Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis.

Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.

Carbazole Substituted BODIPYs: Synthesis, Computational, Electrochemical and DSSC Studies.

Carbazole and p-anisyl substituted BODIPY dyes with a cyanoacetic acid anchoring group have been prepared and their spectral, electrochemical properties and photosensitizing potential in DSSC have been evaluated. X-ray structure of N-phenylcarbazole substituted BODIPY revealed lower torsion angle between BODIPY plane and carbazole plane, suggesting increased communication between the two units. DFT studies indicated effective electronic interactions between the BODIPY unit and carbazole substituents. The N-butylcarbazole and N-phenylcarbazole substituted BODIPYs showed anodic shifts in their reduction potentials, indicating facile reduction process. The predicted HOMO-LUMO gaps are in agreement with the electrochemical result and the lower band gap was observed for the carbazole substituted BODIPYs.

Comparative study of E⋯N (E=Se/Te) intramolecular interactions in organochalcogen compounds using density functional theory.

The intramolecular E⋯N (E=Se, Te) interactions between the selenium (and tellurium) and the nitrogen atom in four series of o-substituted organochalcogen compounds have been analyzed using density functional theory. The nature and the strength of this interactions and their dependence on substituents and the rigidity are predicted using B3LYP/6-31G(d)/LanL2DZ method. The strength of these E⋯N interactions are found to be dependent on the nature of EX (X=Cl, Br, I, SPh, CH2Ph; Ph: Phenyl) acceptor orbitals and follows the order I>Br>Cl>SPh>CH2Ph. The Natural Bond Orbital (NBO) analysis using DFT methods points to nN→σE-X electron delocalization as the key contributing factor toward E⋯N nonbonding interactions. Both NBO and AIM methods suggest that the intramolecular interaction in these compounds is dominantly covalent in nature. Studies on the effect of solvent on the E⋯N interactions show that polar solvent stabilizes these interactions by shortening the E⋯N distances.

On attractive interaction of a colloid pair of like charge at infinite dilution.

Numerical data on the potential of mean force W(r) at infinite dilution of a highly charged colloid pair embedded in a 1:1 electrolyte are reported. The authors obtain attractive minima (W<0) at short interparticle distance in these potential functions in hypernetted chain (HNC) approximation, as salt concentration is increased. These minima, however, disappear in all system sets studied when a self-consistent Zerah-Hansen (ZH) closure is used. The authors infer that the attractive minima obtained in a HNC closure are spurious and result from the neglect of bridge diagrams in HNC approximation. An expression of bridge function, which the ZH closure in effect incorporates in W(r) to remove attractive minima, is derived in terms of modification of correlation functions. Features of repulsive pair potentials obtained using the ZH closure, their dependence on particle charge and salt concentration, and their agreement with those of the Derajguin-Landau-Verwey-Overbeek theory are investigated.

The alpha helix dipole: screened out?

Aligned alpha helix peptide dipoles sum to a "macroscopic" dipole parallel to the helix axis that has been implicated in protein folding and function. However, in aqueous solution the dipole is counteracted by an electrostatic reaction field generated by the solvent, and the strength of the helix dipole may reduce drastically from its value in vacuum. Here, using atomic-detail helix models and Poisson-Boltzmann continuum electrostatics calculations, the net effective dipole moment, mu(eff), is calculated. Some initially surprising results are found. Whereas in vacuum mu(eff) increases with helix length, the opposite is found to be the case for transmembrane helices. In soluble proteins, mu(eff) is found to vary strongly with the orientation and position of the helix relative to the aqueous medium. A set of rules is established to estimate of the strength of mu(eff) from graphical inspection of protein structures.