BCH 330 Exam 2 questions with answers

BCH 330 Exam 2 questions with answers
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Consider the structure of methane. Why are the four sp3
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hybridized orbitals separated as far as they can be from one
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another? - CORRECT ANSWERS ✔✔- bond angle is 109.5 degrees
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- drawing of sp3 hybridized methane
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- an atom will exist in the lowest energy state with the greatest
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frequency
- the most relaxed state will occur with the highest probability
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- repulsive force
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Briefly describe the two major techniques typically used to
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determine the structure of a biological macromolecule. -
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CORRECT ANSWERS ✔✔- nucelar magnetic resonance (NMR)
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- nuclear overhauser effects (NOE)
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- distance between to protons using the transfer of resonant
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energy
- graph of dampened sine wave
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- graph of excited vector + transmitter cell
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- x-ray crystallography
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- x-rays scattered through a protein crystal
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- constructive and deconstructive interference is an additive
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scale and isn't absolute
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- drawing of light wave hitting and scattering on a lattice
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structure

,In a simple way, how is quantum mechanics used to determine
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the energy (and structure) of a molecule? Provide an explanation.
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- CORRECT ANSWERS ✔✔- HY = EY
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- the lowest energy state has the highest probability
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- how to calculate the lowest energy
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Explain the significance of the key general equation. Define the
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Hamiltonian operator and wavefunction. - CORRECT ANSWERS |\ |\ |\ |\ |\ |\ |\


✔✔- HY = EY |\ |\ |\




- Schrodinger equation predicts the most probably structure
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- find the lowest energy state, most probable
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- electron probability distribution
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- the variables are each a matrix defining all points in space
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because they can all potentially hold an atom or bond|\ |\ |\ |\ |\ |\ |\ |\ |\




Write out the Boltzmann's distribution law and define all the
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parameters. - CORRECT ANSWERS ✔✔- state equation |\ |\ |\ |\ |\ |\




- state purpose of equation
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- connection to equilibrium constant k
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- states occupied based on energy available
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What is the relation between probability of a given state and the
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corresponding energy? (Hint: what happens to the distribution |\ |\ |\ |\ |\ |\ |\ |\


when energy is increased?) - CORRECT ANSWERS ✔✔- as
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probability of state (S) increases, probability of states (R) |\ |\ |\ |\ |\ |\ |\ |\ |\


decrease

, - lowest energy states are the most stable and the most likely to
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be occupied
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- deltaEvib/KbT
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- total vibrational states are exhibited
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- distribution is greater when energy is increased
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- lower energy to fight random walk and can't get molecules into
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or out of pocket states
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Given the molecular mechanics master equation, describe what
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each term means. - CORRECT ANSWERS ✔✔- define Vtot
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- first chunk is potential energy of bonds stretching
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- second chunk is bent angles/bond bending
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- third chunk is dihedral angles
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- fourth chunk is Van der Waals interaction energy
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- q is charge
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- the last chunk is hydrogen bonding
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Describe the Lennard-Jones potential energy function and
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contrast it with the hydrogen bonding potential energy function.
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Explain how each depends on the inter-atomic distance. -
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CORRECT ANSWERS ✔✔- Lennard-Jones potential energy function
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- VLJ = E4Eij[(oij/rij)12-(oij/rij)6]
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- Van der Waals interactions
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- hydrogen bonding potential energy
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- exponent is larger
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- atoms must be closer to experience the force
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