = {2008}, date = {2008-09-01}, journal = {LANGMUIR}, volume = {24}, number = {17}, pages = {9598--9606}, abstract = {The lipid bis(guanidinium)-tris(2-aminoethyl)amine-cholesterol (BGTC) is a cationic cholesterol derivative bearing guanidinium polar headgroups which displays high transfection efficiency in vitro and in vivo when used alone or formulated as liposomes with the neutral colipid 1,2-di-[cis-9-octadecenoyl]-sn-glycero-3-phosphoethanolamine (DOPE). Since transfection may be related to the structural and physicochemical properties of the self-assembled supramolecular lipid-DNA complexes, we used the Langmuir monolayer technique coupled with Brewster angle microscopy (BAM) and polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) to investigate DNA-BGTC and DNA-BGTC/DOPE interactions at the air/water interface. We herein show that BGTC forms stable monolayers at the air/water interface. When DNA is injected into the subphase, it adsorbs to BGTC at 20 mN/m. Whathever the (+/-) charge ratio of the complexes used, defined as the ratio of positive charges of BGTC in the monolayer versus negative charges of DNA injected in the subphase, the DNA interacts with the cationic lipid and forms either an incomplete (no constituent in excess) or a complete (DNA in excess) monolayer of oriented double strands parallel to the lipid monolayer plan. We also show that, under a homogeneous BGTC/DOPE (3/2) monolayer at 20 mN/m, DNA adsorbs homogeneously to form an organized but incomplete layer whatever the charge ratio used (DNA in default or in excess). Compression beyond the collapse of these mixed DNA-BGTC/DOPE systems leads to the formation of dense DNA monolayers under an asymmetric lipid bilayer with a bottom layer of BGTC in contact with DNA and a top layer mainly constituted of DOPE. These results allow a better understanding of the mechanisms underlying the formation of the supramolecular BGTC-DNA complexes efficient for gene transfection.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The lipid bis(guanidinium)-tris(2-aminoethyl)amine-cholesterol (BGTC) is a cationic cholesterol derivative bearing guanidinium polar headgroups which displays high transfection efficiency in vitro and in vivo when used alone or formulated as liposomes with the neutral colipid 1,2-di-[cis-9-octadecenoyl]-sn-glycero-3-phosphoethanolamine (DOPE). Since transfection may be related to the structural and physicochemical properties of the self-assembled supramolecular lipid-DNA complexes, we used the Langmuir monolayer technique coupled with Brewster angle microscopy (BAM) and polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) to investigate DNA-BGTC and DNA-BGTC/DOPE interactions at the air/water interface. We herein show that BGTC forms stable monolayers at the air/water interface. When DNA is injected into the subphase, it adsorbs to BGTC at 20 mN/m. Whathever the (+/-) charge ratio of the complexes used, defined as the ratio of positive charges of BGTC in the monolayer versus negative charges of DNA injected in the subphase, the DNA interacts with the cationic lipid and forms either an incomplete (no constituent in excess) or a complete (DNA in excess) monolayer of oriented double strands parallel to the lipid monolayer plan. We also show that, under a homogeneous BGTC/DOPE (3/2) monolayer at 20 mN/m, DNA adsorbs homogeneously to form an organized but incomplete layer whatever the charge ratio used (DNA in default or in excess). Compression beyond the collapse of these mixed DNA-BGTC/DOPE systems leads to the formation of dense DNA monolayers under an asymmetric lipid bilayer with a bottom layer of BGTC in contact with DNA and a top layer mainly constituted of DOPE. These results allow a better understanding of the mechanisms underlying the formation of the supramolecular BGTC-DNA complexes efficient for gene transfection. |
Ramirez, Juan ; Stadler, Adrian-Mihail ; Brelot, Lydia ; Lehn, Jean-Marie Coordinative, conformational and motional behaviour of triazine-based ligand strands on binding of Pb(II) cations Article de journal Dans: TETRAHEDRON, 64 (36), p. 8402–8410, 2008, ISSN: 0040-4020. @article{ramirez_coordinative_2008, title = {Coordinative, conformational and motional behaviour of triazine-based ligand strands on binding of Pb(II) cations}, author = {Ramirez, Juan and Stadler, Adrian-Mihail and Brelot, Lydia and Lehn, Jean-Marie}, doi = {10.1016/j.tet.2008.05.138}, issn = {0040-4020}, year = {2008}, date = {2008-09-01}, journal = {TETRAHEDRON}, volume = {64}, number = {36}, pages = {8402--8410}, abstract = {The coordinative behaviour of two bis(hydrazone)triazine-based ligands in the presence of Pb(II) was investigated. Free ligand, pincer-like and stick-like complexes' X-ray structures are described. The ligands adopt a pyridine-like coordinative behaviour for Pb(II)/ligand molar ratio equal to 1/2 and 1/1, and a pyrimidine-like coordinative behaviour for Pb(II)/ligand molar ratio equal to 2/1. The complexation processes are reversible and may be modulated by external stimuli. They generate conformational and motional behaviour through interconversion of three entities, free ligand, pincer and stick complex. (C) 2008 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The coordinative behaviour of two bis(hydrazone)triazine-based ligands in the presence of Pb(II) was investigated. Free ligand, pincer-like and stick-like complexes' X-ray structures are described. The ligands adopt a pyridine-like coordinative behaviour for Pb(II)/ligand molar ratio equal to 1/2 and 1/1, and a pyrimidine-like coordinative behaviour for Pb(II)/ligand molar ratio equal to 2/1. The complexation processes are reversible and may be modulated by external stimuli. They generate conformational and motional behaviour through interconversion of three entities, free ligand, pincer and stick complex. (C) 2008 Elsevier Ltd. All rights reserved. |
Durot, Stephanie ; Mobian, Pierre ; Collin, Jean-Paul ; Sauvage, Jean-Pierre Synthesis of new copper(I)-complexed rotaxanes via click chemistry Article de journal Dans: TETRAHEDRON, 64 (36), p. 8496–8503, 2008, ISSN: 0040-4020. @article{durot_synthesis_2008, title = {Synthesis of new copper(I)-complexed rotaxanes via click chemistry}, author = {Durot, Stephanie and Mobian, Pierre and Collin, Jean-Paul and Sauvage, Jean-Pierre}, doi = {10.1016/j.tet.2008.05.078}, issn = {0040-4020}, year = {2008}, date = {2008-09-01}, journal = {TETRAHEDRON}, volume = {64}, number = {36}, pages = {8496--8503}, abstract = {The Cu(I)-catalyzed dipolar cycloaddition of azides and terminal alkynes ('click' chemistry) has been used as a mild and efficient stoppering reaction for the preparation of new copper(I)-complexed rotaxanes. (C) 2008 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Cu(I)-catalyzed dipolar cycloaddition of azides and terminal alkynes ('click' chemistry) has been used as a mild and efficient stoppering reaction for the preparation of new copper(I)-complexed rotaxanes. (C) 2008 Elsevier Ltd. All rights reserved. |
Drezet, Aurelien ; Genet, Cyriaque ; Laluet, Jean-Yves ; Ebbesen, Thomas W Optical chirality without optical activity: How surface plasmons give a twist to light Article de journal Dans: OPTICS EXPRESS, 16 (17), p. 12559–12570, 2008, ISSN: 1094-4087. @article{drezet_optical_2008, title = {Optical chirality without optical activity: How surface plasmons give a twist to light}, author = {Drezet, Aurelien and Genet, Cyriaque and Laluet, Jean-Yves and Ebbesen, Thomas W.}, doi = {10.1364/OE.16.012559}, issn = {1094-4087}, year = {2008}, date = {2008-08-01}, journal = {OPTICS EXPRESS}, volume = {16}, number = {17}, pages = {12559--12570}, abstract = {Light interacts differently with left and right handed three dimensional chiral objects, like helices, and this leads to the phenomenon known as optical activity. Here, by applying a polarization tomography, we show experimentally, for the first time in the visible domain, that chirality has a different optical manifestation for twisted planar nanostructured metallic objects acting as isolated chiral metaobjects. Our analysis demonstrate how surface plasmons, which are lossy bidimensional electromagnetic waves propagating on top of the structure, can delocalize light information in the just precise way for giving rise to this subtle effect. (c) 2008 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Light interacts differently with left and right handed three dimensional chiral objects, like helices, and this leads to the phenomenon known as optical activity. Here, by applying a polarization tomography, we show experimentally, for the first time in the visible domain, that chirality has a different optical manifestation for twisted planar nanostructured metallic objects acting as isolated chiral metaobjects. Our analysis demonstrate how surface plasmons, which are lossy bidimensional electromagnetic waves propagating on top of the structure, can delocalize light information in the just precise way for giving rise to this subtle effect. (c) 2008 Optical Society of America. |
Komazin-Meredith, Gloria ; Petrella, Robert J; Santos, Webster L; Filman, David J; Hogle, James M; Verdine, Gregory L; Karplus, Martin ; Coen, Donald M The human cytomegalovirus UL44 C clamp wraps around DNA Article de journal Dans: STRUCTURE, 16 (8), p. 1214–1225, 2008, ISSN: 0969-2126. @article{komazin-meredith_human_2008, title = {The human cytomegalovirus UL44 C clamp wraps around DNA}, author = {Komazin-Meredith, Gloria and Petrella, Robert J. and Santos, Webster L. and Filman, David J. and Hogle, James M. and Verdine, Gregory L. and Karplus, Martin and Coen, Donald M.}, doi = {10.1016/j.str.2008.05.008}, issn = {0969-2126}, year = {2008}, date = {2008-08-01}, journal = {STRUCTURE}, volume = {16}, number = {8}, pages = {1214--1225}, abstract = {Processivity factors tether the catalytic subunits of DNA polymerases to DNA so that continuous synthesis of long DNA strands is possible. The human cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer intermediate in structure between monomeric herpes simplex virus UL42, which binds DNA directly via a basic surface, and the trimeric sliding clamp PCNA, which encircles DNA. To investigate how UL44 interacts with DNA, calculations were performed in which a 12 bp DNA oligonucleotide was docked to UL44. The calculations suggested that UL44 encircles DNA, which interacts with basic residues both within the cavity of the C clamp and in flexible loops of UL44 that complete the “circle.” The results of mutational and crosslinking studies were consistent with this model. Thus, UL44 is a “hybrid” of UL42 and PCNA: its struc ture is intermediate between the two and its mode of interaction with DNA has elements of both.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Processivity factors tether the catalytic subunits of DNA polymerases to DNA so that continuous synthesis of long DNA strands is possible. The human cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer intermediate in structure between monomeric herpes simplex virus UL42, which binds DNA directly via a basic surface, and the trimeric sliding clamp PCNA, which encircles DNA. To investigate how UL44 interacts with DNA, calculations were performed in which a 12 bp DNA oligonucleotide was docked to UL44. The calculations suggested that UL44 encircles DNA, which interacts with basic residues both within the cavity of the C clamp and in flexible loops of UL44 that complete the “circle.” The results of mutational and crosslinking studies were consistent with this model. Thus, UL44 is a “hybrid” of UL42 and PCNA: its struc ture is intermediate between the two and its mode of interaction with DNA has elements of both. |
Cecchini, M; Houdusse, A; Karplus, M Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements Article de journal Dans: PLOS COMPUTATIONAL BIOLOGY, 4 (8), 2008, ISSN: 1553-7358. @article{cecchini_allosteric_2008, title = {Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements}, author = {Cecchini, M. and Houdusse, A. and Karplus, M.}, doi = {10.1371/journal.pcbi.1000129}, issn = {1553-7358}, year = {2008}, date = {2008-08-01}, journal = {PLOS COMPUTATIONAL BIOLOGY}, volume = {4}, number = {8}, abstract = {The rigor to post-rigor transition in myosin, a consequence of ATP binding, plays an essential role in the Lymn-Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke. On the basis of the X-ray structures of myosin V, we have developed a new normal mode superposition model for the transition path between the two states. Rigid-body motions of the various subdomains and specific residues at the subdomain interfaces are key elements in the transition. The allosteric communication between the nucleotide binding site and the U50/L50 cleft is shown to result from local changes due to ATP binding, which induce large amplitude motions that are encoded in the structure of the protein. The triggering event is the change in the interaction of switch I and the P-loop, which is stabilized by ATP binding. The motion of switch I, which is a relatively rigid element of the U50 subdomain, leads directly to a partial opening of the U50/L50 cleft; the latter is expected to weaken the binding of myosin to actin. The calculated transition path demonstrates the nature of the subdomain coupling and offers an explanation for the mutual exclusion of ATP and actin binding. The mechanism of the uncoupling of the converter from the motor head, an essential part of the transition, is elucidated. The origin of the partial untwisting of the central beta-sheet in the rigor to post-rigor transition is described.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The rigor to post-rigor transition in myosin, a consequence of ATP binding, plays an essential role in the Lymn-Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke. On the basis of the X-ray structures of myosin V, we have developed a new normal mode superposition model for the transition path between the two states. Rigid-body motions of the various subdomains and specific residues at the subdomain interfaces are key elements in the transition. The allosteric communication between the nucleotide binding site and the U50/L50 cleft is shown to result from local changes due to ATP binding, which induce large amplitude motions that are encoded in the structure of the protein. The triggering event is the change in the interaction of switch I and the P-loop, which is stabilized by ATP binding. The motion of switch I, which is a relatively rigid element of the U50 subdomain, leads directly to a partial opening of the U50/L50 cleft; the latter is expected to weaken the binding of myosin to actin. The calculated transition path demonstrates the nature of the subdomain coupling and offers an explanation for the mutual exclusion of ATP and actin binding. The mechanism of the uncoupling of the converter from the motor head, an essential part of the transition, is elucidated. The origin of the partial untwisting of the central beta-sheet in the rigor to post-rigor transition is described. |
Cui, Qiang ; Karplus, Martin Allostery and cooperativity revisited Article de journal Dans: PROTEIN SCIENCE, 17 (8), p. 1295–1307, 2008, ISSN: 0961-8368. @article{cui_allostery_2008, title = {Allostery and cooperativity revisited}, author = {Cui, Qiang and Karplus, Martin}, doi = {10.1110/ps.03259908}, issn = {0961-8368}, year = {2008}, date = {2008-08-01}, journal = {PROTEIN SCIENCE}, volume = {17}, number = {8}, pages = {1295--1307}, abstract = {Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid- 60' s ( e. g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/ Pauling- KNF descriptions, and point out that the “ new view” of allostery, emphasizing “ population shifts,” is, in fact, an “ old view.” The presentation offers not only an up- to- date description of allostery from a theoretical/ computational perspective, but also helps to resolve several outstanding issues concerning allostery.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid- 60' s ( e. g., the KNF and MWC models), there is resurgent interest in the topic due to the recent experimental and computational studies that attempted to reveal, at an atomistic level, how allostery actually works. In this review, using systems for which atomistic simulations have been carried out in our groups as examples, we describe the current understanding of allostery, how the mechanisms go beyond the classical MWC/ Pauling- KNF descriptions, and point out that the “ new view” of allostery, emphasizing “ population shifts,” is, in fact, an “ old view.” The presentation offers not only an up- to- date description of allostery from a theoretical/ computational perspective, but also helps to resolve several outstanding issues concerning allostery. |
Nasr, Gihane ; Barboiu, Mihail ; Ono, Takashi ; Fujii, Shunsuke ; Lehn, Jean-Marie Dynamic polymer membranes displaying tunable transport properties on constitutional exchange Article de journal Dans: JOURNAL OF MEMBRANE SCIENCE, 321 (1), p. 8–14, 2008, ISSN: 0376-7388. @article{nasr_dynamic_2008, title = {Dynamic polymer membranes displaying tunable transport properties on constitutional exchange}, author = {Nasr, Gihane and Barboiu, Mihail and Ono, Takashi and Fujii, Shunsuke and Lehn, Jean-Marie}, doi = {10.1016/j.memsci.2008.03.005}, issn = {0376-7388}, year = {2008}, date = {2008-08-01}, journal = {JOURNAL OF MEMBRANE SCIENCE}, volume = {321}, number = {1}, pages = {8--14}, abstract = {Functional dynamic polymers, “dynamers”, are used to design new membrane materials. Our efforts involve the synthesis and the fabrication of dynamic thin-layer supported solid membrane films. The transport performances of (permeability, selectivity and partition coefficients) are evaluated by using the solution-diffusion model. The membrane performances designed to transport ionic salts NaCl and KCl depend and are based on encoded molecular features of the monomeric subcomponents. Thanks to the possibility to combine the structural and functional features of different monomers, the heteropolymeric membrane materials can exhibit very different properties from their original homopolymeric components. In the examples developed here, this strategy revealed itself as a versatile way for the synthesis of new membranes presenting different permeabilities and preserving their selectivity (SK+/Na+ similar to 1.4). (C) 2008 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Functional dynamic polymers, “dynamers”, are used to design new membrane materials. Our efforts involve the synthesis and the fabrication of dynamic thin-layer supported solid membrane films. The transport performances of (permeability, selectivity and partition coefficients) are evaluated by using the solution-diffusion model. The membrane performances designed to transport ionic salts NaCl and KCl depend and are based on encoded molecular features of the monomeric subcomponents. Thanks to the possibility to combine the structural and functional features of different monomers, the heteropolymeric membrane materials can exhibit very different properties from their original homopolymeric components. In the examples developed here, this strategy revealed itself as a versatile way for the synthesis of new membranes presenting different permeabilities and preserving their selectivity (SK+/Na+ similar to 1.4). (C) 2008 Elsevier B.V. All rights reserved. |
Frey, Julien ; Tock, Christian ; Collin, Jean-Paul ; Heitz, Valerie ; Sauvage, Jean-Pierre ; Rissanen, Kari Cyclic [2]pseudorotaxane tetramers consisting of two rigid rods threaded through two bis-macrocycles: Copper(I)-templated synthesis and X-ray structure studies Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (33), p. 11013–11022, 2008, ISSN: 0002-7863. @article{frey_cyclic_2008, title = {Cyclic [2]pseudorotaxane tetramers consisting of two rigid rods threaded through two bis-macrocycles: Copper(I)-templated synthesis and X-ray structure studies}, author = {Frey, Julien and Tock, Christian and Collin, Jean-Paul and Heitz, Valerie and Sauvage, Jean-Pierre and Rissanen, Kari}, doi = {10.1021/ja801924y}, issn = {0002-7863}, year = {2008}, date = {2008-08-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, number = {33}, pages = {11013--11022}, abstract = {Variously substituted coordinating rigid rods have been synthesized which incorporate a central 4,7-phenanthroline nucleus attached to two 2-pyridyl groups via its 3 and 8 positions, so as to yield bis-bidentate chelates, the two-coordinating axes of the chelates being parallel to one another. Regardless of the nature of the substituents borne by the rods, the copper(I)-induced threading reaction of two such rods through the rings of two bis-macrocycles affords in a quantitative yield the 4-copper(I) threaded assembly. The [2]pseudorotaxane tetramers thus obtained have been fully characterized in solution and, for one of them, an X-ray structure could be obtained, confirming the threaded nature of the complex and providing important structural information.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Variously substituted coordinating rigid rods have been synthesized which incorporate a central 4,7-phenanthroline nucleus attached to two 2-pyridyl groups via its 3 and 8 positions, so as to yield bis-bidentate chelates, the two-coordinating axes of the chelates being parallel to one another. Regardless of the nature of the substituents borne by the rods, the copper(I)-induced threading reaction of two such rods through the rings of two bis-macrocycles affords in a quantitative yield the 4-copper(I) threaded assembly. The [2]pseudorotaxane tetramers thus obtained have been fully characterized in solution and, for one of them, an X-ray structure could be obtained, confirming the threaded nature of the complex and providing important structural information. |
Drezet, Aurelien ; Genet, Cyriaque ; Ebbesen, Thomas W Miniature plasmonic wave plates Article de journal Dans: PHYSICAL REVIEW LETTERS, 101 (4), 2008, ISSN: 0031-9007. @article{drezet_miniature_2008, title = {Miniature plasmonic wave plates}, author = {Drezet, Aurelien and Genet, Cyriaque and Ebbesen, Thomas W.}, doi = {10.1103/PhysRevLett.101.043902}, issn = {0031-9007}, year = {2008}, date = {2008-07-01}, journal = {PHYSICAL REVIEW LETTERS}, volume = {101}, number = {4}, abstract = {Linear birefringence, as implemented in wave plates, is a natural way to control the state of polarization of light. We report on a general method for designing miniature planar wave plates using surface plasmons. The resonant optical device considered here is a single circular aperture surrounded by an elliptical antenna grating. The difference between the short and long axis of each ellipsis introduces a phase shift on the surface plasmons which enables the realization of a quarter wave plate. Furthermore, the experimental results and the theoretical analysis show that the general procedure used does not influence the optical coherence of the polarization state and allows us to explore completely the surface of the unit Poincare sphere by changing only the shape of the elliptical grating.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Linear birefringence, as implemented in wave plates, is a natural way to control the state of polarization of light. We report on a general method for designing miniature planar wave plates using surface plasmons. The resonant optical device considered here is a single circular aperture surrounded by an elliptical antenna grating. The difference between the short and long axis of each ellipsis introduces a phase shift on the surface plasmons which enables the realization of a quarter wave plate. Furthermore, the experimental results and the theoretical analysis show that the general procedure used does not influence the optical coherence of the polarization state and allows us to explore completely the surface of the unit Poincare sphere by changing only the shape of the elliptical grating. |
Maragakis, Paul ; Ritort, Felix ; Bustamante, Carlos ; Karplus, Martin ; Crooks, Gavin E Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise Article de journal Dans: JOURNAL OF CHEMICAL PHYSICS, 129 (2), 2008, ISSN: 0021-9606. @article{maragakis_bayesian_2008, title = {Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise}, author = {Maragakis, Paul and Ritort, Felix and Bustamante, Carlos and Karplus, Martin and Crooks, Gavin E.}, doi = {10.1063/1.2937892}, issn = {0021-9606}, year = {2008}, date = {2008-07-01}, journal = {JOURNAL OF CHEMICAL PHYSICS}, volume = {129}, number = {2}, abstract = {The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to nonequilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not been considered previously. Here, we present a Bayesian formalism for estimating free energy changes from nonequilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experiments in which a single RNA hairpin is unfolded and refolded using optical tweezers at three different rates. Interestingly, the fastest and farthest-from-equilibrium measurements contain the least instrumental noise and, therefore, provide a more accurate estimate of the free energies than a few slow, more noisy, near-equilibrium measurements. The methods we propose here will extend the scope of single-molecule experiments; they can be used in the analysis of data from measurements with atomic force microscopy, optical, and magnetic tweezers. (c) 2008 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to nonequilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not been considered previously. Here, we present a Bayesian formalism for estimating free energy changes from nonequilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experiments in which a single RNA hairpin is unfolded and refolded using optical tweezers at three different rates. Interestingly, the fastest and farthest-from-equilibrium measurements contain the least instrumental noise and, therefore, provide a more accurate estimate of the free energies than a few slow, more noisy, near-equilibrium measurements. The methods we propose here will extend the scope of single-molecule experiments; they can be used in the analysis of data from measurements with atomic force microscopy, optical, and magnetic tweezers. (c) 2008 American Institute of Physics. |
Mativetsky, Jeffrey M; Pace, Giuseppina ; Elbing, Mark ; Rampi, Maria A; Mayor, Marcel ; Samori, Paolo Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (29), p. 9192+, 2008, ISSN: 0002-7863. @article{mativetsky_azobenzenes_2008, title = {Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions}, author = {Mativetsky, Jeffrey M. and Pace, Giuseppina and Elbing, Mark and Rampi, Maria A. and Mayor, Marcel and Samori, Paolo}, doi = {10.1021/ja8018093}, issn = {0002-7863}, year = {2008}, date = {2008-07-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, number = {29}, pages = {9192+}, abstract = {Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach. where a metallic AFM tip was used to electrically contact ago-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach. where a metallic AFM tip was used to electrically contact ago-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule. |
Flamigni, Lucia ; Collin, Jean-Paul ; Sauvage, Jean-Pierre Iridium terpyridine complexes as functional assembling units in arrays for the conversion of light energy Article de journal Dans: ACCOUNTS OF CHEMICAL RESEARCH, 41 (7), p. 857–871, 2008, ISSN: 0001-4842. @article{flamigni_iridium_2008, title = {Iridium terpyridine complexes as functional assembling units in arrays for the conversion of light energy}, author = {Flamigni, Lucia and Collin, Jean-Paul and Sauvage, Jean-Pierre}, doi = {10.1021/ar700282n}, issn = {0001-4842}, year = {2008}, date = {2008-07-01}, journal = {ACCOUNTS OF CHEMICAL RESEARCH}, volume = {41}, number = {7}, pages = {857--871}, abstract = {In photosynthesis, sunlight energy is converted into a chemical potential by an electron transfer sequence that is started by an excited state and ultimately yields a long-lived charge-separated state. This process can be reproduced by carefully designed multicomponent artificial arrays of three or more components, and the stored energy can be used to oxidize or reduce molecules in solution, to inject electrons or holes, or to create an electron flow. Therefore, the process is important both for artificial-photosynthesis research and for photovoltaic and optoelectronic applications. Molecular arrays for photoinduced charge separation often use chromophores that resemble the natural ones. However, new synthetic components, including transition metal complexes, have had some success. This Account discusses the use of bis-terpyridine (tpy) metal complexes as assembling and functional units of such multicomponent arrays. M(tpy)(2)(n+) complexes have the advantage of yielding linear rrays with unambiguous geometry. Originally, Ru(tpy)(2)(2+) and Os(tpy)(2)(2+) were used as photosensitizers in triads containing typical organic donors and acceptors. However, it soon became evident that the relatively low excited state of these complexes could act as,an energy drain of the excited state of the photosensitizer and, thus, seriously compete with charge separation. A new metal complex that preserved the favorable tpy geometry and yet had a higher energy level Was needed. We identified Ir(tpy)(2)(3+), which displayed a higher energy level, a more facile reduction that favored charge separation, a longer excited-state lifetime, and strong spectroscopic features that were useful for the identification of intermediates. Ir(tpy)(2)(3+) was used in arrays with electron-donating gold porphyrin and electron-accepting free-base porphyrins. A judicious change of the free-base porphyrin photosensitizer with zinc porphyrin allowed us to shape the photoreactivity and led to charge separation with unity yield and a lifetime on the order of a microsecond. In a subsequent approach, an Ir(tpy)(2)(3+) derivative was connected to an amine electron donor and a bisimide electron acceptor in an array 5 nm long. In this case, the complex acted as photosensitizer, and long-lived charge separation over the extremities (textbackslashtextbackslashtextgreater 100 mu s, nearly independent of the presence of oxygen) was achieved. The efficiency of the charge separation was modest, but it was improved later, after a modification aiming at decoupling the donor and photosensitizer components. This study represents an example of how the performances of an artificial photofunctional array can be modeled by a judicious design assisted by a detailed knowledge of the systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In photosynthesis, sunlight energy is converted into a chemical potential by an electron transfer sequence that is started by an excited state and ultimately yields a long-lived charge-separated state. This process can be reproduced by carefully designed multicomponent artificial arrays of three or more components, and the stored energy can be used to oxidize or reduce molecules in solution, to inject electrons or holes, or to create an electron flow. Therefore, the process is important both for artificial-photosynthesis research and for photovoltaic and optoelectronic applications. Molecular arrays for photoinduced charge separation often use chromophores that resemble the natural ones. However, new synthetic components, including transition metal complexes, have had some success. This Account discusses the use of bis-terpyridine (tpy) metal complexes as assembling and functional units of such multicomponent arrays. M(tpy)(2)(n+) complexes have the advantage of yielding linear rrays with unambiguous geometry. Originally, Ru(tpy)(2)(2+) and Os(tpy)(2)(2+) were used as photosensitizers in triads containing typical organic donors and acceptors. However, it soon became evident that the relatively low excited state of these complexes could act as,an energy drain of the excited state of the photosensitizer and, thus, seriously compete with charge separation. A new metal complex that preserved the favorable tpy geometry and yet had a higher energy level Was needed. We identified Ir(tpy)(2)(3+), which displayed a higher energy level, a more facile reduction that favored charge separation, a longer excited-state lifetime, and strong spectroscopic features that were useful for the identification of intermediates. Ir(tpy)(2)(3+) was used in arrays with electron-donating gold porphyrin and electron-accepting free-base porphyrins. A judicious change of the free-base porphyrin photosensitizer with zinc porphyrin allowed us to shape the photoreactivity and led to charge separation with unity yield and a lifetime on the order of a microsecond. In a subsequent approach, an Ir(tpy)(2)(3+) derivative was connected to an amine electron donor and a bisimide electron acceptor in an array 5 nm long. In this case, the complex acted as photosensitizer, and long-lived charge separation over the extremities (textbackslashtextbackslashtextgreater 100 mu s, nearly independent of the presence of oxygen) was achieved. The efficiency of the charge separation was modest, but it was improved later, after a modification aiming at decoupling the donor and photosensitizer components. This study represents an example of how the performances of an artificial photofunctional array can be modeled by a judicious design assisted by a detailed knowledge of the systems. |
Przybilla, F; Degiron, A; Genet, C; Ebbesen, T W; de Leon-Perez, F; Bravo-Abad, J; Garcia-Vidal, F J; Martin-Moreno, L Efficiency and finite size effects in enhanced transmission through subwavelength apertures Article de journal Dans: OPTICS EXPRESS, 16 (13), p. 9571–9579, 2008, ISSN: 1094-4087. @article{przybilla_efficiency_2008, title = {Efficiency and finite size effects in enhanced transmission through subwavelength apertures}, author = {Przybilla, F. and Degiron, A. and Genet, C. and Ebbesen, T. W. and de Leon-Perez, F. and Bravo-Abad, J. and Garcia-Vidal, F. J. and Martin-Moreno, L.}, doi = {10.1364/OE.16.009571}, issn = {1094-4087}, year = {2008}, date = {2008-06-01}, journal = {OPTICS EXPRESS}, volume = {16}, number = {13}, pages = {9571--9579}, abstract = {We investigate transmission efficiency and finite size effects for the subwavelength hole arrays. Experiments and simulations show how the finite size effects depend strongly on the hole diameter. The transmission efficiency reaches an asymptotic upper value when the array is larger than the surface plasmon propagation length on the corrugated surface. By comparing the transmission of arrays with that of the corresponding single holes, the relative enhancement is found to increase as the hole diameter decreases. In the conditions of the experiments the enhancement is one to two orders of magnitude but there is no fundamental upper limit to this value. (c) 2008 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigate transmission efficiency and finite size effects for the subwavelength hole arrays. Experiments and simulations show how the finite size effects depend strongly on the hole diameter. The transmission efficiency reaches an asymptotic upper value when the array is larger than the surface plasmon propagation length on the corrugated surface. By comparing the transmission of arrays with that of the corresponding single holes, the relative enhancement is found to increase as the hole diameter decreases. In the conditions of the experiments the enhancement is one to two orders of magnitude but there is no fundamental upper limit to this value. (c) 2008 Optical Society of America. |
Spada, Gian Piero ; Lena, Stefano ; Masiero, Stefano ; Pieraccini, Silvia ; Surin, Mathieu ; Samori, Paolo Guanosine-based hydrogen-bonded scaffolds: Controlling the assembly of oligothiophenes Article de journal Dans: ADVANCED MATERIALS, 20 (12), p. 2433+, 2008, ISSN: 0935-9648. @article{spada_guanosine-based_2008, title = {Guanosine-based hydrogen-bonded scaffolds: Controlling the assembly of oligothiophenes}, author = {Spada, Gian Piero and Lena, Stefano and Masiero, Stefano and Pieraccini, Silvia and Surin, Mathieu and Samori, Paolo}, doi = {10.1002/adma.200703177}, issn = {0935-9648}, year = {2008}, date = {2008-06-01}, journal = {ADVANCED MATERIALS}, volume = {20}, number = {12}, pages = {2433+}, abstract = {The scaffolding of a pi-conjugated oligomer, namely terthiophene, is achieved by taking advantage of the self-assembly of a guanosine derivative into highly directional H-bonded networks. Reversible interconversion allows switching between ribbons and quartet-based assemblies in solution. The self-assembly of 1 on surfaces lead to large lamellae of straight ribbons, ultimately forming ID conjugated arrays as prototypes of supramolecular nanowires.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The scaffolding of a pi-conjugated oligomer, namely terthiophene, is achieved by taking advantage of the self-assembly of a guanosine derivative into highly directional H-bonded networks. Reversible interconversion allows switching between ribbons and quartet-based assemblies in solution. The self-assembly of 1 on surfaces lead to large lamellae of straight ribbons, ultimately forming ID conjugated arrays as prototypes of supramolecular nanowires. |
Stefankiewicz, Artur R; Walesa, Monika ; Jankowski, Piotr ; Ciesielski, Artur ; Patroniak, Violetta ; Kubicki, Maciej ; Hnatejko, Zbigniew ; Harrowfield, Jack M; Lehn, Jean-Marie Quaterpyridine ligands forming helical complexes of mono- and dinuclear (helicate) forms Article de journal Dans: EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, (18), p. 2910–2920, 2008, ISSN: 1434-1948. @article{stefankiewicz_quaterpyridine_2008, title = {Quaterpyridine ligands forming helical complexes of mono- and dinuclear (helicate) forms}, author = {Stefankiewicz, Artur R. and Walesa, Monika and Jankowski, Piotr and Ciesielski, Artur and Patroniak, Violetta and Kubicki, Maciej and Hnatejko, Zbigniew and Harrowfield, Jack M. and Lehn, Jean-Marie}, doi = {10.1002/ejic.200800172}, issn = {1434-1948}, year = {2008}, date = {2008-06-01}, journal = {EUROPEAN JOURNAL OF INORGANIC CHEMISTRY}, number = {18}, pages = {2910--2920}, abstract = {The dimethylquaterpyridine ligand L1 reacts with Cu-I and Ag-I to give dinuclear complexes of “helicate” form, in which the metals are in an approximate tetrahedral coordination, whereas reactions with Co-II and Zn-II provide mononuclear complexes, in which the metals are apparently six-coordinate with markedly distorted octahedral coordination, and the ligand retains a helical conformation. Oxidation of the methyl substituents of L1 into carboxylic acid groups, followed by esterification, gives ligand L2, which also forms a dinuclear Cu-I helicate and a mononuclear Coll complex; one of the ester groups appears to be involved in complexation in the latter. All the complexes were characterised by single-crystal X-ray structure determinations. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The dimethylquaterpyridine ligand L1 reacts with Cu-I and Ag-I to give dinuclear complexes of “helicate” form, in which the metals are in an approximate tetrahedral coordination, whereas reactions with Co-II and Zn-II provide mononuclear complexes, in which the metals are apparently six-coordinate with markedly distorted octahedral coordination, and the ligand retains a helical conformation. Oxidation of the methyl substituents of L1 into carboxylic acid groups, followed by esterification, gives ligand L2, which also forms a dinuclear Cu-I helicate and a mononuclear Coll complex; one of the ester groups appears to be involved in complexation in the latter. All the complexes were characterised by single-crystal X-ray structure determinations. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008). |
Pothukanuri, Srinivasu ; Pianowski, Zbigniew ; Winssinger, Nicolas Expanding the scope and orthogonality of PNA synthesis Article de journal Dans: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (18), p. 3141–3148, 2008, ISSN: 1434-193X. @article{pothukanuri_expanding_2008, title = {Expanding the scope and orthogonality of PNA synthesis}, author = {Pothukanuri, Srinivasu and Pianowski, Zbigniew and Winssinger, Nicolas}, doi = {10.1002/ejoc.200800141}, issn = {1434-193X}, year = {2008}, date = {2008-06-01}, journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, number = {18}, pages = {3141--3148}, abstract = {Peptide nucleic acids (PNAs) hybridize to natural oligonucleotides according to Watson and Crick base-pairing rules. The robustness of PNA oligomers and ease of synthesis have made them an attractive platform to encode small or macromolecules for microarraying purposes and other applications based on programmable self assembly. A cornerstone of these endeavors is the orthogonality of PNA synthesis with other chemistries. Herein, we present a thorough investigation of six types of protecting groups for the terminal nitrogen atom (Alloc, Teoc, 4-N(3)Cbz, Fmoc, 4-OTBSCbz, and Azoc) and five protecting groups on the nucleobases (Cl-Bhoc, F-Bhoc, Teoc, 4-OMeCbz, and Boc). ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Peptide nucleic acids (PNAs) hybridize to natural oligonucleotides according to Watson and Crick base-pairing rules. The robustness of PNA oligomers and ease of synthesis have made them an attractive platform to encode small or macromolecules for microarraying purposes and other applications based on programmable self assembly. A cornerstone of these endeavors is the orthogonality of PNA synthesis with other chemistries. Herein, we present a thorough investigation of six types of protecting groups for the terminal nitrogen atom (Alloc, Teoc, 4-N(3)Cbz, Fmoc, 4-OTBSCbz, and Azoc) and five protecting groups on the nucleobases (Cl-Bhoc, F-Bhoc, Teoc, 4-OMeCbz, and Boc). ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008). |
Ebbesen, Thomas W; Genet, Cyriaque ; Bozhevolnyi, Sergey I Surface-plasmon circuitry Article de journal Dans: PHYSICS TODAY, 61 (5), p. 44–50, 2008, ISSN: 0031-9228. @article{ebbesen_surface-plasmon_2008, title = {Surface-plasmon circuitry}, author = {Ebbesen, Thomas W. and Genet, Cyriaque and Bozhevolnyi, Sergey I.}, doi = {10.1063/1.2930735}, issn = {0031-9228}, year = {2008}, date = {2008-05-01}, journal = {PHYSICS TODAY}, volume = {61}, number = {5}, pages = {44--50}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Adamovic, Ivana ; Mijailovich, Srboljub M; Karplus, Martin The elastic properties of the structurally characterized myosin II s2 subdomain: A molecular dynamics and normal mode analysis Article de journal Dans: BIOPHYSICAL JOURNAL, 94 (10), p. 3779–3789, 2008, ISSN: 0006-3495. @article{adamovic_elastic_2008, title = {The elastic properties of the structurally characterized myosin II s2 subdomain: A molecular dynamics and normal mode analysis}, author = {Adamovic, Ivana and Mijailovich, Srboljub M. and Karplus, Martin}, doi = {10.1529/biophysj.107.122028}, issn = {0006-3495}, year = {2008}, date = {2008-05-01}, journal = {BIOPHYSICAL JOURNAL}, volume = {94}, number = {10}, pages = {3779--3789}, abstract = {The elastic properties (stretching and bending moduli) of myosin are expected to play an important role in its function. Of particular interest is the extended alpha-helical coiled-coil portion of the molecule. Since there is no high resolution structure for the entire coiled-coil, a study is made of the scallop myosin II S2 subdomain for which an x-ray structure is available (Protein Data Bank 1nkn). We estimate the stretching and bending moduli of the S2 subdomain with an atomic level model by use of molecular simulations. Results were obtained from nonequilibrium molecular dynamics simulations in the presence of an external force, from the fluctuations in equilibrium molecular dynamics simulations and from normal modes. In addition, a poly-Ala (78 amino acid residues) alpha-helix model was examined to test the methodology and because of its interest as part of the lever arm. As expected, both the alpha-helix and coiled-coil S2 subdomain are very stiff for stretching along the main axis, with the stretching stiffness constant in the range 60-80 pN/nm (scaled to the 60 nm long S2). Both molecules are much more flexible for bending with a lateral stiffness of similar to 0.010pN/nm for the S2 and 0.0055pN/nm for the alpha-helix (scaled to 60 nm). These results are expected to be useful in estimating cross-bridge elasticity, which is required for understanding the strain-dependent transitions in the actomyosin cycle and for the development of three-dimensional models of muscle contraction.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The elastic properties (stretching and bending moduli) of myosin are expected to play an important role in its function. Of particular interest is the extended alpha-helical coiled-coil portion of the molecule. Since there is no high resolution structure for the entire coiled-coil, a study is made of the scallop myosin II S2 subdomain for which an x-ray structure is available (Protein Data Bank 1nkn). We estimate the stretching and bending moduli of the S2 subdomain with an atomic level model by use of molecular simulations. Results were obtained from nonequilibrium molecular dynamics simulations in the presence of an external force, from the fluctuations in equilibrium molecular dynamics simulations and from normal modes. In addition, a poly-Ala (78 amino acid residues) alpha-helix model was examined to test the methodology and because of its interest as part of the lever arm. As expected, both the alpha-helix and coiled-coil S2 subdomain are very stiff for stretching along the main axis, with the stretching stiffness constant in the range 60-80 pN/nm (scaled to the 60 nm long S2). Both molecules are much more flexible for bending with a lateral stiffness of similar to 0.010pN/nm for the S2 and 0.0055pN/nm for the alpha-helix (scaled to 60 nm). These results are expected to be useful in estimating cross-bridge elasticity, which is required for understanding the strain-dependent transitions in the actomyosin cycle and for the development of three-dimensional models of muscle contraction. |
Maragakis, Paul ; Spichty, Martin ; Karplus, Martin A differential fluctuation theorem Article de journal Dans: JOURNAL OF PHYSICAL CHEMISTRY B, 112 (19), p. 6168–6174, 2008, ISSN: 1520-6106. @article{maragakis_differential_2008, title = {A differential fluctuation theorem}, author = {Maragakis, Paul and Spichty, Martin and Karplus, Martin}, doi = {10.1021/jp077037r}, issn = {1520-6106}, year = {2008}, date = {2008-05-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY B}, volume = {112}, number = {19}, pages = {6168--6174}, abstract = {We derive a nonequilibrium thermodynamics identity (the “differential fluctuation theorem”) that connects forward and reverse joint probabilities of nonequilibrium work and of arbitrary generalized coordinates corresponding to states of interest. This identity allows us to estimate the free energy difference between domains of these states. Our results follow from a general symmetry relation between averages over nonequilibrium forward and backward path functions derived by Crooks [Crooks, G. E. Phys. Rev. E 2000, 61, 2361-2366]. We show how several existing nonequilibrium thermodynamic identities can be obtained directly from the differential fluctuation theorem. We devise an approach for measuring conformational free energy differences, and we demonstrate its applicability to the analysis of molecular dynamics simulations by estimating the free energy difference between two conformers of the alanine dipeptide model system. We anticipate that these developments can be applied to the analysis of laboratory experiments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We derive a nonequilibrium thermodynamics identity (the “differential fluctuation theorem”) that connects forward and reverse joint probabilities of nonequilibrium work and of arbitrary generalized coordinates corresponding to states of interest. This identity allows us to estimate the free energy difference between domains of these states. Our results follow from a general symmetry relation between averages over nonequilibrium forward and backward path functions derived by Crooks [Crooks, G. E. Phys. Rev. E 2000, 61, 2361-2366]. We show how several existing nonequilibrium thermodynamic identities can be obtained directly from the differential fluctuation theorem. We devise an approach for measuring conformational free energy differences, and we demonstrate its applicability to the analysis of molecular dynamics simulations by estimating the free energy difference between two conformers of the alanine dipeptide model system. We anticipate that these developments can be applied to the analysis of laboratory experiments. |
Ruff, Yves ; Lehn, Jean-Marie Glycodynamers: Dynamic analogs of arabinofuranoside oligosaccharides Article de journal Dans: BIOPOLYMERS, 89 (5), p. 486–496, 2008, ISSN: 0006-3525. @article{ruff_glycodynamers:_2008, title = {Glycodynamers: Dynamic analogs of arabinofuranoside oligosaccharides}, author = {Ruff, Yves and Lehn, Jean-Marie}, doi = {10.1002/bip.20885}, issn = {0006-3525}, year = {2008}, date = {2008-05-01}, journal = {BIOPOLYMERS}, volume = {89}, number = {5}, pages = {486--496}, abstract = {Dynamic analogs of alpha-(1 -textbackslashtextbackslashtextgreater 5)-D-oligoarabinofuranosides were prepared by oxime polycondensation. These equilibrium polymers were characterized by H-1 NMR studies, NMR DOSY, and MALDI mass spectrometry. Their reversibility under mild acidic conditions was demonstrated by component exchange reaction followed by 1H NMR studies. Their size and composition can be tuned by component exchange emphasizing their constitutionally dynamic character. They represent dynamic versions of biopolymers, biodynamers. (c) 2007 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dynamic analogs of alpha-(1 -textbackslashtextbackslashtextgreater 5)-D-oligoarabinofuranosides were prepared by oxime polycondensation. These equilibrium polymers were characterized by H-1 NMR studies, NMR DOSY, and MALDI mass spectrometry. Their reversibility under mild acidic conditions was demonstrated by component exchange reaction followed by 1H NMR studies. Their size and composition can be tuned by component exchange emphasizing their constitutionally dynamic character. They represent dynamic versions of biopolymers, biodynamers. (c) 2007 Wiley Periodicals, Inc. |
Petitjean, Anne ; Cuccia, Louis A; Schmutz, Marc ; Lehn, Jean-Marie Naphthyridine-based helical foldamers and macrocycles: Synthesis, cation binding, and supramolecular assemblies Article de journal Dans: JOURNAL OF ORGANIC CHEMISTRY, 73 (7), p. 2481–2495, 2008, ISSN: 0022-3263. @article{petitjean_naphthyridine-based_2008, title = {Naphthyridine-based helical foldamers and macrocycles: Synthesis, cation binding, and supramolecular assemblies}, author = {Petitjean, Anne and Cuccia, Louis A. and Schmutz, Marc and Lehn, Jean-Marie}, doi = {10.1021/jo702495u}, issn = {0022-3263}, year = {2008}, date = {2008-04-01}, journal = {JOURNAL OF ORGANIC CHEMISTRY}, volume = {73}, number = {7}, pages = {2481--2495}, abstract = {Unraveling the factors that control the conformation of molecular chains is of great interest both for understanding the shape of biological molecular strands and for designing artificial ones that adopt desired forms. Thus, a variety of artificial folding codons have been identified that enforce the formation, among others, of helices, strands, and loops, the major emphasis being on the shape of the foldamer. We report herein the synthesis and study of a family of foldamers and macrocycles based on the 1,8-naphthyridine and pyrimidine units, whose internal cavity is large enough to accommodate ionic substrates, and focus on the impact of guest binding within a cylindrical environment. Interestingly, the binding event within these large oligomers is translated to the outside of the receptors and affects the interaction of the overall complexes with the outside world. For instance, alkali cations bind to the one-turn helices and macrocycles to promote fibril formation and aggregation. Also, polyammonium substrates are able to tune the length of the overall helix assemblies and the rigidity of long oligomers. The reported data on one-turn, two-turn helices and macrocycles not only allows one to devise a model for the ion-controlled supramolecular assembly of such systems but also provides evidence that such controlled scaffolds bear promise in the design of complex systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Unraveling the factors that control the conformation of molecular chains is of great interest both for understanding the shape of biological molecular strands and for designing artificial ones that adopt desired forms. Thus, a variety of artificial folding codons have been identified that enforce the formation, among others, of helices, strands, and loops, the major emphasis being on the shape of the foldamer. We report herein the synthesis and study of a family of foldamers and macrocycles based on the 1,8-naphthyridine and pyrimidine units, whose internal cavity is large enough to accommodate ionic substrates, and focus on the impact of guest binding within a cylindrical environment. Interestingly, the binding event within these large oligomers is translated to the outside of the receptors and affects the interaction of the overall complexes with the outside world. For instance, alkali cations bind to the one-turn helices and macrocycles to promote fibril formation and aggregation. Also, polyammonium substrates are able to tune the length of the overall helix assemblies and the rigidity of long oligomers. The reported data on one-turn, two-turn helices and macrocycles not only allows one to devise a model for the ion-controlled supramolecular assembly of such systems but also provides evidence that such controlled scaffolds bear promise in the design of complex systems. |
Frey, Julien ; Tock, Christian ; Collin, Jean-Paul ; Heitz, Valerie ; Sauvage, Jean-Pierre A [3]rotaxane with two porphyrinic plates acting as an adaptable receptor Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (14), p. 4592+, 2008, ISSN: 0002-7863. @article{frey_[3]rotaxane_2008, title = {A [3]rotaxane with two porphyrinic plates acting as an adaptable receptor}, author = {Frey, Julien and Tock, Christian and Collin, Jean-Paul and Heitz, Valerie and Sauvage, Jean-Pierre}, doi = {10.1021/ja7110493}, issn = {0002-7863}, year = {2008}, date = {2008-04-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, number = {14}, pages = {4592+}, abstract = {Following a multistep procedure, the copper(I)-templated strategy allowed preparation of a multifunctional [3]rotaxane. The dumbbell consists of a central two-bidentate chelate unit and two terminal stoppers. The two rings threaded on the rotaxane axis consist each of a 1,10-phenanthroline- incorporating macrocycle, rigidly connected to an appended zinc-complexed porphyrin. The copper(I) template can be removed, affording a free rotaxane whose two rings can glide freely along the axis and spin around it. The dumbbell being very long (similar to 85 A in its extended conformation from one stopper to the other), the porphyrin-porphyrin distance can be varied over a wide range. The two porphyrinic plates constitute the key elements of a receptor able to complex various guests between the plates. The ability of the threaded rings to move freely makes the host perfectly adjustable, allowing capture of geometrically very different guests. The copper(I)-complexed rotaxane also acts as an efficient receptor, although its adaptability is obviously more limited than that of its free rotaxane counterpart.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Following a multistep procedure, the copper(I)-templated strategy allowed preparation of a multifunctional [3]rotaxane. The dumbbell consists of a central two-bidentate chelate unit and two terminal stoppers. The two rings threaded on the rotaxane axis consist each of a 1,10-phenanthroline- incorporating macrocycle, rigidly connected to an appended zinc-complexed porphyrin. The copper(I) template can be removed, affording a free rotaxane whose two rings can glide freely along the axis and spin around it. The dumbbell being very long (similar to 85 A in its extended conformation from one stopper to the other), the porphyrin-porphyrin distance can be varied over a wide range. The two porphyrinic plates constitute the key elements of a receptor able to complex various guests between the plates. The ability of the threaded rings to move freely makes the host perfectly adjustable, allowing capture of geometrically very different guests. The copper(I)-complexed rotaxane also acts as an efficient receptor, although its adaptability is obviously more limited than that of its free rotaxane counterpart. |
Strutt, Nathan L; Sauvage, Jean-Pierre PRES 17-Synthesis of a tetra-substituted porphyrin for use in a [6]rotaxane reminiscent of a press Article de journal Dans: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 235 , 2008, ISSN: 0065-7727. @article{strutt_pres_2008, title = {PRES 17-Synthesis of a tetra-substituted porphyrin for use in a [6]rotaxane reminiscent of a press}, author = {Strutt, Nathan L. and Sauvage, Jean-Pierre}, issn = {0065-7727}, year = {2008}, date = {2008-04-01}, journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY}, volume = {235}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lopez-Tejeira, F; Rodrigo, Sergio G; Martin-Moreno, L; Garcia-Vidal, F J; Devaux, E; Dintinger, J; Ebbesen, T W; Krenn, J R; Radko, I P; Bozhevolnyi, S I; Gonzalez, M U; Weeber, J C; Dereux, A Modulation of surface plasmon coupling-in by one-dimensional surface corrugation Article de journal Dans: NEW JOURNAL OF PHYSICS, 10 , 2008, ISSN: 1367-2630. @article{lopez-tejeira_modulation_2008, title = {Modulation of surface plasmon coupling-in by one-dimensional surface corrugation}, author = {Lopez-Tejeira, F. and Rodrigo, Sergio G. and Martin-Moreno, L. and Garcia-Vidal, F. J. and Devaux, E. and Dintinger, J. and Ebbesen, T. W. and Krenn, J. R. and Radko, I. P. and Bozhevolnyi, S. I. and Gonzalez, M. U. and Weeber, J. C. and Dereux, A.}, doi = {10.1088/1367-2630/10/3/033035}, issn = {1367-2630}, year = {2008}, date = {2008-03-01}, journal = {NEW JOURNAL OF PHYSICS}, volume = {10}, abstract = {Surface plasmon-polaritons have recently attracted renewed interest in the scientific community for their potential in sub-wavelength optics, light generation and non-destructive sensing. Given that they cannot be directly excited by freely propagating light due to their intrinsic binding to the metal surface, the light - plasmon coupling efficiency becomes of crucial importance for the success of any plasmonic device. Here, we present a comprehensive study on the modulation ( enhancement or suppression) of such a coupling efficiency by means of one-dimensional surface corrugation. Our approach is based on simple wave interference and enables us to make quantitative predictions which have been experimentally confirmed at both the near-infrared and telecom ranges.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Surface plasmon-polaritons have recently attracted renewed interest in the scientific community for their potential in sub-wavelength optics, light generation and non-destructive sensing. Given that they cannot be directly excited by freely propagating light due to their intrinsic binding to the metal surface, the light - plasmon coupling efficiency becomes of crucial importance for the success of any plasmonic device. Here, we present a comprehensive study on the modulation ( enhancement or suppression) of such a coupling efficiency by means of one-dimensional surface corrugation. Our approach is based on simple wave interference and enables us to make quantitative predictions which have been experimentally confirmed at both the near-infrared and telecom ranges. |
Wenger, Jerome ; Gerard, Davy ; Dintinger, Jose ; Mahboub, Oussama ; Bonod, Nicolas ; Popov, Evgeny ; Ebbesen, Thomas W; Rigneault, Herve E Emission and excitation contributions to enhanced single molecule fluorescence by gold nanometric apertures Article de journal Dans: OPTICS EXPRESS, 16 (5), p. 3008–3020, 2008, ISSN: 1094-4087. @article{wenger_emission_2008, title = {Emission and excitation contributions to enhanced single molecule fluorescence by gold nanometric apertures}, author = {Wenger, Jerome and Gerard, Davy and Dintinger, Jose and Mahboub, Oussama and Bonod, Nicolas and Popov, Evgeny and Ebbesen, Thomas W. and Rigneault, Herve E.}, doi = {10.1364/OE.16.003008}, issn = {1094-4087}, year = {2008}, date = {2008-03-01}, journal = {OPTICS EXPRESS}, volume = {16}, number = {5}, pages = {3008--3020}, abstract = {We detail the role of single nanometric apertures milled in a gold film to enhance the fluorescence emission of Alexa Fluor 647 molecules. Combining fluorescence correlation spectroscopy and lifetime measurements, we determine the respective contributions of excitation and emission in the observed enhanced fluorescence. We characterize a broad range of nanoaperture diameters from 80 to 310 nm, and highlight the link between the fluorescence enhancement and the local photonic density of states. These results are of great interest to increase the effectiveness of fluorescence-based single molecule detection and to understand the interaction between a quantum emitter and a nanometric metal structure. (C) 2008 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We detail the role of single nanometric apertures milled in a gold film to enhance the fluorescence emission of Alexa Fluor 647 molecules. Combining fluorescence correlation spectroscopy and lifetime measurements, we determine the respective contributions of excitation and emission in the observed enhanced fluorescence. We characterize a broad range of nanoaperture diameters from 80 to 310 nm, and highlight the link between the fluorescence enhancement and the local photonic density of states. These results are of great interest to increase the effectiveness of fluorescence-based single molecule detection and to understand the interaction between a quantum emitter and a nanometric metal structure. (C) 2008 Optical Society of America. |
Baudrion, Anne-Laure ; de Leon-Perez, Fernando ; Mahboub, Oussama ; Hohenau, Andreas ; Ditlbacher, Harald ; Garcia-Vidal, Francisco J; Dintinger, Jose ; Ebbesen, Thomas W; Martin-Moreno, Luis ; Krenn, Joachim R Coupling efficiency of light to surface plasmon polariton for single subwavelength holes in a gold film Article de journal Dans: OPTICS EXPRESS, 16 (5), p. 3420–3429, 2008, ISSN: 1094-4087. @article{baudrion_coupling_2008, title = {Coupling efficiency of light to surface plasmon polariton for single subwavelength holes in a gold film}, author = {Baudrion, Anne-Laure and de Leon-Perez, Fernando and Mahboub, Oussama and Hohenau, Andreas and Ditlbacher, Harald and Garcia-Vidal, Francisco J. and Dintinger, Jose and Ebbesen, Thomas W. and Martin-Moreno, Luis and Krenn, Joachim R.}, doi = {10.1364/OE.16.003420}, issn = {1094-4087}, year = {2008}, date = {2008-03-01}, journal = {OPTICS EXPRESS}, volume = {16}, number = {5}, pages = {3420--3429}, abstract = {sThe excitation of surface plasmon polaritons (SPP) by focusing a laser beam on single subwavelength holes opened in a thin gold film is studied both experimentally and theoretically. By means of leakage radiation microscopy, quantitative measurements of the light-SPP coupling efficiency are performed for holes with different sizes and shapes. The system is studied theoretically by using a modal expansion method to calculate the fraction of the incident energy which is scattered by the hole into a surface plasmon. We demonstrate that a single subwavelength hole can be used to generate SPP with an efficiency up to 28%. (C) 2008 Optical Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } sThe excitation of surface plasmon polaritons (SPP) by focusing a laser beam on single subwavelength holes opened in a thin gold film is studied both experimentally and theoretically. By means of leakage radiation microscopy, quantitative measurements of the light-SPP coupling efficiency are performed for holes with different sizes and shapes. The system is studied theoretically by using a modal expansion method to calculate the fraction of the incident energy which is scattered by the hole into a surface plasmon. We demonstrate that a single subwavelength hole can be used to generate SPP with an efficiency up to 28%. (C) 2008 Optical Society of America. |
Laux, Eric ; Genet, Cyriaque ; Skauli, Torbjorn ; Ebbesen, Thomas W Plasmonic photon sorters for spectral and polarimetric imaging Article de journal Dans: NATURE PHOTONICS, 2 (3), p. 161–164, 2008, ISSN: 1749-4885. @article{laux_plasmonic_2008, title = {Plasmonic photon sorters for spectral and polarimetric imaging}, author = {Laux, Eric and Genet, Cyriaque and Skauli, Torbjorn and Ebbesen, Thomas W.}, doi = {10.1038/nphoton.2008.1}, issn = {1749-4885}, year = {2008}, date = {2008-03-01}, journal = {NATURE PHOTONICS}, volume = {2}, number = {3}, pages = {161--164}, abstract = {Colour cameras mimic the human eye and record only a small part of the information contained in the incoming light. Modern image sensing techniques, which subdivide the light spectrally or record information about the polarization of the incoming light, can extract much more information for applications ranging from biological studies to remote sensing(1-5). Spectral imaging techniques(6) typically rely on filters or interferometers combined with scanning or subsampling to record a spectral image `cube' ( which has wavelength as a third dimension). This leads to inefficient use of the incoming light and/ or long recording times. Here, we show that surface plasmons enable direct recording of spectral image cubes in a single exposure. By texturing metal surfaces at the nanometre scale, incoming light is converted to surface plasmons and can then be separated according to wavelength and polarization, before being recoupled to light through subwavelength apertures that illuminate individual photodetector elements. This photon- sorting capability provides a new approach for spectral and polarimetric imaging with extremely compact device archictures.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Colour cameras mimic the human eye and record only a small part of the information contained in the incoming light. Modern image sensing techniques, which subdivide the light spectrally or record information about the polarization of the incoming light, can extract much more information for applications ranging from biological studies to remote sensing(1-5). Spectral imaging techniques(6) typically rely on filters or interferometers combined with scanning or subsampling to record a spectral image `cube' ( which has wavelength as a third dimension). This leads to inefficient use of the incoming light and/ or long recording times. Here, we show that surface plasmons enable direct recording of spectral image cubes in a single exposure. By texturing metal surfaces at the nanometre scale, incoming light is converted to surface plasmons and can then be separated according to wavelength and polarization, before being recoupled to light through subwavelength apertures that illuminate individual photodetector elements. This photon- sorting capability provides a new approach for spectral and polarimetric imaging with extremely compact device archictures. |
Liscio, Andrea ; Palermo, Vincenzo ; Samori, Paolo Probing local surface potential of quasi-one-dimensional systems: A KPFM study of P3HT nanofibers Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (6), p. 907–914, 2008, ISSN: 1616-301X. @article{liscio_probing_2008, title = {Probing local surface potential of quasi-one-dimensional systems: A KPFM study of P3HT nanofibers}, author = {Liscio, Andrea and Palermo, Vincenzo and Samori, Paolo}, doi = {10.1002/adfm.200701142}, issn = {1616-301X}, year = {2008}, date = {2008-03-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {18}, number = {6}, pages = {907--914}, abstract = {A new model for the quantitative analysis of Kelvin Probe Force Microscopy (KPFM) measurements of quasi-one-dimensional systems is presented. It is applied to precisely determine the local surface potential (SP) of semiconducting nanofibers of poly (3-hexylthiophene) (P3HT) self-assembled on various flat substrates. To study these quasi-one dimensional objects, the effective area has been defined. This parameter represents the area of sample surface interacting with the KPFM probe and it plays a crucial role in the estimation of the SP of nanofibers having a cross-section comparable to the apical diameter of the tip, i.e., 20 nm. Therefore our model makes it possible to gain quantitative insight into nano-systems smaller than 20 nm. In particular, through the estimation of the effective area, it allows to determine the local surface potential of single nanofiber as well as to simulate the KPFM image of nano-assemblies adsorbed both on electrically insulating and conducting substrates. This versatile model represents a useful tool to study with a high degree of precision the surface potential characteristics of nanowires paving the way towards their use as building blocks for the fabrication of electronic nanodevices with improved performance.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new model for the quantitative analysis of Kelvin Probe Force Microscopy (KPFM) measurements of quasi-one-dimensional systems is presented. It is applied to precisely determine the local surface potential (SP) of semiconducting nanofibers of poly (3-hexylthiophene) (P3HT) self-assembled on various flat substrates. To study these quasi-one dimensional objects, the effective area has been defined. This parameter represents the area of sample surface interacting with the KPFM probe and it plays a crucial role in the estimation of the SP of nanofibers having a cross-section comparable to the apical diameter of the tip, i.e., 20 nm. Therefore our model makes it possible to gain quantitative insight into nano-systems smaller than 20 nm. In particular, through the estimation of the effective area, it allows to determine the local surface potential of single nanofiber as well as to simulate the KPFM image of nano-assemblies adsorbed both on electrically insulating and conducting substrates. This versatile model represents a useful tool to study with a high degree of precision the surface potential characteristics of nanowires paving the way towards their use as building blocks for the fabrication of electronic nanodevices with improved performance. |
Barboiu, Mihail ; Lehn, Jean-Marie Helical diastereomerism in self-organization of molecular strands Article de journal Dans: REVISTA DE CHIMIE, 59 (3), p. 255–259, 2008, ISSN: 0034-7752. @article{barboiu_helical_2008, title = {Helical diastereomerism in self-organization of molecular strands}, author = {Barboiu, Mihail and Lehn, Jean-Marie}, issn = {0034-7752}, year = {2008}, date = {2008-03-01}, journal = {REVISTA DE CHIMIE}, volume = {59}, number = {3}, pages = {255--259}, abstract = {The polyheterocyclic molecule 2 reported in this paper is a helically-wrapped molecular strand presenting two helical substrands of same helicity separated in space thus forming P-P and M-M helical enantiomers. It represents the case of a molecule presenting two chiral centers of helical type. The dimerization process of the compound described in this paper appears to give rise to heterodimeric and homodimeric species. At high and room temperature the formation of dimeric species is accompanied by folding-unfolding interconversion of single molecular strands. Sliding of the monomers along one another without dissociation at low temperature allows each of two helical partners to associate in dimers stabilized by pronounced pi-pi stacking interactions between the internal heterocycles of the strands.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The polyheterocyclic molecule 2 reported in this paper is a helically-wrapped molecular strand presenting two helical substrands of same helicity separated in space thus forming P-P and M-M helical enantiomers. It represents the case of a molecule presenting two chiral centers of helical type. The dimerization process of the compound described in this paper appears to give rise to heterodimeric and homodimeric species. At high and room temperature the formation of dimeric species is accompanied by folding-unfolding interconversion of single molecular strands. Sliding of the monomers along one another without dissociation at low temperature allows each of two helical partners to associate in dimers stabilized by pronounced pi-pi stacking interactions between the internal heterocycles of the strands. |
Gerard, Davy ; Wenger, Jerome ; Bonod, Nicolas ; Popov, Evgeni ; Rigneault, Herve ; Mahdavi, Farhad ; Blair, Steve ; Dintinger, Jose ; Ebbesen, Thomas W Nanoaperture-enhanced fluorescence: Towards higher detection rates with plasmonic metals Article de journal Dans: PHYSICAL REVIEW B, 77 (4), 2008, ISSN: 1098-0121. @article{gerard_nanoaperture-enhanced_2008, title = {Nanoaperture-enhanced fluorescence: Towards higher detection rates with plasmonic metals}, author = {Gerard, Davy and Wenger, Jerome and Bonod, Nicolas and Popov, Evgeni and Rigneault, Herve and Mahdavi, Farhad and Blair, Steve and Dintinger, Jose and Ebbesen, Thomas W.}, doi = {10.1103/PhysRevB.77.045413}, issn = {1098-0121}, year = {2008}, date = {2008-01-01}, journal = {PHYSICAL REVIEW B}, volume = {77}, number = {4}, abstract = {A bare nanometric aperture milled in a metallic film forms a simple nanophotonic device that can strongly enhance the optical properties of nearby emitters such as fluorescent molecules. In this paper, we experimentally and numerically compare the properties of circular apertures milled in gold and aluminum, and discuss the influence of a noble metal holding plasmonic resonances in the visible range such as gold. We report that nanometric apertures milled in gold exhibit significantly higher fluorescence enhancement factors than apertures in aluminum. We relate this effect to a larger enhancement of the excitation intensity and radiative rate for an aperture milled in gold. A spectrally resolved analysis of the fluorescence emission from apertures is also presented. Comparison with numerical simulations shows that the enhancement factor is maximum when the photonic density of modes is maximum. Altogether, these results provide crucial knowledge for the design of nanoapertures towards high-efficiency single-molecule analysis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A bare nanometric aperture milled in a metallic film forms a simple nanophotonic device that can strongly enhance the optical properties of nearby emitters such as fluorescent molecules. In this paper, we experimentally and numerically compare the properties of circular apertures milled in gold and aluminum, and discuss the influence of a noble metal holding plasmonic resonances in the visible range such as gold. We report that nanometric apertures milled in gold exhibit significantly higher fluorescence enhancement factors than apertures in aluminum. We relate this effect to a larger enhancement of the excitation intensity and radiative rate for an aperture milled in gold. A spectrally resolved analysis of the fluorescence emission from apertures is also presented. Comparison with numerical simulations shows that the enhancement factor is maximum when the photonic density of modes is maximum. Altogether, these results provide crucial knowledge for the design of nanoapertures towards high-efficiency single-molecule analysis. |
Volkov, V S; Bozhevolnyi, S I; Devaux, E; Laluet, J -Y; Ebbesen, T W Nanophotonic components utilizing channel plasmon polaritons Inproceedings Dans: {Kawata, S; Shalaev, VM ; Tsai, DP} (Ed.): PLASMONICS: NANOIMAGING, NANOFABRICATION, AND THEIR APPLICATIONS IV, SPIE, 2008, ISBN: 978-0-8194-7253-3. @inproceedings{volkov_nanophotonic_2008, title = {Nanophotonic components utilizing channel plasmon polaritons}, author = {Volkov, V. S. and Bozhevolnyi, S. I. and Devaux, E. and Laluet, J. -Y. and Ebbesen, T. W.}, editor = {{Kawata, S and Shalaev, VM and Tsai, DP}}, doi = {10.1117/12.794781}, isbn = {978-0-8194-7253-3}, year = {2008}, date = {2008-01-01}, booktitle = {PLASMONICS: NANOIMAGING, NANOFABRICATION, AND THEIR APPLICATIONS IV}, volume = {7033}, publisher = {SPIE}, series = {Proceedings of SPIE}, abstract = {Channel plasmon polaritons (CPPs) propagating along the bottom of subwavelength grooves cut into a metal surface were recently shown to exhibit strong confinement combined with low propagation loss, a feature that makes this guiding configuration very promising for the realisation of ultra-compact photonic components. Here, the results of Our investigations of CPP guiding by V-grooves cut into gold are presented, demonstrating efficient large-angle bending and splitting of radiation as well as waveguide-ring resonators and Bragg grating filters.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Channel plasmon polaritons (CPPs) propagating along the bottom of subwavelength grooves cut into a metal surface were recently shown to exhibit strong confinement combined with low propagation loss, a feature that makes this guiding configuration very promising for the realisation of ultra-compact photonic components. Here, the results of Our investigations of CPP guiding by V-grooves cut into gold are presented, demonstrating efficient large-angle bending and splitting of radiation as well as waveguide-ring resonators and Bragg grating filters. |
Pu, Jingzhi ; Karplus, Martin How subunit coupling produces the gamma-subunit rotary motion in F-1-ATPase Article de journal Dans: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (4), p. 1192–1197, 2008, ISSN: 0027-8424. @article{pu_how_2008, title = {How subunit coupling produces the gamma-subunit rotary motion in F-1-ATPase}, author = {Pu, Jingzhi and Karplus, Martin}, doi = {10.1073/pnas.0708746105}, issn = {0027-8424}, year = {2008}, date = {2008-01-01}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {105}, number = {4}, pages = {1192--1197}, abstract = {F0F1-ATP synthase manufactures the energy “currency,” ATP, of living cells. The soluble F, portion, called F-1-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level of detail how the conformational changes of the catalytic beta-subunits act on the gamma-subunit through repulsive van der Waals interactions to generate a torque that drives unidirectional rotation, as observed experimentally. The simulations suggest that the calculated 85 degrees substep rotation is driven primarily by ATP binding and that the subsequent 35 degrees substep rotation is produced by product release from one beta-subunit and a concomitant binding pocket expansion of another beta-subunit. The results of the simulation agree with single-molecule experiments [see, for example, Adachi K, et al. (2007) Cell 130:3093211 and support a tri-site rotary mechanism for F-1-ATPase under physiological condition.}, keywords = {}, pubstate = {published}, tppubtype = {article} } F0F1-ATP synthase manufactures the energy “currency,” ATP, of living cells. The soluble F, portion, called F-1-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level of detail how the conformational changes of the catalytic beta-subunits act on the gamma-subunit through repulsive van der Waals interactions to generate a torque that drives unidirectional rotation, as observed experimentally. The simulations suggest that the calculated 85 degrees substep rotation is driven primarily by ATP binding and that the subsequent 35 degrees substep rotation is produced by product release from one beta-subunit and a concomitant binding pocket expansion of another beta-subunit. The results of the simulation agree with single-molecule experiments [see, for example, Adachi K, et al. (2007) Cell 130:3093211 and support a tri-site rotary mechanism for F-1-ATPase under physiological condition. |
Chekmarev, Sergei F; Palyanov, Andrey Yu. ; Karplus, Martin Hydrodynamic description of protein folding Article de journal Dans: PHYSICAL REVIEW LETTERS, 100 (1), 2008, ISSN: 0031-9007. @article{chekmarev_hydrodynamic_2008, title = {Hydrodynamic description of protein folding}, author = {Chekmarev, Sergei F. and Palyanov, Andrey Yu. and Karplus, Martin}, doi = {10.1103/PhysRevLett.100.018107}, issn = {0031-9007}, year = {2008}, date = {2008-01-01}, journal = {PHYSICAL REVIEW LETTERS}, volume = {100}, number = {1}, abstract = {A hydrodynamic description of protein folding is proposed and illustrated with a lattice protein model, which has a free energy surface (FES) typical of proteins with two-state folding kinetics. The flows from the unfolded to the native state are concentrated in a limited region of the FES. The rest is occupied by a flow “vortex”, which does not lead to the native state. In contrast with intermediates that are associated with local minima, the vortex is not visible on the FES. The hydrodynamic interpretation thus provides new insights into the mechanism of protein folding and can be a useful complement to standard analyses.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A hydrodynamic description of protein folding is proposed and illustrated with a lattice protein model, which has a free energy surface (FES) typical of proteins with two-state folding kinetics. The flows from the unfolded to the native state are concentrated in a limited region of the FES. The rest is occupied by a flow “vortex”, which does not lead to the native state. In contrast with intermediates that are associated with local minima, the vortex is not visible on the FES. The hydrodynamic interpretation thus provides new insights into the mechanism of protein folding and can be a useful complement to standard analyses. |
Hwang, Wonmuk ; Lang, Matthew J; Karplus, Martin Force generation in kinesin hinges on cover-neck bundle formation Article de journal Dans: STRUCTURE, 16 (1), p. 62–71, 2008, ISSN: 0969-2126. @article{hwang_force_2008, title = {Force generation in kinesin hinges on cover-neck bundle formation}, author = {Hwang, Wonmuk and Lang, Matthew J. and Karplus, Martin}, doi = {10.1016/j.str.2007.11.008}, issn = {0969-2126}, year = {2008}, date = {2008-01-01}, journal = {STRUCTURE}, volume = {16}, number = {1}, pages = {62--71}, abstract = {In kinesin motors, a fundamental question concerns the mechanism by which ATP binding generates the force required for walking. Analysis of available structures combined with molecular dynamics simulations demonstrates that the conformational change of the neck linker involves the nine-residue-long N-terminal region, the cover strand, as an element that is essential for force generation. Upon ATP binding, it forms a beta sheet with the neck linker, the cover-neck bundle, which induces the forward motion of the neck linker, followed by a latch-type binding to the motor head. The estimated stall force and anisotropic response to external loads calculated from the model agree with force-clamp measurements. The proposed mechanism for force generation by the cover-neck bundle formation appears to apply to several kinesin families. It also elucidates the design principle of kinesin as the smallest known processive motor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In kinesin motors, a fundamental question concerns the mechanism by which ATP binding generates the force required for walking. Analysis of available structures combined with molecular dynamics simulations demonstrates that the conformational change of the neck linker involves the nine-residue-long N-terminal region, the cover strand, as an element that is essential for force generation. Upon ATP binding, it forms a beta sheet with the neck linker, the cover-neck bundle, which induces the forward motion of the neck linker, followed by a latch-type binding to the motor head. The estimated stall force and anisotropic response to external loads calculated from the model agree with force-clamp measurements. The proposed mechanism for force generation by the cover-neck bundle formation appears to apply to several kinesin families. It also elucidates the design principle of kinesin as the smallest known processive motor. |
Liscio, Andrea ; De Luca, Giovanna ; Nolde, Fabian ; Palermo, Vincenzo ; Muellen, Klaus ; Samori, Paolo Photovoltaic charge generation visualized at the nanoscale: A proof of principle Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (3), p. 780+, 2008, ISSN: 0002-7863. @article{liscio_photovoltaic_2008, title = {Photovoltaic charge generation visualized at the nanoscale: A proof of principle}, author = {Liscio, Andrea and De Luca, Giovanna and Nolde, Fabian and Palermo, Vincenzo and Muellen, Klaus and Samori, Paolo}, doi = {10.1021/ja075291r}, issn = {0002-7863}, year = {2008}, date = {2008-01-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, number = {3}, pages = {780+}, abstract = {We report for the first time a nanoscale resolved proof of principle of the photovoltaic activity in phase-segregated electron acceptor-donor blend architectures as obtained by Kelvin probe force microscopy. The explored length scale is truly important for organic solar cells since it is comparable to the mean exciton diffusion length. We chose a blend of regioregular poly(3-hexylthiophene) (P3HT) and N,N-bis(1-ethylpropyl)-3,4:9,10- perylenebisdicarboximide) (PDI) as model systems, acting as electron donor and electron. acceptor, respectively. In this work, we demonstrate that the same type of molecular assemblies, obtained from a given electron-accepting material on the same sample, shows different surface potential changes upon white-light illumination when in physical contact with the donor materials or isolated from it. Although excitons are generated by light absorption in all the PDI clusters, we unambiguously proved that only the ones which are in physical contact with P3HT exhibit an appreciable charge transfer because of the existence of a complementary electron donor phase. Such a direct observation is novel and of general applicability and can also be extended to other bicomponent materials for plastic photovoltaics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report for the first time a nanoscale resolved proof of principle of the photovoltaic activity in phase-segregated electron acceptor-donor blend architectures as obtained by Kelvin probe force microscopy. The explored length scale is truly important for organic solar cells since it is comparable to the mean exciton diffusion length. We chose a blend of regioregular poly(3-hexylthiophene) (P3HT) and N,N-bis(1-ethylpropyl)-3,4:9,10- perylenebisdicarboximide) (PDI) as model systems, acting as electron donor and electron. acceptor, respectively. In this work, we demonstrate that the same type of molecular assemblies, obtained from a given electron-accepting material on the same sample, shows different surface potential changes upon white-light illumination when in physical contact with the donor materials or isolated from it. Although excitons are generated by light absorption in all the PDI clusters, we unambiguously proved that only the ones which are in physical contact with P3HT exhibit an appreciable charge transfer because of the existence of a complementary electron donor phase. Such a direct observation is novel and of general applicability and can also be extended to other bicomponent materials for plastic photovoltaics. |
Pace, Giuseppina ; Petitjean, Anne ; Lalloz-Vogel, Marie-Noelle ; Harrowfield, Jack ; Lehn, Jean-Marie ; Samori, Paolo Subnanometer-resolved patterning of bicomponent self-assembled monolayers on Au(111) Article de journal Dans: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47 (13), p. 2484–2488, 2008, ISSN: 1433-7851. @article{pace_subnanometer-resolved_2008, title = {Subnanometer-resolved patterning of bicomponent self-assembled monolayers on Au(111)}, author = {Pace, Giuseppina and Petitjean, Anne and Lalloz-Vogel, Marie-Noelle and Harrowfield, Jack and Lehn, Jean-Marie and Samori, Paolo}, doi = {10.1002/anie.200704731}, issn = {1433-7851}, year = {2008}, date = {2008-01-01}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {47}, number = {13}, pages = {2484--2488}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ferri, Violetta ; Elbing, Mark ; Pace, Giuseppina ; Dickey, Michael D; Zharnikov, Michael ; Samori, Paolo ; Mayor, Marcel ; Rampi, Maria Anita Light-powered electrical switch based on cargo-lifting azobenzene monolayers Article de journal Dans: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47 (18), p. 3407–3409, 2008, ISSN: 1433-7851. @article{ferri_light-powered_2008, title = {Light-powered electrical switch based on cargo-lifting azobenzene monolayers}, author = {Ferri, Violetta and Elbing, Mark and Pace, Giuseppina and Dickey, Michael D. and Zharnikov, Michael and Samori, Paolo and Mayor, Marcel and Rampi, Maria Anita}, doi = {10.1002/anie.200705339}, issn = {1433-7851}, year = {2008}, date = {2008-01-01}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {47}, number = {18}, pages = {3407--3409}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Publications (FR)
2008 |
Interrogation, Recognition, and Repair of Damaged Bases in DNA Article de journal Dans: CHEMICAL RESEARCH IN TOXICOLOGY, 21 (12), p. 2433, 2008, ISSN: 0893-228X. |
Electronic Transport Properties or Ensembles of Perylene-Substituted Poly-isocyanopeptide Arrays Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (24), p. 3947–3955, 2008, ISSN: 1616-301X. |
Luminescence properties and redox behavior of Ru(II) molecular racks Article de journal Dans: COORDINATION CHEMISTRY REVIEWS, 252 (23-24, SI), p. 2480–2492, 2008, ISSN: 0010-8545. |
Resorcylic acid lactones: A pluripotent scaffold with therapeutic potential Article de journal Dans: COMPTES RENDUS CHIMIE, 11 (11-12), p. 1306–1317, 2008, ISSN: 1631-0748. |
Large and flat graphene flakes produced by epoxy bonding and reverse exfoliation of highly oriented pyrolytic graphite Article de journal Dans: NANOTECHNOLOGY, 19 (45), 2008, ISSN: 0957-4484. |
Tip-Sample Interactions in Kelvin Probe Force Microscopy: Quantitative Measurement of the Local Surface Potential Article de journal Dans: JOURNAL OF PHYSICAL CHEMISTRY C, 112 (44), p. 17368–17377, 2008, ISSN: 1932-7447. |
The Relationship between Nanoscale Architecture and Function in Photovoltaic Multichromophoric Arrays as Visualized by Kelvin Probe Force Microscopy Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (44), p. 14605–14614, 2008, ISSN: 0002-7863. |
Generation of surface plasmons at single subwavelength slits: from slit to ridge plasmon Article de journal Dans: NEW JOURNAL OF PHYSICS, 10 , 2008, ISSN: 1367-2630. |
Propagation oscillations in the near-field response of traveling surface waves launched by metallic nanoapertures Article de journal Dans: APPLIED PHYSICS B-LASERS AND OPTICS, 93 (1, SI), p. 171–176, 2008, ISSN: 0946-2171. |
Single Component Self-Assembled Monolayers of Aromatic Azo-Biphenyl: Influence of the Packing Tightness on the SAM Structure and Light-Induced Molecular Movements Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (19), p. 2972–2983, 2008, ISSN: 1616-301X. |
Diffusive reaction dynamics on invariant free energy profiles Article de journal Dans: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (37), p. 13841–13846, 2008, ISSN: 0027-8424. |
Single-molecule transport in three-terminal devices Article de journal Dans: JOURNAL OF PHYSICS-CONDENSED MATTER, 20 (37), 2008, ISSN: 0953-8984. |
Brewster angle microscopy and PMIRRAS study of DNA interactions with BGTC, a cationic lipid used for gene transfer Article de journal Dans: LANGMUIR, 24 (17), p. 9598–9606, 2008, ISSN: 0743-7463. |
Coordinative, conformational and motional behaviour of triazine-based ligand strands on binding of Pb(II) cations Article de journal Dans: TETRAHEDRON, 64 (36), p. 8402–8410, 2008, ISSN: 0040-4020. |
Synthesis of new copper(I)-complexed rotaxanes via click chemistry Article de journal Dans: TETRAHEDRON, 64 (36), p. 8496–8503, 2008, ISSN: 0040-4020. |
Optical chirality without optical activity: How surface plasmons give a twist to light Article de journal Dans: OPTICS EXPRESS, 16 (17), p. 12559–12570, 2008, ISSN: 1094-4087. |
The human cytomegalovirus UL44 C clamp wraps around DNA Article de journal Dans: STRUCTURE, 16 (8), p. 1214–1225, 2008, ISSN: 0969-2126. |
Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements Article de journal Dans: PLOS COMPUTATIONAL BIOLOGY, 4 (8), 2008, ISSN: 1553-7358. |
Allostery and cooperativity revisited Article de journal Dans: PROTEIN SCIENCE, 17 (8), p. 1295–1307, 2008, ISSN: 0961-8368. |
Dynamic polymer membranes displaying tunable transport properties on constitutional exchange Article de journal Dans: JOURNAL OF MEMBRANE SCIENCE, 321 (1), p. 8–14, 2008, ISSN: 0376-7388. |
Cyclic [2]pseudorotaxane tetramers consisting of two rigid rods threaded through two bis-macrocycles: Copper(I)-templated synthesis and X-ray structure studies Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (33), p. 11013–11022, 2008, ISSN: 0002-7863. |
Miniature plasmonic wave plates Article de journal Dans: PHYSICAL REVIEW LETTERS, 101 (4), 2008, ISSN: 0031-9007. |
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise Article de journal Dans: JOURNAL OF CHEMICAL PHYSICS, 129 (2), 2008, ISSN: 0021-9606. |
Azobenzenes as light-controlled molecular electronic switches in nanoscale metal-molecule-metal junctions Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (29), p. 9192+, 2008, ISSN: 0002-7863. |
Iridium terpyridine complexes as functional assembling units in arrays for the conversion of light energy Article de journal Dans: ACCOUNTS OF CHEMICAL RESEARCH, 41 (7), p. 857–871, 2008, ISSN: 0001-4842. |
Efficiency and finite size effects in enhanced transmission through subwavelength apertures Article de journal Dans: OPTICS EXPRESS, 16 (13), p. 9571–9579, 2008, ISSN: 1094-4087. |
Guanosine-based hydrogen-bonded scaffolds: Controlling the assembly of oligothiophenes Article de journal Dans: ADVANCED MATERIALS, 20 (12), p. 2433+, 2008, ISSN: 0935-9648. |
Quaterpyridine ligands forming helical complexes of mono- and dinuclear (helicate) forms Article de journal Dans: EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, (18), p. 2910–2920, 2008, ISSN: 1434-1948. |
Expanding the scope and orthogonality of PNA synthesis Article de journal Dans: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (18), p. 3141–3148, 2008, ISSN: 1434-193X. |
Surface-plasmon circuitry Article de journal Dans: PHYSICS TODAY, 61 (5), p. 44–50, 2008, ISSN: 0031-9228. |
The elastic properties of the structurally characterized myosin II s2 subdomain: A molecular dynamics and normal mode analysis Article de journal Dans: BIOPHYSICAL JOURNAL, 94 (10), p. 3779–3789, 2008, ISSN: 0006-3495. |
A differential fluctuation theorem Article de journal Dans: JOURNAL OF PHYSICAL CHEMISTRY B, 112 (19), p. 6168–6174, 2008, ISSN: 1520-6106. |
Glycodynamers: Dynamic analogs of arabinofuranoside oligosaccharides Article de journal Dans: BIOPOLYMERS, 89 (5), p. 486–496, 2008, ISSN: 0006-3525. |
Naphthyridine-based helical foldamers and macrocycles: Synthesis, cation binding, and supramolecular assemblies Article de journal Dans: JOURNAL OF ORGANIC CHEMISTRY, 73 (7), p. 2481–2495, 2008, ISSN: 0022-3263. |
A [3]rotaxane with two porphyrinic plates acting as an adaptable receptor Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (14), p. 4592+, 2008, ISSN: 0002-7863. |
PRES 17-Synthesis of a tetra-substituted porphyrin for use in a [6]rotaxane reminiscent of a press Article de journal Dans: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 235 , 2008, ISSN: 0065-7727. |
Modulation of surface plasmon coupling-in by one-dimensional surface corrugation Article de journal Dans: NEW JOURNAL OF PHYSICS, 10 , 2008, ISSN: 1367-2630. |
Emission and excitation contributions to enhanced single molecule fluorescence by gold nanometric apertures Article de journal Dans: OPTICS EXPRESS, 16 (5), p. 3008–3020, 2008, ISSN: 1094-4087. |
Coupling efficiency of light to surface plasmon polariton for single subwavelength holes in a gold film Article de journal Dans: OPTICS EXPRESS, 16 (5), p. 3420–3429, 2008, ISSN: 1094-4087. |
Plasmonic photon sorters for spectral and polarimetric imaging Article de journal Dans: NATURE PHOTONICS, 2 (3), p. 161–164, 2008, ISSN: 1749-4885. |
Probing local surface potential of quasi-one-dimensional systems: A KPFM study of P3HT nanofibers Article de journal Dans: ADVANCED FUNCTIONAL MATERIALS, 18 (6), p. 907–914, 2008, ISSN: 1616-301X. |
Helical diastereomerism in self-organization of molecular strands Article de journal Dans: REVISTA DE CHIMIE, 59 (3), p. 255–259, 2008, ISSN: 0034-7752. |
Nanoaperture-enhanced fluorescence: Towards higher detection rates with plasmonic metals Article de journal Dans: PHYSICAL REVIEW B, 77 (4), 2008, ISSN: 1098-0121. |
Nanophotonic components utilizing channel plasmon polaritons Inproceedings Dans: {Kawata, S; Shalaev, VM ; Tsai, DP} (Ed.): PLASMONICS: NANOIMAGING, NANOFABRICATION, AND THEIR APPLICATIONS IV, SPIE, 2008, ISBN: 978-0-8194-7253-3. |
How subunit coupling produces the gamma-subunit rotary motion in F-1-ATPase Article de journal Dans: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105 (4), p. 1192–1197, 2008, ISSN: 0027-8424. |
Hydrodynamic description of protein folding Article de journal Dans: PHYSICAL REVIEW LETTERS, 100 (1), 2008, ISSN: 0031-9007. |
Force generation in kinesin hinges on cover-neck bundle formation Article de journal Dans: STRUCTURE, 16 (1), p. 62–71, 2008, ISSN: 0969-2126. |
Photovoltaic charge generation visualized at the nanoscale: A proof of principle Article de journal Dans: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130 (3), p. 780+, 2008, ISSN: 0002-7863. |
Subnanometer-resolved patterning of bicomponent self-assembled monolayers on Au(111) Article de journal Dans: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47 (13), p. 2484–2488, 2008, ISSN: 1433-7851. |
Light-powered electrical switch based on cargo-lifting azobenzene monolayers Article de journal Dans: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47 (18), p. 3407–3409, 2008, ISSN: 1433-7851. |