Dependence of the constants of binding for nanomarkers of the fluorescein family with human serum albumin on Ph

The effective constants of binding for probes of the fluorescein family (fluorescein and its halogen derivatives, eosin and erythrosin) with human serum albumin (HSA) at different pH were determined. It was found that the introduction of halogen groups into the structural formula of fluorescein changes the character of the dependence on pH of the effective constant of binding of a nanomarker with HSA: the nonlinear dependence of the effective constants of binding with its protein typical for fluorescein, eosin, and erythrosine is characterized by an almost linear reduction with increasing pH dependence of the effective constants of their binding with human serum albumin. It was shown that the presence of more electronegative atoms in the structural formula of nanomarker leads to decrease of values of effective constants of nanomarker binding with HSA.     

Effect of halogenated fluorescent compounds on bioluminescent reactions

The paper investigates an application of luminescent bioassays to monitor the toxicity of organic halides. Effects of xanthene dyes (fluorescein, eosin Y, and erythrosin B), used as model compounds, on bioluminescent reactions of firefly Luciola mingrelica, marine bacteria Photobacterium leiognathi, and hydroid polyp Obelia longissima were studied. Dependence of bioluminescence quenching constants on the atomic weight of halogen substituents in dye molecules was demonstrated. Bacterial bioluminescence was shown to be most sensitive to heavy halogen atoms involved in molecular structure; hence, it is suitable for construction of sensors to monitor toxicity of halogenated compounds. Mechanisms of bioluminescence quenching—energy transfer processes, collisional interactions, and enzyme–dye binding—were considered. Changes of bioluminescence (BL) spectra in the presence of the dyes were analyzed. Interactions of the dyes with enzymes were studied using fluorescence characteristics of the dyes in steady-state and time-resolved experiments. The dependences of fluorescence anisotropy of enzyme-bound dyes, the average fluorescence lifetime, and the number of exponential components in fluorescence decay on the atomic weight of halogen substituents were demonstrated. The results are discussed in terms of “dark effect of heavy halogen atom” in the process of enzyme–dye binding; hydrophobic interactions were assumed to be responsible for the effect.     

Halogen effect on structure and 13C NMR chemical shift of 3,6‐disubstituted‐N‐alkyl carbazoles

Structures of selected 3,6‐dihalogeno‐N‐alkyl carbazole derivatives were calculated at the B3LYP/6‐311++G(3df,2pd) level of theory, and their ¹³C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N‐methyl and N‐ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin–orbit zeroth‐order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~?10 and ~?30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the halogen substituent (F, Cl, Br, and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions of the carbazole ring. The predicted NMR data correctly reproduce the available experimental data for unsubstituted N‐alkylcarbazoles. Copyright © 2013 John Wiley & Sons, Ltd.     

Properties of halogen atoms for representing intermolecular electrostatic interactions related to halogen bonding and their substituent effects

The electrostatic properties of halogen atoms are studied theoretically in relation to their ability of halogen bonding, which is an attractive intermolecular interaction of a covalently bonded halogen atom with a negatively charged atom of a neighboring molecule. The electric quadrupole (of electronic origin) with a positive zz component Θ_zz of a covalently bonded halogen atom, where the z axis is taken along the covalent bond involving the halogen atom, is mainly responsible for the attractive electrostatic interaction with a negatively charged atom. This positive Θ_zz is an intrinsic property of halogen atoms with the p_x²p_y²p_z configuration of the valence electronic shell, as shown by ab initio molecular orbital calculations for isolated halogen atoms with this electronic configuration, and increases in the order of F < Cl < Br < I, in parallel with the known general sequence of the strength of halogen bonding. For halogen‐containing aromatic compounds, the substituent effects on the electrostatic properties are also studied. It is shown that the magnitude of Θ_zz and the electric field originating from it are rather insensitive to the substituent effect, whereas the electric field originating from atomic partial charges has a large substituent effect. The latter electric field tends to partially cancel the former. The extent of this partial cancellation is reduced in the order of Cl < Br < I and is also reducible by proper substitution on or within the six‐membered ring of halobenzene. Perspectives on the development of potential function parameters applicable to halogen‐bonding systems are also briefly discussed. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Mechanisms of circumambulatory rearrangements of 5-halogeno-1,2,3,4,5-pentamethoxycarbonylcyclopentadienes

Possible paths of halogen atom migration in 5-halogeno-1,2,3,4,5-pentamethoxycarbonylcyclopentadienes were studied using the density functional theory. The calculations revealed preferential 1,5(in comparison with 1,3-) sigmatropic shifts of halogen atoms along the perimeter of the five-membered ring with the energy barriers ΔE _ZPE ^≠ = 42.9, 26.9, 19.8, and 15.4 kcal mol^–1 for the fluoro-, chloro-, bromo-, and iodosubstituted derivatives, respectively. The calculated charges of halogen atoms in the structures of transition states for 1,5-shifts change from negative for the fluorine atom to positive for the iodine atom (–0.356 (F), 0.019 (Cl), 0.052 (Br), 0.184 e (I)). The migration capacity increases in the order F < Cl < Br < I with an increase in the atomic radius of halogen.     

Stereochemistry and 13C NMR investigation of 9-halotetrahydro-4H-pyrido[1,2-a]pyrimidin-4-ones

It was shown that the halogen atom occupies the quasi-axial position in the predominant conformer of the 9-halo derivatives of tetrahydro-4H-pyrido[1,2-a]pyrimidin-4-ones. When R³ = Me, the conformational equilibrium is determined by the latter substituent which is always quasi-axial. The effects of the methyl group and the halogen atoms on the ¹³C chemical shifts (SCS values) were used for the identification of cis and trans isomers. Interesting non additivity of substituent effects was found in derivatives bearing quasi-axial substituents at C-6 and C-9: and this was caused by the ring flattening.     

The many flavours of halogen bonds – message from experimental electron density and Raman spectroscopy

Experimental electron‐density studies based on high‐resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl…Cl contacts vary smoothly as a function of the interaction distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitrogen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge–density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron‐rich nucleophiles and heavy halogen atoms resemble three‐centre–four‐electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow intermediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,?1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated interaction. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen–carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen‐bond strength. We find exceptionally long C—I distances for tetrafluorodiiodobenzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations.     

1,2,5-Thiadiazolo[3,4-b]pyrazines

1,2,5-Thiadiazolo[3,4-b]pyrazine and its derivatives were prepared. Nucleophilic displacements of halogen atoms on the nucleus were reported.     

Synthesis of Soluble Quinacridone Photocatalysts for the Homogeneous Oxidation of Thioethers

Evaluation of quinacridone (QA) derivatives as homogeneous metal-free photocatalysts is here presented. QA derivatives were synthetized and systematically characterized, measuring their ground state and excited state redox potentials in dichloromethane (DCM) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), in order to understand how structural modifications influenced their photocatalytic properties. In particular, the effect of dicyanomethylene and nitro EWG groups was investigated, in order to develop a photocatalyst capable of promoting oxidative processes in the presence of molecular oxygen. Among the analyzed derivatives, 2,9-dinitro-N,N′-dibutylquinacridone (DNDBQA) was the one with the highest excited state reduction potential (E_red*=1.60 V in HFIP vs SCE), while N,N’-dibutylquinacridone (DBQA) showed valuable excited state redox potentials (E_red*=1.29 V; E_ox*=−1.28 V in HFIP vs SCE), making it suitable for bimodal applications in oxidative and reductive photocatalytic processes. Afterwards, the synthetized QA derivatives were examined as photocatalysts to promote the selective aerobic oxidation of thioether to sulfoxide. Promising results in thioanisole oxidation were achieved with all the QA derivatives tested as photocatalysts, in terms of yield and selectivity. Remarkably, DBQA showed the best performances, catalyzing the reaction in only 20 minutes, using 0.5 % of the photocatalyst, and showing excellent performances in the oxidation of several thioether derivatives.     

Coupling of Titanacyclopentadienes with a Cp Ligand and Elimination of One Substituent

Titanacyclopentadienes, prepared from [Cp₂TiBu₂] and either two equivalents of an alkyne or a diyne, were treated with PMe₃ (3 equiv) at 50 °C for 3 h and then with azobenzene at room temperature for 12 h to give 4,5,6‐trisubstituted indene derivatives with the loss of one substituent in good yields. This reaction contrasts sharply with our previously reported reaction for the formation of 4,5,6,7‐tetrasubstituted indene derivatives without the loss of substituents by the treatment of titanacyclopentadienes with azobenzene without PMe₃. ¹³C NMR spectroscopy of the product derived from a ¹³C‐enriched complex revealed that the five carbon atoms originating from a Cp ligand were arranged linearly in the trisubstituted indene derivatives, in contrast to the 4,5,6,7‐tetrasubsituted indene derivatives, in which the corresponding five carbon atoms are arranged in a ring.     

Synthesis and Transformations of 3-Ethoxycarbonyl-2-(N-R-thioureido)thiophenes

3-Ethoxycarbonyl-2-(N-R-thioureido)-4,5,6,7-tetrahydrobenzo[b]thiophenes were obtained by the reaction of 2-amino-3-ethoxycarbonyl-4,5,6,7-tetrahydrobenzo[b]thiophene with isothiocyanates and of 3-ethoxycarbonyl-2-isothiocyanato-4,5,6,7-tetrahydrobenzo[b]thiophene with primary and secondary amines. The cyclization paths of the products leading to derivatives of thieno[2,3-d]pyrimidine and thieno[2,3-d]-1,3-thiazine were studied. The corresponding S-substituted derivatives were obtained by the alkylation of 3-R-2-thioxo-3,4,5,6,7,8-hexahydrobenzo[b]thieno[2,3-d]pyrimidin-4-ones.     

Novel Selected Tandem Transformations of the Amino and Carbonyl/Nitrile Groups in the Gewald Thiophenes

Novel transformations of the amino and carbonyl/nitrile groups in the Gewald thiophenes were studied for thienopyrimidine synthesis. It was found that 2-amino-thiophene-3-carboxamides and ethyl 2-(acetylamino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carbo- xylate did not yield tetrazole derivatives, neither in the reaction with triethyl orthoformate and sodium azide, nor in the reaction with phosphorus oxychloride and sodium azide, correspondingly. On the contrary, derivatives of thieno[2,3-d]pyrimidin-4(3H)-one and thieno[2,3-d][1,3]oxazin-4-one were isolated. New 2-azidothiophenes [2-azido-4,5,6,7-tetra hydro-1-benzothiophene-3-carbonitrile and 2-azido-4,5,6,7-tetrahydro-1-benzothiophen-3-yl(phenyl)methanone] were synthesized and used in anionic domino reactions with activated acetonitriles to yield thieno[3,2-e][1,2,3]triazolo[1,5-a]pyrimidines and/or 2-(5-amino-1H-1,2,3-triazol-1-yl)thiophenes. Finally, a new ring system of thieno[3,2-e]pyrazolo[1,5-a]pyrimidine was synthesized via a domino reaction of ethyl 2-[(2Z)-2-(1-chloro-2-ethoxy-2-oxoethylidene)hydrazino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylate with activated acetonitriles.     

Synthetic and Structural Studies of 1‐Halo‐8‐(alkylchalcogeno)naphthalene Derivatives

A series of eight 1‐halo‐8‐(alkylchalcogeno)naphthalene derivatives ( 1 – 8 ; halogen=Br, I; alkylchalcogen=SEt, SPh, SePh, TePh) containing a halogen and a chalcogen atom occupying the peri positions have been prepared and fully characterised by using X‐ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Naphthalene distortion due to non‐covalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X‐ray data for 1 , 2 , 4 and 5 – 8 were compared. Molecular structures were analysed in terms of naphthalene ring torsions, peri‐atom displacement, splay angle magnitude, X???E interactions, aromatic ring orientations and quasi‐linear X???E? C arrangements. A general increase in the X???E distance was observed for molecules that contain bulkier atoms at the peri positions. The I???S distance of 4 is comparable with the I???Te distance of 8 , and is ascribed to a stronger lone pair–lone pair repulsion due to the presence of an axial S(naphthyl) ring conformation. Density functional theory (B3LYP) calculations performed on 5 – 8 revealed Wiberg bond index values of 0.05–0.08, which indicate minor interactions taking place between the non‐bonded atoms in these compounds.     

Cationic polymerization of n‐hexyloxyallene by using halogen‐bonding organocatalysts

The cationic polymerization of n‐hexyloxyallene was investigated by using halogen‐bonding organocatalysts ( Cat A – Cat D ). Although the neutral catalyst Cat C showed a poor polymerization activity, iodine‐carrying bidentate cationic catalyst Cat A brought about the smooth polymerization giving rise to a polymer with M_n of 2710 under [ Cat A ]:[IBVE‐HCl]:[monomer] = 10:10:500 in mM concentrations. Judging from the color change of polymerization system and electrospray ionization mass spectra of recovered catalyst, the decomposition of organocatalyst was suggested. When α‐bromodiphenylmethane was used as an initiator, the relatively controlled polymerization proceeded at the low monomer conversion likely due to the weak halogen‐bonding interaction of Cat A with the bromide anion. On the other hand, bromine‐carrying bidentate catalyst Cat D gave low‐molecular‐weight polymers (M_n < 1550) to be less suitable for polymerization. From the ¹H‐NMR spectrum, it was found that the 1,2‐polymerization unit and 2,3‐polymerization unit are included in 75:25. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 2436–2441     

Halogen-Driven Bandgap Opening in Graphdiyne for Overall Photocatalytic Water Splitting

In this work, we studied the electronic band structure of the halogen (F, Cl, and Br) functionalized graphdiynes (GDYs) by using hybrid density functional theory. The results revealed that the bandgap energies of modified GDYs increase as the number of halogen atoms increases. It is also found that the position of the valence band maximum (VBM) is influenced by the electronegativity of halogen atoms. The higher the electronegativity, the deeper the VBM of the GDYs modified by the same number of halogen atoms. Importantly, our results revealed that the bandgap of GDY could be effectively tuned by mixing types of halogen atoms. The new generated conduction band and valence band edges are properly aligned with the oxidation and reduction potentials of water. Further thermodynamic analysis confirms that some models with mixing types of halogen atoms exhibit higher performance of overall photocatalytic water splitting than non-mixing models. This work provides useful insights for designing efficient photocatalysts that can be used for overall water splitting.     

3,6‐linked 9‐alkyl‐9H‐carbazole main‐chain polymers: Preparation and properties

An investigation into the preparation of poly(9‐alkyl‐9H‐carbazole‐3,6‐diyl)s with palladium catalyzed cross‐coupling reactions of 3‐halo‐6‐halomagnesio‐9‐alkyl‐9H‐carbazoles, generated in situ from their corresponding 3,6‐diiodo‐ and 3,6‐dibromo‐derivatives was undertaken. Monomers with a range of alkyl group substituents with different steric requirements were investigated and their effects on the polymerization were studied. The effects of the nature of halogen substituents on the polymerization reaction were also investigated. Structural analysis of the polymers revealed exclusive 3,6‐linkage between consecutive carbazole repeat units on the polymer chains. The physical properties of these polymers were investigated with spectroscopic, thermal gravimetric analysis, and electrochemical studies. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6041–6051, 2004     

Effect of halogen bonding on supramolecular assembly and photophysical properties of diaryl oxalates

In order to determine the effect of halogen bonding on supramolecular assemblies and photophysical properties of diaryl oxalates, diaryl oxalate itself and its derivatives with fluorine, chlorine, bromine, and iodine substituents in the p-position of phenyl rings were studied and compared. Their single-crystal structures were studied by geometrical analysis and theoretical calculation. The study reveals that different halogen bonds are formed with respect to different halogen atoms, such as C…F and X…X (bromine and iodine atoms) interactions, and molecular stacking modes would be affected by halogen bonds directly. Comparative studies of photophysical properties in dilute solution and solid state indicate that halogen substitutions would not affect the emission processes of diaryl oxalates in dilute solution; this is not the case for their solid state. This work has demonstrated that halogen bonds play an important role in regulating structures and photophysical properties of diaryl oxalates.     

Synthesis of 4,5,6,7‐Tetrabromo‐1H‐benzimidazole Derivatives

A convenient and simple method for the preparation of polybrominated benzimidazole derivatives has been described. Reaction of 4,5,6,7‐tetrabromo‐1‐(3‐chloropropyl)‐1H‐benzimidazole, obtained by alkylation of 4,5,6,7‐tetrabromo‐1H‐benzimidazole (TBBi) with 1‐bromo‐3‐chloropropane in the presence of KOH, with morpholine, aniline, benzylamine, N‐methyl piperazine, and 2‐arylpyrrolidines afforded new TBBi derivatives.     

Electronic structure and models of receptor of monooxygenase inductors from a number of polychlorinated polycyclic compounds. 3. Mndo calculations of chlorine and fluorine derivatives of dibenzo-p-dioxins

MNDO calculations for dibenzo-para-dioxin (DD) and its chlorine- and fluorine-substituted derivatives have shown that the geometric structure of the molecules and the -donor properties are very little dependent on the type of halogen (chlorine or fluorine) or on the position of the halogen in the molecule. The chlorine and fluorine derivatives of the DD do exhibit substantial differences in the charges on the C atoms directly connected to the halogens. The higher atomic charges on the C atoms connected to F atoms suggests that the fluorine-containing DDs will be capable of metabolism to mercapturic acids.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2544–2547, November, 1989.     

Crystal engineering for topochemical polymerization of muconic esters using halogen-halogen and CH/pi interactions as weak intermolecular interactions

We now report the molecular and crystal structure design of muconic ester derivatives on the basis of crystal engineering using halogen-halogen contacts and CH/pi interactions. The solid-state photoreaction pathway of the dibenzyl (Z,Z)-muconates as the 1,3-diene dicarboxylic acid monomers depends on the structure of the ester groups. The substitution of a halogen atom for the aromatic hydrogen of a benzyl group induces topochemical polymerization to produce stereoregular polymers in a crystalline form, whereas the unsubstituted benzyl derivative isomerizes to yield the corresponding E,E isomer under similar conditions. The topochemical polymerization process is directly confirmed by the fact that the single-crystal structures before and after the polymerization are very similar to each other. From the crystal structure analysis for a series of substituted benzyl (Z,Z)- and (E,E)-muconates, it has been revealed that the planar diene moieties are closely packed to form a columnar structure in the crystals. The stacking of the polymerizable monomers is characterized by a stacking distance of 4.9-5.2 A along the columns. This structure is supported by a halogen-halogen interaction between the chlorine or bromine atoms introduced at the p position of the benzyl groups in addition to an aromatic stacking due to the CH/pi interaction between the benzylic methylene hydrogens and aromatic rings. The design of a monomer packing corresponds to the type and position of the introduced halogen atom and also the polymorphs. To make a stacking distance of 5 A using both halogen-halogen and CH/pi interactions as supramolecular synthons is important for the molecular design of muconic ester derivatives appropriate for topochemical polymerization.