Chemical Bonds and Molecular Conformation

Chemical Bonds

• Chemical bonds involve atoms combining to form chemical compounds, bringing stability to the resulting product.
• There are two main types of chemical bonds:
  • Ionic bonds: form when valence electrons are completely removed from an atom and "donated" to the neighboring atom.
  • Covalent bonds: typically have various amounts of flexibility, allowing for movements such as free rotation, bending, compression, extension, and twisting.

Movement in Chemical Bonds and Molecular Conformation

• Forces causing molecule motions can balance restoration force, resulting in atom vibration and various vibrational states with specific frequencies for covalent bonds.
• Bond movements can also allow for multiple paths between two different conformations.
• There are two ways to move from conformation A to conformation B:
  • Through free rotation of the bond between atoms.
  • Through bending.

Forces Affecting Conformation in Biomolecules

• The forces affecting biomolecule conformation are electrical, resulting from charges' attraction or repulsion.
• These forces are manifestations of electromagnetic force generated by protons and electrons in biological molecules.
• Van der Waals forces, other than covalent and ionic bonds, play the largest role in molecular associations, while forces within the molecule indirectly influence conformation.
• Charge-Charge Forces:
  • The force between two electrostatic charges is defined by Coulomb's law.
  • The force F, two charges q1 and q2, distance r, and a constant ke are all crucial factors in a vacuum model.
• Dipole Forces:
  • An electric dipole is defined as two equal and opposite charges separated by a fixed distance.
  • The dipole moment is equal to the magnitude of the charge at one end of the dipole, times the fixed distance between the two charges.

Charge-Dipole Forces

• The potential energy between an ion and a dipole is the sum of the potential energy between the ion and the charges in the dipole.
• It depends on the dipole's orientation relative to the charge and is inversely proportional to the square of the distance between the charge and the dipole.
• The potential energy decreases faster with distance in charge-dipole interactions.

Dipole-Dipole Forces

• The main differences between charge-dipole interactions and dipole-dipole interactions are:
  • Two dipoles interact, resulting in four charges compared to three in a point charge and a dipole.
  • Each dipole has two different angles, unlike a single angle in the orientation between a point charge and a dipole.
• The potential energy function, F(a1, b1, a2, b2), is a function of four angles a1, b1, a2, b2.
• It decreases with distance cube, square, and charge-charge interactions, indicating that more charges have a higher power on the inverse relationship with distance and shorter interaction range.

Hydrogen Bonds in Water

• Water is a highly polar molecule, with a permanent dipole.
• Oxygen atom is partially negative, and hydrogen is partially positive.
• Molecules of water are V-shape, with an unsymmetrical shape and unequal sharing of electrons between the atoms.
• Hydrogen bonds are crucial for preserving the three-dimensional structures of proteins and nucleic acids.

Hydrophobic and Hydrophilic Interactions

• Hydrophobic interactions:
  • Are interactions between water and a non-polar substance.
  • Don't involve a single, physical force.
  • Also called hydrophobic forces.
• Hydrophilic interactions:
  • Easily hydrogen bond with water.
  • Create an attractive force between the hydrophilic structure and water.
• Amphipathic or amphiphilic molecules:
  • Are both hydrophobic and hydrophilic.
  • Examples include phospholipids, which make up the membrane of cells.