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Tutor profile: Maria D.

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Maria D.
Undergraduate Neuroscience and Chemistry Student at Emory University
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Questions

Subject: Organic Chemistry

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Question:

The gauche conformation for 1,2-difluoroethane is more stable than the anti conformation by about 3 kJ/mol. Why?

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Maria D.
Answer:

The gauche conformation of 1,2-difluoroethane has the dihedral angle between the two fluorine atoms at 60 degrees apart, while the anti conformation has them at 180 degrees apart. A steric effect would predict the fluorine atoms to be anti to each other to minimize atomic repulsion. But since the gauche conformation is shown to be more stable than anti, clearly sterics is not playing a role here. This calls into an electronic effect from the overlapping of molecular orbitals. If the gauche conformation is favored, this suggests a HOMO/LUMO overlap is being achieved that isn’t possible in the anti conformation. The orbital overlap must be between the LUMO, a σ* , of one carbon bond and the HOMO, a σ bond, of the other. In the gauche conformation, the fluorine is anti to a hydrogen bonded to the other carbon. So the back-lobe of a σ bond, the electron donor, can overlap with the empty σ* of the neighboring carbon. Between the σ C-F and σ C-H bonds, due to fluorine’s maximum electronegativity, the σ* C-F bond would be a significantly lower LUMO than σ* C-H. This fits with how fluorine holds onto its electrons tighter, so it is a better electron acceptor than a hydrogen, but electrons in the σ C-F bond would be less likely to delocalize to donate electrons. This means the best energy match for orbital stabilization is between the σ* C-F LUMO and σ C-H HOMO, with a π overlap achieved. I really recommended drawing the orbitals and MO diagram out to visualize this.

Subject: Basic Chemistry

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Question:

Why doesn’t carbon hybridize it’s orbitals into s2p to make stronger bonds with better overlap?

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Maria D.
Answer:

It’s true the more s character a bond has, the stronger the bond would be due to larger orbital overlap and electron localization between two positively charged nuclei. However, carbon has only one valence 2s atomic orbital, while its 2p subshell has 3. A s2p hybrid orbital would be ⅔ of the s orbital and ⅓ of each p orbital, so not enough s would remain to make another bond. This prevents carbon from bonding with more than one atom. In the same way, carbon can make 4 sp3 hybridized orbitals since ¼ of s and ¾ of each p orbital is used per hybrid. Multiplying by 4 gives a s to p ratio of 1:3, which matches the number of atomic orbitals in the s and p subshells. In a sp2 hybridized carbon, there’s ⅓ s character and ⅔ p character. This means carbon can make 3 sp2 hybridized orbitals, since multiplying by 3 gives a 1:2 ratio between s and p, leaving one p orbital unhybridized and available to form a π bond. The number and type of bonds an atom can make is determined by the amount of hybridization between atomic orbitals.

Subject: Biology

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Question:

How did scientists determine three nucleotides encode an amino acid?

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Maria D.
Answer:

This was an interesting experiment done in 1961 by Francis Crick (DNA double-helix guy), Sydney Brenner, and others. There are 20 amino acids directly coded for in the human genetic code for protein production, but only 4 nitrogenous bases. In a Goldilocks fashion, scientists knew one nucleotide wouldn’t be enough, since one nucleotide per amino acid can only make 4 amino acids. A doublet code of two nucleotides per amino acid can make 16 amino acids, as any 4 of the nitrogenous bases can be used for either of the two positions, 4 X 4, or 4 squared, gives 16 possible permutations. For this experiment, the T4 bacteriophage, a bacteria-infecting virus, was injected into E. coli bacteria. To settle on the magic number 3, the group did a series of frameshift mutations on the viral DNA sequence. Recall a frameshift mutation involves changing the nucleotide base sequence on DNA so the reading frame for protein translation on RNA shifts. The team made a single base mutation, resulting in a deactivated infectional protein. They then introduced a single frame-shift mutation later on to re-establish the original reading frame. The researchers found when they corrected for a three nucleotide reading frame, a functional protein was produced so the bacteria got infected. Adding or deleting 3 neighboring base pairs could still produce a functional protein, and only non-triplet nucleotide mutations deactivated the protein. This was the first study to show a DNA or RNA nucleotide triplet encodes one amino acid, now referred to as a codon.

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