Atomic Structure and Chemical Bonds

Atoms serve as the fundamental building blocks for all matter in the Universe.
An atom is composed of three primary constituent subatomic particles: electrons, protons, and neutrons.
Electrons: These are negatively charged particles. They are the smallest of the three subatomic particles and are located within orbitals residing in electron shells.
Nucleus: Positioned at the center of the atom, the nucleus typically contains an equal number of protons and neutrons.
Protons: These particles carry a positive charge and are found within the nucleus.
Neutrons: These particles carry no electrical charge and are also found within the nucleus.

Atomic Number: Defined as the total number of protons in the nucleus of an atom.
Atomic Mass Number: Defined as the sum of the number of protons and the number of neutrons ( $\text{Atomic Mass} = \text{Protons} + \text{Neutrons}$ ).
Relative Mass:
- The mass of an electron is effectively $0$ .
- The mass of a proton is $1$ .
- The mass of a neutron is $1$ .
Charge Neutrality: For any given neutral atom, the number of protons is exactly equal to the number of electrons.
Biological Significance: The specific structure and behavior of constituent atoms determine the overall structure and functions of biological molecules.
The Hydrogen Case: A hydrogen atom has an atomic mass of $1$ . It contains $1$ proton and $1$ electron, but contains zero ( $0$ ) neutrons.

Orbital Definition: An orbital is the specific physical region or space where there is a high probability of an electron being present.
Capacity: Any single orbital can be occupied by a maximum of $2$ electrons.
Energy Levels: Orbitals exist at various energy levels. The lowest possible energy level is known as the ground state.
Orbital Types:
- The s orbital has the lowest energy and is represented by sharp spectroscopic lines.
- The p orbital follows the s orbital in energy level and is represented by principle spectroscopic lines.

Innermost Shell (First Shell): Contains exactly one orbital, identified as the $1s$ orbital. It can hold a maximum of $2$ electrons.
Second Shell: This shell contains four orbitals in total:
- One $2s$ orbital.
- Three $2p$ orbitals, specifically designated as $2p_x$ , $2p_y$ , and $2p_z$ .
- Each of these four orbitals can hold $2$ electrons, totaling a maximum capacity of $8$ electrons for the second shell.
Third Shell: Consists of four orbitals, including one $3s$ orbital and three $p$ orbitals.

Hund's Rule: In orbitals of the same energy (also called degenerate orbitals), electrons will occupy each orbital singly before any pairing occurs in a half-filled orbital.
Ground State Behavior: Atoms at ground states prioritize having as many unpaired electrons as possible.
Electron Repulsion: Because electrons are negatively charged, they attempt to stay as far apart as possible within orbitals before being forced to pair up.
Valence Electron Examples:
- Carbon: Possesses four valence electrons.
- Nitrogen: Possesses three valence electrons and one lone pair (a pair of unshared electrons).

A chemical bond is the attraction between atoms that leads to the formation of a chemical compound or molecule consisting of two or more atoms.
Bonds are driven by electrostatic forces of attraction between opposite charges. This occurs either between electrons and protons in the nucleus or through dipole attractions.
Chemical bonds are categorized into two major classes:
1. Covalent bonds.
2. Non-covalent bonds.

Definition: These bonds result from the equal sharing of electrons between two atoms.
Single Covalent Bond: Represents the sharing of two valence electrons, typically contributed by two different atoms.
Bond Stability: Covalent bonds are characterized by high stability. The energy required to break them significantly exceeds the thermal energy available at room temperature ( $25\,^\circ\text{C}$ ) or human body temperature ( $37\,^\circ\text{C}$ ).

Hydrogen ( $H_2$ ): Contains a single covalent bond where two electrons are shared equally ( $H:H$ or $H-H$ ).
Methane ( $CH_4$ ): Features four separate single covalent bonds. Each hydrogen atom shares one pair of electrons with a central carbon atom ( $C:H$ or $C-H$ ).
Ethylene ( $C_2H_4$ ): Contains a double covalent bond ( $H_2C=CH_2$ ), which involves the sharing of two pairs of electrons between the two carbon atoms.
Molecular Nitrogen ( $N_2$ ): Features a triple covalent bond. In this molecule, three pairs of electrons are shared between the two nitrogen atoms, while each nitrogen atom retains one unshared pair of electrons (a lone pair).
Water ( $H_2O$ ): Formed when two hydrogen atoms each share their single electron with one oxygen atom, resulting in two single covalent bonds.
Carbon Dioxide ( $CO_2$ ): Formed when one carbon atom shares two electrons with each of two oxygen atoms. This results in four covalent bonds total, structured as two double bonds ( $O=C=O$ ).

There are four primary types of noncovalent interactions found in biological systems:

Formation: Formed by the attraction of atoms or groups of atoms with opposite charges.
Ions: Atoms that have gained or lost one or more electrons, resulting in a net electrical charge.
Cations: Positively charged ions that are attracted to a negatively charged cathode in an electric field.
Anions: Negatively charged ions that are attracted to a positively charged anode in an electric field.
Structure: Every ionic bond requires at least one cation and one anion.
Example: Sodium Chloride ( $NaCl$ ). Sodium (atomic number $11$ ) forms an ionic bond with Chlorine (atomic number $17$ ).

Mechanism: This is an interaction between a partially positively charged hydrogen atom in a dipolar molecule (such as water) and the unpaired electrons of another atom.
Types: Can be intramolecular (within the same molecule) or intermolecular (between different molecules).
Connectivity: While hydrogen usually forms a covalent bond with only one atom, it can form temporary hydrogen bonds with multiple others.
Water Properties: In liquid water, molecules form a dynamic network of temporary hydrogen bonds. This interaction also occurs between water and peptide or carboxyl groups, explaining the high solubility of organic acids and polypeptides.

Mechanism: Weak, nonspecific attractive forces that occur when any two atoms closely approach one another.
Origin: Caused by temporary and random fluctuations in electron distribution, leading to temporary unequal charges.
Applications: These interactions underlie the attraction between molecules in nonpolar solids and liquids, such as long-chain biological molecules that cannot participate in ionic or hydrogen bonding.

The Hydrophobic Effect: Nonpolar molecules or nonpolar regions of molecules tend to aggregate when placed in water.
Driving Force: By aggregating their hydrophobic surfaces together, nonpolar molecules require less water to surround them. This leads to the spontaneous formation of aggregates.
Solvency: Nonpolar molecules dissolve in nonpolar solvents due to the hydrophobic interactions established between the solute and the solvent.