Thank You To Our Donors!
The department wishes to sincerely thank the following alumni and friends for their generous support of USD Chemistry and Biochemistry.
Denise Andrews-Tang (1987)
Myron Cagan (1972)
Lea Dooley (2002)
David Dorman (1979)
Brian Dorsey (1991)
Williams and Patricia Hastings
Ashraf S. Kasto (1997)
Erin S. Kelly
Brenda Lewis (1992)
Richard Hell (1990)
Ian Maulhardt (1997)
Martha Medina (2000)
Julia Norman (MARS 1997)
Melissa Rosness (1998)
Karen Ann Smith
Ronald and Karen Smith Christopher M. Stafford (1994)
Scott Steingrebe
Lesley Ward

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Chairís Corner

Over the years we have experimented with a variety of ways to stay in communication with our alumni. Given the growth in our department and the number of majors graduating each year, we thought it was time to reach out to more of you on a regular basis. I hope you enjoy reading our newsletter twice each year and that you will share your news with us for upcoming issues. Let me begin by thanking alumna Hailey (Russell) Adams for helping to produce this newsletter and for maintaining our alumni pages on our Web site. If you haven’t checked it out yet, we hope you will log on to our Web site read about what your classmates are up to, and submit a profile.

The first order of business is to update you on some important changes in the department over the last several years. At the top of the list is our new department name: we are now the Department of Chemistry and Biochemistry! More about this change later.

Spring Seminars

March 9th
Dr. John Hutchinson Amira Pharmaceuticals
The Drug Discovery Process - Big Pharma vs. Biotech

March 23rd
Tim Clark (’01)
UC Irvine
The Formation and Synthetic Utility of Oxasilacyclopentenes

April 6th
Dr. Michael Haley
U of Oregon
It Takes Alkynes

April 20th
Dr. Arnold Rheingold
UC San Diego
Organometallic Chemistry Without Carbon

May 4th
Bryan O'Neill ('O1)
Scripps Research Institute
Identification of Novel Eukaryotic DNA Damage Response Components

Seminars are held at 12:15 p.m. in room 133 of The Donald P. Shiley Center for Science and Technology.

Faculty A fantastic faculty, including our newest members who have enhanced both our teaching and research capabilities, anchors the department.

Current members include:

Dr. Jack Opdycke (on phased retirement through 2006-2007)

Dr. Mitch Malachowski (1984; Organic Chemistry)

Dr. Tom Herrinton (1987; currently Associate Provost)

Dr. Tammy Dwyer (1994; Physical Organic Chemistry)

Dr. Leigh Plesniak (1995; Biochemistry)

Dr. Jim Bolender (1996; Physical Chemistry)

Dr. Debbie Tahmassebi (1999; Organic Chemistry)

Dr. David De Haan (2001; Environmental/Analytical Chemistry)

Dr. Tom Shields (2002; Biochemistry)

Dr. Peter Iovine (2002; Organic Chemistry)

Dr. Jeremy Kua (2004; Physical Chemistry)

Dr. Steven Mills (joining us in July 2006; Biochemistry)

We are committed to continuing the outstanding efforts, contributions and traditions established by our emeriti faculty members, Dr. John McDermott, Dr. Donald Peterson, Sr. Agnes Schmit, Sr. Patricia Shaffer and Dr. Patricia Traylor.

In addition, we are fortunate to have a group of highly talented and committed adjunct faculty members who support our teaching mission. In the 2005-2006 academic year these include Ms. Hailey Adams, Mr. Farhad Assad, Dr. Sandrine Berniolles, Ms. Debbie Finocchio, Dr. Hima Joshi, Dr. Kelli Khuong, and Dr. Christine Mullen.

Facilities – If you haven’t had a chance to see our incredible new science building, you are missing out! Since moving over from Camino Hall in June 2003, we’ve settled in nicely to our new home. Fully equipped teaching and research laboratories, instrument rooms plus computational, NMR, and laser facilities have stimulated faculty and students in new ways. We’d love the opportunity to show you around - contact any of us for a tour!

Curriculum – In spring 2005, the department designed a new biochemistry major to replace the chemistry major with biochemistry emphasis. With the support of the Department of Biology, the biochemistry major was officially approved in Fall 2006 and new majors have been declaring in large numbers. Our conversations that led to the new major also prompted us to rename the department to reflect how we truly see ourselves.

Students – Engaging and working with our students continue to be prime motivations for all that we do as a department. As I mentioned above, the number of students declaring both chemistry and biochemistry majors is increasing, as are the numbers of students enrolling in our classes! We are quite literally at capacity with no signs of lessening pressure. Our graduates are having great success in medical school, dental school, graduate school, and in the biotech and pharmaceutical industry throughout the country. We are enormously proud of you and your accomplishments!

Let me close by encouraging you to stay in touch with us – I can’t tell you how thrilled we are to hear from (and get visits from!) our alumni. We are a department on the move and we’d like to make you a part of it!

Warmest wishes,

Discover Biochemistry – A New USD Major

The Department of Chemistry and Biochemistry is launching a new interdisciplinary major in biochemistry. The new major is designed to introduce students to biological and biochemical language and concepts earlier in their studies, to increase the breadth of their biochemical experience, and to enhance the rigor in the overall major. Biochemistry is a diverse field and this major can be tailored for individual student needs and interests. This new degree program requires genetics laboratory, an upper-division laboratory in chemistry, and physical biochemistry lecture. Two electives may be taken from a selection of biology courses.

Physical biochemistry is the only new course that must be created to offer this major. The concept behind this class is to address some of the specific physical chemistry experiments that biochemists encounter in research. In place of gas kinetics, there will be a special focus on enzyme kinetics with more complex models than the classic Michaelis-Menten model. The course will examine thermodynamics of drug binding, using specific examples from the HIV protease family of drugs, identifying entropic and enthalpic contributions to binding energy. It will be team-taught by biochemists and physical chemists in the department in the first two years. Additionally, the department has secured funding to bring an external scholar in the field, Dr. Ernesto Freire of Johns Hopkins University, to come to campus to guest lecture and give a seminar in the field. Dr. Freire is an expert in the technique ITC (isothermal titration calorimetry) and its application to drug binding experiments.

The department is excited about this new major and anticipates that students will be more prepared for programs in graduate study of biochemistry, for jobs in biotechnology, and for the health sciences. Student enrollment has been very enthusiastic since its recent introduction to new majors.

Maria Goeppert-Mayer Interdisciplinary Symposium to be held at USD

For the past 10 years, Dr. Kim Baldridge (formerly of UCSD/San Diego Supercomputer Center and presently at University of Zurich), along with other women scientists in the San Diego area, have organized a one-day symposium in memory of Nobel Laureate Maria Goeppert-Mayer (1963, Atomic Structure), the first female faculty member in physics at UCSD. You can find details of the event over the last 10 years at their Web site. The symposium is comprised of four talks by women scientists in various disciplines followed by lunch and a poster session. The response to this free one-day symposium has been overwhelmingly positive and, due to continued strong interest in making this an annual event, several faculty members in chemistry and biochemistry have agreed to organize it in Dr. Baldridge’s absence, while maintaining her vision and stellar efforts.

This year’s Maria Goeppert-Mayer symposium will be held in the Manchester Conference Center auditorium on Saturday, April 8, 2006. Talks begin at 8:30 a.m., followed by lunch at 12:30 p.m., and poster session at 1:00 p.m. The event will draw attendees and participants including faculty and students (post-doctoral, graduate, and undergraduate). In years past, over 100 participants from UCSD, Scripps Institute of Oceanography, Salk Institute, Scripps Research Institute, UCLA, CalTech, USD, SDSU, UC Irvine, UC Davis, UC Berkeley and from a variety of local industries have enjoyed the symposium. Don’t miss out!

Log on to the Symposium Web site for registration and information.

Meet Emily Perttu Ė USD Goldwater Scholar (Chemistry & Physics 2006)

My decision to attend USD involved scarcely more deliberation than a game of Eeny, Meeny, Miny, Mo, yet is one that I’ve always looked back on favorably. During my five years as a chemistry and physics student, USD provided me with numerous diverse opportunities that ignited my future in research. My first taste of research was with USD’s Zero-Gravity Team during my sophomore year. Our team designed, built, and tested an experiment on board NASA’s KC-135 microgravity aircraft (“The Vomit Comet”) at Johnson Space Center outside of Houston, Texas. For someone who dreams of becoming an astronaut, the experience of touring NASA’s training facilities, going to dinner with astronauts, and feeling weightlessness was invaluable. I now lead the team, and will be flying my third time this spring.

My research continued in the lab of Dr. Peter Iovine of the USD Department of Chemistry. I’ve worked in his lab for three summers, and in 2005 had the opportunity to conduct my research at the Institut Catala de Investigos Quimicas (ICIQ) in Tarragona, Spain. Once again, it was a remarkable experience that helped me prepare for graduate-level studies.

In 2004, I was awarded the Goldwater scholarship for my success in academics and in research, both of which were fueled by the support of my professors and the learning environment they create. The scholarship not only rewarded my past efforts, but also propelled my future studies. It enabled me to spend the extra year at USD needed to complete my double major, and also gave me the confidence that I could compete with other students across the nation. The faculty at USD provides all the necessary resources for a successful undergraduate experience and it is up to the student to take hold of the opportunity and run with it.

Research Updates

Travels to Antarctica (Joanna Kinsey, Chemistry 2006)

When the opportunity arose to participate in a research cruise to Antarctica, I jumped at the chance. I knew that the likelihood of spending a week in Punta Arenas, Chile, and four weeks aboard the R/V Laurence M. Gould off the Antarctica Peninsula would not come along often, and that it would be well worth it. The goal of the research project was to begin a pilot study of how free-floating icebergs effect the surrounding pelagic environment. There were six principle investigators on board, each with their own individual focus, which included plankton studies, bird, and mammal surveys, as well as measuring isotope concentrations in the water surrounding the iceberg.

For me, the project meant sorting and identifying organisms that were caught during MOCNESS (Multiple Opening/Closing Net and Environmental Sampling System) trawls. Spending hours sorting organisms allowed me to get to know some of the other people on the ship as well as seeing the beautiful sunrises and sunsets that were only a few hours apart. Krill was by far the most abundant organism recovered, but other organisms included polychaetes, pteropods, small fish, and medusas. I had seen some of these organisms before, on videotape or as preserved specimens. However, there is no comparison to a living, moving organism, straight out of the Weddell Sea, Antarctica. In addition to the capture of macroscopic organisms, nutrients were analyzed using the Lachet system, and the icebergs were studied using lasers and a remote operated vehicle.

The experience of going to Antarctica, a place where only approximately 3,000 people travel annually, has heightened my interest in field research and love of traveling. The opportunity to participate in a multi-faceted, hands-on research project made the experience more enjoyable and worthwhile and has taught me how much work goes into studying the world around us. Antarctica is an amazingly beautiful place with many untold secrets. It was nothing like I expected it to be, the water was crystal clear, the sunsets astonishing, and the coastline breathtaking. There was wildlife everywhere, whales, seals, birds, and yes, penguins. As for the pilot project, the time spent in the Weddell Sea raised more questions that need to be answered and made all of us realize that it is a more complex project than originally anticipated, and that additional studies need to be and will be conducted.

Malachowski Lab

My research group continues to invest most of its time on synthesizing new organic compounds that can be coordinated to metal complexes. For years our interest was in making models for biological systems that included metals such as iron or copper, but recently we have moved on to a new project that involves synthesizing organic compounds that coordinate to metals that lead to supramolecular systems. Nicole Janet, Christo Dru, and Ryan Wallenberg have been feverishly working on these systems during 2005 and are continuing their work in 2006. They promise that results are forthcoming, maybe even as soon as today.

In the mean time, I have published a paper entitled, “A chiral, heterometallic metal-organic framework derived from a tris(chelate) coordination complex,” in the journal Chemical Communications (pp 5506-5508, 2005) with Professor Seth Cohen of UCSD. In addition, I published an article entitled, “Undergraduate Research as the Next Great Faculty Divide,” in the American Association of Colleges and Universities journal Peer Review.

Dwyer and Tahmassebi Lab

Dwyer Lab

We began talking about our similar interests in DNA structure and function a number of years ago, and when the department was awarded a grant from the NSF to purchase not one, but two, high field NMR spectrometers, we knew we could bring our collaboration to life. Since 2004, we have had four undergraduates and three high school students work on our project. Our goals are to incorporate non-natural bases into DNA oligomers and determine their structures by NMR spectroscopy. We also use drug binding to the DNA as a sensitive probe of local structural details. We are very grateful to Isis Pharmaceuticals for synthesizing large amounts of our designed DNA oligomers for us. Two students, Joanna Cole and Tim Parr, have done remarkable work to collect NMR data on three DNA oligomers and the complexes they form with actinomycin D. Joanna and Tim have mapped out the assignments of the majority of protons in these systems and are currently quantitating the NMR data in preparation for computational modeling studies. One student (John Butler, currently a graduate student in chemistry at University of Texas, Southwestern) began to synthesize large quantities of a mimic of guanine, G, that we call “H” in which the hydrogen bonding groups (containing oxygens and nitrogens) have been replaced byfluorines and carbons. As of this writing, we own the world’s supply of a DNA oligomer containing this new base and we are poised to prepare three new duplexes for study. Joanna, John, and Tim presented their results at the American Chemical Society national meeting in March 2005 (see above picture).

De Haan Lab

De Haan Lab

Over the past year, research in David De Haan’s smog research group has been conducted by Charlie Koehler and Will Hastings (seniors), Kirsten Loeffler (junior), Nichole Paul (freshman), and Neeraj Sathnur (high school volunteer). Together, we have studied the way that reactive gas-phase chemicals interact with cloud droplets and form haze. We published a paper in the November 15, 2005 issue of Environmental Science & Technology describing how glyoxal (which forms from evaporated gasoline) is taken up by haze particles, making them grow – a process that is probably happening outside your window at this moment if you live in Southern California. The article, for those of you who are interested, can be downloaded free of charge on the web).

Our most recent work shows that glyoxal won’t evaporate once it gets into a wet particle – unless, paradoxically, you make no attempt at evaporating the water. We are close to explaining why this is, we think, but of course our hypothesis will need to be tested in the lab this coming summer!

Iovine Lab

The year 2005 was a productive and exciting one in the Iovine research lab. Supported by grants from Research Corporation and the American Chemical Society, the group made excellent progress on developing the chemistry of a class of boron-containing organic materials. We have published two papers this year. One of the papers was in collaboration with Dr. Jeremy Kua, a colleague at USD. Several students participated in 2005 research efforts: Jennie Fong, Ashley Sullivan, Emily Perttu, Matt Fletcher, and Chris Allen (UCLA student).

We have also established a new collaboration with Dr. Edward Neuwelt at Oregon Health Sciences University (OHSU) in Portland. In collaboration with OHSU we are looking at the chemistry of chemoprotectants – small molecule compounds that offer protection from several side effects associated with platinum chemotherapy.

Kua Lab

This past fall, the Kua lab added another 16 processors to a growing Linux cluster. We are making good progress on several research fronts in our two main research projects: thermodynamics and kinetics of boroxine chemistry, and preliminary steps towards simulating the self-assembly of inorganic frameworks. A joint paper (with the Iovine lab) was published in the Journal of Physical Chemistry last fall, and several more are in the works to be submitted this spring. Keaton Tomlin ('08) will be continuing to calculate transition metal-benzene complexes and Charles Gyselbrecht ('08) is just coming on-board to study boroxine kinetics.

Alumni News

Our Newest Alumni
Chemistry & Biochemistry Class of 2005  

Matthias Barden - employed at Pharmatek

Jennifer Bart - employed at NeoMPS Inc.

John Butler - graduate student in Chemistry at University of Texas, Southwestern

Ashley Dunn - graduate student in Chiropracty at University of Texas, Southwestern

Jennie Fong - graduate student in Chemistry at Massachusetts Institute of Technology (MIT)

Erin Fuller - employed at Pharmatek

Nicholas Marinkovich - employed at Takeda

Makala Maybury - graduate student in Pharmacy at UC San Francisco

Stephanie Sandoval - employed at Diagnostics Products Corporation

Jennifer Schollee - employed at MEC Analytical

Uyen-Uyen Vo - employed at Atmospheric Analysis and Consulting

We look forward to hearing from these alumni:

Tara O’Leary

Zulaika Marty

Kari Mikkelson

Kyle Ries

Lauren Rodgers

Tad Rowe

Gilbert Saguid

Kennedy, Sheila (1976): Safety Coordinator at UCSD.  I've been married to Carl Luster ('76) since that summer; we now have two 6-foot red-haired sons.  Since 1997 I've been part of the lab support staff to the Chem&Biochem department at UCSD.  Now I coordinate health and safety programs, teach lab safety and assist the lab instructors and TAs.

Finocchio (McIntire), Debbie (1988): Chemistry Instructor/General Chemistry Lab Coordinator.

Arruda, Jeannie (1998): Research Associate at Amira Pharmaceuticals ( San Diego).

de la Fuente, Tania (1998): Graduate Student.  I am currently back home getting my Ph.D. in Medicinal Chemistry at Universidad Complutense de Madrid and hopefully will be reading next summer. After that I am still not sure if I will go back to the states for a post doc. I am also teaching chemistry at St. Louis University ( Madrid campus).

Cordaro, Joseph (1999): Post-doc. After graduating from USD in 1999 I went to UC Berkeley and completed my PhD in the summer of 2004. Since then, I have been a post-doc at the ETH in Zurich, Switzerland. This summer I'll return to California for a second post-doc at UCSB.

Medina , Martha (2000): Scientist at Proctor & Gamble.  After USD I graduated from Arizona State with a Ph.D. in Biochemistry in August 2004, where I worked on proteomics of secreted proteins from the fungus Aspergillus flavus. After some time off traveling around the world, I joined Proctor & Gamble in Cincinnati, where I work on hair biology (very different!). I recently bought a house and I am trying to enjoy the cold midwest weather! 

Bailey (Dunn), Denise (2001): Graduate Student. I am in my last year (hopefully) of graduate school getting my Ph.D. in Organic Chemistry. I am working on more of a Chemical Biology project and hope to start interviewing soon for a job in industry. I’ve been running into alumni lately and would love to hear from more of you. I am glad to hear that everyone is doing well. 

Clark, Tim (2001): Graduate Student.  I am in my final year at UC Irvine getting my Ph.D. in Organic Chemistry. In the spring I will start a post-doctoral fellowship at the University of Wisconsin, Madison. 

O'Neill, Bryan (2001): Graduate Student.  I am in my last year at The Scripps Research Institute and I am hoping to defend in August of 2006. My next move will likely be away from traditional science, but I'm not sure what that will be yet. 

Adams (Russell), Hailey (2002): Adjunct Faculty at the University of San Diego.  I'm teaching DNA Science & Technology and Physical Science for K-8 Teachers. 

Burghardt, Ted (2002): Veterinary Student.  I am in my first year of veterinary school at CSU. After USD I worked for 2 years at The Scripps Research Institute and I received my Masters degree in Anatomy. 

Christian, Nilesh (2002): Air Force Officer and Program Manager as of May 2003. I am currently working on the development of new acquisition for the Air Force. It's very exciting to work with and experience future technology for tomorrow's world although it has nothing to do with chemistry. I’m thinking about getting back into chemistry and will soon pursue a graduate degree so I can become a chemistry instructor at USAFA.

Clarke, Kristine (2002): Chemistry Instructor.  I am teaching and coaching softball at Dana Hills High School.

Dooley, Lea (2002): Nuclear Engineer. I'm working onboard USS John C. Stennis (CVN-74). I spent the last year at Naval Nuclear Power School and Prototype, got engaged, and bought a house along the way! Jeff and I will be married later this summer in Alaska.

Humkey, Robert (2002): Graduate Student. I am a 4th year graduate student in Dr. Nigel Richards' group at the University of Florida pursuing a Ph.D. in computational biochemistry.

Fillo, Jeremiah (2004): Research Associate at BioSite, Inc. & Future Medical Student at Creighton University.   I am working in the R&D Chemistry department at Biosite. I have just received a letter of acceptance from the Creighton University School of Medicine! At this time I plan to continue working in San Diego at BioSite Inc. until the end of the summer 2006, at which point I will move to Omaha to attend medical school.

Sullivan, Brian (2004): Systems Engineer. I am working at Raytheon Integrated Defense Systems in San Diego. I am currently applying to Notre Dame for a Master’s program in Mechanical Engineering.

Bart, Jennifer (2005): QC Chemist I at NeoMPS Inc., Inc.  I have been working at NeoMPS, Inc. in Miramar the past couple of months and it’s going great. The people are very nice and I’m using things I learned at USD in chemistry that I never thought I would. I know I have graduated, but I still feel like I am on an extended summer break. I live with Ashley (a chemistry senior at USD) and when I see her studying for a test and registering for classes it makes me realize that I am done with school, for now. I’d love to hear from everyone and I hope all is well!

Fong, Jennie (2005): Graduate Student.  I am a 1 st year graduate student pursuing a Ph.D. in Chemistry at MIT. I am excited to announce that I am now a member of Rick Danheiser's group in the Organic Division. My project(s) will include developing synthetic methodology, total synthesis of natural products, or ideally both. I'm looking forward to the end of classes next summer so I can focus on research. Feel free to contact me with questions about graduate school life or getting into graduate school.

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