Interactions between DNA and the acridine intercalator: A computational study.

Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits well-defined π orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine… ODNA with bond lengths ranging from 2.370 Što 3.472 Å. The Binding energy (ΔEBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter (∇2ρ(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids.

Theoretical study of the adsorption capacity of potentially toxic Cd2+, Pb2+, and Hg2+ ions in hemicellulose matrices.

Hemicellulose is widely available in nature, is a sustainable resource and has a wide range of applications. Among them, adsorption stands out for the removal of potentially toxic ions. Thus, in the study, the adsorption of Cd2+, Pb2+ and Hg2+ ions in two hemicellulose matrices were elucidated through computational simulations using density functional theory. Molecular electrostatic potential and frontier molecular orbitals demonstrated whether the interactions could happen. Four interaction complexes were highlighted due to the interaction energy criteria, ΔEBind, ΔH and ΔG < 0.00 kcal mol-1, that is: Hm1… Pb (1); Hm2… Pb (3); Hm2…Cd (4) and Hm2…Hg (4) and the results show that they occur through physisorption. In structural parameter studies, interaction distances smaller than 3000 Å were identified, which ranged from 2.253 Å to 2.972 Å. From the analysis of the topological parameters of QTAIM, it was possible to characterize the intensities of the interactions, as well as their nature, which were partially covalent or electrostatic in nature. Finally, based on the theoretical results, it can be affirmed that the hemicellulose can interact with Cd2+, Pb2+ and Hg2+ ions, evidencing that this study can support further experimental essays to remove contaminants from effluents.

Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis.

CONTEXT: Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood. METHODS: Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.

Theoretical and experimental study of the diastereoisomers (2S) and (2R)-naringenin-6-C-ß-D-glucopyranoside obtained from Clitoria guianensis.

In this work the diastereoisomers (2S) and (2R)-naringenin-6-C-ß-D-glucopyroside, isolated for the first time from Clitoria guianensis, were studied using the density functional theory. The frontier molecular orbitals and structural properties showed that the diastereoisomers exhibit the same energy gap 166.61 kcal mol-1 and structural properties different, where in the S diastereoisomer, the bond length between the chiral carbon and the phenolic group is greater (difference of 0.0126 Å). The HPLC data showed that the retention time of the S-diastereoisomer (16.7 min) is shorter than that of R, suggesting that the S compound is more polar than R. The HPLC results corroborates with the molecular electrostatic potential which showed that in the S configuration, the electronegative density was more intense overall, particularly in the glucose molecule. The reactivity indices showed that the diastereoisomers are good electrophiles and reactive species. Finally, the absolute configuration of the diastereoisomers were determined using electronic circular dichroism (ECD) spectroscopy and the theoretical spectra were similar to the experimental. METHODS : All calculations of Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) were performed using the program Gaussian 09 and the structures of the diastereoisomers were generated and analyzed using the GaussView program. The optimization and vibrational frequency calculations were performed using the functional CAM-B3LYP and 6-311 + + G(2d,2p) basis set. Conformational searches were performed for R configuration, by molecular mechanics using the MM + , MMFF, and OPLS05 force fields; the entire molecular mechanics simulation was performed using the Maestro/MacroModel software. The calculations for the simulations of the ECD spectra were performed for the eight lowest energy conformers obtained in the geometric optimization step, and the TDDFT at the CAM-B3LYP/6-311 + + G(2d,2p) theory level used. The effects of methanol and chloroform were calculated using the SMD implicit solvent model.

Brueckner Doubles variation of W1 theory (W1BD) adapted to pseudopotential: W1BDCEP theory.

Composite methods are the combination of ab initio calculations used to achieve high precision in the face of a computational reduction. Weizmann-n theories (n = 1, 2, 3, and 4) stand out for presenting a high precision, and a version of the W1 theory is the W1BD theory that uses ab initio Brueckner Doubles (BD) methods. One way to reduce the computational cost of composite methods and maintain accuracy is to use pseudopotentials in the calculation steps; in this context, W1BDCEP composite method was developed from the respective W1BD all-electron version by considering the implementation of compact effective pseudopotential (CEP). The test set used to evaluate the theory were 8 proton affinities (PA0), 46 electron affinities (EA0), 54 ionization energies (IE0), 80 enthalpies of formation (ΔfH0), and 10 bond dissociation energies (BDE). The mean absolute deviation values (MADs) for W1BD and for the version adapted to the pseudopotential, W1BDCEP, were similar, with values of 0.97 kcal mol-1 and 1.03 kcal mol-1, respectively, when the properties PA0, EA0, IE0, and ΔfH0 were evaluated together. Comparing the versions of the theories that employ ab initio Brueckner Doubles calculations with the W1 and W1CEP theories, it is possible to observe that the W1BD and W1BDCEP theories are more accurate than the W1 theory (MADW1 = 1.25 kcal mol-1) and W1CEP (MADW1CEP = 1.44 kcal mol-1), proving the accuracy of using the BD method. Pseudopotential reduces computational time by up to 30% and thus enables more accurate calculations with less computational time.

Computational study of the interaction of heavy metal ions, Cd(II), Hg(II), and Pb(II) on lignin matrices.

Contamination by heavy metal ions, particularly in water resources, is a severe environmental problem. In this study, the interaction of metal ions, namely, Cadmium Cd(II), Mercury Hg(II), and Lead Pb(II), on lignin matrices was investigated based on theoretical calculations. Binding energy (ΔEBind) values proved that the Pb(II) interacted better with lignin matrices than Cd(II) or Hg(II), having energy values between -8.4 kcal mol-1 to -20.2 kcal mol-1. The Gibbs energy (ΔG) and enthalpy (ΔH) values for Pb(II) were <0, indicating that the process was spontaneous and released heat. However, the lignin matrices studied in this work did not interact efficiently with Cd(II) and Hg(II) ions because almost all ΔEBind, ΔG, and ΔH values were positive. The bond length of the interaction proved that the Pb ions yielded the smallest values, ratifying the values for the interaction energy. Analyses based on the quantum theory of atoms in molecules showed that the interactions between Pb(II) and the matrices were partially covalent, whereas the interactions of Cd(II) and Hg(II) were predominantly electrostatic, justifying the positive values of ΔEBind, ΔG, and ΔH. The natural bond orbital results showed that the ligand orbitals of the matrix interacted with the lone pair antibonding orbital (LP*) of the metal ions. The theoretical results of the study show the possibility of applying lignin to remove heavy metal ions, especially Pb, and providing information for research related to wastewater treatment.

Interaction of glyphosate in matrices of cellulose and diethylaminoethyl cellulose biopolymers: theoretical viewpoint of the adsorption process.

Glyphosate is an herbicide widely used in agricultural activities causing contamination of soils and bodies of water and damage to the biodiversity of ecosystems. In this context, the present study aimed to theoretically study the adsorption potential of the biopolymer cellulose (CE) and its diethylaminoethyl cellulose derivative (DEAEC) with the herbicide glyphosate (GLY). Theoretical calculations were performed using the density functional theory. Molecular electrostatic potential and frontier molecular orbital analyses were performed, which allowed identifying the possible sites of interaction of biopolymers that were in the functional groups -OH and O- of cellulose and in the groups -O- and -NH+(CH2CH3)2 of the DEAEC. Reactivity indices chemical softness and hardness showed that both adsorbents could interact with adsorbate. Simulated IR indicated that the interactions could be evinced in experimental measurements by changes in the bands of glyphosate (ν(P = O), δ(P-O-H), δ(C-N-H)) or in the bands of CE and DEAEC (ν(C-O), ν(C-H), ν(N-H)). The binding energies showed that the GLY interacts more effectively with CE than DEAEC. The ΔH prove that all processes are exothermic and the CE-GLY1 interaction showed value of ΔG < 0. The topological results showed a greater number of interactions with electrostatic nature. The results found in the study show that the theoretical data provides useful information to support the use of biopolymers as matrices for glyphosate adsorption or other contaminants.

When treatment increases the contaminant's ecotoxicity: A study of the Fenton process in the degradation of methylene blue.

The degradation of dyes can generate harmful by-products, thereby requiring the need to evaluate the toxicity to aquatic organisms. This study aims to evaluate the chronic ecotoxicity of methylene blue dye degraded by the Fenton process using the non-target planarian Girardia tigrina as a sensitive bioindicator of environmental contamination. The bioassays evaluated the lethality of several concentrations of the untreated and degraded dye methylene blue (MB), as well as, their sub-lethal effects on locomotion, feeding, regeneration, and reproduction. In both acute and chronic tests, the degraded dye had a stronger toxic effect when compared to the untreated dye. This negative effect after treatment was mainly associated with the presence of residual hydrogen peroxide and iron (and consequently the hydroxyl radical formed). We conclude that the utilization of the Fenton process using less oxidizing agents should be considered as important alternatives for the protection of aquatic ecosystems, without compromising the efficient removal of MB.

Fenton-type process using peracetic acid: Efficiency, reaction elucidations and ecotoxicity.

Recent studies on Fenton-type processes involving peracetic acid (PAA) stimulated further development of advanced oxidative processes (AOPs). The objective of this work was to provide new information about such processes, elucidate their reaction mechanisms both experimentally and theoretically, and verify their possible uses. The Fenton-type reaction of PAA with Fe3+ exhibited a greater dye degradation efficiency than the Fenton process, while the efficiency of the PAA reaction with Fe2+ was very close of Fenton process. Moreover, the processes photocatalyzed by solar radiation demonstrated comparable efficiencies due to the photoreduction of Fe3+ to Fe2+. By conducting theoretical calculations, it was found that the formation of oxidizing radicals during the reaction of PAA with Fe2+ was not thermodynamically favorable and, therefore, unsuitable for practical use. In contrast, the processes occurred in the PAA/Fe3+ system included thermodynamically spontaneous reactions that generated peroxyl (CH3C(O)OO•), alkoxyl (CH3C(O)•), and hydroperoxyl (HO2•) radicals. The ecotoxicological tests demonstrated that the toxicity of the PAA to the organism Dugesia tigrina can be attributed to the presence of H2O2.

Theoretical study of internal rotational barriers of electrons donating and electrons withdrawing groups in aromatic compounds.

The presence of internal rotation in sigma bonds is essential for conformational analysis of organic molecules and its understanding is of great relevance in chemistry, as well as in several other areas. However, for aromatic compounds that have substituent groups, withdrawers or donors of electron, there are no data in the literature to explain their rotational barriers. In this context, the work studied the internal rotational barriers of electron donating and withdrawing groups in aromatic compounds using the MP3, MP4, and CCSD(T) methods and the influence of substituents' nature on barrier heights was investigated through calculations based on the theory of Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results obtained showed that the CCSD(T) method is the one that best describes the internal rotational barriers, followed by MP4 and MP3 and the electron donating groups decrease the barrier, whereas electron withdrawing groups increase. Through the NBO analysis it was possible to observe that for withdrawing groups the interaction of the molecular orbitals is more accentuated promoting the increase of the rotational barrier of these compounds. Through the QTAIM analysis it was possible to show that, for electron donating groups, the internal rotation is influenced by the loss of electronic density when the substituents is perpendicular to the ring plane, however, for withdrawing groups the density is little influenced, regardless of the two conformations (minimum and maximum energy). Two molecules showed free rotation, trichloromethylbenzene and methylbenzene, and the theoretical calculations NBO and QTAIM showed that for these species there is no difference in the properties studied when there is rotation of the dihedral angle.

Peracetic acid: Structural elucidation for applications in wastewater treatment.

Peracetic acid (PAA) is an oxidizer widely used for the sterilization of equipment in hospitals, pharmaceutical, cosmetic and food industries and also for water and wastewater disinfection. Even with its increasing applications, there have been no previous theoretical studies that explain the experimental results based on its molecular behavior. In this context, this work used calculations based on the density functional theory (DFT) combined with experimental results to elucidate the decomposition mechanisms of PAA for predicting its stability and the possible products generated from its decomposition. The results obtained showed that the protonation of PAA promoted its spontaneous decomposition in acetic acid and molecular oxygen. The hydrolysis mechanism of PAA in acidic medium indicated that the low energy difference involved in the mechanism's stages is responsible for the equilibrium between PAA and H2O2. The structural and electronic comparison of PAA with H2O2 showed that the O-O bond length of PAA is longer than that of H2O2 and is also weaker, therefore may demonstrate greater efficiency in advanced oxidative processes by photocatalysis.

Phe-Phe Di-Peptide Nanostructure Self-Assembling Modulated by Luminescent Additives.

In this work, supramolecular l-l-diphenylalanine (Phe-Phe) nanostructures were self-assembled in solvents of distinct polarity and in the presence of luminescent additives of distinct conjugation length that physically adhere to the nanostructures to provide growth environments of distinct properties. When the additive is poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene], an electron donor polymer, and solvent is tetrahydrofuran (THF), Phe-Phe vesicle-like structures are obtained, whereas in water and in the presence of a similar additive in structure, poly[5-methoxy-2-(3-sulfopropoxy)-1,4-phenylenevinylene], nanotubes are formed. In contrast, when 9-vinyl-carbazole, an electron acceptor additive is used, nanotubes are formed even when THF is the solvent. The same structures are obtained when the additive is the macromolecule poly(vinyl carbazole). The morphologies of these self-assembled structures were observed by scanning electron microscopy, and their photophysical behavior was determined by steady-state fluorescence spectroscopy and time-resolved fluorescence spectroscopy. These data analyzed altogether inform about the formation mechanisms of such structures and about the influence that distinct interactions exert on self-assembling and charge-transfer processes through formation of complexes between the luminescent additives and the Phe-Phe nano- and microstructures.

A DFT-based analysis of adsorption of Cd2+, Cr3+, Cu2+, Hg2+, Pb2+, and Zn2+, on vanillin monomer: a study of the removal of metal ions from effluents.

The density functional theory was used to understand the adsorption process of Cd(II), Cr(III), Cu(II), Hg(II), Pb(II), and Zn(II) ions with the methacrylate monomer derived of vanillin (VMA). Different analyses were carried out: Conformational analysis, molecular electrostatic potential (MEP), adsorption energy, frontier orbitals, hardness, and softness, all of which are necessary to predict the formation of complexes. By means of the molecular electrostatic potential and frontier molecular orbital (FMOs), the best region for adsorption was found, so each metallic ion of the study was placed close to the nitrogen and oxygen atoms of the imine and carboxyl groups of vanillin monomer, respectively. The bond of the metal ions with the nitrogen atom was shown to be stronger than with oxygen atoms, because the charge density of the nitrogen is increased in the formation of the Schiff base with the proximity of the aromatic ring. The monomer showed to be more adsorbent for the Cu(II), Cr(III), and Pb(II) ions because of the high energy values involved. The analysis QTAIM was investigated to understand the character of the interaction between vanillin monomer and metal species, which were shown in almost all cases as covalent partial. Thus, the monomer derived from vanillin has good stability in water and is therefore considered a good material for the remediation of effluents and poisonings.

G4CEP: A G4 theory modification by including pseudopotential for molecules containing first-, second- and third-row representative elements.

The G4CEP composite method was developed from the respective G4 all-electron version by considering the implementation of compact effective pseudopotential (CEP). The G3/05 test set was used as reference to benchmark the adaptation by treating in this work atoms and compounds from the first and second periods of the periodic table, as well as representative elements of the third period, comprising 440 thermochemical data. G4CEP has not reached a so high level of accuracy as the G4 all-electron theory. G4CEP presented a mean absolute error around 1.09 kcal mol(-1), while the original method presents a deviation corresponding to 0.83 kcal mol(-1). The similarity of the optimized molecular geometries between G4 and G4CEP indicates that the core-electron effects and basis set adjustments may be pointed out as a significant factor responsible for the large discrepancies between the pseudopotential results and the experimental data, or even that the all-electron calculations are more efficient either in its formulation or in the cancellation of errors. When the G4CEP mean absolute error (1.09 kcal mol(-1)) is compared to 1.29 kcal mol(-1) from G3CEP, it does not seem so efficient. However, while the G3CEP uncertainty is ±4.06 kcal mol(-1), the G4CEP deviation is ±2.72 kcal mol(-1). Therefore, the G4CEP theory is considerably more reliable than any previous combination of composite theory and pseudopotential, particularly for enthalpies of formation and electron affinities.

G3(MP2)-CEP theory and applications for compounds containing atoms from representative first, second and third row elements of the periodic table.

The compact effective potential (CEP) pseudopotential was adapted to the G3(MP2) theory, herein referred to as G3(MP2)-CEP, and applied to the calculation of enthalpies of formation, ionization energies, atomization energies, and electron and proton affinities for 446 species containing elements of the 1st, 2nd, and 3rd rows of the periodic table. A total mean absolute deviation of 1.67 kcal mol(-1) was achieved with G3(MP2)-CEP, compared with 1.47 kcal mol(-1) for G3(MP2). Electron affinities and enthalpies of formation are the properties exhibiting the lowest deviations with respect to the original G3(MP2) theory. The use of pseudopotentials and composite theories in the framework of the G3 theory is feasible and compatible with the all electron approach. Graphical Abstract Application of composite methods in high-level ab initio calculations.

A study of the rotational barriers for some organic compounds using the G3 and G3CEP theories.

The G3, G3CEP, MP4, MP4CEP, QCISD(T), and QCISD(T)CEP methods were applied to study 43 internal rotational barriers of different molecules. The calculated G3 and G3CEP barriers were accurate with respect to those obtained experimentally, typically showing deviations of <0.50 kcal mol⁻¹. The results for the MP4CEP, MP4, QCISD(T), and QCISD(T)CEP calculations were less accurate, and larger deviations of approximately ±1 kcal mol⁻¹ were observed. The accuracy of G3CEP was comparable to that of G3, but a reduction in CPU time of between 5 and 35 % was observed when the dependence of the pseudopotentials on the size of the molecule and atom type was taken into account. The behaviors of the energy components show that these corrections depend on the molecular environment and whether the calculations are performed with all electrons or pseudopotentials. Usually, the predominance of a specific effect follows a distinct pattern when the G3 and G3CEP results are compared. For the G3 calculations, the most important component of the corrected MP4/6-31G(d) rotational energy is ΔE(2df,p). Among the 43 molecules, 29 were dependent on polarization effects, ΔE(2df,p); 19 were dependent on diffuse functions, ΔE +; and 13 depended on the effects of more elaborate basis functions (ΔE(G3large)). Similar behavior was observed for the G3CEP calculations: polarization effects were more important for 25 molecules, followed closely by the effect of diffuse functions for 23 molecules, and finally the effect of large basis sets (19 molecules). ΔE(QCI) correction seldom resulted in significant effects on the G3 and G3CEP calculations.

Assessment of G3(MP2)∕∕B3 theory including a pseudopotential for molecules containing first-, second-, and third-row representative elements.

G3(MP2)∕∕B3 theory was modified to incorporate compact effective potential (CEP) pseudopotentials, providing a theoretical alternative referred to as G3(MP2)∕∕B3-CEP for calculations involving first-, second-, and third-row representative elements. The G3∕05 test set was used as a standard to evaluate the accuracy of the calculated properties. G3(MP2)∕∕B3-CEP theory was applied to the study of 247 standard enthalpies of formation, 104 ionization energies, 63 electron affinities, 10 proton affinities, and 22 atomization energies, comprising 446 experimental energies. The mean absolute deviations compared with the experimental data for all thermochemical results presented an accuracy of 1.4 kcal mol(-1) for G3(MP2)∕∕B3 and 1.6 kcal mol(-1) for G3(MP2)∕∕B3-CEP. Approximately 75% and 70% of the calculated properties are found with accuracy between ±2 kcal mol(-1) for G3(MP2)∕∕B3 and G3(MP2)∕∕B3-CEP, respectively. Considering a confidence interval of 95%, the results may oscillate between ±4.2 kcal mol(-1) and ±4.6 kcal mol(-1), respectively. The overall statistical behavior indicates that the calculations using pseudopotential present similar behavior with the all-electron theory. Of equal importance to the accuracy is the CPU time, which was reduced by between 10% and 40%.

Implementation of pseudopotential in the G3 theory for molecules containing first-, second-, and non-transition third-row atoms.

Compact effective pseudopotential (CEP) is adapted in the G3 theory providing a theoretical alternative referred to as G3CEP for calculations involving the first-, second-, and non-transition third-row elements. These modifications tried to preserve as much as possible the original characteristics of G3. G3CEP was used in the study of 247 enthalpies of formation, 22 atomization energies, 104 ionization potentials, 63 electron affinities, and 10 proton affinities, resulting in the calculation of 446 species for the first-, second-, and third-row atoms. The final average total absolute deviation was of 1.29 kcal mol(-1) against 1.16 kcal mol(-1) from all-electron G3 for the same calculations. The CPU time has been reduced by 7% to 56%, depending on the size of the molecules and the type of atoms considered.