Density Functional Studies of Oxidized and Reduced Methane Monooxygenase. Optimized Geometries and Exchange Coupling of Active Site Clusters

2001 ◽  
Vol 40 (20) ◽  
pp. 5251-5266 ◽  
Author(s):  
Timothy Lovell ◽  
Jian Li ◽  
Louis Noodleman
Keyword(s):  
Active Site ◽  
Exchange Coupling ◽  
Density Functional ◽  
Methane Monooxygenase ◽  
Functional Studies ◽  
Optimized Geometries

On the role of lysine in the active site Ser-X-X-Lys region of penicillin-recognizing enzymes

2010 ◽  
Vol 88 (1) ◽  
pp. 1-4
Author(s):  
Saul Wolfe ◽  
Kiyull Yang
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Basis Set ◽  
Penicillin G ◽  
Hydroxyl Group ◽  
Functional Theory ◽  
One Step ◽  
Optimized Geometries

Using Autodock, docking of penicillin G to the crystal structures of penicillin-recognizing enzymes leads to an alignment in the active site Ser-X-X-Lys region consisting of the serine hydroxyl group, the terminal amino group of lysine, a second hydroxyl group, and the N–C=O of the β-lactam. This alignment is consistent with the notion that acylation of the serine hydroxyl group proceeds by a one-step cooperative mechanism in which C–O bond formation and proton transfer to the β-lactam nitrogen take place through a heteroatom bridge. For the cooperative ring opening of penam by two molecules of methanol and one molecule of methylamine or one molecule of water, density functional theory with the B3LYP DFT gradient-corrected functional and the 6–31G(d) basis set reproduces the alignment seen in the docked structures. Methylamine lowers the barrier calculated at MP2/6–31G(d) from the DFT-optimized geometries by 3 kcal/mol; water increases the barrier by 4 kcal/mol. The function of the conserved lysine in the active sites of penicillin-recognizing enzymes is therefore to catalyze the formation of an acyl enzyme by a cooperative mechanism.

Spectroscopic and Density Functional Studies of the Red Copper Site in Nitrosocyanin:  Role of the Protein in Determining Active Site Geometric and Electronic Structure

2005 ◽  
Vol 127 (10) ◽  
pp. 3531-3544 ◽  
Author(s):  
Lipika Basumallick ◽  
Ritimukta Sarangi ◽  
Serena DeBeer George ◽  
Brad Elmore ◽  
Alan B. Hooper ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Active Site ◽  
Density Functional ◽  
Functional Studies ◽  
Copper Site

Assessing the Calculation of Exchange Coupling Constants and Spin Crossover Gaps Using the Approximate Projection Model to Improve Density Function Calculations

2019 ◽  
Author(s):  
Xianghai Sheng ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Density Functional Theory ◽  
Exchange Coupling ◽  
Density Functional ◽  
Spin Crossover ◽  
Coupling Constants ◽  
Spin Projection ◽  
Coupling Constant ◽  
Projection Model ◽  
Functional Theory

This work evaluates the quality of exchange coupling constant and spin crossover gap calculations using density functional theory corrected by the Approximate Projection model. Results show that improvements using the Approximate Projection model range from modest to significant. This study demonstrates that, at least for the class of systems examined here, spin-projection generally improves the quality of density functional theory calculations of J-coupling constants and spin crossover gaps. Furthermore, it is shown that spin-projection can be important for both geometry optimization and energy evaluations. The Approximate Project model provides an affordable and practical approach for effectively correcting spin-contamination errors in molecular exchange coupling constant and spin crossover gap calculations.

Density functional studies on the adsorption and decomposition of SO2 on Cu(100)

2001 ◽  
Vol 115 (1) ◽  
pp. 454-465 ◽  
Author(s):  
José A. Rodriguez ◽  
Josep M. Ricart ◽  
Anna Clotet ◽  
Francesc Illas
Keyword(s):  
Density Functional ◽  
Functional Studies
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