Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design

Proton transfer reactions and hydrogen-bond networks in protein environments.

In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond dono...

pH-Dependent Protein Electrostatics – Hydrogen Bond Networks Perspective

Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation

Selective ion separation is a major challenge with far-ranging impact from water desalination to product separation in catalysis. Recently introduced ferrocene (Fc)/ ferrocenium (Fc+) polymer electrode materials have been demonstrated experimentally and theoretically to selectively bind carboxylates over perchlorate through weak C−H···O hydrogen bond (HB) interactions that favor carboxylates, d...

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.

A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, side-chain confor...

investigating the feasibility of a proposed model for geometric design of deployable arch structures

deployable scissor type structures are composed of the so-called scissor-like elements (sles), which are connected to each other at an intermediate point through a pivotal connection and allow them to be folded into a compact bundle for storage or transport. several sles are connected to each other in order to form units with regular polygonal plan views. the sides and radii of the polygons are...