Topological indices and QSPR analysis of some chemical structures applied for the treatment of heart patients

Posted on 11 October 2023 by nMehri Hasani, nMasoud Ghodsn

The results showed that certain topological indices had strong correlations with specific physicochemical properties. Quantitative structure property relationship modeling demonstrated that the best predictor of topological indices for physicochemical features was the H(G) index for (BP), (FP), and (E), the ReZG3$$ {}_3 $$ index for (P), (MR), and (MV), the I(G) index for (MR), the mM2$$ {}_2 $$ (G) index for (T) in linear regression models.

Abstract

In this study, various beta-blocker drugs used for heart disease were analyzed, and their degree-based topological indices derived from the M-polynomial were calculated. Linear and quadratic regression analysis was used to obtain quantitative structure-property relationship models between the topological indices and eight the physicochemical properties of the drugs to determine their effectiveness. The results show that the harmonic index was the best predictor for boiling point, flashpoint, and enthalpy of vaporization, while the redefined third Zagreb index was effective for polarizability, molar refractivity, and molar volume. The inverse sum indeg index was found to be effective for molar refractivity, and the second modified Zagreb index was surface tension in linear regression models. In addition, the redefined third Zagreb index was the best predictor for polarizability and molar refractivity, while the second modified Zagreb index was effective for molar volume. The SDD index was found to be effective for surface tension in quadratic regression models.

Transition metal embedded in two‐dimensional bi‐BN as high activity single atom electrocatalyst for oxygen reduction reactions

Posted on 8 October 2023 by

Au-bi-BN as high activity single atom electrocatalyst for ORR.

Abstract

Searching for stable, highly effective and cost-efficient catalysts for the oxygen reduction reaction (ORR) is important to addressing the energy crisis and environmental issues. A single atom embedded in two-dimensional boron nitride materials is a viable candidate for the ORR to replace Pt-based catalysts. Herein, by making use of density functional theory (DFT) simulations, we systematically study a novel two-dimensional boron nitride materials (bi-BN) embedded by 23 kinds of transition metal (TM) atoms ranging from Ti to Au as high activity single atom electrocatalyst for the ORR. According to the initial screening criteria (−4.92 eV < ΔG _O* < 0 eV), 13 kinds of TM-bi-BN (TM = Ti, V, Cr, Mn, Fe, Co, Ni, Ru, Rh, Pd, Ag, Pt, Au) meet the criteria and are selected to study their ORR performance in this work. Our calculations indicate that Au-bi-BN has the most superior ORR performance with the lowest overpotential (0.43 V), which was lower than that of Pt (0.45 V) as ORR catalyst. The origin of the catalytic activity of the ORR is studied by the linear correlation between these oxygen-containing intermediates, the volcanic curve, the d-band center and the crystal orbital Hamilton populations. Ab Initio Molecular Dynamics simulation suggests that Au-bi-BN is thermodynamically stable at 300 K. Our results not only offer valuable insights into the utility of boron-nitride materials as catalysts for ORR, but also facilitate the development of novel catalysts for ORR through improved comprehension of the material properties.

Issue Information

Posted on 8 October 2023 by Wiley: International Journal of Quantum Chemistry: Table of Contents

International Journal of Quantum Chemistry, Volume 123, Issue 22, November 15, 2023.

Modeling of the photophysical and photovoltaic properties of an active layer based on the organic composite poly(2‐methoxy‐5‐(2‐ethyl‐hexyloxy)‐1,4‐phenylene‐vinylene) (MEH‐PPV)–poly(3‐hexylthiophene) (P3HT): (6,6)‐phenyl C61 butyric acid methyl ester (PCBM)

Posted on 8 October 2023 by nM. Ltayef, nM. Mbarek, nM. M. Almoneef, nK. Alimin

Solar cells active layer energy based MEH-PPV-P3HT and PCBM

Abstract

In this work, two different composite architectures have been investigated. These materials are formed by the block and ramified MEHPPV-P3HT copolymers mixing with the PCBM. Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculation methods have been used to simulate the properties of the photo-physical and photovoltaic material. The results show that adding the PCBM decreases the HOMO–LUMO gap energy to approximately 1.4 eV compared to the basic copolymers. This reduction implies a higher charge transfer between the donor and acceptor materials. Therefore, these composites can be implemented as an active layer in bulk heterojunction organic solar cells. Furthermore, the coupling between the polymers MEH-PPV and P3HT improves their performance order by 5.2%.

Topological indices of molecular graphs of monkeypox drugs for QSPR analysis to predict physicochemical and ADMET properties

Posted on 8 October 2023 by nM. Kalaimathi, nB. J. Balamurugann

Density based topological indices are computed for the antiviral drugs used to treat monkeypox disease. The quantitative structure property relationship analysis is carried out to predict the physicochemical and pharmacokinetic properties of the drugs through quadratic regression. The results show that the computed topological indices exhibit a strong correlation for physicochemical/pharmacokinetic properties of the drugs.

Abstract

Numerous viral diseases endure to develop causing serious community health issues. One of such diseases is monkeypox, which is a viral zoonotic disease, found primarily in remote areas of Central and West African countries and is sporadically spread to other countries. The virus is transmitted to people through contact with infected animals and also from person to person through respiratory droplets, bodily fluids and skin lesions of infected individuals. There are no specific drugs to treat monkeypox virus. This virus is similar to smallpox and belongs to Orthopoxvirus family. The smallpox drugs are recommended to treat monkeypox disease. There are few antiviral drugs such as Cidofovir, Valacyclovir, Famciclovir, Acyclovir, Tecovirimat, and Brincidofovir used for treating monkeypox disease. A chemical molecule/structure can be considered as a graph G=V,E where V is the set of atoms and E is the set of bonds between the atoms. A molecular descriptor of the molecular graph/structure G is a numerical value of G. The numerical values of molecular descriptors are used to quantitatively describe the physical and chemical information of the molecules. In this article, density based topological descriptors are computed for the molecular graphs of the above aforesaid drugs to treat monkeypox disease to carry out QSPR analysis through the quadratic regression to predict physicochemical and ADMET properties of monkeypox drugs.

QSPR analysis through graph models for predicting ADMET properties of antifungal drugs to treat fungal diseases

Posted on 8 October 2023 by nS. Thilsath Parveen, nB. J. Balamurugann

Domination numbers of anti-fungal drugs are computed for the prediction of absorption, distribution, metabolism, excretion, and toxicity properties associated with the drugs used to treat the fungal disease. A quantitative structure property relationship analysis using cubic regression between these domination numbers and properties has been investigated. The findings show that the computed domination numbers exhibit a strong correlation for ADMET properties namely, water solubility, caco-2 permeability, fraction unbound, BBB permeability, acute toxicity, and total clearance.

Abstract

The chemical structure of a drug is considered as a chemical graph G=V,E, where the vertex set V is the set of atoms and the edge set E is the set of bonds between the atoms. Fungi-related diseases are becoming a more serious medical problem as a result of changes in the worldwide environment. In this article, the QSPR analysis is performed to predict the ADMET properties of the drugs used to treat fungal infections such as mucormycosis, blastomycosis, invasive candidiasis, talaromycosis, cryptococcus, neoformans, and so forth. The antifungal drugs posaconazole, isavuconazole, and amphotericin B and its analogs are considered to carry out the QSPR analysis. The domination numbers of these drugs are determined to correlate with their ADMET properties through cubic regression and the analysis suggests a high association between the domination numbers of drugs and their ADMET properties. The ADMET properties of the analog structures of the drug amphotericin B are also predicted in this QSPR analysis.

DFT‐based systematic study on the structural, optoelectronic, thermodynamic, vibrational, and mechanical behavior of Ruddlesden Popper perovskites Sr2XO4 (X = Zr, Hf) for optoelectronic applications

Posted on 8 October 2023 by

Grafical abstract of layered perovskites Sr₂XO₄ (X = Zr, Hf).

Abstract

DFT study on the structural, optoelectronic, thermodynamic, vibrational, and mechanical properties of Ruddlesden Popper (RP) perovskites Sr₂XO₄ (X = Zr, Hf) is made with the help of first principle simulation in the framework of WIEN2K code. The lattice constants in bohr unit are found to be a=7.313,b=7.313,c=23.346 for Sr₂ZrO₄, and a=7.310,b=7.310,andc=23.368 for Sr₂HfO₄. The calculated band gap values are 2.65 eV for Sr₂ZrO₄ and 2.58 eV for Sr₂HfO₄. The band structure and electronic density of states reveal the semiconductor nature of these materials having an indirect band gap. Also, Kramers–Krönig relations are used for optical analysis which unveils that these compounds are suitable for applications in optoelectronic. The vibrational investigations are done while using harmonic approximation. Phonon dispersion curves are plotted to observe the vibrational modes by DFPT to confirm the dynamical stability of studied compounds. Although few soft modes have appeared, however, these compounds are found to be thermally stable. Raman modes appeared at low and high frequencies whereas IR modes are noticed at intermediate frequencies for considered compounds. Upon thermodynamical examination, the maximum value of free energy at 1000 K is noted to be −1.95 eV for Sr₂ZrO₄ and −2.25 eV for Sr₂HfO₄. The elastic constants are calculated by using the Voigt–Reuss–Hill approximation. The calculated anisotropic values for these compounds are 1.077 (A) and 0.913 (A) which indicate that Sr₂ZrO₄ has isotropic behavior and Sr₂HfO₄ has anisotropic behavior. From our calculations, Voigt Young's modulus of Sr₂ZrO₄ and Sr₂HfO₄ is 266.99 (GPa) and 279.42 (GPa) along with Poison's ratio of 0.29 and 0.26, respectively.

Does alkyl chain unsaturation affect tunability of the aryl alkyl imidazolium‐based ion pairs?

Posted on 8 October 2023 by nBehzad Khalili, nMehdi Sheykhan, nMarziye Ali Jan Pour, nKhatereh Ghaurin

Unsaturation effect on the tunability of Ionic liquids.

Abstract

Three series of functionalized ion pairs composed of ethyl phenyl imidazolium [PhIM(C₂H₅)]⁺, (vinyl) ethenyl phenyl imidazolium [PhIM(C₂H₃)]⁺ and ethynyl phenyl imidazolium [PhIM(C₂H)]⁺ cations and acetate ([Y1]⁻), nitrate ([Y2]⁻), tetrafluoroborate ([Y3]⁻) and perchlorate ([Y4]⁻) anions were designed and their physical and chemical properties were analyzed at M06-2X-GD3/AUG-cc-pVDZ level of theory. The effect of alkyl chain unsaturation on structural characteristics, energetic parameters, electronic and topological properties, and the global reactivity parameters and also on some physical and chemical properties such as dipole moment, melting point, and electrochemical window of the introduced IPs was discussed. Based on electrochemical window values, the studied IPs including alkyl chain unsaturation in the cation and [Y1-2]⁻ anions have no suitable electrochemical stability for use in electrochemical devices.

Curl condition: Existence of sub‐Hilbert space for molecular species or chemical processes

Posted on 8 October 2023 by

While exploring the practical workability of Beyond Born-Oppenheimer theory for the construction of "accurate" diabatic potential energy surfaces and couplings, one has to find a "true" sub-Hilbert space (SHS) of dimension "N" within the interested domain of nuclear configuration space (CS). The existence of such sub-space can be affirmed only when the vector field originated from nonadiabatic coupling terms fulfill the Curl Condition. In case of Q_12x-Q_12y pair of 1,3,5-C₆H₃F₃ ⁺ radical cation, the magnitudes of Mathematical and ADT Curls are non-zero, but their difference (Curl Condition) is negligibly small validating the three state SHS as a “true” subspace.

Abstract

The “accuracy” of diabatic Hamiltonian matrix elements solely depends on the level of ab initio calculation and on the included set of coupled electronic manifold forming a “true” sub-Hilbert space (SHS). If ab initio calculations are performed with enough accuracy, existence of SHS can be validated only when the Curl Condition attains zero within numerical precision. For the first time, we depict a theoretical and algorithmic formulation on the calculation of Curl Condition to demonstrate the existence of SHS on molecular processes or chemical reactions.

First principle determination of stability constants of metal complexes by cellmetry method

Posted on 8 October 2023 by nMihály Purgel, nJan Heinrich Schuurn

By scanning the cell sizes of the complexes, characteristic breakpoints and motifs appear from which determining the logK or logß values is possible. To do that, the choice of relevant references is necessary. DFT calculations were performed by the Quantum Espresso software to study different types of complexes.

Abstract

The stability constants of 81 metal complexes were calculated using the newly-developed method which was previously used for determining pK values of acid–base dissociation constants by plane wave functions. Fifteen metal ions and 36 ligands were chosen, and a wide range of the complexes was studied to calculate the logK and logß stability constants. The large variety of geometries and coordination modes allowed us to see the limitation of the method. In some cases, good agreements could be found with the experimental data with an accuracy of .5–1 unit. Results howed that for smaller structural changes, the stability constants can be calculated easily by using the determined parameters. For larger structural differences, rough estimations by 2–4 logK units can be conducted. Correlations could be found among the data which can help further studies as well as aid in the prediction of some unknown complexes. The pK of a hexaaqua metal complex was determined as well.