DFT and Docking Study of Potential Transition State Analogue Inhibitors of Glycosyltransferases

2008 ◽  
Vol 73 (5) ◽  
pp. 591-607 ◽  
Author(s):  
Lucie Sihelniková ◽  
Stanislav Kozmon ◽  
Igor Tvaroška
Keyword(s):  
Transition State ◽  
Density Functional ◽  
Density Functional Theory Method ◽  
Docking Study ◽  
Binding Mode ◽  
Functional Theory ◽  
Sulfate Anion ◽  
Transition State Analogue ◽  
Transition State Analogue Inhibitors ◽  
Energy Maps

Conformational behavior of the [(2S,3R,4R,5S)-3,4,5-trihydroxy-2-(phenylsulfanyl)tetrahydrofuran-2-yl]methyl sulfate anion (2), which is the potential transition state (TS) analogue of the inverting glycosyltransferases, was studied by means of two-dimensional potential-energy maps, using a density functional theory method at the B3LYP/6-31+G* level. The maps revealed the presence of eight low-energy domains which were refined at the B3LYP/6-311++G** level and led to six conformers in vacuum. In aqueous solution, two conformers dominate at equilibrium. The preferred conformers superimpose well with the transition state structure, as determined previously for glycosyltransferase GnT-I. The conformations of 2 in the active site of glycosyltransferase GnT-I were obtained by docking methods. It was found that one of the two best docking poses mimics the binding mode of TS. These results suggest that the proposed TS mimics 2 have the potential to be used as a scaffold for the design of TS analogue inhibitors.

Study of the Stability and Chemical Reactivity of a Series of Tetrazole Pyrimidine Hybrids by the Density Functional Theory Method (DFT)

2021 ◽  
Vol 37 (4) ◽  
pp. 805-812
Author(s):  
Ahissandonatien Ehouman ◽  
Adjoumanirodrigue Kouakou ◽  
Fatogoma Diarrassouba ◽  
Hakim Abdel Aziz Ouattara ◽  
Paulin Marius Niamien
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Molecular Descriptors ◽  
Chemical Reactivity ◽  
Density Functional Theory Method ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
The Density Functional Theory ◽  
The Stability ◽  
Global Reactivity Descriptors

Our theoretical study of stability and reactivity was carried out on six (06) molecules of a series of pyrimidine tetrazole hybrids (PTH) substituted with H, F, Cl, Br, OCH3 and CH3 atoms and groups of atoms using the density function theory (DFT). Analysis of the thermodynamic formation quantities confirmed the formation and existence of the series of molecules studied. Quantum chemical calculations at the B3LYP / 6-311G (d, p) level of theory determined molecular descriptors. Global reactivity descriptors were also determined and analyzed. Thus, the results showed that the compound PTH_1 is the most stable, and PTH_5 is the most reactive and nucleophilic. Similarly, the compound PTH_4 is the most electrophilic. The analysis of the local descriptors and the boundary molecular orbitals allowed us to identify the preferred atoms for electrophilic and nucleophilic attacks.

A novel mechanism of spin-orientation dependence of O2 reactivity from first principles methods

2017 ◽  
Vol 7 (5) ◽  
pp. 1040-1044 ◽  
Author(s):  
M. C. S. Escaño ◽  
H. Kasai
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Transition State ◽  
First Principles ◽  
Density Functional ◽  
Orientation Dependence ◽  
Coupling Mechanism ◽  
Spin Moment ◽  
Spin Orientation ◽  
Functional Theory

A novel mechanism of oxygen reaction on a metal surface beyond the present charge transfer or hybridization mechanism, spin-orientation dependence via a coupling mechanism due to the finite spin moment of O2 at the transition state, is obtained using a combination of spin density functional theory (SDFT) and constrained DFT.

scholarly journals Transition State Analogue Inhibitors of 5′-Deoxyadenosine/5′-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis

Biochemistry ◽  
2017 ◽  
Vol 56 (38) ◽  
pp. 5090-5098 ◽  
Author(s):  
Hilda A. Namanja-Magliano ◽  
Gary B. Evans ◽  
Rajesh K. Harijan ◽  
Peter C. Tyler ◽  
Vern L. Schramm
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Transition State ◽  
Transition State Analogue ◽  
Transition State Analogue Inhibitors

scholarly journals Practical and Theoretical Study on the Inhibitory Influences of New Azomethine Derivatives Containing an 8-Hydroxyquinoline Moiety for the Corrosion of Carbon Steel in 1 M HCl

2018 ◽  
Vol 34 (6) ◽  
pp. 3016-3029 ◽  
Author(s):  
A. El-Yaktini ◽  
A. Lachiri ◽  
M. El-Faydy ◽  
F. Benhiba ◽  
H. Zarrok ◽  
...  
Keyword(s):  
Carbon Steel ◽  
Density Functional ◽  
Electrochemical Impedance ◽  
Density Functional Theory Method ◽  
Steel Corrosion ◽  
Experimental Results ◽  
Chemical Parameters ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Inhibition Ability

The inhibition ability of a new Azomethine derivatives containing the 8-hydroxyquinoline (BDHQ and MDHQ) towards carbon steel corrosion in HCl solution was studied at various concentrations and temperatures using weight loss, polarization curves and electrochemical impedance spectroscopy (EIS) methods. The experimental results reveal that BDHQ and MDHQ are efficient mixed type corrosion inhibitors, and their inhibition efficiencies increase with increasing concentration. The adsorption of these inhibitors on mild steel surface obeys Langmuir isotherm. Quantum chemical parameters are calculated using the Density Functional Theory method (DFT) and Monte Carlo simulations. Correlation between theoretical and experimental results is discussed.

scholarly journals Popular Integration Grids Can Result in Large Errors in DFT-Computed Free Energies

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Steven Wheeler
Keyword(s):  
Transition State ◽  
Molecular Orientation ◽  
Density Functional ◽  
Basis Sets ◽  
Free Energies ◽  
Functional Theory ◽  
Metal Free ◽  
Stereoselective Reactions ◽  
Functionalization Reaction ◽  
Transition State Structures

<div>Density functional theory (DFT) has emerged as a powerful tool for analyzing organic and organometallic systems and proved remarkably accurate in computing the small free energy differences that underpin many chemical phenomena (e.g. regio- and stereoselective reactions). We show that the lack of rotational invariance of popular DFT integration grids reveals large uncertainties in computed free energies for isomerizations, torsional barriers, and regio- and stereoselective reactions. The result is that predictions based on DFT-computed free energies for many systems can change qualitatively depending on molecular orientation. For example, for a metal-free propargylation of benzaldehyde, predicted enantioselectivities based on B97-D/def2-TZVP free energies using the popular (75,302) integration grid can vary from 62:38 to 99:1 by simply rotating the transition state structures. Relative free energies for the regiocontrolling transition state structures for an Ir-catalyzed C–H functionalization reaction computed using M06/6-31G(d,p)/LANL2DZ and the same grid can vary by more than 5 kcal mol–1, resulting in predicted regioselectivities that range anywhere from 14:86 to >99:1. Errors of these magnitudes occur for different functionals and basis sets, are widespread among modern applications of DFT, and can be reduced by using much denser integration grids than commonly employed.</div>

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