This research is designed to further understand the effects of the novel drug MDMA on biologic receptor of DNA. The ultimate goal is to design drugs that have higher affinity with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA should ultimately enable the rational design of novel anticancer or antiviral drugs. Molecular modeling on the complex formed between MDMA and DNA presented this complex to be fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MDMA and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized with the aid of the B3LYP ⁄ 6-31G* method. The properties of the isolated intercalator and its stacking interactions with adenineAEAEAEthymine (AT) and guanineAEAEAEcytosine (GC) nucleic acid base pairs were studied with the DFTB method. DFTB method is an approximate version of the DFT method that was extended to cover the London dispersion energy. The B3LYP ⁄ 6-31G* stabilization energies of the intercalatorAEAEAEbase pair complexes were found to be )9.40 and )12.57 kcal ⁄ mol for ATAEAEAEMDMA and GCAEAEAEMDMA, respectively. Results from comparison of the DFTB method and HF method conclude close results and support each other. MDMA (3,4-methylenedioxy-N-methylamphetamine) is a ring-substituted amphetamine derivative that is structurally related to hallucinogenic drugs (1). Nowadays, MDMA used as ''ecstasy'' is becoming increasingly widespread among young adults in universities and high schools even though the side-effects of MDMA on the human body are those such as: neuronal damage and DNA damage (2,3).In recent years, the DFT method was applied in different branches of chemistry (4-11) a . This paper presents the recently introduced approximate DFT method, DFTB technique (density functional tight-binding), empirical London dispersion energy term, which is accurate and reliable for computational studies (12), and calculations performed using the DFTB technique for H-bonded and stacked DNA base pairs (13). Furthermore, this computationally very efficient procedure can yet be used in quantum mechanical (QM) and QM ⁄ molecular mechanical (MM) MD simulations very conveniently and accurately (14,15).The quantum mechanical description of interactions between MDMA and DNA base pairs (Watson-Crick base pairing) employing the DFTB method are reported in this paper. To achieve this goal, MDMA and DNA base pairs were simulated; atomic charges, geometrical values (bond lengths, bond angles and dihedral angles), dipole moment, polarizability, and energies of the frontier molecular orbitals [high occupied molecular orbital (HOMO) and low unoccupied molecular orbital (LUMO)] were obtained. According to a literature survey, this is the first paper that studies MDMA and DNA base pair intercalations using the DFT method.In recent years, the DFT method was applied in different branches of chemistry (16)(17)(18)(19)(20)(21)(22). In this paper, we have used DFTB technique (...

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.

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