Hydrogen bond cooperativity in dimers of hydroxamic acids

Molecular orbital calculations are performed on various dimeric forms of four tautomers each of thioformohydroxamic acid and formohydroxamic acid. The analysis of stabilization energies associated with the dimerization and their correlation to proton affinities and deprotonation enthalpies of different potential sites present in the molecules indicate that the highest stabilization results when the most basic, site of the molecule acts as hydrogen bond acceptor but combination of the most acidic and the most basic site does not result in the largest stabilization when dimerization occurs. The presence of hydrogen bond cooperativity is indicated and the reasons for the observed cooperativity are explored in this study. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Proton-induced tuning of metal-metal communication in rack-type dinuclear Ru complexes containing benzimidazolyl moieties

Ru complexes bearing a bis-tridentate benzimidazolyl ligand have been synthesized. The dinuclear ones act as a bibasic acid with pK(a1)=4.36 and pK(a2)=5.90. The protonated form of the dinuclear complex exhibited two one-electron oxidations at +0.91 and +1.02 V versus the ferrocenium/ferrocene (Fc/Fc(+)) couple (the potential difference (ΔE)=0.11 V), but the di-deprotonated form showed two waves at +0.50 and +0.58 V versus Fc/Fc(+) (ΔE=0.08 V). Since the potential difference between two waves reflects the strength of the metal-metal interaction, the deprotonation of the benzimidazole moieties in the complexes weakened the Ru-Ru communication. The degree of electronic coupling between two metal centers, estimated from the intervalence charge transfer (IVCT) band, was greater for the protonated form. DFT calculations for the protonated and deprotonated forms of the dinuclear complex suggest that the Ru(II)-L(H(2)) π* interaction plays a key role in the Ru-Ru interaction.     

Isocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]‐Hydrogenases

The presence of Fe‐bound cyanide ligands in the active site of the proton‐reducing enzymes [FeFe]‐hydrogenases has led to the hypothesis that such Brønsted–Lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (HNC) might have a relevant role in such crucial microbial metabolic paths. We present a hybrid quantum mechanical/molecular mechanical (QM/MM) study of the energetics of CN^? protonation in the enzyme, and of the effects that cyanide protonation can have on [FeFe]‐hydrogenase active sites. A detailed analysis of the electronic properties of the models and of the energy profile associated with H₂ evolution clearly shows that such protonation is dysfunctional for the catalytic process. However, the inclusion of the protein matrix surrounding the active site in our QM/MM models allowed us to demonstrate that the amino acid environment was finely selected through evolution, specifically to lower the Brønsted–Lowry basicity of the cyanide ligands. In fact, the conserved hydrogen‐bonding network formed by these ligands and the neighboring amino acid residues is able to impede CN^? protonation, as shown by the fact that the isocyanide forms of [FeFe]‐hydrogenases do not correspond to stationary points on the enzyme QM/MM potential‐energy surface.     

meso-Aryl phenanthroporphyrins: synthesis and spectroscopic properties

The successful synthesis of tetraphenyltetraphenanthroporphyrin (TPTPhenP; 5a) in 2006 under modified Rothemund-Lindsey conditions yielded a tetraphenyl porphyrinoid with a B band redshifted to an unprecedented 576 nm. Radially symmetric fused-ring expansion of tetraphenylporphyrin with phenanthrene moieties results in very deep saddling due to steric crowding and very marked redshifts of the Q and B (or Soret) porphyrinoid absorption bands. The extent to which the TPTPhenP structure can be further modified is explored, and the optical properties of TPTPhenPs are analyzed based on a perimeter model approach that makes use of time-dependent DFT calculations and magnetic circular dichroism spectroscopy and also based on a detailed analysis of the fluorescence emission. Attempts to introduce substituents at the ortho and meta positions of the meso-phenyl groups and to insert a central metal proved unsuccessful. The synthesis of a series of TPTPhenPs with strong electron-withdrawing (-CN, -NO(2)) and -donating (-CH(3), -N(CH(3))(2)) substituents at the para positions of the meso-phenyl rings is reported. Marked redshifts of the main spectral bands were consistently observed. The most pronounced spectral changes were observed with -N(CH(3))(2) groups (5i) due to a marked destabilization of the HOMO, which has large MO coefficients on the meso-carbon atoms. Protonation of 5i at both the ligand core and at the -N(CH(3))(2) groups resulted in unprecedented Q(00) band absorption at wavelengths greater than 1200 nm.     

Benzo[e]pyrene skeleton dipyrylium dication with a strong donor-acceptor-donor interaction, and its two-electron reduced molecule

The donor-acceptor-donor (D-A-D) conjugated molecules 1,4-bis(diarylaminophenylethynyl)anthraquinone (1,4-Am(2)Aq) and 1,4-bis(ferrocenylethynyl)anthraquinone (1,4-Fc(2)Aq), undergo a double proton cyclization reaction with bis(trifluoromethanesulfone)imide acid (TFSIH) to yield 1,4-bis(diarylaminophenyl or ferrocenyl) dipyrylium salts [1,4-R(2)Pyl(2)](TFSI)(2) (R=Am or Fc) with novel planar pentacyclic structures similar to the aromatic benzo[e]pyrene-type skeleton. [1,4-Am(2)Pyl(2)](TFSI)(2) could be reduced to give the neutral molecule [1,4-Am(2)Pyl(2)](0), which is stable and maintains the benzo[e]pyrene-type skeleton. To the best of our knowledge, this is the first oxygen-atom-containing polycyclic aromatic hydrocarbon with 22 (4n+2) π-electrons. The obtained condensed-ring benzo[e]pyrene-type skeleton compounds show physical and chemical properties that are significantly different from those of [1,5-Am(2)Pyl(2)](TFSI)(2), which has a perylene-type skeleton.     

Protonation of Tetrapropoxy-4-tert-butylcalix[4]arene: NMR Study of Interaction and Probable Structures of the Product

Using ¹H and ¹³C NMR spectroscopy, the interaction of tetrapropoxy-p-tert-butyl-calix[4]arene (1) with H₃O⁺ ions produced by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and traces of water was studied in nitrobenzene-d ₅. It was shown that 1 readily forms an equimolecular complex with H₃O⁺. The equilibrium constant K of its formation is 2.6 at 296 K. Exchange between bound and free 1 is fast even under mild excess of HDCC, the correlation time τ_ex being about 0.13 ms. NMR shows that H₃O⁺ is bound to the aryl-oxygen atoms and this binding forces the calixarene cup to adopt a more open and symmetrical conformation. This conclusion is in full accord with high precision quantum DFT calculations which find one structure of the complex corresponding to a global energy minimum, in which the H₃O⁺ ion is bound to three of the oxygen atoms by strong hydrogen bonds and to the remaining oxygen by two weaker hydrogen bonds. The calixarene part is forced into a C₄ symmetrical opened form.

When stored for weeks, the complex gradually transforms into other forms, most probably its hydrates, according to spectral evidence and DFT calculations.     

Protonation Curves of the D10N Variant of Endoglucanase Cel45 Catalytic Domain From Humicola Insolens. Isothermal calorimetry and combined isoelectric focusing-electrophoresis

Titration of ionizable groups of D10N variant catalytic domain has been performed by isothermal calorimetric technique and by combined isoelectric focusing-electrophoresis in the range of pH 3–9. pK ₀ ⁱ andΔH ⁰ _i related to the ionizable groups have been estimated using Lindestrøm–Lang equation. Both experimental techniques are in agreement and confirm the validity of the applied theory. Slight differences in protonation enthalpies of carboxyl groups are caused by Asp10 interaction with the other part of the macromolecule.

     

Protonation effects on electron transport through diblock molecular junctions:A theoretical study

Diblock oligomers are widely used in molecular electronics. Based on fully self-consistent nonequilib-rium Green's function method and density functional theory, we study the electron transport properties of the molecular junction with a dipyrimidinyl-diphenyl (PMPH) diblock molecule sandwiched between two gold electrodes. Effects of different kinds of molecule-electrode anchoring geometry and protona-tion of the PMPH molecule are studied. Protonation leads to both conductance and rectification en-hancements. However, the experimentally observed rectifying direction inversion is not found in our calculation. The preferential current direction is always from the pyrimidinyl to the phenyl side. Our calculations indicate that the protonation of the molecular wire is not the only reason of the rectification inversion.