| 1. |
- Behzadi, Hadi, et al.
(författare)
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Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors
- 2018
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Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280 .- 0022-2860. ; 1151, s. 34-40
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Tidskriftsartikel (refereegranskat)abstract
- In light of the importance of developing novel corrosion inhibitors, a series of quantum chemical calculations were carried out to evaluate 15N chemical shielding CS tensors as well as aromaticity indexes including NICS, HOMA, FLU, and PDI of three pyrazine derivatives, 2-methylpyrazine (MP), 2-aminopyrazine (AP) and 2-amino-5-bromopyrazine (ABP). The NICS parameters have been shown in previous studies to be paramount to the prediction of anti-corrosion properties, and have been combined here with HOMA, FLU and PDI and detailed wavefunction analysis to determine the effects from bromination and methylation on pyrazine. The results show that the electron density around the nitrogens, represented by CS tensors, can be good indicators of anti-corrosion efficiency. Additionally, the NICS, FLU and PDI, as aromaticity indicators of molecule, are well correlated with experimental corrosion inhibition efficiencies of the studied inhibitors. Bader sampling and detailed wavefunction analysis shows that the major effects from bromination on the pyrazine derivatives affect the Laplacian of the electron density of the ring, delocalizing the aromatic electrons of the carbon atoms into lone pairs and increasing polarization of the Laplacian values. This feature is well agreement with empirical studies, which show that ABP is the most efficient anti-corrosion compound followed by AP and MP, a property which can be attributed and predicted by derivation of the Laplacian of the electron density of the ring nuclei. This study shows the importance of devising DFT methods for development of new corrosion inhibitors, and the strength of electronic and nuclear analysis, and depicts most importantly how corrosion inhibitors composed of aromatic moieties may be modified to increase anti-corrosive properties.
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| 2. |
- Behzadi, Hadi, et al.
(författare)
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Relationship between electronic properties and drug activity of seven quinoxaline compounds : A DFT study
- 2015
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1091, s. 196-202
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Tidskriftsartikel (refereegranskat)abstract
- The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including E-HOMO, E-LUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.
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| 3. |
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Benchmark study of bond dissociation energy of Si-X (X=F, Cl, Br, N, O, H and C) bond using density functional theory (DFT)
- 2017
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Ingår i: Journal of Molecular Structure. - : Elsevier. - 0022-2860 .- 1872-8014. ; 1143, s. 8-19
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Tidskriftsartikel (refereegranskat)abstract
- A benchmark study of Bond Dissociation Energies (BDEs) of various chemical bonds is carried out by Density Functional theory (DFT) method. The aim of the present research study was to find out the best suited functional and basis set to calculate BDEs of selected bonds of silicon with halogens (F, Cl, Br), N, H, C and O. Six different functionals (CAM/B3LYP, B3LYP, B3PW91, PBEPBE, TPSSTPSS) were applied on 36 molecules of different nature. Furthermore, six different basis sets 3-21G, aug-cc-pVTZ, 6-31G, aug-cc-pVDZ, DGDZVP and DGDZVP2 were also applied on these molecules with the best suited functional CAM/B3LYP. After rigorous effort it can be safely said that the best basis set for calculating BDEs for Si H, Si-C, Si-N bonds using CAM-B3LYP functional is 3-21G and for Si-halogens,aug-cc-pVTZ was found to be best basis set.
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| 4. |
- Blokhin, Dimitry S., et al.
(författare)
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Spatial structure of fibrinopeptide B in water solution with DPC micelles by NMR spectroscopy
- 2015
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1102, s. 91-94
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Tidskriftsartikel (refereegranskat)abstract
- Fibrinopeptide B (GluFib) is one of the factors of thrombosis. Normal blood protein soluble, fibrinogen (fibrinopeptide A and fibrinopeptide B), is transformed into the insoluble, fibrin, which in the form of filaments adheres to the vessel wall at the site of injury, forming a grid. However, the spatial structure of this peptide has not been established till now. In this article, GluFib peptide is investigated together with dodecylphosphocholine (DPC) micelles which were used for mimicking the environment of peptide in blood vessels. The spatial structure was obtained by applying 1D and 2D 1H-1H NMR spectroscopy (TOCSY, NOESY). It was shown that the fibrinopeptide B does not have a secondary structure but we can distinguish the fragment Gly 9 – Arg 14 with a good convergence (the backbone RMSD for the Gly9 – Arg14 is 0.18 ± 0.08 Å).
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| 5. |
- Davidovich, P. B., et al.
(författare)
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Synthesis, structure, biochemical, and docking studies of a new dinitrosyl iron complex [Fe-2(mu-SC4H3SCH2)(2)(NO)(4)]
- 2015
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1092, s. 137-142
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Tidskriftsartikel (refereegranskat)abstract
- A new dinitrosyl iron complex of binuclear structure [Fe-2(mu-S-2-methylthiophene)(2)(NO)(4)] was first synthesized and structurally characterized by XRD and theoretical methods. Using caspase-3 as an example it was shown that [Fe-2(mu-S-2-methylthiophene)(2)(NO)(4)] and its analog [Fe-2(mu-S-2-methylfurane)(2)(NO)(4)] can inhibit the action of active site cysteine proteins; the difference in inhibitory activity was explained by molecular docking studies. Biochemical and in silico studies give grounds that the biological activity of dinitrosyl iron complexes is a mu-SR bridging ligand structure function. Thus the rational design strategy of [Fe-2(mu-SR)(2)(NO)(4)] complexes can be applied to make NO prodrugs with high affinity to therapeutically significant targets involved in cancer and inflammation.
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| 6. |
- El Hachmi, Abdelhadi, et al.
(författare)
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Temperature induced structural phase transition in Sr3-xCaxFe2TeO9 (0 <= x <= 1) probed by Raman and Mossbauer techniques
- 2017
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1141, s. 484-494
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Tidskriftsartikel (refereegranskat)abstract
- A series of perovskites Sr3-xCaxFe2TeO9 (0 <= x <= 1) have been prepared in polycrystalline form by solid-state reaction method in air. These materials have been studied by X-ray powder diffraction method (XRPD) and Raman spectroscopy. An analysis of the XRD patterns at room temperature has shown that these compounds crystallize in a tetragonal system, space group I4/m. The structure contains alternating (Fe/Te)(2a)O-6 and (Fe/Te)(2b)O-6 octahedra, tilted in anti-phase in the basal ab-plane. The study of Raman spectroscopy at various temperatures shows a transition from tetragonal to cubic phase: I4/m -> Fm (3) over bar m. This phase transition occurs at high-temperature. Analysis of Raman spectra recorded at several temperatures shows that this phase transition appears near similar to 375 degrees C for (x = 0), similar to 435 degrees C for (x = 0.5) and similar to 451 degrees C for (x = 1). A proportional and gradual increase of temperature phase transition is observed as function of the calcium amount.
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| 7. |
- Faccio, Ricardo, et al.
(författare)
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Using density functional theory to increase the accuracy of experimental crystal structures : The case of potassium peroxocarbonate
- 2017
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Ingår i: Journal of Molecular Structure. - : Elsevier. - 0022-2860 .- 1872-8014. ; 1146, s. 1-4
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Tidskriftsartikel (refereegranskat)abstract
- A first principles simulation of the crystal structure of potassium peroxocarbonate is presented, using density functional methods (both local and semilocal) for the calculations. An experimental crystal structure with a seemingly inconsistent disposition of the peroxide bonds was used as initial input. Both geometry optimizations of the molecular structure and optimization of the cell size were performed. While cell parameters and heavier atom positions determined at the GGA level are very close to the experimental ones, there are important discrepancies in the positioning of the hydrogen atoms. As a result of these calculations, it was shown that the assignment of the peroxydic hydrogens and the peroxydic bond in the experimental structure was incorrect. A more accurate structure is presented and geometrical as well as cell parameters described. It is also shown that LDA is not accurate enough to describe this type of ionic crystals, because of overbinding of the ions, leading to incorrect cell parameters and volume. Our methodology was validated using DFT methods with several basis sets. (C) 2017 Elsevier B.V. All rights reserved.
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| 8. |
- Irfan, Muhammad, et al.
(författare)
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Benchmark study of UV/Visible spectra of coumarin derivatives by computational approach
- 2017
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1130, s. 603-616
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Tidskriftsartikel (refereegranskat)abstract
- A benchmark study of UV/Visible spectra of Simple coumarins and Furanocoumarins derivatives was conducted by employing the Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) approaches. In this study the geometries of ground and excited states, excitation energy and absorption spectra were estimated by using the DFT functional CAM-B3LYP, WB97XD, HSEH1PBE, MPW1PW91 and TD-B3LYP with 6-31 + G (d,p) basis set. CAM-B3LYP functional was found to have close agreement with the experimental values of Furranocoumarin class of coumarins while MPW1PW91 gave close results for simple coumarins. This study provided an insight about the electronic characteristics of the selected compounds and provided an effective tool for developing and designing the better UV absorber compounds.
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| 9. |
- Kasza, P., et al.
(författare)
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Fluorescent triazolyl spirooxazolidines : Synthesis and NMR stereochemical studies
- 2019
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Ingår i: Journal of Molecular Structure. - : Elsevier. - 0022-2860 .- 1872-8014. ; 1183, s. 157-167
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Tidskriftsartikel (refereegranskat)abstract
- Carbon-heteoratom chemistry is a method of choice for rapid construction of complex molecules. In the recent decade, its various applications flourished thanks to the click chemistry approach. Herein, we use a combination of C-X bond formation reactions to complete the synthesis of 1,2,3-triazolyl spirooxazolidines, bearing the fluorenylmethoxycarbonyl (fmoc) substituent. Thanks to the application of 2D-NMR spectroscopic methods and a multilevel computational approach, including a medicinal chemistry – inspired conformational search, PM7 semiempirical and DFT-based geometry optimization finalized with DFT-GIAO NMR shielding constant calculation, we were able to investigate the conformational space and assign cis/trans configuration in complex NMR spectra. For the obtained fmoc derivatives we recorded UV-VIS absorption and emission spectra. The obtained compounds contain pharmacophoric groups characteristic for endocannabinoid system modulators- CB1 receptor ligands or FAAH inhibitors.
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| 10. |
- Prajapati, Preeti, et al.
(författare)
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Combined spectroscopic and quantum chemical studies of ezetimibe
- 2016
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1125, s. 193-203
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Tidskriftsartikel (refereegranskat)abstract
- Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.
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