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Chapter 8 Self-test questions
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Chapter 8 Self-test questions
Hybrid and Multi-Scale Methods
Quiz Content
*
not completed
.
The dielectric constant of the common solvent acetonitrile is 37.5. What is the free energy of solvation of the formate anion HCOO
^{-}
in acetonitrile, assuming that it becomes solvated in a spherical cavity with radius 2.1 Å.
-322 kJ mol
^{-1}
correct
incorrect
-644 kJ mol
^{-1}
correct
incorrect
-161 kJ mol
^{-1}
correct
incorrect
-483 kJ mol
^{-1}
correct
incorrect
*
not completed
.
Which of the following pairs cannot usually be described in terms of a system:environment pair?
Solute:solvent
correct
incorrect
Defect:crystal
correct
incorrect
Active site:protein bulk
correct
incorrect
Reactant A:Reactant B
correct
incorrect
*
not completed
.
Which of the following acronyms does not describe a common method for predicting solvation free energies?
SMD
correct
incorrect
PCM
correct
incorrect
CCSD
correct
incorrect
COSMO
correct
incorrect
*
not completed
.
One of the simplest approaches for constructing hybrid methods is the
subtractive
approach, whereby the energy of the system formed by a core A and environment B is given by:
V
^{HL}
(AB) =
V
^{HL}
(A) +
V
^{LL}
(AB) –
V
^{LL}
(A). HL denotes a high-level of theory and LL a low level. This method can be very simple because:
Only three terms are needed in the energy expression, so the maths is very simple.
correct
incorrect
The low level of theory is used to describe the environment, unlike in other hybrid methods.
correct
incorrect
It only requires carrying out standard
V
^{HL}
and
V
^{LL}
calculations on A or AB.
correct
incorrect
*
not completed
.
In a typical QM/MM calculation in which the core region is treated with a QM method, with embedding in an MM environment described by point charges, which of the following effects is not included?
Polarization of the atoms of the core due to interactions with the environment.
correct
incorrect
Polarization of some of the atoms in the core region due to interactions with other atoms in the core.
correct
incorrect
Repulsion at short range between non-bonded atoms in the core and the environment.
correct
incorrect
Polarization of the atoms of the environment due to interactions with the core.
correct
incorrect
*
not completed
.
Consider a metal-phosphine complex [M]-PR
_{3}
, where R is the cyclohexyl group, and [M] denotes the metal together with ancillary ligands. If this complex is modelled using a hybrid QM-MM method in which for the QM calculations on the core the R group is replaced by H atoms, which of the following can be stated concerning the results?
The QM calculation will reflect the electronic structure expected for the PH
_{3}
ligand, but perhaps perturbed by the fact that the molecular structure will reflect that expected for PCy
_{3}
.
correct
incorrect
PCy
_{3}
ligands are very bulky and steric bulk is not well described by molecular mechanics.
correct
incorrect
This type of calculation is not at all useful nowadays, because PCy
_{3}
ligands are small enough to be modelled with QM methods.
correct
incorrect
As a means of studying the electronic effect of the PCy
_{3}
ligand, this calculation will not be successful as the calculated QM properties will be those expected for the PH
_{3}
ligand.
correct
incorrect
*
not completed
.
The Cope rearrangement, in its simplest form, converts 1,5-hexadiene to an isomer of itself through a 6-membered ring TS. At the B3LYP/6-31G level of theory, the reactant and TS return energies of -234.5535 and -234.5054 hartree respectively, while B3LYP together with the SMD continuum solvent model, with parameters for acetonitrile, returns energies of -234.5594 and -234.5112 hartree respectively. What is the effect (in kJ mol
^{-1}
, 1 hartree = 2625.5 kJ mol
^{-1}
) of including the solvent on (a) the energy of the TS, (b) the activation energy?
(a) -15 kJ mol
^{-1}
and (b) 0 kJ mol
^{-1}
.
correct
incorrect
(a) +15 kJ mol
^{-1}
and (b) 22 kJ mol
^{-1}
.
correct
incorrect
(a) -45 kJ mol
^{-1}
and (b) 5 kJ mol
^{-1}
.
correct
incorrect
(a) -125 kJ mol
^{-1}
and (b) 12 kJ mol
^{-1}
.
correct
incorrect
*
not completed
.
Coarse-grained molecular mechanics models can be more easily evaluated as they involve fewer interaction sites. Consider modelling of a system using an all-atom MM model and a coarse-grained model. Assume that, in the coarse-grained model, on average 6 atoms are grouped together into one interaction site. Assuming that the number of energy terms varies as the square of the number of sites, what is the expected change in computational effort from the atomistic model to the coarse-grained one?
The calculation will be about 30 times faster with the coarse-grained model.
correct
incorrect
The calculation will be about six times faster with the coarse-grained model.
correct
incorrect
The coarse-grained and atomistic models will take roughly the same amount of time to evaluate.
correct
incorrect
The atomistic model will be roughly 30 times faster to evaluate than the coarse-grained model.
correct
incorrect
*
not completed
.
One way to treat an environment is to include relevant atoms in an all-atom model. Assuming the computational effort associated with a calculation (evaluating the energy + optimizing the structure) scales as the square of the number of atoms, what would be the effect of including histidine (CH
_{3}
C
_{3}
H
_{3}
N
_{2}
) and aspartate (CH
_{3}
CO
_{2}
^{-}
) side chains in a calculation on an acetyl-coenzyme A model CH
_{3}
COSCH
_{3}
?
The calculation will be roughly three times slower.
correct
incorrect
The calculation will be roughly ten times slower.
correct
incorrect
The calculation will be roughly thirty times slower.
correct
incorrect
The calculation will be roughly a hundred times slower.
correct
incorrect
*
not completed
.
Which of the following chemical reactions would you expect to proceed
much
faster in a polar solvent than in vacuum?
Diels-Alder cycloaddition of a dienophile to butadiene.
correct
incorrect
Abstraction of a hydrogen atom from the methyl group in toluene by a chlorine atom.
correct
incorrect
S
_{N}
1 substitution of chloride in tert-butyl chloride.
correct
incorrect
Dissociation of a phosphine ligand PPh
_{3}
from a metal site [M].
correct
incorrect
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