Introduction to Chemical Dynamics and Molecular Bonding

Basic chemical dynamics are essential for understanding human biology and the interaction between biological systems and drugs.
Melanoma, a form of skin cancer, is a focus of modern research regarding biological molecules.
mRNA technology, while famously used in vaccines, is being adapted for cancer treatments. There are successful studies and clinical trials indicating that cancer vaccines using mRNA molecules and delivery systems can prevent melanoma from recurring.

Atoms are composed of a nucleus containing protons and neutrons, surrounded by electron shells.
Protons carry a positive charge, while electrons carry a negative charge.
An atom with a positive charge contains more protons than electrons.
Electrons represent a negative charge; therefore, the balance between protons and electrons determines the overall charge of an atom.

Electrons exist in specific orbitals within shells surrounding the nucleus.
There are exactly two electrons per orbital.
Shell capacities follow a specific hierarchy:
- First Shell: Contains $1$ orbital, holding a maximum of $2$ electrons.
- Second Shell: Contains $4$ orbitals, holding a maximum of $8$ electrons.
- Third Shell: For introductory purposes, this is considered to have $4$ orbitals, holding $8$ electrons.

The valence shell is the outermost shell of any atom.
Valence electrons are the electrons located in the outermost shell and are the primary determinants of how an atom interacts and bonds with other atoms to form molecules.
Atoms are most stable when their valence shell is completely filled.
Unfilled valence shells drive atoms to seek bonds with other atoms to achieve stability.

Hydrogen ( $H$ ): Consists of one shell with one electron. Because the first shell requires $2$ electrons to be full, hydrogen needs $1$ additional electron to achieve stability.
Carbon ( $C$ ): A fundamental element of life. Carbon has $4$ electrons in its second shell. Since the second shell consists of $4$ orbitals (requiring $8$ electrons total), carbon needs $4$ more electrons to be complete and stable.
Group 7 Elements: These atoms have $7$ electrons in their outer shell and require only $1$ additional electron to be filled.
Inert Gases (Noble Gases): These are located in the last column of the periodic table. They are highly stable and "inert" because their valence shells are already complete.

The behavior of the outer portion of an atom determines chemical reactivity, including how combinations happen, how molecules break apart, and the speed of reactions.
Reactants: The substances or "ingredients" used at the beginning of a chemical reaction.
Products: The results or substances formed by the chemical reaction.
Example Reaction: The breakdown of hydrogen peroxide ( $H_2O_2$ ) results in the products water ( $H_2O$ ) and oxygen ( $O_2$ ).

Chemical bonding is classified into three primary types based on the interaction of electrons and electrostatic forces.

Definition: An exchange where one atom gives up one or more electrons to another atom.
Memory Cue: "Give and Take."
Example: Sodium Chloride ( $NaCl$ ), commonly known as table salt.

Definition: Atoms share pairs of electrons to form stable molecules. This is the primary bond type for building complex biological molecules.
Memory Cue: "Share."
Double Bonds: Occur when two pairs of electrons are shared between atoms, often represented by double lines in chemical diagrams (e.g., $O=O$ in an oxygen molecule, $O_2$ ).
Example: Water ( $H_2O$ ).

Definition: Not a true bond, but an attraction or interaction between molecules caused by electromagnetic charges. It is similar to the pull between two opposite poles of magnets.
Memory Cue: "Attract."
Significance: Critical for the existence of life. Without hydrogen bonding, water and gases necessary for survival would not behave as they do.
Water Expansion: Water expands when it freezes because hydrogen bonds organize into a crystallized structure.
Biological Context: The human body is composed of approximately $85\%$ water.

The way chemicals are ingested and processed in the body is determined by molecular bonding.
Drugs enter the bloodstream and bind to specifically shaped receptors (docking points) on the outside of cells, creating a drug-receptor complex that elicits a biological response.

Transient (Short-term) Responses: Most medications taken daily (e.g., for chronic conditions) do not form covalent bonds. They rely on weaker interactions like hydrogen bonds or ionic bonds. This allows the effect to wear off, requiring subsequent doses.
Irreversible (Long-term) Responses: These involve covalent bonding, where the drug sticks to the target indefinitely.
- Antibiotics: Drugs like Penicillin form strong bonds to kill bacteria. If an antibiotic course (e.g., $7$ or $10$ days) is not finished, resistant bacteria survive and multiply, leading to antibiotic resistance.
- Nerve Gas: Functions as a bioweapon by forming irreversible covalent bonds that stop bodily functions.
- Anti-cancer Drugs: Often designed to covalently bond to cancer cells to ensure they are destroyed.

Polar Covalent Bonds: Occur when electrons are shared unequally between atoms because one atom is "greedier."
Electronegativity: The scientific term for an atom's tendency to attract electrons.
Example of Polarity: In water ( $H_2O$ ), oxygen is more electronegative than hydrogen. Oxygen pulls the shared electrons closer to itself, gaining a slight negative charge, while the hydrogens becomes slightly positive.

Question: How does a hydrogen atom achieve stability?
Answer: It is missing one electron because there is only one orbital in the first shell, which requires two electrons to be full.
Question: What subatomic particle has a positive charge?
Answer: Protons.
Question: Does an atom with a positive charge have more electrons than protons?
Answer: No, it has more protons than electrons.
Question: Why do we care about what is on the outside of an atom?
Answer: Because it determines how different chemicals react, what combinations happen, and how quickly reactions occur.
Question: What kind of bond exists between a drug and its target if the effect is short-term?
Answer: Likely ionic or hydrogen bonds (hydrostatic interactions), as they are not permanent like covalent bonds.
Class Exercise: Students were asked to rank the four most common elements in living organisms (found in previous notes) from highest to lowest electronegativity for the next session.