Crystallography Aided by Atomic Core-Level Binding Energies: Proton Transfer versus Hydrogen Bonding in Organic Crystal Structures

Ionic bond or hydrogen bridge? Br?nsted proton transfer to nitrogen acceptors in organic crystals causes strong N1s core-level binding energy shifts. A study of 15 organic cocrystal and salt systems shows that standard X-ray photoelectron spectroscopy (XPS) can be used as a complementary method to X-ray crystallography for distinguishing proton transfer from H-bonding in organic condensed matter.     

Dihydronaphthalene‐Fused Boron–Dipyrromethene (BODIPY) Dyes: Insight into the Electronic and Conformational Tuning Modes of BODIPY Fluorophores

A new series of boron–dipyrromethene (BDP, BODIPY) dyes with dihydronaphthalene units fused to the β‐pyrrole positions ( 1 a – d , 2 ) has been synthesised and spectroscopically investigated. All the dyes, except pH‐responsive 1 d in polar solvents, display intense emission between 550–700 nm. Compounds 1 a and 1 b with a hydrogen atom and a methyl group in the meso position of the BODIPY core show spectroscopic properties that are similar to those of rhodamine 101, thus rendering them potent alternatives to the positively charged rhodamine dyes as stains and labels for less polar environments or for the dyeing of latex beads. Compound 1 d , which carries an electron‐donating 4‐(dimethylamino)phenyl group in the meso position, shows dual fluorescence in solvents more polar than dibutyl ether and can act as a pH‐responsive “light‐up” probe for acidic pH. Correlation of the pK_a data of 1 d and several other meso‐(4‐dimethylanilino)‐substituted BODIPY derivatives allowed us to draw conclusions on the influence of steric crowding at the meso position on the acidity of the aniline nitrogen atom. Preparation and investigation of 2 , which carries a nitrogen instead of a carbon as the meso‐bridgehead atom, suggests that the rules of colour tuning of BODIPYs as established so far have to be reassessed; for all the reported couples of meso‐C‐ and meso‐N‐substituted BODIPYs, the exchange leads to pronounced redshifts of the spectra and reduced fluorescence quantum yields. For 2 , when compared with 1 a , the opposite is found: negligible spectral shifts and enhanced fluorescence. Additional X‐ray crystallographic analysis of 1 a and quantum chemical modelling of the title and related compounds employing density functional theory granted further insight into the features of such sterically crowded chromophores.     

Synthesis and Supramolecular Functional Assemblies of Ratiometric pH Probes

Tracking pH with spatiotemporal resolution is a critical challenge for synthetic chemistry, chemical biology and beyond. Over the last decade, different small probes and supramolecular systems have emerged for in cellulo or in vivo pH tracking. However, pH reporting still presents critical limitations, such as background reduction, improved sensor stability, cell targeting, endosomal escape, near- and far-infrared ratiometric pH tracking and adaption to new imaging techniques (i.e., super-resolution). These challenges will require the combined efforts of synthetic and supramolecular chemistry working together to develop the next generation of smart materials that will resolve current limitations. Herein, recent advances in the synthesis of small fluorescent probes, together with new supramolecular functional systems employed for pH tracking, are described with an emphasis on ratiometric probes. The combination of organic synthesis and stimuli-responsive supramolecular functional materials will be essential to solve future challenges of pH tracking, such as improved signal to noise ratio, on target activation and microenvironment reporting.     

Tetranuclear Copper(I) Complex Containing Bis (Diphenylphosphino) Methane Bridging Ligands. Crystal Structure of [Cu 4 (C 7 H 4 NO 4 ) 2 (dppm) 4 ] (NO 3 ) 2

The tetranuclear copper complex [Cu 4 (C 7 H 4 NO 4 ) 2 (dppm) 4 ] (NO 3 ) 2 (C 7 H 4 NO 4 =pyridine-2, 6-dicarboxylic acid) has been synthesized and characterized spectroscopically. The compound crystallizes in the triclinic space group $P{\bar 1}$     

Protonation Sequence Study of the Solution Structure of DTPA by 1H NMR

The protonation sequence of DTPA is evaluated using a 300 MHz H NMR instrument. A terminal nitrogen is protonated first (pK_a1,2=10.02, 8.45). Upon the first protonation a dynamic hydrogen bonded five membered ring is formed between the terminal nitrogen and the central nitrogen. The second equivalent of protons protonates the opposite terminal amine and causes the ring to open. The third protonation (pK_a3=4.65) takes place on the central acetate and forms a ring with the central amine. The fourth protonation is assigned to a terminal acetate. The formation of five membered rings involving hydrogen bonding gives a better quantitative and qualitative account for the unusual shifts observed in the H NMR spectra than previous explanations.     

Effects of protonation and deprotonation on the reactivity of quinolone: A theoretical study

Quinolones are the subject of much research as antibacterial compounds and as a new class of antitumor agents.The protonation(P) and deprotonation(D) sites and conformations of quinolone were investigated.The proton affinity(PA) on each of the possible sites in 4-oxo-1,4-dihydroquinoline has been calculated by the restricted Hartree-Fock(HF) and density functional theory(DFT) methods with the basis set 6-311G**.The O-site of protonation was found to be strongly favored over the N-site for the studied compound in the gas phase.Deprotonation takes place in quinolone by detachment of the N-H and COOH protons.The PA of the simple quinolone molecule was used to characterize quinolone reactivity with DNA binding sites.The relative stabilities of the syn and anti conformations were investigated at the B3LYP/6-311G** level of theory;the syn form was shown to be slightly more stable.Its conformation seems to be intrastabilized by hydrogen-bonds consisting of a hydroxyl proton with the O10 atom as the acceptor.We computed and discussed the charge-density distribution and electrostatic potential to explain the reactivity of quinolone.     

Organophosphorous ligands in hydrogenase‐inspired iron‐based catalysts: A DFT study on the energetics of metal protonation as a function of P‐atom substitution

The present paper reports a study on the energetics of protonation of a hydrogenase biomimetic complex, [Fe₂(μ‐adt)(CO)₄(PMe₃)₂] (adt = N‐benzylazadithiolate), and of its homologue featuring triphenylphosphine ligands in place of trimethylphosphines. Formation of a terminal hydride on one of the Fe centres was considered first, given the key relevance of terminal hydride species in the enzymatic mechanism. Theoretical calculations highlight that, in a vacuum, terminal protonation of the selected Fe ion in the PPh₃‐bearing organometallic complex is highly favoured when compared to the analogous reaction involving the PMe₃‐containing species, but the trend is inverted in the case of models optimized in a continuum polarizable. An unexpected parallel is thus established between relative basicities of PPh₃ and PMe₃ in vacuum or in solution phase [C. A. Tolman, J. Am. Chem. Soc. 1970 , 92, 2953; G. M. Bancroft, Inorg. Chem. 1986 , 25, 3675], and the energetics of terminal hydride formation upon protonation of [FeFe]‐hydrogenase biomimetic complexes bearing such organophosphorous ligands. Bridging hydride formation was also considered in the present study: calculations showed that protonation of the PMe₃‐bearing organometallic complex is again strongly favoured in vacuo, as compared to the case of the PPh₃‐containing model. However, protonation energies become significantly smaller when solvent effects are taken into account. Such differences between protonation reactions modelled in vacuo and in the polarizable continuum are rationalized in light of the different electrostatic properties of the diiron complexes here considered. Implications for the design and modelling of biomimetic catalysts are briefly discussed in light of recent literature.     

Protonation of captodative trifluoromethylated aminoalkenes and isomerization of their salts. An ab initio study

A study of the regioselectivity of protonation of captodative trifluoromethylated enamines was carried out using MP2/6‐311 + G(d,p) calculations and the natural bond orbital analysis. The central issue of this research concerns the influence of the electron‐withdrawing group, which is not capable of the π,π‐conjugation, on the properties of captodative enamines and their salts. The presence of CF₃ group in such type of enamines levels the energy of their N‐protonated and C‐protonated forms. The transition states were found for both intramolecular and intermolecular processes of the proton transfer. The more possible mechanism of the isomerization of enammonium and iminium cations includes the proton transfer from N‐protonated form to olefinic carbon atom of the starting enamine. The transition state energies, which correspond to intermolecular process, are relatively low (11–13 kcal mol^–1) in contrast to the intramolecular pathway (64–69 kcal mol^–1). Copyright © 2011 John Wiley & Sons, Ltd.     

Novel heterocyclic poly(pyridine‐imide)s with unsymmetric carbazole substituent and noncoplanar structure: High thermal,mechanical and optical transparency,electrochemical, and electrochromic properties

A diamine containing heterocyclic pyridine and unsymmetrical carbazole substituents, 4‐(9‐ethyl‐3‐carbazole)‐2,6‐bis(4‐aminophenyl)pyridine ( CBAPP ), was prepared for use in the synthesis of poly(pyridine‐imide)s PI‐1–8 by direct polycondensation with dianhydrides in N,N‐dimethylacetamide (DMAc). The poly(pyridine‐imide)s derived from the diamine are highly soluble in solvents such as N‐Methyl‐2‐pyrrolidone (NMP) and DMAc at room temperature. Noncoplanar polyimide (PI‐1) showed excellent solubility, high transparency, and high‐performance mechanical properties. These polymers had relatively high glass transition temperatures and exhibited good thermal stability in both nitrogen (T_d10 > 470 °C) and air (T_d10 > 450 °C). The PI‐3～5 cannot form flexible and tough films due to the unsymmetrical carbazole moiety, rigid structure, and polar–polar interaction. However, through copolymerization technique these polymers (PI‐6～8) could be enhanced through the solubility, mechanical, and thermal properties. The optical properties included a strong orange fluorescence (540 nm) after protonation with acid. When the HCl concentration was increased, a new absorption band at approximately 350 nm appeared, and the intensity of the fluorescent peak at 380 nm observed in the neutral polymer solution decreased, along with the appearance of the new fluorescent peak at 540 nm. The poly(pyridine‐imide)s presented here showed only slight fluorescence quenching in the presence of methanol. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 405–412