Multi-Orbital Molecular Compound (TTM-TTP)I_3: Effective Model and Fragment Decomposition

The electronic structure of the molecular compound (TTM-TTP)I_3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.Comment: 5 pages, 4 figures, published versio

Finite-Temperature Properties across the Charge Ordering Transition -- Combined Bosonization, Renormalization Group, and Numerical Methods

We theoretically describe the charge ordering (CO) metal-insulator transition based on a quasi-one-dimensional extended Hubbard model, and investigate the finite temperature ($T$) properties across the transition temperature, $T_{\rm CO}$. In order to calculate $T$ dependence of physical quantities such as the spin susceptibility and the electrical resistivity, both above and below $T_{\rm CO}$, a theoretical scheme is developed which combines analytical methods with numerical calculations. We take advantage of the renormalization group equations derived from the effective bosonized Hamiltonian, where Lanczos exact diagonalization data are chosen as initial parameters, while the CO order parameter at finite-$T$ is determined by quantum Monte Carlo simulations. The results show that the spin susceptibility does not show a steep singularity at $T_{\rm CO}$, and it slightly increases compared to the case without CO because of the suppression of the spin velocity. In contrast, the resistivity exhibits a sudden increase at $T_{\rm CO}$, below which a characteristic $T$ dependence is observed. We also compare our results with experiments on molecular conductors as well as transition metal oxides showing CO.Comment: 9 pages, 8 figure

Charge-ordering and optical transitions of LiV2O5 and NaV2O5

We present the measurements of the polarized optical spectra of NaV2O5 and LiV2O5. In an energy range from 0.5 to 5.5 eV we observe similar peaks in the E parallel a spectra of LiV2O5 and NaV2O5, which suggests similar electronic structure along the a axis in both materials. On the other hand, we find an almost complete suppression of the peaks in sigma_b of LiV2O5 around 1 and 5 eV. We attribute this suppression to the charge localization originating from the existence of double-chain charge-ordering patterin in LiV2O5.Comment: 7 pages, 3 figures final version, to appear in PR

Theoretical Aspects of Charge Ordering in Molecular Conductors

Theoretical studies on charge ordering phenomena in quarter-filled molecular (organic) conductors are reviewed. Extended Hubbard models including not only the on-site but also the inter-site Coulomb repulsion are constructed in a straightforward way from the crystal structures, which serve for individual study on each material as well as for their systematic understandings. In general the inter-site Coulomb interaction stabilizes Wigner crystal-type charge ordered states, where the charge localizes in an arranged manner avoiding each other, and can drive the system insulating. The variety in the lattice structures, represented by anisotropic networks in not only the electron hopping but also in the inter-site Coulomb repulsion, brings about diverse problems in low-dimensional strongly correlated systems. Competitions and/or co-existences between the charge ordered state and other states are discussed, such as metal, superconductor, and the dimer-type Mott insulating state which is another typical insulating state in molecular conductors. Interplay with magnetism, e.g., antiferromagnetic state and spin gapped state for example due to the spin-Peierls transition, is considered as well. Distinct situations are pointed out: influences of the coupling to the lattice degree of freedom and effects of geometrical frustration which exists in many molecular crystals. Some related topics, such as charge order in transition metal oxides and its role in new molecular conductors, are briefly remarked.Comment: 21 pages, 19 figures, to be published in J. Phys. Soc. Jpn. special issue on "Organic Conductors"; figs. 4 and 11 replaced with smaller sized fil

A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System

Signal transduction systems and ABC transporters often contribute jointly to adaptive bacterial responses to environmental changes. In Bacillus subtilis, three such pairs are involved in responses to antibiotics: BceRSAB, YvcPQRS and YxdJKLM. They are characterized by a histidine kinase belonging to the intramembrane sensing kinase family and by a translocator possessing an unusually large extracytoplasmic loop. It was established here using a phylogenomic approach that systems of this kind are specific but widespread in Firmicutes, where they originated. The present phylogenetic analyses brought to light a highly dynamic evolutionary history involving numerous horizontal gene transfers, duplications and lost events, leading to a great variety of Bce-like repertories in members of this bacterial phylum. Based on these phylogenetic analyses, it was proposed to subdivide the Bce-like modules into six well-defined subfamilies. Functional studies were performed on members of subfamily IV comprising BceRSAB from B. subtilis, the expression of which was found to require the signal transduction system as well as the ABC transporter itself. The present results suggest, for the members of this subfamily, the occurrence of interactions between one component of each partner, the kinase and the corresponding translocator. At functional and/or structural levels, bacitracin dependent expression of bceAB and bacitracin resistance processes require the presence of the BceB translocator loop. Some other members of subfamily IV were also found to participate in bacitracin resistance processes. Taken together our study suggests that this regulatory mechanism might constitute an important common antibiotic resistance mechanism in Firmicutes. [Supplemental material is available online at http://www.genome.org.

Identification of Lysine 37 of Histone H2B as a Novel Site of Methylation

Recent technological advancements have allowed for highly-sophisticated mass spectrometry-based studies of the histone code, which predicts that combinations of post-translational modifications (PTMs) on histone proteins result in defined biological outcomes mediated by effector proteins that recognize such marks. While significant progress has been made in the identification and characterization of histone PTMs, a full appreciation of the complexity of the histone code will require a complete understanding of all the modifications that putatively contribute to it. Here, using the top-down mass spectrometry approach for identifying PTMs on full-length histones, we report that lysine 37 of histone H2B is dimethylated in the budding yeast Saccharomyces cerevisiae. By generating a modification-specific antibody and yeast strains that harbor mutations in the putative site of methylation, we provide evidence that this mark exist in vivo. Importantly, we show that this lysine residue is highly conserved through evolution, and provide evidence that this methylation event also occurs in higher eukaryotes. By identifying a novel site of histone methylation, this study adds to our overall understanding of the complex number of histone modifications that contribute to chromatin function

Polaronic states with Spin-Charge-Coupled Excitation in a 1D Mott Insulator K-TCNQ

We discuss photogenerated midgap states of a one-dimensional (1D) dimerized Mott insulator, potassium-tetracyanoquinodimethane (K-TCNQ). Two types of phonon modes are taken into account: intermolecular and intramolecular vibrations. We treat these phonon modes adiabatically and analyze a theoretical model by using the density-matrix renormalization group (DMRG). Our numerical results demonstrate that the intermolecular lattice distortion is necessary to reproduce the photoinduced midgap absorption in K-TCNQ. We find two types of midgap states. One is a usual polaronic state characterized by a localized elementary excitation. The other is superposition of two types of excitations, a doped-carrier state and a triplet-dimer state, which can be generally observed in 1D dimerized Mott insulators, not limited to K-TCNQ.Comment: 6 pages, 8 figures, to appear in J. Phys. Soc. Jpn. Vol.77, No.7 (2008

Acetic Acid Bacteria: Physiology and Carbon Sources Oxidation

Acetic acid bacteria (AAB) are obligately aerobic bacteria within the family Acetobacteraceae, widespread in sugary, acidic and alcoholic niches. They are known for their ability to partially oxidise a variety of carbohydrates and to release the corresponding metabolites (aldehydes, ketones and organic acids) into the media. Since a long time they are used to perform specific oxidation reactions through processes called “oxidative fermentations”, especially in vinegar production. In the last decades physiology of AAB have been widely studied because of their role in food production, where they act as beneficial or spoiling organisms, and in biotechnological industry, where their oxidation machinery is exploited to produce a number of compounds such as l-ascorbic acid, dihydroxyacetone, gluconic acid and cellulose. The present review aims to provide an overview of AAB physiology focusing carbon sources oxidation and main products of their metabolism

Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11

The proteasome is a vital cellular machine that maintains protein homeostasis, which is of particular importance in multiple myeloma and possibly other cancers. Targeting of proteasome 20S peptidase activity with bortezomib and carfilzomib has been widely used to treat myeloma. However, not all patients respond to these compounds, and those who do eventually suffer relapse. Therefore, there is an urgent and unmet need to develop new drugs that target proteostasis through different mechanisms. We identified quinoline-8-thiol (8TQ) as a first-in-class inhibitor of the proteasome 19S subunit Rpn11. A derivative of 8TQ, capzimin, shows >5-fold selectivity for Rpn11 over the related JAMM proteases and >2 logs selectivity over several other metalloenzymes. Capzimin stabilized proteasome substrates, induced an unfolded protein response, and blocked proliferation of cancer cells, including those resistant to bortezomib. Proteomic analysis revealed that capzimin stabilized a subset of polyubiquitinated substrates. Identification of capzimin offers an alternative path to develop proteasome inhibitors for cancer therapy