November 8, 2013




fun with animated gifs, part 41.







Article in Journal of Organic Chemistry

March 9, 2010

Some of the NMR studies that I completed at Pomona College back in the Summer of 2005 have appeared in the Journal of Organic Chemistry!  During the revision process, we decided that the visual abstract needed more “punch.”  So, Dan O’Leary convinced one of his organic chemistry students to design a new abstract featuring the “elves” of entropy and enthalpy bending our molecules to their whims.  JOC liked the idea so much that they put the elves on the cover!

As you can see at the bottom, the black haired Enthalpy is pulling the deuterium to the position where it can have a lower zero-point vibrational energy while Entropy, the trickster, is doing just the opposite.  The NMR spectrum of these “cage diol” systems look quite different depending on how much water is present in the solution.  So, much of the summer that I worked with these molecules was spent at the argon-filled glove-box, trying to keep any trace of water out of the NMR tube.  Those cheeky elves don’t seem to have any problem with water in their solvents!

Check out the article:

Longs Peak Bike and Hike

July 17, 2009

After reading about people doing Longs Peak in a day from Boulder by bicycle, I decided that this was something that I had to try. This past weekend (July 11-12, 2009) I succeeded in biking from my house in Boulder to the Longs Peak trailhead, hiking the Keyhole route to the summit, and biking back home, for a total of about 80 miles of biking and 15 miles of hiking. Since the only time estimates that I could find were for the record-setting ascents:
I thought that I would post a quick report here to give an idea of how long the different legs of the trip might take.

This was the first time that I had made it to the top of Longs Peak and I thought that it would be a good idea to start hiking around 3 am in order to avoid the afternoon thunderstorms. This meant that I would have to do the bike ride in the dark. The quickest way to ride from Boulder to the Longs Peak Trailhead is by taking the mostly flat Highway 36 to Lyons and then the steadily climbing Highway 7 for about 15 miles to the Peak-to-Peak Highway. I decided against riding up Highway 7 in the middle of the night since the speed limit on the road is generally 50 mph and I thought that it would see a fair amount of traffic, even in the middle of the night. I instead took Lee Hill Road to James Canyon Road, through Jamestown, and to the Peak-to-Peak Highway via the overland dirt road. This route did succeed in avoiding traffic, but it involved lots of huge hills and, if I bike to Longs again, I will probably just go through Lyons.

The singlespeed ready for action!

The singlespeed ready for action!

I would have liked to have a road bike for this ride, but, being a impoverished graduate student, I had to make due with my trusty Redline singlespeed mountainbike. As can be seen in the picture, I applied lots of reflective tape to be sure that I wouldn’t get hit by any cars.  I had two lights on the front of my bike and I also attached a headlamp to my helmet, a technique that I highly recommend as it made it much easier to read the map and look at signs.

I left my house in Boulder (near 6th and College) at 10:05 pm on Saturday night under mostly clear skies and pleasant 70’s temperatures. I got to Broadway and Lee Hill Road at 10:26. I think that this is the traditional starting point for the Longs Duathalon, so I this is where I start the clock officially. After passing Old Stage Road, Lee Hill Road climbs a number of huge hills before losing almost all the elevation gained on the descent down to Left Hand Canyon Road (damn!). I made a right on Left Hand Canyon Rd, blasted down the hill, and hung a left on James Canyon Road, climbing a gradual hill and reaching Jamestown at 11:40 pm.  Despite being many miles into the hills, the general store (and bar?) in Jamestown was still buzzing with merrymakers.  After Jamestown, the Overland Road got me to the Peak-to-Peak Highway via a giant lung-busting climb and a few miles of dirt road. I reached Highway 72 (the Peak-to-Peak) at 12:43 am and took a well-earned break. After a few quick miles of downhill riding I reached Highway 7 at 1:11 am, and then made it to the trailhead at 2:25 am, for a total riding time of 3:59 from Lee Hill Road (4:21 from my house).

The gang (Laura, Erin, and Weeze) at dawn on the hike up to Longs Peak.

The gang (left to right: Weeze, Erin, and Laura) at dawn on the hike up to Longs Peak.

At the trailhead I met up with Laura, Erin, and Weeze. We started hiking at 2:45 am, and, after a glorious sunrise, arrived at the Keyhole at 6:20 am. Erin and Weeze turned around at the bottom of the trough, but Laura and I continued up, finding the route to be mostly free of snow, though there was some snow of the homestretch that forced us to scramble up some wet rocks, still third class though.

Walking across the boulderfield towards the Keyhole

Walking across the boulderfield towards the Keyhole

Laura and I made it to the summit at 8:10 am and we scrambled back to the keyhole by 9:45. We met up with Erin and Weeze near the campsites in the Boulderfield and we scampered back to the trailhead, arriving at the car at 1:00 pm, with a few stops to take some pictures of the wildflowers.

Laura and I on the summit of Longs Peak (14,259 feet (4,346 m))

Laura and I on the summit of Longs Peak (14,259 feet (4,346 m))

I started biking back to Boulder around 1:15 pm. The biking along the Peak-to-Peak highway was nicer on the way back down and I wished that I had a road bike so that I could have drafted one of the pelotons that were cruising the highway. I made it to the junction with Highway 7 at 1:57 pm. After a quick descent on the nice downhill I arrived in Lyons just in time for a huge thunderstorm that saw me riding through 6 inches of water. Luckily, the storm only lasted about 10 minutes and, by the time I turned onto 36, the sun was shining again. After a tired slog on 36, I reached Lee Hill Road at 4:00 pm, for a bike descent time of 2:45 and a total “Duathlon time” of 17:34. I made it back to the house at 4:26, for a Door-to-door time of 18:21. After a burger I fell asleep for the next 13 hours!

I also made a (terribly produced) video of the Longs Peak Duathlon experience:


April 8, 2009

I’ve made a few panorama photographs from my recent trip to Montana and I’ve been looking for the best way to put them online.  Flickr, facebook, shutterfly, and photobucket only display the low quality image which works fine for normal photographs, but poorly for a long panorama.  Lets see how good they look on wordpress:

Backcountry skiing in the Absaroka mountains

Backcountry skiing in the Absaroka mountains

The thumbnail doesn’t work on this next one for some reason (maybe because it’s so long) so you’ve got to click on the link to see the full size image:

The view from Kiira's house.  I've been having trouble getting this one to be flat...

The view from Kiira's house. I've been having trouble getting this one to be flat...

Closeup of the panorama at Kiira's place.

Closeup of the panorama at Kiira's place.

WordPress limits me to jpeg format and the file size to 8 MB, but it would appear that clicking on the thumbnail provides the full size jpeg file.  Great success!  Now I just have to figure out how to make the colors look nice.

Tonto – quickly look at data from output files

July 16, 2008

Often I want to quickly grab the same numbers from a whole series of Tonto output files.  Here is an easily modified python script that saves me some time:

#, a script for extracting values
# for various properties from a Tonto calculation.
# call with: python
# modify the 'if' statements to grab the properties that you want
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Thesis 2008 – Rotating ZTS movies

July 9, 2008

As part of my thesis work at Cambridge, I have used the Tonto program to fit the electron density of tris zinc thiourea sulphate to a high resolution x-ray diffraction study. I used two different sets of coordinates and atomic displacement parameters (ADPs): those from a multipole refinement in XD2006 and those generated by a ‘Hirshfeld Atom Refinement’ in Tonto (Jayatilaka and Dittrich, Acta. Cryst. A 2008). It has been proposed that the Hirshfeld atom coordinates might serve as a better starting point for the x-ray constrained Hartree-Fock calculation than the multipole refinement coordinates, as the Hirshfeld refinement coordinates have been optimized to the basis set (in this case 6-31G*) being used for the x-ray constrained Hartree-Fock calculation. Most of the molecules that I study lie nicely in a plane, so a slice of the electron density can be easily viewed in two dimensions. ZTS, on the other hand, refuses to lay flat on a sheet of paper, and so the electron density is best viewed in this rotating mode.

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Convert gaussian cube files from bohr to angstroms

July 8, 2008

Tonto outputs all of it’s grid and cube files in electrons per bohr-cubed and I don’t think there is a way to change it (actually, “plot_units= angstrom^-3” converts the plot).  However, some other programs (namely XD2006) output in electrons per angstrom-cubed.  All you have to do is multiply the values by 1/0.529^3, but this gets a little tedious, so here is a script that converts a gaussian cube file from bohr (atomic units) to angstroms:

# - converts .cube files from electrons per au
# to electrons per angstrom.
# Call with: python input-file [output-file-name]
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