In press, in Crystal Growth and Design.  A short paper with an important message.  In principle, solid-state quantum chemical methods provide the tools for both the prediction of crystal polymorphs and the calculation of the relative energies of characterized crystal forms to determine why one version forms preferentially.  That said, modern solid-state quantum chemical methods are dominated by density functional theory which, although work is being performed to address this issue, are fundamentally incapable of accounting for all of the energy terms in the complete lattice energy calculation of solid-state materials because dispersion forces are not accounted for (there are methods around this, be they empirical or by way of solid-state Moeller-Plesset Perturbation Theory, which we may even have the computing power to handle someday…).

In molecular polymorphs, the energies of the crystal cells per molecule may be quite similar to one another because, being molecules with polar and non-polar regions, specific functional groups tend to bind preferentially to other specific functional groups, which all may involve similar interaction energies.  The point is that the lattice energy differences between different polymorphs may be quite small.  In such cases, the vibrational zero-point energy of the crystal cells may be very important contributors to the experimentally determined polymorph energy differences.  Such is found to be the case for the alpha- and gamma- polymorphs of glycine.

Specifically in the glycine example and other polymorphs for which proper thermochemistry is available, we even have a means to estimating what SHOULD be the lattice energy of the crystal without relying on theoretical models (and their inherent limitations).  For glycine, the experimental enthalpies for both crystal forms have been measured.  We have the experimental vibrational spectrum available against which to compare the theoretical work, from which we can determine the zero-point energy for the unit cell (simply 1/2 the sum of the vibrational mode energies).  With that information, we can determine (to a first approximation, there are many other factors to consider that play lesser roles in the final value) the experimental lattice energies.  These values then provide a benchmark for determining the abilities of theoretical models to reproduce this most fundamental of the solid-state quantum chemical properties.

Sharon A. Rivera^1,2, Damian G. Allis^1,3, Bruce S. Hudson¹

1. Department of Chemistry, Syracuse University, Syracuse, NY 13224-4100
2. School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
3. Nanorex, Inc., Bloomfield Hills, MI 48302-4100

Abstract: The relative stability of polymorphic crystal forms is a challenging conceptual problem of considerable technical interest.  Current estimates of relative polymorph energies concentrate on lattice energy.  In this work the contribution of differences in zero-point energy and vibrational enthalpy to the enthalpy difference for polymorphs is investigated.  The specific case investigated is that of alpha- and gamma-glycine, for which the experimental enthalpy difference is known.  Periodic lattice DFT computations are used to provide the vibrational spectrum at the Gamma-point.  It is confirmed that these methods provide reasonable descriptions of the inelastic neutron scattering spectra of these two crystals.  It is found that the difference in the zero-point energy is about 1.9 kJ/mol and that the vibrational thermal population difference is 0.9 kJ/mol in the opposite sense.  The overall vibrational contributions to the enthalpy difference are much larger than the observed value of ca. 0.3 kJ/mol.  The vibrational contribution must be largely compensated by the lattice energy difference.  The polymorphs of glycine differ in the pattern of their hydrogen bonds, a feature common to many polymorphs of interest.  The consequent difference in the N-H stretching frequencies is a contributor to the zero-point correction but the major effect stems from changes in the bending vibrations.

pubs.acs.org/journals/cgdefu/index.html
en.wikipedia.org/wiki/Quantum_chemistry
en.wikipedia.org/wiki/Polymorphism_(materials_science)
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/M%C3%B8ller-Plesset_perturbation_theory
en.wikipedia.org/wiki/Functional_group
en.wikipedia.org/wiki/Zero-point_energy
en.wikipedia.org/wiki/Glycine
en.wikipedia.org/wiki/Enthalpy
creativecraftychemist.blogspot.com
hudsonlab.syr.edu
chemistry.syr.edu
www.syr.edu
www.unsw.edu.au
www.nanorex.com

A repost of the original at the Syracuse Astronomical Society website. And official blog post #100 for somewhereville.com.

Greetings fellow astrophiles! We’ll get right to the news…

Summer Seminar 2008 Recap

We managed two beautiful nights this past August 22/23, which was a feat in itself given the limited number of good evenings we’ve had for viewing this year. The usual day-long festivities of past Summer Seminars were collapsed into two evenings of lectures by noted author and Baltimore Woods astro-organizer Bob Piekiel. Perhaps best known (certainly how I knew of him) for his beyond-comprehensive history of a scope-making giant, “Celestron, The Early Years“, the focus of his two lectures was “Testing and Evaluating the Optics of Schmidt-Cassegrain Telescopes,” also the subject of his new, very recently published book (those in attendance who bought copies had the foreword pasted into place, as these books really were “hot off the press”). With nearly 300 lbs. worth of gear brought into the Observatory, Bob covered a number of tests used to evaluate the quality of scope mirrors, doing so with the help of his own projector system to give everyone in the room a view down the eyepiece. We were also thrilled to host members of CNY-SPARC on Friday night and were pleased that the skies held up for a few hours of near-perfect naked eye viewing.

Bob Piekiel hard at play…

The Saturday program became a hands on for attendees, with Bob performing the same tests on the scopes of Mike Brady, Jeff Funk, and my own “Stu Special,” which will receive its own little article in the near future. We’ll have a copy of both the Celestron ebook and Bob’s new SCT book for perusing at Darling Hill. For those of you interested in purchasing your own copy (two great gifts for when the skies cloud over), you can get them directly from Bob at piekielrl@netzero.com.

SDSS 1: “Cosmic Haul” Reminds That “Data” Is Plural, After All

The BBC Sky at Night featured a short article on the recent identification of 50 new objects in the outer reaches of our Solar System, a number that will no doubt grow tremendously as more of the same data are analyzed and more powerful telescopes are pointed to the heavens. Of specific interest is the discovery of the aptly-named 2006 SQ372, an object that may be an old Oort Cloud resident but is now in an eccentric orbit that has it at about the distance of Neptune but will, at its maximum, distance itself from the Sun 75 times beyond its current 2 billion mile position.

2006 SQ372 (red ring not included). See article for more info.

The discoveries of these new objects demonstrate the power of recycling. The data used for these findings come from the Sloan Digital Sky Survey and were part of a survey of supernovae that finds the telescopes and cameras pointed at the same strip of sky every three days. Instead of looking for new pinpoints of light in distant galaxies, the Solar System researchers simply performed image overlays to look for before-and-after shifts in the position of objects that existed in both images. With Stripe 82 successfully analyzed (the origin of these first discoveries), researchers can continue to work backwards and forwards, with all of us looking forward to the identification of new objects in our own backyard.

SDSS 2: Do Dwarf Galaxies Stick To The Roof Of Your Mouth?

In an odd twist, it seems that the Milky Way has quite an appetite. A second study from the Sloan Digital Sky Survey has revealed that the outer galaxy contains “streams” of stars that originate from satellite galaxies that were torn apart but still remain connected through their motions. In short, ribbons of stars from entire dwarf galaxies are moving within the outer halo of the Milky Way, gravitationally bound to the galaxy center. Using the Sloan data, researchers have been able to identify 14 such distinct ribbons of stars by observing the motions of each. Further, this same data was used to identify 14 dwarf Milky Way companions that remain intact within the dark matter halo of the Milky Way.

A model of the Milky Way. By. K. Johnston, J. Bullock. See article for more info.

The separation of these 14 ribbons is quite a mess of correlated motion and rigorous tracking of untold numbers of stars, but understanding the origins and results are straightforward here on Earth. Those that know of the American composer Charles Ives know that a major inspiration for his compositional approach came from hearing two marching bands playing different tunes simultaneously. In effect, the 14 ribbons of stars are the marching bands playing distinct songs in Ives’ parade, with gravitational forces playing the roles of the drum majors directing the bands along their paths. As long as you know the different songs (and, thanks to Newton and Einstein, every good physicist can hum along to those tunes), you can work back and identify the bands. While these bands are playing too far away for us to observe even in the 16″ Cave, it is worth noting that our Milky Way plays host to an increasingly more complex arrangement than we’re capable of hearing, although our speakers are improving all the time.

We’re Unique, Just Like All The Rest Of Them

It appears as though Extra-Solar Systems may be common, but our particular arrangement may be a lot harder to come by. A computational study predicts that our Solar System is the result of a delicate balance of initial stellar disk mass (how much matter the Solar System had to work with) and viscosity (a measure of the primordial “soupiness” of this gaseous disk of matter). Using computationally demanding simulations (as a computational chemist, I can attest to how long one has to wait to have an answer show up on a computer screen) and available data on the 250 identified planetary systems (including our own, of course), researchers identified that the wrong combinations of mass and viscosity can lead to no planets forming (low mass, high viscosity) or planets forming quickly and falling towards the center of the disk (high mass and low viscosity. Note the number of systems discovered with massive planets sitting quite close to their associated stars), while the right combinations can yield systems just like our own (warm porridge and large spoons).

Who are the planets in your neighborhood?

As equipment improves and we’re capable of identifying ever-smaller planets around reasonable stars, we’ll begin to test the accuracy of the theoretical models. When presenting the results of theoretical work (including my own), I often find myself quoting the great one, Han Solo. “Hokey religions and ancient weapons are no match for a good blaster at your side, kid.”

I’ll Take A Shallow Pothole Any Day

From aero-news.net. Most debris in space from old missions, damaged satellites, and stalled UFOs scoot around the Earth at a non-trivial 17,500 miles/hour. The world’s astronauts (and our space-enthusiast tax dollars) find no small amount of comfort in knowing that simple equations provide very accurate predictions of the motions of this debris. But what do you do when that debris is shooting straight at you? Crew members of the International Space Station opted to err on the side of caution and used booster rockets to move the ISS clearly out of the path of a piece of the Russian Cosmos-2421 surveillance satellite that was blown up earlier in 2008.

The International Space Station (from above). See article for more info.

This relocation of the ISS is noteworthy because, well, they did move their house to avoid the baseball from the kids next door and, despite all the green-friendly efforts we make here on Earth to cut fuel usage, this ISS motion was a “wasteful” endeavor. While the ISS uses rockets to move itself away from the planet on a regular basis (because of drag from the far, far upper atmosphere that causes the station to fall closer to Earth by several hundred feet every day), this move pushed the station closer to Earth (because it was already at its maximum preferred distance). Interestingly, Russians deny the existence of the debris (well, the satellite), while the ISS crew has had to keep track of quite the messy debris field.

When crossing the street, look both ways. Then, look up.

Clash Of The Titaniums (And Assorted Elements)

While a number of us enjoyed the Perseid meteor shower from the comfort of the Darling Hill Observatory, two amateur astronomers set their sights (and their scopes) on the Moon to watch for visible explosions resulting from impacts. This article from NASA reports on astronomers taking images of flashes of light on the Moon using reasonable scopes, recording equipment, and LunarScan, a freely available program for detecting lunar explosions. Anyone pointing a scope of any kind at the Moon knows just how hard the lunar surface has been hit in its 4.5-or-so billion year history (our own surface would look much the same if not for tectonic shifting, large bodies of water, and atmospheric phenomena).

George Varros, Mt. Airy, Maryland. See article for more info.

I cannot overstate just how cool the links associated with this article are. Do have a look at www.gvarros.com.

Extreme Extremophiles, Or Don’t Try This At Home Or In Low Earth Orbit

This article from LiveScience reports on a group of “water bears” that don’t believe in stay-cations. Or probably wouldn’t, even if they had a choice. A sample of tardigrades (see the cute picture) were sent into Low-Earth Orbit (LEO) aboard a FOTON-M3 and left to experience the harshest the void of LEO had to offer: high vacuum and deadly cosmic and solar radiation. Amazingly, a number of these critters returned to Earth no (or little) worse for wear and even managed to produce completely normal offspring, no doubt in the hopes of telling their several thousand grandkids the ultimate bedtime story.

The tardigrade (water bear). By Rick Gillis and Roger J. Haro, Department of Biology, University of Wisconsin – La Crosse.

The Earth is covered in extremophiles, organisms that exist (in fact, thrive) in conditions that most every other life form on the planet would cook, freeze, squeeze, or dissolve in. There are bacteria that literally eat heavy metals for lunch, microbes that thrive in water as high as 122 degrees Celsius (and those of you that remember your conversions will note that this is 22 degrees hotter than boiling water), and organisms that grow at pH levels of 3 and below (as in their prefer their hydrochloric acid undiluted, thank you). As for setting the record for most cost spent and least damage done, the simple water bear holds the new World+ Record.

Space is the place,
Damian Allis, Ph.D.
sas@somewhereville.com

Links Used Above (Subject To Web Changes)

www.takeahike.org
www.astromart.com/articles/article.asp?article_id=167
tech.groups.yahoo.com/group/sct-user/message/105312
www.cnysparc.org
www.bbc.co.uk
www.bbc.co.uk/skyatnight
news.bbc.co.uk/2/hi/science/nature/7580539.stm
en.wikipedia.org/wiki/Solar_System
en.wikipedia.org/wiki/2006_SQ372
en.wikipedia.org/wiki/Oort_Cloud
en.wikipedia.org/wiki/Neptune
www.sdss.org
en.wikipedia.org/wiki/Supernova
en.wikipedia.org/wiki/Milky_Way
www.spaceflightnow.com/news/n0808/18halo/
en.wikipedia.org/wiki/Satellite_galaxies
en.wikipedia.org/wiki/Dwarf_galaxies
en.wikipedia.org/wiki/Dark_matter
en.wikipedia.org/wiki/Earth
www.charlesives.org
en.wikipedia.org/wiki/Isaac_Newton
en.wikipedia.org/wiki/Einstein
en.wikipedia.org/wiki/Extrasolar_planet
thefutureofthings.com/news/1295/new-study-shows-solar-system-is…
en.wikipedia.org/wiki/Viscosity
www.princeton.edu/%7Ewillman/planetary_systems
en.wikipedia.org/wiki/Han_Solo
www.aero-news.net/news/aerospace.cfm?ContentBlockID=65c21c04…
en.wikipedia.org/wiki/International_Space_Station
en.wikipedia.org/wiki/List_of_Cosmos_satellites
science.nasa.gov/headlines/y2008/02sep_lunarperseids.htm
en.wikipedia.org/wiki/Perseids
en.wikipedia.org/wiki/Moon
www.nasa.gov
gvarros.com
en.wikipedia.org/wiki/Plate_tectonics
en.wikipedia.org/wiki/Tardigrad
www.livescience.com/space/080908-space-creature.html
en.wikipedia.org/wiki/Low-earth_orbit
en.wikipedia.org/wiki/Foton
en.wikipedia.org/wiki/Extremophiles

Amidst all the high explosives and illicit drugs comes a positive site addition about two very nasty toxins.  Several science news services (Eureka Alert, bio-medicine.org, and firstscience.com to start) posted the following article from Judy Holmes, the Dean of Arts and Sciences Senior Publications Coordinator, about a new project being started up to develop new oral vaccines for both tetanus and rotavirus.  Details below.

• www.eurekalert.org/pub_releases/2008-09/su-sup090408.php

• www.bio-medicine.org/biology-news-1/Syracuse-University-partners-with-Serum-Institute-of-India-to-develop-vaccines-for-children-4733-3/

• www.firstscience.com/home/news/biology/syracuse-university-partners-with-serum-institute-of-india-to-develop-vaccines-for-children-page-2-1_52028.html

• thecollege.syr.edu/pressrelease/seruminstitute.htm

Chemistry assistant professor Robert Doyle will lead the research project.

A unique partnership between Syracuse University and the Serum Institute of India could lead to better access to life-saving vaccines for children living in some of the most impoverished areas of the world. The Institute recently awarded $250,000 to a team of SU researchers led by Robert Doyle, assistant professor of chemistry in the College of Arts and Sciences, to develop new oral vaccines against tetanus and rotavirus, a severe form of diarrhea that affects infants and young children worldwide.

Tetanus is caused by a toxin produced by bacteria naturally found in soil. The vaccine is only available by injection. While the disease is rare in the Western world, tetanus caused an estimated 257,000 deaths in low-income countries between 2000 and 2003, according to the World Health Organization‘s (WHO) latest report. A significant percentage involved infants born in predominately rural areas who were exposed to the tetanus bacteria during unsanitary delivery procedures. Likewise, infants and young children in these same countries have a much higher risk of dying from rotavirus than those living in Western nations. The disease killed an estimated 500,000 children in developing nations during 2004, according to a 2007 WHO report.

“We are very excited to be working with the Serum Institute of India on these projects,” Doyle says. “This is a difficult area of research due to the nature of the molecules we will be working with. But, if we are successful, our work could have an enormously positive impact on the lives of people well beyond Syracuse University. This is truly scholarship in action.”

Founded in 1966, the Serum Institute of India produces and supplies low-cost, life-saving vaccines for children and adults living in low-income countries. It is the world’s largest producer of measles and diphtheria-tetanus-pertussis (DPT) vaccines. An estimated two out of every three immunized children in the world have received a vaccine manufactured by the Serum Institute.

“Our company’s philanthropic philosophy is to make high-quality, affordable, life-saving vaccines available for under-privileged children in both India and in more than 140 countries across the world,” says S.V.Kapre, executive director of the Serum Institute of India. “This new partnership with Syracuse University will help the Serum Institute further this endeavor as it will open new doors of vaccine usage.”

The Institute approached Doyle because of his successful research to develop an oral form of insulin, which may someday enable people with insulin-dependent diabetes to take fewer daily injections. An oral vaccine for tetanus would enhance distribution in impoverished countries. Doyle’s team will also explore new ways to synthesize the rotavirus vaccine to make it more accessible to children in developing nations.

A new laboratory has been established in SU’s Center for Science and Technology for the research, which poses a number of challenges. Similarly to insulin, the protein molecules used in the tetanus vaccine are destroyed in the digestive system. However, the tetanus molecules are 30 times larger than insulin, making them more difficult to transport. The vaccine is created by literally boiling the tetanus bacteria in a chemical solution, causing the protein to completely unfold. In its new, unfolded state, the tetanus protein is harmless, but is still recognized as tetanus by the immune system so as to trigger a response that protects the person from the disease.

“It’s like frying an egg,” Doyle says. “The egg white, which is a protein, is clear when you crack the egg into a pan. When the egg heats up, the egg white becomes opaque as the protein unfolds. You still recognize it as an egg, but you can’t make the egg white clear again after it’s been heated.”

The challenge is to figure out how to package this large molecule, sneak it through the digestive system unharmed, and transport it through the wall of the small intestine where it can be absorbed into the bloodstream. “Tetanus is a strange and wonderful molecule,” Doyle says. “We need to get a better idea of what the unfolded protein looks like and try to predict areas that would make good targets for attaching a transport vehicle.”

Problem is, you can’t actually see a protein molecule or the thousands of chemical reactions that take place within it over nanoseconds of time. However, researchers can develop computerized models of the molecules to predict their behavior and zoom in on possible targets. Damian Allis, research professor in the chemistry department, will be developing models for both projects. “The simulations allow us to view the process and identify sticky ends of the proteins that could potentially be used as binding sites for transport molecules,” Allis says.

Unlike the tetanus vaccine molecule, the rotavirus molecule Doyle’s team will be working with is not a protein; it is a viral capsule—the outer core of which is coated with proteins. “It’s a totally different problem,” Doyle says. “We need to deliver the viral capsid to the wall of the small intestine and keep it there long enough to trigger an immune response directly in the intestine, which is the first line of defense against the disease.”

Current oral rotavirus vaccines use tiny amounts of weakened, live bacteria. The vaccines’ possible side effects limit distribution in countries where access to health care is not readily available, according to the World Health Organization. Doyle’s aim is to develop a vaccine that does not contain live bacteria and has fewer side effects. The results could lead to wider distribution in low-income countries, ultimately saving hundreds of thousands of lives.

“We have some strong ideas and some good people on our team who bring very different skill sets to these projects,” Doyle says. “The University has been very supportive of this research. Every penny of the grant will go into research. It’s now up to us; we are excited about the possibilities.”

… and a pruned flavor of the same article with hard numbers from genengnews.com below.

• www.genengnews.com/news/bnitem.aspx?name=41348596

Syracuse University (SU) and the Serum Institute of India will partner to develop new oral vaccines against tetanus and rotavirus. The institute awarded $250,000 to SU.

The aim of the rotavirus research is to develop a vaccine that does not contain live bacteria and has fewer side effects. Research will also explore new ways to synthesize the rotavirus vaccine to make it more accessible to children in developing nations, according to the companies.

The challenge with the tetanus protein is to figure out how to package this large molecule, get it through the digestive system unharmed, and transport it through the wall of the small intestine where it can be absorbed into the bloodstream. The SU team will develop computerized models to predict the behavior of these molecules

“The simulations allow us to view the process and identify sticky ends of the proteins that could potentially be used as binding sites for transport molecules,� explains Damian Allis, research professor in the chemistry department who will create these models.

For more information about the articles, contact Judy Holmes (jlholmes@syr.edu, 315-443-8085).  For more about the project, myself or Rob Doyle.

www.somewhereville.com/?p=123
www.somewhereville.com/?p=126
www.eurekalert.org
www.bio-medicine.org
www.firstscience.com
www.eurekalert.org/pub_releases/2008-09/su-sup090408.php
www.bio-medicine.org/biology-news-1/Syracuse-University-partners-with-Serum-Institute-of-India…
www.firstscience.com/home/news/biology/syracuse-university-partners-with-serum-institute-of-india…
thecollege.syr.edu/pressrelease/seruminstitute.htm
thecollege.syr.edu
en.wikipedia.org/wiki/Tetanus
en.wikipedia.org/wiki/Rotavirus
chemistry.syr.edu/faculty/doyle.html
www.syr.edu
www.seruminstitute.com
en.wikipedia.org/wiki/Vaccine
www.who.int/en
www.somewhereville.com/?p=103
www.genengnews.com
www.genengnews.com/news/bnitem.aspx?name=41348596
chemistry.syr.edu/faculty/doyle_group/index.html