On the role of the basis set and electron correlation in the description of stacking interactions
ABSTRACT Ab initio SCF and Möller-Plesset electron correlations, up to fourth-order calculations, have been performed for a very simple model system of stacking interactions—the water dimer with parallel and antiparallel dipole-dipole orientations. The performance of a variety of basis sets in evaluating the basis set superposition error and the interaction energy has been systematically examined. It is shown that for a proper description of the stacking interaction the diffuse sp-functions as well as the multiple sets of polarization functions are required. Additional calculations were carried out with popular semi-empirical methods (MNDO, AMI and PM3). All of the applied semi-empirical methods greatly overestimate the interaction forces and give qualitatively incorrect results.
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ABSTRACT: The present study has intended to have a better understanding of physicochemical interaction between platinum drugs and DNA base pairs. The interactions of platinum drugs Cisplatin (Cis-Pt), Carboplatin (Carb-Pt), Oxaliplatin (Oxali-Pt), and Nedaplatin (Neda-Pt) with AT and GC base pairs were studied with two main orientations using quantum chemical methods. The planar and stacked complex geometries were optimized by B3LYP, M05-2X, and M05 of density functional theory methods; HF and MP2 levels of theory of ab initio method by employing LANL2DZ and SDD basis sets. The influence of solvent on the stacked complex geometries has been studied at M05/LANL2DZ, M05/SDD, MP2/LANL2DZ, and MP2/SDD levels of theory. The role of vertical distance and twist angle between the stacked molecules on the interaction energy were investigated by the above methods. The present study reveals that the computational methods with electron correlation and newly developed density functional method (M05) are preferred for interaction of base pairs with intercalator. It is observed that the platinum drugs which are intercalated with the AT and GC base pairs through hydrogen bonding alter the geometry, dipole moment, and polarization of base pairs. The cross-link of these molecules with DNA strand prevents the replication and transcription of DNA. It is also interesting to note that after the interaction of platinum drugs, an intermolecular C–H···O hydrogen bond has formed between Adenine and Thymine in AT base pair and the values ranges between 2.348 and 2.399 Å. The calculated results favor that the platinum molecules are good candidates for the cancer drug.Structural Chemistry 04/2012; 24(2). DOI:10.1007/s11224-012-0087-y · 1.90 Impact Factor
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ABSTRACT: A rigid-body systematic search technique was applied to stacked complexes of the novel AT-specific intercalator, amiloride, with each of the four DNA bases (A, T, C, G) and two Watson−Crick base pairs (AT and GC). Gas-phase calculations were carried out using the Cornell empirical molecular potential with a set of ab initio-optimized atomic charges. At selected points on the ligand−nucleobase potential energy surface, empirical intermolecular interaction energy values were found to be in good agreement with the ab initio MP2/6-31++G(d,p) energies corrected for basis set superposition errors. This result supports the application of the systematic search technique to larger model systems. The general features of the amiloride−base and amiloride−base pair intermolecular potential energy surfaces were found to be different in the case of adenine and thymine compared to guanine and cytosine, resulting in more orientational and translational freedom for amiloride in the former case. In addition, the interaction of amiloride with adenine and thymine nucleobases is significantly more dispersion-controlled than that with guanine and cytosine, where the electrostatic energy contributes up to a third of the total intermolecular energy. Amiloride in the base pair complexes is overlapped with guanine and adenine. Thymine and cytosine are exposed, and the interaction of the ligand with the pyrimidine nucleobases appears to be exclusively due to electrostatic forces.The Journal of Physical Chemistry B 01/2000; 104(4). DOI:10.1021/jp9926140 · 3.38 Impact Factor
- Physical Chemistry Chemical Physics 01/2003; 5(21):4932-. DOI:10.1039/b309328j · 4.20 Impact Factor