1st Hour Exam Notes

From WikidChem

Test Prep Maybe post your test related questions here and then move this page out of the way once the test is done so that people in the future can get to it/use it as a resource? Add to the outline to help everyone out!

If anyone is looking at old exams, in the 2001 exam, question five talks about a wave function for a Hydrogen electron. Do we need to know how to do this? And if we do, can someone explain it? Gozde told me tonight that we did not need to know how to do this question because he never taught it to us and we were only looking at particles.

Are there molecules and Atoms? What force holds atoms together? Functional Groups Memorize them, and remember that the C=O in an amide or ester is not a ketone! Similarly, the –OH in a carboxylic acid is not an alcohol

Rough Bond Lengths, etc. It is always good to keep in mind the rough length of a bond (order of magnitude, at least), the size of an atom, the size of a small molecule, etc. Most of these numbers were mentioned in the lectures.

-1 nm is 10A

-atom length 1 A

-bond length 1.5 A

Lewis structures What they represent well, what they represent poorly, why they are useful to us

-They are useful because they help to visualize the bonding that goes on between atoms. X-ray diffraction with difference density plot shows that the actual sharing of electrons is much less than 2e- and is more like .2e-. -useful for book keeping for charges.

Other theories and ideas that emerged to compete with Lewis’ idea - be able to recognize and explain the quotations in the lectures (associate people with ideas) Pepys, Lewis, Thomson, Dunitz, etc.

Thomson-Plum Pudding Model

Formal charges Are theoretical Zeff= valence electrons- (half bonding electrons + lone pair electrons) Ex: N with four bonds and no lone pairs) 5-(4+0)=+1 just think about the electron balance if it has more bonds than it wants than it is a + but if it has less than it’s a negative.

Resonance vs. Equilibrium  single vs. double minimum, arrow conventions (double-headed arrow vs. two arrows in opposite directions)

Charge Separation! Causes a double minimum Think about the carboxylic acid. It can be two different species because the O can be O16 or O18. However if you take away the H in the –OH then its missing an electron and it’s electron paramagnetic resonance which is unusually stable (bonds are an intermediate length). There is no change in the positions of the nuclei but the drawings are limited. In experiments, there is only one real species. These have a single minimum because they are in the middle of a double minimum. They have a balanced energy minimum sum (single minimum). In experiments, when in equilibrium there are two different real species found. They cannot have a balanced minimum (double minimum).

X-ray diffraction Why we need to use x-rays to see small particles

we use x-rays to see small particles because scanning probe microscopy is not precise enough to show the very small particles.

Difference between electron density maps and electron difference density maps and how to convert one to the other Electron density maps show the electron density in different areas of the structures. Electron difference density maps actually show the difference between what the electron density would be of a "nonintereacting" atom and the observed electron density. That is why there are dotted lines on those maps, they represent the negative differences because these would be the areas of large electron densities for noninteracting atoms but actually have very little electron densities because bonding is occuring.

Relation between cross-sectional shape of electron difference density and type of bond (C-C, C=C, C=C=C, C-F, etc.)

How diffraction pattern in reciprocal space changes when pattern in real space changes, i.e. closer objects in real space give diffraction patterns with spots that are farther apart

Scattering pattern and intensity of spots

DNA pattern  correlating diffraction pattern in reciprocal space to 2- or 3-D structure in real space, i.e. know what each spot (and in some cases its intensity) on the diffraction pattern means  this information is clearly given in the lectures

Microscopy Three types of Scanning Probe Microscopy (SPM): Scanning Tunneling Microscopy (STM) Atomic Force Microscopy (AFM) Scanning Near-Field Optical Microscopy (SNOM)

Know what the probe is, how they work, the approximate resolution (and what that means you can see), advantages and disadvantages of each. Wikipedia seems to have decent articles for these forms of microscopy, but no guarantees

NONE OF THESE CAN SEE BONDS WHICH IS WHY WE NEED X-RAY DIFFRACTION particularly the density differences plots The advantage of SPM is that they all operate in real space as opposed to x-ray diffraction that shows everything in reciprocal space

Scanning Tunneling Microscopy -There is a constant current of electrons and based on the differences in distance it makes a profile of the substance -never touches sample -disadvantage: needs a conductor underneath the substance attempting to "see"

Atomic Force Microscopy -it has a 20nm cantilever that actually touches the substance -the moving up and down of the cantilever shows the size of the molecules and you can see this through the voltage changes -PROBLEM: how sharp the tip can be because it can tear through substance -also can put function groups at end of cantilever

Scanning Near-Field Optical Microscopy -shining light absorbs a photon -works with fluorescent light -set a detector to certain wavelength -tells separate bodies by variation of intensity as a function of scattering angles as a result of interference -the wavelength differences "show" separate bodies -PROBLEM shortest visible wavelength is 400nm which is much bigger than a molecule (although tiny aperture solves this problem) but atoms do not fluoresce, so can still only see molecules

Quantum Mechanics Schrodinger equation and what constitutes a solution

Given a Psi graph, be able to draw the potential energy and vise versa Keep in mind inflection points, curvature over psi ratio (remember the negative sign in the equation), regions of negative kinetic energy, non-classically allowed regions, recognize psi as it corresponds to common potentials (i.e. sine wave for constant positive kinetic energy, exponential decay for negative KE, etc.)

Effect of mass on psi, relation between number of nodes and energy  more nodes imply more curvature and therefore higher energy

Normalization  the reason for normalizing, interpretation of psi and psi squared

Bonding  more electron density between the nuclei than one would expect from the overlapping of the electron density from two isolated nuclei; in the double-minimum potential, the “bonding” wavefunction results from positive overlap of the individual wavefunctions from the harmonic potential, the “anti-bonding” wavefunction is the difference  see the lecture slides from today

Why are the allowable energy solutions for a harmonic oscillator evenly spaced? -YMT

Why can Erwin Meets Goldilocks assume a slope of zero at the far left when beginning to trace out a wave function for any of these three potentials? - DC

Multiplying psi by a constant does not change the value of the kinetic energy because the second derivative of psi (the curvature) also gets mutiplied by the same value (take the second derivative of constant * function and it will be the same constant * second derive of fcn). So, you can assign any arbitrary value of psi, slope of psi, and curvature of psi to start with just to make life easier for yourself. -ADK What is the goal of normalization and what constitutes whether a function can be normalized?

Not sure on this, but this is my feeling. What we are usually normalizing is psi squared. We want to normalize it so that all the probability densities add up to 1 because all probabilities of where a particle can be add up to one. So if a particle can be in region A and region B and it is twice as likely to be in A than in B, then after normalization you get 66.6% in A and 33.3% in B. For a function to be normalized, it needs to not have an infinite number of regions of electron density (the way say a sine psi curve would). It should probably also not have a psi that goes off to infinity as then psi^2 wouldn't be a pretty number. When would you use AFM versus STM? Why can't you use AFM to locate atoms on the surface of organic solid (resolution not good enough for that? or would it destroy the solid?) Is there a single advantage to using AFM?

AFM uses a tip that is about 5 nm (according to a website here http://spm.phy.bris.ac.uk/techniques/AFM/) so it would not be able to detect the end of one atom and the beginning of another. It's too big to fit into the bond areas between the atoms, which is only about .15 nm wide. I think. Please correct me if I'm wrong. - JY 9/27/06

Actually, I think the tip of the AFM is about 20 nm.

With AFM, because the tip is too wide, you can only see molecules, not atoms, as you scrape the surface with the cantilever. If the tip was any tinier, it might puncture or destroy the molecule as it scrapes the surface. Therefore, STM is better for seeing atoms, as it can "see" the height differences as small as an atom because it isn't actually touching the surface but it instead uses current. However, with STM I believe you need a thin layer of the material you are looking at over a conducting surface for the current to work… could this somehow be a disadvantage/inconvenience? (ECM 9/27) Can someone re-explain why the C-F bond cannot be seen?

The scientists making the electron density difference graph assume that F is a sphere that has evenly distributed electrons, attributing 7/4 of an electron to each position in the octet, all at regular intervals. Thus, there is no electron difference when this symmetrical model of the F is subtracted from the bonded F. In reality, however, the F atom changes and leaves one electron by itself, ready for bonding. If that electron density was subtracted from the bonded F, one would see a difference and the C-F bond would be seen. - JY 9/27/06 What do we learn about tunneling from knowing that more massive atoms move in a smaller range than less massive ones? - JY 9/27/06

In regards to the DNA x-ray diffraction, can someone explain the demonstration of stacking and pitch?

Stacking: You are looking at the DNA from the side. So, you see lots of base pairs going parallel to each other from one side of the helix to the other. They are also pretty close together and have a pretty high electron density (lots of carbon and other atoms). So, if you draw planes with all the base pairs, then draw a perpendicular line to that plane, you will get a line that goes from the top of the helix down. Because the original base pairs are close together, the reciprical image will be a very strong one at the top and bottom of the X-ray image. -ADK Pitch: Draw a "squished" helix, a "normal" helix, and a really really "stretched out" helix. Then, draw planes (lines) through the tilted sides of the helix and then draw lines perpendicular to those lines. These will form the X you are talking about. Notice how if your helix is flat, then the lines will form a very very sharp X and if your helix is stretched, then the lines will form a really flat X. That is pitch, I think. -ADK Why does the carbon nitrogen triple bond, as shown in the difference density map, appear as a circle rather than a clover shape?

Because our model of triple bonds (orbitals, Lewis, etc) is not perfect and does not perfectly represent reality. It appears more circular and not a clover/diamond as we'd expect. -ADK Can someone explain the weak-strong-strong-weak banding patterns on the "x" seen in the x-ray diffraction image for DNA? -YMT

Can someone review the differences between real and reciprocal space and how that applies to diffraction?

For a Morse Potential, does low KE mean low curvature? Why or why not?

I read in my notes that a double minimum means there are two orbitals: one bonding, one anti-bonding, and that if an electron is in the higher orbital, it will move away from the middles region and form an anti-bond. Is this correct? Explain.

Is the process of coupling (the amount by which you decide to lower the energy at otherwise sharp intersection of the two parabolas in a double minimum potential) related to the use of a catalyst? -VWC

Single and triple bonds have circular cross-sections on a difference density chart, but aromatic have ovular. Why?