Week 2 - Molecular Forces Flashcards
What is a covalent bond?
when two atoms with unfilled electronic shells overlap, increasing the electron density, and forming a bond.
Is H+ or H2 more stable? and why?
H2 because it is covalently bonded with itself to make it nonpolar, therefor strengthening its stature among other molecules.
What is hydrogen bonding?
The force of attraction between a hydrogen atom in one molecule and a small atom of high electronegativity in another molecule; O, F, N.
Is hydrogen a proton donor?
Yes
What is Ionic bonding?
When atoms of opposite ionic charge attract each other by donating or receiving electrons (E.g. Na and Cl to form NaCl (sodium chloride)).
What is a polar covalent bond?
Where the pair of electrons is shared unequally between two attoms. - H2O: The electrons are unequally shared, with the oxygen atom spending more time with the electrons than the hydrogen atom.
What does the term dipole mean?
Dipoles occur when two atoms in a molecule have different electronegativity
What are Dipole-Dipole forces?
Dipole‐dipole forces are attractive forces between the positive end of one polar molecule and the negative end of another polar molecule.
What type of interaction does a hydrogen bond contain?
A hydrogen bond can be considered to be a type of dipole‐dipole interaction.
What are Van Der Waals forces?
These are weak forces between atoms and/or molecules that can either be attractive or repulsive.
What are Hydrophobic interactions?
Hydrophobic interaction involves bulk water molecules excluding non-polar molecules and is an affect of an increase in entropy rather than an effect of enthalpy.
Hydrophobic forces in combination with dispersion forces keep non-polar molecules together in water but a separate phase may form
What are some Biochemical examples of hydrophobic interactions?
- Cell membranes - Protein folding - Insertion of membrane proteins into the nonpolar lipid environment
What is an Ion-Induced dipole attraction?
When a permanent charge, or other dipole, induces polarization in another molecule. Results in electrostatic attraction between the permanent charge and the partial charges induced in the other molecules.
What type of interaction occurs between H and Cl?
Dipole-Dipole interaction, the positive end of the Hydrogen atom attracts the negative end of the Chlorine atom and influences the position.
Why do atoms or molecules interact?
Electrons distribute, and rearrange, within atomic and molecular orbitals to maintain a combination of the lowest possible potential energy and greatest dispersion of energy. This leads to greater stability.
Ethane is an example of what type of interaction?
A Covalent interaction
Why are covalent bonds important in biomolecules?
Essential in forming biomolecules and form the polymer ‘backbones’ of macromolecules from monomer units.
What is an Isomer?
Two or more compounds with the same formula but a different arrangement of atoms in the molecule and different properties.
What would be meant if a carbon was chiral?
That the Carbon was attached to 4 different groups. If you were to draw a mirror image of the molecule and it is the same, it would be ACHIRAL if it was different, it would be CHIRAL
What is a stereoisomer?
2 or more molecules that have the same chemical formula, the same connections, BUT the three dimensional configuration is different.
What are geometric (Cis-Trans) Isomers?
Double or triple bonds that prevent or restrict rotation of functional groups or hydrogen atoms around the bond. - Cis configuration: Functional groups and hydrogen atoms are of the same side of the double bond respectively. - Trans Configuration: Functional groups and hydrogen atoms are on opposite sides of the double bond respectively.
What are Chiral Isomers (enantiomers)?
- have a Non superimposable mirror image. - 4 Different types of atoms attached to the carbon atom - Same chemical properties but a difference in interactions.
Why are chiral isomers important?
Many interactions in biochemistry are stereospecific. For example: - Enzyme to substrate - Protein to Ligand Stereoisomers can elicit different biological responses.
What is the relationship between Stereoisomers and Configuration?
- A sterioisomer defines a particular configuration of the atoms. - Can only convert from one arrangement to another by breaking one or more covalent bonds.
What is Conformational Isomerism (Conformation)?
A form of stereoisomerism in which the isomers can be interconverted exclusively by ROTATIONS about formally SINGLE bonds.
What is polarity?
- An unequal distribution of electrons that causes slight differences in charge over throughout the molecule.
How is a dipole indicated between two atoms?
With an arrow pointing FROM the positive charge TOWARDS the negative charge.
What is a molecule with a permanent dipole moment known as?
A polar molecule.
How are permanent dipoles formed?
When there is a large difference in electronegativity between two atoms bonded together in a covalent bond. This causes the shared pair of electrons to be shared unequally. They are pulled towards the more electronegative atom.
True or False: Not all molecules that contain a polar bond are polar
True: They can be overall non-polar. Generally, a molecule needs to be asymmetric to have a dipole.
Are hydrocarbons polar or non-polar?
hydrocarbons are non polar. This is due to the hydrogen that is covalently bound to the carbon being non polar.
what are the two different types of Van Der Waals forces?
Repulsion interactions and dipole interactions
List the 4 main characteristics of covalent interactions
- Effective at small internuclear distances less than 2Å (2 angstrom = 0.2nm) - Electron clouds overlap, exchange, or share electrons between two particular atoms - Mainly intramolecular - Higher bond energy
List the 4 main characteristics of non-covalent interactions
- Effective up to 10Å or more but increases in strength at small distances between molecules - Little or no overlap, exchange, or sharing electrons between atoms - Mainly intermolecular - Lower bond energy
What is the “rough” strength of the bonds in kJ/mol for Non-Covalent, Ionic and Covalent bonds?
- Non-Covalent: between about 350 and 400kJ/mol - Ionic: About 250kJ/mol - Non-Covalent: Hydrogen bonds ~ 20, Dispersion ~ 2, and Dipole-Dipole ~ 2 (kJ/mol)
how are non-covalent bond interactions important when it comes to DNA?
Non-Covalent hydrogen bonds are important for helix base pairing in the DNA double helix.
How can Non-Covalent interactions be strong?
In quantity lots of non-covalent molecules can be collectively strong.
Do non-polar molecules increase or decrease macromolecular flexibility?
Increase
What does the term “Salt bridge” mean?
The attractive interaction between oppositely charged amino acids in a protein structure
How do you calculate the attractive or repulsive force between 2 charged atoms?
By using the Coulombs law equation: F = k q(one)q(two) / r^2
What is does Coulomb’s law calculate?
How strong the force will be between two electrostatic charges
what is the van der waal radius?
Van der Waals radii is the closest distance of approach for another atom with an atom (without electron clouds overlapping)
What happens to the van der waal radii in a covalent bond?
They overlap
What are dispersion forces?
weak Temporary attractions due to opposite charges induced in each molecule over relatively short distances
How are dispersion forces influenced?
- Shape of the molecule (E.g regular or planar shapes have greater dispersion forces due to more contact points) - Size of the molecule (E.g. Large molecules have more contact points than smaller molecules)
What is repulsion?
Electrostatic repulsion between molecules that prevents them from getting too close to each other
What is interaction is being demonstrated here?
Ion-Induced Dipole interaction; the Fe2+ molecule is a positive ion inducing the polerization (distortion of the electron cloud) of the O2 (nonpolar) molecule.
What interactions are being demonstrated by the blue dashes?
Hydrogen bonding
