Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach

Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Recoil effects in high-energy photoemission beyond single-site approximation

Recoil effects of photoelectrons excited by high-energy X-rays are studied beyond the simplest approximation where elastic scatterings of photoelectrons are completely neglected (single-site approximation). At first we have shown that the simple free atom energy shift is accurately obtained within the harmonic and the single-site approximations. Beyond the single-site approximation, this simple formula does not work, but still simple classically acceptable formula can be used to explain the recoil energy shift. Illustrative numerical calculations show that the energy shifts caused by the photoelectron diffraction amounts to 5–8 meV for graphite-like carbon and about 100 meV for LiI₆${\text{LiI}}_6$ cluster at _?k=5${?}_k=5$–7 keV, and show oscillations as functions of the photoelectron energy. Furthermore we discuss the recoil effects in photoemission from extended levels by use of the tight-binding approach. Our approach naturally provides not only Debye–Waller factors but also the recoil factors. In addition to the phonon excitation, we also study the recoil effects associated with plasmon losses where intrinsic and extrinsic processes can interfere each other. Only the latter can contribute to the recoil energy shift.     

Synthesis,Structures, and Properties of Highly Strained Cyclophenylene–Ethynylenes with Axial and Helical Chirality

Single and double cyclophenylene–ethynylenes (CPEs) with axial and helical chirality have been synthesized by the Sonogashira cross-coupling of di- and tetraethynyl biphenyls with a U-shaped prearomatic diiodoparaphenylene followed by reductive aromatization. X-ray crystallographic analyses and DFT calculations revealed that the CPEs possess highly twisted bent structures. Bend angles on the edge of the paraphenylene units were close to the value of [5]cycloparaphenylene (CPP)—the smallest CPP to date. The double and single CPEs possessed stable chirality despite flexible biphenyl structures because of the high strain in the diethynyl–paraphenylene moiety. In both the single and double CPEs, orbital interactions along the biphenyl axis were observed by DFT calculations in LUMO and LUMO+2 of the single CPE and LUMO+1 of the double CPE, which likely cause lowering of these orbital energies. Concerning chiroptical properties: boosting of the g_abs value was observed in the biphenyl-based double CPE, as well as the binaphthyl-based single CPE, compared to the biphenyl-based single CPE.     

Enantioselective Synthesis of Polycyclic Aromatic Hydrocarbon (PAH)-Based Planar Chiral Bent Cyclophanes by Rhodium-Catalyzed [2+2+2] Cycloaddition

The enantioselective synthesis of polycyclic aromatic hydrocarbon (PAH)-based planar chiral cyclophanes was achieved for the first time by the rhodium-catalyzed intramolecular regio- and enantioselective [2+2+2] cycloaddition of tethered diyne-benzofulvenes followed by stepwise oxidative transformations. The thus synthesized planar chiral bent cyclophanes, that possess bent p-terphenyl- and 9-fluorenone-cores, were converted to 9-fluorenol-based ones with excellent ee values of >99 % by diastereoselective 1,2-reduction. These 9-fluorenol-based cyclophanes exhibited high fluorescence quantum yields, which were significantly higher than that of an acyclic reference molecule (78–82 % vs. 48 %). The bending effect on the chiroptical property was also examined, which revealed that the anisotropy factors (g_abs values) for electronic circular dichroism (ECD) of these 9-fluorenol-based planar chiral bent cyclophanes increase as the tether length becomes shorter.     

Direct synthesis of 1,3-diketones by Rh-catalyzed reductive alpha-acylation of enones

1,3-Diketones were synthesized from alpha,beta-unsaturated ketones by treatment with acid chlorides and Et(2)Zn in the presence of RhCl(PPh(3))3. This is a very simple and extremely chemoselective reaction to give the adduct at the alpha-position of alpha,beta-unsaturated ketones.     

Stir bar sorptive extraction and thermal desorption-gas chromatography-mass spectrometry for trace analysis of triclosan in water sample

A simple and highly sensitive method called stir bar sorptive extraction (SBSE) and thermal desorption (TD)-gas chromatography-mass spectrometry (GC-MS), which is used for the determination of trace amounts of 5-chloro-2-(2,4-dichlorophenoxy)phenol (triclosan) in river water samples, is described. A stir bar coated with polydimethylsiloxane (PDMS) is added to a 10mL water sample and stirring is carried out for 120min at room temperature (25 degrees C) in a vial. Then, the PDMS stir bar is subjected to TD-GC-MS. The detection limit of triclosan is 5ngL(-1) (ppt). The method shows linearity over the calibration range (0.02-20mugL(-1)) and the correlation coefficient is higher than 0.997 for triclosan standard solution. The recovery of triclosan in river water samples ranges from 91.9 to 108.3% (RSD: 4.0-7.0%). This simple, accurate, sensitive, and selective analytical method may be used in the determination of trace amounts of triclosan in river water samples.     

Mercury speciation and analysis in drinking water by stir bar sorptive extraction with in situ propyl derivatization and thermal desorption-gas chromatography-mass spectrometry

A method for mercury analysis and speciation in drinking water was developed, which involved stir bar sorptive extraction (SBSE) with in situ propyl derivatization and thermal desorption (TD)-GC-MS. Ten millilitre of tap water or bottled water was used. After a stir bar, pH adjustment agent and derivatization reagent were added, SBSE was performed. Then, the stir bar was subjected to TD-GC-MS. The detection limits were 0.01 ng mL(-1) (ethylmercury; EtHg), 0.02 ng mL(-1) (methylmercury; MeHg), and 0.2 ng mL(-1) (Hg(II) and diethylmercury (DiEtHg)). The method showed good linearity and correlation coefficients. The average recoveries of mercury species (n=5) in water samples spiked with 0.5, 2.0, and 6.0 ng mL(-1) mercury species were 93.1-131.1% (RSD<11.5%), 90.1-106.4% (RSD<7.8%), and 94.2-109.6% (RSD<8.8%), respectively. The method enables the precise determination of standards and can be applied to the determination of mercury species in water samples.     

Simultaneous analysis of benzophenone sunscreen compounds in water sample by stir bar sorptive extraction with in situ derivatization and thermal desorption-gas chromatography-mass spectrometry

A method for the simultaneous measurement of benzophenone (BP) sunscreen compounds, its derivatives 2,4-dihydroxybenzophenone (BP-1), 2-hydroxy-4-methoxybenzophenone (BP-3), 2-hydroxy-4-methoxy-4'-methylbenzophenone (BP-10), 2-hydroxybenzophenone (2OH-BP), 3-hydroxybenzophenone (3OH-BP) and 4-hydroxybenzophenone (4OH-BP), in water samples was developed using stir bar sorptive extraction (SBSE) with in situ derivatization followed by thermal desorption (TD)-gas chromatography-mass spectrometry (GC-MS). The detection limit is 0.5-2 ng L(-1) (ppt) for the seven BPs. The method shows good linearity and the correlation coefficients are equal to or higher than 0.990 for all the analyte. The average recoveries of BPs range from 102.0 to 128.1% (RSD<15.4%, n=6). Trace amounts of BPs in river water samples were determined by the present method.     

Single-crystal X-ray study of Ba2Cu2Te4O11Br2 and its incommensurately modulated superstructure companion

Compounds containing lone-pair elements such as Te(IV) are very interesting from the structural point of view, as the lone-pair nonbonding regions create low-dimensional geometrical arrangements. We have synthesized two new compounds with these features-Ba(2)Cu(2)Te(4)O(11)Br(2) (I) and Ba(2)Cu(2)Te(4)O(11-delta)(OH)(2delta)Br(2) (II, delta approximately equal to 0.57)-as members of the AE-M-Te-O-X (AE=alkaline-earth metal, M=transition metal, X=halide) family of compounds by solid-state reactions. Preliminary single-crystal X-ray analysis indicated that compound I crystallizes in the orthorhombic system, but attempts at refinement proved unsatisfactory. Closer inspection of the reciprocal lattice revealed systematic, non-crystallographic absences that indicate twinning. The structure is in fact triclinic, space group C_1 (equivalent to P_1), with unit cell parameters (at 120 K) of a=10.9027(9), b=15.0864(7), c=9.379(2) A, beta=106.8947 degrees . It is layered and built from [TeO(3)E] tetrahedra, [TeO(3+1)E] trigonal bipyramids (where E is the lone pair of Te(IV)), [CuO(4)] squares and irregular [BaO(10)Br] polyhedra. The crystal structure of II shows the same basic structure as I but contains additional oxygen, probably in the form of OH groups. The presence of satellites reveals that ordering on this O site creates an incommensurate modulation, primarily affecting Br and Te. The modulated structure of II was solved in the triclinic superspace group X$\bar 1$(alphabetagamma)0 with the vector q approximately equal to1/16 c*.     

Polymer-like polyphenols of black tea and their lipase and amylase inhibitory activities

Lipase and amylase inhibitory activities of black tea were examined. After solvent partitioning of a black tea extract with the ethyl acetate and n-butanol, the two soluble fractions showed comparable inhibitory activities. Activity in the ethyl acetate fraction was mainly attributable to polyphenols with low-molecular weights, such as theaflavin gallates. On the other hand, the active substance in the n-butanol layer was ascertained to be a polymer-like substance. 1H- and 13C-NMR spectra showed signals arising from the flavan A-ring and galloyl groups, although signals due to flavan B-rings were not detected, suggesting that the polymer-like substances were generated by oxidative condensation of flavan B-rings, a result which was previously deduced from our results of in vitro catechin oxidation experiments. Enzymatic oxidation of epicatechin 3-O-gallate produced a similar polymer-like substance and suggested that condensation between a B-ring and galloyl groups was involved in the polymerization reaction.