scholarly journals Estudo Teórico in silico da Interação entre Geraniol e o Sítio Ativo da Opsina Bovina

2020 ◽  
Author(s):  
Vanessa Regina Miranda ◽  
Nelson Henrique Morgon
Keyword(s):  
Molecular Structure ◽  
Active Site ◽  
Density Functional ◽  
Bos Taurus ◽  
Adult Stage ◽  
Antioxidant Activities ◽  
Theoretical Calculations ◽  
Interaction Process ◽  
Functional Theory ◽  
Maximum Value

The bovine opsin protein, 6PGS, is present in the eye of the Bos taurus species, and has activity throughout the period of development of the retina, remaining until its adult stage. The interaction of the geraniol ligand, which has anti-inflammatory, antimicrobial and antioxidant activities, with the active site of the protein was studied through theoretical calculations using Density Functional Theory. The molecular structure results show that in the interaction process of geraniol with the active site of 6PGS there is a distortion in the geometry of the ligand. Through the UV-Vis spectra, a shift of the wavelength maximum value in relation to the free geraniol is observed, of the order of 50 nm.

A Combined Experimental and Theoretical Study on the Reaction Mechanism and Molecular Structure of 4-(Diphenylamino)-3-iodo-2(5H)-furanone

2017 ◽  
Vol 70 (7) ◽  
pp. 837
Author(s):  
Xiumei Song ◽  
Fuling Xue ◽  
Zongcai Feng ◽  
Yun Wang ◽  
Zhaoyang Wang ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Density Functional ◽  
Reaction Pathway ◽  
Theoretical Calculations ◽  
Calculation Model ◽  
Basis Set ◽  
Functional Theory ◽  
Evaporation Technique ◽  
Molecular Structure Analysis ◽  
Semi Empirical

The simultaneous α-iodination and Nβ-arylation mechanism of 5-alkyloxy-4-phenylamino-2(5H)-furanone by (diacetoxyiodo)benzene was investigated by means of density functional theory (DFT) with B3LYP/6-31G*//LANL2DZ, selecting 4-(diphenylamino)-5-methyloxy-3-iodo-2(5H)-furanone as the calculation model. In addition, the effect of solvent on the reaction pathway was investigated using the Polarisable Continuum Model (PCM). Good agreement was found between the computational and the experimental results. Furthermore, single crystals of 4-(diphenylamino)-5-ethoxy-3-iodo-2(5H)-furanone were grown by slow evaporation technique. The molecular structure analysis was performed by single crystal X-ray analysis and theoretical calculations using a semi-empirical quantum chemical method and DFT/B3LYP methods with a LANL2DZ as basis set.

scholarly journals Computational Modeling of the Mechanism of Urease

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Håkan Carlsson ◽  
Ebbe Nordlander
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Hydrolytic Enzyme ◽  
Nickel Atom ◽  
Nickel Ion ◽  
Functional Theory ◽  
Amine Nitrogen ◽  
Tetrahedral Intermediate ◽  
Oxygen Donor

In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).

scholarly journals Crystal structure ofN,N′-didecylpyromellitic diimide

2017 ◽  
Vol 73 (6) ◽  
pp. 838-841 ◽  
Author(s):  
Hansu Im ◽  
Myong Yong Choi ◽  
Cheol Joo Moon ◽  
Tae Ho Kim
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Density Functional Theory ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Asymmetric Unit ◽  
Functional Theory ◽  
Compound C ◽  
Herringbone Structure

The title compound, C30H44N2O4[systematic name: 2,6-didecylpyrrolo[3,4-f]isoindole-1,3,5,7(2H,6H)-tetraone], consists of a central pyromellitic diimide moiety with terminal decyl groups at the N-atom positions. The centre of the molecule lies on a crystallographic inversion centre so the asymmetric unit contains one half-molecule. The molecule exhibits a rod-shaped conformation, like other similar compounds of this type, the distance between the ends of terminal decyl groups being 32.45 Å. The packing is dominated by a lamellar arrangement of the molecules, which is reinforced by C—H...O hydrogen bonds and C—O...π interactions, forming a classic herringbone structure. The molecular structure is consistent with the theoretical calculations performed by density functional theory (DFT).

scholarly journals Crystal structure ofN-[2-(cyclohexylsulfanyl)ethyl]quinolinic acid imide

2017 ◽  
Vol 73 (9) ◽  
pp. 1372-1374
Author(s):  
Hyunjin Park ◽  
Myong Yong Choi ◽  
Cheol Joo Moon ◽  
Tae Ho Kim
Keyword(s):  
Molecular Structure ◽  
Quinolinic Acid ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Ladder Structure ◽  
Functional Theory ◽  
Compound C ◽  
Imide Ring ◽  
The Mean ◽  
Ring Centroid

The title compound, C15H18N2O2S {systematic name: 6-[2-(cyclohexylsulfanyl)ethyl]-5H-pyrrolo[3,4-b]pyridine-5,7(6H)-dione}, was obtained from the reaction of pyridine-2,3-dicarboxylic anhydride (synonym: quinolinic anhydride) with 2-(cyclohexylsulfanyl)ethylamine. The dihedral angle between the mean plane of the cyclohexyl ring and the quinolinic acid imide ring is 25.43 (11)°. In the crystal, each molecule forms two C—H...O hydrogen bonds and one weak C—O...π [O...ring centroid = 3.255 (2) Å] interaction with neighbouring molecules to generate a ladder structure along theb-axis direction. The ladders are linked by weak C—O...π [O...ring centroid = 3.330 (2) Å] interactions, resulting in sheets extending parallel to theabplane. The molecular structure is broadly consistent with theoretical calculations performed by density functional theory (DFT).

Theoretical and Experimental Evaluation of the Effect of Fluorinated Substituent on the Topological Landscape and Thermodynamic Stability of Zeolitic Imidazolate Framework Polymorphs

2018 ◽  
Author(s):  
Mihails Arhangelskis ◽  
Athanassis Katsenis ◽  
Novendra Novendra ◽  
Zamirbek Akimbekov ◽  
Dayaker Gandrath ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Mechanochemical Synthesis ◽  
Thermodynamic Stability ◽  
Experimental Evaluation ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Zeolitic Imidazolate Framework ◽  
Functional Theory ◽  
Calorimetric Measurements ◽  
And Calorimetry

By combining mechanochemical synthesis and calorimetry with theoretical calculations, we demonstrate that dispersion-corrected periodic density functional theory (DFT) can accurately survey the topological landscape and predict relative energies of polymorphs for a previously inaccessible fluorine-substituted zeolitic imidazolate framework (ZIF). Experimental screening confirmed two out of three theoretically anticipated polymorphs, and the calorimetric measurements provided an excellent match to theoretically calculated energetic difference between them.<br>

Synthesis, Conformational Analysis and Crystal Structure of New Thioxo, Oxo, Seleno Diastereomeric Cyclophosphamides Containing 1,3,2-dioxaphosphorinane

2019 ◽  
Vol 23 (2) ◽  
pp. 205-213
Author(s):  
Dorra Kanzari-Mnallah ◽  
Med L. Efrit ◽  
Jiří Pavlíček ◽  
Frédéric Vellieux ◽  
Habib Boughzala ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Density Functional ◽  
Chemical Shifts ◽  
Structural Determination ◽  
Conformational Study ◽  
Functional Theory ◽  
One Step ◽  
High Resolution Mass Spectroscopy ◽  
Resolution Mass

Thioxo, Oxo and Seleno diastereomeric cyclophosphamides containing 1,3,2- dioxaphosphorinane are prepared by a one-step chemical reaction. Their structural determination is carried out by means of Nuclear Magnetic Resonance NMR (31P, 1 H, 13C) and High-Resolution Mass Spectroscopy (HRMS). The conformational study of diastereomeric products is described. Density Functional Theory (DFT) calculations allowed the identification of preferred conformations. Experimental and calculated 31P, 13C, 1H NMR chemical shifts are compared. The molecular structure of the 2-Benzylamino-5-methyl-5- propyl-2-oxo-1,3,2-dioxaphosphorinane (3d) has been determined by means of crystal Xray diffraction methods.

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