* not completed

. The dielectric constant of the common solvent acetonitrile is 37.5. What is the free energy of solvation of the formate anion HCOO^- in acetonitrile, assuming that it becomes solvated in a spherical cavity with radius 2.1 Å.

-322 kJ mol^-1 correct incorrect

-644 kJ mol^-1 correct incorrect

-161 kJ mol^-1 correct incorrect

-483 kJ mol^-1 correct incorrect

* not completed

. Which of the following pairs cannot usually be described in terms of a system:environment pair?

Solute:solvent correct incorrect

Defect:crystal correct incorrect

Active site:protein bulk correct incorrect

Reactant A:Reactant B correct incorrect

* not completed

. Which of the following acronyms does not describe a common method for predicting solvation free energies?

SMD correct incorrect

PCM correct incorrect

CCSD correct incorrect

COSMO correct incorrect

* not completed

. One of the simplest approaches for constructing hybrid methods is the subtractive approach, whereby the energy of the system formed by a core A and environment B is given by: V^HL(AB) = V^HL(A) + V^LL(AB) – V^LL(A). HL denotes a high-level of theory and LL a low level. This method can be very simple because:

Only three terms are needed in the energy expression, so the maths is very simple. correct incorrect

The low level of theory is used to describe the environment, unlike in other hybrid methods. correct incorrect

It only requires carrying out standard V^HL and V^LL calculations on A or AB. correct incorrect

* not completed

. In a typical QM/MM calculation in which the core region is treated with a QM method, with embedding in an MM environment described by point charges, which of the following effects is not included?

Polarization of the atoms of the core due to interactions with the environment. correct incorrect

Polarization of some of the atoms in the core region due to interactions with other atoms in the core. correct incorrect

Repulsion at short range between non-bonded atoms in the core and the environment. correct incorrect

Polarization of the atoms of the environment due to interactions with the core. correct incorrect

* not completed

. Consider a metal-phosphine complex [M]-PR₃, where R is the cyclohexyl group, and [M] denotes the metal together with ancillary ligands. If this complex is modelled using a hybrid QM-MM method in which for the QM calculations on the core the R group is replaced by H atoms, which of the following can be stated concerning the results?

The QM calculation will reflect the electronic structure expected for the PH₃ ligand, but perhaps perturbed by the fact that the molecular structure will reflect that expected for PCy₃. correct incorrect

PCy₃ ligands are very bulky and steric bulk is not well described by molecular mechanics. correct incorrect

This type of calculation is not at all useful nowadays, because PCy₃ ligands are small enough to be modelled with QM methods. correct incorrect

As a means of studying the electronic effect of the PCy₃ ligand, this calculation will not be successful as the calculated QM properties will be those expected for the PH₃ ligand. correct incorrect

* not completed

. The Cope rearrangement, in its simplest form, converts 1,5-hexadiene to an isomer of itself through a 6-membered ring TS. At the B3LYP/6-31G level of theory, the reactant and TS return energies of -234.5535 and -234.5054 hartree respectively, while B3LYP together with the SMD continuum solvent model, with parameters for acetonitrile, returns energies of -234.5594 and -234.5112 hartree respectively. What is the effect (in kJ mol^-1, 1 hartree = 2625.5 kJ mol^-1) of including the solvent on (a) the energy of the TS, (b) the activation energy?

(a) -15 kJ mol^-1 and (b) 0 kJ mol^-1. correct incorrect

(a) +15 kJ mol^-1 and (b) 22 kJ mol^-1. correct incorrect

(a) -45 kJ mol^-1 and (b) 5 kJ mol^-1. correct incorrect

(a) -125 kJ mol^-1 and (b) 12 kJ mol^-1. correct incorrect

* not completed

. Coarse-grained molecular mechanics models can be more easily evaluated as they involve fewer interaction sites. Consider modelling of a system using an all-atom MM model and a coarse-grained model. Assume that, in the coarse-grained model, on average 6 atoms are grouped together into one interaction site. Assuming that the number of energy terms varies as the square of the number of sites, what is the expected change in computational effort from the atomistic model to the coarse-grained one?

The calculation will be about 30 times faster with the coarse-grained model. correct incorrect

The calculation will be about six times faster with the coarse-grained model. correct incorrect

The coarse-grained and atomistic models will take roughly the same amount of time to evaluate. correct incorrect

The atomistic model will be roughly 30 times faster to evaluate than the coarse-grained model. correct incorrect

* not completed

. One way to treat an environment is to include relevant atoms in an all-atom model. Assuming the computational effort associated with a calculation (evaluating the energy + optimizing the structure) scales as the square of the number of atoms, what would be the effect of including histidine (CH₃C₃H₃N₂) and aspartate (CH₃CO₂^-) side chains in a calculation on an acetyl-coenzyme A model CH₃COSCH₃?

The calculation will be roughly three times slower. correct incorrect

The calculation will be roughly ten times slower. correct incorrect

The calculation will be roughly thirty times slower. correct incorrect

The calculation will be roughly a hundred times slower. correct incorrect

* not completed

. Which of the following chemical reactions would you expect to proceed much faster in a polar solvent than in vacuum?

Diels-Alder cycloaddition of a dienophile to butadiene. correct incorrect

Abstraction of a hydrogen atom from the methyl group in toluene by a chlorine atom. correct incorrect

S_N1 substitution of chloride in tert-butyl chloride. correct incorrect

Dissociation of a phosphine ligand PPh₃ from a metal site [M]. correct incorrect