BCH 330 TEST 2 QUESTIONS & ANSWERS
Consider the structure of methane. Why are the four sp3 hybridized orbitals separated
as far as they can be from one another? - answer -- 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? - answer -- 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 - answer -- 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. - answer -- 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)𝑑𝑉=(𝜓^2)4𝜋(𝑟^2)𝑑𝑟 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 - answer --
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? - answer
-- 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) - answer -- 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 - answer -- 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 - answer -- equation (figures):
allows you to calc delta g from delta e, which are both potential energies.
- g: gibbs free energy
- n number of electrons transferred
- f: faradays constant (converts voltz to j/mol)
- delta e prime: standard state reduction potential, units: voltz
- a different nernst equation is used to calc delta e
- equation 3, circled
Given the following equation: w(theta)=eq1(cos(theta)op-cos(theta)cl)=(-psi q 1/d) delta
cos (theta), how could the work of an applied electrostatic field be minimized. - answer
-- decrease l of dipole, decrease membrane thickness d, decrease delta cos theta,
increasing voltage psi, - work is minimized when zeff is + and q is -
A linear dna polymer that aligns parallel to a magnetic field is considered to be in state
s. Assume that state r represents all possible states of orientation in space. Using the
equation for the boltzmann distribution: (given equation) explain what you expect to
Consider the structure of methane. Why are the four sp3 hybridized orbitals separated
as far as they can be from one another? - answer -- 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? - answer -- 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 - answer -- 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. - answer -- 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)𝑑𝑉=(𝜓^2)4𝜋(𝑟^2)𝑑𝑟 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 - answer --
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? - answer
-- 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) - answer -- 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 - answer -- 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 - answer -- equation (figures):
allows you to calc delta g from delta e, which are both potential energies.
- g: gibbs free energy
- n number of electrons transferred
- f: faradays constant (converts voltz to j/mol)
- delta e prime: standard state reduction potential, units: voltz
- a different nernst equation is used to calc delta e
- equation 3, circled
Given the following equation: w(theta)=eq1(cos(theta)op-cos(theta)cl)=(-psi q 1/d) delta
cos (theta), how could the work of an applied electrostatic field be minimized. - answer
-- decrease l of dipole, decrease membrane thickness d, decrease delta cos theta,
increasing voltage psi, - work is minimized when zeff is + and q is -
A linear dna polymer that aligns parallel to a magnetic field is considered to be in state
s. Assume that state r represents all possible states of orientation in space. Using the
equation for the boltzmann distribution: (given equation) explain what you expect to
