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). · 1.90 Impact Factor
- Physical Chemistry Chemical Physics 01/2003; 5(21):4932-. · 4.20 Impact Factor
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ABSTRACT: In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.Journal of Theoretical and Computational Chemistry 11/2011; 09(05). · 0.52 Impact Factor