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Halogen Bonding

Mengxi Liu, Shichao Li, Jingyuan Zhou, Zeqi Zha, Jinliang Pan, Xin Li, Jin Zhang, Zhongfan Liu, Yuanchang Li, Xiaohui Qiu
Rationally designed halogenated hydrocarbons are widely used building blocks to fabricate covalent-bonded carbon nanostructures on surface through a reaction pathway involving generation and dissociation of organometallic intermediates and irreversible covalent bond formation. Here we provide a comprehensive picture of the on-surface-assisted homocoupling reaction of 1,3-bis(2-bromoethynyl)benzene on Au(111), aiming for the synthesis of graphdiyne nanostructures. Submolecular resolution scanning tunneling microscopy and noncontact atomic force microscopy observations identify the organometallic intermediates and their self-assemblies formed in the dehalogenation process...
December 4, 2018: ACS Nano
Jiyu Sun, Asia Marie S Riel, Orion B Berryman
Herein, we present on two 2,6-bis(4-ethynylpyridinyl)-4-fluoroaniline receptors that display solvatochromic absorption and emission. Neutral derivatives displayed opposite solvatochromic behavior as compared to the alkylated receptors. Adding anions induced changes in the absorption and emission spectra. In general, the fluorescence of the halogen bonding receptor was quenched less efficiently when compared to the hydrogen bonding receptor.
July 7, 2018: New Journal of Chemistry, Nouveau Journal de Chimie
Felix Allum, Michael Burt, Kasra Amini, Rebecca Boll, Hansjochen Köckert, Pavel K Olshin, Sadia Bari, Cédric Bomme, Felix Brauße, Barbara Cunha de Miranda, Stefan Düsterer, Benjamin Erk, Marie Géléoc, Romain Geneaux, Alexander S Gentleman, Gildas Goldsztejn, Renaud Guillemin, David M P Holland, Iyas Ismail, Per Johnsson, Loïc Journel, Jochen Küpper, Jan Lahl, Jason W L Lee, Sylvain Maclot, Stuart R Mackenzie, Bastian Manschwetus, Andrey S Mereshchenko, Robert Mason, Jérôme Palaudoux, Maria Novella Piancastelli, Francis Penent, Dimitrios Rompotis, Arnaud Rouzée, Thierry Ruchon, Artem Rudenko, Evgeny Savelyev, Marc Simon, Nora Schirmel, Henrik Stapelfeldt, Simone Techert, Oksana Travnikova, Sebastian Trippel, Jonathan G Underwood, Claire Vallance, Joss Wiese, Farzaneh Ziaee, Mark Brouard, Tatiana Marchenko, Daniel Rolles
The photodissociation dynamics of CH3 I and CH2 ClI at 272 nm were investigated by time-resolved Coulomb explosion imaging, with an intense non-resonant 815 nm probe pulse. Fragment ion momenta over a wide m / z range were recorded simultaneously by coupling a velocity map imaging spectrometer with a pixel imaging mass spectrometry camera. For both molecules, delay-dependent pump-probe features were assigned to ultraviolet-induced carbon-iodine bond cleavage followed by Coulomb explosion. Multi-mass imaging also allowed the sequential cleavage of both carbon-halogen bonds in CH2 ClI to be investigated...
November 28, 2018: Journal of Chemical Physics
Zoltán Varga, Pragya Verma, Donald G Truhlar
This work explores possible reaction paths for the inversion of a series of trigonal pyramidal phosphorus trihalides, PF3, PCl3, PBr3, and PI3, and it especially addresses the question of whether and when the bonding of the lowest-energy species along the inversion paths should be described as a hyper open-shell diradical. The various paths for inversion are calculated using a single-reference method within the framework of Kohn-Sham density functional theory and also with multi-reference wave function methods...
November 28, 2018: Journal of Physical Chemistry. A
Rubik Asatryan, Yudhajit Pal, Johannes Hachmann, Eli Ruckenstein
Diol radicals (DRs) are important intermediates in biocatalysis, atmospheric chemistry and biomass combustion. They are particularly generated from photolysis of halogenated diols and a barrierless addition of hydroxyl radical to a double bond of unsaturated alcohols, such as lignols. The energized DRs further isomerize / decompose to form products, including water. Aqueous-phase dehydration in radiolytic and biomimetic systems typically occurs at low temperatures, with or without catalysis, whereas the gas-phase dehydration is usually considered energetically unfavorable...
November 28, 2018: Journal of Physical Chemistry. A
Alavi Karim, Nils Schulz, Hanna Andersson, Bijan Nekoueishahraki, Anna-Carin C Carlsson, Daniel Sarabi, Arto Valkonen, Kari Rissanen, Jürgen Gräfenstein, Sandro Keller, Máté Erdélyi
Tetrel bonding is the noncovalent interaction of Group IV elements with electron donors. It is a weak, directional interaction that resembles hydrogen and halogen bonding, yet remains barely explored. Herein, we present the experimental investigation of the carbon-centered, three-center four-electron tetrel bond, [N-C-N]+ , formed by capturing a carbenium ion with a bidentate Lewis base. NMR spectroscopic, titration calorimetric and reaction kinetic evidences for the existence and structure of this species are reported...
November 28, 2018: Journal of the American Chemical Society
Aisen Li, Jing Wang, Yingjie Liu, Shuping Xu, Ning Chu, Yijia Geng, Bao Li, Bin Xu, Haining Cui, Weiqing Xu
A series of two-component co-crystals driven by IN interactions based on the bipyridine (BIPY) chromophore with one among three different co-former building blocks, iodopentafluorobenzene (IPFB), 1,4-diiodotetrafluorobenzene (DITFB) and 1,3,5-trifluoro-2,4,6-triiodobenzene (IFB), were prepared and analysed via infared spectroscopy and single-crystal X-ray diffraction. By comparing the IN distances in the co-crystal structures, we found that the higher the -F ratio in the building blocks the closer the contact of the IN bond, enhancing the intermolecular interactions in these co-crystals as well...
November 28, 2018: Physical Chemistry Chemical Physics: PCCP
Sourav Ghosh, Balaji R Jagirdar
We report a general strategy for the synthesis of metal nanosponges (M = Ag, Au, Pt, Pd, and Cu) using a capping agent dissolution method where addition of water to the M@BNHx nanocomposite affords the metal nanosponges. The B-H bond of the BNHx polymer gets hydrolysed upon addition of water and produces hydrogen gas bubbles which act as dynamic templates leading to the formation of nanosponges. The rate of B-H bond hydrolysis has a direct impact on the final nanostructure of the materials. The metal nanosponges were characterized using powder XRD, electron microscopy, XPS, and BET surface area analyzer techniques...
November 27, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Ryan G Anderson, Brianna M Jett, Andrew McNally
Heteroaryl thioethers, comprised of pyridines and diazines, are an important class of compounds with relevance to medicinal chemistry. Metal-catalyzed cross-couplings and SN Ar are traditionally used to form C-S bonds in these systems but are limited by available halogenated precursors. An alternative approach is presented where pyridines and diazines are transformed into heterocyclic phosphonium salts and then C-S bonds are formed by adding thiolate nucleophiles. The process is 4-selective for pyridines, simple to execute and can be used to make derivatives of complex pharmaceuticals...
June 21, 2018: Tetrahedron
Wataru Ichinose, Tsukasa Sawato, Haruna Kitano, Yasuhiro Shinozaki, Mieko Arisawa, Nozomi Saito, Takeo Yoshikawa, Masahiko Yamaguchi
Optically active helicene derivatives inhibit the activity on histamine N-methyl transferase (HNMT). Specifically, methyl (P)-1,12-dimethylbenzo[c]phenanthrene-8-carboxylate with 6-iodo and 5-trifluoromethanesulfonyloxy groups inhibits HNMT activity on the μM order of IC50 . Chirality is important, and (M)-isomers exhibits substantially reduced activity. The 6-iodo group is also essential, which suggests the involvement of halogen bonds in protein binding. Substituents on the sulfonate moiety also affect the inhibitory activity...
November 20, 2018: Journal of Antibiotics
Mónica Mamián-López, Marcia L A Temperini
The nature of the cooperativity effect of hydrogen bonds in Watson & Crick and wobble base pairs formed with thymine, uracil and its 5-halogenated derivatives (5-fluoro, -chloro and -bromouracil) have been studied through SERS, and using chemometric tools to process data and extract relevant information. Remarkable differences between the two kinds of pairs were clearly observed and the behavior correlated to the withdrawing character of different substituents at the 5- position of uracil was verified. Multivariate analyses have also unveiled information about pair's stability and a stronger cooperativity effect seems to rule the Watson & Crick pairs when compared to wobble pairs...
November 20, 2018: Analytical Chemistry
Zhiqiang Fu, Jingwen Chen, Yong Wang, Huixiao Hong, Hongbin Xie
The metabolic fate and toxicokinetics of organic phosphorus flame retardants catalyzed by cytochrome P450 enzymes (CYPs) are here investigated by in silico simulations, leveraging an active center model to mimic the CYPs, triphenyl phosphate (TPHP), tris(2-butoxyethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate as substrates. Our calculations elucidated key main pathways and predicted products, which were corroborated by current in vitro data. Results showed that alkyl OPFRs are eliminated faster than aryl and halogenated alkyl-substituted OPFRs...
November 20, 2018: Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews
Seyed Morteza Alavi, Saied Yeganegi
In this paper, the structures and energetics of 1,3-bis[3-methylimidazolium-yl] pentane ([bis-Mim]2+ ) dication and bis(mandelato) borate [BMB]- and bis(salicylato) borate [BScB]- anions in isolated forms, ion pairs (IPs) and dicationic ionic liquids (DILs) were studied by Density Functional Theory (DFT) at the M06-2X/6-31G(d,p) level of theory. According to the IUPAC criteria, the hydrogen bonds between anion and cation were characterized and classified in the optimized geometries of the isolated ions, IPs and DILs...
November 13, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Adam C Pearcy, Kyle A Mason, M Samy El-Shall
Herein, we report on the gas phase association of the small polar and aprotic solvent molecules acetonitrile (CH3CN) and acetone (CH3COCH3) with the halogenated benzene radical cations (C6H5X+•, X=F, Cl, Br, and I) using the mass-selected ion mobility technique and density functional theory calculations. The association energies (-ΔH°) of CH3CN (CH3COCH3) with C6H5F+• and C6H5I+• are similar [13.0 (13.3) and 13.2 (14.1) kcal/mol, respectively] but higher than those of CH3CN (CH3COCH3) with C6H5Cl+• and C6H5Br+• [10...
November 19, 2018: Journal of Physical Chemistry. A
Chen-Hui Shu, Shao-Ze Zhang, Cheng-Xin Wang, Jian-Le Chen, Yan He, Ke-Ji Shi, Pei-Nian Liu
Diverse self-assembled structures were obtained on Cu(111) and Ag(111) surfaces by using a simple and small 4,4''-dichloro-1,1':4',1''-terphenyl molecule. Surprisingly, a complicated supramolecular self-assembled vortex structure, composed of 15 molecules in a large unit, was realized through the collaboration of hydrogen bonding and halogen bonding.
November 19, 2018: Chemical Communications: Chem Comm
Fang Cheng, Xue-Jun Wu, Zhixin Hu, Xuefeng Lu, Zijing Ding, Yan Shao, Hai Xu, Wei Ji, Jishan Wu, Kian Ping Loh
Molecular tessellations are often discovered serendipitously, and the mechanisms by which specific molecules can be tiled seamlessly to form periodic tessellation remain unclear. Fabrication of molecular tessellation with higher symmetry compared with traditional Bravais lattices promises potential applications as photonic crystals. Here, we demonstrate that highly complex tessellation can be constructed on Au(111) from a single molecular building block, hexakis(4-iodophenyl)benzene (HPBI). HPBI gives rise to two self-assembly phases on Au(111) that possess the same geometric symmetry but different packing densities, on account of the presence of halogen-bonded and halogen-metal coordinated networks...
November 19, 2018: Nature Communications
Roderick C Jones, Brendan Twamley
Two independent samples of the title compound, alternatively 2-chloro- N -(4-methylphenyl)prop-an-amide, C10 H12 ClNO, 1 , were studied using Cu K α, 1a , and Mo K α, 1b , radiation as part of a continuous crystallization study. The mol-ecule crystallizes with disorder in the Cl/terminal methyl positions [occupancies for the major disorder component of 0.783 (2) in 1a and and 0.768 (2) in 1b ] and exhibits N-C bond lengths of 1.3448 (19), 1.344 (2) Å, C=O bond lengths of 1.2233 (18) and 1.2245 (19) Å and an acetamide moiety C-N-C-C torsion angle of 179...
November 1, 2018: Acta Crystallographica. Section E, Crystallographic Communications
Manman Chu, Bing Qiu, Wei Zhang, Zhonghao Zhou, Xinzheng Yang, Yongli Yan, Jiannian Yao, Yong Jun Li, Yong Sheng Zhao
Organic cocrystals with unique energy-level structures are potentially a new class of materials for the development of versatile solid-state lasers. However, till now, the stimulated emission in cocrystal materials remains a big challenge possibly because of the nonradiative charge-transfer (CT) transitions. Here, for the first time, we report organic cocrystal microlasers constructed by simultaneously tailoring the energy levels and cavity structures based on the intermolecular halogen-bonding interactions...
November 28, 2018: ACS Applied Materials & Interfaces
Dmitry I Bugaenko, Anastasia A Dubrovina, Marina A Yurovskaya, Alexander V Karchava
A new protocol for the preparation of N-substituted indole-3-carboxylates has been developed. The key C-N bond formation occurs under transition-metal-free conditions employing a t-BuOK/DMF system without special initiators or additives. Across a number of substrates, indoles were afforded in yields higher or comparable to those obtained under transition-metal-catalyzed conditions. While demonstrating high functional group tolerance, new conditions are particularly attractive for manufacturing halogenated indoles that cannot be made in a pure form using other metal-based catalytic methods...
November 15, 2018: Organic Letters
Guneet Guram, Junaid Ahmed Shaik
Aims and Objectives: Conventionally, composites are cured using halogen-based light-curing units (LCUs). However, recently, light-emitting diode (LED) LCUs have been introduced commercially, claiming many advantages, yet producing comparable bond strength even when cured with single LED LCUs. This present study was undertaken to compare the shear bond strength of orthodontic brackets bonded to teeth with conventional halogen LCU (3M ESPE Elipar 2500) and LED LCU (3M ESPE Elipar FreeLight 2) and to determine the site of bond failure...
September 2018: Journal of International Society of Preventive & Community Dentistry
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