28 Questions
What is a limitation of the MM3 force field with regard to vibrational spectra?
Vibrational spectra are not accurately calculated
Which of the following is affected by hyperconjugation according to the text?
Bond length changes in conjugated molecules
What dependency does hyperconjugation have on bond characteristics in molecules?
Bond length changes due to higher H+ character
In CHARMM, what type of chemistry is focused on by Harvard Macromolecular Mechanics?
Macromolecular mechanics
What is a limitation of the MM4 force field in relation to saturated hydrocarbons?
High rotational barriers
What type of force field parameter is used for electrostatic calculations?
Atom-centered monopole
Which type of experiments are used for parametrization in proteins according to the text?
Microwave and X-ray
What module in AMBER is used for minimization, molecular dynamics, and NMR refinements?
SANDER
Which AMBER force field is generally recommended for proteins?
ff14SB
What does the Replica exchange calculations in force field parameterization allow?
Simultaneous sampling at a variety of conditions
In which type of calculations are provisions made for handling NOESY intensities and proton chemical shifts?
QM calculations
What is the force field that accounts for all atoms in the periodic table?
UFF
What type of potential is used to describe bond stretching in the UFF force field?
Morse potential
What is the term used to describe the electrostatic interaction between charged atoms in the UFF force field?
Charge-Charge interaction
How many atom types are defined in the UFF force field?
126
What type of torsion term is used in the UFF force field?
Cosine torsion term
What is the primary focus of the CHARMM22 force field reoptimization mentioned in the text?
Achieving equilibrium between A and B forms of DNA
What aspect of the force field was specifically optimized for the TIP3P water model?
Scaling factors and offsets of interaction energies
In what solvent was the stabilization of the B form of DNA observed during the simulation?
Aqueous solution
What are the major simulations conducted for further validation of the reoptimized force field?
Structural, dynamic, and hydration parameters
Which force field is specifically designed for all-atom simulations of proteins?
CHARMM36
What was noted as a limitation in the CHARMM22 force field reoptimization according to the text?
Equilibrium between helical and extended conformations
What improvement was made to the CMAP potential in the experiment described?
Refining with solution NMR data
Which part of the backbone CMAP potential was corrected in the study?
α-helix and extended regions
What aspect of the CHARMM22 Gly and Pro CMAPs was corrected?
Correcting α-helical bias
What was the main focus of the experiments conducted with Ala3, Ala5, Ala7, Val3, and Gly3?
Equilibrium folding of β-hairpins
Which technique was used to validate the experiments?
Comparison with backbone scalar couplings
In what type of proteins did the MacKerell Group focus their study on, according to the text?
Unfolded proteins
Learn about the need for a consistent force field in chemistry to accurately calculate structures, spectra, and heat parameters. Explore the limitations of MM3 parameters and the inaccuracies in vibrational spectra and rotational barriers calculations.
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