Molecular Modeling Quizzes

Classically, particles have three well-defined quantities – what are these?

mass, location , speed

Waves do have a well-defined _________, __________, and _________ but not a well-defined ________ or _________

wavelength, frequency, speed, mass, location

What are the areas that we mentioned as applications of computational chemistry?

properties, processes, populations, and pictures

What is kinetic energy?

energy of motion

What is potential energy?

energy stored due to location

What is a dihedral angle?

the angle between two planes, where each plane is defined by three atoms

Which has a dihedral angle of 60°?

staggered conformation

What is the purpose of the clean button in GaussView?

it adjusts the geometry of the molecule to match chemical intuition

What is purpose of the symmetrize button in GaussView?

it imposes the maximum identifiable point group on the molecule

What does QSAR stand for?

quantitative structure-activity relationship

What is the key assumption in the QSAR approach?

the activity of a certain chemical compound is related to its structure

The key to the QSAR approach is that:

Human Experts identified links between structure and toxicity or other important functions

A “descriptor” in QSAR is:

a physical or chemical parameter of a molecule which is considered the independent variables

An “effect” in QSAR is:

the medicinal or chemical activity we seek to maximize or minimize and is the dependent variable

The algorithm in QSAR is:

the mathematical function that predicts the dependence of the effect on the descriptors

Validation of the QSAR model is:

testing the algorithm on new molecules with known descriptors and effects that were NOT used in the development of the algorithm

Types of descriptors include: (need to give just one of the examples below)

informational (MW, formula)

Why would you want to use QSAR compared to in vivo approaches?

Time, money, and ethics

How does a QSAR approach increase the possibility for innovation?

as we amass data on descriptors and effects QSAR will allow us to predict effects for millions of substances based on their descriptors, including molecules we are considering synthesizing

What equation does the Gaussian program solve for us?

Schrodinger equation

What are the three required inputs for the Gaussian program?

Molecular geometry, basis set, approximate scheme to solve the SE

What is a basis set?

Set of mathematical functions used to describe the electron distribution

Classical mechanics is governed by whose laws?

Newton’s laws

A characteristic phenomenon associated with waves that we mentioned in class is

Interference effects

Waves do have a well-defined ____________________________ but not a well-defined _______

Kinetic Energy, Position

Waves are described by a ____________________ represented by the symbol _____

Wave function, psi

The unique interpretation of quantum wave functions is that …

The particle is not in anyone place but has a distribution of positions given by psi²

What Do the symbols psi, and E represent in the Schrodinger equation?

Psi is the wave function, E is the total energy (kinetic + potential)

Which is more computationally more difficult to solve numerically for similar systems: the Schrodinger equation or Newton’s equations?

SE

What two things do you obtain when you solve the Schrodinger equation?

Psi, E

Once you have psi, you can …

Obtain all available information about the system

In our solution of the Schrodinger equation, the wave functions we obtain are standing waves, which means …

The are a repeated oscillation with no change in the shape of the electron probability distribution

State the uncertainty principle in words.

There is a limit to the precision of some simultaneously measured quantities, such as x, v_x

For systems with more than two interacting bodies, can an exact solution be found to either Newton’s equations or the Schrodinger equation?

Neither can be solved exactly

Classical mechanics is most appropriate for modeling …

Motion of nuclei and larger objects

Quantum mechanics is most appropriate for modeling …

Electrons

What physical parameter determines whether quantum mechanics is necessary in modeling the motion of a given system?  Explain.

The mass.  Large masses have smaller uncertainties, making classical mechanics more appropriate.

Does the MOE program use classical or quantum modelling?

Classical

The MOE program requires what two things?

The atomic positions and a force field

What is the mathematical form of an atomic 1s orbital?

Ae^-pr

Atomic orbitals are often referred to as _________________ orbitals

Slater

What is the mathematical for of a Gaussian orbital?

Ae^-αr²

Gaussian orbitals give a poor representation of atomic orbitals in two places. What are these?  Illustrate the problem with a graph (label the axes)

Very near and very far from the nucleus

What does it mean to refer to a function as a “tight” basis function?  What does this tell you about the magnitude of the Gaussian exponent (a)?

It means that the function dies off quickly as r increases due to a large value of alpha

What does it mean to refer to a function as a “diffuse” basis function?  What does this tell you about the magnitude of the Gaussian exponent (a)?

It means that the function dies off slowly as r increases due to a small value of α

What is a contracted Gaussian-type basis function and how does it improve on a single Gaussian function as a representation of a Slater orbital?

A contracted gaussian-type basis function is a fixed sum of gaussian functions and allows a better matching to a slater orbital.

Why is a contracted Gaussian-type basis function preferred over the same number of independent Gaussian functions?

While the UNCONTRACTED gaussians allow greater flexibility the cpu time for calculations scales as the number of independent basis functions raises to a power (the power is between 4 and 7).  A contracted basis function counts as only one independent function.

Enumerate the basis functions contained a minimum basis set for Al (note this should NOT include the 3d subshell as this is not occupied in the ground state of Al).

3s functions and 2 sets of p functions = 9

What are the two main drawbacks of a minimum basis set?

Lack of flexibility is in the size and shape of the electron distribution

Using a split valence basis set is a strategy used to overcome what insufficiency in a minimal basis set?

Inflexibility in size of electron distribution (not shape)

Using a polarization functions is a strategy used to overcome what insufficiency in a minimal basis set?

Inflexibility in shape of electron distribution (not size)

The prefix “aug” indicates that the basis set includes _________________________

One set of diffuse gaussian functions for each angular momentum present in the basis set.

An “aug” basis set might be used for modeling what two chemical situations?

Anions and excited states

Enumerate the functions contained in the aug-cc-pVQZ basis set for C.

1s for the core

4s and 4 sets of p for the valence

3 sets of d, 2 sets of f and one set of g for the polarization

One set of s, p, d, f, and g for the “aug”

Most basis sets are split valence but do NOT “split” the core.  Why is this a reasonable strategy?

We do not expect the core orbitals to change much as the chemical bonding environment changes.

There are three ways to indicate the presence of polarization functions in a basis set.  These are:

a “*”, the letter “p” and an angular momentum letter in parentheses after the basis set as in 6-31g(d)

What are the two ways to indicate the presence of additional diffuse functions in the basis set?

Aug or “+”