Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory

2014 ◽  
Vol 28 (3) ◽  
pp. 299-304 ◽  
Author(s):  
Jia Fu ◽  
Yu Liu ◽  
Jianzhong Wu
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Free Energies ◽  
Blind Test ◽  
Functional Theory ◽  
Fast Prediction

Bisoxazoline–copper(I)-catalyzed aziridination of diazoacetate with imines — A DFT study

2010 ◽  
Vol 88 (10) ◽  
pp. 981-990 ◽  
Author(s):  
Qingxi Meng ◽  
Fen Wang ◽  
Ming Li
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Mode I ◽  
Mode Ii ◽  
Free Energies ◽  
Functional Theory ◽  
Carboxylate Complex ◽  
Calculation Results ◽  
Favorable Reaction ◽  
Level Calculation

Density functional theory (DFT) has been used to study bisoxazoline–copper(I)-catalyzed aziridination of diazoacetate with syn-imines or anti-imines. All the intermediates and transition states were optimized completely at the B3LYP/6-31G(d) level. Calculation results confirm that Cu(I)-catalyzed aziridination goes mainly through the catalyst–diazoacetate complex (M1), the copper(I)–carbene intermediate (M2), the copper–carbene–imine complex (M3), and the catalyst–aziridine carboxylate complex (M4). For syn-imines, the reaction mode I (C3–N5 bond attacking the Cu–C1 bond of M2) is more dominant than the reaction mode II (C3–N5 bond attacking the carbene–carbon C1 of M2), and the attack from the si-surface of M2 is prior to the re-surface. For anti-imines, the reaction modes and attacks from the si- or re-surface coexist. The reactivity of syn-imines is stronger than anti-imines. The favorable reaction channel is CA2 → M1b → TS1b → M2 → syn-TS2b → syn-M3b → syn-TS3b → syn-M4b → syn-P2. The dominant product theoretically predicted is of (S,S)-chirality. On the whole, the solvent effect decreases the free energies of the species.

scholarly journals Theoretical calculation for the phonon spectrum and thermodynamic functions of vanadium and its hydride

2021 ◽  
Vol 252 ◽  
pp. 03039
Author(s):  
Qiang Wei-rong ◽  
Wang Xiao-mei ◽  
Liu Wei-qi
Keyword(s):  
Experimental Data ◽  
Density Functional Theory ◽  
Density Functional ◽  
Free Energies ◽  
Generalized Gradient ◽  
Virtual Crystal Approximation ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
Density Functional Perturbation Theory ◽  
Densities Of States

Based on density functional theory(DFT), using virtual crystal approximation and generalized gradient approximation(GGA)with pseudopotential method, the lattices and energies for five crystallines of vanadium hydrides are optimized and calculated. The phonon densities of states are calculated based on density functional perturbation theory(DFPT). The standard Heat capacities, Entropies, Helmholtz free energies and Gibbs functions of vanadium and its hydride are deduced at 298.15K. The calculated results are discussed and compared with experimental data.

Nucleophilic Substitution Reactions of Cyclic Thiosulfinates Are Accelerated by Hyperconjugative Interactions

2019 ◽  
Author(s):  
Daniel Donnelly ◽  
Jeffrey Agar ◽  
Steven Lopez
Keyword(s):  
Density Functional Theory ◽  
Nucleophilic Substitution ◽  
Strain Energy ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Free Energies ◽  
Substitution Reactions ◽  
Functional Theory ◽  
Nucleophilic Substitution Reactions

Strain energy has been shown to promote the nucleophilic substitution reactions of cyclic disulfides, the reactivities of cyclic thiosulfinate nucleophilic substitution is unexplored. We used density functional theory calculations [M06-2X/6-311++G(d,p)] to determine the activation and reaction free energies for the reactions of 3—10-membered cyclic thiosulfinates and cyclic disulfides with methyl thiolate.

RANK-ORDERING THE BINDING AFFINITY FOR FKBP12 AND H1N1 NEURAMINIDASE INHIBITORS IN THE COMBINATION OF A PROTEIN MODEL WITH DENSITY FUNCTIONAL THEORY

2011 ◽  
Vol 10 (04) ◽  
pp. 541-565 ◽  
Author(s):  
GANG HE ◽  
JUYING SHI ◽  
YANTAO CHEN ◽  
YI CHEN ◽  
QIANLING ZHANG ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Interaction Energy ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Mechanical Interaction ◽  
Functional Theory ◽  
Protein Model ◽  
Autodock 4.0 ◽  
Binding Free Energies

The quantum mechanical interaction energies between FKBP12 as well as H1N1 neuraminidase and their inhibitors were directly calculated with an efficient density functional theory by mimicking the whole protein with a protein model composed of the amino acids surrounding the ligands. It was found that the calculated quantum mechanical interaction energies correlate well with the experimental binding free energies with the correlation coefficients of 0.88, 0.86, and the standard deviation of 0.93 and 1.00 kcal/mol, respectively. To compare with force field approach, the binding free energies with the correlation coefficient R = 0.80 and 0.47 were estimated by AutoDock 4.0 programs. It was indicated that the quantum interaction energy shows a better performance in rank-ordering the binding affinity between FKBP12 and H1N1 neuraminidase inhibitors than those of AutoDock 4.0 program. In combination protein model with density functional theory, the estimated quantum interaction energy could be a good predictor or scoring function in structure-based computer-aided drug design. Finally, five new FKBP12 inhibitors were designed based on calculated quantum mechanical interaction energy. In particular, the theoretical K i value of one compound is as low as 0.05 nM, nearly 8-fold more active than FK506.

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