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Molecular Modeling: Molecular MechanicsPowerPoint Presentation

Molecular Modeling: Molecular Mechanics

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Presentation Transcript

Guidelines for Use

- What systems were used to parameterize
- How is energy calculated
- What assumptions are used in the force field
- How has it performed in the past

Transferability

- AMBER (Assisted Model Building Energy Refinement)
- Specific to proteins and nucleic acids

- CHARMM (Chemistry at Harvard Macromolecular Mechanics)
- Specific to proteins and nucleic acids
- Widely used to model solvent effects
- Molecular dynamics integrator

Transferability

- MM? – (Allinger et. al.)
- Organic molecules

- MMFF (Merck Molecular Force Field)
- Organic molecules
- Molecular Dynamics

- Tripos/SYBYL
- Organic and bio-organic molecules

Transferability

- UFF (Universal Force Field)
- Parameters for all elements
- Inorganic systems

- YETI
- Parameterized to model non-bonded interactions
- Docking (AmberYETI)

How is Energy Calculated

- Valence Terms
- Cross Terms
- Non-bonding Terms
- Induced Dipole-Induced Dipole
- Electrostatic/Ionic (Permanent Dipole) System not far from equilibrium geometry (harmonic)

- Energy is ?
- Strain Energy (E=0 at equilibrium bond length/angle)
- Field Energy (Energy due to Non-bonding terms)
- Atomistic Heats of Formation (Parameterized so as to yield chemically meaningful values for thermodynamics)
- K. Gilbert: This is only in the MM?-type force fields

Assumptions

- Hydrogens often not explicitly included (intrinsic hydrogen methods)
- “Methyl carbon” equated with 1 C and 3 Hs

- System not far from equilibrium geometry (harmonic)
- Solvent is vacuum or simple dielectric

Assumptions:Harmonic Approximation

Assumptions:Harmonic Approximation

Determining k?

Assumptions:Harmonic Approximation

Assumptions:Harmonic Approximation

Assumptions

- Hydrogens often not explicitly included (intrinsic hydrogen methods)
- “Methyl carbon” equated with 1 C and 3 Hs

- System not far from equilibrium geometry (harmonic)
- Solvent is vacuum or simple dielectric

MMFF Energy

- Electrostatics (ionic compounds)
- D – Dielectric Constant
- d - electrostatic buffering constant

MMFF Energy

- Analogous to Lennard-Jones 6-12 potential
- London Dispersion Forces
- Van der Waals Repulsions

The form for the repulsive part has no physical basis and is for computational convenience when working with largemacromolecules. K. Gilbert: Force fields like MM2 which is used for smaller organic systems will use a Buckingham potential (or expontential) which accurately reflects the

chemistry/physics.

Easily constructed

Accuracy

Not robust enough to describe subtle chemical effects

Hydrophobicity

Excited States

Radicals

Does not reproduce quantal nature

Pros and ConsCaveats

- Compare energy differences NOT energies
- Always compare results with higher order theory (ab initio) and/or experiments

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