Quantum Chemical DFT Methods Research Articles

Schizocommunin analogues and derivatives as G-quadruplex ligands and anticancer agents

G-quadruplexes (GQs) have become valid targets for anticancer efforts in the recent couple of decades due to their extremely multifaceted biological functions. Our goal is to quantify interactions within GQs, as well as their interactions with potential ligands (Ls). As secondary nucleic acid (NA) structures, GQs may be understood as a central channel of stacked G-quartets, interlinked into a G-stem (GS) with nucleotide loops. Computational data on full GQ energetics are, however, increasingly noisy. Therefore, we have chosen to simplify our GQ model by stripping it off all nucleotide residues into a “naked” GQ. The GQ-L stacking model allows computing of intrinsic interaction energies, as well as external ligand stacking affinities with “chemical precision”. To relate computed ligand – G4 affinities to their biological activity, we use published inhibitory activities (IC50 values) of several groups of heterocycles. Some of our results provide a good linear relationship between ligand stacking affinities to GQ, calculated by quantum chemical DFT methods, and corresponding log(IC50) values. Herewith we discuss the obtained results in terms of a mechanism of anticancer activity of heterocyclic ligands via complexation with GQs and thereby control of GQ cell regulatory activity.

Исследование возможности создания композитов на основе биополимера, армированного углеродными нанотрубками, для использования их в протезировании

One of the main and fairly new materials for prosthetics are polymers. Among the most commonly used materials nowadays in the design and manufacture of prostheses are polyetheretherketones (PEEK), which have excellent stiffness and strength. They can be modified with fillers to improve their already impressive properties. This results in increased durability of the materials, so that prosthetic components remain strong and viable even after years of use. There are many ways to obtain structural materials with improved functional properties, one of which is the introduction of carbon nanotubes (CNTs) into the matrix of polymer composite material (PCM), which, having unique physical and chemical properties, modify the polymer-matrix for further use in special-purpose products. This paper presents the results of the study of the possibility of creating composites based on biopolymer polyetheretherketone reinforced with carbon nanotubes for their use as a material for prostheses that can be produced by 3D printing. The interaction of a single-layer carbon nanotube (6, 6) with a polyetheretherketone monomer and with a fragment consisting of four PEEK monomers was modeled and studied. One-center and two-center interactions have been studied. The calculations were performed within the framework of the quantum-chemical DFT method with different basis sets. The main interaction parameters were determined and the possibility of realizing the modification of the polymer by nanotubes was proved, which can serve as a stimulus for the creation of a new material that will have new unique properties for the creation of durable prosthetic limbs.

Studies of the interaction of modified nitro group boronitride nanotubes with gas-phase carbon-containing molecules to create sensor devices

Recently, the environmental situation in the world has been deteriorating everywhere and there is a need to find new effective means of detecting harmful substances in the air. Every year, the content of carbon dioxide in the air is growing, which in the end can lead to a deterioration in the health of people. Various types of sensor devices are currently used to timely fix the increase in the gas level. As the active material of such a sensor, modern unique materials can be used – nanotubes, which, due to their sorption properties, are able to detect the presence of harmful impurities in the air space of the premises. It is also possible to use such sensors as detectors of some human diseases by analyzing exhaled air, which makes their use in medicine possible. The results of a theoretical study of the sorption interaction of modified boronitride nanotubes with molecules of carbon dioxide and acetone, obtained using the quantum-chemical DFT method, are presented, which prove the possibility of using this type of nanotubes as a sensor material for sensor devices.

Plant-Derived and Dietary Hydroxybenzoic Acids-A Comprehensive Study of Structural, Anti-/Pro-Oxidant, Lipophilic, Antimicrobial, and Cytotoxic Activity in MDA-MB-231 and MCF-7 Cell Lines.

Seven derivatives of plant-derived hydroxybenzoic acid (HBA)—including 2,3-dihydroxybenzoic (2,3-DHB, pyrocatechuic), 2,4-dihydroxybenzoic (2,4-DHB, β-resorcylic), 2,5-dihydroxybenzoic (2,5-DHB, gentisic), 2,6-dihydroxybenzoic (2,6-DHB, γ-resorcylic acid), 3,4-dihydroxybenzoic (3,4-DHB, protocatechuic), 3,5-dihydroxybenzoic (3,5-DHB, α-resorcylic), and 3,4,5-trihydroxybenzoic (3,4,5-THB, gallic) acids—were studied for their structural and biological properties. Anti-/pro-oxidant properties were evaluated by using DPPH• (2,2-diphenyl-1-picrylhydrazyl), ABTS•+ (2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), FRAP (ferric-reducing antioxidant power), CUPRAC (cupric-reducing antioxidant power), and Trolox oxidation assays. Lipophilicity was estimated by means of experimental (HPLC) and theoretical methods. The antimicrobial activity against Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), Bacillus subtilis (B. subtilis), Salmonella enteritidis (S. enteritidis), and Candida albicans (C. albicans) was studied. The cytotoxicity of HBAs in MCF-7 and MDA-MB-231 cell lines was estimated. Moreover, the structure of HBAs was studied by means of experimental (FTIR, 1H, and 13C NMR) and quantum chemical DFT methods (the NBO and CHelpG charges, electrostatic potential maps, and electronic parameters based on the energy of HOMO and LUMO orbitals). The aromaticity of HBA was studied based on the calculated geometric and magnetic aromaticity indices (HOMA, Aj, BAC, I6, NICS). The biological activity of hydroxybenzoic acids was discussed in relation to their geometry, the electronic charge distribution in their molecules, their lipophilicity, and their acidity. Principal component analysis (PCA) was used in the statistical analysis of the obtained data and the discussion of the dependency between the structure and activity (SAR: structure–activity relationship) of HBAs. This work provides valuable information on the potential application of hydroxybenzoic acids as bioactive components in dietary supplements, functional foods, or even drugs.

Pivotal Neighboring‐Group Participation in Substitution versus Elimination Reactions – Computational Evidence for Ion Pairs in the Thionation of Alcohols with Lawesson's Reagent

The mechanism of the thionation of alcohols with Lawesson's reagent was explored through quantum chemical DFT methods. Evidence that carbocations are involved was found. The mechanism is completely different to that established recently for the thionation of carbonyls. The presence of a phenyl ring at the alcoholic carbon atom exerts a pivotal role in the stability of the carbocation and enables a S–π interaction, which is crucial for favoring thionation instead of undesired elimination. The influence of the solvent was also studied, and elimination is preferred in toluene, whereas substitution leading to thionation is favored in acetonitrile. A clear correlation between solvent polarity and elimination was observed. The study is in complete agreement with the different behavior observed experimentally for primary, secondary, and tertiary alcohols (bearing a phenyl ring or not), and the best conditions for minimizing undesired elimination can be predicted.

Lithium Diffusion Pathways in β-Li2TiO3: A Theoretical Study

In recent experimental studies based on NMR techniques, the ion dynamics in β-Li2TiO3 has been discussed controversially. In order to shed light on this discussion, Li ion diffusion processes in β-Li2TiO3 are investigated theoretically using periodic quantum–chemical DFT methods. It is observed that Li+ migrates along the ab plane as well as in the direction perpendicular to the LiTi2 layers with the activation energies ranging between 0.44 and 0.54 eV, suggesting a slow ion dynamics. In addition, the structural, electronic, and defect properties and the electric field gradient (EFG) parameters at Li positions of β-Li2TiO3 are calculated. According to our results, β-Li2TiO3 is a wide gap insulator with an indirect band gap at Γ–C. The calculated defect formation energy values as well as the EFG parameters show that there are three different Li sites in the structure, namely, Li(1), Li(2), and Li(3), which are in well accord with the experiment.

Binuclear copper(II) complex with bis(azomethine) based on 1,3-diaminopropan-2-ol and 4-hydroxy-3-formylcoumarin: Crystal structure and magnetic properties

The binuclear copper(II) complex [Cu2(L)(Mp)(H2O)((CH3)2SO)] (Mp is 6-methoxypurinate anion) with the heterocyclic azomethine ligand, which is the condensation product of 1,3-diaminopropan-2-ol and 4-hydroxy-3-formylcoumarin (H3L), is synthesized and structurally characterized (CIF file CCDC no. 982199). The temperature dependence of the magnetic susceptibility is measured and shows a significant exchange interaction of the antiferromagnetic type (2J = −348 cm−1) in the compound. This sharply distinguishes the new complex from the earlier studied compounds with a similar exchange fragment characteristic of the ferromagnetic exchange. The antiferromagnetic exchange parameter is calculated by the quantum-chemical DFT method in the broken symmetry approximation.

Theoretical Investigation on Rearrangement Mechanism of Fluoroalkylsilane

Fluoroalkylsilanes are a kind of important carbofunctionalized silanes and applied in many fields. while the rearrangement and decomposition reactions could easily occur for these compounds under a certain high temperature or catalysis. In this work, we selected CH3H2SiCH2F as the molecular sample and investigated the mechanism of rearrangement reaction by using quantum chemical DFT methods. The results showed the rearrangement occurred via a transition state, in which the fluorine atom migrated from carbon to silicon and the hydrogen atom migrated from silicon to carbon. To understant the the process details the atomic charge distribution and electronic transfer were analyzed. And atomic vibrations spectra was discussed as well.

Stabilizing hydrogen-hydrogen interactions in cationic indopolycarbocyanine dyes

A quantum chemical DFT method with the hybrid B3LYP functional in the 6-31G(d) basis set is employed to calculate the equilibrium geometric parameters of the ground and excited states of cationic symmetric indopolycarbocyanine dyes. Based on the Bader topological analysis of the electron density distribution function, it is found that there are hydrogen-hydrogen bonding interactions in the ground, first singlet, and first triplet states of the studied compounds. These interactions are assumed to have the dispersion character. The effect of the stabilization of the conformational position of methyl groups due to hydrogenhydrogen interatomic interactions on fluorescence deactivation processes is shown. The total stabilization energy of hydrogen-hydrogen interatomic interactions in dye cations is found, which is ≈9 kcal/mol.

Theoretical study of the conformational structure and thermodynamic properties of 5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine and ethyl-5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine-3-acetic acid as acceptor groups of indoline dyes

The quantum chemical DFT method with the B3LYP hybrid functional in 6–31++G(d,p) and 6–311+G(d,p) basis sets is used to calculate the equilibrium geometric parameters of different conformations of 5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine and its substituted form ethyl–5-(4-oxo-1,3-thiazolidine-2-ylidene)-rhodanine-3′-acetic acid applied in the synthesis of indoline and some other sensitizing dyes for solar cells. The thermodynamic parameters of four conformers and their synthesis reactions are calculated. The effect of substituents on the thermodynamic stability of the studied isomers is shown.

Quantum-Chemical Study of the Effect of Triethylaluminum on the Chain-End Structure, Reactivity, and Microtacticity of Poly(N,N-dimethylacrylamide) with Lithium Counterion in Nonpolar Solvents

Reactions of chain growth in the anionic polymerization of N,N-dimethylacrylamide (DMAAm) with lithium counterion in the presence of triethylaluminum (Et3Al) were studied using quantum-chemical DFT methods. The active sites were simulated by chain fragments consisting of two DMAAm units, the lithium counterion being coordinated to carbonyl oxygen atoms of both ultimate and penultimate units. For all local minima and transition states zero-point vibration energies and free energies, ΔG, at 200 K were calculated. It was shown that in the absence of Et3Al iso-addition of the monomer to the model chain end is the most favorable, while in the presence of two Et3Al molecules syndio- and iso-additions of DMAAm are equally probable. In the presence of one Et3Al molecule, an unambiguous prediction of the prevailing stereomode of DMAAm addition is impossible because different stereomodes are preferred at the BHLYP/SVP (syndio-addition via 1LA-DAS mechanism) and BHLYP/aug-cc-pVTZ//BHLYP/SVP (iso-addition via 1LA-AM ...

Calculations of dissociation constants of carboxylic acids by empirical and quantum-chemical DFT methods

Dissociation constants of 15 carboxylic acids in water, methanol, and DMSO were calculated by empirical and quantum-chemical DFT methods. The maximal error of the empirical calculation was 1.4%. A comparative analysis of the results obtained was carried out.

Formation of meso-1,2-Bis(dimethylamino)-1,2-diphenylethane by Oxidative C-C Coupling Reaction

The title compound was obtained from the reaction of N,N-dimethylbenzylamine with n-butyl lithium and sulfur in tetrahydrofuran at room temperature. Its molecular structure was investigated by means of single crystal X-ray diffraction and quantum chemical DFT methods. The formation of meso-1,2-bis(dimethylamino)-1,2-diphenylethane is likely to be due to an unusual α-deprotonation of N,N-dimethylbenzylamine, instead of the well known ortho-lithiation, with a subsequent oxidative C-C coupling of the anions. Ab initio calculations of the corresponding α- and o-deprotonated anions of N,N-dimethylbenzylamine showed the former to be more stable than the latter, due to delocalisation of the negative charge over the π-system of the phenyl ring. The choice of solvent and temperature is seen as the main reason for the unusual course of the reaction.

Quantum-Chemical and Force-Field Investigations of Ice Ih: Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies

The different possible proton-ordered structures of ice Ih for an orthorombic unit cell with 8 water molecules were derived. The number of unique structures was found to be 16. The crystallographic coordinates of these are reported. The energetics of the different polymorphs were investigated by quantum-mechanical density-functional theory calculations and for comparison by molecular-mechanics analytical potential models. The polymorphs were found to be close in energy, i.e., within approximately 0.25 kcal/mol H2O, on the basis of the quantum-chemical DFT methods. At 277 K, the different energy levels are about evenly populated, but at a lower temperature, a transition to an ordered form is expected. This form was found to agree with the ice phase XI. The difference in lattice energies among the polymorphs was rationalized in terms of structural characteristics. The most important parameters to determine the lattice energies were found to be the distributions of water dimer H-bonded pair conformations, in...

Molecular Structure and C−O Stretch Frequencies of the Cobalt Carbonyls Co(CO)n, n = 1, 4, As Studied by Density Functional Theory

Gas-phase geometries and carbon−oxygen stretch frequencies for the binary cobalt carbonyl molecules CoCO, Co(CO)2, Co(CO)3, and Co(CO)4 have been calculated using quantum chemical DFT methods. The results are compared to earlier experimental results from gas-matrix vibrational spectroscopy. Where experimental results are available, the computed results show good agreement. A reinterpretation of the experimental IR and ESR spectra of Co(CO)2 and Co(CO)3 is proposed.