Potential Energy Surface (PES) and the Basic Force Field (Molecular mechanics)

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Potential Energy Surface(PES)and the Basic
Force Field (Molecular mechanics)

• Lecture 2 08.2.19CH418 computational Chemistry
• KAIST

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This lecture is mostly from Prof. Cramers of
UMN, tRNA example is probably from the following
paper

• Wild-type RNA MicrohelixAla and 370 Variants
  Molecular Dynamics Analysis of Tightly Bound
  Water and Local Helical Structure
• Nagan, M. C. Kerimo, S. S. Musier-Forsyth, K.
  Cramer, C. J. J. Am. Chem. Soc. 1999, 121, 7310.
• Molecular dynamics simulations of RNA
  microhelixAla indicate that GU and other 370
  purinepyrimidine wobble pairs induce local
  deviations from A-form geometry in their
  respective microhelices the helix is underwound
  at the base-pair step above and overwound at the
  base-pair step below, in each case by about 7 to
  9 degrees compared to canonical A-form RNA. Based
  on analysis of average water densities and
  residence lifetimes, the wild-type microhelix
  strongly binds a water molecule in the minor
  groove of the 370 base pair, consistent with
  crystallographic analyses of an RNA duplex
  derived from the acceptor stem of Escherichia
  coli tRNAAla. Other wobble pairs show water
  binding at this position but to a lesser degree
  the strength of water binding correlates directly
  with the measured aminoacylation activities of
  the microhelices as substrates for E. coli
  alanyl-tRNA synthetase (GU gt 2AAIsoC gt GdU gt
  IU). Watson-Crick base pairs at the 370
  position show no tendency towards specific
  hydration. This tightly bound minor-groove water
  in the microhelices with 370 wobble pairs
  evidently does not function to stabilize a
  particular local helical structure, but it may
  play a role as a specific recognition element or
  serve as an indicator of interaction specificity
  between the microhelix and a hydroxylated residue
  of the aminoacyl-tRNA synthetase.

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• Deeper Aspects of the PES
• Depends in a fundamental way on the
• Born-Oppenheimer approximation
• Inherently a classical construct with
• respect to the nuclei (but quantum in
• the electronics)
• Corresponds to a single molecule
• thinking about a collection of molecules
• requires us to bring in thermodynamics
• (which well discuss later)

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• More Deeper Aspects of the PES
• Does not show kinetic energy! So, everyones
• favorite picture of a dynamic molecule being a
  ball
• rolling on the surface is misleading if you think
  of the
• energy decreasing as you go downhill. Total
  energy
• (PE KE) is conserved at a constant value.
  Again,
• this is something well discuss later.
• At T 0 K (no KE), the rules of our universe
  say that
• our molecule will want to be at the lowest
  possible
• potential energy, i.e., at a minimum on the PES.
  It
• sure would be nice to have ways of finding the
• locations of minima efficiently
• Between any two minima (valley bottoms) the
  lowest
• energy path will pass through a maximum at a
  saddle
• point. In chemistry, we call that saddle point a
• transition-state structure. Theyd be nice to
  find too

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• Valence force field parameters are available for
  limited set of atom types
• Minimization trivial for isolated small molecules
• Large molecule, solvation and other environmental
  effect make application of straightforward
  minimization difficult

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Modeling programs needs structure files (in
different format)
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