Resolution of intramolecular dipoles and push-back effect of individual molecules on a metal surface

Molecules consisting of a donor and an acceptor moiety can exhibit large intrinsic dipole moments. Upon deposition on a metal surface, the dipole may be effectively screened and the charge distribution altered due to hybridization with substrate electronic states. Here, we deposit Ethyl-Diaminodicyanoquinone molecules, which exhibit a large dipole moment in gas phase, on a Au(111) surface. Employing a combination of scanning tunneling microscopy and non-contact atomic force microscopy, we find that a significant dipole moment persists in the flat-lying molecules. Density-functional theory calculations reveal that the dipole moment is even increased on the metal substrate as compared to the gas phase. We also show that the local contact potential across the molecular islands is decreased by several tens of meV with respect to the bare metal. We explain this by the induced charge-density redistribution due to the adsorbed molecules, which confine the substrate's wavefunction at the interface. Our local measurements provide direct evidence of this so-called push-back or cushion effect at the scale of individual molecules.Comment: This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Journal of Physical Chemistry

Variations of vibronic states in densely-packed structures of molecules with intramolecular dipoles

Electrostatic potentials strongly affect molecular energy levels and charge states, providing the fascinating opportunity of molecular gating. Their influence on molecular vibrations remains less explored. Here, we investigate Ethyl-Diaminodicyanoquinone molecules on a monolayer of MoS$_2$ on Au(111) using scanning tunneling and atomic force microscopy and spectroscopy. These molecules exhibit a large dipole moment in gas phase, which we find to (partially) persist on the MoS$_2$ monolayer. The self-assembled structures consist of chains, where the dipoles of neighboring molecules are aligned anti-parallel. Thanks to the decoupling efficiency of the molecular states from the metal by the MoS$_2$ interlayer, we resolve vibronic states of the molecules, which vary in intensity depending on the molecular surrounding. We suggest that the vibrations are strongly damped by electrostatic interactions with the environment

Weak splittings of quotients of Drinfeld and Heisenberg doubles

We investigate the fine structure of the simplectic foliations of Poisson homogeneous spaces. Two general results are proved for weak splittings of surjective Poisson submersions from Heisenberg and Drinfeld doubles. The implications of these results are that the torus orbits of symplectic leaves of the quotients can be explicitly realized as Poisson-Dirac submanifolds of the torus orbits of the doubles. The results have a wide range of applications to many families of real and complex Poisson structures on flag varieties. Their torus orbits of leaves recover important families of varieties such as the open Richardson varieties.Comment: 20 pages, AMS Late

Expert system for predicting reaction conditions: The Michael reaction case

© 2015 American Chemical Society. A generic chemical transformation may often be achieved under various synthetic conditions. However, for any specific reagents, only one or a few among the reported synthetic protocols may be successful. For example, Michael β-addition reactions may proceed under different choices of solvent (e.g., hydrophobic, aprotic polar, protic) and catalyst (e.g., Brønsted acid, Lewis acid, Lewis base, etc.). Chemoinformatics methods could be efficiently used to establish a relationship between the reagent structures and the required reaction conditions, which would allow synthetic chemists to waste less time and resources in trying out various protocols in search for the appropriate one. In order to address this problem, a number of 2-classes classification models have been built on a set of 198 Michael reactions retrieved from literature. Trained models discriminate between processes that are compatible and respectively processes not feasible under a specific reaction condition option (feasible or not with a Lewis acid catalyst, feasible or not in hydrophobic solvent, etc.). Eight distinct models were built to decide the compatibility of a Michael addition process with each considered reaction condition option, while a ninth model was aimed to predict whether the assumed Michael addition is feasible at all. Different machine-learning methods (Support Vector Machine, Naive Bayes, and Random Forest) in combination with different types of descriptors (ISIDA fragments issued from Condensed Graphs of Reactions, MOLMAP, Electronic Effect Descriptors, and Chemistry Development Kit computed descriptors) have been used. Models have good predictive performance in 3-fold cross-validation done three times: balanced accuracy varies from 0.7 to 1. Developed models are available for the users at http://infochim.u-strasbg.fr/webserv/VSEngine.html. Eventually, these were challenged to predict feasibility conditions for ∼50 novel Michael reactions from the eNovalys database (originally from patent literature)

Mask formulas for cograssmannian Kazhdan-Lusztig polynomials

We give two contructions of sets of masks on cograssmannian permutations that can be used in Deodhar's formula for Kazhdan-Lusztig basis elements of the Iwahori-Hecke algebra. The constructions are respectively based on a formula of Lascoux-Schutzenberger and its geometric interpretation by Zelevinsky. The first construction relies on a basis of the Hecke algebra constructed from principal lower order ideals in Bruhat order and a translation of this basis into sets of masks. The second construction relies on an interpretation of masks as cells of the Bott-Samelson resolution. These constructions give distinct answers to a question of Deodhar.Comment: 43 page

Generalizing Tanisaki's ideal via ideals of truncated symmetric functions

We define a family of ideals $I_h$ in the polynomial ring $\mathbb{Z}[x_1,...,x_n]$ that are parametrized by Hessenberg functions $h$ (equivalently Dyck paths or ample partitions). The ideals $I_h$ generalize algebraically a family of ideals called the Tanisaki ideal, which is used in a geometric construction of permutation representations called Springer theory. To define $I_h$, we use polynomials in a proper subset of the variables ${x_1,...,x_n}$ that are symmetric under the corresponding permutation subgroup. We call these polynomials {\em truncated symmetric functions} and show combinatorial identities relating different kinds of truncated symmetric polynomials. We then prove several key properties of $I_h$, including that if $h>h'$ in the natural partial order on Dyck paths then $I_{h} \subset I_{h'}$, and explicitly construct a Gr\"{o}bner basis for $I_h$. We use a second family of ideals $J_h$ for which some of the claims are easier to see, and prove that $I_h = J_h$. The ideals $J_h$ arise in work of Ding, Develin-Martin-Reiner, and Gasharov-Reiner on a family of Schubert varieties called partition varieties. Using earlier work of the first author, the current manuscript proves that the ideals $I_h = J_h$ generalize the Tanisaki ideals both algebraically and geometrically, from Springer varieties to a family of nilpotent Hessenberg varieties.Comment: v1 had 27 pages. v2 is 29 pages and adds Appendix B, where we include a recent proof by Federico Galetto of a conjecture given in the previous version. We also add some connections between our work and earlier results of Ding, Gasharov-Reiner, and Develin-Martin-Reiner. v3 corrects a typo in Valibouze's citation in the bibliography. To appear in Journal of Algebraic Combinatoric

Cloning, expression, purification and characterization of a DsbA-like protein from Wolbachia pipientis

Wolbachia pipientis are obligate endosymbionts that infect a wide range of insect and other arthropod species. They act as reproductive parasites by manipulating the host reproduction machinery to enhance their own transmission. This unusual phenotype is thought to be a consequence of the actions of secreted Wolbachia proteins that are likely to contain disulfide bonds to stabilize the protein structure. In bacteria, the introduction or isomerization of disulfide bonds in proteins is catalyzed by Dsb proteins. The Wolbachia genome encodes two proteins, a-DsbA1 and a-DsbA2, that might catalyze these steps. In this work we focussed on the 234 residue protein a-DsbA1; the gene was cloned and expressed in Escherichia coli, the protein was purified and its identity confirmed by mass spectrometry. The sequence identity of a-DsbA1 for both dithiol oxidants(E. coli DsbA, 12%) and disulfide isomerases(E. coli DsbC, 14%) is similar. We therefore sought to establish whether a-DsbA1 is an oxidant or an isomerase based on functional activity. The purified a-DsbA1 was active in an oxidoreductase assay but had little isomerase activity, indicating that a-DsbA1 is DsbA-like rather than DsbC-like. This work represents the first successful example of the characterization of a recombinant Wolbachia protein. Purified a-DsbA1 will now be used in further functional studies to identify protein substrates that could help explain the molecular basis for the unusual Wolbachia phenotypes, and in structural studies to explore its relationship to other disulfide oxidoreductase proteins. Copyright © 2008 Elsevier In

Disruption of reducing pathways is not essential for efficient disulfide bond formation in the cytoplasm of E. coli

<p>Abstract</p> <p>Background</p> <p>The formation of native disulfide bonds is a complex and essential post-translational modification for many proteins. The large scale production of these proteins can be difficult and depends on targeting the protein to a compartment in which disulfide bond formation naturally occurs, usually the endoplasmic reticulum of eukaryotes or the periplasm of prokaryotes. It is currently thought to be impossible to produce large amounts of disulfide bond containing protein in the cytoplasm of wild-type bacteria such as <it>E. coli </it>due to the presence of multiple pathways for their reduction.</p> <p>Results</p> <p>Here we show that the introduction of Erv1p, a sulfhydryl oxidase and FAD-dependent catalyst of disulfide bond formation found in the inter membrane space of mitochondria, allows the efficient formation of native disulfide bonds in heterologously expressed proteins in the cytoplasm of <it>E. coli </it>even without the disruption of genes involved in disulfide bond reduction, for example <it>trxB </it>and/or <it>gor</it>. Indeed yields of active disulfide bonded proteins were higher in BL21 (DE3) pLysSRARE, an <it>E. coli </it>strain with the reducing pathways intact, than in the commercial Δ<it>gor </it>Δ<it>trxB </it>strain rosetta-gami upon co-expression of Erv1p.</p> <p>Conclusions</p> <p>Our results refute the current paradigm in the field that disruption of at least one of the reducing pathways is essential for the efficient production of disulfide bond containing proteins in the cytoplasm of <it>E. coli </it>and open up new possibilities for the use of <it>E. coli </it>as a microbial cell factory.</p

Modulation of Bacterial Type III Secretion System by a Spermidine Transporter Dependent Signaling Pathway

10.1371/journal.pone.0001291PLoS ONE212