The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experime...

Carotenoids play the dual function of light harvesting and photoprotection in photosynthetic organisms. Despite their functional importance, the molecular basis for binding of carotenoids in the photosynthetic proteins is poorly understood. We have discovered that all carotenoids are surrounded either by aromatic residues or by chlorophylls in all known crystal structures of the photosynthetic ...

Solvothermal reactions of trans-stilbene-4,4'-dicarboxylic acid (H(2)STDC) and zinc(ii) acetate in the presence of systematically varied terminal ligands afforded a series of supramolecular architectures with formula [Zn(STDC)(py)(2)].py (1), [Zn(STDC)(bipy)(H(2)O)].0.5py.H(2)O (2), [Zn(STDC)(biql)] (3), [Zn(STDC)(phen)].solv (solv = DMSO, 4a; DMF, 4b), where py = pyridine, bipy = 2,2'-bipyridi...

The understanding of folding and function of RNA molecules depends on the identification and classification of interactions between ribonucleotide residues. We developed a new method named ClaRNA for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of sp...

We investigate using Monte Carlo simulations in the NPT ensemble the self-assembly of disk-coil macromolecules with stacking interactions. The disk-coil molecules are composed of a planar disk that is covalently bonded to a single coil. In addition to commonly used amphiphilic interactions between the disk and coil portion of the molecules, we employ an attractive interaction between central mo...

Spin polarization and stacking are interesting effects in complex molecular systems and are both presented in graphene-based materials. Their possible combination may provide a new perspective in understanding the intermolecular force. The nanoscale graphene structures with zigzag edges could possess spin-polarized ground states. However, the mechanical effect of spin polarization in stacking o...

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimi...

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 Å). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150–200 atoms with enough large basis sets (for example,...