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PubMed2001

Identification of halogen atoms in scanning tunneling microscopy images of substituted phenyl octadecyl ethers.

A homologous series of para-substituted phenyl octadecyl ethers (X-POEs, where X = H, Cl, Br, I) was prepared using the Williamson ether synthesis and characterized by 1H NMR and GC/MS. Scanning tunneling microscopy images acquired from these ethers revealed a bias-dependent contrast corresponding to electron density contours of various X-POE molecular orbitals. Images reflecting the electron density contour of the highest occupied molecular orbital exhibited four bright spots--one for the halogen atom, two representing the pair of lobes of the phenyl ring, and one for the oxygen/alpha-carbon atoms. For each X-POE, the intensities (Zmax) of the spots for the halogen atom and the lobe of the phenyl ring closest to the halogen were measured and their ratio was calculated (Cl-POE 0.49 +/- 0.06; Br-POE 0.59 +/- 0.06; I-POE 0.75 +/- 0.07). Analysis of variance at the 95% confidence level revealed that the intensity ratios were consistent from molecule to molecule, image to image, and day to day. According to the Student t-test, the average Zmax ratios for Cl-POE, Br-POE, and I-POE are different at the 95% confidence level. In addition, they follow a trend that corresponds favorably with that of the atomic radii of the halogens. The probability of classifying a single X-POE molecule as Cl-POE, Br-POE, or I-POE is variable and depends on the magnitude of the Zmax ratio.

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PubMed2005

Halogen bonding based recognition processes: a world parallel to hydrogen bonding.

Halogen bonding is the noncovalent interaction between halogen atoms (Lewis acids) and neutral or anionic Lewis bases. The main features of the interaction are given, and the close similarity with the hydrogen bonding will become apparent. Some heuristic principles are presented to develop a rational crystal engineering based on halogen bonding. The focus is on halogen-bonded supramolecular architectures given by halocarbons. The potential of the interaction is shown by useful applications in the field of synthetic chemistry, material science, and bioorganic chemistry.

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PubMed2002

Weakly coordinating anions: crystallographic and NQR studies of halogen-metal bonding in silver, thallium, sodium, and potassium halomethanesulfonates.

35Cl, (79,81)Br, and (127)I NQR (nuclear quadrupole resonance) spectroscopy in conjunction with X-ray crystallography is potentially one of the best ways of characterizing secondary bonding of metal cations such as Ag(+) to halogen donor atoms on the surfaces of very weakly coordinating anions. We have determined the X-ray crystal structure of Ag(O(3)SCH(2)Cl) (a = 13.241(3) A; b = 7.544(2) A; c = 4.925(2) A; orthorhombic; space group Pnma; Z = 4) and compared it with the known structure of Ag(O(3)SCH(2)Br) (Charbonnier, F.; Faure, R.; Loiseleur, H. Acta Crystallogr., Sect. B 1978, 34, 3598-3601). The halogen atom in each is apical (three-coordinate), being weakly coordinated to two silver ions. (127)I NQR studies on Ag(O(3)SCH(2)I) show the expected NQR consequences of three-coordination of iodine: substantially reduced NQR frequencies nu(1) and nu(2) and a fairly small NQR asymmetry parameter eta. The reduction of the halogen NQR frequency of the coordinating halogen atom in Ag(O(3)SCH(2)X) becomes more substantial in the series X = Cl < Br < I, indicating that the coordination to Ag(+) strengthens in this series, as expected from hard-soft acid-base principles. The numbers of electrons donated by the organic iodine atom to Ag(+) have been estimated; these indicate that the bonding to the cation is weak but not insignificant. We have not found any evidence for the bonding of these organohalogen atoms to another soft-acid metal ion, thallium. A scheme for recycling of thallium halide wastes is included.

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PubMed2003

Novel halogen and interhalogen adducts of nanoscale magnesium oxide.

The difference in the adsorption properties of magnesium oxide in two different physical forms--large micron-sized crystals (CM-MgO) and nanoscale crystals (AP-MgO)--is described. The highly energetic surface of the nanoparticles is significantly more active than the bulk surface in adsorption of nonpolar halogens (Cl(2), Br(2), and I(2)) and dipole interhalogen molecules (ICl, IBr, and ICl(3)). The nanocrystalline and microcrystalline MgO adducts with halogens and interhalogens were characterized by thermogravimetric analysis (TGA), UV-vis and Raman spectroscopies, and transmission electron microscopy (TEM). The bonds of the adsorbates were considerably strained upon adsorption on the nanocrystalline MgO without a molecular dissociation. The results presented in the paper explain the enhanced reactivities of the nanoscale MgO, halogen adducts as halogenating agents of organic molecules and their noticeable biocidal activity.

Journal Article↗

PubMed1980

Halogenated L-fucose and D-galactose analogues: synthesis and metabolic effects.

Several new analogues of L-fucose modified in the 2 position and the 5-methyl group have been synthesized as potential plasma-membrane glycoconjugate inhibitors or modifiers, and their biological effects have been studied. 2-Chloro-, 2-bromo-, and 2-iodo-2-deoxy-L-fucose (9a, 9b, and 13, respectively) have been prepared by addition of the appropriate halogen to 3,4-di-O-acetyl-L-fucal, followed by hydrolysis of the anomeric halogen and the acetyl groups. A series of four halogenated 5-methyl analogues of L-fucose (4, X = F, Cl, Br, and I) have been obtained starting from 1,2:3,4-di-O-isopropylidene-L-galactose. The synthesis of this latter compound has been improved. A corresponding series of 6-deoxy-6-halo-D-galactose analogues, which are enantiomers of the 5-(halomethyl)-L-fucose analogues, has also been synthesized. Analogues 4b, 4c, and 9b at 1 x 10(-3) M specifically inhibited the incorporation of L-[3H]fucose into macromolecular components of SW613 human mammary tumor cells. Analogue 13 inhibited the growth of L1210 murine leukemic cells with an IC50 of 6 x 10(5) M in culture. 6-Deoxy-6-fluoro-D-galactose and its enantiomer 4a were found to be effective inhibitors of D-[3H]galactose and L-[3H]fucose incorporation, respectively, into macromolecular components of human mammary tumor cells. The effectiveness of inhibition was reduced with an increase in size of the halogen atom. Analogue 4a and its enantiomer have been tritiated at C-1 and both were found to be activated to a nucleotide sugar, which was followed by incorporation into the macromolecular fraction of SW613 human mammary tumor cells in vitro.

Animals↗

PubMed2005

Polymer-supported organotin reagents for regioselective halogenation of aromatic amines.

[reaction: see text] Polymer-supported triorganotin halides were used in the halogenation reaction of aromatic amines. Treatment of aromatic amines with n-butyllithium and polymer-supported organotin halides gave the corresponding polymer-bound N-triorganostannylamines, which by treatment with bromine or iodine monochloride gave the para-halogenated aromatic amines with high yields and high selectivities. The polymer-supported organotin halides reagents regenerated during the course of the halogenation reaction can be reused without loss of efficiency. The presence of tin residues in halogenated aromatic amines was also investigated and evaluated at under 20 ppm after three runs.

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PubMed1998

Intramolecular Homolytic Translocation Chemistry: An ab Initio Study of 1,n-Halogen Atom Transfer Reactions in Some omega-Haloalkyl Radicals.

Ab initio calculations using all-electron (3-21G(()()), 6-311G) and pseudopotential (DZP) basis sets, with (MP2, QCISD) and without (UHF) the inclusion of electron correlation, predict that 1,n-halogen transfer reactions in the 5-halo-1-pentyl (6), 6-halo-1-hexyl (7), and 7-halo-1-heptyl radicals (8) proceed via C(s)- and/or C(2)-symmetric transition states (9-11), except for the 5-bromo-1-pentyl (6, X = Br) radical for which a C(s)-symmetric transition state (9) was located only at the UHF/3-21G(()()) level of theory and the 5-iodo-1-pentyl radical (6, X = I) for which no transition state (9) could be located at any level of theory used in this study. Energy barriers for these translocation reactions of between 120.0 (1,7-iodine transfer) and 191.0 kJ mol(-)(1) (1,5-chlorine transfer) are predicted at the MP2/DZP level of theory; QCISD/DZP (single-point) calculations predict similar energy barriers. These high energy barriers are a consequence of unfavorable factors associated with ring size and long carbon-halogen separations in transition states (9-11) which lead to significant deviations from the collinear arrangement of attacking and leaving radicals preferred in transition states involved in homolytic substitution reactions at halogen. The dependence of transition state energy on attack angle at halogen has been explored for the attack of methyl radical at chloromethane. At the MP2/DZP level of theory, attack angles of between 80 and 90 degrees are calculated to lead to increases in energy barrier of about 100 kJ mol(-)(1) when compared with the collinear (180 degrees ) arrangement of attacking and leaving groups. The mechanistic implications of these predictions are discussed.

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PubMed2000

Halogenations of anthracenes and Dibenz

Halogenation of dibenz[a,c]anthracene (1) by NBS in CCl(4) affords the products of 9- and 10-monobromination in the ratio of 9:1. The reaction is accelerated by iodine, and HBr effects rearrangement of 9-bromo product to the sterically less crowded 10-bromo isomer. The mechanism is proposed to involve reversible addition of Br(2), followed by elimination of HBr. Reaction of NCS with 1 in CCl(4) requires addition of HCl and affords exclusively 9-chlorination. The different reactivities of NBS and NCS are ascribed to the relative amounts of free halogen produced (due to differences in N-X bond strengths involving Br and Cl), and the different sizes of the halogens. Under similar conditions, NCS chlorinates 9-bromoanthracene (2a) to afford 9,10-dichloroanthracene and 9-bromo-10-chloroanthracene in the ratio of 65:35. This reaction ostensibly occurs by addition of Cl(2) to 2a, followed by preferential loss of HBr rather than HCl. 9-Methylanthracene (3) affords exclusively 9-(bromomethyl)anthracene with NBS in the absence of iodine, but mainly (67%) 9-bromo-10-methylanthracene in the presence of iodine. Chlorination of 3 with NCS in the presence of HCl also affords mostly (65%) nuclear halogenation. Nuclear bromination of anthracene, 9-methylanthracene, and dibenz[a, c]anthracene by NBS in the absence of added HBr is accelerated by iodine. This effect is probably due to an increase in the amount of bromine produced from NBS in the presence of iodine.

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PubMed2006

Spectroscopic signatures of halogens in clathrate hydrate cages. 1. Bromine.

We report the first UV-vis spectroscopic study of bromine molecules confined in clathrate hydrate cages. Bromine in its natural hydrate occupies 51262 and 51263 lattice cavities. Bromine also can be encapsulated into the larger 51264 cages of a type II hydrate formed mainly from tetrahydrofuran or dichloromethane and water. The visible spectra of the enclathrated halogen molecule retain the spectral envelope of the gas-phase spectra while shifting to the blue. In contrast, spectra of bromine in liquid water or amorphous ice are broadened and significantly more blue-shifted. The absorption bands shift by about 360 cm-1 for bromine in large 51264 cages of type II clathrate, by about 900 cm-1 for bromine in a combination of 51262 and 51263 cages of pure bromine hydrate, and by more than 1700 cm-1 for bromine in liquid water or amorphous ice. The dramatic shift and broadening in water and ice is due to the strong interaction of the water lone-pair orbitals with the halogen sigma* orbital. In the clathrate hydrates, the oxygen lone-pair orbitals are all involved in the hydrogen-bonded water lattice and are thus unavailable to interact with the halogen guest molecule. The blue shifts observed in the clathrate hydrate cages are related to the spatial constraints on the halogen excited states by the cage walls.

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PubMed2004

The synthesis and crystal structures of halogenated tolans p-X-C6H4-C[triple bond]C-C6F5 and p-X-C6F4-C[triple bond]C-C6H5(X=F, Cl, Br, I).

A series of halogenated, partially fluorinated tolans of general formula p-X-C6H4-C[triple bond]C-C6F5[X=I (1), Br (2), Cl (3), F (4)] and p-X-C6F4-C[triple bond]C-C6H5[X=I (5), Br (6)] have been prepared via palladium-catalysed Sonogashira cross-coupling, or for X=Cl (7), by nucleophilic aromatic substitution reactions. The single-crystal X-ray structures of 1-3 and 5-6 have been determined. The structures reveal that the molecular packing is characterized by either arene-perfluoroarene interactions (3), or halogen-halogen interactions (isomorphous 1 and 2), or neither (isomorphous 5 and 6). The structure of represents the first fully determined crystal structure of a compound that contains a halogen atom other than fluorine, in which arene-perfluoroarene interactions are present.

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PubMed1978

The specificity of the interaction of bovine pancreatic ribonuclease A with natural and halogenated purine nucleotides.

The interaction between bovine pancreatic ribonuclease A (EC 3.1.4.22) and the purine nucleotides AMP, GMP, 6-chloropurine 5'-ribonucleotide and 8-bromoadenosine 5'-monophosphate was studied by u.v. difference spectroscopy. The stoicheiometry of the binding of the halogenated nucleotides to the enzyme shows a 1:1 ratio, as for the natural ones. The binding constants, Ka, for all four nucleotides at pH 5.5 were determined. They are within the same order of magnitude, though the nucleotides with a 6-amino group show a stronger interaction. The magnitude of the binding shows a reciprocal dependence on the ionic strength, which indicates an electrostatic interaction between ligand and enzyme. Finally, solvent-perturbation experiments show that all four nucleotides bind to the enzyme in a partially hydrophobic region. It is concluded that both halogenated and natural purine ribonucleotides interact in a similar manner with the enzyme molecule. The special synthesis and identification of 6-chloropurine 5'-ribonucleotide are discussed extensively. It is concluded that both halogenated and natural purine ribonucleotides interact in a similar manner with the enzyme molecule and thus the halogenated analogues are potential reagents for the affinity labelling of the purine-binding site.

Binding Sites↗

PubMed2004

Endogenous formation of novel halogenated 2'-deoxycytidine. Hypohalous acid-mediated DNA modification at the site of inflammation.

A potential role of DNA damage by leukocyte-derived reactive species in carcinogenesis has been suggested. Leukocyte-derived peroxidases, such as myeloperoxidase and eosinophil peroxidase, use hydrogen peroxide and halides (Cl- and Br-) to generate hypohalous acids (HOCl and HOBr), halogenating intermediates. It has been suggested that these oxidants lead to the formation of halogenated products upon reaction with nucleobases. To verify the consequences of phagocyte-mediated DNA damage at the site of inflammation, we developed a novel monoclonal antibody (mAb2D3) that recognizes the hypohalous acid-modified DNA and found that the antibody most significantly recognized HOCl/HOBr-modified 2'-deoxycytidine residues. The immunoreactivity of HOCl-treated oligonucleotide was attenuated by excess methionine, suggesting that chloramine-like species may be the plausible epitopes of the antibody. On the basis of further characterization combined with mass spectrometric analysis, the epitopes of mAb2D3 were determined to be novel N4,5-dihalogenated 2'-deoxycytidine residues. The formation of the dihalogenated 2'-deoxycytidine in vivo was immunohistochemically demonstrated in the lung and liver nuclei of mice treated with lipopolysaccharides, an experimental inflammatory model. These results strongly suggest that phagocyte-derived oxidants, hypohalous acids, endogenously generate the halogenated DNA bases such as a novel dihalogenated 2'-deoxycytidine in vivo. Halogenation (chlorination and/or bromination) of DNA therefore may constitute one mechanism for oxidative DNA damage at the site of inflammation.

Animals↗

PubMed1999

A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives: Monte Carlo simulation.

An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy preference is determined by water-water interaction. For other dimers conformational energy is the most important factor, or both the factors are of nearly equal importance. The introduction of the methyl group into the 5-position of uracil ring most noticeably influences the conformational energy and leads to the decrease of its stabilizing contribution to the total interaction energy. The introduction of halogen atoms increases the relative content of anti-syn and syn-anti conformations of DNPs as compared to the parent ones due to the formation of an energetically more favorable water structure around these conformations. A correlation is observed between the Monte Carlo results for the halogenated DNPs and their experimental photoproduct distribution. The data obtained demonstrates a sequence dependence in the photochemistry of the halogenated dinucleoside monophosphates.

Dinucleoside Phosphates↗

PubMed1975

E.s.r. studies of halogenated pyrimidines in gamma-irradiated alkaline glasses.

The reactions of mobile electrons (em-) and oxygen radical anions (O--) with halogenated bases and nucleosides have been studies in gamma-irradiated alkaline glasses by e.s.r. and specific halogen-ion electrode techniques. It is shown that electrons react with halogenated uracil bases (XUr where X = Cl, Br. I but not F) by dissociative electron attachment to form uracil-5-yl radicals (U-) and halogen anions. The relative rates of reaction of em- with XUr decrease in the sequence BrUr greater than ClUr greater than FUr greater than IUr. Thermal annealing studies carried out on U- in H2O and D2O matrices support the hypothesis that U- in H2O hydrates across the 5-6 double bond in the temperature region 135 degrees-155 degrees K, and deuterates to a much smaller extent in D2O at temperatures above 155 degrees K. Studies on bromouridine and bromodeoxyurinde suggest that em- reacts with the base moieties to form U- type radicals which abstract H- from the sugar moieties of adjacent nucleosides.

Bromouracil↗

PubMed1981

E.S.R. of spin-trapped radicals in gamma-irradiated polycrystalline nucleic acid constituents and their halogenated derivatives.

Free radicals in gamma-irradiated polycrystalline nucleic acid constituents and their 5-halogenated derivatives have been studied by e.s.r. and spin-trapping. After gamma-irradiation at room temperature, the polycrystalline samples were dissolved in aqueous solutions of t-nitrosobutane (tNB) in the absence or presence of oxygen. For many of the nucleic acid constituents, two types of radicals, -C(5)RH-C(6)H- and -C(5)R-C(6)H2-, formed by H-addition to the double bond [-C(5)R=C(6)H-] of the base, were observed, where R is -CH3 or -H. In addition, radicals formed on the sugar moiety were found for some nucleosides. When oxygen was present in the tNB solution, the relative stability of trapped radicals was changed, and thus the presence of more than one radical species could be established. For halogenated bases, the radical produced by H-abstraction from N(1) was observed, and an additional radical species formed by H-addition to the C(6) position was found for 5-fluorouracil. For halogenated nucleosides, the same spectrum was observed in all compounds except the 5-fluoroderivatives, and was assigned to the radicals produced on the sugar moiety. For 5-fluorodeoxyuridine and 5-fluorouridine, the radical formed by H-addition to the C(6) position of the base was observed. In general, the present results are in good agreement with those of previous single crystal studies, but in the case of halogenated compounds other than the 5-fluoroderivatives, it was not possible to spin-trap the alpha-halo radicals which were the most prominent radicals formed from gamma-irradiation of single crystals at room temperature.

Cobalt Radioisotopes↗

PubMed1983

Reactions of the hydrated electron with pyrimidine nucleosides halogenated at the sugar moiety: e.s.r. and spin-trapping with 2-methyl-2-nitrosopropane.

Free radicals produced by the reactions of hydrated electrons with pyrimidine nucleosides halogenated at the sugar moiety (2'-chloro-2'-deoxyuridine and 2'-chlorothymidine) were studied by e.s.r. and spin-trapping. 2-Methyl-2-nitrosopropane was used as the spin-trap. The usual spin-trapping technique was extended to frozen and deoxygenated systems to avoid contamination of the trapped radicals with side-products by spin-trapping 2-methyl-2-nitrosopropane itself. When this method was applied to 2'-chloro-2'-deoxyuridine, a free radical at the C-2' position of the sugar moiety was spin-trapped together with a free radical at the C-5 position of the base moiety. This indicates that hydrated electrons both add to the base moiety and eliminate halogen anions from the halogenated sugar moiety. In the case of 2'-chlorothymidine, however, only a free radical attributed to H-addition at the C-6 position of the thymine base was observed. No radicals produced by the reaction of hydrated electrons with the halogenated sugar could be spin-trapped.

Deoxyuridine↗

PubMed1990

Potent genotoxicity of halogen lamps, compared to fluorescent light and sunlight.

The light emitted by halogen lamps induced mutations in Salmonella typhimurium and DNA damage in Escherichia coli, as shown by the hypersensitivity of DNA repair-deficient strains. The mutagenicity of halogen lamps was considerably higher than that of fluorescent light and of sunlight, even at much lower illuminance levels. Excision mechanisms and SOS functions were involved in repairing light-induced base-pair substitutions and frameshift errors in bacterial DNA. At variance with solar irradiation, which produces mutagenic effects over a wide UV spectrum, genotoxicity of halogen lamps was almost exclusively due to far-UV wavelengths transmissible through UV-R-250 and UV-R-280 interference filters. The main mutagenic component of fluorescent light (254 nm) were almost 10(4)-fold more mutagenic than near-UV wavelengths (365 nm). All light sources exhibited some residual mutagenicity even following filtration through various cloths. On the other hand, appropriate glass or plastic covers consistently prevented mutagenic effects. This emphasizes the urgent need for a compulsory shielding of halogen and fluorescent lamps in order to prevent unnecessary exposures to genotoxic and potentially carcinogenic UV radiations.

DNA Damage↗

PubMed2002

Spontaneous roughening: fundamental limits in Si(100) halogen etch processing.

A dynamical scanning tunneling microscopy and density functional theory study of the thermodynamic stability of halogen-terminated Si(100) surfaces is presented. Significant steric repulsion is shown to exist on all halogen-terminated Si(100) surfaces. This repulsion is the driving force for a roughening phenomenon, which is favored for all halogens except fluorine. Since roughening is an intrinsic property of these surfaces, it sets a lower bound on the atomic scale perfection that can be achieved using halogen etch processing.

Journal Article↗