BCH 330 Test 2 Questions with Correct Answers Latest Update 2025/2026
consider the structure of methane. why are the four sp3 hybridized orbitals separated as far as
they can be from one another? - Answers - draw methane with phi angle 109.5
- overlap integral: the phenomena of staying as separated as far apart as possible
- lower e- e- repulsion when doing this, more stable
briefly describe the two major techniques typically used to determine the structure of a
biological macromolecule? - Answers - x ray Crystallography: shooting specific wavelengths (10-
0.01nm) at a crystal lattice containing molecule. they hit and bounce off and are measured and
produce a globular shape using computers. the intensity of spots related to atomic arrangement,
position is related to unit cell arrangement, and the phase problem arrises from squaring
amplitude and losing phase.
- x ray lattice diagram
- Nuclear magnetic resonance: measuring orientation of a spin vector of an atom before and
after a radio frequency pulse. This gives hydrogen atom peaks and small atomic distances
between atoms of 5 angstroms.
- pulse x/y/z diagram
in a simple way, how is quantum mechanics used to determine the energy and structure of a
molecule? provide an explanation - Answers - key equation: schrodenger equation (hy=ey)
- hamiltonion operator: used to find lowest energy, finds the energy produced by a specific wave
function. describes various electron density clouds
- figure: real thing from wave function derivation
explain the significance of the schrodinger key equation. define the hamiltonion operator and
wave function. - Answers - significance: allows one to find the energy level of a system and use
the wave function to find probability of a particle in space/time
- wave function/the electron probability distribution function: (𝜓 ^2)𝑑 𝑉 =(𝜓 ^2)4𝜋 (𝑟 ^2)𝑑 𝑟 is
used to find these probabilities of electrons in space/time
- hamiltonion operator: produces the energy associated with a specific wave function/finds
structure based on lowest energy
write out/define boltzmanns distribution law and define all the parameters - Answers - the
probability that a molecule will be in a certain state, varies exponentially
- figure: equation 1 (is a canonical ensemble)
, - Ns: average over micro states in the canonical ensemble
- N: population of individuals
- -E(): energies of states ()
- Kb: boltzmanns constant
- T: temperature in Kelvin
- Z: the sum of exponentials corresponding to all possible states
what is the relation between probability of a given states and the corresponding energy? Hint:
what happens to the distribution when the energy is increased? - Answers - possibility of a given
states decreases exponentially as the energy of state R increases. This is because a single
higher energy state has few occupants then a lower energy state.
- when energy is low, only 18% (delta Evib/KbT=0.2) of total states are occupied.
- At high energy 98% of lowest energy states are occupied (delta Evib/KbT=4)
given the molecular mechanics master equation, describe what each term means (equation
given) - Answers - overall equation describes how a mechanical model can be applied to
Boltzmann temp scenario to determine potential energy of a system (Vtot) (single
configuration).
- 1st term: covalent bond stretching (diagram)
- 2nd: covalent angle stretching (diagram)
- 3rd: covalent dihedral stretching (diagram)
- 4th: Lennard jones potential (diagram)
- 5th: electrostatic energy (diagram)
- 6th: hydrogen bond interacting
describe the Lennard-jones potential energy function and contrast it with the hydrogen bonding
potential energy function. Explain how each depends on the inter-atomic distance - Answers -
the equations give potential energy associated with favorable interactions (figures!)
- GRAPHS! graphs show differences in how distance affects attraction and repulsion.
- H bonding has a narrower range than Lennard jones.
- H bonding has no charge-charge interaction
give the Nernst equation and define its parameters - Answers - equation (figures): allows you to
consider the structure of methane. why are the four sp3 hybridized orbitals separated as far as
they can be from one another? - Answers - draw methane with phi angle 109.5
- overlap integral: the phenomena of staying as separated as far apart as possible
- lower e- e- repulsion when doing this, more stable
briefly describe the two major techniques typically used to determine the structure of a
biological macromolecule? - Answers - x ray Crystallography: shooting specific wavelengths (10-
0.01nm) at a crystal lattice containing molecule. they hit and bounce off and are measured and
produce a globular shape using computers. the intensity of spots related to atomic arrangement,
position is related to unit cell arrangement, and the phase problem arrises from squaring
amplitude and losing phase.
- x ray lattice diagram
- Nuclear magnetic resonance: measuring orientation of a spin vector of an atom before and
after a radio frequency pulse. This gives hydrogen atom peaks and small atomic distances
between atoms of 5 angstroms.
- pulse x/y/z diagram
in a simple way, how is quantum mechanics used to determine the energy and structure of a
molecule? provide an explanation - Answers - key equation: schrodenger equation (hy=ey)
- hamiltonion operator: used to find lowest energy, finds the energy produced by a specific wave
function. describes various electron density clouds
- figure: real thing from wave function derivation
explain the significance of the schrodinger key equation. define the hamiltonion operator and
wave function. - Answers - significance: allows one to find the energy level of a system and use
the wave function to find probability of a particle in space/time
- wave function/the electron probability distribution function: (𝜓 ^2)𝑑 𝑉 =(𝜓 ^2)4𝜋 (𝑟 ^2)𝑑 𝑟 is
used to find these probabilities of electrons in space/time
- hamiltonion operator: produces the energy associated with a specific wave function/finds
structure based on lowest energy
write out/define boltzmanns distribution law and define all the parameters - Answers - the
probability that a molecule will be in a certain state, varies exponentially
- figure: equation 1 (is a canonical ensemble)
, - Ns: average over micro states in the canonical ensemble
- N: population of individuals
- -E(): energies of states ()
- Kb: boltzmanns constant
- T: temperature in Kelvin
- Z: the sum of exponentials corresponding to all possible states
what is the relation between probability of a given states and the corresponding energy? Hint:
what happens to the distribution when the energy is increased? - Answers - possibility of a given
states decreases exponentially as the energy of state R increases. This is because a single
higher energy state has few occupants then a lower energy state.
- when energy is low, only 18% (delta Evib/KbT=0.2) of total states are occupied.
- At high energy 98% of lowest energy states are occupied (delta Evib/KbT=4)
given the molecular mechanics master equation, describe what each term means (equation
given) - Answers - overall equation describes how a mechanical model can be applied to
Boltzmann temp scenario to determine potential energy of a system (Vtot) (single
configuration).
- 1st term: covalent bond stretching (diagram)
- 2nd: covalent angle stretching (diagram)
- 3rd: covalent dihedral stretching (diagram)
- 4th: Lennard jones potential (diagram)
- 5th: electrostatic energy (diagram)
- 6th: hydrogen bond interacting
describe the Lennard-jones potential energy function and contrast it with the hydrogen bonding
potential energy function. Explain how each depends on the inter-atomic distance - Answers -
the equations give potential energy associated with favorable interactions (figures!)
- GRAPHS! graphs show differences in how distance affects attraction and repulsion.
- H bonding has a narrower range than Lennard jones.
- H bonding has no charge-charge interaction
give the Nernst equation and define its parameters - Answers - equation (figures): allows you to
