scholarly journals Mechanisms and Parameters of the Binding of Amitozinoberamid to DNA in the Aqueous Solution

2018 ◽  
Vol 63 (8) ◽  
pp. 709 ◽  
Author(s):  
S. Yu. Kutovyy ◽  
R. S. Savchuk ◽  
N. V. Bashmakova ◽  
D. M. Hovorun ◽  
L. A. Zaika
Keyword(s):  
Aqueous Solution ◽  
Density Functional ◽  
Spectral Characteristics ◽  
Dna Interaction ◽  
Base Pairs ◽  
Electron Absorption ◽  
Dna Base ◽  
The Density Functional Theory ◽  
Dna Base Pairs ◽  
The One

The interaction between the amitozinoberamid preparation (thiotepa-alkylated berberine) and a DNA macromolecule in the aqueous solution has been studied, by using the optical spectroscopy methods: electron absorption and fluorescence. The dependence of spectral characteristics on the concentration ratio N/c between the DNA base pairs and the ligand molecules is plotted. Using the system of modified Scatchard and McGhee–von Hippel equations, the parameters of the binding of amitozinoberamid to DNA are determined. A comparative analysis of the DNA interaction with amitozinoberamid, on the one hand, and berberine and sanguinarine alkaloids, on the other hand, is carried out. The structure and the spectra of electron absorption of thiotepa, berberine, and amitozinoberamid molecules are calculated in the framework of the density functional theory at the DFT B3LYP/6-31G(d,p) level.

DFT/TDDFT STUDY ON DNA-BINDING AND SPECTRAL PROPERTIES OF "LIGHT SWITCH" COMPLEX [Ru(phen)2 (taptp)]2+ IN AQUEOUS SOLUTION

2008 ◽  
Vol 07 (06) ◽  
pp. 1147-1158 ◽  
Author(s):  
JUN LI ◽  
LIAN-CAI XU ◽  
SI-YAN LIAO ◽  
KANG-CHENG ZHENG ◽  
LIANG-NIAN JI
Keyword(s):  
Aqueous Solution ◽  
Dna Binding ◽  
Solvent Effect ◽  
Spectral Properties ◽  
Density Functional ◽  
Frontier Molecular Orbital ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Planar Area

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.

scholarly journals Computational Evidence Suggests That 1-chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-chloroethanol into Acetaldehyde and HCl

2019 ◽  
Author(s):  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Oscar Ventura ◽  
Vincenzo Barone
Keyword(s):  
Aqueous Solution ◽  
Water Molecule ◽  
Gas Phase ◽  
Density Functional ◽  
Water Molecules ◽  
Functional Theory ◽  
Direct Transformation ◽  
The Density Functional Theory ◽  
Successive Step ◽  
The One

<p>The dehalogenation of 2-chloroethanol (2ClEtOH) in gas phase with and without participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route towards oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. This species is more stable than 2ClEtOH by about 6 kcal mol<sup>-1</sup>, and the reaction barrier is 22 kcal mol<sup>-1</sup> vs 55 kcal mol<sup>-1</sup> for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol<sup>-1</sup>) than that of VA to the same products (55 kcal mol<sup>-1</sup>). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol<sup>-1</sup>, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 6 kcal mol<sup>-1</sup>). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 22 to 12 kcal mol<sup>-1</sup>). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is competitive with the VA alcohol path.</p>

Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

2016 ◽  
Vol 27 (10) ◽  
pp. 1650119 ◽  
Author(s):  
Mohammad Zarei ◽  
Abdolvahab Seif ◽  
Khaled Azizi ◽  
Mohanna Zarei ◽  
Jamil Bahrami
Keyword(s):  
Hydrogen Bond ◽  
Dft Calculations ◽  
Base Pair ◽  
Density Functional ◽  
Base Pairs ◽  
Water Solvent ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Phenoxy Radicals ◽  
Dna Base Pair

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

B-DNA model systems in non-terran bio-solvents: implications for structure, stability and replication

2017 ◽  
Vol 19 (26) ◽  
pp. 16969-16978 ◽  
Author(s):  
Trevor A. Hamlin ◽  
Jordi Poater ◽  
Célia Fonseca Guerra ◽  
F. Matthias Bickelhaupt
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Model Systems ◽  
Structure Stability ◽  
Implicit Solvation ◽  
Base Pairs ◽  
Functional Theory ◽  
Dna Base ◽  
Dna Base Pairs

We have computationally analyzed a comprehensive series of Watson–Crick and mismatched B-DNA base pairs, in the gas phase and in several solvents, including toluene, chloroform, ammonia, methanol and water, using dispersion-corrected density functional theory and implicit solvation.

Actinomin und 4.6-Didesmethyl-4.6-di-tert.-butyl-actinomin-Modellverbindungen zum Studium der Actinomycin/DNA-Wechselwirkung / Actinomine and 4,6-Didemethyl-di-tert-butyl-actinomine-Model Compounds for Studies of the Actinomycin-DNA Interaction

1971 ◽  
Vol 26 (9) ◽  
pp. 875-878 ◽  
Author(s):  
Frank Seela
Keyword(s):  
Model Compound ◽  
Dna Interaction ◽  
Methyl Groups ◽  
Model Compounds ◽  
Base Pairs ◽  
Tert Butyl ◽  
Dna Base ◽  
Dna Base Pairs

The synthesis of actinomine, a model compound for the investigation of the actinomycin-DNA interaction is discribed. In place of the pentapeptide lactone rings, actinomin has N,N-diethyl-ethylenediamine groups; it binds to DNA as strongly as actinomycin C1 (D) does. Additional replacement of the 4,6 methyl groups of the chromophore by tert-butyl residues strongly reduces the binding of actinomine to DNA. This result is consistent with intercalation of the actinomine chromophore between the DNA base-pairs, a reaction that is sterically blocked by the tert-butyl groups.

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