No abstract

The finite size effects on the electronic structure of graphene ribbons are studied using first principles density functional techniques. The energy gap [difference between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)] dependence for finite width and length is computed for both armchair and zigzag ribbons and compared to their one-dimensional (infinite length) cases. The results suggest, in addition to quantum confinement along the width of the ribbon, an additional finite size effect emerges along the length of ribbons only for metallic armchair ribbons. The origin of additional quantum confinement in these structures is analyzed based on the energy states near the Fermi energy: both HOMO and LUMO energy levels for metallic armchair ribbons are delocalized entirely on the ribbons while for nonmetallic ribbons, these states are localized at the edges only. The results are discussed in light of effect of passivation on the electronic properties of graphenes and their impact on nanoelectronic devices based on graphenes.

Protein splicing is a precise auto-catalytic process in which an intein excises itself from a precursor with the concomitant ligation of the flanking sequences. Protein splicing occurs through acid-base catalysis in which the ionization states of active site residues are crucial to the reaction mechanism. In inteins, several conserved histidines have been shown to play important roles in protein splicing, including the most conserved "B-block" histidine. In this study, we have combined NMR pK a determination with quantum mechanics/molecular mechanics (QM/MM) modeling to study engineered inteins from Mycobacterium tuberculosis (Mtu) RecA intein. We demonstrate a dramatic pK a shift for the invariant B-block histidine, the most conserved residue among inteins. The B-block histidine has a pK a of 7.3 ± 0.6 in a precursor and a pK a of < 3.5 in a spliced intein. The pK a values and QM/MM data suggest that the B-block histidine has a dual role in the acid-base catalysis of protein splicing. This histidine likely acts as a general base to initiate splicing with an acyl shift and then as a general acid to cause the breakdown of the scissile bond. The proposed pK a shift mechanism accounts for the biochemical data supporting the essential role for the B-block histidine and for the absolute sequence conservation of this residue.