In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck-Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER...

The new iron carbonyl cyanide trans-[Fe(CN)(2)(CO)(3)](2)(-), [2](2)(-), forms in high yield via photosubstitution of Fe(CO)(5) with 2 equiv of Et(4)NCN. Protonation of [2](2)(-) generated [HFe(CN)(2)(CO)(3)](-), [2H](-), the first H-Fe-CN-CO species. Further protonation gives dihydrogen. This simple system provides insights into hydrogen evolution by the hydrogenase enzymes, which also feature...

Electronic circular dichroism and circularly polarized luminescence acid/base switching activity has been demonstrated in helicene-bipyridine proligand 1 a and in its "rollover" cycloplatinated derivative 2 a. Whereas proligand 1 a displays a strong bathochromic shift (>160 nm) of the nonpolarized and circularly polarized luminescence upon protonation, complex 2 a displays slightly stronger emi...

We describe effects of a mutation, Ile-67-->Asn, in subunit I of yeast cytochrome c oxidase on redox-linked protonation processes within the protein. The mutation lowers the midpoint potential of haem a and weakens its pH dependency, but has little effect on the potential of haem a3. The residue is close to a conserved glutamate (Glu-243) in the crystal structure. We propose that protonation of...

Water clusters of protonated substituted anilines generated by an electrospray ion source have been investigated using a Fourier Transform ion cyclotron resonance mass spectrometer. It is observed that evaporation kinetics and cluster distributions are highly dependent on sites of protonation in the substituted anilines. Based on the examination of the water cluster distributions of protonated ...

Hydrogen sulfide (H2S) is an important signaling molecule that exerts action on various bioinorganic targets. Despite this importance, few studies have investigated the differential reactivity of the physiologically relevant H2S and HS(-) protonation states with metal complexes. Here we report the distinct reactivity of H2S and HS(-) with zinc(II) and cobalt(II) phthalocyanine (Pc) complexes an...

The emission wavelength shift in mechanochromic luminescence is extended via protonation of pyridyl-substituted imidazole molecules near the crystal surface.

The p K(a) values of 6-fluoro-4,8-diazadodecane-1,12-diamine (6-fluorospermine) (1), 6,6-difluoro-4,8-diazadodecane-1,12-diamine (6,6-difluorospermine) (2), 6-fluoro-4-azaoctane-1,8-diamine (6-fluorospermidine) (3) and 6,6-difluoro-4-azaoctane-1,8-diamine (6,6-difluorospermidine) (4) in D(2)O solution have been determined at 40 degrees C from (13)C NMR chemical shifts data using the new compute...

Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resol...