Problem 1: Near infrared (NIR) fluorescence is used in tumor imaging due to high tissue penetration depth as well as low tissue autofluorescence in this EM band. One of the dyes, a squaraine KSQ-4-H, has two characteristic wavelengths: 760 nm and 812 nm. Which wavelength corresponds to the excitation frequency and which one to the emission frequency?
Answers:

• excitation 812 nm, emission 760 nm
• depends on the specific technique and the imaging equipment used
• emission 812 nm, excitation 760 nm

Problem 2: What is the main determinant of neutral atom repulsion at very short distances(much smaller than the sum of two van der Waals radii of two atoms)?
Answers:

• electrostatics
• dipole-dipole interaction
• entropic contribution
• Pauli exclusion principle

Problem 3: What is the formal charge of a hydrogen in ammonium cation (NH₄₎₊ ?
Answers:

• -1/4
• 0
• -1
• 1/4
• +1

Problem 4: Salbutamol, a short-acting β2-adrenergic receptor agonist used for the relief of bronchospasm in asthma, has an amine group with nitrogen attached to two carbons and two hydrogens. What is its formal charge?
Answers:

• +1
• 3
• +2
• -2
• -1
• 0

Problem 5: The electrostatic interaction energy of two charges at a distance of 4Å in water is approximately the same as the electrostatic interaction energy of the same charges at a distance of X in vacuum. Evaluate X:
Answers:

• 4.8 Å
• 8Å
• 160 Å
• 80 Å
• 32 nm
• 4*(80)^-½

Problem 6: Estimate the desolvation energy of a mole of ions with formal charge of 1 unit and the Born radius of 2A. Ions are transferred from water to a membrane (dielectric constant of 2). C = 332 (kcal A)(el.u)^-2 . Note that the desolvation and solvation are the opposite processes. (Hint, use the Born formula)
Answers:

• 90 kcal/mol
• -10 kcal/mol
• -80 kcal/mol
• -40 kcal/mol
• 10 kcal/mol
• -20 kcal/mol
• 20 kcal/mol
• 40 kcal/mol

Problem 7: The main determinant of the low drug permeation is the following energy term:
Answers:

• the torsion strain in the membrane
• entropic loss due to internal rotatable bonds
• the high number of hydrophobic atoms in a drug
• high positive desolvation energy of the charged and polar atoms
• electrostatic interactions of the drug charges with the lipid heads

Problem 8: Choose the right statement about the Lennard-Jones (LJ) potential:
Answers:

• LJ potential combines the entropic component related to water cage formation around hydrophobic substances with the favorable energy of solvation of polar and charge atoms
• LJ potential describes the atomic attracton at long distances due to Pauli exclusion principle in relation to water
• LJ potential describes the atomic repulsion at long distances due to electrostatic effect
• LJ potential combines the atomic attraction at short distances due to transient fluctuating dipoles with atomic repulsion due to the Pauli exclusion principle

Problem 9: An optimal van der Waals interaction between two carbon atoms is closer to the following range of values:
Answers:

• 100-400 kcal/mol
• 2-5 kcal/mol
• 0.01 cal/mol
• 30-40 cal/mol

Problem 10: The interaction of two neutral atoms with van der Waals radii of 1.6A at a distance of 3.8A can be best characterized as follows:
Answers:

• strong repulsion
• weak repulsion
• interaction energy exactly equal to zero
• attraction as (distance)^-2
• weak attraction