Chair’s Column
New Tenure-Track Faculty
New Staff Members
Training Future Faculty
Post Doctoral Fellowship
Student News
Chem Club Highlights
Alumni Highlight
Creative Collaborations
Faculty Research Highlights
Research Corporation Update
New Director Positions
New External Grants

University of San Diego
Department of Chemistry and Biochemistry

5998 Alcalá Park
San Diego, CA 92110-2492
(619) 260-7512

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Chair’s Column

Artwork by Shannen Cravens '11
It is very exciting to share news about the activities of the department over the past year. Our faculty, students and alumni continue to work hard and I am very excited to share some of the results with you in this issue of The Spin.

First, on behalf of the Department, I would like to offer a huge thank you to Dr. Tammy Dwyer for serving as Chair for the past eight years. In the past eight years, we have been through some tremendous changes and growth. These accomplishments were the result of several years of dedicated planning, always working towards our goal of making this department one of the best places for undergraduate students to study chemistry and biochemistry. As examples, we completed the planning process and moved into the new Shiley Center for Science and Technology in 2003. In 2005, we started offering a major in biochemistry and the department changed names to reflect the addition. Based on a 5-year department plan, in 2008 we were awarded a Department Development Award from the Research Corporation for approximately $500K. That funding allowed us to introduce a new research requirement so now all majors in the department participate in undergraduate research. In the Research Updates section below, you will be able to read about the results of their tremendous work in collaboration with faculty in the department. Dr. Dwyer will be focusing her energy on her research program and is currently working on a novel electronic general chemistry interactive “textbook” along with Dr. Charlie Grisham.

In this issue, you will be introduced to some new people and notice the absence of others. We are thrilled to have hired Dr. Lauren Benz as the Clare Boothe Luce Assistant Professor. Her hire is the result of the department being awarded a prestigious named professorship from The Luce Foundation. Mia White, executive assistant, returned to Arkansas to be closer to her family and Desiree Harpe has joined the department. She is a great friendly face and the first place that most people stop when visiting the department. Alnelis Rodriguez, lab technician, moved back to Puerto Rico. We welcome Jessica Kramer as our new lab technician. We look forward to the arrival of Lelia Hawkins in early summer. We wish Dr. Kris Koudelka and Dr. Namandje Bumpus, both JUST Fellows, good luck with their new tenure-track faculty positions. Also, we welcome back Dr. David De Haan from his year-long sabbatical in Colorado. Dr. De Haan was awarded a very prestigious Visiting Fellowship at CU’s Cooperative Institute for Research in Environmental Sciences to support his sabbatical research.

It’s always wonderful to hear from our alumni so feel free to e-mail me just to keep us up to date with where you are and what you’re up to.

Debbie Tahmassebi

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New Tenure-Track Faculty Members:

Dr. Lauren Benz – Clare Boothe Luce Assistant Professor
Dr. Benz joined USD in August 2009 as the recipient of the first named professorship in the department. Dr. Benz is originally from Rhode Island, where she graduated from the University of Rhode Island with a B.S. in Chemistry. She later went on to earn her Ph.D. in Inorganic Chemistry at UC Santa Barbara working with Dr. Steven Buratto, and she completed her post-doctoral research with Dr. Cynthia Friend at Harvard University. Dr. Benz will be teaching General Chemistry, Inorganic Chemistry and Physical Chemistry in the near future. Her research interests are in the general area of surface chemistry, with a focus on energy-related questions. Specifically, she studies surface structure-reactivity relationships and the chemical reactivity and catalytic properties of supported nanostructures.

New Staff Members:

Desiree Harpe

Desiree Harpe joined the department in April 2009 as the Executive Assistant. She supports the Department Chair and provides administrative support for all members of the department.

Jessica Kramer

Jessica Kramer joined the department as Laboratory Technician for the General and Analytical Chemistry courses in March 2010 She obtained her B.S. in chemistry from Marist College in Poughkeepsie, NY in 2009. After completing some graduate courses at UCSB she’s happy to find herself at USD. Growing up on the east coast she always dreamed California was the ideal place to live, which was proven correct on her first trip to Santa Barbara. The minute she stepped off the plane to 70 degree weather in March she knew she never wanted to leave (although she’ll always be an NY sports fan at heart, go Jets!). Jess is constantly fascinated and perplexed by existence, atoms, and consciousness, which leads to a love of chemistry and philosophy (of mind/human action).

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Training Future Faculty: JUST Fellowship Program

The Joint USD-Scripps Training (JUST) for future faculty program offers fellowships to post-doctoral students to complete research at The Scripps Research Institute (TSRI) and mentored teaching at USD. The goal of the program is to prepare JUST Fellows for careers that involve teaching and research with undergraduate students. The progress of our two current fellows is below. We wish both Dr. Koudelka and Dr. Bumpus good luck as they start their careers as Assistant Professors this summer. Congratulations to both of them.

Dr. Kristopher Koudelka

Dr. Kristopher Koudelka is completing his second year as a JUST Fellow. He is particularly interested in understanding events at the molecular scale. In his current class, BIOL 482: Molecular Biology, he uses chemical reactions coupled with protein structures to help his students understand the cellular processes of DNA replication, transcription, and translation. He is also continuing his research on creating viral nanoparticles that specifically target cancer. During the previous summer, he and USD undergraduate student, Shannon Ippoliti, chemically conjugated cancer-homing ligands to bacteriophage lambda (a common virus that infects E.coli). Efficacy and optimization of this formulation are currently being pursued in cell culture experiments. He also welcomes a new baby girl to his family and has accepted a tenure-track faculty position at Carthage College in Kenosha, WI beginning in August 2010.

Dr. Namandje Bumpus

Dr. Namandjé N. Bumpus received a B.A. in biology from Occidental College and Ph.D. in pharmacology from the University of Michigan. Her postdoctoral research, in the lab of Dr. Eric F. Johnson at The Scripps Research Institute, has focused on the regulation of lipid metabolizing enzymes. Namandjé is currently transitioning her research towards investigating the role of drug metabolism in the adverse events associated with HIV therapy. At USD she is teaching an organic chemistry laboratory and is being mentored by Dr. Dwyer. Namandjé is very interested in introducing undergraduate students to the field of pharmacology through both teaching and research. She will begin a position as a faculty member at Johns Hopkins this summer.

Post Doctoral Fellowship Program

Dr. Andrew Korich

Andrew Korich earned his Ph.D. from the University of Vermont in late 2008 where he studied alknye and imine shape persistent macrocycles. In early 2009 he joined Prof. Peter Iovine at the University of San Diego as a post-doctoral fellow. His current research focuses on the preparation of novel boronic acid containing materials with a particular focus on polymers. These polymers are currently being studied as macromolecular reagents for modifying biopolymers, such as lignin. In addition to his research here at USD, Dr. Korich taught organic chemistry laboratory this past Fall and is currently teaching organic chemistry.

Dr. Lelia Hawkins

Lelia Hawkins will be a postdoctoral fellow in the laboratory of Dr. David De Haan starting this summer. Lelia received her B.S. in Environmental Chemistry and Environmental Systems from University of California, San Diego in 2005 and will receive her Ph.D. from Scripps Institution of Oceanography at UCSD in May of this year. Her graduate work has focused on characterization of atmospheric organic aerosol particles from both natural and anthropogenic sources using FTIR spectroscopy, aerosol mass spectrometry, and x-ray spectromicroscopy. At USD, she will be investigating the role of organic nitrogen compounds in secondary organic aerosol formation from glyoxal and mentoring undergraduate students on their research projects. As a graduate student, Lelia enjoyed working with undergraduates and younger graduate students in her research group, in addition to being a teaching assistant in atmospheric chemistry in UCSD's Chemistry department. USD's focus on teaching and commitment to undergraduate research is what drew her to apply for the postdoctoral position here. In Fall 2009, she will be co-teaching Analytical Chemistry with Dr. De Haan.

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Student News:

Stefanie Sacknoff (Biochem '10) Receives the American Chemical Society's 2009 Overcoming Challenges Award
Each year, the Women Chemists Committee of the ACS presents a national award to one undergraduate who has overcome hardships in pursuit of her education. At the ACS conference in Washington DC in August 2009, USD biochemistry major Stefanie Sacknoff was the center of attention as she accepted the award at a luncheon attended by nearly 200 chemists. Stefanie stood before the crowd with poise and confidence as she told the story of her battle with aplastic anemia, a blood disorder marked by the body's inability to produce red or white blood cells and platelets. She also told of being diagnosed as legally blind at the age of eight years. During her second year at USD, Stefanie's condition had progressed to cancer of the bone marrow and she took a leave of absence from her studies to combat the illness. In February 2007, Stefanie underwent a successful bone marrow transplant that gave her new life (plus a new blood type and a taste for coffee!) Stefanie returned to USD in Fall 2008, resumed her studies with gusto and will finish her degree at the end of summer 2010. Following graduation, Stefanie plans to attend graduate school and "give back" by becoming a physician's assistant.

Stefanie and her mother, Valeri, have founded a non-profit bone marrow donor project called "Perfect Match" ( that links donors and recipients. Registration as a potential bone marrow donor requires a simple cheek swab that is taken at the dentist's office.

In a show of support for and immense pride in Stefanie, several faculty members (Tammy Dwyer - who nominated Stefanie for the award), Jeremy Kua and Debbie Tahmassebi, and fellow student Michelle Grau (Biochem '10) attended the luncheon in Washington DC. Congratulations, Stefanie!

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Bridges to Doctoral Institutions – Caitlin Stevens and Hadley Krizner

In concert with the Clare Boothe Luce professorship, the department established a program called “Bridges to Doctoral Institutions” that provides support for two female undergraduate students seeking to pursue graduate studies in Chemistry and Biochemistry. The program pays a summer research stipend for students to spend ten weeks at a top-ranked research institution. This gives the students the opportunity to experience an environment quite different from USD, and gives them a taste of what being in a top-flight Ph.D. program would be like. Faculty work closely with the students in selecting potential mentors that will provide the best possible summer research experience that will encourage students to apply to and be successful in graduate school.

Our first two students were Hadley Krizner and Caitlin Stevens, both Chemistry majors. Their research experience took place in the summer between their junior and senior years. Both students had previously done research at USD. Hadley worked with Dr. Kua calculating the thermodynamics and kinetics of methylglyoxal oligomerization. Caitlin worked with Dr. Iovine on developing novel polyester polymers that feature “sticky ends” capable of binding to and physically modifying certain types of natural polymers.

Hadley joined the research group of Prof. Mark Thiemens at UCSD. Her project was two-fold. Under the close guidance of a senior graduate student, Lauren Brothers, Hadley tested water in fog samples to determine the isotopic ratios of nitrate and sulfate. These samples came from a protected rainforest, and the purpose of the study was to track where pollutants were coming from. Hadley was involved with processing the samples, using chemical separation techniques including ion chromatography, and then analyzing the data after running the samples through a mass spectrometer. Hadley also worked closely with a postdoctoral research fellow, Dr. Gerardo Dominguez, using mathematical tools (MatLab) to analyze back trajectories of pollutants based on experimental data.

Caitlin joined the research group of Prof. Heather Maynard at UCLA. The Maynard group at UCLA is interested in developing novel polymeric materials that marry synthetic polymer scaffolds and biologically-derived molecules such as peptides and proteins. Caitlin was involved in a diverse array of projects that dealt mainly with synthesizing these types of synthetic polymer-biological molecule hybrids. Caitlin learned basic methods in polymer chemistry including instrumental techniques to characterize fundamental physical properties of the newly synthesized materials.

This past Fall, both Hadley and Caitlin applied to Ph.D. programs in Chemistry around the country. They both received multiple acceptances into top-ranked programs. Both Caitlin and Hadley are headed to UCLA. We wish them a successful career in graduate school and look forward to inviting them back to USD to give seminars on new and exciting chemistry.

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In the Navy and Dental School – Stephanie Roadarmel

Stephanie Roadarmel, class of 2010, shares thoughts about her experiences in the Department of Chemistry and Biochemistry and her plans for the future. Stephanie has been an exceptional work study student, twice nominated for WS Student of the year. Additionally, she is the current President of the Chemistry Club.

What are your plans after graduating?

I will be joining the Navy while attending the University of California San Francisco School of Dentistry. (UCSF)

When did you decide to go to dental school, was it something that you wanted to do before you came to USD or was there a particular experience here that leaned you in that direction?

I have always been a very visual person and have been fascinated with teeth and people’s smiles ever since I was about 5 years old. I enjoy the personal aspect of dentistry, interacting with patients and getting to know them.

Tell us about your decision to join the Navy as your pathway to dental school

With today’s economy, I saw it as a great opportunity to finance my education, giving me one less thing to worry about, in addition, it is a great way to travel!

Can you think of a particular class that had a big impact on your academic career?

There have been several classes but the one that stands out would have to be Physical Chemistry. It was so intense and challenging that it taught me to have a strong work ethic, something that I will take with me wherever I go. I learned that with hard work and dedication, anything is possible. It gave me a great sense of accomplishment to conquer P. Chem, and gave me the confidence to meet the challenge of dental school.

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Chem Club Highlights

This year, the USD Chem Club has made successful progress in its hosted events, student involvement, and community outreach. The year kicked off with Chem Club officers visiting all General Chemistry and Organic Chemistry classes to tell students about the opportunities and fun events that Chem Club is involved in. With events like Sundaes on Monday, they were able to successfully bring together students and faculty for a quick chat over a homemade Sundae various times throughout the year. Last semester, they also hosted two “Movie Nights” behind the Shiley Science and Technology building in the DNA garden for a viewing of I Love You, Man and Fast Times at Ridgemont High. Of course they also did their share of helping out the surrounding community by volunteering at events like the ChemExpo at Balboa Park where they presented three demonstrations. During the Spring Semester Chem Club participated in the Annual Expand Your Horizons Conference hosted by USD. The Club hosted a workshop named Household Acids and Bases, where girls were able to play the lab detectives in full lab gear. Chem Club also hosted a booth at the San Diego Science Festival at Petco Park. By focusing on Green Chemistry the club brought along fun demos of solar powered homemade cars, a hydrogen fueled car, and wind powered demos. The club has also made new sweatshirts and t-shirts, which have been a hit even outside of the Chemistry Department. This year Chem Club also co-hosted the beginning of the year Faculty/Student BBQ, and Health Careers Club’s Glasses Drive. Of course the year is not quite over and a Chem Club hosted lunch at the new restaurant on campus, La Gran Terraza, is coming up, along with a visit to a local forensics lab, and to finish out the year, the annual BBQ where this year a competition between homemade solar powered cars is in the works.

Stephanie Roadarmel – Chem Club President

Alumni Highlight:

Dr. Edward (Eddie) Merino; Assistant Professor of Chemistry, University of Cincinnati
Eddie, Renee and Natalie Merino
Dr. Merino was born in San Diego, CA in the neighborhood of South San Diego. He is the son of a gardener and a homemaker whose parents immigrated to this country from Mexico. He had an interest in science from a young age that began with astronomy, moved to exercise physiology in high school and now focused on nucleic acids. After completing his degree at USD (2000), he earned his Ph.D. at UNC-Chapel Hill, working with Professor Kevin Weeks. He completed his post-doctoral research with Dr. Jacqueline K. Barton at Cal-Tech then took a position as an Assistant Professor in 2008.

Tell us about what you do for fun.

I like to play with my 4-month old daughter Natalie, watch Reds games, and walk around the city (doubles as exercise).

How did your USD education prepare you for success in graduate school?

One word comes to mind: Fundamentals. Biochemists are like Jacks-of-all-trades and need to be able to know their fundamentals. You would be surprised how far you can go with just your general and organic textbook. There is a reason those books each have 50 chapters.

When/how did you decide to pursue a career in academia, specifically teaching and research with undergraduate and graduate students?

Side story. In high school I used to play football. I would think to myself how can I get the big hit? Which way should I turn to get the big interception? Despite all this thinking I would never get the big play. Then one day a coach told me “to just focus on the ball and not the play.” After that I would be in just the right place to make a big play. Same went for science. I love nucleic acids. They are just fascinating to me. I always read as many papers on nucleic acids as I can. I would focus on experiments. The papers followed. Soon I landed a great postdoctoral position. After that I found a great place to continue with my research interests.

What classes do you teach at the University of Cincinnati?

I have taught Biochemistry and Biochemistry Lab. I am probably slated to teach general chemistry next year. In graduate school I entered as an organic chemist. I have been moving towards biochemistry ever since.

Can you describe your research program? How did you end up doing research to fight against cancer?

I have two projects. Both projects deal with nucleic acid modification. The first project tries to understand and describe novel means to quantify DNA damage in cancer cells. The second project is aimed at synthesizing DNA damaging agents based on our expertise in DNA modification. I have always wanted to do work that had meaning and purpose. Working on the great cancer problem gets me excited to wakeup and go to work everyday.

What stands out for you about your time as a student at USD that most prepared you for your career at University of Cincinnati?

My research time with Dr. Malachowski. It helped cement my love of academia and research. He allowed us to go into lab and try things. I still study copper, although I examine how it modified DNA.

What advice would you give to current USD students considering graduate school and a similar career path?

Do research in a lab and ask yourself if you could do this 60 hours a week for 8 or so years. If so, you love research. The crazy part of this whole thing is that when you’re a professor, someone else does the work. Always do what you love…don’t just get a PhD. It’s not for everyone.

How did you decided between searching for a faculty position at a Ph.D. granting institution vs. a primarily undergraduate institution (PUI), such as USD?

To tell you the truth I am not sure. I just went with what felt natural.

What do you most value about your USD training?

The positive influence the faculty had. I learned a lot those years.

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Creative Collaborations – A Growing Celebration

Winner of the iPod Touch door prize, Paulo Cortes (left) with the Chem Club President Stephanie Roadarmel (center), and the student invited seminar speaker Professor Eric T. Kool of Stanford University (right).
The annual Creative Collaborations event to celebrate the collaborative research performed by undergraduates in conjunction with faculty at USD was held on April 15, 2010. The event has grown terrifically in the last several years such that it now takes up all of the Halls at the newly renovated UC (University Center)! Our department was represented by 17 posters from our undergraduates and their faculty advisors. To increase the impact of the celebration this year, the Chem Club, in conjunction with the department, coordinated the student invited seminar speaker’s visit to coincide with Creative Collaborations. The goal being that the speaker would be able to see first-hand the highly involved and successful undergraduate research program in our department by interacting with the students during Creative Collaborations as well as to provide the capstone seminar to complete the day of celebration. This year’s student invited speaker was Professor Eric Kool of Stanford University. Professor Kool presented his seminar “DNA Base Replacements: Synthesis, Applications and Cellular Activity” to a packed house of over 100 people in the Manchester Executive Conference Center main auditorium. His talk was very well received by the students and faculty in attendance, especially Paulo Cortes (see photo) who was the winner of the door prize for students in attendance – an iPod Touch! We are grateful to Professor Kool for his involvement with the students: he engaged students at their posters during Creative Collaborations and he made himself available to answer questions at his post-seminar reception and at dinner.

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Faculty Research Highlights:

Benz Research Update

Two new students joined the Benz lab: Tran Le and Karen Cesafsky.

We just received an ultra high vacuum chamber to begin work on studying the decomposition of heteroatom-containing molecules, representative of contaminant structures in petroleum, over the surface of titanium dioxide. We are also gearing up to do some magnetic levitation experiments which involving reactions over polystyrene beads.

Bolender Research Update

Ashley Cobb, Alana Calise and Denise Do overlooking the Rift Valley

One would figure that any sane person, taking on the duties as Honors Director would scale back his research group. Not so…The Bolender Group has expanded to seven students this year. Ashley Cobb (Biochem ’10) and Denise Do (Biochem ’10) have continued their projects on blue crabs and white clams from Magdalena Bay. Both presented their work at the Society for Environmental Toxicology and Chemistry meeting in New Orleans, and both will complete their Honors Theses this semester. Shane Smith (Bio ’12) joined the group this spring. He is currently working with Ashley on the blue crab work and will go with us to Baja to collect his own samples this coming summer.

Alana Calise (Chem ’11) joined the group in the fall semester and is pursuing work on the samples we have brought back from Mbarara, Uganda. Alana joined Ashley, Denise, and myself for our annual visit to Mbarara in January. For the first time, the hospital was up and running, and packed full of patients. Our entire group consisted of 25 people and these included 17 nursing students and faculty, the four of us, and four doctors from Rady Children’s Hospital and Oakland Children’s Hospital. We arrived in high malaria season, and got to see first hand the hospital in action. During our short two-week stay, we got to see the ups and downs of this type of work in Uganda. Six children passed away due to malaria and associated issues during our stay. This led to some very intense discussions on medical ethics and our roll in this realm. You can read more about our journey at:

Sadly, our work in Jamaica will probably never get off the ground. Dr. Rafik Mohammed left USD to take a position in Atlanta. Between Rafik’s departure, and Dr. Carlton Floyd’s elevation to the Associate Provost for Inclusion and Diversity, it is highly likely that our work there will progress no further.

The nanocrystal side of my lab has continued to progress with two students and one alumna working in the lab. Erica Hewitt (Chem ’09), Taylor Caldwell (Biochem ’11) and Scott Belding (Chem ’11) are working projects to optimize the synthesis of these materials to make them more reproducible spectroscopically and to see if we can resolve various size fractions of these nanocrystals. All three will be working on their projects this summer.

Daley Research Update

Lauren Schopp, Grant Ferrell, Christopher Daley, Kyle Cordova and Jessica Cryder

The Daley research group has had a large turnover since the last SPIN with only Jessica Cryder and Kyle Cordova remaining. Since then we have had Grant Ferrell, Lauren Schopp, Amber Vitalo, and Kent Lee pass through our lab. Lauren worked in the lab over the summer after graduating in May ‘09, Kent Lee worked alongside Jessi as a PURE student during summer ‘09, and Amber Vitalo worked in the group for fall ‘09 and will rejoin the group in fall ‘10 to complete her Chem 396W work. Kyle and Grant worked since the spring and summer of ‘09, respectively and are set to graduate this May ‘10. To accommodate the large turnover, we are welcoming Lauren Bernier (joined spring ‘10), Jessica Rodriguez, Daniel Huh, and Eric Czer to the group beginning summer ‘10.

On the research front, our group continues to make strides with significant progress on our enantioselective catalysis project, which is spearheaded by Jessi Cryder. Jessi has synthesized four metal complexes and two key free chiral ligands and characterized all of them by X-ray crystallography! It is rare that an undergraduate will graduate with 6 crystal structures to their name. So, if you see Jessi around, please give her a big “congrats”. Also, Dr. Daley would appreciate it if you could call her “Crystal” Cryder as he is trying to get the nickname to stick.

The bioinorganic research has also had successes with the isolation and structural characterization (including X-ray crystallography) of five key compounds. This work was led by the efforts of Kyle Cordova, Grant Ferrell, Lauren Schopp, and Amber Vitalo all of whom played a significant role in the research.

Owing to all our successes, most of the group (Dr. Daley, Kyle, Grant, Jessi, and Lauren Schopp) went to the American Chemical Society National Meeting in Washington, DC (August ’09) to present our work. The group did a wonderful job with their presentations and they also got the opportunity to visit museums and several other sites on the trip.

Overall, the Daley Group had a great year and we hope to have more of the same in the upcoming one. As always, while we will have four new members in the group this summer, we will be looking for 1-3 more students to join the group come Fall ‘10, whether for Chem 396W, Chem 496, or just as volunteers.

While Dr. Daley does not Blog, Text, or Tweet, you can still follow the group’s progress (including each individual research member) on the Daley Group Webpage at .

De Haan Research Update

David De Haan, Jake Turley and Vanessa Blasic

The De Haan research group is up and running at USD again after a temporarily relocation to the University of Colorado for Dr. De Haan’s sabbatical. USD students Kyle Cordova, Grant Ferrell, Stephanie Wood, and Jake Turley enjoyed summer research experiences in Boulder working with Dr. De Haan on the atmospheric chemistry of small aldehyde molecules and also characterizing the ability of simulated Martian soils to destroy atmospheric methane with CU’s Margaret Tolbert. Back at USD, students Vanessa Blasic, Hiromi Takano, Jake Turley, and Julia Kononenko have been busy measuring reaction rates and characterizing products of the reactions of small aldehydes with amines, determining the importance of these reactions in clouds and atmospheric particles.

Major findings from our group this year include the discovery of two new pathways to atmospheric particle formation. The first is a reaction between glyoxal and amines, which produces nitrogen-containing ring structures, and, in some cases, polymers. One of these amines, methylamine, a volatile molecule with a molecular mass of only 31, had not previously been implicated in aerosol formation. This work was published in early and mid-2009 (D. O. De Haan, M. A. Tolbert, J. L. Jimenez, “Atmospheric condensed-phase reactions of glyoxal with methylamine.” Geophys. Res. Lett. 36 L12201 (2009), doi:10.1029/2009GL037441; D. O. De Haan, A. L. Corrigan,* K. W. Smith,* D. R. Stroik,* J. J. Turley,* F. E. Lee,* M. A. Tolbert, J. L. Jimenez, K. E. Cordova,* G. R. Ferrell,* “Secondary organic aerosol-forming reactions of glyoxal with amino acids.” Environ. Sci. Technol. 43 (8) 2818-2824 (2009), doi:10.1021/es803534f). The second set of new pathways to particle formation are the self-reactions of glyoxal and methylglyoxal, which can polymerize rather than just evaporating from cloud droplets, as was previously assumed. This work, based on data collected by Ashley Corrigan, Stephanie Wood, and Jake Turley, showed that 33% of glyoxal and 19% of methylglyoxal polymerize under atmospheric conditions (D. O. De Haan, A. L. Corrigan,* M. A. Tolbert, J. L. Jimenez, S. E. Wood,* J. J. Turley,* “Secondary organic aerosol formation by self-reactions of methylglyoxal and glyoxal in evaporating droplets.” Environ. Sci. Technol. 43 (21) 8184-8190 (2009), doi: 10.1021/es902152t).

Dr. De Haan used his sabbatical to establish new collaborations with CU Professors Margaret Tolbert, Jose Jimenez, and Veronica Vaida. Collaborative projects continued within the department (Dr. Jeremy Kua) and with the Energy Policy Initiatives Center (Director Scott Anders) at USD’s School of Law. These projects resulted in several additional publications (S. J. Anders, D. O. De Haan, N. Silva-Send, S. Tanaka, L. Tyner,* “Applying California’s AB 32 targets to the regional level: a study of San Diego County greenhouse gases and reduction strategies.” Energy Policy (2009), doi:10.1016/j.enpol.2009.03.009; . H. E. Krizner,* D. O. De Haan, J. Kua, “Thermodynamics and kinetics of methylglyoxal dimer formation: a computational study.” J. Phys. Chem. A 113 (25) 6994-7001 (2009), doi:10.1021/jp903213k; J. L. Axson, K. Takahashi, D. O. De Haan and V. Vaida, “Gas-Phase Water Mediated Equilibrium Study Between Methylglyoxal and its Geminal Diol.” Proc. Nat. Acad. Sci., in press, 2010).

Finally, there was a notable personnel ‘trade’ with the group of Scripps Institution of Oceanography Professor Lynn Russell: Ashley Corrigan, winner of multiple research awards at USD, left the De Haan group upon graduation from USD to become a graduate student in the Russell lab, while Lelia Hawkins will be finishing her Ph.D. in the Russell group this May and joining the De Haan lab as a post-doctoral fellow.

Dutnall Research Update

Elyssa Pickle, Bob Dutnall and Ryan Brennan

The Dutnall research group is moving forward in its studies of proteins involved in packaging DNA in cells. We have submitted a paper describing a novel method we have developed for making histones in bacteria and are continuing our studies of the structure and function of a histone acetyltransferase enzyme (Hat1) that is involved in gene regulation.

Ryan Brennan has been working on Hat1 in a project that is aimed at understanding how it recognizes and modifies a specific histone target. Ryan has been supported by a SURE fellowship (Summer ’09) and a Lawrence Hinman Honors Research Grant. Ryan has expressed mutant versions of the yeast Hat1 protein that lack one of its two structural domains. He is currently trying to purify the mutant proteins so that he can measure their enzymatic activity and compare it to the intact Hat1 protein. This will allow him to determine whether or not the deleted domain plays a significant role in histone recognition. Ryan will graduate this year and we wish him well as he moves on to dental school in the Fall.

Two new students, Elyssa Pickle and Allison Bigeh, also recently joined the lab. Allison is working on cloning and expressing the human Hat1 protein. Her studies of the human enzyme will complement our previous work on yeast Hat1 and will allow us to more directly investigate the role of Hat1 in human diseases such as cancer. Elyssa is working on a protein called Hif1 that interacts with Hat1 and histones and helps package DNA. She is currently purifying Hif1 and histones and using our novel histone expression methodology to create co-expression plasmids to produce Hif1-histone complexes in bacteria. Elyssa aims to understand how Hif1 interacts with histones and how this complex interacts with Hat1 and helps assemble histones onto DNA. Elyssa will continue her work in Summer ‘10 supported by a SURE fellowship.

Dwyer Research Update

Shannen Cravens, Alyssa Navapanich and Shannon Ippoliti

My research group has continued to focus on determining solution structures of DNA oligomers containing novel, non-natural nucleobases. Shannen Cravens (Chem '11) has done a marvelous job completing the structure of a duplex containing a GT base pair in complex with the drug actinomycin and she is currently putting the finishing touches on a complex between actinomycin and a duplex containing a guanine:difluorotoluene pair. Stefanie Sacknoff (Biochem '10; not pictured), Shannen Cravens and Alyssa Navapanich (Chem '11) have contributed to completing NMR assignments of a duplex containing a non-hydrogen bonding mimic of guanine (that we call H) paired with a thymine. Alyssa is beginning to compute the solution structure of that duplex as I write this update. Finally, I've just co-authored a manuscript with Floyd Romesberg at the Scripps Research Institute on the solution structure (our contribution), mechanism of replication and optimization (their contribution) of an unnatural base pair that, despite having little in common with a natural base pair (except aromaticity), is processed nearly as well by polymerases! Danielle Pfaff (Biochem '08) and Shannon Ippoliti (Biochem '11) made significant contributions to the project. Finally, I am excited about a new project I've undertaken. Along with my terrific colleague and friend, Charlie Grisham at the University of Virginia, I will be writing a new digital textbook for General Chemistry! We are under contract with W.H. Freeman and so far so great - we hope to bring the project to completion in 2013.

Iovine Research Update

Andrew Korich, Abe Ichinoe, Amanda Walker, Caitlin Stevens, Peter Iovine and Chris HIncke

Research in the Iovine lab continues to expand in scope with the lab moving more and more towards a polymeric materials focus. The group recently returned from the ACS Meeting in San Francisco where Caitlin Stevens and Christopher Hincke presented a poster. In 2010 our group published a review article focusing on the chemistry and applications of boroxine chemistry. Review articles are a great opportunity to summarize a field but it was of great surprise that we were awarded the journal cover. The review appears in Dalton Transactions.

In August of 2009 Ben Streifel presented a poster at the 236th ACS National Meeting in Philadelphia. Ben graduated in the spring of 2009 and began his Ph.D. studies at Johns Hopkins University. Ben has skillfully navigated his first year course work and indicates that he recently joined the Tovar Lab.

Current Iovine group members include Abe Ichinoe, Christopher Hincke, Amanda Walker, and Caitlin Stevens. Chris and Caitlin will graduate in the spring of 2010 While Abe and Amanda will conduct full-time research during the summer of 2010. Chris and Caitlin will begin graduate school next fall but have not finalized their plans. Abe is medical school bound while Amanda looks forward to graduate school.

One of the biggest changes in the Iovine Lab has been the arrival of post-doctoral fellow Andrew Korich. Andrew completed his Ph.D. at the University of Vermont and joined the lab in February 2009. Andrew has already made substantial contributions to our research agenda and continues to provide fantastic mentoring to undergraduate students. Andrew is currently teaching second semester organic chemistry!

Kua Research Update

Chris Lee, Lorenzo Bautista, Rowena Daly, Elizabeth Cummings, Jeremy Kua and Hadley Krizner

ch group has made progress in several fronts. Hadley Krizner ('10) published her first paper on the oligomerization of methylglyoxal, and is now working on understanding the reaction of glyoxal and amines to form imidazoles. Elizabeth Cummings ('10) is working on the cyclization of nitriles to form triazines catalyzed by zinc chloride. Rowena Daly ('10) had her first paper published on the self-assembly of antimony trichloride and dioxane published. Keaton Tomlin ('08) who started the project is a co-author. Lorenzo Bautista ('11) has made good progress in parameterizing a reactive force field for boroxines. Christopher Lee ('12) is taking over preparing metal-benzene self-assembly force fields started by Calvin Schneider ('09) who has started graduate school at UC-Irvine. Hadley, Elizabeth, Rowena, Lorenzo and Chris had their poster abstracts accepted at the American Chemical Society national conference in San Francisco this March so we'll be having a group trip!

Malachowski Research Update

Lindsay Row and Michelle Grau

Our research continues to evolve as we have moved into making organic molecules called dipyrromethenes that can bind to metal ions. Not only do they bind to metals but they make the most beautiful, intense colored compounds imaginable. We are particularly fond of the orange ruthenium complexes and the green copper complexes. My students (Michelle Grau, Alex Dru, Taylor Hepp, Jordan Thomas and Lindsay Row) have made some impressive progress this year as we have been able to make a large series of new metal complexes. With the help of Arnie Rheingold at UCSD, we have solved the structures of twelve new compounds and are in the process of writing up many of these new results. We seem to spend lots of time in the lab and not enough time writing up the results as we have a nice backlog of work to publish. Summer is coming so the amount of time available to write will increase.

We did publish two papers detailing our chemical results from an earlier project. These publications were, “Copper(II) Complexes of a Biphenyl-based Ligand: Tuning the Needs of the Metal with those of the Ligand,” Polyhedron, 28, 393-397, 2009, Mitchell R. Malachowski, Ashraf S. Kasto, Mark E. Adams, Arnold L. Rheingold, Lev N. Zakharov, Lawrence D. Margerum, Matthew Greaney. The second one was: Mitchell R. Malachowski, Mark E. Adams, Daniel Murray, Ryan White, Nadia Elia, Arnold L. Rheingold, Lev. N. Zakharov and Richard S. Kelly, “Copper(II) Complexes of Bidentate Ligands Containing Nitrogen and Sulfur Donors,” Inorganica Chimica Acta, 362, 1247-1252, 2009.

I also have continued to pursue my work on the impact of undergraduate research on students and student learning and have published a series of articles and chapters in books on this topic during 2009. I have run many workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities. This work will accelerate over the next four years as I (along with three colleagues from other institutions) have received a $1,000,000 grant from the National Science Foundation to work with state systems of higher education that are interested in doing more undergraduate research. Let the fun continue.

Matulef Research Update

Sabrina Phillips and Jennifer Wooley

From unpacking boxes to lipid bilayer recordings, the Matulef lab has had a busy first year at USD. Our lab began by focusing on two projects both aiming to help understand the molecular mechanism and physiological importance of a chloride-proton antiporter found in E. coli (called CLC-ec1).

Jennifer Wooley (’10) began her work in the lab by unpacking LOTS of glassware just before the start of the spring 2009 semester. CLC-ec1 had been reported to be important in helping bacteria survive at low pH and also helping bacteria to swarm properly. Jenny set out to test whether proton movement or chloride movement are critical for extreme acid resistance. Holly Hinderberger (’09) joined her efforts at understanding the physiological roles of CLC-ec1 last summer by examining the importance of CLC-ec1 in swarming assays.

Our lab is also interested in using small molecule inhibitors as tools to probe the mechanism of CLC-ec1 function. Sabrina Philips (’12) spent the summer in the lab testing the mechanism of a novel inhibitor of CLC-ec1 recently discovered by the Maduke and Du Bois labs at Stanford University. In order to do this, Sabrina learned how to purify CLC-ec1 protein, reconstitute it into lipid vesicles, and perform proton flux assays to measure protein activity with a variety of inhibitor concentrations. She found that this inhibitor prevented proton flux through CLC-ec1. In order to characterize the properties of inhibition in more detail, we built a lipid bilayer rig. This allows us to measure activity (in the form of current) while controlling the voltage across the membrane along with the chloride and proton concentrations across the membrane. Jennifer Wooley worked through the fall semester and then Sabrina came back to join her this spring. Both Jenny and Sabrina have been working diligently to learn how to do lipid bilayer recordings and find partitions that produce the most stable bilayers. We are looking forward to hopefully having some more thorough characterization of this inhibitor to report in the next edition of the Spin.

Mills Research Update

Kaitlyn Dang and Michelle Dominguez

The Mills research group continues to make progress in understanding the role of metals in proteins and how they get there. We have expressed and purified Fur proteins from 2 bacteria – Shewanella oneidensis, and Pseudomonas aeruginosa. We have also been able to titrate several metals into each of these proteins. Joseph Schneider, Julia Becherer and Shayna Herskovic had all been working on this project but graduated in May of 2009. Michelle Dominguez, Jamie Custodio and Jourdain Artz took over from them. Michelle will graduate this May and Jamie moved away, so Jourdain will be on his own for a while. Jourdain is starting to work with our instrument from Silicon Kinetics to measure Fur-DNA binding. Our work with the copper amine oxidases has also been progressing. Kaitlyn Dang has been working to understand cofactor reactivity and the role of copper in these enzymes. Through a collaboration with a lab in Montana, we have been supplied with the amine oxidase from pea seedlings. Jennifer Nguyen spent last summer and the fall developing methods for removing copper from this enzyme and replacing it with cobalt. Kaitlyn and Jenn are now characterizing the kinetics of the cobalt-substituted PSAO. Both of them will graduate this May.

Tahmassebi Research Update

Debbie Tahmassebi, Michael Harlander-Locke and Michael Hughes

o have been hard at work in the Tahmassebi group over the past year and a couple of excellent students graduated in May 2009. Ben Huebner graduated and started medical school in Nebraska. Will Porterfield also graduated and is taking a few years off before heading to graduate school.

Over the summer, Jennifer Fleischmann focused on the synthesis of several Ru(bipy)3 amino acid complexes, working to determine if the syntheses proceed with enantiomeric selectivity. She completed several syntheses and the analysis of structure by NMR. Currently, Michael Harlander-Locke is continuing work on the project. Michelle Grau received funding, based on a research proposal that she had written, from the prestigious American Chemical Society Division of Organic Chemistry Summer Undergraduate Research Fellowship. Over the summer, her work in the lab focused on the multi-step synthesis of a DNA nucleoside analog of cytosine. Michael Hughes is continuing work on the synthesis and we are very close to the final product. Along with a high school teacher and USD alum Kristy Clarke, Michael will continue work on the project this summer. We are hopeful that we can complete the synthesis, scale it up, get the nucleoside into DNA and then collaborate with the Dwyer group on the NMR structure determination. Last summer I also hosted a high school teacher, Susanne Nelson who worked to determine a method for measuring the concentration of ascorbic acid in Kool-Aid samples using stop-flow fluorescence. Katie Scott continued the project in the fall and put the finishing touches on the data collection and methodology. We expect to complete a manuscript detailing their work and results this summer. This past year, a manuscript detailing several years of excellent work completed by alum Will Porterfield was published : “Synthesis of a Fluorescence 2’3’-Dideoxycytosine Analog, tCdd” Porterfield, William; Tahmassebi, Deborah; Bioorganic and Medicinal Chemistry Letters 19 (2009) pp. 111-113. 10.1016/j.bmcl.2008.11.015.

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Research Corporation Update

Summer 2009 Research Faculty and Students in Chemistry and Biochemistry

We completed our first year of the Research Corporation Department Development Award. The award has had significant impact on the level of undergraduate research and scholarship in the department. The graph below comes from the sponsored programs annual reports and clearly indicates the pay-off from the hard work that the faulty in the department have put into increasing the level of external funding for research with our students.

As part of the Department Development Award, we committed to achieve the benchmarks shown below. We were very pleased to be able to report to the Research Corporation that we surpassed every single one of our benchmarks. Additionally, we are on target to surpass our Year 2 benchmarks as well. This impressive result would not be possible without the dedication of everyone in the department and the excellent work of our students.

Department Totals

June 1, 2009

Year 1

1. Peer-reviewed research publications (published or in press)



2. Conference presentations by faculty member (research, national)



3. External research funding obtained



4. Research proposals submitted and/or funded



5. Percentage of graduates who have research experience



6. Number of student presentations at non-USD conferences



We have just implemented a research requirement for all chemistry and biochemistry majors. The percentage of graduates who have research experience will be at 100% by the end of 2011.

Funding from The Research Corporation allows us to take many more students to national conferences to present their research results. Check out this huge group from the recent national American Chemical Society meeting in San Francisco.


Students and Faculty out for some great Indian Food in San Francisco
Students and Faculty out for some great Indian Food in San Francisco
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New Director Positions

With funding from the Research Corporation, we made a few changes to the structure of the department in order to facilitate and support our research activities. We have introduced new Directors of General, Organic and Biochemistry.

Debbie Finocchio – Director of General Chemistry

In this new position, I teach three classes per semester and coordinate the general chemistry lecture and laboratory curricula. I also write all lab materials and maintain the student and instructor resource sites. In addition to regular lab instructor meetings, those of us teaching lecture have been meeting for “coffee chats” where we discuss pedagogy and ideas. I have also been organizing our demo kits/info to make it more convenient for lecturers to do demonstrations.

In the past couple of years we’ve been inundated with students wanting to take general chemistry. (Forty students on a wait list last fall! An extra section of lecture/lab added this spring! One of this summer’s courses already full!) Because of these enrollment challenges, I was asked to participate in a committee whose goal is to modernize/revamp the college’s system for summer freshman advising. This new system will organize data to make advising more efficient, benefit incoming freshman and preceptors, and will also help departments identify early on if they need to add extra sections of a course.

One perk of this position is that I now have summers off, which gives me time to explore extracurricular interests, one of which is watercolor painting. Last summer I participated in a juried art show in Pacifica called the “50/50 show”. Each of the 64 artists completed a themed piece of artwork every day for 50 days straight and exhibited the 50 works for a month in late summer.

This year I’ve particularly enjoyed teaching my first preceptorial and planning/hosting a wine appreciation workshop and a series of book club dinner meetings (Napoleon’s Buttons: 17 Molecules that Changed History – highly recommend it!) Both events were funded by USD’s Enhanced Student-Faculty Interaction grants.

Kelli Khuong – Director of Organic Chemistry

In the last couple of years, I have overseen several changes to organic chemistry lab. One big change was the creation of an organic chemistry lab website in place of a traditional textbook. This change has allowed me to tailor the weekly experiments: (a) the background information is written knowing exactly what material the students have already covered in lecture, (b) the procedure matches the equipment and instruments that are available to our students, and (c) I am able to include links to videos that highlight the new techniques. Another big change is the implementation of majors’-only lab sections in Chem 302L (second semester organic lab). The majors’-only lab sections are reserved for declared chemistry and biochemistry majors and the maximum number of students in these sections is limited to 12 (instead of the usual 15). The instructors for these sections have really focused on creating a community among the majors while allowing these students to have more individual time on the various instruments. These students have also piloted several new experiments. Finally, while the general structure of the two semesters of lab remains the same (first semester features a variety of organic techniques and second semester focuses on using those techniques in the context of synthesis), I have intentionally chosen to implement new experiments that involve the answering of a question or the solving of a puzzle in addition to the synthesis of a particular molecule.

Bridget Salzameda – Director of Biochemistry

As the director of biochemistry, Dr. Salzameda maintains biochemistry lecture and laboratory curricula and assists with course technology and administration. She continues to teach courses in biochemistry and also works with Sharon Ferguson, the biochemistry lab technician to coordinate biochemistry laboratory experiments. For Fall 2008, Dr. Salzameda helped develop and implement departmental course assessment of CHEM 331 (biochemistry lecture) and provided results to the university. Dr. Salzameda has also been active in research at USD resulting in the publication of two scientific articles with Dr. Leigh Plesniak - one in FEBS letters and the other in Chemical Biology & Drug Design. In addition to teaching, she has also participated in Expanding Your Horizons (EYH), a group dedicated to encouraging young women in science and mathematics.
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New External Grants Obtained by Chemistry and Biochemistry Faculty in 2009

Faculty and Student Co-Authored Research Publications in 2009 (student co-authors designated by *):

  • Kua, J.; Daly, R. C.*; Tomlin, K. M*.; van Duin, A. C. T.; Brill, T. B.; Beal, R. W.; Rheingold, A. L. J. Phys. Chem. A, 2009, 113, 11443-11453. 
-assembly of SbCl3 and 1,4-dioxane: A cubic structure connected by very weak bonds."
  • David O. De Haan, Ashley L. Corrigan,* Margaret A. Tolbert, Jose L. Jimenez, Stephanie E. Wood,* Jacob J. Turley,* “Secondary organic aerosol formation by self-reactions of methylglyoxal and glyoxal in evaporating droplets.” Environ. Sci. Technol. 43 (21) 8184-8190 (2009), doi: 10.1021/es902152t
  • S. J. Anders, D. O. De Haan, N. Silva-Send, S. Tanaka, L. Tyner,* "Applying California╒s AB 32 targets to the regional level: a study of San Diego County greenhouse gases and reduction strategies." Energy Policy (2009), doi:10.1016/j.enpol.2009.03.009
  • D. O. De Haan, A. L. Corrigan,* K. W. Smith,* D. R. Stroik,* J. J. Turley,* F. E. Lee,* M. A. Tolbert, J. L. Jimenez, K. E. Cordova,* G. R. Ferrell,* "Secondary organic aerosol-forming reactions of glyoxal with amino acids." Environ. Sci. Technol. 43 (8) 2818-2824 (2009), doi:10.1021/es803534f
  • D. O. De Haan, M. A. Tolbert, J. L. Jimenez, “Atmospheric condensed-phase reactions of glyoxal with methylamine.” Geophys. Res. Lett. 36 L12201 (2009), doi:10.1029/2009GL037441
  • Korich, Andrew; Clarke, Kristine; Wallace, David; Iovine, Peter M. “Chemical Modification of a Lignin Model Polymer via Arylboronte Ester Formation Under Mild Reaction Conditions”. Macromolecules 2009, 42(16), 5906-5908.
  • H. E. Krizner,* D. O. De Haan, J. Kua, “Thermodynamics and kinetics of methylglyoxal dimer formation: a computational study.” J. Phys. Chem. A 113 (25) 6994-7001 (2009), doi:10.1021/jp903213k.
  • Boyd, M.; Wesemann, J. Eds;. "Broadening Participation in Undergraduate Research: Fostering Excellence and Enhancing the Impact."Council on Undergraduate Research; Anticipated publication date: February 2009.
  • Porterfield, W.*; Tahmassebi, D.;" Synthesis of a Fluorescent 2'3'-Dideoxycytosine Analog, tCdd." Bioorganic & Medicinal Chemistry Letters 19, 111-113 (2009).
  • Mitchell R. Malachowski, Ashraf S. Kasto, Mark E. Adams*, Arnold L. Rheingold, Lev N. Zakharov, Lawrence D. Margerum, Matthew Greaney, “Copper(II) Complexes of a Biphenyl-based Ligand: Tuning the Needs of the Metal with those of the Ligand,” Polyhedron, 28, 393-397, 2009.
  • Mitchell R. Malachowski, Mark E. Adams*, Daniel Murray, Ryan White*, Nadia Elia, Arnold L. Rheingold, Lev. N. Zakharov and Richard S. Kelly, “Copper(II) Complexes of Bidentate Ligands Containing Nitrogen and Sulfur Donors,” Inorganica Chimica Acta, 362, 1247-1252, 2009.

Please consider a donation to support the Department of Chemistry and Biochemistry. We would love to start a special alumni fund to support the research and scholarship of current students.

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