Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

1997 ◽  
Vol 18 (12) ◽  
pp. 1496-1512 ◽  
Author(s):  
Peter L. Cummins ◽  
Jill E. Gready
Keyword(s):  
Aqueous Solution ◽  
Molecular Mechanics ◽  
Molecular Orbital ◽  
Organic Molecules ◽  
Mechanics Model ◽  
Molecular Mechanics Model ◽  
Semiempirical Molecular Orbital

Molecular Mechanics Studies on MFI Type Zeolites. 1. Effect of p-Xylene Adsorption on the Zeolite Structure

1992 ◽  
Vol 57 (4) ◽  
pp. 675-680 ◽  
Author(s):  
Erik de Vos Burchart ◽  
Bert van der Linden ◽  
Herman van Bekkum ◽  
Bastiaan van de Graaf
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Organic Molecules ◽  
Monoclinic Space Group ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Mechanics Model ◽  
Organic Zeolite ◽  
Molecular Mechanics Model ◽  
Mm3 Force Field

The effect of the adsorption of p-xylene on the all-silica MFI-structure is simulated with our molecular mechanics model. From experimental measurements it is known that the symmetry of the framework changes from monoclinic (space group P21/n.1.1.) towards orthorhombic (space group P212121) upon adsorption of p-xylene up to eight molecules per unit cell. The experimentally observed change in the geometry of the zeolite upon p-xylene adsorption is compared with that calculated by molecular mechanics. For the calculations our force field for all-silica zeolites is used in combination with the MM3 force field for organic molecules. Parameters for the organic-zeolite interactions are obtained by combination of the two force fields.

An Efficient Multigrid Method for Molecular Mechanics Modeling in Atomic Solids

2011 ◽  
Vol 10 (1) ◽  
pp. 70-89 ◽  
Author(s):  
Jingrun Chen ◽  
Pingbing Ming
Keyword(s):  
Molecular Mechanics ◽  
Multigrid Method ◽  
Tensile Deformation ◽  
Initial Guess ◽  
Iterative Solvers ◽  
Linear Scaling ◽  
One Dimensional ◽  
Mechanics Model ◽  
Molecular Mechanics Model ◽  
Deformed State

AbstractWe propose a multigrid method to solve the molecular mechanics model (molecular dynamics at zero temperature). The Cauchy-Born elasticity model is employed as the coarse grid operator and the elastically deformed state as the initial guess of the molecular mechanics model. The efficiency of the algorithm is demonstrated by three examples with homogeneous deformation, namely, one dimensional chain under tensile deformation and aluminum under tension and shear deformations. The method exhibits linear-scaling computational complexity, and is insensitive to parameters arising from iterative solvers. In addition, we study two examples with inhomogeneous deformation: vacancy and nanoindentation of aluminum. The results are still satisfactory while the linear-scaling property is lost for the latter example.

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