A computational study of the main degradation product of antitumor drug imexon

2017 ◽  
Vol 16 (04) ◽  
pp. 1750037
Author(s):  
Djaffar Kheffache ◽  
Ourida Ouamerali

We theoretically study, from the thermodynamic point of view, the possibility of the two degradation pathways of antitumor drug of imexon. According to the theoretical results obtained at DFT level in both gas and aqueous phases, the two degradation pathways of imexon are characterized by negative reaction Gibbs free energies. It has been found that 4-imino-5-methylene-imidazolidin-2-one is the favored degradation product of imexon. Herein, the focus of this work has been on calculating the geometries, relative energies and electronic properties of all possible prototropic tautomers of 4-imino-5-methylene-imidazolidin-2-one using the DFT and MP2 levels. The bulk water environment has been simulated by continuum model using Solvation Model based on Density (SMD). The UV spectra of two dominant tautomers of 4-imino-5-methylene-imidazolidin-2-one are also predicted using time-dependent density functional theory and the results are compared with the available experimental data. The comparison of the simulated and the experimental absorption spectra has allowed us to accurately characterize the predominant tautomer of the degradation product in aqueous medium.

2021 ◽  
Vol 11 (9) ◽  
pp. 4045
Author(s):  
Amilcar Duque-Prata ◽  
Carlos Serpa ◽  
Pedro J. S. B. Caridade

The photodegradation mechanism of 1-phenyl-4-allyl-tetrazol-5-one has been studied using (time-dependent) density functional theory with the M06-HF, B3LYP, and PBE0 functionals and the VDZ basis set. All calculations have been carried out using the polarizable continuum model to simulate the solvent effects of methanol. The reaction pathway evolution on the triplet state has been characterised to validate a previously postulated experimental-based mechanism. The transition states and minimums have been initially located by local scanning in partial constrained optimisation, followed by a fully relaxed search procedure. The UV spectra has shown to be better described with PBE0 functional when compared with the experimental results, having the M06-HF a shift of 40 nm. From the energetic point of view, the postulated mechanism has been validated in this work showing a concerted photoextrusion of the N2 molecule. The intramolecular proton transfer occurs at a later stage of the mechanism after cyclization of the allyl group on a triplet biradical intermediate. The photoproduct observed experimentally, a pyrimidinone, has been characterised. The infrared spectroscopic reaction profile has also been proposed.


2019 ◽  
Author(s):  
Michael Fischer

<p>The silicoaluminophosphate zeotype ECR-40, which has the MEI topology, contains linkages of AlO<sub>4</sub> tetrahedra via a common oxygen atom, thereby violating the famous “Löwenstein’s rule”. Due to the proven existence of Al-O-Al linkages in this material, it constitutes an ideal model system to study the acidity and mobility of protons associated with such unusual linkages. In addition, their properties can be directly compared to those of protons associated with more common Si-O-Al linkages, which are also present in ECR-40. In this work, static density functional theory (DFT) calculations including a dispersion correction were employed to study the preferred proton sites as well as the Brønsted acidity of the framework protons, followed by DFT-based ab-initio molecular dynamics (AIMD) to investigate the proton mobility in guest-free and hydrated ECR-40. Initially, two different proton arrangements were compared, one containing both H[O6] protons associated with Al-O-Al linkages and H[O10] protons at Si-O-Al linkages, the other one containing only H[O10] protons. The former model was found to be thermodynamically favoured, as a removal of protons from the Al-O-Al linkages causes a local accumulation of negative charge. Calculations of the deprotonation energy showed a moderately higher Brønsted acidity of the H[O10] protons, at variance with previous empirical explanations, which attributed the exceptional performance of ECR-40 as acid catalyst to the presence of Al‑O‑Al linkages. The AIMD simulations (<i>T</i> = 298 K) delivered no appreciable proton mobility for guest-free ECR-40 and for low levels of hydration (one H<sub>2</sub>O per framework proton). Under saturation conditions, framework deprotonation occurred, leading to the formation of protonated water clusters in the pores. Pronounced differences between the two types of framework protons were observed: While the H[O10] protons were always removed from the Si-O-Al linkages, the Al-O-Al linkages remained mostly protonated, but deprotonation did occur to a minor extent. The observation of a degree of framework deprotonation of Al-O-Al linkages differs from the findings reported in a recent computational study of hydrated aluminosilicate zeolites with such linkages (Heard et al., <i>Chem. Sci.</i> <b>2019</b>, <i>10</i>, 5705), pointing to an influence of the overall framework composition. Further inspection of the AIMD results showed that a coordination of water molecules to framework Al atoms occurred in many cases, especially in the vicinity of the Al-O-Al linkages, sometimes resulting in a pronounced modification of the linkages through additional bridging oxygen atoms. Given the changes in the local structure, it can be expected that such modified linkages are especially prone to break upon dehydration. Thus, in addition to elucidating the deprotonation behaviour of protons associated with different types of linkages, the calculations also provide insights into possible reasons for the instability of Al-O-Al linkages, clarifying why Löwenstein’s rule is mostly obeyed in materials that are formed via a hydrothermal route.</p>


2020 ◽  
Vol 17 (11) ◽  
pp. 884-889
Author(s):  
Somayeh Mirdoraghi ◽  
Hamed Douroudgari ◽  
Farideh Piri ◽  
Morteza Vahedpour

For (Z)-(Z)-N-(λ5-phosphanylidene) formohydrazonic formic anhydride, Aza-Wittig reaction and Mumm rearrangement are studied using both density functional and coupled cluster theories. For this purpose, two different products starting from one substrate are considered that are competing with each other. The obtained products, P1 and P2, are thermodynamically favorable. The product of the aza-Wittig reaction, P1, is more stable than the product of Mumm rearrangement (P2). For the mentioned products, just one reliable pathway is separately proposed based on unimolecular reaction. Therefore, the rate constants based on RRKM theory in 300-600 K temperature range are calculated. Results show that the P1 generation pathway is a suitable path due to low energy barriers than the path P2. The first path has three steps with three transition states, TS1, TS2, and TS3. The P2 production path is a single-step reaction. In CCSD level, the computed barrier energies are 14.55, 2.196, and 10.67 kcal/mol for Aza-Wittig reaction and 42.41 kcal/mol for Mumm rearrangement in comparison with the corresponding complexes or reactants. For final products, the results of the computational study are in a good agreement with experimental predictions.


Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1947
Author(s):  
Delano P. Chong

After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.


RSC Advances ◽  
2021 ◽  
Vol 11 (30) ◽  
pp. 18246-18251
Author(s):  
Selçuk Eşsiz

A computational study of metal-free cyanomethylation and cyclization of aryl alkynoates with acetonitrile is carried out employing density functional theory and high-level coupled-cluster methods, such as [CCSD(T)].


1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic

High level ab initio and density functional theory studies are performed on highly protonated methane species.


Inorganics ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 20
Author(s):  
Antonio A. García-Valdivia ◽  
Estitxu Echenique-Errandonea ◽  
Gloria B. Ramírez-Rodríguez ◽  
José M. Delgado-López ◽  
Belén Fernández ◽  
...  

Two new coordination polymers (CPs) based on Zn(II) and Cd(II) and 1H-indazole-6-carboxylic acid (H2L) of general formulae [Zn(L)(H2O)]n (1) and [Cd2(HL)4]n (2) have been synthesized and fully characterized by elemental analyses, Fourier transformed infrared spectroscopy and single crystal X-ray diffraction. The results indicate that compound 1 possesses double chains in its structure whereas 2 exhibits a 3D network. The intermolecular interactions, including hydrogen bonds, C–H···π and π···π stacking interactions, stabilize both crystal structures. Photoluminescence (PL) properties have shown that compounds 1 and 2 present similar emission spectra compared to the free-ligand. The emission spectra are also studied from the theoretical point of view by means of time-dependent density-functional theory (TD-DFT) calculations to confirm that ligand-centred π-π* electronic transitions govern emission of compound 1 and 2. Finally, the PL properties are also studied in aqueous solution to explore the stability and emission capacity of the compounds.


Minerals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 607
Author(s):  
Raquel Chuliá-Jordán ◽  
David Santamaria-Perez ◽  
Javier Ruiz-Fuertes ◽  
Alberto Otero-de-la-Roza ◽  
Catalin Popescu

The structure of the naturally occurring, iron-rich mineral Ca1.08(6)Mg0.24(2)Fe0.64(4)Mn0.04(1)(CO3)2 ankerite was studied in a joint experimental and computational study. Synchrotron X-ray powder diffraction measurements up to 20 GPa were complemented by density functional theory calculations. The rhombohedral ankerite structure is stable under compression up to 12 GPa. A third-order Birch–Murnaghan equation of state yields V0 = 328.2(3) Å3, bulk modulus B0 = 89(4) GPa, and its first-pressure derivative B’0 = 5.3(8)—values which are in good agreement with those obtained in our calculations for an ideal CaFe(CO3)2 ankerite composition. At 12 GPa, the iron-rich ankerite structure undergoes a reversible phase transition that could be a consequence of increasingly non-hydrostatic conditions above 10 GPa. The high-pressure phase could not be characterized. DFT calculations were used to explore the relative stability of several potential high-pressure phases (dolomite-II-, dolomite-III- and dolomite-V-type structures), and suggest that the dolomite-V phase is the thermodynamically stable phase above 5 GPa. A novel high-pressure polymorph more stable than the dolomite-III-type phase for ideal CaFe(CO3)2 ankerite was also proposed. This high-pressure phase consists of Fe and Ca atoms in sevenfold and ninefold coordination, respectively, while carbonate groups remain in a trigonal planar configuration. This phase could be a candidate structure for dense carbonates in other compositional systems.


Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 693
Author(s):  
Christian Ludt ◽  
Elena Ovchinnikova ◽  
Anton Kulikov ◽  
Dmitri Novikov ◽  
Sibylle Gemming ◽  
...  

This work focuses on the validation of a possible connection of the known Ruddlesden-Popper (RP) phases and the novel concept of the migration-induced field-stabilized polar (MFP) phase. To study this subject, model structures of RP phases in bulk strontium titanate are analyzed by means of density functional theory (DFT). The obtained geometries are compared to experimental MFP data. Good agreement can be found concerning atomic displacements in the pm range and lattice strain inferred by the RP phases. Looking at the energy point of view, the defect structures are on the convex hull of the Gibb’s free energy. Although the dynamics to form the discussed defect models are not addressed in detail, the interplay and stability of the described defect model will add to the possible structure scenarios within the near-surface region of strontium titanate. As a result, it can be suggested that RP phases generally favor the MFP formation.


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