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Chapter 4 Self-test questions
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Chapter 4 Self-test questions
Molecular Mechanics Methods
Quiz Content
*
not completed
.
The bond-bending contribution to the molecular mechanics energy of a water molecule, for a structure with an angle of 120.6°, is 4.34 kcal mol
^{-1}
. If the bending force constant
k
_{bend}
of equation (4.1) is 55 kcal mol
^{-1}
radian
^{-2}
, what is the equilibrium bond angle θ
_{0}
?
104.5°
correct
incorrect
102°
correct
incorrect
97.8°
correct
incorrect
136.7°
correct
incorrect
*
not completed
.
Which of the following is not the name of a forcefield?
CHARMM
correct
incorrect
TIP3P
correct
incorrect
AMBER
correct
incorrect
AM1
correct
incorrect
*
not completed
.
For an MM model of a system containing four water molecules, the forcefield includes eight bond stretching terms and 6 oxygen-oxygen non-bonded terms. How many of each would be present in a system with 10,000 water molecules?
10,000 and 10,002
correct
incorrect
20,000 and 5 x 10
^{7}
correct
incorrect
20,000 and 15,000
correct
incorrect
10,000 and 5 x 10
^{6}
correct
incorrect
*
not completed
.
A peptide carbonyl carbon atom is positioned 10 Å from the peptide nitrogen atom of another residue. What is the Lennard-Jones interaction energy of eq. (4.5) if the σ
_{CC}
and σ
_{NN}
parameters are 2.00 and 1.85 Å, ε
_{CC}
and ε
_{NN}
are 0.11 and 0.20 kcal mol
^{-1}
, and the combining rules of eq. (4.7) are used?
5.4 x 10
^{-6}
kcal mol
^{-1}
correct
incorrect
-3.0 x 10
^{-5}
kcal mol
^{-1}
correct
incorrect
-7.5 x 10
^{-6}
kcal mol
^{-1}
correct
incorrect
-7.5 kcal mol
^{-1}
correct
incorrect
*
not completed
.
How many methanol molecules (RMM 32.04 g mol
^{-1}
) are present in a cubic box with an edge length of 30 Å, assuming a density of 0.792 g cm
^{-3}
?
402
correct
incorrect
402,020
correct
incorrect
134
correct
incorrect
264
correct
incorrect
*
not completed
.
When using periodic boundary conditions, every atom present in the simulation box, with coordinates (
x
,
y
,
z
), is accompanied by an infinite number of periodic images with coordinates (
x+n
_{x}
L
_{x}
,
y+n
_{y}
L
_{y}
,
z+n
_{z}
L
_{z}
), where the
n
's are integers, and
L
_{x}
,
L
_{y}
and
L
_{z}
are the length of the box in each direction. Consider a cubic box (
L
= 30 Å in each direction) and two atoms A and B with (
x
_{A}
,
y
_{A}
,
z
_{A}
) = (29, 14, 28) and (
x
_{B}
,
y
_{B}
,
z
_{B}
) = (2, 15, 1). What is the distance between the two
closest
images of A and B?
38.2 Å
correct
incorrect
4.36 Å
correct
incorrect
3.21 Å
correct
incorrect
7 Å
correct
incorrect
*
not completed
.
A molecular mechanics calculation is carried out on a protein which is roughly spherical, with a diameter of 40 Å. Periodic boundary conditions are used with a cubic box, whose length
L
is chosen so that if the protein is in the centre of the box, each part of the protein is at least 20 Å from the edge of the box. How many water molecules will be needed to fill the rest of the box, assuming that one water molecule occupies 29.9 Å
^{3}
?
17,120
correct
incorrect
160,000
correct
incorrect
1,600
correct
incorrect
16,000
correct
incorrect
*
not completed
.
A Ca
^{2+}
ion interacts with a sulfate ion SO
_{4}
^{2-}
that is 20 Å away. How strong is the interaction due to Coulomb's law?
278 kJ mol
^{-1}
correct
incorrect
278,000 kJ mol
^{-1}
correct
incorrect
69.5 kJ mol
^{-1}
correct
incorrect
69,500 kJ mol
^{-1}
correct
incorrect
*
not completed
.
Combination rules lead to a requirement for many fewer parameters when developing forcefields. Consider a forcefield that is to be used for a system with 100 different atom types. How many Lennard-Jones radius parameters σ must be obtained if they are defined for each pair of atoms, or if combining rules are used, respectively?
10,000 and 100
correct
incorrect
5,050 and 100
correct
incorrect
20 and 50
correct
incorrect
100 and 100
correct
incorrect
*
not completed
.
Calculations are performed on a water droplet with radius
r
= 80 Å. Assuming each water molecule occupies 29.9 Å
^{3}
, and that the layer with thickness 3.85 Å at the surface of the sphere corresponds to 'surface' molecules, how many molecules are present in total and at the surface, respectively?
17,100 and 2,438
correct
incorrect
71,730 and 2,438
correct
incorrect
17,100 and 9,865
correct
incorrect
71,730 and 9,865
correct
incorrect
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