University:
The University Of Western Ontario
Course:
Biology 2290F | Scientific Method in Biology
Academic year:

2022
Views:

187

Pages:

4
Author:

Kyuwon J.

Molecular modeling ● a technique for the investigation of molecular structures and properties using computational chemistry and graphical visualization techniques ● Proves plausible three-dimensional representation under a given set of circumstances Quantum Mechanics ● Calculations using all electron and nuclei of the molecules Molecular mechanics ● Equations used to calculate interactions and energies(force fields) Quantum Mechanics (QM) ● Quantum Mechanics tires toi understand all interactions found in a molecule ● In principle quantum mechanics considers the electron and nuclei in a molecule together ● Foundation is the Schrodinger Equations ● Finds for all interaction in molecule ○ Distance, Charge ● The Schrodinger equation allows us to calculate the energy (E) of a system as a function of geometry ● ● ● ● ab initio(from the beginning method) Only experimental fundamental constants In principle very high accuracy Complete( all interactions are inclined ) Very time consuming, limited to small systems ● ● ● Density Functional Theory in principle accurate Faster than traditional ab initio time consuming ● ● ● Semi-empirical methods valence electron only ○ cut out non-important portion of the analysis to fasten up the process reduced accuracy Fast, can be used for larger systems. Flow Chart for QM calculation ● ● ● ● molecule(2D): Draw a structure in Chemdraw Molecular coordinates(3D): Converts 2D to 3D structure ○ Chemdraw can also do this ○ DS visualizer Program: Gaussian, Games, Mopac Level of theory: Different basic set fives different level of accuracy MO energies, orbitals, heat formation electrostatic potentials, dipole moments, transition states and geometries could be analyzed . An example of QM calculation Semi-empirical method PM6 Seems to have 4 H-bond Through analysis, could find 5 H-bonds are present in most stable state(even though one of them are 3.3A apart) Molecular Mechanics(MM) Molecular mechanism treats ● Atom as a single particles ● Molecules as bonded particles ● Bonds as springs ● ● The energy will increase as the Bonds are stretched The energy will increase as the Bonds are compressed