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 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.

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>

scholarly journals Experimental and Density Functional Theory Characteristics of Ibrutinib, a Bruton’s Kinase Inhibitor Approved for Leukemia Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Ali I. Ismail
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Kinase Inhibitor ◽  
Theoretical Calculations ◽  
Dft Method ◽  
Vibrational Frequencies ◽  
Basis Sets ◽  
Electronic Transitions ◽  
Functional Theory ◽  
Leukemia Treatment

Ibrutinib, a Bruton’s tyrosine kinase that plays an essential role in the B-cell development and cancer cells, has been recently approved to treat chronic, lymphocytic, and other types of leukemia. This study focused on investigating ibrutinib by its electronic transitions, vibrational frequencies, and electrospray mass spectra. The experimental peaks for electronic spectrum were found at 248.0 and 281.0 nm, whereas the νC = 0 stretching frequency was found at 1652.4 and 1639.19 cm−1. These experimental properties were compared with the corresponding theoretical calculations in which density functional theory was applied. The optimized structure was obtained with the calculations using a hybrid function (B3LYP) and high-level basis sets [6-311G++(d,p)]. Most of the calculated vibrational frequencies showed a relatively good agreement with the experimental ones. The electronic transitions of ibrutinib calculated using time-dependent DFT method were performed at two different solvation methods: PCM and SMD. The mass spectrum of ibrutinib, its fragments, and its isotopic pattern agreed well with the expected spectra.

Excitation spectra of cubic perovskite titanates

2021 ◽  
Vol 32 ◽  
Author(s):  
Hieu Nguyen-Truong
Keyword(s):  
Density Functional Theory ◽  
Local Field ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Plasmon Mode ◽  
Time Dependent ◽  
Excitation Spectra ◽  
Functional Theory ◽  
Field Effects ◽  
Dependent Density

We calculate excitation spectra of cubic perovskites ATiO3 (A = Ca, Sr, Ba, Pb). The calculations are performed within the time-dependent density functional theory, including local field effects. The theoretical calculations show that the perovskites have a plasmon mode at around 12 eV, which is not observed in experiments.

scholarly journals Selective Hydrogenation of Acetylene Catalysed by a B12N12 Cluster Doped with a Single Nickel Atom: A DFT Study

Catalysts ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 115 ◽  
Author(s):  
Yun Wang ◽  
Lihua Kang
Keyword(s):  
Selective Hydrogenation ◽  
Density Functional ◽  
Reaction Path ◽  
Nickel Atom ◽  
Single Atom ◽  
Functional Theory ◽  
Acetylene Hydrogenation ◽  
Selective Hydrogenation Of Acetylene ◽  
New Type ◽  
Catalytic Performances

To obtain a catalyst based on a non-precious metal that can replace traditional palladium-based selective catalysts of acetylene hydrogenation, the catalytic performances of two different configurations of a B12N12 cluster doped with a single nickel atom were studied by a density functional theory computational approach. After analysing the effect that the adsorption of reactants onto the clusters has on the reaction path, we determined the lowest energy path for the acetylene double hydrogenation. Comparing the acetylene hydrogenation activities and ethylene product selectivities of the B11N12Ni and B12N11Ni clusters, which have different doping sites, we determined the activities of these two catalysts to be similar to each other; however, the B11N12Ni cluster was calculated to have higher selectivity for ethylene as a product. This difference may be related to the moderate adsorption of hydrogen and acetylene on the B11N12Ni cluster. As a new type of nickel-based single-atom catalyst, B11N12Ni clusters may have research value in the selective hydrogenation of acetylene.

scholarly journals 1,3-Di(hetero)aryl-7-substituted Pyrenes—An Undiscovered Area of Important Pyrene Derivatives

Proceedings ◽  
2019 ◽  
Vol 41 (1) ◽  
pp. 28
Author(s):  
Dawid Zych
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Basis Set ◽  
Functional Theory ◽  
Td Dft ◽  
Pyrene Derivatives ◽  
Osmium Complexes ◽  
The Subject ◽  
Theoretical Considerations

In this work, the necessity of synthesis of 1,3-di(hetero)aryl-7-substituted pyrenes is presented based on the results of theoretical calculations by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) by using Gaussian 09 program with B3LYP exchange-correlation functional and 6-31G** basis set. What is more, the synthetic routes with feasible reagents and conditions are presented. The subject of theoretical considerations are two pyrene derivatives which contain at position 1 and 3 pyrazolyl substituents and at position 7 amine (1) or boron (2) derivative. The theoretical calculations were also performed for the osmium complexes with mentioned ligands (3 and 4). The influence of electron-donating/accepting character of the substituent at position 7 of pyrene on the properties of molecules has been established.

scholarly journals Understanding the Lack of Reactivity of 2,4-Dihydroxybenzaldehyde Towards the Biginelli Adduct Using Density Functional Theory Molecular Modeling

Processes ◽  
2019 ◽  
Vol 7 (8) ◽  
pp. 521
Author(s):  
Virginia Flores-Morales ◽  
Eduardo D. Ayala-Medrano ◽  
José García-Elías ◽  
Margarita L. Martínez-Fierro ◽  
Edgar Marquez ◽  
...  
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Activation Enthalpy ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Condensation Reaction ◽  
Biginelli Reaction ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
Multiple Substitution

The Biginelli reaction is a multicomponent reaction for obtaining dihydropyrimidinthiones quickly, with multiple substitution patterns. The reaction mechanism remains unclear. Three possible pathways proposed for the reaction are the iminium route, an enamine intermediate, and the Knoevenagel pathway. However, when thiourea was used, no theoretical calculations were reported. Thus, based on the literature, the iminium pathway was used to obtain evidence explaining the lack of reactivity of 2,4-dihydroxybenzaldehyde towards the Biginelli adduct, compared with 4-hydroxybenzaldehyde. This computational study, carried out using the B3LYP/6-31++G(d,p) level of theory, showed an increment of 150 kJ/mol in the activation energy of the slowest pathway, due to the presence of a hydroxyl group in position 2 (ortho) of the aromatic aldehyde, decreasing its reactivity. Natural bond orbital (NBO) calculations suggest that the determinant steps are simultaneous, i.e., the polarization of the carbonyl group and its corresponding protonation by the hydrogen of the SH fragment of the thiourea tautomer. The activation enthalpy values suggest that the nucleophile attack takes place later on the compound 2,4-dihydroxybenzaldehyde compared to 4-hydroxybenzaldehyde-TS, confirming that the OH group in position 2 hinders the condensation reaction.

scholarly journals Computational Study of Methane C–H Activation by Main Group and Mixed Main Group–Transition Metal Complexes

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2794
Author(s):  
Carly C. Carter ◽  
Thomas R. Cundari
Keyword(s):  
Transition Metal Complexes ◽  
Active Site ◽  
Density Functional ◽  
Computational Study ◽  
Divalent Metal ◽  
Main Group ◽  
Free Energies ◽  
Functional Theory ◽  
Activation Barriers ◽  
Experimental Values

In the present density functional theory (DFT) research, nine different molecules, each with different combinations of A (triel) and E (divalent metal) elements, were reacted to effect methane C–H activation. The compounds modeled herein incorporated the triels A = B, Al, or Ga and the divalent metals E = Be, Mg, or Zn. The results show that changes in the divalent metal have a much bigger impact on the thermodynamics and methane activation barriers than changes in the triels. The activating molecules that contained beryllium were most likely to have the potential for activating methane, as their free energies of reaction and free energy barriers were close to reasonable experimental values (i.e., ΔG close to thermoneutral, ΔG‡ ~30 kcal/mol). In contrast, the molecules that contained larger elements such as Zn and Ga had much higher ΔG‡. The addition of various substituents to the A–E complexes did not seem to affect thermodynamics but had some effect on the kinetics when substituted closer to the active site.

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