8. Cytosine can act as a base and accept a proton to form the charged species shown below. Label the hydrogen bond donors (D) and acceptors (A) on the protonated cytosine. Then, draw the hydrogen bound dimer between neutral cytosine and the protonated cytosine.

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## Understanding Protonated Cytosine and Hydrogen Bonding

### Question 8
Cytosine can act as a base and accept a proton to form the charged species shown below. Label the hydrogen bond donors (D) and acceptors (A) on the protonated cytosine. Then, draw the hydrogen-bound dimer between neutral cytosine and the protonated cytosine.

### Protonated Cytosine Structure
Below is the chemical structure of protonated cytosine:

```
NH₂
 \ 
  C
  |  \
N=C   N^+
 |   /
C=O
 | 
 H
(Cytosine-H+)
```

### Explanation
Here is the step-by-step analysis of the molecule:

1. **Hydrogen Bond Donors (D)**:
    - These are typically hydrogen atoms attached to more electronegative atoms like nitrogen (N) or oxygen (O), which can participate in hydrogen bonding by donating their hydrogen.
    - In the given cytosine-H⁺ structure, hydrogen bond donors are hydrogens attached to nitrogen atoms or others suitably positioned in cytosine.

2. **Hydrogen Bond Acceptors (A)**:
    - These are atoms with lone pairs of electrons that can accept hydrogen bonds, typically nitrogen (N) or oxygen (O) atoms.
    - In the protonated cytosine, nitrogen and oxygen atoms with lone pairs can act as hydrogen bond acceptors.

### Labeling Donors and Acceptors:
- In the given molecule, label as follows:
    - The NH₂ group has two hydrogen atoms attached to nitrogen, which are hydrogen bond donors (D).
    - The nitrogen atom attached to the proton (N^+H) is a hydrogen bond donor (D) due to the newly added hydrogen.
    - The carbonyl oxygen (=O) and the nitrogen within the ring (not attached to H) are hydrogen bond acceptors (A) because they have lone pairs.

### Drawing the Dimer:
The diagram should show two cytosine molecules interacting through hydrogen bonds. One part of the diagram illustrates neutral cytosine; the other shows protonated cytosine. Ensure to clearly show the hydrogen bonds (typically represented by dotted lines) connecting donors (D) and acceptors (A).

For demonstrating hydrogen bonding in the dimer form:
- Highlight the hydrogen bond interactions between:
    - The amine group (NH₂) of
Transcribed Image Text:## Understanding Protonated Cytosine and Hydrogen Bonding ### Question 8 Cytosine can act as a base and accept a proton to form the charged species shown below. Label the hydrogen bond donors (D) and acceptors (A) on the protonated cytosine. Then, draw the hydrogen-bound dimer between neutral cytosine and the protonated cytosine. ### Protonated Cytosine Structure Below is the chemical structure of protonated cytosine: ``` NH₂ \ C | \ N=C N^+ | / C=O | H (Cytosine-H+) ``` ### Explanation Here is the step-by-step analysis of the molecule: 1. **Hydrogen Bond Donors (D)**: - These are typically hydrogen atoms attached to more electronegative atoms like nitrogen (N) or oxygen (O), which can participate in hydrogen bonding by donating their hydrogen. - In the given cytosine-H⁺ structure, hydrogen bond donors are hydrogens attached to nitrogen atoms or others suitably positioned in cytosine. 2. **Hydrogen Bond Acceptors (A)**: - These are atoms with lone pairs of electrons that can accept hydrogen bonds, typically nitrogen (N) or oxygen (O) atoms. - In the protonated cytosine, nitrogen and oxygen atoms with lone pairs can act as hydrogen bond acceptors. ### Labeling Donors and Acceptors: - In the given molecule, label as follows: - The NH₂ group has two hydrogen atoms attached to nitrogen, which are hydrogen bond donors (D). - The nitrogen atom attached to the proton (N^+H) is a hydrogen bond donor (D) due to the newly added hydrogen. - The carbonyl oxygen (=O) and the nitrogen within the ring (not attached to H) are hydrogen bond acceptors (A) because they have lone pairs. ### Drawing the Dimer: The diagram should show two cytosine molecules interacting through hydrogen bonds. One part of the diagram illustrates neutral cytosine; the other shows protonated cytosine. Ensure to clearly show the hydrogen bonds (typically represented by dotted lines) connecting donors (D) and acceptors (A). For demonstrating hydrogen bonding in the dimer form: - Highlight the hydrogen bond interactions between: - The amine group (NH₂) of
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