scholarly journals DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Sandra Cotes Oyaga ◽  
José Cotuá Valdés ◽  
Sigrid Borja Paez ◽  
Keylin Hurtado Marquez

The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e)), DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO), and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e) with GC are the strongest. 9-AA 1(d) displayed the strongest interaction and 9-AA 1(b) the weakest.

2008 ◽  
Vol 07 (06) ◽  
pp. 1147-1158 ◽  
Author(s):  
JUN LI ◽  
LIAN-CAI XU ◽  
SI-YAN LIAO ◽  
KANG-CHENG ZHENG ◽  
LIANG-NIAN JI

The theoretical studies on the electronic structure, DNA-binding, and absorption-spectral properties of "light switch" complex [ Ru ( phen )2( taptp )]2+ (phen = 1,10-phenanthroline; taptp = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene) in aqueous solution have been carried out using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. The results show the following: (i) The solvent effect makes all the frontier molecular orbital energies of complex to increase to a certain extent; however, the energies (ε LUMO + x) of some frontier unoccupied molecular orbitals (MOs) in aqueous solution are still negative and rather lower than those of the energies (ε HOMO - x) of some frontier-occupied MOs of DNA-base pairs, and thus the complex in aqueous solution is still an excellent electron-acceptor in its DNA-binding. (ii) The solvent effect further shows that simply increasing the conjugative planar area of intercalative ligand may be ineffective on the improvement of DNA-binding of the resulting complex because of going along with the increase in the LUMO (and LUMO + x) energy. It is the reason why the DNA-binding affinity of "light switch" complex [ Ru ( phen )2( taptp )]2+ is not better than that of the well-known complex [ Ru ( phen )2( dppz )]2+ yet. (iii) The three main experimental bands (~450 nm, ~360 nm, and ~290 nm) of the studied complex in aqueous solution were further well calculated, simulated, and explained by the TDDFT computations.


2018 ◽  
Vol 5 (2) ◽  
pp. 27 ◽  
Author(s):  
Tahar Abbaz ◽  
Amel Bendjeddou ◽  
Didier Villemin

Objective: Optimized molecular structures have been investigated by DFT/B3LYP method with 6-31G (d,p) basis set. Stability of Benzo and anthraquinodimethane derivatives 1-4, hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed by using natural bond orbital (NBO) analysis. Electronic structures were discussed and the relocation of the electron density was determined. Molecular electrostatic potential (MEP), local density functional descriptors has been studied. Nonlinear optical (NLO) properties were also investigated. In addition, frontier molecular orbitals analyses have been performed from the optimized geometries. An ionization potential (I), electron affinity (A), electrophilicity index (ω), chemical potential (µ), electronegativity (χ), hardness (η), and softness (S), have been investigated. All the above calculations are made by the method mentioned above.Methods: The most stable optimized geometries obtained from DFT/B3LYP method with 6-31G(d,p) basis set were investigated for the study of molecular structures, nonlinear properties, natural bond orbital (NBO), molecular electrostatic potential (MEP) and frontier molecular orbital of Benzo and anthraquinodimethane derivatives.Results: Reactive sites of electrophilic and nucleophilic attacks for the investigated molecule were predicted using MEP at the B3LYP/6-31G(d,p). Compound 4 possesses higher electronegativity value than all compounds so; it is the best electron acceptor; the more reactive sites for electrophilic attacks are shown in compounds 1 and 4, for nucleophilic attacks are indicated in compounds 2 and 3 and the more reactive sites in radical attacks are detected in compounds 2 and 4.Conclusions: Compound 1 is softest, best electron donor and more reactive than all compounds. The calculated first order hyperpolarizability was found much lesser than reported in literature for urea.


2020 ◽  
Vol 17 (2) ◽  
pp. 124-137 ◽  
Author(s):  
Adel Mahmoud Attia ◽  
Ahmed Ibrahin Khodair ◽  
Eman Abdelnasser Gendy ◽  
Mohammed Abu El-Magd ◽  
Yaseen Ali Mosa Mohamed Elshaier

Background:Perturbation of nucleic acids structures and confirmation by small molecules through intercalation binding is an intriguing application in anticancer therapy. The planar aromatic moiety of anticancer agents was inserted between DNA base pairs leading to change in the DNA structure and subsequent functional arrest.Objective:The final scaffold of the target compounds was annulated and linked to a benzotriazole ring. These new pharmacophoric features were examined as antiviral and anticancer agents against MCF7 and their effect on DNA damage was also assessed.Methods:A new series of fully substituted 2-oxopyridine/2-thioxopyridine derivatives tethered to a benzotriazole moiety (4a-h) was synthesized through Michael cyclization of synthesized α,β- unsaturated compounds (3a-e) with appropriate active methylene derivatives. The DNA damage study was assessed by comet assay. In silico DNA molecular docking was performed using Open Eye software to corroborate the experimental results and to understand molecule interaction at the atomic level.Results:The highest DNA damage was observed in Doxorubicin, followed by 4h, then, 4b, 4g, 4f, 4e, and 4d. The docking study showed that compound 4h formed Hydrogen Bonds (HBs) as a standard ligand with GSK-3. Compound 4h was the most active compound against rotavirus Wa, HAVHM175, and HSV strains with a reduction of 30%, 40%, and 70%, respectively.Conclusion:Compound 4h was the most active compound and could act as a prospective lead molecule for anticancer agent.


1988 ◽  
Vol 53 (9) ◽  
pp. 1943-1945
Author(s):  
Pavel Hobza ◽  
Camille Sandorfy

The interaction of the 6-O methylguanine cation with cytosine and thymine was studied using the ab initio SCF method in combination with a London type expression for dispersion energy. The structure of the complex formed with cytosine differs from that found previously with guanine itself.


MRS Advances ◽  
2020 ◽  
Vol 5 (16) ◽  
pp. 815-823
Author(s):  
Ian Sands ◽  
Jinhyung Lee ◽  
Wuxia Zhang ◽  
Yupeng Chen

AbstractRNA delivery into deep tissues with dense extracellular matrix (ECM) has been challenging. For example, cartilage is a major barrier for RNA and drug delivery due to its avascular structure, low cell density and strong negative surface charge. Cartilage ECM is comprised of collagens, proteoglycans, and various other noncollagneous proteins with a spacing of 20nm. Conventional nanoparticles are usually spherical with a diameter larger than 50-60nm (after cargo loading). Therefore, they presented limited success for RNA delivery into cartilage. Here, we developed Janus base nanotubes (JBNTs, self-assembled nanotubes inspired from DNA base pairs) to assemble with small RNAs to form nano-rod delivery vehicles (termed as “Nanopieces”). Nanopieces have a diameter of ∼20nm (smallest delivery vehicles after cargo loading) and a length of ∼100nm. They present a novel breakthrough in ECM penetration due to the reduced size and adjustable characteristics to encourage ECM and intracellular penetration.


2020 ◽  
Vol 56 (2) ◽  
pp. 201-204 ◽  
Author(s):  
Kinga E. Szkaradek ◽  
Petr Stadlbauer ◽  
Jiří Šponer ◽  
Robert W. Góra ◽  
Rafał Szabla

Formation of an excited-state complex enables ultrafast photorelaxation of dark nπ* states in GC and HC base pairs.


2015 ◽  
Vol 127 (49) ◽  
pp. 14932-14935 ◽  
Author(s):  
Katharina Röttger ◽  
Hugo J. B. Marroux ◽  
Michael P. Grubb ◽  
Philip M. Coulter ◽  
Hendrik Böhnke ◽  
...  

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