Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies

Tailoring metal–organic hybrid interfaces: heteromolecular structures with varying stoichiometry on Ag(111)

The physical properties of interfaces between organic semiconductors and metal surfaces crucially influence the performance of organic electronic devices. In order to enable the tailoring of such metal–organic hybrid interfaces we study the adsorption of heteromolecular thin films containing the prototypical molecules copper-II-phthalocyanine (CuPc) and 3,4,9,10-perylene-tetra-carboxylic-dianhydride (PTCDA) on the Ag(111) surface. Here, we demonstrate how the lateral order can be tuned by changing the relative coverage of both adsorbates on the surface. The layer growth has been studied in real time with low energy electron microscopy, and—for different stoichiometries—the geometric properties of three heteromolecular submonolayer phases have been investigated using high resolution low energy electron diffraction and low temperature scanning tunneling microscopy. Furthermore, we have used a theoretical approach based on van der Waals and electrostatic potentials in order to reveal the influence of the intermolecular and the molecule–substrate interactions on the lateral order of heteromolecular films

Copper Phthalocyanine Monolayers and Multilayers on Ag(110) and Ag(111) Surfaces

Organic semiconductors and their potential for applications in electronic devices such as solar cells and organic light emitting diodesmake them interesting for fundamental research. Especially interfaces between different organic layers, e.g. PTCDA and CuPc, are subjects of experiments. To create a basis for the understanding of heteroorganic systems, the corresponding homomolecular phases are investigated regarding their geometric and electronic structure upon adsorption on a metal surface. While homomolecular phases of PTCDA on different noble metal surfaces are well-studied, less is known about adsorption and ordering of CuPc. Here we present a combined study employing (SPA)LEED, STM, STS and ARUPS to CuPc monolayers and multilayers adsorbed on the Ag(110) and Ag(111) surfaces

Single Component and Compound Monolayers of CuPc and PTCDA on a Ag(110) Surface

This work is motivated by the recent international effort to create an experimentally self-sustained dynamo. The dynamo effect, whose existence was proposed by Larmor at the beginning of the 20th century, is believed to be the explanation for the magnetic field of Earth and other celestial bodies due to the flow of a conducting fluid. In order to numerically study the von Kármán flow, which models the configuration of the dynamo experiment implemented at Cadarache, we have developed a new numerical approach for solving the magnetohydrodynamic equations in potential formulation in a finite cylindrical geometry. The poloidal-toroidal decomposition has been used to ensure the solenoidal character of the velocity and magnetic fields. We use the influence matrix technique to impose the boundary conditions for the velocity and the continuity between the internal and external magnetic fields. The computational power of the code, which is the result of the MPI-based parallelization, enabled us to investigate two problems concerning turbulence in cylindrical geometry: axisymmetric turbulence and a bifurcation between turbulent flows.Ce travail est motivé par l'effort international actuel de créer expérimentalement une dynamo fluide auto-entretenue. L'effet dynamo, dont l'existence a été prevu par Larmor au début du XXème siècle, est considéré comme étant responsable de la production du champ matnétique terrestre et d'autres objets célestes par l'intermédiaire de l'écoulement d'un fluide conducteur. Afin d'étudier numériquement l'écoulement de von Kármán, qui modélise la configuration d'une expérience dynamo mise en place à Cadarache, nous avons développé une approche numérique originale permettant la résolution des équations magnétohydrodynamiques dans une géométrie dylindrique en formulation potentielle. La décomposition en potentiels poloïdal et toroïdal a été utilisée pour garantir la nature solénoïdale des champs de vitesse et magnétique. Nous utilisons la technique de la matrice d'influence pour satisfaire aux conditions aux limites et aux conditions de continuité du champ magnétique à la paroi du cylindre. La grande puissance de calcul, résultant de la parallélisation MPI du code, a presmis de l'appliquer deux problèmes concernant la turbulence dans la géométrie cylindrique : la turbulence axisymétrique et une bifurcation entre états turbulents

Single Component and Compound Monolayers of CuPc and PTCDA on a Ag(110) Surface

Organic semiconductors are of great interest for research due to their potential application in organic electronics. Organic layers of one component on top of a metal crystal, traditionally, (111) surfaces of Ag, Au and Cu single crystals, have been studied for decades. Here, we report on the structure of ordered monolayers of CuPc and PTCDA on a Ag(110) surface, both single component and compound.The geometric arrangement and the electronic structure of the n-type semiconducting molecule PTCDA adsorbed on Ag(110) are well known. [1,2,3] On the contrary, the structure of the p-type semiconducting molecule CuPc on the same Ag(110) surface has been investigated only rarely, mainly by Low Energy Electron Diffraction (LEED) and Photoemission Spectroscopy (PES). [4,5] Wewill offer further results on this sample system gained by Angle-Resolved Photoemission Spectroscopy (ARUPS) and Orbital Tomography (OT).Recently, binary and multinary molecular film also have come into focus, e.g. for the application in organic p-n junctions and all-organic solar cells. We will present results obtained by LEED, ARUPS and OT on a laterally mixed layer of CuPc and PTCDA on Ag(110). In order to complete our investigations, in the next step Scanning Tunneling Microscopy and Scanning Tunneling Spectroscopy (STM, STS) will be applied to the mixed monolayer of CuPc and PTCDA on Ag(110) as well as to the monolayer ofpure CuPc on Ag(110).[1] Willenbockel et al., NJP 15 033017, 2013[2] Puschnig et al., PRB 84 235427, 2011[3] Ziroff et al., PRL 104 233004, 2010[4] Schäfer et al., Adv. Funct. Mat. 11 193, 2001[5] Song at al., JoP: Cond. Matt. 19 136002, 200

Single Component and Compound Monolayers of CuPc and PTCDA on a Ag(110) Surface

Organic semiconductors are of great interest for research due to their potential application in organic electronics. Organic layers of one component on top of a metal crystal have been studied for decades. Recently binary and multinary molecular films also have come into focus, e.g., for the application in organic p-n junctions and all-organic solar cells. Traditionally, (111) surfaces of Ag, Au and Cu single crystals were used for experimental studies. Here we report on the structure of ordered monolayers of CuPc and PTCDA on a Ag(110) surface, both single component and compound. Scanning Tunneling Microscopy and Low Energy Electron Diffraction were used

Adsorption height determination of nonequivalent C and O species of PTCDA on Ag(110) using x-ray standing waves

The normal incidence x-ray standing wave (NIXSW) technique is used to determine the adsorption geometry of submonolayer 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) adsorbed on the Ag(110) surface. An accurate analysis of both C1s and O1s photoemission (PE) spectra allows the respective adsorption heights of carbon and oxygen atoms in different chemical environments within PTCDA to be distinguished. Due to the intricacy of the PE fitting models, a systematic error analysis of NIXSW structural parameters was developed and employed. Based on the adsorption geometry of PTCDA on Ag(110) a bonding mechanism is discussed