Molecular modelling Flashcards
What is molecular modelling?
Molecular modelling is the science and art of studying a molecular structure and function through model building and computation.
What do molecular models usually represent?
Molecular models represent a highly-simplified version of the complex cellular environment.
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A molecule is represented as a mechanical system in which the particles – atoms – are connected by springs – the bonds. The molecules rotate, vibrate, and translate to assume favored conformations in the space as a collective response to the inter- and intramolecular forces acting upon them.
How is the total energy of the molecule calculated?
Etot = Estr + Ebend + Etors + Evdw + Eele +…
What are reference values and force constants known as?
Known as the force field.
Where are the parameters in the force fields derived from?
From both experiment and quantum mechanical calculations.
What is total energy a measure of?
The total energy is a measure of intramolecular strain relative to a hypothetical molecule with ideal geometry.
Energy = Ebonded + Enon-bonded
What energies comprise the Ebonded energy?
Ebonded = Ebond-stretch + Eangle-bend + Erotate-along-bond.
Energy = Ebonded + Enon-bonded
What energies comprise the Enon-bonded energy?
Enon-bonded = Evan-der-Waals + Eelectrostatic
What does Van-der-Waals Energy calculate?
Van-der-Waals Energy calculates the intramolecular attractions between two non-bonded hydrophobic regions with opposite temporary dipoles in the molecule. The dipoles arise from uneven electron distributions with time.
What does electrostatic energy calculate?
Electrostatic Energy calculates a non-covalent bonding interactions between two molecular regions having opposite charges in the molecule.
When and why should minimisation of the structure be carried out?
The minimisation should be carried out only when the structure is built. This is because the construction process may have resulted in unfavourable bond lengths, bond angles or torsion angles. Unfavourable non-bonded interactions may also be present i.e. atoms from different parts of the molecule occupying the same regions of space.
How is the energy minimisation process usually carried out?
The energy minimization process is usually carried out by a molecular mechanics program, which calculates the energy of the starting molecule, then varies the bond lengths, bond angles and torsion angles to create a new structure.
The energy of the new structure is calculated to see whether it is energetically more stable or not. If the structure is unstable, a slight alteration in bond angle or bond length will have a large effect on the overall energy of the molecule resulting in a large energy difference (ΔE). The program will recognize this and carry out the overall changes.
At what point will the energy minimisation program stop?
The program will stop when it interprets the structure as being stable. The structure will have structural variation which will have slight changes in energy = an energy minimum.
What is molecular graphics?
Molecular graphics provides different graphical visualisation of small molecules.
