From The Chair...
A few years ago the department decided to provide chemistry majors with a key to Mudd Hall upon request. Students will be allowed to keep this key until the end of Spring Term of their senior year. Therefore, if you are interested in being able to access Mudd Hall after midnight, you should send a request for a key to Wendy Zimmerman by email (firstname.lastname@example.org). She will submit your request to facilities, and they will contact you when your key is ready for pick up at the facilities office. Note that the department has only approved the general issuance of building keys. Individual room keys will continue to be available only to students involved in research who have received appropriate safety training.
Friday, September 23, 2005
Computational Studies of the Photodynamics of Retinal
Retinal protonated Schiff base (RPSB) is a versatile, well-studied molecule with an important place in biological photochemistry. In proteins such as rhodopsin, conversion of 11-cis RPSB to all-trans RPSB is the primary trigger for vision while the protein bacteriorhodopsin (bR) uses the photoisomerization of all-trans RPSB to 13-cis RPSB to transport protons against the gradient across the cell membrane. bR is a particularly interesting system in which the protein environment works to steer the photochemical reaction; changing the selectivity, quantum yield, and timescale of the reaction. As is generally true for photochemical reactions, the molecular dynamics occurring between photon absorption and the initial observation of ground state intermediates is not well understood for RPSB either in solution or in bR.
Molecular dynamics calculations can directly probe the photodynamics of RPSB but require characterization of the local potential energy surface at each dynamics timestep as well as a mechanism for transitioning between potential energy surfaces of different electronic states. Using ab initio calculations for this purpose is likely to be prohibitively time-consuming even for gas-phase calculations. Calculations with molecular-mechanics-type forcefields are considerably faster but, lacking a quantum mechanics formalism, are not well suited to multi-state calculations. Based in quantum mechanics and much faster than ab initio calculation, NDDO type semi-empirical calculations seem an ideal solution but do not often accurately reproduce excited-state ab initio potential energy surfaces. However re-parameterizing these methods to better describe select excited state potential energy surfaces is a promising possibility.
A re-optimization of a semi-empirical parameter set to better reproduce the results of excited state ab initio calculations of an RPSB analog was accomplished. Results using this new parameter set compare favorably with experiment and with high-level calculations. Multi-state dynamics simulations performed with this new set yield insight into the relationships among potential energy surfaces, dynamics, and photoproducts. Future work to explore the effect of a protein environment on RPSB photodynamics is promising.
Journal Club Meets This Week
Journal Club meets this Thursday at noon in Mudd 171 to discuss a paper relating to this week's seminar. For information about what to read beforehand, see the seminar web page: http://apps.carleton.edu/curricular/chem/seminars/.
Annual Report of the Chemistry Department
Copies of the August 2005 Annual Report of the Chemistry Department are now available. Among other things, this report has information on the chemistry majors who graduated in 1995 and 2005 and what the faculty did last year when they weren’t teaching. If you’d like a copy of this report, email Wendy (email@example.com), and she will send you one through campus mail.