Molecular QTAIM Topology Is Sensitive to Relativistic Corrections

The topology of the molecular electron density of benzene dithiol gold cluster complex Au₄−S−C₆H₄−S′−Au′₄ changed when relativistic corrections were made and the structure was close to a minimum of the Born–Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.     

A Theoretical study on the charge and discharge states of Na-ion battery cathode material,Na1+xFePO4F

Na₂FePO₄F is a promising cathode material for a Na-ion battery because of its high electronic capacity and good cycle performance. In this work, first principle calculations combined with cluster expansion and the Monte Carlo method have been applied to analyze the charge and discharge processes of Na₂FePO₄F by examining the voltage curve and the phase diagram. As a result of the density functional theory calculation and experimental verification with structural analysis, we found that the most stable structure of Na_1.5FePO₄F has the P2₁/b11 space group, which has not been reported to date. The estimated voltage curve has two clear plateaus caused by the two-phase structure composed of P2₁/b11 Na_1.5FePO₄F and Pbcn Na₂FePO₄F or Na₁FePO₄F and separated along the c-axis direction. The phase diagram shows the stability of the phase-separated structure. Considering that Na₂FePO₄F has diffusion paths in the a- and c-axis directions, Na₂FePO₄F has both innerphase and interphase diffusion paths. We suggest that the stable two-phase structure and the diffusion paths to both the innerphase and interphases are a key for the very clear plateau. We challenge to simulate a nonequilibrium state at high rate discharge with high temperature by introducing a coordinate-dependent chemical potential. The simulation shows agreement with the experimental discharge curve on the disappearance of the two plateaus. © 2018 Wiley Periodicals, Inc.     

Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo-Ring Formation with 8π-6π Electrocyclization

Shimalactones A and B are neuritogenic polyketides possessing characteristic oxabicyclo[2.2.1]heptane and bicyclo[4.2.0]octadiene ring systems that are produced by the marine fungus Emericella variecolor GF10. We identified a candidate biosynthetic gene cluster and conducted heterologous expression analysis. Expression of ShmA polyketide synthase in Aspergillus oryzae resulted in the production of preshimalactone. Aspergillus oryzae and Saccharomyces cerevisiae transformants expressing ShmA and ShmB produced shimalactones A and B, thus suggesting that the double bicyclo-ring formation reactions proceed non-enzymatically from preshimalactone epoxide. DFT calculations strongly support the idea that oxabicyclo-ring formation and 8π-6π electrocyclization proceed spontaneously after opening of the preshimalactone epoxide ring through protonation. We confirmed the formation of preshimalactone epoxide in vitro, followed by its non-enzymatic conversion to shimalactones in the dark.     

A theory of reflection and refraction of light by a metal

Optical Review - The optical properties of a metal are revisited. Starting from Maxwell’s equations, a rigorous calculation on the reflection and refraction of light at the interface between...     

Coronenetetraimide‐Centered Cruciform Pentamers Containing Multiporphyrin Units: Synthesis and Sequential Photoinduced Energy‐ and Electron‐Transfer Dynamics

A series of coronenetetraimide (CorTIm)‐centered cruciform pentamers containing multiporphyrin units, in which four porphyrin units are covalently linked to a CorTIm core through benzyl linkages, were designed and synthesized to investigate their structural, spectroscopic, and electrochemical properties as well as photoinduced electron‐ and energy‐transfer dynamics. These systems afforded the first synthetic case of coroneneimide derivatives covalently linked with dye molecules. The steady‐state absorption and electrochemical results indicate that a CorTIm and four porphyrin units were successfully characterized by the corresponding reference monomers. In contrast, the steady‐state fluorescence measurements demonstrated that strong fluorescence quenching relative to the corresponding monomer units was observed in these pentamers. Nanosecond laser flash photolysis measurements revealed the occurrence of intermolecular electron transfer from triplet excited state of zinc porphyrins to CorTIm. Femtosecond laser‐induced transient absorption measurements for excitation of the CorTIm unit clearly demonstrate the sequential photoinduced energy and electron transfer between CorTIm and porphyrins, that is, occurrence of the initial energy transfer from CorTIm (energy donor) to porphyrins (energy acceptor) and subsequent electron transfer from porphyrins (electron donor) to CorTIm (electron acceptor) in these pentamers, whereas only the electron‐transfer process from porphyrins to CorTIm was observed when we mainly excite porphyrin units. Finally, construction of high‐order supramolecular patterning of these pentamers was performed by utilizing self‐assembly and physical dewetting during the evaporation of solvent.     

Reconstitution of Biosynthetic Machinery for the Synthesis of the Highly Elaborated Indole Diterpene Penitrem

Penitrem A is one of the most elaborated members of the fungal indole diterpenes. Two separate penitrem gene clusters were identified using genomic and RNA sequencing data, and 13 out of 17 transformations in the penitrem biosynthesis were elucidated by heterologous reconstitution of the relevant genes. These reactions involve 1) a prenylation‐initiated cationic cyclization to install the bicyclo[3.2.0]heptane skeleton (PtmE), 2) a two‐step P450‐catalyzed oxidative processes forming the unique tricyclic penitrem skeleton (PtmK and PtmU), and 3) five sequential oxidative transformations (PtmKULNJ). Importantly, without conventional gene disruption, reconstitution of the biosynthetic machinery provided sufficient data to determine the pathway. It was thus demonstrated that the Aspergillus oryzae reconstitution system is a powerful method for studying the biosynthesis of complex natural products.     

Towards the chiral metabolomics: Liquid chromatography–mass spectrometry based dl-amino acid analysis after labeling with a new chiral reagent, (S)-2,5-dioxopyrrolidin-1-yl-1-(4,6-dimethoxy-1,3,5-triazin-2-yl)pyrrolidine-2-carboxylate,and the application to saliva of healthy volunteers

A novel triazine-type chiral derivatization reagent, i.e., (S)-2,5-dioxopyrrolidin-1-yl-1-(4,6-dimethoxy-1,3,5-triazin-2-yl) pyrrolidine-2-carboxylate (DMT-(S)-Pro-OSu), was developed for the highly sensitive and selective detection of chiral amines and amino acids by UPLC–MS/MS analysis. The enantiomers of amino acids were easily labeled with the reagents at room temperature within 40 min in an alkaline medium containing triethylamine. The diastereomers derived from proteolytic amino acids, except serine, were well separated under isocratic elution conditions by reversed-phase chromatography using an ODS column (R_s = 1.2–9.0). dl-Serine was separated by use of an ADME column which has relatively higher polar surface than the conventional ODS column. The characteristic product ions, i.e., m/z 195.3 and m/z 209.3, were detected from all the diastereomers by the collision-induced dissociation of the protonated molecule. A highly sensitive detection on the amol–fmol level was obtained from the selected reaction monitoring (SRM) chromatogram. The chiral amines (e.g., adrenaline and noradrenaline) labeled with DMT-(S)-Pro-OSu were also well separated and sensitively detected by the present procedure. The method using DMT-(S)-Pro-OSu was used for the determination of dl-amino acids in the human saliva from healthy volunteers. Various l-amino acids were identified in the saliva. Furthermore, d-alanine (d-Ala) and d-proline (d-Pro) were also detected in relatively high concentrations (>5%). The ratio was higher in male saliva than in female saliva. However, the difference in the ratio of d-Ala for one day was not very high and the effect of foods and beverage seemed to be negligible. Based on the results using l-Ala-d₃, the d-Ala in saliva seemed to be produced due to the racemization with some enzymes such as racemase. The racemization reaction was reversible, i.e., d-Ala-d₃ was also racemized to l-Ala-d₃ in saliva. Thus, care should be taken during the analysis of dl-amino acids in saliva. The present method using DMT-(S)-Pro-OSu may be applicable for the determination of chiral amine metabolomics, because the resulting derivatives produce the same product ions without relation to the compounds and show highly sensitive detection in the SRM mode of MS/MS. Consequently, DMT-(S)-Pro-OSu seems to be a useful chiral derivatization reagent for the determination of amines and amino acids in biological samples.