Acceleration of self‐consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function

The Lagrange interpolation of molecular orbital (LIMO) method, which reduces the number of self‐consistent field iterations in ab initio molecular dynamics simulations with the Hartree–Fock method and the Kohn–Sham density functional theories, is extended to the theory of multiconfigurational wave functions. We examine two types of treatments for the active orbitals that are partially occupied. The first treatment, as denoted by LIMO(C), is a simple application of the conventional LIMO method to the union of the inactive core and the active orbitals. The second, as denoted by LIMO(S), separately treats the inactive core and the active orbitals. Numerical tests to compare the two treatments clarify that LIMO(S) is superior to LIMO(C). Further applications of LIMO(S) to various systems demonstrate its effectiveness and robustness. © 2014 Wiley Periodicals, Inc.     

Imaging mass spectrometry distinguished the cancer and stromal regions of oral squamous cell carcinoma by visualizing phosphatidylcholine (16:0/16:1) and phosphatidylcholine (18:1/20:4)

Most oral cancers are oral squamous cell carcinoma (OSCC). The anatomical features of OSCC have been histochemically evaluated with hematoxylin and eosin. However, the border between the cancer and stromal regions is unclear and large portions of the cancer and stromal regions are resected in surgery. To reduce the resected area and maintain oral function, a new method of diagnosis is needed. In this study, we tried to clearly distinguish the border on the basis of biomolecule distributions visualized by imaging mass spectrometry (IMS). In the IMS dataset, eleven signals were significantly different in intensity (p?<?0.01) between the cancer and stromal regions. Two signals at m/z 770.5 and m/z 846.6 were distributed in each region, and a clear border was revealed. Tandem mass spectrometric (MS/MS) analysis identified these signals as phosphatidylcholine (PC) (16:0/16:1) at m/z 770.5 in the cancer region and PC (18:1/20:4) at m/z 846.6 in the stromal region. Moreover, the distribution of PC species containing arachidonic acid in the stromal region suggests that lymphocytes accumulated in response to the inflammation caused by cancer invasion. In conclusion, the cancer and stromal regions of OSCCs were clearly distinguished by use of these PC species and IMS analysis, and this molecular identification can provide important information to elucidate the mechanism of cancer invasion.     

Function and association of CyanoP in photosystem II of Synechocystis sp. PCC 6803

The CyanoP protein is a cyanobacterial homolog of the PsbP protein, which is an extrinsic subunit of photosystem II (PSII) in green plant species. The molecular function of CyanoP has been investigated in mutant strains of Synechocystis but inconsistent results have been reported by different laboratories. In this study, we generated and characterized a Synechocystis mutant in which entire region of the CyanoP gene was eliminated. After repeated subculture in CaCl₂-depleted medium, growth retardation was clearly observed for a CyanoP knockout mutant of Synechocystis sp. PCC 6803 (?P). The PSII-mediated oxygen-evolving activity of the ?P cells was more susceptible to depletion of CaCl₂ than that of wild-type cells. The 77 K fluorescence emission spectra indicated that energy coupling between phycobilisome and PSII was perturbed in both wild-type and ?P cells under CaCl₂-depleted conditions, and was more evident for the ?P mutant. To examine the association of CyanoP with PSII complexes, we tested several detergents for solubilization of thylakoid membranes and showed that CyanoP was partly included in fractions containing large protein complexes in gel-filtration analysis. These results indicate that CyanoP constitutively stabilizes PSII functionality in vivo.     

Highly Mesoporous Metal‐Organic Frameworks as Synergistic Multimodal Catalytic Platforms for Divergent Cascade Reactions

Rational engineering and assimilation of diverse chemo‐ and biocatalytic functionalities in a single nanostructure is highly desired for efficient multistep chemical reactions but has so far remained elusive. Here, we design and synthesize multimodal catalytic nanoreactors (MCNRs) based on a mesoporous metal‐organic framework (MOF). The MCNRs consist of customizable metal nanocrystals and stably anchored enzymes in the mesopores, as well as coordinatively unsaturated cationic metal MOF nodes, all within a single nanoreactor space. The highly intimate and diverse catalytic mesoporous microenvironments and facile accessibility to the active site in the MCNR enables the cooperative and synergistic participation from different chemo‐ and biocatalytic components. This was shown by one‐pot multistep cascade reactions involving a heterogeneous catalytic nitroaldol reaction followed by a [Pd/lipase]‐catalyzed chemoenzymatic dynamic kinetic resolution to yield optically pure (>99 % ee) nitroalcohol derivatives in quantitative yields.     

An “OFF–ON–OFF” fluorescence protein-labeling probe for real-time visualization of the degradation of short-lived proteins in cellular systems

The ability to monitor proteolytic pathways that remove unwanted and damaged proteins from cells is essential for understanding the multiple processes used to maintain cellular homeostasis. In this study, we have developed a new protein-labeling probe that employs an ‘OFF–ON–OFF’ fluorescence switch to enable real-time imaging of the expression (fluorescence ON) and degradation (fluorescence OFF) of PYP-tagged protein constructs in living cells. Fluorescence switching is modulated by intramolecular contact quenching interactions in the unbound probe (fluorescence OFF) being disrupted upon binding to the PYP-tag protein, which turns fluorescence ON. Quenching is then restored when the PYP-tag–probe complex undergoes proteolytic degradation, which results in fluorescence being turned OFF. Optimization of probe structures and PYP-tag mutants has enabled this fast reacting ‘OFF–ON–OFF’ probe to be used to fluorescently image the expression and degradation of short-lived proteins.

An “OFF–ON–OFF” fluorescence probe for real-time imaging of the expression (fluorescence ‘OFF’) and degradation (fluorescence ‘ON’) of short lived PYP-tag proteins in cellular systems.     

Proton Conduction at High Temperature in High-Symmetry Hydrogen-Bonded Molecular Crystals of RuIII Complexes with Six Imidazole-Imidazolate Ligands

A new H-bonded crystal [Ru^III(Him)₃(Im)₃] with three imidazole (Him) and three imidazolate (Im⁻) groups was prepared to obtain a higher-temperature proton conductor than a Nafion membrane with water driving. The crystal is constructed by complementary N−H⋅⋅⋅N H-bonds between the Ru^III complexes and has a rare Icy-c* cubic network topology with a twofold interpenetration without crystal anisotropy. The crystals show a proton conductivity of 3.08×10⁻⁵ S cm⁻¹ at 450 K and a faster conductivity than those formed by only HIms. The high proton conductivity is attributed to not only molecular rotations and hopping motions of HIm frameworks that are activated at ∼113 K, but also isotropic whole-molecule rotation of [Ru^III(Him)₃(Im)₃] at temperatures greater than 420 K. The latter rotation was confirmed by solid-state ²H NMR spectroscopy; probable proton conduction routes were predicted and theoretically considered.     

Mean dimension of $${\mathbb{Z}^k}$$-actions

Mean dimension is a topological invariant for dynamical systems that is meaningful for systems with infinite dimension and infinite entropy. Given a \({\mathbb{Z}^k}\)-action on a compact metric space X, we study the following three problems closely related to mean dimension.

1. (1)
   When is X isomorphic to the inverse limit of finite entropy systems?
    
2. (2)
   Suppose the topological entropy \({h_{\rm top}(X)}\) is infinite. How much topological entropy can be detected if one considers X only up to a given level of accuracy? How fast does this amount of entropy grow as the level of resolution becomes finer and finer?
    
3. (3)
   When can we embed X into the \({\mathbb{Z}^k}\)-shift on the infinite dimensional cube \({([0,1]^D)^{\mathbb{Z}^k}}\)?
    

These were investigated for \({\mathbb{Z}}\)-actions in Lindenstrauss (Inst Hautes Études Sci Publ Math 89:227–262, 1999), but the generalization to \({\mathbb{Z}^k}\) remained an open problem. When X has the marker property, in particular when X has a completely aperiodic minimal factor, we completely solve (1) and a natural interpretation of (2), and give a reasonably satisfactory answer to (3).A key ingredient is a new method to continuously partition every orbit into good pieces.     

Conducting polymer based hybrid structure as transparent and flexible field electron emitter

An efficient cathode material with high transparency (93%) based on conducting polymer poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and single wall carbon nanotubes (SWCNTs) has been developed for the fabrication of highly transparent and flexible field electron emitters (FEE). This kind of material showed superior field emission (FE) performance with very high current density (10^–3A/cm²) at very low electric field. The FE performance of the hybrid materials was dramatically improved compared to either SWCNTs and PEDOT:PSS. Thus the hybrid structures of conducting polymer and SWCNTs might be a good choice for use as a cathode material to enhance the FE performance and for potential application in future portable displays. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)