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Halogen Bonding

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https://read.qxmd.com/read/30776228/in-situ-measure-of-intrinsic-bond-strength-in-crystalline-structures-local-vibrational-mode-theory-for-periodic-systems
#1
Yunwen Tao, Wenli Zou, Daniel Sethio, Niraj Verma, Yue Qui, Chuan Tian, Dieter Cremer, Elfi Kraka
The local vibrational mode analysis developed by Konkoli and Cremer has been successfully applied to characterize the intrinsic bond strength via local bond stretching force constants in molecular systems. A wealth of new insights into covalent bonding and weak chemical interactions ranging from hydrogen, halogen, pnicogen, chalcogen to tetrel bonding has been obtained. In this work we extend the local vibrational mode analysis to periodic systems, i.e. crystals, allowing for the first time a quantitative in situ measure of bond strength in extended systems of one-, two- and three-dimensions...
February 18, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30759226/understanding-the-role-of-intermolecular-interactions-between-lissoclimides-and-the-eukaryotic-ribosome
#2
Simone Pellegrino, Mélanie Meyer, Zef A Könst, Mikael Holm, Vamsee K Voora, Daniya Kashinskaya, Camila Zanette, David L Mobley, Gulnara Yusupova, Chris D Vanderwal, Scott C Blanchard, Marat Yusupov
Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity. Toward this goal, we have previously established a short synthesis pathway that grants access to multiple congeners of the lissoclimide family. Here we present the X-ray co-crystal structure at 3...
February 13, 2019: Nucleic Acids Research
https://read.qxmd.com/read/30758372/oxidative-addition-of-arsenic-halides-to-platinum-0
#3
Jonas H Muessig, Tom E Stennett, Uwe Schmidt, Rian D Dewhurst, Lisa Mailänder, Holger Braunschweig
Reaction of AsCl3 with Pt(0) complexes [Pt(PCy3)2], [Pt(PCy3)(IMes)] and [Pt(IMes)2] (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene) resulted in oxidative addition of As-Cl bonds at the Pt centres to form complexes of the form trans-[PtCl(AsCl2)L2]. Two of these compounds were characterised by X-ray diffraction, making them the first structurally characterised examples of AsX2 ligands (X = halogen). AsBr3 also underwent oxidative addition to [Pt(PCy3)2], forming trans-[PtBr(AsBr2)(PCy3)2] in situ, as judged by 31P NMR spectroscopy...
February 13, 2019: Dalton Transactions: An International Journal of Inorganic Chemistry
https://read.qxmd.com/read/30742711/not-your-usual-bioisostere-solid-state-study-of-3d-interactions-in-cubanes
#4
Keith Flanagan, Stefan S R Bernhard, Shane Plunkett, Mathias O Senge
Previous studies by Desiraju and co-workers have implicated the acidic hydrogen atoms of cubane as a support network for hydrogen-bonding groups. Herein we report a detailed structural analysis of all currently available 1,4-disubstituted cubane structures with an emphasis on how the cubane scaffold interacts in its solid-state environment. In this regard, the interactions between the cubane hydrogen atoms and acids, ester, halogens, ethynyl, nitrogenous groups, and other cubane scaffolds were cataloged. The goal of this study was to investigate the potential of cubane as a substitute for phenyl...
February 11, 2019: Chemistry: a European Journal
https://read.qxmd.com/read/30741547/gfn2-xtb-an-accurate-and-broadly-parametrized-self-consistent-tight-binding-quantum-chemical-method-with-multipole-electrostatics-and-density-dependent-dispersion-contributions
#5
Christoph Bannwarth, Sebastian Ehlert, Stefan Grimme
An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction energies for molecular systems with roughly 1000 atoms. The essential novelty in this so-called GFN2-xTB method is the inclusion of anisotropic second order density fluctuation effects via short-range damped interactions of cumulative atomic multipole moments. Without noticeable increase in the computational demands, this results in a less empirical and overall more physically sound method, which does not require any classical halogen or hydrogen bonding corrections and which relies solely on global and element-specific parameters (available up to radon, Z = 86)...
February 11, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30740979/anomalous-halogen-halogen-interaction-assists-radial-chromophoric-assembly
#6
M A Niyas, Remya Ramakrishnan, Vishnu Vijay, Ebin Sebastian, Mahesh Hariharan
The design of highly efficient supramolecular architectures that mimic competent natural systems requires a comprehensive knowledge of noncovalent interactions. Halogen bonding is an excellent noncovalent interaction that forms halogen-halogen (X2 ) as well as trihalogen interacting synthons. Herein, we report the first observation of a symmetric radial assembly of chromophores ( R-3 c space group) composed of a stable hexabromine interacting synthon (Br6 ) that further push the limits of our understanding on the nature, role and potential of noncovalent halogen bonding...
February 11, 2019: Journal of the American Chemical Society
https://read.qxmd.com/read/30735618/synergistic-dual-role-of-hmim-br-arso2cl-in-cascade-sulfenylation-halogenation-of-indole-mechanistic-insight-into-regioselective-c-s-and-c-s-c-x-x-cl-br-bonds-formation-in-one-pot
#7
Danish Equbal, Richa Singh, Saima Malik, Aditya Gandhidas Lavekar, Arun K Sinha
Bifunctionalized indoles are an important class of biologically active heterocyclic compounds and potential drug candidates. Because of the lack of efficient synthetic methods, one pot cascade synthesis of these compounds is rare and remains a challenge. To expand this field, we herein disclose a step-economic and temperature tunable strategy wherein the synergistic effect between [hmim]Br-ArSO2Cl leads exclusively to the formation of 3-arylthio indole via sulfenylation of indole at room temperature while heating the reaction mixture at 50 ºC provided an unexpected 2-halo-3-arylthio indole with construction of C-S and C-S/C-X (X= Br & Cl) bonds without addition of any external halogenating agent via cascade sulfenylation-halogenation reactions under metal-oxidant-base-free condition...
February 8, 2019: Journal of Organic Chemistry
https://read.qxmd.com/read/30734873/effect-of-external-electric-field-on-c-x-%C3%A2-%C3%A2-%C3%A2-%C3%AF-halogen-bonds
#8
Ahmet Tokatlı, Fatmagül Tunç, Fatih Ucun
In this study, ab initio calculations (RI-MP2(full)/aug-cc-pVDZ) are performed to investigate the effect of an external electric field (EEF) on the nature, properties, and structures of C-X ··· π halogen bonds in CF3 Br complexes with π systems (benzene, ethene, and ethyne), for the first time. This EEF effect is analyzed by a myriad of methods, including molecular electrostatic potential (MEP), symmetry adapted perturbation theory (SAPT), natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and noncovalent interaction (NCI) methods...
February 8, 2019: Journal of Molecular Modeling
https://read.qxmd.com/read/30721807/degradation-of-benzophenone-4-in-a-uv-chlorine-disinfection-process-mechanism-and-toxicity-evaluation
#9
Xiaorui Jia, Jing Jin, Rui Gao, Tianyu Feng, Yan Huang, Qing Zhou, Aimin Li
This study investigated the degradation of benzophenone-4 (BP-4) in a UV/chlorine disinfection process, with chlorination and UV disinfection as comparisons. With a degradation efficiency of 80% after 10 s, the UV/chlorine process significantly enhanced the degradation of BP-4. However, a rebound of 36% of the initial concentration was observed in the UV/chlorine process ([free active chlorine (FAC)]0 :[BP-4]0  = 1:1, pH = 7). The same tendency appeared under the addition of alkalinity, Cl- , and humic acid (HA)...
January 31, 2019: Chemosphere
https://read.qxmd.com/read/30716620/discovery-of-potent-ptp1b-inhibitors-via-structure-based-drug-design-synthesis-and-in-vitro-bioassay-of-norathyriol-derivatives
#10
Wenjie Xue, Jinlong Tian, Xiang Simon Wang, Jie Xia, Song Wu
Protein tyrosine phosphatase 1B (PTP1B) has recently been identified as a potential target of Norathyriol. Unfortunately, Norathyriol is not a potent PTP1B inhibitor, which somewhat hinders its further application. Based on the fact that no study on the relationship of chemical structure and PTP1B inhibitory activity of Norathyriol has been reported so far, we attempted to perform structural optimization so as to improve the potency for PTP1B. Via structure-based drug design (SBDD), a rational strategy based on the binding mode of Norathyriol to PTP1B, we designed 26 derivatives with substitutions at the four phenolic hydroxyl groups of Norathyriol...
January 28, 2019: Bioorganic Chemistry
https://read.qxmd.com/read/30713734/crystal-structure-hirshfeld-surface-analysis-and-dft-studies-of-e-1-4-bromo-phen-yl-3-3-fluoro-phen-yl-prop-2-en-1-one
#11
Muhamad Fikri Zaini, Ibrahim Abdul Razak, Mohamad Zahid Anis, Suhana Arshad
The asymmetric unit of the title halogenated chalcone derivative, C15 H10 BrFO, contains two independent mol-ecules, both adopting an s-cis configuration with respect to the C=O and C=C bonds. In the crystal, centrosymmetrically related mol-ecules are linked into dimers via inter-molecular hydrogen bonds, forming rings with R 1 2 (6), R 2 2 (10) and R 2 2 (14) graph-set motifs. The dimers are further connected by C-H⋯O inter-actions into chains parallel to [001]. A Hirshfeld surface analysis suggests that the most significant contribution to the crystal packing is by H⋯H contacts (26...
January 1, 2019: Acta Crystallographica. Section E, Crystallographic Communications
https://read.qxmd.com/read/30701641/selective-emergence-of-halogen-bond-in-ground-and-excited-states-of-noble-gas-chlorine-systems
#12
Fernando Pirani, David Cappelletti, Stefano Falcinelli, Diego Cesario, Francesca Nunzi, Leonardo Belpassi, Francesco Tarantelli
Molecular-beam scattering experiments and theoretical calculations prove the nature, strength and selectivity of halogen-bond (XB) in the interaction of halogen molecules with the series of noble-gas (Ng) atoms. The XB, accompanied by charge transfer from the Ng to the halogen, is shown to take place in, and measurably stabilize, the collinear conformation of the adducts, which thus becomes - in contrast to what happens for other Ng-molecule systems - approximately as bound as the T-shaped one. Remarkably, we also show how and why XB is inhibited when the halogen molecule is in the 3Πu excited state...
January 31, 2019: Angewandte Chemie
https://read.qxmd.com/read/30698963/forging-ru-c-sp-2-bonds-in-paddlewheel-complexes-using-the-lithium-halogen-exchange-reaction
#13
Adharsh Raghavan, Brandon L Mash, Tong Ren
Reported herein are the first examples of the formation of Ru-Csp2 bonds in paddlewheel diruthenium species. A series of six Ru2 ( ap)4 (C6 H4 -4-X) type compounds ( ap = 2-anilinopyridinate; X = NMe2 (1), N,N-(C6 H4 -4-OMe)2 (2), t Bu (3), H (4), Br (5), CF3 (6)) was synthesized by employing the lithium-halogen exchange reaction with a variety of para-substituted aryl halides. These compounds have been characterized via electronic absorption spectroscopy, cyclic voltammetry, mass spectrometry, and magnetism studies, and their molecular structures have been established by single-crystal X-ray diffraction studies...
January 30, 2019: Inorganic Chemistry
https://read.qxmd.com/read/30687859/electrochemically-driven-interfacial-halogen-bonding-on-self-assembled-monolayers-for-anion-detection
#14
Hussein Hijazi, Antoine Vacher, Sihem Groni, Dominique Lorcy, Eric Levillain, Claire Fave, Bernd Schöllhorn
Electrochemically driven interfacial halogen bonding between redox-active SAMs and halide anions was quantitatively studied for the first time. The halogen bond donor properties were switched on by electrochemically controlling the oxidation state of the adsorbates. Experimental data and simulation show high binding enhancement towards halide anions compared to homogeneous systems.
January 28, 2019: Chemical Communications: Chem Comm
https://read.qxmd.com/read/30681189/the-role-of-the-halogen-bond-in-iodothyronine-deiodinase-dependence-on-chalcogen-substitution-in-naphthyl-based-mimetics
#15
Diego Cesario, Mariagrazia Fortino, Tiziana Marino, Francesca Nunzi, Nino Russo, Emilia Sicilia
The effects on the activity of thyroxine (T4) due to the chalcogen replacement in a series of peri-substituted naphthalenes mimicking the catalytic function of deiodinase enzymes are computationally examined using density functional theory. In particular, T4 inner-ring deiodination pathways assisted by naphthyl-based models bearing two tellurols and a tellurol-thiol pair in peri-position are explored and compared with the analogous energy profiles for the naphthalene mimic having two selenols. The presence of a halogen bond (XB) in the intermediate formed in the first step and involved in the rate-determining step of the reaction is assumed to facilitate the process increasing the rate of the reaction...
March 30, 2019: Journal of Computational Chemistry
https://read.qxmd.com/read/30680824/weak-pnictogen-bond-with-bismuth-experimental-evidence-based-on-bi-p-through-space-coupling
#16
Dominikus Heift, Réka Mokrai, Jamie Barrett, David Apperley, Andrei Batsanov, Zoltán Benkő
To study pnictogen bonding involving bismuth, flexible accordion-like molecular complexes of the composition [P(C6H4-o-CH2SCH3)3BiX3], (X = Cl, Br, I) have been synthesised and characterised. The strength of the weak and mainly electrostatic interaction between the Bi and P centres strongly depends on the character of the halogen substituent on bismuth, which is confirmed by single crystal X-ray diffraction analyses, DFT and ab initio computations. Significantly, 209Bi-31P through-space coupling (J = 2560 Hz) is observed in solid-state 31P-NMR spectra, which is so far unprecedented in the literature, delivering direct information on the magnitude of this interpnictogen interaction...
January 24, 2019: Chemistry: a European Journal
https://read.qxmd.com/read/30680467/structural-energetic-and-vibrational-properties-of-the-homodimers-of-the-silyl-germyl-and-stannyl-halides-mh-3-x-2-m-si-ge-sn-x-f-cl-br-i
#17
Ponnadurai Ramasami, Thomas A Ford
A number of properties of the homodimers of the three families of molecules MH3 X, where M is Si, Ge, and Sn and X is F, Cl, Br, and I are computed. The results are compared with those of a similar study of the homodimers of the methyl halides containing the same four halogen atoms, and some notable differences are observed among related sets of monomer species. The interaction energies, the primary intermolecular geometrical parameters, the changes in the intramolecular bond lengths, and the vibrational data (wavenumber shifts and dimer/monomer infrared intensity ratios) of some of the modes most closely associated with the site of interaction show, for the most part, regular variations as the central atom and the halogen atom are systematically varied...
January 24, 2019: Journal of Molecular Modeling
https://read.qxmd.com/read/30680378/methanesulfonyl-polarized-halogen-bonding-enables-strong-halide-recognition-in-an-arylethynyl-anion-receptor
#18
Jessica A Lohrman, Chun-Lin Deng, Trevor A Shear, Lev N Zakharov, Michael M Haley, Darren W Johnson
A 3,5-bis((2-iodophenyl)ethynyl)pyridinium scaffold was synthesized which introduces the use of methanesulfonyl withdrawing groups to polarize iodine halogen bonding units for anion binding. We investigate the capability of this receptor to bind halides in polar media, while further probing the structure-property relationship of this well-polarized yet under-explored halogen bonding system.
January 25, 2019: Chemical Communications: Chem Comm
https://read.qxmd.com/read/30679372/an-enantioconvergent-halogenophilic-nucleophilic-substitution-s-n-2x-reaction
#19
Xin Zhang, Jingyun Ren, Siu Min Tan, Davin Tan, Richmond Lee, Choon-Hong Tan
Bimolecular nucleophilic substitution (SN 2) plays a central role in organic chemistry. In the conventionally accepted mechanism, the nucleophile displaces a carbon-bound leaving group X, often a halogen, by attacking the carbon face opposite the C-X bond. A less common variant, the halogenophilic SN 2X reaction, involves initial nucleophilic attack of the X group from the front and as such is less sensitive to backside steric hindrance. Herein, we report an enantioconvergent substitution reaction of activated tertiary bromides by thiocarboxylates or azides that, on the basis of experimental and computational mechanistic studies, appears to proceed via the unusual SN 2X pathway...
January 25, 2019: Science
https://read.qxmd.com/read/30678158/is-the-fluorine-in-molecules-dispersive-is-molecular-electrostatic-potential-a-valid-property-to-explore-fluorine-centered-non-covalent-interactions
#20
Arpita Varadwaj, Helder M Marques, Pradeep R Varadwaj
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T)...
January 22, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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