Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be us...

BACKGROUND Among the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful. RESULTS Four interaction types of histidine are quantitatively cal...

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both ...

The use of appropriate level of theories for studying weak interactions such as stacking of aromatic molecules has been an important aspect, since the high level methods have limitations for application to large molecules. The differences in the stacking energies of various structures are found significant for identifying the most favored stacked benzene rings and the pyridine rings. The most f...

Thiosemicarbazones (TSCs) possess significant antimalarial properties believed to be linked to the inhibition of major cysteine proteases, such as falcipain-2, in Plasmodium falciparum. However, the binding modes of TSCs to the active site of these enzymes are not clear. As a result of this, the nature of the bonding interactions between the active site of falcipain-2 and different derivatives ...

The strongest gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass. Our calculations reveal that the stacking i...

The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti or...

A new class of platinum(II) terpyridine complexes with a phosphole-derived bridging alkynyl ligand have been prepared. The X-ray crystal structure of complex 2 has been determined, and reveals a polymeric zig-zag chain structure with the existence of p–p stacking interactions. The photophysical properties have also been studied, with MLCT/LLCT phosphorescence exhibited in degassed CH2Cl2; the e...

A new class of platinum(ii) terpyridine complexes with a phosphole-derived bridging alkynyl ligand have been prepared. The X-ray crystal structure of complex 2 has been determined, and reveals a polymeric zig-zag chain structure with the existence of π-π stacking interactions. The photophysical properties have also been studied, with 3MLCT/3LLCT phosphorescence exhibited in degassed CH2Cl2; the...

Aromatic π-π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA-polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and ...