Extended implementation of canonical transformation theory: parallelization and a new level-shifted condition

The canonical transformation (CT) theory has been developed as a multireference electronic structure method to compute high-level dynamic correlation on top of a large active space reference treated with the ab initio density matrix renormalization group method. This article describes a parallelized algorithm and implementation of the CT theory to handle large computational demands of the CT calculation, which has the same scaling as the coupled cluster singles and doubles theory. To stabilize the iterative solution of the CT method, a modification to the CT amplitude equation is introduced with the inclusion of a level shift parameter. The level-shifted condition has been found to effectively remove a type of intruder state that arises in the linear equations of CT and to address the discontinuity problems in the potential energy curves observed in the previous CT studies.     

Exploring chemistry with the fragment molecular orbital method

The fragment molecular orbital (FMO) method makes possible nearly linear scaling calculations of large molecular systems, such as water clusters, proteins and DNA. In particular, FMO has been widely used in biochemical applications involving protein-ligand binding and drug design. The method has been efficiently parallelized suitable for petascale computing. Many commonly used wave functions and solvent models have been interfaced with FMO. We review the historical background of FMO, and summarize its method development and applications.     

High-volume production of single and compound emulsions in a microfluidic parallelization arrangement coupled with coaxial annular world-to-chip interfaces

This study describes a microfluidic platform with coaxial annular world-to-chip interfaces for high-throughput production of single and compound emulsion droplets, having controlled sizes and internal compositions. The production module consists of two distinct elements: a planar square chip on which many copies of a microfluidic droplet generator (MFDG) are arranged circularly, and a cubic supporting module with coaxial annular channels for supplying fluids evenly to the inlets of the mounted chip, assembled from blocks with cylinders and holes. Three-dimensional flow was simulated to evaluate the distribution of flow velocity in the coaxial multiple annular channels. By coupling a 1.5 cm × 1.5 cm microfluidic chip with parallelized 144 MFDGs and a supporting module with two annular channels, for example, we could produce simple oil-in-water (O/W) emulsion droplets having a mean diameter of 90.7 μm and a coefficient of variation (CV) of 2.2% at a throughput of 180.0 mL h(-1). Furthermore, we successfully demonstrated high-throughput production of Janus droplets, double emulsions and triple emulsions, by coupling 1.5 cm × 1.5 cm - 4.5 cm × 4.5 cm microfluidic chips with parallelized 32-128 MFDGs of various geometries and supporting modules with 3-4 annular channels.     

A thiol-mediated active membrane transport of selenium by erythroid anion exchanger 1 protein

In this paper, we describe a thiol-mediated and energy-dependent membrane transport of selenium by erythroid anion exchanger 1 (AE1, also known as band 3 protein). The AE1 is the most abundant integral protein of red cell membranes and plays a critical role in the carbon dioxide transport system in which carbon dioxide is carried as bicarbonate in the plasma. This protein mediates the membrane transport of selenium, an essential antioxidant micronutrient, from red cells to the plasma in a manner that is distinct from the already known anion exchange mechanism. In this pathway, selenium bound to the cysteine 93 of the hemoglobin β chain (Hb-Cysβ93) is transported by the relay mechanism to the Cys317 of the amino-terminal cytoplasmic domain of the AE1 on the basis of the intrinsic interaction between the two proteins and is subsequently exported to the plasma via the Cys843 of the membrane-spanning domain. The selenium export did not occur in plain isotonic buffer solutions and required thiols, such as albumin, in the outer medium. Such a membrane transport mechanism would also participate in the export pathways of the nitric oxide vasodilator activity and other thiol-reactive substances bound to the Hb-Cysβ93 from red cells to the plasma and/or peripherals.     

Eu(III) emission band changes caused by peripheral C-H/O hydrogen bonding

We synthesized Eu(III) and Sm(III) complexes with tridentate phosphine oxide ligands, Eu(hfa)(3)(TPPM) and Sm(hfa)(3)(TPPM) (hfa: hexafluoroacetylacetonato, TPPM: tris(diphenylphosphinyl)methane), and we then examined their luminescent properties. In the complexes the Eu(III) and Sm(III) centres were fully surrounded by low-vibrational frequency ligands, which led to relatively high emission quantum yields (Φ(Eu) = 30%, Φ(Sm) = 4.7%). The X-ray single crystal structures of the Eu(hfa)(3)(TPPM) revealed nona-coordinated Eu(III) complexes and C-H/O hydrogen bonding formations between the acidic hydrogen atom of the TPPM ligand and oxygen atoms of solvent molecules. The C-H/O hydrogen bonding slightly affected the coordination structure around the Eu(III) ion. Despite the seemingly small effect on the structural change, because the emission band profile of the (5)D(0)→(7)F(2) transition is sensitive to changes in the coordination environment of the Eu(III) complex, we observed a red shift in the emission spectral line.     

Protein conformational gating of enzymatic activity in xanthine oxidoreductase

In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 ? resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.     

Chemical understanding of carbide cluster metallofullerenes: a case study on Sc2C2@C2v(5)-C80 with complete X-ray crystallographic characterizations

Little is known about the chemical properties of carbide cluster metallofullerenes (CCMFs). Here we report the photochemical reaction of a newly assigned CCMF Sc(2)C(2)@C(2v)(5)-C(80) with 2-adamantane-2,3-[3H]-diazirine (AdN(2), 1), which provides a carbene reagent under irradiation. Five monoadduct isomers (2a-2e), with respective abundances of 20%, 40%, 25%, 5%, and 10%, were isolated and characterized with a combination of experimental techniques including unambiguous single-crystal X-ray crystallography. Results show that the two Sc atoms of the bent Sc(2)C(2) cluster tend to move in most cases, whereas the C(2)-unit is almost fixed. Accordingly, it is difficult to explain the addition patterns by considering the strain and charge density on the cage with a fixed cluster, and thus a moving cluster may account for the addition patterns. These results show that the situation of CCMFs is more complicated than those in other metallofullerenes. Furthermore, a thermal isomerization process from 2b to 2c was observed, confirming that the most abundant isomer 2b is a kinetically favored adduct. Finally, it is revealed that the electronic and electrochemical properties of pristine Sc(2)C(2)@C(2v)(5)-C(80) have been markedly altered by exohedral modification.     

Enol ethers as substrates for efficient Z- and enantioselective ring-opening/cross-metathesis reactions promoted by stereogenic-at-Mo complexes: utility in chemical synthesis and mechanistic attributes

The first examples of catalytic enantioselective ring-opening/cross-metathesis (EROCM) reactions that involve enol ethers are reported. Specifically, we demonstrate that catalytic EROCM of several oxa- and azabicycles, cyclobutenes and a cyclopropene with an alkyl- or aryl-substituted enol ether proceed readily in the presence of a stereogenic-at-Mo monopyrrolide-monoaryloxide. In some instances, as little as 0.15 mol % of the catalytically active alkylidene is sufficient to promote complete conversion within 10 min. The desired products are formed in up to 90% yield and >99:1 enantiomeric ratio (er) with the disubstituted enol ether generated in >90% Z selectivity. The enol ether of the enantiomerically enriched products can be easily differentiated from the terminal alkene through a number of functionalization procedures that lead to the formation of useful intermediates for chemical synthesis (e.g., efficient acid hydrolysis to afford the enantiomerically enriched carboxaldehyde). In certain cases, enantioselectivity is strongly dependent on enol ether concentration: larger equivalents of the cross partner leads to the formation of products of high enantiomeric purity (versus near racemic products with one equivalent). The length of reaction time can be critical to product enantiomeric purity; high enantioselectivity in reactions that proceed to >98% conversion in as brief a reaction time as 30 s can be nearly entirely eroded within 30 min. Mechanistic rationale that accounts for the above characteristics of the catalytic process is provided.     

Laser induced threshold photoemission magnetic circular dichroism and its application to photoelectron microscope

This work enlightens the threshold photoemission magnetic circular dichroism (MCD) and its adaption on photoemission electron microscopy (PEEM) using lasers. MCD is a simple and efficient way to investigate magnetic properties since it does not need any spin analyzers with low efficiency, and thus the MCD related techniques have developed to observe magnetic domains. Usually, MCD in a total yield measurement in the valence band with weak spin–orbit coupling (SOC) excited by low photon energy (hν≤ 6 eV) does not compete with the X-ray magnetic circular dichroism (XMCD) with strong SOC. XMCD PEEM observation of magnetic domains has been successfully established while MCD PEEM derived from valence bands has not been. However, using angle and energy resolved photoelectron, valence band MCD provides large asymmetry similar to that by XMCD. Threshold measurement of photoelectron in a total electron yield procedure can take advantage of the measurement of photoelectrons with a limited angle and energy mode. This restriction of the photoelectron makes the threshold MCD technique an efficient way to get magnetic information and gives more than 10% asymmetry for Ni/Cu(0 0 1), which is comparable to that obtained by angle resolved photoemission. Thus the threshold MCD technique is a suitable method to observe magnetic domains by PEEM. For threshold MCD, incident angle dependence and high sensitivity to out-of-plane magnetized films compared with in-plane ones are discussed. Ultrashort pulse lasers make it feasible to measure two photon photoemission MCD combined with PEEM, where resonant excitation has a possibility to enhance dichroic asymmetry. Recent results for valence band magnetic dichroism PEEM are presented.