Asymmetric alkylations on chiral formamidines. Molecular mechanics studies relating to the facial selectivity of the lithiated intermediates

1992 ◽  
Vol 57 (14) ◽  
pp. 3819-3821 ◽  
Author(s):  
Laurie A. Castonguay ◽  
Joseph W. Guiles ◽  
A. K. Rappe ◽  
A. I. Meyers
Keyword(s):  
Molecular Mechanics ◽  
Facial Selectivity ◽  
Asymmetric Alkylations

The conformational properties of calix[4]arenes 1h NMR and molecular mechanics calculations

1989 ◽  
Vol 86 ◽  
pp. 945-954 ◽  
Author(s):  
F. Bayard ◽  
D. Decoret ◽  
D. Pattou ◽  
J. Royer ◽  
A. Satrallah ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
1H Nmr ◽  
Molecular Mechanics Calculations ◽  
Conformational Properties

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

π-Facial Selectivity in 1,3-Dipolar Cycloaddition Reactions of α-Methylidene-γ-lactone Substituted by 4-Methyl-2,6,7-trioxabicyclo[2.2.2]octan-1-yl Group in γ-Position

2002 ◽  
Vol 67 (3) ◽  
pp. 353-364 ◽  
Author(s):  
Petr Melša ◽  
Ctibor Mazal
Keyword(s):  
Double Bond ◽  
Carboxylic Acid ◽  
Nitrile Oxide ◽  
Dipolar Cycloaddition ◽  
Cycloaddition Reactions ◽  
Enantiomerically Pure ◽  
Nitrile Imine ◽  
Facial Selectivity ◽  
Excellent Selectivity

Diastereoselectivity of 1,3-dipolar cycloaddition reactions of benzyl azide, diazomethane, a nitrile oxide and a nitrile imine to α-methylidene-γ-lactone dipolarophile was effectively controlled by a bulky γ-substituent, 4-methyl-2,6,7-trioxabicyclo[2.2.2]octan-1-yl in γ-position of the dipolarophile. The dipoles added from the less hindered face of the double bond with an excellent selectivity. Enantiomerically pure dipolarophile was prepared from the easily available (S)-5-oxotetrahydrohydrofuran-2-carboxylic acid.

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