2011 |
Ovchinnikov, V; Cecchini, M; Vanden-Eijnden, E; Karplus, M A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size Journal Article In: BIOPHYSICAL JOURNAL, 101 (10), pp. 2436–2444, 2011, ISSN: 0006-3495. @article{ovchinnikov_conformational_2011, title = {A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size}, author = {Ovchinnikov, V. and Cecchini, M. and Vanden-Eijnden, E. and Karplus, M.}, doi = {10.1016/j.bpj.2011.09.044}, issn = {0006-3495}, year = {2011}, date = {2011-11-01}, journal = {BIOPHYSICAL JOURNAL}, volume = {101}, number = {10}, pages = {2436--2444}, abstract = {Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter conformation and the conventional conformation found in other myosins. This result suggests that MVI can bind to actin with the converter in either conformation. Models of MVI/MV chimeric dimers show that the variability in the tilting angle of the lever arm that results from the two converter conformations can lead to step-size variations of similar to 12 nm. These variations, in combination with other proposed mechanisms, could explain the experimentally determined step-size variability of similar to 25 nm for wild-type MVI. Mutations to test the findings by experiment are suggested.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter conformation and the conventional conformation found in other myosins. This result suggests that MVI can bind to actin with the converter in either conformation. Models of MVI/MV chimeric dimers show that the variability in the tilting angle of the lever arm that results from the two converter conformations can lead to step-size variations of similar to 12 nm. These variations, in combination with other proposed mechanisms, could explain the experimentally determined step-size variability of similar to 25 nm for wild-type MVI. Mutations to test the findings by experiment are suggested. |
Roethlingshoefer, Manuel ; Gorska, Katarzyna ; Winssinger, Nicolas Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (45), pp. 18110–18113, 2011, ISSN: 0002-7863. @article{roethlingshoefer_nucleic_2011, title = {Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response}, author = {Roethlingshoefer, Manuel and Gorska, Katarzyna and Winssinger, Nicolas}, doi = {10.1021/ja2086504}, issn = {0002-7863}, year = {2011}, date = {2011-11-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {133}, number = {45}, pages = {18110--18113}, abstract = {The photocleavage of a nitrobenzyl-type linker (NPPOC) at 405 nm wavelength was enabled by nucleic acid-templated energy transfer from a sensitizer (thioxanthenone) to the linker. This strategy was used to release profluorescent rhodamine, which facilitated monitoring of the reaction via fluorescence measurement in a nonoverlapping window with the sensitizer/photocleavage reaction. The rate acceleration of the templated reaction was greater than 20-fold over the background reaction. The templated reaction was used in conjunction with strand displacement to design four-component systems that responded to an analyte (DNA). Programming a specific hierarchical relationship among the four components enabled the design of a system that responded first positively and then negatively to increasing levels of an analyte.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The photocleavage of a nitrobenzyl-type linker (NPPOC) at 405 nm wavelength was enabled by nucleic acid-templated energy transfer from a sensitizer (thioxanthenone) to the linker. This strategy was used to release profluorescent rhodamine, which facilitated monitoring of the reaction via fluorescence measurement in a nonoverlapping window with the sensitizer/photocleavage reaction. The rate acceleration of the templated reaction was greater than 20-fold over the background reaction. The templated reaction was used in conjunction with strand displacement to design four-component systems that responded to an analyte (DNA). Programming a specific hierarchical relationship among the four components enabled the design of a system that responded first positively and then negatively to increasing levels of an analyte. |
Sievers, Fabian ; Wilm, Andreas ; Dineen, David ; Gibson, Toby J; Karplus, Kevin ; Li, Weizhong ; Lopez, Rodrigo ; McWilliam, Hamish ; Remmert, Michael ; Soeding, Johannes ; Thompson, Julie D; Higgins, Desmond G Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Journal Article In: MOLECULAR SYSTEMS BIOLOGY, 7 , 2011, ISSN: 1744-4292. @article{sievers_fast_2011, title = {Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega}, author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J. and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and Soeding, Johannes and Thompson, Julie D. and Higgins, Desmond G.}, doi = {10.1038/msb.2011.75}, issn = {1744-4292}, year = {2011}, date = {2011-10-01}, journal = {MOLECULAR SYSTEMS BIOLOGY}, volume = {7}, abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. Molecular Systems Biology 7: 539; published online 11 October 2011; doi:10.1038/msb.2011.75}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. Molecular Systems Biology 7: 539; published online 11 October 2011; doi:10.1038/msb.2011.75 |
Ullah, Ehsan ; Lehn, Jean-Marie Rational enthusiasm Journal Article In: NATURE, 478 (7368), pp. S8–S9, 2011, ISSN: 0028-0836. @article{ullah_rational_2011, title = {Rational enthusiasm}, author = {Ullah, Ehsan and Lehn, Jean-Marie}, doi = {10.1038/478S8a}, issn = {0028-0836}, year = {2011}, date = {2011-10-01}, journal = {NATURE}, volume = {478}, number = {7368}, pages = {S8--S9}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Merle, Patrick ; Evrard, Bertrand ; Petitjean, Anne ; Lehn, Jean-Marie ; Teulade-Fichou, Marie-Paule ; Chautard, Emmanuel ; De Cian, Anne ; Guittat, Lionel ; Tran, Phong Lan Thao ; Mergny, Jean-Louis ; Verrelle, Pierre ; Tchirkov, Andrei Telomere Targeting with a New G4 Ligand Enhances Radiation-Induced Killing of Human Glioblastoma Cells Journal Article In: MOLECULAR CANCER THERAPEUTICS, 10 (10), pp. 1784–1795, 2011, ISSN: 1535-7163. @article{merle_telomere_2011, title = {Telomere Targeting with a New G4 Ligand Enhances Radiation-Induced Killing of Human Glioblastoma Cells}, author = {Merle, Patrick and Evrard, Bertrand and Petitjean, Anne and Lehn, Jean-Marie and Teulade-Fichou, Marie-Paule and Chautard, Emmanuel and De Cian, Anne and Guittat, Lionel and Tran, Phong Lan Thao and Mergny, Jean-Louis and Verrelle, Pierre and Tchirkov, Andrei}, doi = {10.1158/1535-7163.MCT-10-0664}, issn = {1535-7163}, year = {2011}, date = {2011-10-01}, journal = {MOLECULAR CANCER THERAPEUTICS}, volume = {10}, number = {10}, pages = {1784--1795}, abstract = {The aim of this study was to test in vitro the efficacy of TAC, an original G-quadruplex ligand, as a potential radiosensitizing agent for glioblastoma multiforme (GBM). Two human radioresistant telomerase-positive GBM cell lines (SF763 and SF767) were analyzed, with and without TAC treatment, for telomere length, cell proliferation, apoptosis, cell-cycle distribution, gene expression, cytogenetic aberrations, clonogenic survival assay, 53BP1 immunofluorescence staining, and gamma H2AX phosphorylation. We found that low concentrations of TAC (0.5 and 1 mu mol/L) inhibited the proliferation of GBM cells in a concentration-dependent manner after only 1 week of treatment, with minimal effects on cell cycle and apoptosis. TAC treatment had no visible effect on average telomere length but modified expression levels of telomere-related genes (hTERT, TRF1, and TRF2) and induced concentration-dependent DNA damage response and dicentric chromosomes. Survival curves analysis showed that exposure to nontoxic, subapoptotic concentrations of TAC enhanced radiation-induced killing of GBM cells. Analysis of DNA repair after irradiation revealed delayed repair kinetics in GBM cells treated with TAC. Furthermore, the combined treatment (TAC and radiation) significantly increased the frequency of chromosomal aberrations as compared with radiation alone. These findings provide the first evidence that exposure to a G4 ligand radiosensitizes human glioblastoma cells and suggest the prospect of future therapeutic applications. Mol Cancer Ther; 10(10); 1784-95. (C) 2011 AACR.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this study was to test in vitro the efficacy of TAC, an original G-quadruplex ligand, as a potential radiosensitizing agent for glioblastoma multiforme (GBM). Two human radioresistant telomerase-positive GBM cell lines (SF763 and SF767) were analyzed, with and without TAC treatment, for telomere length, cell proliferation, apoptosis, cell-cycle distribution, gene expression, cytogenetic aberrations, clonogenic survival assay, 53BP1 immunofluorescence staining, and gamma H2AX phosphorylation. We found that low concentrations of TAC (0.5 and 1 mu mol/L) inhibited the proliferation of GBM cells in a concentration-dependent manner after only 1 week of treatment, with minimal effects on cell cycle and apoptosis. TAC treatment had no visible effect on average telomere length but modified expression levels of telomere-related genes (hTERT, TRF1, and TRF2) and induced concentration-dependent DNA damage response and dicentric chromosomes. Survival curves analysis showed that exposure to nontoxic, subapoptotic concentrations of TAC enhanced radiation-induced killing of GBM cells. Analysis of DNA repair after irradiation revealed delayed repair kinetics in GBM cells treated with TAC. Furthermore, the combined treatment (TAC and radiation) significantly increased the frequency of chromosomal aberrations as compared with radiation alone. These findings provide the first evidence that exposure to a G4 ligand radiosensitizes human glioblastoma cells and suggest the prospect of future therapeutic applications. Mol Cancer Ther; 10(10); 1784-95. (C) 2011 AACR. |
Dalmonte, M; Zoller, P; Pupillo, G Trimer Liquids and Crystals of Polar Molecules in Coupled Wires Journal Article In: PHYSICAL REVIEW LETTERS, 107 (16), 2011, ISSN: 0031-9007. @article{dalmonte_trimer_2011, title = {Trimer Liquids and Crystals of Polar Molecules in Coupled Wires}, author = {Dalmonte, M. and Zoller, P. and Pupillo, G.}, doi = {10.1103/PhysRevLett.107.163202}, issn = {0031-9007}, year = {2011}, date = {2011-10-01}, journal = {PHYSICAL REVIEW LETTERS}, volume = {107}, number = {16}, abstract = {We investigate pairing and crystalline instabilities of bosonic and fermionic polar molecules confined to a ladder geometry. Combining analytical and numerical techniques, we show that gases of composite molecular dimers as well as trimers can be stabilized as a function of the density difference between the wires. A shallow optical lattice can pin both liquids, realizing crystals of composite bosons and fermions. We show that these exotic quantum phases are robust against conditions of confinement of the molecular gas to harmonic finite-size potentials.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigate pairing and crystalline instabilities of bosonic and fermionic polar molecules confined to a ladder geometry. Combining analytical and numerical techniques, we show that gases of composite molecular dimers as well as trimers can be stabilized as a function of the density difference between the wires. A shallow optical lattice can pin both liquids, realizing crystals of composite bosons and fermions. We show that these exotic quantum phases are robust against conditions of confinement of the molecular gas to harmonic finite-size potentials. |
Beyler, Maryline ; Heitz, Valerie ; Taesch, Julien ; Sauvage, Jean-Pierre Templated synthesis of catenanes incorporating Zn(II) or Rh(III)-complexed porphyrins: the coordination chemistry-only approach Journal Article In: JOURNAL OF PORPHYRINS AND PHTHALOCYANINES, 15 (9-10), pp. 848–857, 2011, ISSN: 1088-4246. @article{beyler_templated_2011, title = {Templated synthesis of catenanes incorporating Zn(II) or Rh(III)-complexed porphyrins: the coordination chemistry-only approach}, author = {Beyler, Maryline and Heitz, Valerie and Taesch, Julien and Sauvage, Jean-Pierre}, doi = {10.1142/S1088424611004002}, issn = {1088-4246}, year = {2011}, date = {2011-10-01}, journal = {JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, volume = {15}, number = {9-10}, pages = {848--857}, abstract = {Porphyrin-containing [2]catenanes were obtained from relatively simple organic precursors thanks to “coordination chemistry-only”. When the central porphyrin metal is Zn2+ the [2] catenanes were assembled in two steps by using Cu(I)-N interactions to assemble acyclic complexes and Zn(II)-N interactions to generate rings. These sophisticated architectures were obtained in excellent yield since the formation of the thermodynamic products is favored over that of kinetic products. This also explains why a perfect fit in terms of distances and angles between the components to assemble leads to highly stable coordination chemistry-assembled species. When a second row metal with an inert coordination sphere, like Rh(III) was chosen as metal centre of the porphyrins, direct metalation of porphyrinic compounds with [Rh(CO)(2)Cl](2) was not met with success when the bidentate chelate used as connector was metal free. A three-step strategy was used for the synthesis of a tetra-rhodiumporphyrin[2]-catenane: (i) copper(I)-driven entwining of two free-base porphyrin-bearing bidentate chelates followed (ii) by insertion of rhodium in the porphyrin nuclei and finally (iii) cyclisation via formation of N-Rh coordination bonds.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Porphyrin-containing [2]catenanes were obtained from relatively simple organic precursors thanks to “coordination chemistry-only”. When the central porphyrin metal is Zn2+ the [2] catenanes were assembled in two steps by using Cu(I)-N interactions to assemble acyclic complexes and Zn(II)-N interactions to generate rings. These sophisticated architectures were obtained in excellent yield since the formation of the thermodynamic products is favored over that of kinetic products. This also explains why a perfect fit in terms of distances and angles between the components to assemble leads to highly stable coordination chemistry-assembled species. When a second row metal with an inert coordination sphere, like Rh(III) was chosen as metal centre of the porphyrins, direct metalation of porphyrinic compounds with [Rh(CO)(2)Cl](2) was not met with success when the bidentate chelate used as connector was metal free. A three-step strategy was used for the synthesis of a tetra-rhodiumporphyrin[2]-catenane: (i) copper(I)-driven entwining of two free-base porphyrin-bearing bidentate chelates followed (ii) by insertion of rhodium in the porphyrin nuclei and finally (iii) cyclisation via formation of N-Rh coordination bonds. |
Baron, Alexandre ; Devaux, Eloise ; Rodier, Jean-Claude ; Hugonin, Jean-Paul ; Rousseau, Emmanuel ; Genet, Cyriaque ; Ebbesen, Thomas W; Lalanne, Philippe Compact Antenna for Efficient and Unidirectional Launching and Decoupling of Surface Plasmons Journal Article In: NANO LETTERS, 11 (10), pp. 4207–4212, 2011, ISSN: 1530-6984. @article{baron_compact_2011, title = {Compact Antenna for Efficient and Unidirectional Launching and Decoupling of Surface Plasmons}, author = {Baron, Alexandre and Devaux, Eloise and Rodier, Jean-Claude and Hugonin, Jean-Paul and Rousseau, Emmanuel and Genet, Cyriaque and Ebbesen, Thomas W. and Lalanne, Philippe}, doi = {10.1021/nl202135w}, issn = {1530-6984}, year = {2011}, date = {2011-10-01}, journal = {NANO LETTERS}, volume = {11}, number = {10}, pages = {4207--4212}, abstract = {Controlling the launching efficiencies and the directionality of surface plasmon polaritons (SPPs) and their decoupling to freely propagating light is a major goal for the development of plasmonic devices and systems. Here, we report on the design and experimental observation of a highly efficient unidirectional surface plasmon launcher composed of eleven subwavelength grooves, each with a distinct depth and width. Our observations show that, under normal illumination by a focused Gaussian beam, unidirectional SPP launching with an efficiency of at least 52% is achieved experimentally with a compact device of total length smaller than 8 mu m. Reciprocally, we report that the same device can efficiently convert SPPs into a highly directive light beam emanating perpendicularly to the sample.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Controlling the launching efficiencies and the directionality of surface plasmon polaritons (SPPs) and their decoupling to freely propagating light is a major goal for the development of plasmonic devices and systems. Here, we report on the design and experimental observation of a highly efficient unidirectional surface plasmon launcher composed of eleven subwavelength grooves, each with a distinct depth and width. Our observations show that, under normal illumination by a focused Gaussian beam, unidirectional SPP launching with an efficiency of at least 52% is achieved experimentally with a compact device of total length smaller than 8 mu m. Reciprocally, we report that the same device can efficiently convert SPPs into a highly directive light beam emanating perpendicularly to the sample. |
Mativetsky, Jeffrey M; Liscio, Andrea ; Treossi, Emanuele ; Orgiu, Emanuele ; Zanelli, Alberto ; Samori, Paolo ; Palermo, Vincenzo Graphene Transistors via in Situ Voltage-Induced Reduction of Graphene-Oxide under Ambient Conditions Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (36), pp. 14320–14326, 2011, ISSN: 0002-7863. @article{mativetsky_graphene_2011, title = {Graphene Transistors via in Situ Voltage-Induced Reduction of Graphene-Oxide under Ambient Conditions}, author = {Mativetsky, Jeffrey M. and Liscio, Andrea and Treossi, Emanuele and Orgiu, Emanuele and Zanelli, Alberto and Samori, Paolo and Palermo, Vincenzo}, doi = {10.1021/ja202371h}, issn = {0002-7863}, year = {2011}, date = {2011-09-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {133}, number = {36}, pages = {14320--14326}, abstract = {Here, we describe a simple approach to fabricate graphene-based field-effect-transistors (FETs), starting from aqueous solutions of graphene-oxide (GO), processed entirely under ambient conditions. The process relies on the site-selective reduction of GO sheets deposited in between or on the surface of micro/nanoelectrodes. The same electrodes are first used for voltage-induced electrochemical GO reduction, and then as the source and drain contacts of FETs, allowing for the straightforward production and characterization of ambipolar graphene devices. With the use of nanoelectrodes, we could reduce different selected areas belonging to one single sheet as well.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Here, we describe a simple approach to fabricate graphene-based field-effect-transistors (FETs), starting from aqueous solutions of graphene-oxide (GO), processed entirely under ambient conditions. The process relies on the site-selective reduction of GO sheets deposited in between or on the surface of micro/nanoelectrodes. The same electrodes are first used for voltage-induced electrochemical GO reduction, and then as the source and drain contacts of FETs, allowing for the straightforward production and characterization of ambipolar graphene devices. With the use of nanoelectrodes, we could reduce different selected areas belonging to one single sheet as well. |
Roy, Nabarun ; Lehn, Jean-Marie Dynamic Covalent Chemistry: A Facile Room-Temperature, Reversible, Diels-Alder Reaction between Anthracene Derivatives and N-Phenyltriazolinedione Journal Article In: CHEMISTRY-AN ASIAN JOURNAL, 6 (9), pp. 2419–2425, 2011, ISSN: 1861-4728. @article{roy_dynamic_2011, title = {Dynamic Covalent Chemistry: A Facile Room-Temperature, Reversible, Diels-Alder Reaction between Anthracene Derivatives and N-Phenyltriazolinedione}, author = {Roy, Nabarun and Lehn, Jean-Marie}, doi = {10.1002/asia.201100244}, issn = {1861-4728}, year = {2011}, date = {2011-09-01}, journal = {CHEMISTRY-AN ASIAN JOURNAL}, volume = {6}, number = {9}, pages = {2419--2425}, abstract = {A series of readily accessible, dynamic Diels-Alder reactions that are reversible at room temperature have been developed between anthracene derivatives as dienes and N-phenyl-1,2,4-triazoline-3,5-dione as the dienophile. The adducts formed undergo reversible component exchange to form dynamic libraries of equilibrating cycloadducts. Furthermore, reversible adduct formation allows temperature-dependent modulation of the fluorescent properties of anthracene components; a feature of potential interest for the design of optodynamic polymeric materials by careful selection and manipulation of these simple dienes and dienophiles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A series of readily accessible, dynamic Diels-Alder reactions that are reversible at room temperature have been developed between anthracene derivatives as dienes and N-phenyl-1,2,4-triazoline-3,5-dione as the dienophile. The adducts formed undergo reversible component exchange to form dynamic libraries of equilibrating cycloadducts. Furthermore, reversible adduct formation allows temperature-dependent modulation of the fluorescent properties of anthracene components; a feature of potential interest for the design of optodynamic polymeric materials by careful selection and manipulation of these simple dienes and dienophiles. |
El Debs, Bachir W; Tschulena, Ulrich ; Griffiths, Andrew D; Merten, Christoph A A competitive co-cultivation assay for cancer drug specificity evaluation Journal Article In: Journal of Biomolecular Screening, 16 (8), pp. 818–824, 2011, ISSN: 1552-454X. @article{el_debs_competitive_2011, title = {A competitive co-cultivation assay for cancer drug specificity evaluation}, author = {El Debs, Bachir W. and Tschulena, Ulrich and Griffiths, Andrew D. and Merten, Christoph A.}, doi = {10.1177/1087057111414898}, issn = {1552-454X}, year = {2011}, date = {2011-09-01}, journal = {Journal of Biomolecular Screening}, volume = {16}, number = {8}, pages = {818--824}, abstract = {The identification of compounds that specifically inhibit or kill cancer cells without affecting cells from healthy tissues is very challenging but very important for reducing the side effects of current cancer therapies. Hence, there is an urgent need for improved assays allowing the selectivity of a given compound to be monitored directly. The authors present an assay system based on the competitive co-cultivation of an excess of cancer cells with a small fraction of noncancer human indicator cells generating a fluorescence signal. In the absence of a specific anticancer compound, the cancer cells outgrow the indicator cells and abolish the fluorescence signal. In contrast, the presence of specific anticancer drugs (such as Tyrphostin-AG1478 or PLX4720) results in the selective growth of the indicator cells, giving rise to a strong fluorescence signal. Furthermore, the authors show that the nonspecific cytotoxic compound sodium azide kills both cancer and noncancer cells, and no fluorescence signal is obtained. Hence, this assay system favors the selection of compounds that specifically target cancer cells and decreases the probability of selecting nonspecific cytotoxic molecules. Z factors of up to 0.85 were obtained, indicating an excellent assay that can be used for high-throughput screening.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The identification of compounds that specifically inhibit or kill cancer cells without affecting cells from healthy tissues is very challenging but very important for reducing the side effects of current cancer therapies. Hence, there is an urgent need for improved assays allowing the selectivity of a given compound to be monitored directly. The authors present an assay system based on the competitive co-cultivation of an excess of cancer cells with a small fraction of noncancer human indicator cells generating a fluorescence signal. In the absence of a specific anticancer compound, the cancer cells outgrow the indicator cells and abolish the fluorescence signal. In contrast, the presence of specific anticancer drugs (such as Tyrphostin-AG1478 or PLX4720) results in the selective growth of the indicator cells, giving rise to a strong fluorescence signal. Furthermore, the authors show that the nonspecific cytotoxic compound sodium azide kills both cancer and noncancer cells, and no fluorescence signal is obtained. Hence, this assay system favors the selection of compounds that specifically target cancer cells and decreases the probability of selecting nonspecific cytotoxic molecules. Z factors of up to 0.85 were obtained, indicating an excellent assay that can be used for high-throughput screening. |
Fylaktakidou, Konstantina C; Duarte, Carolina D; Jogireddy, Rajamalleswaramma ; Koumbis, Alexandros E; Nicolau, Claude ; Lehn, Jean-Marie Polyphosphates and Pyrophosphates of Pentopyranoses and Pentofuranoses as Allosteric Effectors of Human Hemoglobin: Synthesis, Molecular Recognition, and Oxygen Release Journal Article In: CHEMMEDCHEM, 6 (8), pp. 1495–1508, 2011, ISSN: 1860-7179. @article{fylaktakidou_polyphosphates_2011, title = {Polyphosphates and Pyrophosphates of Pentopyranoses and Pentofuranoses as Allosteric Effectors of Human Hemoglobin: Synthesis, Molecular Recognition, and Oxygen Release}, author = {Fylaktakidou, Konstantina C. and Duarte, Carolina D. and Jogireddy, Rajamalleswaramma and Koumbis, Alexandros E. and Nicolau, Claude and Lehn, Jean-Marie}, doi = {10.1002/cmdc.201100110}, issn = {1860-7179}, year = {2011}, date = {2011-08-01}, journal = {CHEMMEDCHEM}, volume = {6}, number = {8}, pages = {1495--1508}, abstract = {Perphosphorylated pentopyranoses and pentofuranoses were synthesized from parent carbohydrates as potential allosteric effectors of hemoglobin (Hb). The construction of seven-and eight-membered cyclic pyrophosphates was also carried out successfully on most of the pentoses. All final compounds were tested for their efficiency on oxygen release from human Hb. Most proved to be efficient allosteric effectors, some of them with an affinity toward Hb and an effect on oxygen release from Hb approaching that of myo-inositol hexakisphosphate, which is one of the most active allosteric effectors of Hb. The efficacy was higher for free phosphates than for pyrophosphates.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Perphosphorylated pentopyranoses and pentofuranoses were synthesized from parent carbohydrates as potential allosteric effectors of hemoglobin (Hb). The construction of seven-and eight-membered cyclic pyrophosphates was also carried out successfully on most of the pentoses. All final compounds were tested for their efficiency on oxygen release from human Hb. Most proved to be efficient allosteric effectors, some of them with an affinity toward Hb and an effect on oxygen release from Hb approaching that of myo-inositol hexakisphosphate, which is one of the most active allosteric effectors of Hb. The efficacy was higher for free phosphates than for pyrophosphates. |
Zheng, Guishan ; Niklasson, Anders M N; Karplus, Martin Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method Journal Article In: JOURNAL OF CHEMICAL PHYSICS, 135 (4), 2011, ISSN: 0021-9606. @article{zheng_lagrangian_2011, title = {Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method}, author = {Zheng, Guishan and Niklasson, Anders M. N. and Karplus, Martin}, doi = {10.1063/1.3605303}, issn = {0021-9606}, year = {2011}, date = {2011-07-01}, journal = {JOURNAL OF CHEMICAL PHYSICS}, volume = {135}, number = {4}, abstract = {An important element determining the time requirements of Born-Oppenheimer molecular dynamics (BOMD) is the convergence rate of the self-consistent solution of Roothaan equations (SCF). We show here that improved convergence and dynamics stability can be achieved by use of a Lagrangian formalism of BOMD with dissipation (DXL-BOMD). In the DXL-BOMD algorithm, an auxiliary electronic variable (e. g., the electron density or Fock matrix) is propagated and a dissipative force is added in the propagation to maintain the stability of the dynamics. Implementation of the approach in the self-consistent charge density functional tight-binding method makes possible simulations that are several hundred picoseconds in lengths, in contrast to earlier DFT-based BOMD calculations, which have been limited to tens of picoseconds or less. The increase in the simulation time results in a more meaningful evaluation of the DXL-BOMD method. A comparison is made of the number of iterations (and time) required for convergence of the SCF with DXL-BOMD and a standard method (starting with a zero charge guess for all atoms at each step), which gives accurate propagation with reasonable SCF convergence criteria. From tests using NVE simulations of C2F4 and 20 neutral amino acid molecules in the gas phase, it is found that DXL-BOMD can improve SCF convergence by up to a factor of two over the standard method. Corresponding results are obtained in simulations of 32 water molecules in a periodic box. Linear response theory is used to analyze the relationship between the energy drift and the correlation of geometry propagation errors. (C) 2011 American Institute of Physics.[doi:10.1063/1.3605303]}, keywords = {}, pubstate = {published}, tppubtype = {article} } An important element determining the time requirements of Born-Oppenheimer molecular dynamics (BOMD) is the convergence rate of the self-consistent solution of Roothaan equations (SCF). We show here that improved convergence and dynamics stability can be achieved by use of a Lagrangian formalism of BOMD with dissipation (DXL-BOMD). In the DXL-BOMD algorithm, an auxiliary electronic variable (e. g., the electron density or Fock matrix) is propagated and a dissipative force is added in the propagation to maintain the stability of the dynamics. Implementation of the approach in the self-consistent charge density functional tight-binding method makes possible simulations that are several hundred picoseconds in lengths, in contrast to earlier DFT-based BOMD calculations, which have been limited to tens of picoseconds or less. The increase in the simulation time results in a more meaningful evaluation of the DXL-BOMD method. A comparison is made of the number of iterations (and time) required for convergence of the SCF with DXL-BOMD and a standard method (starting with a zero charge guess for all atoms at each step), which gives accurate propagation with reasonable SCF convergence criteria. From tests using NVE simulations of C2F4 and 20 neutral amino acid molecules in the gas phase, it is found that DXL-BOMD can improve SCF convergence by up to a factor of two over the standard method. Corresponding results are obtained in simulations of 32 water molecules in a periodic box. Linear response theory is used to analyze the relationship between the energy drift and the correlation of geometry propagation errors. (C) 2011 American Institute of Physics.[doi:10.1063/1.3605303] |
Karplus, Martin Behind the folding funnel diagram Journal Article In: NATURE CHEMICAL BIOLOGY, 7 (7), pp. 401–404, 2011, ISSN: 1552-4450. @article{karplus_behind_2011, title = {Behind the folding funnel diagram}, author = {Karplus, Martin}, doi = {10.1038/nchembio.565}, issn = {1552-4450}, year = {2011}, date = {2011-07-01}, journal = {NATURE CHEMICAL BIOLOGY}, volume = {7}, number = {7}, pages = {401--404}, abstract = {This Commentary clarifies the meaning of the funnel diagram, which has been widely cited in papers on protein folding. To aid in the analysis of the funnel diagram, this Commentary reviews historical approaches to understanding the mechanism of protein folding. The primary role of free energy in protein folding is discussed, and it is pointed out that the increase in the configurational entropy as the native state is approached hinders folding, rather than guiding it. Diagrams are introduced that provide a less ambiguous representation of the factors governing the protein folding reaction than the funnel diagram.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This Commentary clarifies the meaning of the funnel diagram, which has been widely cited in papers on protein folding. To aid in the analysis of the funnel diagram, this Commentary reviews historical approaches to understanding the mechanism of protein folding. The primary role of free energy in protein folding is discussed, and it is pointed out that the increase in the configurational entropy as the native state is approached hinders folding, rather than guiding it. Diagrams are introduced that provide a less ambiguous representation of the factors governing the protein folding reaction than the funnel diagram. |
Folmer-Andersen, Frantz J; Lehn, Jean-Marie Thermoresponsive Dynamers: Thermally Induced, Reversible Chain Elongation of Amphiphilic Poly(acylhydrazones) Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (28), pp. 10966–10973, 2011, ISSN: 0002-7863. @article{folmer-andersen_thermoresponsive_2011, title = {Thermoresponsive Dynamers: Thermally Induced, Reversible Chain Elongation of Amphiphilic Poly(acylhydrazones)}, author = {Folmer-Andersen, J. Frantz and Lehn, Jean-Marie}, doi = {10.1021/ja2035909}, issn = {0002-7863}, year = {2011}, date = {2011-07-01}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {133}, number = {28}, pages = {10966--10973}, abstract = {A nanostructured poly(acylhydrazone), which is reversibly formed in acidic aqueous solution from di(aldehyde) and di(acylhydrazine) monomers with appended hexaglyme groups, was found to display lower critical solution (LCS) behavior. Remarkably, under acidic conditions in which polymerization is reversible, large and reversible molecular weight (M(w)) increases were observed in response to elevated temperatures, both below and above the LCS temperature. No variation in M, was evident under neutral and alkaline conditions, in which the acylhydrazone condensation is essentially irreversible. Results of turbidometry studies, size-exclusion chromatography-multiangle laser light scattering (SEC-MALLS), and transmission electron microscopy (TEM) suggest that heating the polymer below the LCS temperature leads to polymer growth with preservation of the characteristic nanostructured morphology, whereas the onset of the microphase separated state causes a fundamental change in morphology, in which the polymer chains aggregate into larger bundles and fibers. van't Hoff analysis of a small molecule model system indicates that the acylhydrazone condensation is enthalpy driven (Delta H(eq) = -8.2 +/- 0.2 kcal.mol(-1) and Delta S(eq) = -11.1 +/- 0.4 = cal.mol(-1) .K(-1)), which suggests that the observed polymer growth with temperature is not a consequence of the intrinsic thermodynamics of the intermonomer linkage but is likely the result of the thermoresponsive characteristics conferred by the multiple hexaglyme groups. The system described displays double control of the dynamer state by two orthogonal agents, heat and protons (pH). It also represents a prototype for dynamic materials displaying multiple control adaptive behavior.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A nanostructured poly(acylhydrazone), which is reversibly formed in acidic aqueous solution from di(aldehyde) and di(acylhydrazine) monomers with appended hexaglyme groups, was found to display lower critical solution (LCS) behavior. Remarkably, under acidic conditions in which polymerization is reversible, large and reversible molecular weight (M(w)) increases were observed in response to elevated temperatures, both below and above the LCS temperature. No variation in M, was evident under neutral and alkaline conditions, in which the acylhydrazone condensation is essentially irreversible. Results of turbidometry studies, size-exclusion chromatography-multiangle laser light scattering (SEC-MALLS), and transmission electron microscopy (TEM) suggest that heating the polymer below the LCS temperature leads to polymer growth with preservation of the characteristic nanostructured morphology, whereas the onset of the microphase separated state causes a fundamental change in morphology, in which the polymer chains aggregate into larger bundles and fibers. van't Hoff analysis of a small molecule model system indicates that the acylhydrazone condensation is enthalpy driven (Delta H(eq) = -8.2 +/- 0.2 kcal.mol(-1) and Delta S(eq) = -11.1 +/- 0.4 = cal.mol(-1) .K(-1)), which suggests that the observed polymer growth with temperature is not a consequence of the intrinsic thermodynamics of the intermonomer linkage but is likely the result of the thermoresponsive characteristics conferred by the multiple hexaglyme groups. The system described displays double control of the dynamer state by two orthogonal agents, heat and protons (pH). It also represents a prototype for dynamic materials displaying multiple control adaptive behavior. |
Zhong, Qun ; Bhattacharya, Smiti ; Kotsopoulos, Steven ; Olson, Jeff ; Taly, Valérie ; Griffiths, Andrew D; Link, Darren R; Larson, Jonathan W Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR Journal Article In: Lab on a Chip, 11 (13), pp. 2167–2174, 2011, ISSN: 1473-0189. @article{zhong_multiplex_2011, title = {Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR}, author = {Zhong, Qun and Bhattacharya, Smiti and Kotsopoulos, Steven and Olson, Jeff and Taly, Valérie and Griffiths, Andrew D. and Link, Darren R. and Larson, Jonathan W.}, doi = {10.1039/c1lc20126c}, issn = {1473-0189}, year = {2011}, date = {2011-07-01}, journal = {Lab on a Chip}, volume = {11}, number = {13}, pages = {2167--2174}, abstract = {Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (textbackslashtextbackslashtextbackslashtextgreater10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815AtextbackslashtextbackslashtextbackslashtextgreaterG, SMN1). Results of a pilot study with SMA patients are presented.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (textbackslashtextbackslashtextbackslashtextgreater10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815AtextbackslashtextbackslashtextbackslashtextgreaterG, SMN1). Results of a pilot study with SMA patients are presented. |
Pekin, Deniz ; Skhiri, Yousr ; Baret, Jean-Christophe ; Le Corre, Delphine ; Mazutis, Linas ; Salem, Chaouki Ben ; Millot, Florian ; El Harrak, Abdeslam ; Hutchison, Brian J; Larson, Jonathan W; Link, Darren R; Laurent-Puig, Pierre ; Griffiths, Andrew D; Taly, Valérie Quantitative and sensitive detection of rare mutations using droplet-based microfluidics Journal Article In: Lab on a Chip, 11 (13), pp. 2156–2166, 2011, ISSN: 1473-0189. @article{pekin_quantitative_2011, title = {Quantitative and sensitive detection of rare mutations using droplet-based microfluidics}, author = {Pekin, Deniz and Skhiri, Yousr and Baret, Jean-Christophe and Le Corre, Delphine and Mazutis, Linas and Salem, Chaouki Ben and Millot, Florian and El Harrak, Abdeslam and Hutchison, J. Brian and Larson, Jonathan W. and Link, Darren R. and Laurent-Puig, Pierre and Griffiths, Andrew D. and Taly, Valérie}, doi = {10.1039/c1lc20128j}, issn = {1473-0189}, year = {2011}, date = {2011-07-01}, journal = {Lab on a Chip}, volume = {11}, number = {13}, pages = {2156--2166}, abstract = {Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(®) assays and pyrosequencing, while quantitative, cannot detect less than ∼1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(®) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(®) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to screen the six common mutations in KRAS codon 12 in parallel in a single experiment.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(®) assays and pyrosequencing, while quantitative, cannot detect less than ∼1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(®) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(®) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to screen the six common mutations in KRAS codon 12 in parallel in a single experiment. |
Aouani, Heykel ; Mahboub, Oussama ; Devaux, Eloise ; Rigneault, Herve ; Ebbesen, Thomas W; Wenger, Jerome Large molecular fluorescence enhancement by a nanoaperture with plasmonic corrugations Journal Article In: OPTICS EXPRESS, 19 (14), pp. 13056–13062, 2011, ISSN: 1094-4087. @article{aouani_large_2011, title = {Large molecular fluorescence enhancement by a nanoaperture with plasmonic corrugations}, author = {Aouani, Heykel and Mahboub, Oussama and Devaux, Eloise and Rigneault, Herve and Ebbesen, Thomas W. and Wenger, Jerome}, doi = {10.1364/OE.19.013056}, issn = {1094-4087}, year = {2011}, date = {2011-07-01}, journal = {OPTICS EXPRESS}, volume = {19}, number = {14}, pages = {13056--13062}, abstract = {We investigate the influence of circular corrugations surrounding a central nanoaperture to further enhance the fluorescence count rate per emitter and control its emission directionality. Adding a single corrugation already allows to significantly increase the fluorescence signal as compared to a bare nanoaperture. A complete fluorescence characterization quantifies the excitation and emission gains contributing to the fluorescence enhancement process as the number of corrugations is increased. (C) 2011 Optical Society of America}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigate the influence of circular corrugations surrounding a central nanoaperture to further enhance the fluorescence count rate per emitter and control its emission directionality. Adding a single corrugation already allows to significantly increase the fluorescence signal as compared to a bare nanoaperture. A complete fluorescence characterization quantifies the excitation and emission gains contributing to the fluorescence enhancement process as the number of corrugations is increased. (C) 2011 Optical Society of America |
Zenin, Vladimir A; Volkov, Valentyn S; Han, Zhanghua ; Bozhevolnyi, Sergey I; Devaux, Eloisa ; Ebbesen, Thomas W Dispersion of strongly confined channel plasmon polariton modes Journal Article In: JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, 28 (7), pp. 1596–1602, 2011, ISSN: 0740-3224. @article{zenin_dispersion_2011, title = {Dispersion of strongly confined channel plasmon polariton modes}, author = {Zenin, Vladimir A. and Volkov, Valentyn S. and Han, Zhanghua and Bozhevolnyi, Sergey I. and Devaux, Eloisa and Ebbesen, Thomas W.}, doi = {10.1364/JOSAB.28.001596}, issn = {0740-3224}, year = {2011}, date = {2011-07-01}, journal = {JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS}, volume = {28}, number = {7}, pages = {1596--1602}, abstract = {We report on experimental (by use of scanning near-field optical microscopy) and theoretical investigations of strongly confined (similar to lambda/5) channel plasmon polariton (CPP) modes propagating at telecom wavelengths (1425-1630 nm) along V-grooves cut in a gold film. The main CPP characteristics (mode index, width, and propagation length) are determined directly from the experimental near-field images and compared to theoretical results obtained using an analytic description of CPP modes supported by (infinitely deep) V-grooves and finite-element simulations implemented in COMSOL. (c) 2011 Optical Society of America}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report on experimental (by use of scanning near-field optical microscopy) and theoretical investigations of strongly confined (similar to lambda/5) channel plasmon polariton (CPP) modes propagating at telecom wavelengths (1425-1630 nm) along V-grooves cut in a gold film. The main CPP characteristics (mode index, width, and propagation length) are determined directly from the experimental near-field images and compared to theoretical results obtained using an analytic description of CPP modes supported by (infinitely deep) V-grooves and finite-element simulations implemented in COMSOL. (c) 2011 Optical Society of America |
Palma, Carlos-Andres ; Samori, Paolo Blueprinting macromolecular electronics Journal Article In: NATURE CHEMISTRY, 3 (6), pp. 431–436, 2011, ISSN: 1755-4330. @article{palma_blueprinting_2011, title = {Blueprinting macromolecular electronics}, author = {Palma, Carlos-Andres and Samori, Paolo}, doi = {10.1038/NCHEM.1043}, issn = {1755-4330}, year = {2011}, date = {2011-06-01}, journal = {NATURE CHEMISTRY}, volume = {3}, number = {6}, pages = {431--436}, abstract = {Recently, by mastering either top-down or bottom-up approaches, tailor-made macromolecular nano-objects with semiconducting properties have been fabricated. These engineered nanostructures for organic electronics are based on conjugated systems predominantly made up of sp(2)-hybridized carbon, such as graphene nanoribbons. Here, we describe developments in a selection of these nanofabrication techniques, which include graphene carving, stimulus-induced synthesis of conjugated polymers and surface-assisted synthesis. We also assess their potential to reproduce chemically and spatially precise molecular arrangements, that is, molecular blueprints. In a broad context, the engineering of a molecular blueprint represents the fabrication of an integrated all-organic macromolecular electronic circuit. In this Perspective, we suggest chemical routes, as well as convergent on-surface synthesis and microfabrication approaches, for the ultimate goal of bringing the field closer to technology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recently, by mastering either top-down or bottom-up approaches, tailor-made macromolecular nano-objects with semiconducting properties have been fabricated. These engineered nanostructures for organic electronics are based on conjugated systems predominantly made up of sp(2)-hybridized carbon, such as graphene nanoribbons. Here, we describe developments in a selection of these nanofabrication techniques, which include graphene carving, stimulus-induced synthesis of conjugated polymers and surface-assisted synthesis. We also assess their potential to reproduce chemically and spatially precise molecular arrangements, that is, molecular blueprints. In a broad context, the engineering of a molecular blueprint represents the fabrication of an integrated all-organic macromolecular electronic circuit. In this Perspective, we suggest chemical routes, as well as convergent on-surface synthesis and microfabrication approaches, for the ultimate goal of bringing the field closer to technology. |
Luo, Guobin ; Karplus, Martin Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis Journal Article In: JOURNAL OF PHYSICAL CHEMISTRY B, 115 (24), pp. 7991–7995, 2011, ISSN: 1520-6106. @article{luo_determining_2011, title = {Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis}, author = {Luo, Guobin and Karplus, Martin}, doi = {10.1021/jp201998c}, issn = {1520-6106}, year = {2011}, date = {2011-06-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY B}, volume = {115}, number = {24}, pages = {7991--7995}, abstract = {The response of a protein to variation of a specific coordinate can provide insights into the role of the overall architecture in the structural change. Given that the calculated potential of mean force governing the fluctuation of an electron transfer donor-acceptor distance in the NAD(P)H:Flavin oxidoreductase (Fre)/FAD complex was shown to agree with experiment, an analysis of the structural response of the rest of the protein to that distance change was made. Significant displacements are found throughout much of the protein, and the coupling pathway resulting in the structural changes was determined. A covariance analysis based on the quasiharmonic modes of the unperturbed protein was used to provide information concerning how the residue motions are correlated. It is found that, of the three regions identified as moving together in an NMR study, two undergo significant structural changes when the electron donor acceptor distance is varied, and the third does not.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The response of a protein to variation of a specific coordinate can provide insights into the role of the overall architecture in the structural change. Given that the calculated potential of mean force governing the fluctuation of an electron transfer donor-acceptor distance in the NAD(P)H:Flavin oxidoreductase (Fre)/FAD complex was shown to agree with experiment, an analysis of the structural response of the rest of the protein to that distance change was made. Significant displacements are found throughout much of the protein, and the coupling pathway resulting in the structural changes was determined. A covariance analysis based on the quasiharmonic modes of the unperturbed protein was used to provide information concerning how the residue motions are correlated. It is found that, of the three regions identified as moving together in an NMR study, two undergo significant structural changes when the electron donor acceptor distance is varied, and the third does not. |
Beermann, Jonas ; Sondergaard, Thomas ; Novikov, Sergey M; Bozhevolnyi, Sergey I; Devaux, Eloise ; Ebbesen, Thomas W Field enhancement and extraordinary optical transmission by tapered periodic slits in gold films Journal Article In: NEW JOURNAL OF PHYSICS, 13 , 2011, ISSN: 1367-2630. @article{beermann_field_2011, title = {Field enhancement and extraordinary optical transmission by tapered periodic slits in gold films}, author = {Beermann, Jonas and Sondergaard, Thomas and Novikov, Sergey M. and Bozhevolnyi, Sergey I. and Devaux, Eloise and Ebbesen, Thomas W.}, doi = {10.1088/1367-2630/13/6/063029}, issn = {1367-2630}, year = {2011}, date = {2011-06-01}, journal = {NEW JOURNAL OF PHYSICS}, volume = {13}, abstract = {We investigate field enhancements by one-dimensional periodic arrays of tapered slits fabricated to a high quality (nm precision) using focused ion beam milling in a 180 nm-thick gold film. Tapering of periodic slits in metal was recently shown to boost the extraordinary optical transmission (EOT) exhibited by similar, but non-tapered, plasmonic structures. Here, both simulated and experimental reflection spectra, along with high-resolution two-photon luminescence (TPL) scanning optical images and simulated electric field plots of the metal slits, are compared, revealing good correspondence between spectral dependences and field intensity enhancements (FEs) estimated via the local TPL. Experimentally investigated structures had a fixed taper angle alpha = 20.5 degrees for two different widths}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigate field enhancements by one-dimensional periodic arrays of tapered slits fabricated to a high quality (nm precision) using focused ion beam milling in a 180 nm-thick gold film. Tapering of periodic slits in metal was recently shown to boost the extraordinary optical transmission (EOT) exhibited by similar, but non-tapered, plasmonic structures. Here, both simulated and experimental reflection spectra, along with high-resolution two-photon luminescence (TPL) scanning optical images and simulated electric field plots of the metal slits, are compared, revealing good correspondence between spectral dependences and field intensity enhancements (FEs) estimated via the local TPL. Experimentally investigated structures had a fixed taper angle alpha = 20.5 degrees for two different widths |
Aouani, Heykel ; Mahboub, Oussama ; Devaux, Eloise ; Rigneault, Herve ; Ebbesen, Thomas W; Wenger, Jerome Plasmonic Antennas for Directional Sorting of Fluorescence Emission Journal Article In: NANO LETTERS, 11 (6), pp. 2400–2406, 2011, ISSN: 1530-6984. @article{aouani_plasmonic_2011, title = {Plasmonic Antennas for Directional Sorting of Fluorescence Emission}, author = {Aouani, Heykel and Mahboub, Oussama and Devaux, Eloise and Rigneault, Herve and Ebbesen, Thomas W. and Wenger, Jerome}, doi = {10.1021/nl200772d}, issn = {1530-6984}, year = {2011}, date = {2011-06-01}, journal = {NANO LETTERS}, volume = {11}, number = {6}, pages = {2400--2406}, abstract = {Spontaneous emission of fluorescent molecules or quantum dots is radiated along all directions when emitters are diluted in a liquid solution, which severely limits the amount of collected light. Besides, the emission direction does not carry any useful information and cannot be used to sort different molecules. To go beyond these limits, optical antennas have been recently introduced as conceptual tools to control the radiation properties for nanoemitters fixed on a substrate. Despite intense recent research, controlling the luminescence directivity remains a challenge for emitters with random positions and orientations, which is a key for several biomolecular screening applications. Here, we present full directional control of the fluorescence emission from molecules in water solution by an optical antenna made of a nanoaperture surrounded by a periodic set of shallow grooves in a gold film. For each emission wavelength, the fluorescence beam can be directed along a specific direction with a given angular width, hereby realizing a micrometer-size dispersive antenna. We demonstrate the fluorescence beaming results from an interference phenomenon and provide physical optics guidelines to control the fluorescence directivity by tuning the groove-nanoaperture distance. This photon-sorting capability provides a new approach for high-sensitivity screening of molecular species in solution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Spontaneous emission of fluorescent molecules or quantum dots is radiated along all directions when emitters are diluted in a liquid solution, which severely limits the amount of collected light. Besides, the emission direction does not carry any useful information and cannot be used to sort different molecules. To go beyond these limits, optical antennas have been recently introduced as conceptual tools to control the radiation properties for nanoemitters fixed on a substrate. Despite intense recent research, controlling the luminescence directivity remains a challenge for emitters with random positions and orientations, which is a key for several biomolecular screening applications. Here, we present full directional control of the fluorescence emission from molecules in water solution by an optical antenna made of a nanoaperture surrounded by a periodic set of shallow grooves in a gold film. For each emission wavelength, the fluorescence beam can be directed along a specific direction with a given angular width, hereby realizing a micrometer-size dispersive antenna. We demonstrate the fluorescence beaming results from an interference phenomenon and provide physical optics guidelines to control the fluorescence directivity by tuning the groove-nanoaperture distance. This photon-sorting capability provides a new approach for high-sensitivity screening of molecular species in solution. |
Bonini, Massimo ; Zalewski, Leszek ; Orgiu, Emanuele ; Breiner, Thomas ; Doetz, Florian ; Kastler, Marcel ; Samori, Paolo H-Bonding Tuned Self-Assembly of Phenylene-Thiophene-Thiophene-Phenylene Derivatives at Surfaces: Structural and Electrical Studies Journal Article In: JOURNAL OF PHYSICAL CHEMISTRY C, 115 (19), pp. 9753–9759, 2011, ISSN: 1932-7447. @article{bonini_h-bonding_2011, title = {H-Bonding Tuned Self-Assembly of Phenylene-Thiophene-Thiophene-Phenylene Derivatives at Surfaces: Structural and Electrical Studies}, author = {Bonini, Massimo and Zalewski, Leszek and Orgiu, Emanuele and Breiner, Thomas and Doetz, Florian and Kastler, Marcel and Samori, Paolo}, doi = {10.1021/jp201556y}, issn = {1932-7447}, year = {2011}, date = {2011-05-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY C}, volume = {115}, number = {19}, pages = {9753--9759}, abstract = {Several physicochemical properties of molecular ensembles can be modulated by controlling intermolecular interactions. The design and synthesis of pi-conjugated rodlike molecules exposing groups that can undergo H-bondings was exploited to develop materials featuring tunable 2D self-assembly at surfaces, thermal stability, order in micrometer-thick films, and electrical characteristics in organic field-effect transistors (OFETs). As a model system, we have chosen phenylene thiophene thiophene phenylene derivatives with side groups exposing either COOH or COOMe moieties. The structure and dynamics within monolayers at the solid-liquid interface was explored by in-situ scanning tunneling microscopy (STM) experiments. The thermal behavior of the materials was investigated by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The order in micrometer-thick films was studied by grazing-incidence small-angle X-ray scattering (GISAXS), whereas the electrical characteristics of the different systems were studied when self-assembled in thin films in a bottom-gate and bottom-contact field-effect transistor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several physicochemical properties of molecular ensembles can be modulated by controlling intermolecular interactions. The design and synthesis of pi-conjugated rodlike molecules exposing groups that can undergo H-bondings was exploited to develop materials featuring tunable 2D self-assembly at surfaces, thermal stability, order in micrometer-thick films, and electrical characteristics in organic field-effect transistors (OFETs). As a model system, we have chosen phenylene thiophene thiophene phenylene derivatives with side groups exposing either COOH or COOMe moieties. The structure and dynamics within monolayers at the solid-liquid interface was explored by in-situ scanning tunneling microscopy (STM) experiments. The thermal behavior of the materials was investigated by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The order in micrometer-thick films was studied by grazing-incidence small-angle X-ray scattering (GISAXS), whereas the electrical characteristics of the different systems were studied when self-assembled in thin films in a bottom-gate and bottom-contact field-effect transistor. |
Voignier, Julie ; Frey, Julien ; Kraus, Tomas ; Budesinsky, Milos ; Cvacka, Josef ; Heitz, Valerie ; Sauvage, Jean-Pierre Transition-Metal-Complexed Cyclic [3]- and [4]Pseudorotaxanes Containing Rigid Ring-and-Filament Conjugates: Synthesis and Solution Studies Journal Article In: CHEMISTRY-A EUROPEAN JOURNAL, 17 (19), pp. 5404–5414, 2011, ISSN: 0947-6539. @article{voignier_transition-metal-complexed_2011, title = {Transition-Metal-Complexed Cyclic [3]- and [4]Pseudorotaxanes Containing Rigid Ring-and-Filament Conjugates: Synthesis and Solution Studies}, author = {Voignier, Julie and Frey, Julien and Kraus, Tomas and Budesinsky, Milos and Cvacka, Josef and Heitz, Valerie and Sauvage, Jean-Pierre}, doi = {10.1002/chem.201003592}, issn = {0947-6539}, year = {2011}, date = {2011-05-01}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {17}, number = {19}, pages = {5404--5414}, abstract = {By using the “gathering-and-threading” effect of copper(I) with rigid ring-and-string conjugates, daisy-chain-type [3]- and [4]pseudorotaxanes could be prepared in high yields. The organic fragment used consisted of a 2,9-diphenyl-1,10-phenanthroline (dpp)-containing ring attached to a coordinating filament capable of threading through the ring of another molecule by coordination to copper(I). The bidentate chelate introduced in the axis was also a 1,10-phenanthroline (phen) derivative with two methyl groups ortho to the nitrogen atoms of the phen unit. The organic component was prepared following a multistep strategy, one of the key steps being the attachment of the ring to the lateral axis. This connection was done by a condensation reaction between an ortho dione located at the back of a ring-incorporated phen and an aromatic aldehyde, which was the end-function of the thread. An oxazole nucleus was obtained after the condensation, which provided a rigid connection between the ring and the axis. In this way, the coordination axes of the ring-incorporated bidentate chelate and of the ligand belonging to the lateral filament were approximately orthogonal to one another. The design was such that the tetrameric complex, a [4]pseudorotaxane, seemed to be the most stable species, owing to the mutual geometrical arrangement of the filament and the ring. Various spectroscopic techniques, such as (1)H NMR spectroscopy, including DOSY, and electrospray ionization mass spectroscopy (ESI-MS), clearly demonstrated that a mixture of cyclic [3]- and [4]pseudorotaxane was obtained; the proportions of both components depended on concentration and temperature. Copper(I) was not the only metal center leading to the formation of cyclic pseudorotaxanes. A similar effect was observed with silver(I) as the templating metal: quantitative formation of threaded species was observed, with a higher proportion of trimer over tetramer than in the copper(I) case. Concentration and temperature effects were investigated for both series of Cu(I)- and Ag(I)-complexed threaded species showing that formation of the trimer was favored upon dilution or heating of the solution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } By using the “gathering-and-threading” effect of copper(I) with rigid ring-and-string conjugates, daisy-chain-type [3]- and [4]pseudorotaxanes could be prepared in high yields. The organic fragment used consisted of a 2,9-diphenyl-1,10-phenanthroline (dpp)-containing ring attached to a coordinating filament capable of threading through the ring of another molecule by coordination to copper(I). The bidentate chelate introduced in the axis was also a 1,10-phenanthroline (phen) derivative with two methyl groups ortho to the nitrogen atoms of the phen unit. The organic component was prepared following a multistep strategy, one of the key steps being the attachment of the ring to the lateral axis. This connection was done by a condensation reaction between an ortho dione located at the back of a ring-incorporated phen and an aromatic aldehyde, which was the end-function of the thread. An oxazole nucleus was obtained after the condensation, which provided a rigid connection between the ring and the axis. In this way, the coordination axes of the ring-incorporated bidentate chelate and of the ligand belonging to the lateral filament were approximately orthogonal to one another. The design was such that the tetrameric complex, a [4]pseudorotaxane, seemed to be the most stable species, owing to the mutual geometrical arrangement of the filament and the ring. Various spectroscopic techniques, such as (1)H NMR spectroscopy, including DOSY, and electrospray ionization mass spectroscopy (ESI-MS), clearly demonstrated that a mixture of cyclic [3]- and [4]pseudorotaxane was obtained; the proportions of both components depended on concentration and temperature. Copper(I) was not the only metal center leading to the formation of cyclic pseudorotaxanes. A similar effect was observed with silver(I) as the templating metal: quantitative formation of threaded species was observed, with a higher proportion of trimer over tetramer than in the copper(I) case. Concentration and temperature effects were investigated for both series of Cu(I)- and Ag(I)-complexed threaded species showing that formation of the trimer was favored upon dilution or heating of the solution. |
Sauvage, Jean-Pierre ; Trolez, Yann ; Canevet, David ; Salle, Marc Intercalation of Tetrathiafulvalene between the Two Plates of a Copper(I)-Complexed [4]Rotaxane Journal Article In: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (13), pp. 2413–2416, 2011, ISSN: 1434-193X. @article{sauvage_intercalation_2011, title = {Intercalation of Tetrathiafulvalene between the Two Plates of a Copper(I)-Complexed [4]Rotaxane}, author = {Sauvage, Jean-Pierre and Trolez, Yann and Canevet, David and Salle, Marc}, doi = {10.1002/ejoc.201100142}, issn = {1434-193X}, year = {2011}, date = {2011-05-01}, journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, number = {13}, pages = {2413--2416}, abstract = {The ability of a cyclic copper(I)-complexed [4]rotaxane to act as a receptor towards organic electron donors has been studied. In particular, tetrathiafulvalene (TTF), which is a flat and electron-rich molecule, forms a relatively stable complex with the rotaxane host. H-1 NMR spectroscopic measurements strongly suggest that the coordination mode involves intercalation of the TTF motif between the two electron-poor plates of the [4]rotaxane. By contrast, extended TTF (exTTF), which possesses pi-donating ability similar to that of TTF but which is a significantly bulkier molecule due to a concave structure, was not able to form any detectable complex. This observation tends to indicate that the recognition site of the [4]rotaxane receptor is rigid and can not adapt to thick substrates.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The ability of a cyclic copper(I)-complexed [4]rotaxane to act as a receptor towards organic electron donors has been studied. In particular, tetrathiafulvalene (TTF), which is a flat and electron-rich molecule, forms a relatively stable complex with the rotaxane host. H-1 NMR spectroscopic measurements strongly suggest that the coordination mode involves intercalation of the TTF motif between the two electron-poor plates of the [4]rotaxane. By contrast, extended TTF (exTTF), which possesses pi-donating ability similar to that of TTF but which is a significantly bulkier molecule due to a concave structure, was not able to form any detectable complex. This observation tends to indicate that the recognition site of the [4]rotaxane receptor is rigid and can not adapt to thick substrates. |
Carretero-Palacios, S; Mahboub, O; Garcia-Vidal, F J; Martin-Moreno, L; Rodrigo, Sergio G; Genet, C; Ebbesen, T W Mechanisms for extraordinary optical transmission through bull's eye structures Journal Article In: OPTICS EXPRESS, 19 (11), pp. 10429–10442, 2011, ISSN: 1094-4087. @article{carretero-palacios_mechanisms_2011, title = {Mechanisms for extraordinary optical transmission through bull's eye structures}, author = {Carretero-Palacios, S. and Mahboub, O. and Garcia-Vidal, F. J. and Martin-Moreno, L. and Rodrigo, Sergio G. and Genet, C. and Ebbesen, T. W.}, doi = {10.1364/OE.19.010429}, issn = {1094-4087}, year = {2011}, date = {2011-05-01}, journal = {OPTICS EXPRESS}, volume = {19}, number = {11}, pages = {10429--10442}, abstract = {We analyze both experimentally and theoretically the physical mechanisms that determine the optical transmission through deep subwavelength bull's eye structures (concentric annular grooves surrounding a circular hole). Our analysis focus on the transmission resonance as a function of the distance between the central hole and its nearest groove. We find that, for that resonance, each groove behaves almost independently, acting as an optical cavity that couples to incident radiation, and reflecting the surface plasmons radiated by the other side of the same cavity. It is the constructive contribution at the central hole of these standing waves emitted by independent grooves which ends up enhancing transmission. Also for each groove the coupling and reflection coefficients for surface plasmons are incorporated into a phenomenological Huygens-Fresnel model that gathers the main mechanisms to enhance transmission. Additionally, it is shown that the system presents a collective resonance in the electric field that does not lead to resonant transmission, because the fields radiated by the grooves do not interfere constructively at the central hole. (C) 2011 Optical Society of America}, keywords = {}, pubstate = {published}, tppubtype = {article} } We analyze both experimentally and theoretically the physical mechanisms that determine the optical transmission through deep subwavelength bull's eye structures (concentric annular grooves surrounding a circular hole). Our analysis focus on the transmission resonance as a function of the distance between the central hole and its nearest groove. We find that, for that resonance, each groove behaves almost independently, acting as an optical cavity that couples to incident radiation, and reflecting the surface plasmons radiated by the other side of the same cavity. It is the constructive contribution at the central hole of these standing waves emitted by independent grooves which ends up enhancing transmission. Also for each groove the coupling and reflection coefficients for surface plasmons are incorporated into a phenomenological Huygens-Fresnel model that gathers the main mechanisms to enhance transmission. Additionally, it is shown that the system presents a collective resonance in the electric field that does not lead to resonant transmission, because the fields radiated by the grooves do not interfere constructively at the central hole. (C) 2011 Optical Society of America |
Schwartz, T; Hutchison, J A; Genet, C; Ebbesen, T W Reversible Switching of Ultrastrong Light-Molecule Coupling Journal Article In: PHYSICAL REVIEW LETTERS, 106 (19), 2011, ISSN: 0031-9007. @article{schwartz_reversible_2011, title = {Reversible Switching of Ultrastrong Light-Molecule Coupling}, author = {Schwartz, T. and Hutchison, J. A. and Genet, C. and Ebbesen, T. W.}, doi = {10.1103/PhysRevLett.106.196405}, issn = {0031-9007}, year = {2011}, date = {2011-05-01}, journal = {PHYSICAL REVIEW LETTERS}, volume = {106}, number = {19}, abstract = {We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room temperature, corresponding to 32% of the molecular transition energy. A similar coupling strength is demonstrated in a plasmonic structure. Such systems present a unique combination of coupling strength and functional capacities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room temperature, corresponding to 32% of the molecular transition energy. A similar coupling strength is demonstrated in a plasmonic structure. Such systems present a unique combination of coupling strength and functional capacities. |
Samori, Paolo ; Helman, Ana ; Biscarini, Fabio ; Cacialli, Franco Mastering Self-Organization of Functional Materials at Different Length Scale Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (7, SI), pp. 1210–1211, 2011, ISSN: 1616-301X. @article{samori_mastering_2011, title = {Mastering Self-Organization of Functional Materials at Different Length Scale}, author = {Samori, Paolo and Helman, Ana and Biscarini, Fabio and Cacialli, Franco}, doi = {10.1002/adfm.201100462}, issn = {1616-301X}, year = {2011}, date = {2011-04-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {21}, number = {7, SI}, pages = {1210--1211}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
De Luca, Giovanna ; Pisula, Wojciech ; Credgington, Dan ; Treossi, Emanuele ; Fenwick, Oliver ; Lazzerini, Giovanni Mattia ; Dabirian, Reza ; Orgiu, Emanuele ; Liscio, Andrea ; Palermo, Vincenzo ; Muellen, Klaus ; Cacialli, Franco ; Samori, Paolo Non-conventional Processing and Post-processing Methods for the Nanostructuring of Conjugated Materials for Organic Electronics Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (7, SI), pp. 1279–1295, 2011, ISSN: 1616-301X. @article{de_luca_non-conventional_2011, title = {Non-conventional Processing and Post-processing Methods for the Nanostructuring of Conjugated Materials for Organic Electronics}, author = {De Luca, Giovanna and Pisula, Wojciech and Credgington, Dan and Treossi, Emanuele and Fenwick, Oliver and Lazzerini, Giovanni Mattia and Dabirian, Reza and Orgiu, Emanuele and Liscio, Andrea and Palermo, Vincenzo and Muellen, Klaus and Cacialli, Franco and Samori, Paolo}, doi = {10.1002/adfm.201001769}, issn = {1616-301X}, year = {2011}, date = {2011-04-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {21}, number = {7, SI}, pages = {1279--1295}, abstract = {In the search for new ways to combine the appealing simplicity of solution processing methods and the need for a high performance of the active layer of organic (opto)electronic devices, the possibilities given by the joint use of well-established casting techniques and post-treatment procedures are explored, as well as new and unconventional deposition protocols to tailor self-assembled architectures with a high degree of order at different length scales, from the subnanometer up to the macroscopic scale. In fact, even the same organic molecule can give rise to different molecular architectures which, in turn, may offer the possibility to exploit a large variety of new functionalities of the deposited materials, paving the way towards the fabrication multifunctional organic-based devices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In the search for new ways to combine the appealing simplicity of solution processing methods and the need for a high performance of the active layer of organic (opto)electronic devices, the possibilities given by the joint use of well-established casting techniques and post-treatment procedures are explored, as well as new and unconventional deposition protocols to tailor self-assembled architectures with a high degree of order at different length scales, from the subnanometer up to the macroscopic scale. In fact, even the same organic molecule can give rise to different molecular architectures which, in turn, may offer the possibility to exploit a large variety of new functionalities of the deposited materials, paving the way towards the fabrication multifunctional organic-based devices. |
Fischer, Stefan ; Olsen, Kenneth W; Nam, Kwangho ; Karplus, Martin Unsuspected pathway of the allosteric transition in hemoglobin Journal Article In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108 (14), pp. 5608–5613, 2011, ISSN: 0027-8424. @article{fischer_unsuspected_2011, title = {Unsuspected pathway of the allosteric transition in hemoglobin}, author = {Fischer, Stefan and Olsen, Kenneth W. and Nam, Kwangho and Karplus, Martin}, doi = {10.1073/pnas.1011995108}, issn = {0027-8424}, year = {2011}, date = {2011-04-01}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {108}, number = {14}, pages = {5608--5613}, abstract = {Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228: 726-734], the subunit motions do not follow the textbook description of a simple rotation of one alpha beta-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 mu s) as well as a slow (20 mu s) component and provide a testable model for single molecule FRET experiments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228: 726-734], the subunit motions do not follow the textbook description of a simple rotation of one alpha beta-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 mu s) as well as a slow (20 mu s) component and provide a testable model for single molecule FRET experiments. |
Lehn, Jean-Marie Beyond synthesis: Self-organization Journal Article In: COMPTES RENDUS CHIMIE, 14 (4), pp. 348–361, 2011, ISSN: 1631-0748. @article{lehn_beyond_2011, title = {Beyond synthesis: Self-organization}, author = {Lehn, Jean-Marie}, doi = {10.1016/j.crci.2009.12.003}, issn = {1631-0748}, year = {2011}, date = {2011-04-01}, journal = {COMPTES RENDUS CHIMIE}, volume = {14}, number = {4}, pages = {348--361}, abstract = {The evolution of the universe from the particle to the thinking organism has taken place through self-organization. Chemistry has a major role to play in understanding these processes leading to the generation of complex matter. Chemistry has developed a highly powerful molecular synthetic chemistry, mastering the combination and recombination of atoms into increasingly complex molecules through selective chemical reactions. Supramolecular chemistry is harnessing intermolecular forces for the generation of informed supramolecular systems and processes through supramolecular synthetic chemistry implementing molecular information carried by electromagnetic interactions. Supramolecular chemistry has been actively exploring systems undergoing self-organization, i.e., systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, under the control of interactional molecular recognition events, thus behaving as programmed chemical systems. Molecular chemistry may similarly take advantage of the selectivity of covalent reactions to assemble complex molecular architectures through self-organization processes implementing functional molecular recognition. Supramolecular/non-covalent and molecular/covalent SELF-ORGANIZATION may thus be considered as the ULTIMATE SYNTHETIC CHEMISTRY, whereby chemical objects at both levels are generated on the basis of recognition processes involving either interactional or reactional features. Illustrations from the supramolecular domain will serve as illustrations. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus leads towards the emergence of adaptive and evolutive chemistry. (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The evolution of the universe from the particle to the thinking organism has taken place through self-organization. Chemistry has a major role to play in understanding these processes leading to the generation of complex matter. Chemistry has developed a highly powerful molecular synthetic chemistry, mastering the combination and recombination of atoms into increasingly complex molecules through selective chemical reactions. Supramolecular chemistry is harnessing intermolecular forces for the generation of informed supramolecular systems and processes through supramolecular synthetic chemistry implementing molecular information carried by electromagnetic interactions. Supramolecular chemistry has been actively exploring systems undergoing self-organization, i.e., systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, under the control of interactional molecular recognition events, thus behaving as programmed chemical systems. Molecular chemistry may similarly take advantage of the selectivity of covalent reactions to assemble complex molecular architectures through self-organization processes implementing functional molecular recognition. Supramolecular/non-covalent and molecular/covalent SELF-ORGANIZATION may thus be considered as the ULTIMATE SYNTHETIC CHEMISTRY, whereby chemical objects at both levels are generated on the basis of recognition processes involving either interactional or reactional features. Illustrations from the supramolecular domain will serve as illustrations. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus leads towards the emergence of adaptive and evolutive chemistry. (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved. |
Besenius, Pol ; van den Hout, Kelly P; Albers, Harald M H G; de Greef, Tom F A; Olijve, Luuk L C; Hermans, Thomas M; de Waal, Bas F M; Bomans, Paul H H; Sommerdijk, Nico A J M; Portale, Giuseppe ; Palmans, Anja R A; van Genderen, Marcel H P; Vekemans, Jef A J M; Meijer, E W Controlled Supramolecular Oligomerization of C-3-Symmetrical Molecules in Water: The Impact of Hydrophobic Shielding Journal Article In: CHEMISTRY-A EUROPEAN JOURNAL, 17 (18), pp. 5193–5203, 2011, ISSN: 0947-6539. @article{besenius_controlled_2011, title = {Controlled Supramolecular Oligomerization of C-3-Symmetrical Molecules in Water: The Impact of Hydrophobic Shielding}, author = {Besenius, Pol and van den Hout, Kelly P. and Albers, Harald M. H. G. and de Greef, Tom F. A. and Olijve, Luuk L. C. and Hermans, Thomas M. and de Waal, Bas F. M. and Bomans, Paul H. H. and Sommerdijk, Nico A. J. M. and Portale, Giuseppe and Palmans, Anja R. A. and van Genderen, Marcel H. P. and Vekemans, Jef A. J. M. and Meijer, E. W.}, doi = {10.1002/chem.201002976}, issn = {0947-6539}, year = {2011}, date = {2011-04-01}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {17}, number = {18}, pages = {5193--5203}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Woronoff, Gabrielle ; El Harrak, Abdeslam ; Mayot, Estelle ; Schicke, Olivier ; Miller, Oliver J; Soumillion, Patrice ; Griffiths, Andrew D; Ryckelynck, Michael New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications Journal Article In: Analytical Chemistry, 83 (8), pp. 2852–2857, 2011, ISSN: 1520-6882. @article{woronoff_new_2011, title = {New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications}, author = {Woronoff, Gabrielle and El Harrak, Abdeslam and Mayot, Estelle and Schicke, Olivier and Miller, Oliver J. and Soumillion, Patrice and Griffiths, Andrew D. and Ryckelynck, Michael}, doi = {10.1021/ac200373n}, issn = {1520-6882}, year = {2011}, date = {2011-04-01}, journal = {Analytical Chemistry}, volume = {83}, number = {8}, pages = {2852--2857}, abstract = {Droplet-based microfluidics is a powerful tool for biology and chemistry as it allows the production and the manipulation of picoliter-size droplets acting as individual reactors. In this format, high-sensitivity assays are typically based on fluorescence, so fluorophore exchange between droplets must be avoided. Fluorogenic substrates based on the coumarin leaving group are widely used to measure a variety of enzymatic activities, but their application in droplet-based microfluidic systems is severely impaired by the fast transport of the fluorescent product between compartments. Here we report the synthesis of new amidase fluorogenic substrates based on 7-aminocoumarin-4-methanesulfonic acid (ACMS), a highly water-soluble dye, and their suitability for droplet-based microfluidics applications. Both substrate and product had the required spectral characteristics and remained confined in droplets from hours to days. As a model experiment, a phenylacetylated ACMS was synthesized and used as a fluorogenic substrate of Escherichia coli penicillin G acylase. Kinetic parameters (k(cat) and K(M)) measured in bulk and in droplets on-chip were very similar, demonstrating the suitability of this synthesis strategy to produce a variety of ACMS-based substrates for assaying amidase activities both in microtiter plate and droplet-based microfluidic formats.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Droplet-based microfluidics is a powerful tool for biology and chemistry as it allows the production and the manipulation of picoliter-size droplets acting as individual reactors. In this format, high-sensitivity assays are typically based on fluorescence, so fluorophore exchange between droplets must be avoided. Fluorogenic substrates based on the coumarin leaving group are widely used to measure a variety of enzymatic activities, but their application in droplet-based microfluidic systems is severely impaired by the fast transport of the fluorescent product between compartments. Here we report the synthesis of new amidase fluorogenic substrates based on 7-aminocoumarin-4-methanesulfonic acid (ACMS), a highly water-soluble dye, and their suitability for droplet-based microfluidics applications. Both substrate and product had the required spectral characteristics and remained confined in droplets from hours to days. As a model experiment, a phenylacetylated ACMS was synthesized and used as a fluorogenic substrate of Escherichia coli penicillin G acylase. Kinetic parameters (k(cat) and K(M)) measured in bulk and in droplets on-chip were very similar, demonstrating the suitability of this synthesis strategy to produce a variety of ACMS-based substrates for assaying amidase activities both in microtiter plate and droplet-based microfluidic formats. |
Crivillers, Nuria ; Orgiu, Emanuele ; Reinders, Federica ; Mayor, Marcel ; Samori, Paolo Optical Modulation of the Charge Injection in an Organic Field-Effect Transistor Based on Photochromic Self-Assembled-Monolayer-Functionalized Electrodes Journal Article In: ADVANCED MATERIALS, 23 (12), pp. 1447–1452, 2011, ISSN: 0935-9648. @article{crivillers_optical_2011, title = {Optical Modulation of the Charge Injection in an Organic Field-Effect Transistor Based on Photochromic Self-Assembled-Monolayer-Functionalized Electrodes}, author = {Crivillers, Nuria and Orgiu, Emanuele and Reinders, Federica and Mayor, Marcel and Samori, Paolo}, doi = {10.1002/adma.201003736}, issn = {0935-9648}, year = {2011}, date = {2011-03-01}, journal = {ADVANCED MATERIALS}, volume = {23}, number = {12}, pages = {1447--1452}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zalewski, Leszek ; Brovelli, Sergio ; Bonini, Massimo ; Mativetsky, Jeffrey M; Wykes, Michael ; Orgiu, Emanuele ; Breiner, Thomas ; Kastler, Marcel ; Doetz, Florian ; Meinardi, Francesco ; Anderson, Harry L; Beljonne, David ; Cacialli, Franco ; Samori, Paolo Self-Assembled Conjugated Thiophene-Based Rotaxane Architectures: Structural, Computational, and Spectroscopic Insights into Molecular Aggregation Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (5), pp. 834–844, 2011, ISSN: 1616-301X. @article{zalewski_self-assembled_2011, title = {Self-Assembled Conjugated Thiophene-Based Rotaxane Architectures: Structural, Computational, and Spectroscopic Insights into Molecular Aggregation}, author = {Zalewski, Leszek and Brovelli, Sergio and Bonini, Massimo and Mativetsky, Jeffrey M. and Wykes, Michael and Orgiu, Emanuele and Breiner, Thomas and Kastler, Marcel and Doetz, Florian and Meinardi, Francesco and Anderson, Harry L. and Beljonne, David and Cacialli, Franco and Samori, Paolo}, doi = {10.1002/adfm.201001135}, issn = {1616-301X}, year = {2011}, date = {2011-03-01}, journal = {ADVANCED FUNCTIONAL MATERIALS}, volume = {21}, number = {5}, pages = {834--844}, abstract = {A comparative study of the self-assembly at a variety of surfaces of a dithiophene rotaxane 1 subset of beta-CD and its corresponding dumbbell, 1, by means of atomic force microscopy (AFM) imaging and scanning tunneling microscopy (STM) imaging on the micrometer and nanometer scale, respectively. The dumbbell is found to have a greater propensity to form ordered supramolecular assemblies, as a result of pi-pi interactions between dithiophenes belonging to adjacent molecules, which are hindered in the rotaxane. The fine molecular structure determined by STM was compared to that obtained by molecular modelling. The optical properties of both rotaxane and dumbbell in the solid state were investigated by steady-state and time-resolved photoluminescence (PL) experiments on spin-cast films and diluted solutions. The comparison between the optical features of the threaded and unthreaded systems reveals an effective role of encapsulation in reducing aggregation and exciton migration for the rotaxanes with respect to the dumbbells, thus leading to higher PL quantum efficiency and preserved single-molecule photophysics for longer times after excitation in the threaded oligomers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A comparative study of the self-assembly at a variety of surfaces of a dithiophene rotaxane 1 subset of beta-CD and its corresponding dumbbell, 1, by means of atomic force microscopy (AFM) imaging and scanning tunneling microscopy (STM) imaging on the micrometer and nanometer scale, respectively. The dumbbell is found to have a greater propensity to form ordered supramolecular assemblies, as a result of pi-pi interactions between dithiophenes belonging to adjacent molecules, which are hindered in the rotaxane. The fine molecular structure determined by STM was compared to that obtained by molecular modelling. The optical properties of both rotaxane and dumbbell in the solid state were investigated by steady-state and time-resolved photoluminescence (PL) experiments on spin-cast films and diluted solutions. The comparison between the optical features of the threaded and unthreaded systems reveals an effective role of encapsulation in reducing aggregation and exciton migration for the rotaxanes with respect to the dumbbells, thus leading to higher PL quantum efficiency and preserved single-molecule photophysics for longer times after excitation in the threaded oligomers. |
Liscio, Andrea ; Palermo, Vincenzo ; Fenwick, Oliver ; Braun, Slawomir ; Muellen, Klaus ; Fahlman, Mats ; Cacialli, Franco ; Samori, Paolo Local Surface Potential of pi-Conjugated Nanostructures by Kelvin Probe Force Microscopy: Effect of the Sampling Depth Journal Article In: SMALL, 7 (5), pp. 634–639, 2011, ISSN: 1613-6810. @article{liscio_local_2011, title = {Local Surface Potential of pi-Conjugated Nanostructures by Kelvin Probe Force Microscopy: Effect of the Sampling Depth}, author = {Liscio, Andrea and Palermo, Vincenzo and Fenwick, Oliver and Braun, Slawomir and Muellen, Klaus and Fahlman, Mats and Cacialli, Franco and Samori, Paolo}, doi = {10.1002/smll.201001770}, issn = {1613-6810}, year = {2011}, date = {2011-03-01}, journal = {SMALL}, volume = {7}, number = {5}, pages = {634--639}, abstract = {Kelvin probe force microscopy (KPFM) is usually applied to map the local surface potential of nanostructured materials at surfaces and interfaces. KPFM is commonly defined as a `surface technique', even if this assumption is not fully justified. However, a quantification of the surface sensitivity of this technique is crucial to explore electrical properties at the nanoscale. Here a versatile 3D model is presented which provides a quantitative explanation of KPFM results, taking into account the vertical structure of the sample. The model is tested on nanostructured films obtained from two relevant semiconducting systems for field-effect transistor and solar cell applications showing different interfacial properties, i.e., poly(3-hexylthiophene) (P3HT) and perylene-bis-dicarboximide (PDI). These findings are especially important since they enable quantitative determination of the local surface potential of conjugated nanostructures, and thereby pave the way towards optimization of the electronic properties of nanoscale architectures for organic electronic applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Kelvin probe force microscopy (KPFM) is usually applied to map the local surface potential of nanostructured materials at surfaces and interfaces. KPFM is commonly defined as a `surface technique', even if this assumption is not fully justified. However, a quantification of the surface sensitivity of this technique is crucial to explore electrical properties at the nanoscale. Here a versatile 3D model is presented which provides a quantitative explanation of KPFM results, taking into account the vertical structure of the sample. The model is tested on nanostructured films obtained from two relevant semiconducting systems for field-effect transistor and solar cell applications showing different interfacial properties, i.e., poly(3-hexylthiophene) (P3HT) and perylene-bis-dicarboximide (PDI). These findings are especially important since they enable quantitative determination of the local surface potential of conjugated nanostructures, and thereby pave the way towards optimization of the electronic properties of nanoscale architectures for organic electronic applications. |
Aprahamian, Marc ; Bour, Gaetan ; Akladios, Cherif Y; Fylaktakidou, Konstantina ; Greferath, Ruth ; Soler, Luc ; Marescaux, Jacques ; Egly, Jean-Marc ; Lehn, Jean-Marie ; Nicolau, Claude Myo-InositolTrisPyroPhosphate Treatment Leads to HIF-1 alpha Suppression and Eradication of Early Hepatoma Tumors in Rats Journal Article In: CHEMBIOCHEM, 12 (5), pp. 777–783, 2011, ISSN: 1439-4227. @article{aprahamian_myo-inositoltrispyrophosphate_2011, title = {Myo-InositolTrisPyroPhosphate Treatment Leads to HIF-1 alpha Suppression and Eradication of Early Hepatoma Tumors in Rats}, author = {Aprahamian, Marc and Bour, Gaetan and Akladios, Cherif Y. and Fylaktakidou, Konstantina and Greferath, Ruth and Soler, Luc and Marescaux, Jacques and Egly, Jean-Marc and Lehn, Jean-Marie and Nicolau, Claude}, doi = {10.1002/cbic.201000619}, issn = {1439-4227}, year = {2011}, date = {2011-03-01}, journal = {CHEMBIOCHEM}, volume = {12}, number = {5}, pages = {777--783}, abstract = {Myo-inositol trispyrophosphate (ITPP), a synthetic allosteric effector of hemoglobin, increases the regulated oxygen-releasing capacity of red blood cells (RBCs), leading to suppression of hypoxia-inducible factor 1 alpha (HIF-1 alpha) and to down-regulation of hypoxia-inducible genes such as vascular endothelial growth factor (VEGF). As a consequence, tumor growth is markedly affected. The effect of weekly intravenous injection of ITPP on an orthotopic, syngenic rat hepatocellular carcinoma (HCC) model was compared to that for untreated animals and animals subjected to conventional Doxorubicin chemotherapy. The longitudinal examination of HCC was performed by microCT imaging, and the cellular and molecular changes were evaluated by histology and Western blotting analysis of HIF-1 alpha, VEGF, and caspase-3 gene expression in the tumor and in the surrounding liver. Hematologic impact was evaluated by blood cell-count measurement and determination of P50 (oxygen partial pressure for a 50% oxygen saturation of hemoglobin). The HCC evaluation by microCT revealed a high potency of ITPP for tumor growth inhibition, thus allowing long-term survival and even cure of almost all the treated animals. The P50 value of hemoglobin in RBCs underwent a shift of 30% following ITPP injection. Under these conditions, HIF-1 alpha activity was strongly decreased, VEGF expression was down-regulated, and apoptosis was induced in HCC and surrounding liver cells, as indicated by Caspase-3 expression. ITPP did not affect hematologic parameters during treatment. The observations of in vivo tumor eradication suggest a significant clinical potential for ITPP in cancer therapy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Myo-inositol trispyrophosphate (ITPP), a synthetic allosteric effector of hemoglobin, increases the regulated oxygen-releasing capacity of red blood cells (RBCs), leading to suppression of hypoxia-inducible factor 1 alpha (HIF-1 alpha) and to down-regulation of hypoxia-inducible genes such as vascular endothelial growth factor (VEGF). As a consequence, tumor growth is markedly affected. The effect of weekly intravenous injection of ITPP on an orthotopic, syngenic rat hepatocellular carcinoma (HCC) model was compared to that for untreated animals and animals subjected to conventional Doxorubicin chemotherapy. The longitudinal examination of HCC was performed by microCT imaging, and the cellular and molecular changes were evaluated by histology and Western blotting analysis of HIF-1 alpha, VEGF, and caspase-3 gene expression in the tumor and in the surrounding liver. Hematologic impact was evaluated by blood cell-count measurement and determination of P50 (oxygen partial pressure for a 50% oxygen saturation of hemoglobin). The HCC evaluation by microCT revealed a high potency of ITPP for tumor growth inhibition, thus allowing long-term survival and even cure of almost all the treated animals. The P50 value of hemoglobin in RBCs underwent a shift of 30% following ITPP injection. Under these conditions, HIF-1 alpha activity was strongly decreased, VEGF expression was down-regulated, and apoptosis was induced in HCC and surrounding liver cells, as indicated by Caspase-3 expression. ITPP did not affect hematologic parameters during treatment. The observations of in vivo tumor eradication suggest a significant clinical potential for ITPP in cancer therapy. |
Leproult, Emeline ; Barluenga, Sofia ; Moras, Dino ; Wurtz, Jean-Marie ; Winssinger, Nicolas Cysteine Mapping in Conformationally Distinct Kinase Nucleotide Binding Sites: Application to the Design of Selective Covalent Inhibitors Journal Article In: JOURNAL OF MEDICINAL CHEMISTRY, 54 (5), pp. 1347–1355, 2011, ISSN: 0022-2623. @article{leproult_cysteine_2011, title = {Cysteine Mapping in Conformationally Distinct Kinase Nucleotide Binding Sites: Application to the Design of Selective Covalent Inhibitors}, author = {Leproult, Emeline and Barluenga, Sofia and Moras, Dino and Wurtz, Jean-Marie and Winssinger, Nicolas}, doi = {10.1021/jm101396q}, issn = {0022-2623}, year = {2011}, date = {2011-03-01}, journal = {JOURNAL OF MEDICINAL CHEMISTRY}, volume = {54}, number = {5}, pages = {1347--1355}, abstract = {Kinases have emerged as one of the most prolific therapeutic targets. An important criterion in the therapeutic success of inhibitors targeting the nucleotide binding pocket of kinases is the inhibitor residence time. Recently, covalent kinase inhibitors have attracted attention since they confer terminal inhibition and should thus be more effective than reversible inhibitors with transient inhibition. The most robust approach to design irreversible inhibitors is to capitalize on the nucleophilicity of a cysteine thiol group present in the target protein. Herein, we report a systematic analysis of cysteine residues present in the nucleotide binding site of kinases, which could be harnessed for irreversible inhibition, taking into consideration the different kinase conformations. We demonstrate the predictive power of this analysis with the design and validation of an irreversible inhibitor of KIT/PDGFR kinases. This is the first example of a covalent kinase inhibitor that combines a pharmacophore addressing the DFG-out conformation with a covalent trap.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Kinases have emerged as one of the most prolific therapeutic targets. An important criterion in the therapeutic success of inhibitors targeting the nucleotide binding pocket of kinases is the inhibitor residence time. Recently, covalent kinase inhibitors have attracted attention since they confer terminal inhibition and should thus be more effective than reversible inhibitors with transient inhibition. The most robust approach to design irreversible inhibitors is to capitalize on the nucleophilicity of a cysteine thiol group present in the target protein. Herein, we report a systematic analysis of cysteine residues present in the nucleotide binding site of kinases, which could be harnessed for irreversible inhibition, taking into consideration the different kinase conformations. We demonstrate the predictive power of this analysis with the design and validation of an irreversible inhibitor of KIT/PDGFR kinases. This is the first example of a covalent kinase inhibitor that combines a pharmacophore addressing the DFG-out conformation with a covalent trap. |
Ciesielski, Artur ; Stefankiewicz, Artur R; Hanke, Felix ; Persson, Mats ; Lehn, Jean-Marie ; Samori, Paolo Rigid Dimers Formed through Strong Interdigitated Ħ-Bonds Yield Compact 1D Supramolecular Helical Polymers Journal Article In: SMALL, 7 (3), pp. 342–350, 2011, ISSN: 1613-6810. @article{ciesielski_rigid_2011, title = {Rigid Dimers Formed through Strong Interdigitated Ħ-Bonds Yield Compact 1D Supramolecular Helical Polymers}, author = {Ciesielski, Artur and Stefankiewicz, Artur R. and Hanke, Felix and Persson, Mats and Lehn, Jean-Marie and Samori, Paolo}, doi = {10.1002/smll.201001419}, issn = {1613-6810}, year = {2011}, date = {2011-02-01}, journal = {SMALL}, volume = {7}, number = {3}, pages = {342--350}, abstract = {Hierarchical self-assembly of small abiotic molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by using conformationally rigid molecular modules undergoing self-assembly through strong H-bonds. Their binding strength depends on the multiplicity of the H-bonds, the nature of donor/acceptor pairs and their secondary attractive/repulsive interactions. Here a functionalized molecular module is described, which is capable of self-associating through self-complementary H-bonding patterns comprising four strong and two medium-strength H-bonds to form dimers. The self-association of these phenylpyrimidine-based dimers through directional H-bonding between two lateral pyridin-2(1H)-one units of neighboring molecules allows the formation of highly compact 1D supramolecular polymers by self-assembly on graphite. A concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional studies, reveals the controlled generation of either linear supramolecular 2D arrays, or long helical supramolecular polymers with a high shape persistence.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hierarchical self-assembly of small abiotic molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by using conformationally rigid molecular modules undergoing self-assembly through strong H-bonds. Their binding strength depends on the multiplicity of the H-bonds, the nature of donor/acceptor pairs and their secondary attractive/repulsive interactions. Here a functionalized molecular module is described, which is capable of self-associating through self-complementary H-bonding patterns comprising four strong and two medium-strength H-bonds to form dimers. The self-association of these phenylpyrimidine-based dimers through directional H-bonding between two lateral pyridin-2(1H)-one units of neighboring molecules allows the formation of highly compact 1D supramolecular polymers by self-assembly on graphite. A concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional studies, reveals the controlled generation of either linear supramolecular 2D arrays, or long helical supramolecular polymers with a high shape persistence. |
Ovchinnikov, Victor ; Karplus, Martin ; Vanden-Eijnden, Eric Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI Journal Article In: JOURNAL OF CHEMICAL PHYSICS, 134 (8), 2011, ISSN: 0021-9606. @article{ovchinnikov_free_2011, title = {Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI}, author = {Ovchinnikov, Victor and Karplus, Martin and Vanden-Eijnden, Eric}, doi = {10.1063/1.3544209}, issn = {0021-9606}, year = {2011}, date = {2011-02-01}, journal = {JOURNAL OF CHEMICAL PHYSICS}, volume = {134}, number = {8}, abstract = {A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepower-stroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS. R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. (C) 2011 American Institute of Physics. [doi:10.1063/1.3544209]}, keywords = {}, pubstate = {published}, tppubtype = {article} } A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepower-stroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS. R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. (C) 2011 American Institute of Physics. [doi:10.1063/1.3544209] |
Buchs (nee Levrand), Barbara ; Godin, Guillaume ; Trachsel, Alain ; de Saint Laumer, Jean-Yves ; Lehn, Jean-Marie ; Herrmann, Andreas Reversible Aminal Formation: Controlling the Evaporation of Bioactive Volatiles by Dynamic Combinatorial/Covalent Chemistry Journal Article In: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (4), pp. 681–695, 2011, ISSN: 1434-193X. @article{buchs_nee_levrand_reversible_2011, title = {Reversible Aminal Formation: Controlling the Evaporation of Bioactive Volatiles by Dynamic Combinatorial/Covalent Chemistry}, author = {Buchs (nee Levrand), Barbara and Godin, Guillaume and Trachsel, Alain and de Saint Laumer, Jean-Yves and Lehn, Jean-Marie and Herrmann, Andreas}, doi = {10.1002/ejoc.201001433}, issn = {1434-193X}, year = {2011}, date = {2011-02-01}, journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, number = {4}, pages = {681--695}, abstract = {Dynamic mixtures generated by reversible aminal formation efficiently prolong the duration of evaporation of bioactive volatile aldehydes. Secondary diamines used for the generation of dynamic mixtures are obtained by treatment of primary diamines with carbonyl compounds and reduction of the diimines with NaBH(4). The reversibilities of the reactions were demonstrated by NMR measurements in buffered aqueous solutions. Kinetic rate constants and equilibrium constants for the formation and hydrolysis of aminals were determined. The performance of dynamic mixtures as delivery systems for perfumery ingredients was tested after deposition onto cotton, and the long-lastingness of fragrance evaporation was investigated by dynamic headspace analysis against a reference sample. The simplicity of the concept together with its excellent performance makes this delivery system highly interesting for applied perfumery. Reversible aminal formation might also be successfully applicable to dynamic combinatorial/covalent chemistry for screening of pharmaceutically or catalytically active ligands and receptors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dynamic mixtures generated by reversible aminal formation efficiently prolong the duration of evaporation of bioactive volatile aldehydes. Secondary diamines used for the generation of dynamic mixtures are obtained by treatment of primary diamines with carbonyl compounds and reduction of the diimines with NaBH(4). The reversibilities of the reactions were demonstrated by NMR measurements in buffered aqueous solutions. Kinetic rate constants and equilibrium constants for the formation and hydrolysis of aminals were determined. The performance of dynamic mixtures as delivery systems for perfumery ingredients was tested after deposition onto cotton, and the long-lastingness of fragrance evaporation was investigated by dynamic headspace analysis against a reference sample. The simplicity of the concept together with its excellent performance makes this delivery system highly interesting for applied perfumery. Reversible aminal formation might also be successfully applicable to dynamic combinatorial/covalent chemistry for screening of pharmaceutically or catalytically active ligands and receptors. |
Smith, Thierry ; Dupuis, Christian ; Folie, Annelise ; Quesnel, Florence ; Storme, Jean-Yves ; Iacumin, Paola ; Riveline, Janine ; Missiaen, Pieter ; Ladeveze, Sandrine ; Yans, Johan A new terrestrial vertebrate site just after the Paleocene-Eocene boundary in the Mortemer Formation of Upper Normandy, France Journal Article In: COMPTES RENDUS PALEVOL, 10 (1), pp. 11–20, 2011, ISSN: 1631-0683. @article{smith_new_2011, title = {A new terrestrial vertebrate site just after the Paleocene-Eocene boundary in the Mortemer Formation of Upper Normandy, France}, author = {Smith, Thierry and Dupuis, Christian and Folie, Annelise and Quesnel, Florence and Storme, Jean-Yves and Iacumin, Paola and Riveline, Janine and Missiaen, Pieter and Ladeveze, Sandrine and Yans, Johan}, doi = {10.1016/j.crpv.2010.11.004}, issn = {1631-0683}, year = {2011}, date = {2011-02-01}, journal = {COMPTES RENDUS PALEVOL}, volume = {10}, number = {1}, pages = {11--20}, abstract = {European terrestrial vertebrate sites of the Upper Paleocene-Lower Eocene deposits are predominantly known from the central and eastern parts of the Paris Basin. However, several outcrops covering this interval are scattered along the Upper Normandy coast, in the western part of the Paris Basin. Here we report the discovery of a new terrestrial vertebrate site in the Mortemer Formation, at the top of the cliffs of Sotteville-sur-Mer in Upper Normandy, France. The vertebrate level is situated about 1.5 m above the onset of the Paleocene Eocene Carbon Isotope Excursion (CIE) based on dispersed organic carbon and is therefore Earliest Eocene in age. The vertebrate fauna is composed of fish, amphibians, lizards and mammals, including the earliest peradectid marsupials and paromomyid plesiadapiform of Europe. A diverse and rich charophyte flora is well represented throughout the lower part of the outcrop and allows the conclusion that the CIE falls in the Peckichara disermas biozone. (C) 2010 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } European terrestrial vertebrate sites of the Upper Paleocene-Lower Eocene deposits are predominantly known from the central and eastern parts of the Paris Basin. However, several outcrops covering this interval are scattered along the Upper Normandy coast, in the western part of the Paris Basin. Here we report the discovery of a new terrestrial vertebrate site in the Mortemer Formation, at the top of the cliffs of Sotteville-sur-Mer in Upper Normandy, France. The vertebrate level is situated about 1.5 m above the onset of the Paleocene Eocene Carbon Isotope Excursion (CIE) based on dispersed organic carbon and is therefore Earliest Eocene in age. The vertebrate fauna is composed of fish, amphibians, lizards and mammals, including the earliest peradectid marsupials and paromomyid plesiadapiform of Europe. A diverse and rich charophyte flora is well represented throughout the lower part of the outcrop and allows the conclusion that the CIE falls in the Peckichara disermas biozone. (C) 2010 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved. |
Briggs, Breeze N; Durola, Fabien ; McMillin, David R; Sauvage, Jean-Pierre Luminescence studies of copper(I)-containing [2]pseudorotaxanes Journal Article In: CANADIAN JOURNAL OF CHEMISTRY, 89 (2), pp. 98–103, 2011, ISSN: 0008-4042. @article{briggs_luminescence_2011, title = {Luminescence studies of copper(I)-containing [2]pseudorotaxanes}, author = {Briggs, Breeze N. and Durola, Fabien and McMillin, David R. and Sauvage, Jean-Pierre}, doi = {10.1139/V10-093}, issn = {0008-4042}, year = {2011}, date = {2011-02-01}, journal = {CANADIAN JOURNAL OF CHEMISTRY}, volume = {89}, number = {2}, pages = {98--103}, abstract = {This report describes photoluminescence studies of copper-containing [2]pseudorotaxanes that mimic elements of functioning molecular machines. Excitation with visible light induces a formal oxidation of the metal center and simulates an actuation process. In all four [2] pseudorotaxanes studied, the ring ligand is the same, but the thread ligand is variable, namely 2,9-di(anisol-4-yl)-1,10-phenanthroline (dap), 6,6'-di(anisol-4-yl)-2,2'-bipyridine (o-dabipy), 5,5'-di(anisol-4-yl)-2,2'-bipyridine (m-dabipy), or 8,8'-di(anisol-4-yl)-3,3'-bi-isoquinoline (dabiiq). The absorbance bandshapes suggest that aryl substituents extending from the core ligands engage in stacking interactions and induce a partially flattened structure in the ground state. More severe flattening occurs in the excited state and precludes the observation of emission if inter-ligand steric forces do not limit the distortion. Thus, the [2] pseudorotaxanes containing dap or o-dabipy as the thread ligand exhibit uncorrected emission maxima at around 720 nm in room-temperature dichloromethane, while the less constrained analogues, containing dabiiq or m-dabipy, are not emissive in fluid solution and barely exhibit a signal in rigid media. In dichloromethane, the luminescence quantum yields of the dap- and o-dabipy-containing systems are 6 x 10(-4) and 4 x 10(-4), and the excited-state lifetimes are 98 ns and 90 ns, respectively.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This report describes photoluminescence studies of copper-containing [2]pseudorotaxanes that mimic elements of functioning molecular machines. Excitation with visible light induces a formal oxidation of the metal center and simulates an actuation process. In all four [2] pseudorotaxanes studied, the ring ligand is the same, but the thread ligand is variable, namely 2,9-di(anisol-4-yl)-1,10-phenanthroline (dap), 6,6'-di(anisol-4-yl)-2,2'-bipyridine (o-dabipy), 5,5'-di(anisol-4-yl)-2,2'-bipyridine (m-dabipy), or 8,8'-di(anisol-4-yl)-3,3'-bi-isoquinoline (dabiiq). The absorbance bandshapes suggest that aryl substituents extending from the core ligands engage in stacking interactions and induce a partially flattened structure in the ground state. More severe flattening occurs in the excited state and precludes the observation of emission if inter-ligand steric forces do not limit the distortion. Thus, the [2] pseudorotaxanes containing dap or o-dabipy as the thread ligand exhibit uncorrected emission maxima at around 720 nm in room-temperature dichloromethane, while the less constrained analogues, containing dabiiq or m-dabipy, are not emissive in fluid solution and barely exhibit a signal in rigid media. In dichloromethane, the luminescence quantum yields of the dap- and o-dabipy-containing systems are 6 x 10(-4) and 4 x 10(-4), and the excited-state lifetimes are 98 ns and 90 ns, respectively. |
Winssinger, Nicolas Translating instructions into function by nucleic acid programmed self-assembly Journal Article In: ACTUALITE CHIMIQUE, (348-49), pp. 42–48, 2011, ISSN: 0151-9093. @article{winssinger_translating_2011, title = {Translating instructions into function by nucleic acid programmed self-assembly}, author = {Winssinger, Nicolas}, issn = {0151-9093}, year = {2011}, date = {2011-02-01}, journal = {ACTUALITE CHIMIQUE}, number = {348-49}, pages = {42--48}, abstract = {The predictable nature of nucleic acid hybridization offers a simple platform to program assemblies with emerging function. This review will highlight some examples from our laboratory towards the use of this concept in chemical biology. These developments capitalize on peptide nucleic acids (PNAs), a functional analogue of natural oligonucleotides to program assemblies. In the first example, hybridization is used to organize mixtures of molecules tagged with PNAs into a microarray format; in the second example, the PNA tags are used to program the dimerization of ligands onto a nucleic acid template which translates into enhanced affinity for a biomolecule; in the third one, hybridization is used to program a reaction by aligning reactive functional groups and translated into a fluorescent signal. While these examples are only a prelude in translating instructions into a function, we hope that they can be the basis of more complex network and inspire further developments in the broader context of system chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The predictable nature of nucleic acid hybridization offers a simple platform to program assemblies with emerging function. This review will highlight some examples from our laboratory towards the use of this concept in chemical biology. These developments capitalize on peptide nucleic acids (PNAs), a functional analogue of natural oligonucleotides to program assemblies. In the first example, hybridization is used to organize mixtures of molecules tagged with PNAs into a microarray format; in the second example, the PNA tags are used to program the dimerization of ligands onto a nucleic acid template which translates into enhanced affinity for a biomolecule; in the third one, hybridization is used to program a reaction by aligning reactive functional groups and translated into a fluorescent signal. While these examples are only a prelude in translating instructions into a function, we hope that they can be the basis of more complex network and inspire further developments in the broader context of system chemistry. |
Aouani, Heykel ; Mahboub, Oussama ; Bonod, Nicolas ; Devaux, Eloise ; Popov, Evgeny ; Rigneault, Herve ; Ebbesen, Thomas W; Wenger, Jerome Bright Unidirectional Fluorescence Emission of Molecules in a Nanoaperture with Plasmonic Corrugations Journal Article In: NANO LETTERS, 11 (2), pp. 637–644, 2011, ISSN: 1530-6984. @article{aouani_bright_2011, title = {Bright Unidirectional Fluorescence Emission of Molecules in a Nanoaperture with Plasmonic Corrugations}, author = {Aouani, Heykel and Mahboub, Oussama and Bonod, Nicolas and Devaux, Eloise and Popov, Evgeny and Rigneault, Herve and Ebbesen, Thomas W. and Wenger, Jerome}, doi = {10.1021/nl103738d}, issn = {1530-6984}, year = {2011}, date = {2011-02-01}, journal = {NANO LETTERS}, volume = {11}, number = {2}, pages = {637--644}, abstract = {Controlling the fluorescence emission from nanoscale quantum emitters is a key element for a wide range of applications,; from efficient analytical sensing to quantum information processing. Enhancing the fluorescence intensity and narrowing the emission directivity are both essential features to achieve a full control of fluorescence, yet this is rarely obtained simultaneously with optical nanoantennas. Here we report that gold nanoapertures surrounded by periodic corrugations transform standard fluorescent molecules into bright unidirectional sources. We obtain enhancement factors of the fluorescence count rate per molecule up to 120 fold simultaneously with a directional emission of the fluorescence into a narrow angular cone in the direction normal to the sample plane. The bright emission and,wow directionality enable the detection of single molecules with a low numerical aperture objective, and improve the effectiveness of fluorescence based applications. We thoroughly quantify the increased light-matter coupling as well as the radiation pattern intensity. These results are highly relevant for the development of single molecule sensing, single-photon sources, and light emitting devices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Controlling the fluorescence emission from nanoscale quantum emitters is a key element for a wide range of applications,; from efficient analytical sensing to quantum information processing. Enhancing the fluorescence intensity and narrowing the emission directivity are both essential features to achieve a full control of fluorescence, yet this is rarely obtained simultaneously with optical nanoantennas. Here we report that gold nanoapertures surrounded by periodic corrugations transform standard fluorescent molecules into bright unidirectional sources. We obtain enhancement factors of the fluorescence count rate per molecule up to 120 fold simultaneously with a directional emission of the fluorescence into a narrow angular cone in the direction normal to the sample plane. The bright emission and,wow directionality enable the detection of single molecules with a low numerical aperture objective, and improve the effectiveness of fluorescence based applications. We thoroughly quantify the increased light-matter coupling as well as the radiation pattern intensity. These results are highly relevant for the development of single molecule sensing, single-photon sources, and light emitting devices. |
Cadeddu, Andrea ; Ciesielski, Artur ; El Malah, Tamer ; Hecht, Stefan ; Samori, Paolo Modulating the self-assembly of rigid “clicked” dendrimers at the solid-liquid interface by tuning non-covalent interactions between side groups Journal Article In: CHEMICAL COMMUNICATIONS, 47 (38), pp. 10578–10580, 2011, ISSN: 1359-7345. @article{cadeddu_modulating_2011, title = {Modulating the self-assembly of rigid “clicked” dendrimers at the solid-liquid interface by tuning non-covalent interactions between side groups}, author = {Cadeddu, Andrea and Ciesielski, Artur and El Malah, Tamer and Hecht, Stefan and Samori, Paolo}, doi = {10.1039/c1cc13099d}, issn = {1359-7345}, year = {2011}, date = {2011-01-01}, journal = {CHEMICAL COMMUNICATIONS}, volume = {47}, number = {38}, pages = {10578--10580}, abstract = {First generation poly(triazole-phenylene) dendrimers equipped with peripheral alkyl or carboxylic acid groups to engage in van der Waals and hydrogen-bonding interactions, respectively, assemble into distinct two-dimensional nano-structures at the solid-liquid interface as revealed by high resolution STM investigations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } First generation poly(triazole-phenylene) dendrimers equipped with peripheral alkyl or carboxylic acid groups to engage in van der Waals and hydrogen-bonding interactions, respectively, assemble into distinct two-dimensional nano-structures at the solid-liquid interface as revealed by high resolution STM investigations. |
Ciesielski, Artur ; Colella, Silvia ; Zalewski, Leszek ; Bruchmann, Bernd ; Samori, Paolo Nanopatterning the graphite surface with ordered macrocyclic or ribbon-like assemblies of isocytosine derivatives: an STM study Journal Article In: CRYSTENGCOMM, 13 (18), pp. 5535–5537, 2011, ISSN: 1466-8033. @article{ciesielski_nanopatterning_2011, title = {Nanopatterning the graphite surface with ordered macrocyclic or ribbon-like assemblies of isocytosine derivatives: an STM study}, author = {Ciesielski, Artur and Colella, Silvia and Zalewski, Leszek and Bruchmann, Bernd and Samori, Paolo}, doi = {10.1039/c1ce05521f}, issn = {1466-8033}, year = {2011}, date = {2011-01-01}, journal = {CRYSTENGCOMM}, volume = {13}, number = {18}, pages = {5535--5537}, abstract = {STM studies of the self-assembly at the solid-liquid interface of substituted isocytosine derivatives exposing side groups featuring different steric hindrance revealed the formation of distinct crystalline nanopatterns.}, keywords = {}, pubstate = {published}, tppubtype = {article} } STM studies of the self-assembly at the solid-liquid interface of substituted isocytosine derivatives exposing side groups featuring different steric hindrance revealed the formation of distinct crystalline nanopatterns. |
Savage, Rebecca C; Mativetsky, Jeffrey M; Orgiu, Emanuele ; Palma, Matteo ; Gbabode, Gabin ; Geerts, Yves H; Samori, P Integration of self-assembled discotic-based fibres into field-effect transistors: a comparison of preparation approaches Journal Article In: JOURNAL OF MATERIALS CHEMISTRY, 21 (1), pp. 206–213, 2011, ISSN: 0959-9428. @article{savage_integration_2011, title = {Integration of self-assembled discotic-based fibres into field-effect transistors: a comparison of preparation approaches}, author = {Savage, Rebecca C. and Mativetsky, Jeffrey M. and Orgiu, Emanuele and Palma, Matteo and Gbabode, Gabin and Geerts, Yves H. and Samori, P.}, doi = {10.1039/c0jm01754j}, issn = {0959-9428}, year = {2011}, date = {2011-01-01}, journal = {JOURNAL OF MATERIALS CHEMISTRY}, volume = {21}, number = {1}, pages = {206--213}, abstract = {The role played by the preparation method upon the morphological and electrical properties of alkyl substituted thio-triphenylene-based self-assembled fibres is explored by comparing two processing approaches, termed solvent vapour annealing (SVA) and solvent induced precipitation (SIP). Both approaches led to fibres having widths of several hundred nanometres and lengths of tens of micrometres. SVA formed isolated fibres which were tens of nanometres high, flat, and tapered at the ends. Conversely, SIP fibres exhibited nearly matching heights and widths, but organized into bundles. Despite these morphological differences, the same intermolecular packing is found by XRD in each type of structure, albeit with differing degrees of long-range order. The fibres were integrated into bottom-gate bottom-contact field-effect transistors. The density and configuration of the fibres with respect to the electrodes and gate dielectric were found to play an important role in the transport properties. SIP devices yielded the highest mobilities compared to SVA and spin-coated devices, largely owing to their high degree of internal order and the possibility to achieve high fibre densities within the transistor channel.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The role played by the preparation method upon the morphological and electrical properties of alkyl substituted thio-triphenylene-based self-assembled fibres is explored by comparing two processing approaches, termed solvent vapour annealing (SVA) and solvent induced precipitation (SIP). Both approaches led to fibres having widths of several hundred nanometres and lengths of tens of micrometres. SVA formed isolated fibres which were tens of nanometres high, flat, and tapered at the ends. Conversely, SIP fibres exhibited nearly matching heights and widths, but organized into bundles. Despite these morphological differences, the same intermolecular packing is found by XRD in each type of structure, albeit with differing degrees of long-range order. The fibres were integrated into bottom-gate bottom-contact field-effect transistors. The density and configuration of the fibres with respect to the electrodes and gate dielectric were found to play an important role in the transport properties. SIP devices yielded the highest mobilities compared to SVA and spin-coated devices, largely owing to their high degree of internal order and the possibility to achieve high fibre densities within the transistor channel. |
Liscio, Andrea ; Veronese, Giulio Paolo ; Treossi, Emanuele ; Suriano, Francesco ; Rossella, Francesco ; Bellani, Vittorio ; Rizzoli, Rita ; Samori, Paolo ; Palermo, Vincenzo Charge transport in graphene-polythiophene blends as studied by Kelvin Probe Force Microscopy and transistor characterization Journal Article In: JOURNAL OF MATERIALS CHEMISTRY, 21 (9), pp. 2924–2931, 2011, ISSN: 0959-9428. @article{liscio_charge_2011, title = {Charge transport in graphene-polythiophene blends as studied by Kelvin Probe Force Microscopy and transistor characterization}, author = {Liscio, Andrea and Veronese, Giulio Paolo and Treossi, Emanuele and Suriano, Francesco and Rossella, Francesco and Bellani, Vittorio and Rizzoli, Rita and Samori, Paolo and Palermo, Vincenzo}, doi = {10.1039/c0jm02940h}, issn = {0959-9428}, year = {2011}, date = {2011-01-01}, journal = {JOURNAL OF MATERIALS CHEMISTRY}, volume = {21}, number = {9}, pages = {2924--2931}, abstract = {Blends of reduced graphene oxide (RGO) and poly(3-hexylthiophene) (P3HT) are used as the active layer of field-effect transistors (FETs). By using sequential deposition of the two components, the density of RGO sheets can be tuned linearly, thereby modulating their contribution to the charge transport in the transistors, and the onset of charge percolation. The surface potential of RGO, P3HT and source-drain contacts is measured on the nanometric scale with Kelvin Probe Force Microscopy (KPFM), and correlated with the macroscopic performance of the FETs. KPFM is also used to monitor the potential decay along the channel in the working FETs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Blends of reduced graphene oxide (RGO) and poly(3-hexylthiophene) (P3HT) are used as the active layer of field-effect transistors (FETs). By using sequential deposition of the two components, the density of RGO sheets can be tuned linearly, thereby modulating their contribution to the charge transport in the transistors, and the onset of charge percolation. The surface potential of RGO, P3HT and source-drain contacts is measured on the nanometric scale with Kelvin Probe Force Microscopy (KPFM), and correlated with the macroscopic performance of the FETs. KPFM is also used to monitor the potential decay along the channel in the working FETs. |
Publications
2011 |
A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size Journal Article In: BIOPHYSICAL JOURNAL, 101 (10), pp. 2436–2444, 2011, ISSN: 0006-3495. |
Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (45), pp. 18110–18113, 2011, ISSN: 0002-7863. |
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Journal Article In: MOLECULAR SYSTEMS BIOLOGY, 7 , 2011, ISSN: 1744-4292. |
Rational enthusiasm Journal Article In: NATURE, 478 (7368), pp. S8–S9, 2011, ISSN: 0028-0836. |
Telomere Targeting with a New G4 Ligand Enhances Radiation-Induced Killing of Human Glioblastoma Cells Journal Article In: MOLECULAR CANCER THERAPEUTICS, 10 (10), pp. 1784–1795, 2011, ISSN: 1535-7163. |
Trimer Liquids and Crystals of Polar Molecules in Coupled Wires Journal Article In: PHYSICAL REVIEW LETTERS, 107 (16), 2011, ISSN: 0031-9007. |
Templated synthesis of catenanes incorporating Zn(II) or Rh(III)-complexed porphyrins: the coordination chemistry-only approach Journal Article In: JOURNAL OF PORPHYRINS AND PHTHALOCYANINES, 15 (9-10), pp. 848–857, 2011, ISSN: 1088-4246. |
Compact Antenna for Efficient and Unidirectional Launching and Decoupling of Surface Plasmons Journal Article In: NANO LETTERS, 11 (10), pp. 4207–4212, 2011, ISSN: 1530-6984. |
Graphene Transistors via in Situ Voltage-Induced Reduction of Graphene-Oxide under Ambient Conditions Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (36), pp. 14320–14326, 2011, ISSN: 0002-7863. |
Dynamic Covalent Chemistry: A Facile Room-Temperature, Reversible, Diels-Alder Reaction between Anthracene Derivatives and N-Phenyltriazolinedione Journal Article In: CHEMISTRY-AN ASIAN JOURNAL, 6 (9), pp. 2419–2425, 2011, ISSN: 1861-4728. |
A competitive co-cultivation assay for cancer drug specificity evaluation Journal Article In: Journal of Biomolecular Screening, 16 (8), pp. 818–824, 2011, ISSN: 1552-454X. |
Polyphosphates and Pyrophosphates of Pentopyranoses and Pentofuranoses as Allosteric Effectors of Human Hemoglobin: Synthesis, Molecular Recognition, and Oxygen Release Journal Article In: CHEMMEDCHEM, 6 (8), pp. 1495–1508, 2011, ISSN: 1860-7179. |
Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method Journal Article In: JOURNAL OF CHEMICAL PHYSICS, 135 (4), 2011, ISSN: 0021-9606. |
Behind the folding funnel diagram Journal Article In: NATURE CHEMICAL BIOLOGY, 7 (7), pp. 401–404, 2011, ISSN: 1552-4450. |
Thermoresponsive Dynamers: Thermally Induced, Reversible Chain Elongation of Amphiphilic Poly(acylhydrazones) Journal Article In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133 (28), pp. 10966–10973, 2011, ISSN: 0002-7863. |
Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR Journal Article In: Lab on a Chip, 11 (13), pp. 2167–2174, 2011, ISSN: 1473-0189. |
Quantitative and sensitive detection of rare mutations using droplet-based microfluidics Journal Article In: Lab on a Chip, 11 (13), pp. 2156–2166, 2011, ISSN: 1473-0189. |
Large molecular fluorescence enhancement by a nanoaperture with plasmonic corrugations Journal Article In: OPTICS EXPRESS, 19 (14), pp. 13056–13062, 2011, ISSN: 1094-4087. |
Dispersion of strongly confined channel plasmon polariton modes Journal Article In: JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, 28 (7), pp. 1596–1602, 2011, ISSN: 0740-3224. |
Blueprinting macromolecular electronics Journal Article In: NATURE CHEMISTRY, 3 (6), pp. 431–436, 2011, ISSN: 1755-4330. |
Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis Journal Article In: JOURNAL OF PHYSICAL CHEMISTRY B, 115 (24), pp. 7991–7995, 2011, ISSN: 1520-6106. |
Field enhancement and extraordinary optical transmission by tapered periodic slits in gold films Journal Article In: NEW JOURNAL OF PHYSICS, 13 , 2011, ISSN: 1367-2630. |
Plasmonic Antennas for Directional Sorting of Fluorescence Emission Journal Article In: NANO LETTERS, 11 (6), pp. 2400–2406, 2011, ISSN: 1530-6984. |
H-Bonding Tuned Self-Assembly of Phenylene-Thiophene-Thiophene-Phenylene Derivatives at Surfaces: Structural and Electrical Studies Journal Article In: JOURNAL OF PHYSICAL CHEMISTRY C, 115 (19), pp. 9753–9759, 2011, ISSN: 1932-7447. |
Transition-Metal-Complexed Cyclic [3]- and [4]Pseudorotaxanes Containing Rigid Ring-and-Filament Conjugates: Synthesis and Solution Studies Journal Article In: CHEMISTRY-A EUROPEAN JOURNAL, 17 (19), pp. 5404–5414, 2011, ISSN: 0947-6539. |
Intercalation of Tetrathiafulvalene between the Two Plates of a Copper(I)-Complexed [4]Rotaxane Journal Article In: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (13), pp. 2413–2416, 2011, ISSN: 1434-193X. |
Mechanisms for extraordinary optical transmission through bull's eye structures Journal Article In: OPTICS EXPRESS, 19 (11), pp. 10429–10442, 2011, ISSN: 1094-4087. |
Reversible Switching of Ultrastrong Light-Molecule Coupling Journal Article In: PHYSICAL REVIEW LETTERS, 106 (19), 2011, ISSN: 0031-9007. |
Mastering Self-Organization of Functional Materials at Different Length Scale Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (7, SI), pp. 1210–1211, 2011, ISSN: 1616-301X. |
Non-conventional Processing and Post-processing Methods for the Nanostructuring of Conjugated Materials for Organic Electronics Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (7, SI), pp. 1279–1295, 2011, ISSN: 1616-301X. |
Unsuspected pathway of the allosteric transition in hemoglobin Journal Article In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108 (14), pp. 5608–5613, 2011, ISSN: 0027-8424. |
Beyond synthesis: Self-organization Journal Article In: COMPTES RENDUS CHIMIE, 14 (4), pp. 348–361, 2011, ISSN: 1631-0748. |
Controlled Supramolecular Oligomerization of C-3-Symmetrical Molecules in Water: The Impact of Hydrophobic Shielding Journal Article In: CHEMISTRY-A EUROPEAN JOURNAL, 17 (18), pp. 5193–5203, 2011, ISSN: 0947-6539. |
New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications Journal Article In: Analytical Chemistry, 83 (8), pp. 2852–2857, 2011, ISSN: 1520-6882. |
Optical Modulation of the Charge Injection in an Organic Field-Effect Transistor Based on Photochromic Self-Assembled-Monolayer-Functionalized Electrodes Journal Article In: ADVANCED MATERIALS, 23 (12), pp. 1447–1452, 2011, ISSN: 0935-9648. |
Self-Assembled Conjugated Thiophene-Based Rotaxane Architectures: Structural, Computational, and Spectroscopic Insights into Molecular Aggregation Journal Article In: ADVANCED FUNCTIONAL MATERIALS, 21 (5), pp. 834–844, 2011, ISSN: 1616-301X. |
Local Surface Potential of pi-Conjugated Nanostructures by Kelvin Probe Force Microscopy: Effect of the Sampling Depth Journal Article In: SMALL, 7 (5), pp. 634–639, 2011, ISSN: 1613-6810. |
Myo-InositolTrisPyroPhosphate Treatment Leads to HIF-1 alpha Suppression and Eradication of Early Hepatoma Tumors in Rats Journal Article In: CHEMBIOCHEM, 12 (5), pp. 777–783, 2011, ISSN: 1439-4227. |
Cysteine Mapping in Conformationally Distinct Kinase Nucleotide Binding Sites: Application to the Design of Selective Covalent Inhibitors Journal Article In: JOURNAL OF MEDICINAL CHEMISTRY, 54 (5), pp. 1347–1355, 2011, ISSN: 0022-2623. |
Rigid Dimers Formed through Strong Interdigitated Ħ-Bonds Yield Compact 1D Supramolecular Helical Polymers Journal Article In: SMALL, 7 (3), pp. 342–350, 2011, ISSN: 1613-6810. |
Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI Journal Article In: JOURNAL OF CHEMICAL PHYSICS, 134 (8), 2011, ISSN: 0021-9606. |
Reversible Aminal Formation: Controlling the Evaporation of Bioactive Volatiles by Dynamic Combinatorial/Covalent Chemistry Journal Article In: EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (4), pp. 681–695, 2011, ISSN: 1434-193X. |
A new terrestrial vertebrate site just after the Paleocene-Eocene boundary in the Mortemer Formation of Upper Normandy, France Journal Article In: COMPTES RENDUS PALEVOL, 10 (1), pp. 11–20, 2011, ISSN: 1631-0683. |
Luminescence studies of copper(I)-containing [2]pseudorotaxanes Journal Article In: CANADIAN JOURNAL OF CHEMISTRY, 89 (2), pp. 98–103, 2011, ISSN: 0008-4042. |
Translating instructions into function by nucleic acid programmed self-assembly Journal Article In: ACTUALITE CHIMIQUE, (348-49), pp. 42–48, 2011, ISSN: 0151-9093. |
Bright Unidirectional Fluorescence Emission of Molecules in a Nanoaperture with Plasmonic Corrugations Journal Article In: NANO LETTERS, 11 (2), pp. 637–644, 2011, ISSN: 1530-6984. |
Modulating the self-assembly of rigid “clicked” dendrimers at the solid-liquid interface by tuning non-covalent interactions between side groups Journal Article In: CHEMICAL COMMUNICATIONS, 47 (38), pp. 10578–10580, 2011, ISSN: 1359-7345. |
Nanopatterning the graphite surface with ordered macrocyclic or ribbon-like assemblies of isocytosine derivatives: an STM study Journal Article In: CRYSTENGCOMM, 13 (18), pp. 5535–5537, 2011, ISSN: 1466-8033. |
Integration of self-assembled discotic-based fibres into field-effect transistors: a comparison of preparation approaches Journal Article In: JOURNAL OF MATERIALS CHEMISTRY, 21 (1), pp. 206–213, 2011, ISSN: 0959-9428. |
Charge transport in graphene-polythiophene blends as studied by Kelvin Probe Force Microscopy and transistor characterization Journal Article In: JOURNAL OF MATERIALS CHEMISTRY, 21 (9), pp. 2924–2931, 2011, ISSN: 0959-9428. |