An algorithm for mass matrix calculation of internally constrained molecular geometries.
Dynamic models for molecular systems require the determination of corresponding mass matrix. For constrained geometries, these computations are often not trivial but need special considerations. Here, assembling the mass matrix of internally constrained molecular structures is formulated as an optimization problem. Analytical expressions are derived for the solution of the different possible cases depending on the rank of the constraint matrix. Geometrical interpretations are further used to enhance the solution concept. As an application, we evaluate the mass matrix for a constrained molecule undergoing an electron-transfer reaction. The preexponential factor for this reaction is computed based on the harmonic model.
Aryanpour
Masoud
M
Department of Mechanical Engineering, Stanford University, Stanford, California 94305, USA. ma526@cornell.edu
Dhanda
Abhishek
A
Pitsch
Heinz
H