Molecular Modeling

What is a “polarization” basis set?

adding the next function up (d-function to p-block)

How does the use of polarization basis set allow calculations to reflect actual electron behavior in molecules and ions?

move the electrons off the nucleus which is more accurate and can improve the molecular models

what are “diffuse functions”

made up functions that describe the electrons far from the nucleus that the gaussians can’t accurately describe

Why are diffuse functions added to basis sets?

added to improve electron descriptions for more accurate calculations

How is a basis set containing diffuse functions denoted?

with a + plus

What is the difference between * and **

one indicates the addition of polarization to basis set only to heavy atoms while the other indicates polarization is added to all atoms

what does 6-311+G** mean

split valence basis set with 3 orbitals. 3 contracted, 1 diffuse, and 1 intermediate. 6 guassians used for core electrons. + is adding diffuse functions then both ** indicates polarization to all atoms

How are molecular orbitals obtained in quantum mechanics calculations?

by combining atomic orbitals to create the molecular orbitals

what is a “basis set”?

electron description in a wave function

What are slater Type orbitals

orbitals produced from atomic functions obtained from solution of 1 electron shrodinger equation (s,p,d)

describe two ways that the Gaussian function differs from Slater Type Orbitals

very far from the nucleus and very near the nucleus

given these differences where might the use of Gaussian functions introduce error in quantum calculations?

for core electrons and for anions and etc.

what does STO-3G stand?

slater type orbitals -3 gaussians

Describe the STO-3G

three gaussian functions to describe slater type orbitals

The STO-3G basis set is a “minimal” basis set. What does this mean?

using only as many functions as needed to represent valence and core shells

what are the two major shortcomings of a minimal basis set?

sum of minimal basis set in a sphere. sum of minimal basis set is nuclear-centered

what is a “split-valence” basis set?

splitting every valence shell in 2

what is meant by “contracted” or a “diffuse” orbital

a condensed orbital or a spread orbital

How does the split-valence basis set address one of the shortcomings of a minimal basis set?

gets rid of the spherical symmetry

What magnetic property arises when a molecule or ion has unpaired electrons?

magnetic susceptibility

Does the electron dot structure of oxygen predict that it will be paramagnetic of diamagnetic?

diamagnetic

What are the basic tenets of the molecular orbital model?

Adjacent atomic orbitals combine and make MOs. MOs only form from AO with approximately similar energies and symmetry. there are bonding, antibonding, and non-bonding MO.

What is a MO diagram?

a diagram that shows how e- are distributed in orbitals.

what is a “bonding” MO? How is it characterized?

attractive form between nuclei. characterized by lower energy than the AOs from which the electrons come from?

what is an “anti-bonding” MO? how is it characterized?

repulsive force between nuclei. characterized by higher energy then the AOs from which the electrons came from. nodal plane.

what is a nonbonding molecular orbital? how is it characterized

like lone pairs. characterized by being comparable energies to the original AOs the electrons were originally pulled from. centered on an atom.

according to MO model, why would H2 form but He2 would not

the first is lower in energy than the original atoms alone and the second is higher in energy than the original atoms alone.

How would a MO diagram demonstrate a paramagnetic molecule?

by having at least one MO with an unpaired electron

Experimentally, how do we know that the ordering of the MOs is different for N2 than O2

photoelectron spectroscopy

What property of O2 does the MO model get right that the other models fail to predict

the proper magnetism

What is a LUMO

the lowest unoccupied molecular orbital

what information does the LUMO provide?

what spot can accept an electron. ability to accept an electron

What is a HOMO

highest occupied molecular orbital

What information does the HOMO provide?

where donated electrons come from

What would happen to the bon length if an electron were removed from an antibonding orbital forming a cation.

would get shorter

what would happen to the bond length if an electron were removed from a bonding orbital forming a cation?

would get longer

What are conformations?

2 different structures for the same molecule

will two equilibrium geometry calculations always result in the same structure

no, they could have different starting structures with different minimums

What is the difference between a global minimum and a local minimum

the first is an overall minimum. the second is the minimum in that area

What is a single point energy calculation

you build and calculate without changing the geometry

why does the time taken to perform a single point energy calculation scale more linearly than a geometry optimization as the number of atoms

for the first, it only matters that you’re adding an atom so it is linear. The second adds multiple degrees of freedom per atom which is why its not linear

What is symmetry?

when there is a line of symmetry on a molecule’s connectivity

why does invoking symmetry decrease the time it takes for a calculation to finish?

it forces certain points to be the same

What is a geometric constraint?

a constraint that usually applies that a certain measure should be applied to another as well

When would a geometric constraint be used?

when you just want to calculate what the molecule you’ve drawn’s energy is

What is a potential energy surface?

graph of potential energy of a molecule at different lengths/angles/dihedrals

what is meant by geometric degrees of freedom

length, angle, or dihedral angle

What is an energy gradient?

the slope of the line tangent to the potential energy surface.

What determines the magnitude of the energy gradient?

how fast the potential energy changes, slope

How does a modeling program locate an energy minimum?

taking small steps to find lower energy until no possible step brings energy down

what is meant by “convergence”

converging on a minimum single, stable structure

Why do the calculations for some species have difficulty converging?

can happen by characterizing unstable molecules with shallow, broad potential energy surfaces

What can be done to improve the chances of convergence of a high-energy species

taking bigger steps

why does the time it takes to perform an equilibrium geometry optimization scale exponentially as the number of atoms increases?

exponentially increasing energy and degrees of freedom

what are the typical parameters used in molecular mechanics?

length at equilibrium, bond angle at equilibrium, dihedral angle at equilibrium, spring constant, and size of molecules

What is the primary molecular mechanics model used in spartan

SYBL and MMFF (mainly MMFF)

Why SYBL and MMFF molecular mechanics methods yield different results for the energy of a molecule

they have different parameters and assumptions. they work better on different types of molecules

if strain energy is always positive, how can the total energy difference obtained from a molecular mechanics calculation be negative?

electrostatics can cause this. can be negative if there are opposite charges attracting and causing “strain”

what limitations are there for comparing energies obtained from molecular mechanics

to compare energies, have to typically be same bonds and same bond types

why is it important that each bond type be defined for any structure on which a molecular mechanics calculation is performed

you have to know the bond order to compare the the bond to known values

why is molecular mechanics used to describe the energies of proteins?

because we can. can’t use some other models because of protein molecule size.

parameters such as bond lengths, bond angles, and vibrational frequiencies seem to be transferable between similar types of molecules. for example, such that most C=C bonds are similar. how does this observation lead to the concept of molecular mechanics?

parameters help set a standard for these and molecular mechanics can then use these but also somewhat predict deviations

how are the bonds and angles described in molecular mechanics

they are described as springs

what is a “strain energy”

energy it takes to deviate from equilibrium position

how is the energy from molecular mechanics determined?

hooke’s law

given that molecular mechanics assumes bonds to be atoms held together by springs, why does this method work reasonably well

because at equilibrium bonds behave exactly like springs

what is the force constant in molecular mechanics

parameter the represents bond stiffness in a chemical bond. essentially how much force per unit length taken to stretch or compress

how are force constants determined experimentally

by IR. Using different methods then analyzing the vibrational frequency

why is molecular mechanics sometimes called “atoms on springs”

treating the bonds like springs. its the basis of the method

what is “parameterization”

you set different parameters for the different methods. basis of models are determined by parameters

do equivalent electron dot structures contribute equally to the observed structure

yes

do non-equivalent electron dot structures contribute equally to the observed structure?

no

Why can S atoms have more than 8 electrons

they have access to the d orbitals

for elements beyond the second period, how can formal charge be reduced

using the d valence shell

what must be remembered about the connectivity of the atoms in oxy-acids

typically connected in layers

what is a peroxide bond

O single bonded to O

why are peroxide bonds generally uncommon in naturally occurring compounds

they are unstable and highly reductive

which structure for sulfuric acid best describes the molecule and why

a sulfuric acid structure with the 0 formal charge as S has access to the d valence shell so it can have the extra connectivity

what is an electron dot structure

demonstrating atomic connectivity using letter abbreviations for atoms and dots for electrons

what is the physical basis of the octet rule.

if an atom is in p-block, the typical valence shell is usually 8 electrons so an “octet” fills its valence shell

what is a bond pair of electrons

a line aka electrons shared behind two bonded atoms

what are lone pair electrons

valence electrons that are not shared between atoms

how can formal charge be used to predict the relative stability of two species

typically species without formal charge are most stable or whichever has the least formal charge

what is bond order

measure of multiplicity of a covalent bond between two atoms. single bond= 1st order. double bond=2nd order. triple bond=3rd order

what is the relationship between bond order, bond length, and bond strength

higher order means stronger and shorter

what is the process of using two or more electron dot structures to represent a single molecule called

resonance

what is the difference between equivalent and non-equivalent electron dot strucutre

equivalent: each contribute equally to actual connectivity of a molecule. non-equivalent: don’t contribute equally, typically electrons in very different spots

what determines the chemical properties of an atom, ion, molecule

mainly the valence shell but overall the electron configuration dictates the chemical behavior

what is meant by ab initio

“from beginning”, starting with nuclei and electrons

who was Erwin Schrodinger and how did he describe an atom

He was an austrian physicist who described an atom. he had the model of an atom that described electrons more as waves

what is a wave function

a mathematical function that relates the location of an electron at a given point in space to the amplitude of its wave

how is a wavefunction related to an electron orbital

An orbital is a region of space where there is a high probability of finding an electron the wavefunction provides the mathematical description of that region

The Schrodinger equation is given by (image). what does the H mean

its a Hamiltonian operator, its a mathematical function

Who was Henri Poincare?

french math person. says you can't solve the three body problem. can’t describe electron-electron interactions if there’s more than 2. can’t understadn the movement

Poincare’s theorem states “when multiple bodies interact, their equations of motion become coupled, and thus nonlinear. this means that the motion of one body depends on all the others in a complex way, making it impossible to find a general closed-form solution solution” what does this theorem mean for the use of the schrodinger equation?

can not get a close answer with the equation for a multielectron atom

based on poincare’s theorem, what species can schrodinger’s approach be used to obtain an exact solution

one electron species

since it is theoretically impossible for the schrodinger equation be used to obtain an exact solution for a species with two or more electrons, what must be done to solve the equation for any many-electron species

you must create many one electron problems

is it reasonable to expect that the calculated electronic structure of a species to be exactly the same as that found experimentally

no, its incredibly impossible to estimate exactly but can get close

if approximation to the schrodinger equation are made, what two conditions are required of the model

the model must have a unique solution and it must be practical

if approximation to the schrodinger equation are made, what to conditions are desirable for the model

it should preferably be variational and size consistent