Structural study of 2-(1-oxo-1 H-inden-3-yl)-2H-indene-1,3-dione by DFT calculations, NMR and IR spectroscopy

Riahi, Siavash; Ganjali, Mohammad Reza; Moghaddam, Abdolmajid Bayandori; Norouzi, Parviz; Davarani, Saied Saeed Hosseiny

doi:10.1016/j.saa.2007.07.024

Cited by 44 publications

(14 citation statements)

References 23 publications

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“…After interacting with AQ molecule, bond angles of each nucleobase and also base pairs have changed in the previously mentioned area for both AT and GC, i.e. A (17,16,18), A (16,18,19), and A (18,19,23) in AT and A (1,10,29), A (18,17,23), and A (17,23,19) in GC show the highest differences. Changes in dihedral angles show that the base pairs structure have shifted from the planar, i.e.…”

Section: Resultsmentioning

confidence: 98%

“…Changes in dihedral angles show that the base pairs structure have shifted from the planar, i.e. D (12,24,16,18) and D (26,2,3,4) in AT and D (22,21,24,12) and D (15,24,21,22) in GC display the highest differences. Table 5 presents one-electron properties (dipole moment and polarizability) and energies of frontier molecular orbital's of AQ, AT, and GC (HOMO and LUMO) of the investigated bases and base pair using DFTB method.…”

Section: Resultsmentioning

confidence: 99%

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Quantum Mechanical Description of the Interactions Between Dna and 9,10-Anthraquinone

Riahi

Norouzi

2008

J. Theor. Comput. Chem.

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Molecular geometries of the 9,10-anthraquinone (AQ) and DNA bases (Adenine, Guanine, Cytosine, and Thymine) were optimized using B3LYP/6-31G * * method. Properties of isolated intercalator (9,10-anthraquinone) and their stacking interactions with adenine · · · thymine (AT) and guanine · · · cytosine (GC) nucleic acid base pairs were investigated by means of DFTB method. DFTB method, an approximate version of the DFT method, was extended to cover London dispersion energy. AQ exhibits a large charge delocalization and it has no site with dominant charge. This intercalator has a large polarizability and is a good electron acceptor, while base pairs are good electron donors. B3LYP/6-31G * * stabilization energies of intercalator · · · base pair complexes are large (−18.83 kcal/mol for AT · · · AQ and −15.69 kcal/mol for GC · · · AQ). It is concluded that, the dispersion energy predominantly contributes to the stability of intercalator · · · DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation. The results showed that AQ changes the structure of DNA on bond length, bond angle, torsion angle, and charges.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Quantum Mechanical Description of the Interactions Between Dna and 9,10-Anthraquinone

Riahi

Norouzi

2008

J. Theor. Comput. Chem.

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“…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 (density functional tight-binding), which is accurate and reliable for computational studies, especially for H-bonded and stacked DNA base pairs (23,24).…”

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confidence: 99%

“…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 (density functional tight-binding), which is accurate and reliable for computational studies, especially for H-bonded and stacked DNA base pairs (23,24).…”

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Computational Studies on Effects of MDMA as an Anticancer Drug on DNA

Riahi

Eynollahi

2010

Chem Biol Drug Des

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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 (...

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“…[11][12][13][14][15] Computational work is also valuable in the drug development, where medium-sized organic pharmaceuticals are selected as candidates and are made in larger quantities. Instead of modeling interactions with macromolecules, the prediction of molecular properties for small molecules is more essential in the development stage.…”

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confidence: 99%

A new homatropine potentiometric membrane sensor as a useful device for homatropine hydrobromide analysis in pharmaceutical formulation and urine: a computational study

Ganjali¹,

Memari²,

Riahi³

et al. 2009

J. Braz. Chem. Soc.

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Homatropina ("Equipin, Isopto Homatropine") é um medicamento anticolinérgico que inibe receptores muscarínicos de acetilcolina e, consequentemente, o sistema nervoso parassimpático. É encontrado na forma de sal, bromoidrato ou metilbrometo. Neste estudo, foi construído um sensor potenciométrico de membrana líquida para determinação rápida e simples de bromoidrato de homatropina em formulações farmacêuticas e em urina. Para a preparação da membrana, complexos homatropina-tetrafenilborato foram empregados como materiais eletroativos na membrana. O sensor proposto apresenta um intervalo linear amplo (10), e resposta rápida (ca. 10 s). A validação do método mostra que os sensores são adequados para aplicação em análises de controle de qualidade de bromoidrato de homatropina em formulações farmacêuticas e urina.Homatropine (Equipin, Isopto Homatropine) is an anticholinergic medication that inhibits muscarinic acetylcholine receptors and thus the parasympathetic nervous system. It is available as the hydrobromide or methylbromide salt. In this study, a potentiometric liquid membrane sensor for simple and fast determination of homatropine hydrobromide in pharmaceutical formulation and urine was constructed. For the membrane preparation, homatropine-tetraphenylborate complexes were employed as electroactive materials in the membrane. The proposed sensor presents wide linear range (10 ), and fast response time (ca. 10 s). Validation of the method shows suitability of the sensors for applicability in the quality control analysis of homatropine hydrobromide in pharmaceutical formulation and urine.

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Structural study of 2-(1-oxo-1 H-inden-3-yl)-2H-indene-1,3-dione by DFT calculations, NMR and IR spectroscopy

Cited by 44 publications

References 23 publications

Quantum Mechanical Description of the Interactions Between Dna and 9,10-Anthraquinone

Quantum Mechanical Description of the Interactions Between Dna and 9,10-Anthraquinone

Computational Studies on Effects of MDMA as an Anticancer Drug on DNA

A new homatropine potentiometric membrane sensor as a useful device for homatropine hydrobromide analysis in pharmaceutical formulation and urine: a computational study

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