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Department of

Chemistry and Biochemistry

Chemistry Newsletter 2012

Chair’s Column

It has been another tremendous year in the department. The Department of Chemistry and Biochemistry remains one of the most vibrant areas on campus. The quality of our students, staff and faculty allow us to achieve great success. Most important this year is a huge THANK YOU to our wonderful alumna/e who supported an important new fellowship for Chemistry and Biochemistry majors. Read about Michael Bagley, the first awardee. We plan to continue and even expand this fellowship so please consider attending our second annual Summer Reunion and Fundraiser in June and/or contributing to the Fellowship. The department is working very hard in order to provide as much support to our undergraduate research students as we can.  Please consider making a donation directly to the department.

Dr. Tahmassebi - Artwork by Shannen Cravens '11

Artwork by Shannen Cravens '11

This past year, we lost some dear friends and gained some new ones. Thank you to Mitch Malachowski for writing such a thoughtful dedication to Dr. Jack Opdycke. One thing that has not changed over time in this department is our amazing students. There is nothing more satisfying than hearing from our majors who have gone on to great success in a multitude of areas. Often, people end up in careers they could not even fathom while undergraduates here. In this issue, you’ll hear from four different alumna/e. What grabbed me the most is that the common thread they all share is experience in undergraduate research while at USD. At the time they all graduated, research was not required for our majors. However, undergraduate research has always been an important part of our curriculum. Their experiences exemplify the value that undergraduate research has – especially in ways that are not always obvious at the time.

Lastly, we are working hard to stay in touch with everyone. Please stay connected by “liking” our new department Facebook page and by joining the University of San Diego Department of Chemistry and Biochemistry Alumni Group on LinkedIn.

Welcome to the Department Back to top

Timothy Clark, PhD Timothy Clark, PhD joined the department in July 2011 as an assistant professor in organic chemistry. He was born and raised near San Diego, CA, and obtained his BA degree in chemistry at the University of San Diego in 2001. For his graduate work, Dr. Clark attended the University of California, Irvine, where he worked with Professor Keith Woerpel, and obtained his Ph.D. in organic chemistry in 2006. After completing his Ph.D., Dr. Clark was a Ruth L. Kirschstein NIH postdoctoral fellow at the University of Wisconsin-Madison with Professor Charles Casey. He then held a faculty position at Western Washington University from 2007–2001. Dr. Clark will primarily teach in the area of organic chemistry and his research area involves the development of catalysts that mediate organic reactions. Dr. Clark and his wife Nicole have three daughters, Hannah (6), Hope (3), and Miriam (1).



Andrew Roering, PhDAndrew Roering, PhD received his PhD in March 2011 with Rory Waterman at the University of Vermont studying catalytic phosphorus bond forming reactions.  He joined the group of Tim Clark as a post-doctoral fellow in the summer of 2011 to work on copper catalyzed diboration and iridium catalyzed ortho-borylations. Although formally trained in organometallic chemistry, he is excited to learn more about organic transformations and to teach organic chemistry. Dr. Roering is currently teaching organic chemistry and plans on pursuing a job in academia as a professor at a PUI (Primarily Undergraduate Institution).




Transitions Back to top

Dr. Kim Matulef

A new baby and an unsolicited job opportunity for Dr. Matulef’s husband to work close to their families in Portland, OR, led to the difficult decision for her to resign from her position USD this past January. She is just starting a position as a Senior Research Scientist at Oregon Health & Science University studying potassium ion channels in the lab of Dr. Francis Valiyaveetil. She is  excited to learn how to do unnatural amino acid mutagenesis to introduce precise chemical changes into ion channels.

Bridget Salzameda

Since her departure from USD Bridget (’01) has relocated to Orange County to join her husband, Nicholas (’01) who is an assistant professor of chemistry at CSU Fullerton. Dr. Salzameda took a position as a chemistry lecturer and general chemistry coordinator in the Schmid College of Science at Chapman University. She is enjoying her work at Chapman and her time with her family.

Jack Opdycke (1935-2011)

We were saddened by the death of retired USD physical chemistry professor Jack Opdycke who passed away on May 25, 2011. Dr. Opdycke, who retired in 2007, was a fixture in the chemistry department as he taught at USD for 40 years as one of the most student friendly faculty members in the history of the College.

Jack received his bachelor’s and Ph.D. degrees from UC Riverside and then went off to Fort Collins College in Durango, CO where he took his first teaching job. After teaching at Fort Collins for two years, Jack came back to southern California and took a position at the San Diego University College for Men (the men’s college portion of what is now USD).

Jack was one of the first to teach “across colleges,” and that experience helped to foster communication between the two schools. Jack was among a group of about six professors who started a grassroots effort to link the men’s and women’s colleges. This group organized a week-long seminar in which the faculty from the two colleges met to discuss important issues common to both. The outcomes of these brainstorming sessions led to the development of the merger of the two colleges, which took place in 1971. How many of us can say that we helped start a University? Over the years, Jack was a force at USD as he served the University in many capacities including functioning as chair of the faculty on two occasions and by serving on just about every committee that ever existed.

Early in his career, Jack published a number of research articles on topics such as molar volumes and compressibilities, along with probing heat capacities and designing improved calorimeters. He also was an expert glass blower as he was part of a generation that still made their own scientific apparati. He was a master at saving broken glassware and at fabricating amazingly intricate vacuum lines and various set-ups and he saved the department unfathomable amounts of money via his glasswork. Later in his career he developed an interest in membranes and did considerable research in this area for local chemical companies.

Jack was frequently referred to as “Smiling Jack” because of his warm personality and his approach to students. He most commonly taught Physical Chemistry, General Chemistry and Chemistry and Society and his office was frequently packed to the gills with students. He gave his students constant attention and had an endless capacity to help them maximize their potential and they responded with some of their best work.

In many ways, Jack was way ahead of his time. For example, he was on the leading edge of implementing technology in the classroom. He and Sister Pat Shaffer received funding for and implemented Class Talk, a computer-based classroom student response system (the current rage is using clickers to do the same thing 20 years later) and he used many technologies in his courses, including smart boards, WebCT and PowerPoint presentations long before they became fashionable.

Jack was a life long tennis player and his competitive nature came out on the court. He spent countless lunchtime hours on the courts behind Camino Hall where he frequently got the best of other faculty and students with his patience, wild spins and nuanced game. Jack and his wife Judy have six children and six grandchildren and amazingly, five of their children attended USD.

Over the years, Jack saw many changes at USD as we went from two colleges to one, we grew by five-fold, and the chemistry department moved from Serra Hall to Camino Hall and then to the Shiley Science Center. What has remained the same is the commitment of the Chemistry and Biochemistry Department to our students as we have continued to take our cues from our predecessors such as Jack Opdycke. In this way, his legacy lives on in all of us.

Student News Back to top

Chem Club and Social Events

The Chem Club remains very active and engages students in social and outreach events. One of the highlights is the end of the year BBQ when student awards are given out and the students and faculty share a friendly softball game (had to rub those results in one more time!). The Chem Club received a Commendable Award for its activities during 2010-2011 which was recently presented at the National ACS meeting in San Diego.

StudentsEnd of the Year BBQ and Awards: Faculty - 18; Students - 8

Bridges to Doctoral Institutions

The Bridges to Doctoral Institutions program was created to give female USD students in chemistry and biochemistry the opportunity to experience life at a graduate degree-granting institution for one summer prior to applying to graduate school. Students chosen for this program work closely with faculty to identify an appropriate mentor with a research program in their field of interest. The goal of this program is to increase the number of women successfully earning their Ph.D.’s in Chemistry and Biochemistry.

In its third iteration, USD students Amanda Walker (’12) and Elyssa Pickle (’12) worked for 10 weeks over the summer to hone their research skills and experience what it would be like to be a graduate student. Amanda worked with Paula Hammond on the development of fuel cells at MIT, and has recently been accepted to a number of graduate schools. Elyssa studied an enzyme important to the repair of DNA in the laboratory of Lorraine Pillus at UCSD. She currently holds a position in the pharmaceutical industry. We wish them both much success in their future careers.

Student and Alumni Awards

Jean Dreyfus Boissevain Scholars – Jeff O’Brien ’13, Randall Clendenen ’14, Wendy Guan ‘14
The Jean Dreyfus Boissevain Lectureship awards provide an $18,500 grant to bring a leading researcher to a primarily undergraduate institution to give a series of lectures in the chemical sciences. The lecturer is expected to substantially interact with undergraduate students and faculty over the period of the visit. The program provides funds to host the speaker and support of summer research opportunities. Next month, Dr. Colin Nuckolls from Columbia University will be our guest on campus. The three students above were selected for the prestigious fellowship based on their current academic strengths and potential for success in graduate school.

Hayes Scholarships – Courtney Chow ’12, Kevin Forey and Kent Lee
June 2003 marked the grand opening of the Donald P. Shiley Center for Science and Technology and the retirement of Alice B. Hayes, Ph.D., as president of the university. As part of the opening of the Shiley Center, a scholarship fund in honor of Hayes was established in support of sophomore and junior level students who display merit (a minimum cumulative GPA of 3.25) and who are majoring in Biology, Chemistry, Biochemistry, Marine Science, Environmental Studies, or Physics.

NIH Biotechnology Training Grant – Danielle Pfaff ’08
Danielle is a 2nd year PhD student at the University of Colorado, Boulder having completed a Master’s Degree at Western Washington University. She is working in the Wutke lab on projects that include the study of DNA binding activity of S. cerivisiae and the determination of a novel oligonucleotide/oligosaccharide/oligopeptide fold by NMR and x-ray crystallography.

Owen Fellowship – Shannen Cravens ‘11
Shannen is a 1st year PhD student at Johns Hopkins University. The Owen Fellowship is a prestigious award that reflects the high regard that the biophysics faculty and admissions committee have for an applicant's distinguished academic record and their belief that they show promise of an outstanding career in scientific research.

Poster Award –Michelle Mezher ’12 and Aileen Park ‘14
Michelle Mezher (’12) and Aileen Park (’14) received an award for the presentation of their work on petroleum-based organosulfur compounds from the Division of Colloid and Surface Chemistry at the March 2012 national ACS conference in San Diego. This award recognizes excellence in research, and was given out to only 5 of approximately 150 posters presented during the session. The award included dinner at Donovan’s steakhouse and an award luncheon with several top scientists in the field, as well as a cash prize of $250. Way to go Michelle and Aileen!!

Poster Award Poster Award

National Meetings Back to top

The most recent American Chemical Society National meeting was in San Diego and we had a great showing by USD students and faculty – check out our lunch at The Old Spaghetti Factory.

National Meeting

Alumni News Back to top

2012 Summer Reunion & Research Fundraiser

Our second Summer Reunion and Research Fundraiser will take place on Saturday, June 9, 2012 from 6 – 8 p.m. in the Shiley Center for Science and Technology Atrium, and you are cordially invited to attend!  Tickets are $50 per person and include dinner reception with beer / wine and dessert.  At the event, you’ll have time to mingle with fellow alums, take a tour of the Shiley Center, check out some research poster displays, participate in a raffle of some really fun prizes, and hear a brief talk from the recipient of our first Alumni Research Fellowship, Michael Bagley.

As the recipient of the 2012 Alumni Research Fellowship, Michael Bagley will receive a $4000 summer research stipend and up to $1000 for campus housing. (All proceeds from our first Summer Reunion & Research Fundraiser last summer went towards funding this fellowship, so a special “thank you” to those who attended the 2011 event.)  Michael will be working with Dr. Bob Dutnall this summer, where he has been doing research since the summer before his freshman year. Michael started out with aspirations of going to medical school, but discovered he loves doing research, and is now thinking about becoming a teacher. Here you can read the “Inside USD” article about Michael Bagley.

It is our hope that we can continue to fund at least one student research position each summer with the Alumni Research Fellowship.  100% of all proceeds from the event as well as all donations will continue to go towards funding this fellowship. If you wish to contribute to the Alumni Research Fellowship you can:

  • Click this link to order tickets to the June 9th event.
  • Click this link to make a donation.
  • Click this link to learn more about the President’s Club (where you can direct your donation to Chemistry & Biochemistry).
  • Send an email to us at if you’d like to donate a raffle item.
  • Help us with a special display at the event, highlighting alumni who graduated in a year ending in a “2”.  These graduates, please send us a current picture and a short description about your current professional and/or family life. Please email an electronic copy to

You can check out the Department Facebook page for pictures from the event last year. We hope to see you at this year’s event!

Alumni Highlights Back to top

Dr. Joe CordaroDr. Joe Cordaro earned his B.A. in Chemistry from USD in 1999 then completed a Ph.D. in Chemistry at UC Berkeley. He was first a post-doctoral fellow at the Swiss Federal Institute of Technology, ETH in Zurich then completed a post-doc at UCSB.  He is now working at Sandia National Laboratories as a Principle Member of the Technical Staff in Livermore, CA since 2007. Dr. Cordaro was recently on campus giving a scientific seminar in the department in honor of Sister Pat Shaffer.

It sounds amazing to have spent time in Zurich as a post-doc. What got you interested in an international post-doc and the ETH in particular?

 For as long as I can remember, I wanted to try living in Europe. My original plan had been to get a post-doc in Italy, not Switzerland. I even took a semester of Italian during grad school. However, when I told my PhD advisor, Robert Bergman, that I applied for positions in Italy his response was “What? Why did you do that? Do you want to get anything done?!” Despite the cultural draws to Italy, I followed my advisor’s suggestion and applied for a position at the ETH in Zurich working for Hansjörg Grützmacher. It was still a huge change going from Berkeley to the ETH, but in the end, I am very happy that I landed a position in Switzerland. They have a strong work ethic and a good infrastructure for science, which made getting things done possible.

What were some of your most interesting experiences while abroad?

There were not any single events that specifically stand out as the most interesting for me. I spent nearly two years in Zurich and the experience as a whole was really fantastic. In addition to working at the ETH and being exposed to new science, I traveled a fair amount and learned to appreciate other ways of living. For example, I don’t think I ever really understood the perspective many Europeans have on America’s cultural and political dominance. I took it for granted that America was perceived as a positive influence throughout Europe but my colleagues and friends in Switzerland frequently had a different opinion. It was also very interesting to be in a location (central Europe) with so much cultural diversity, albeit mainly European in origin. I could be at lunch and hear five different languages spoken at one table. Luckily most people also spoke English. I do have to say, however, that traveling around the south of Italy or the Basque region in France were two of my favorite trips.

Were there challenges securing a position in the US after studying abroad?

The short answer is yes. Fortunately, I had taken my PhD advisor’s advice and gotten a post-doc at the ETH. It could have been much more difficult had I gone to a lesser known university without a decent reputation. So even before I went to Zurich, I knew I could have a difficult time finding a job back in the US. For this reason, I started early looking for positions, specifically for a second post-doc rather than a permanent job. Most employers are not going to fly someone from Europe to the US for an interview. However, post-doc positions are frequently secured only through email correspondences and your letters of recommendation.

Your post-doctoral research focused on the synthesis of phosphorus based heterocycles and polymers. As a graduate student, you worked in the field of organometallic chemistry. Now your research emphasizes hydrogen storage technologies and thermal energy storage for concentrated solar power. Can you explain how your undergraduate, graduate and post-doctoral education and experiences prepared you for your current work?

It’s been an interesting journey going from USD to UC Berkeley to Switzerland and then returning to the US to work at UCSB and now Sandia. Each place was different and taught me a lot in regards to doing science and life in general.

I think I’ve always been interested in making stuff but I’ve also had an interest in the physical and electronic properties of materials. My undergraduate experiences in Dr. Jim Bolender’s lab gave me my first insights into photophysics and dynamics of small molecules. I spent two summers as an REU intern, first doing electrochemistry at the University of New Mexico for Ignacio Villegas and the second at Columbia University working for Ged Parkin. It was in the latter REU program at Columbia that I really became totally immersed in a research culture. I had a great experience working at Columbia, which definitely influenced my decision to apply to top-tier graduate schools and to work in the area of organometallic chemistry. As a graduate student, I actually started off working on a project trying to do light-activated C-H bond activation and other photophysical related chemistry projects. I think I was trying to combine the themes of my research background from Dr. Bolender’s work with the research I did at Columbia. This project was ultimately unsuccessful but I was exposed to ultrafast spectroscopy methods though a collaboration with a group in the physical chemistry division at Berkeley.

My course work from USD also had a big effect on the direction I chose in graduate school. Dr. Herrington’s classes in inorganic and bioinorganic chemistry hugely influenced my decisions to lean more towards inorganic synthesis rather than organic chemistry. However, Dr. Dywer’s classes in experimental physical organic chemistry and a special course on computational chemistry were put to use as I dabbled in DFT calculations later on in my PhD career. Eventually, my work as a graduate student focused primarily on the synthesis and reactivity of organometallic complexes but I never stopped thinking about kinetics, physical organic chemistry, and reaction mechanisms.

Going to the ETH was more synthesis but I appreciated the uniqueness of main group chemistry and some of the unexplored or forgotten reaction mechanisms only available to heavier atoms. While academically very interesting, a lot of the work I did as a graduate student and a post-doc in Switzerland did not make me a competitive candidate for jobs back in the US.

I was pretty set on coming back to California but I also knew that I probably needed to expand my skill-set and learn something new. Therefore, I got my second post-doc at UCSB in the materials and polymer group of Craig Hawker. It was rapid immersion into a field that I knew nothing about. Fortunately, Craig was very generous in letting me spend a year in Santa Barbara learning about polymer chemistry.

When I finally went on the job market, I think my research experience gave me a breadth of skills that significantly helped me to get a job at the national labs. My strong foundation in chemistry rooted in USD’s small classroom sizes and great teachers gave me the confidence to branch out into other areas or research like hydrogen storage and concentrated solar power. At the moment, I’ve come back full circle and am currently pursuing small molecule synthesis, polymer chemistry, and even trying to get funding to study the photoluminescence of scintillators for radiation detection.

What are the advantages and disadvantages of working at a national lab?

Sandia National Labs is an engineering lab, which is different than some of the other labs that are more focused on science. This creates some advantages and disadvantages for scientists trying to work in an engineering environment. For one, it is not that easy to secure research grants from outside government agencies to do basic research when it’s thought that we are an engineering lab. However, Sandia has an internal mechanism to support basic research ideas which funds many scientists like me. I find working at an engineering lab very rewarding despite some of the challenges encountered when trying to explain why science is important. For example, it is exciting to work on a project that is actually going to be deployed into a product in under 10 years. The past couple years I have worked on developing new heat transfer fluids that could actually be utilized in solar thermal fields to generate electricity. I’ve also worked on projects to improve the physical properties of Kevlar to better protect soldiers. More recently, I’m starting to look at materials compatibility issues of plastics, foams and rubbers in parts that are expected to last for up to 30 years under extreme conditions. Some of these projects can at first glance seem boring, but if you ask the right questions it can become an exciting problem. Working at a national lab, in particular at Sandia, has really given me the opportunity to participate on a lot of different projects while still asking good science questions.

Other advantages to working at the national labs compared to an academic position include a very nice live-work balance, decent pay, and very understandable and friendly colleagues. I think my biggest complaint about working at the national labs has to do with our funding cycle. It literally takes an act of Congress to approve our budget. So as you can imagine, when there is gridlock in DC, our budget is held up and we stand by waiting for approval to work. Then, when a budget is finally passed (sometimes nine months late!) we are given all the funds to spend in the remaining months of the fiscal year. It makes for poor long-term planning and hiring decisions, which frustrate everyone.

As an undergraduate at USD, along with completing your degree in Chemistry, you were a Choral Scholar. It must have been challenging to balance your time between the two. What advice do you have for current students trying to balance seemingly competing demanding interests?

Make a schedule, establish a routine, and be strict about it! As an undergrad at USD, I worked harder than I ever did in graduate school or as a post-doc but I think it was all worth it. I’d budget time for every class, including on the weekends, so that I could get the reading done before attending a lecture. I’d also study in the law library because none of my friends went there so it was less distracting. Lastly, I didn’t own a TV. I was out of touch with pop culture but I knew my music for when the Choral Scholars performed and I knew my chemistry. It was definitely hard but the work paid off. Education pays off. The more you can invest now in learning, the more opportunities you will have in the future.

Dr. Ellen EberhardDr. Ellen Eberhard graduated with a B.A. in Chemistry in 1996.  While at USD, she was a Trustee Scholar and was awarded the Outstanding Senior Student in Chemistry when she graduated. After that, she worked for a year then completed her Ph.D. in Chemistry at the University of Illinois at Urbana-Champaign.

There are several times that you have had international positions. The first dates back to a summer internship at Bayer Agrochemicals the summer after your sophomore year. How did you get that position and did it impact your interest in further work abroad?

I got that position, as I’ve gotten all of my jobs, by networking. In this case, my grandmother’s good friends had retired from Bayer in Leverkusen, Germany, and I think they brought my application in to the company and asked if they had any summer internships for me. Soon after that, I received an offer letter in the mail. It was so easy, I didn’t fully realize at the time how lucky I was to have such an opportunity!

My interest in working internationally stems from my upbringing. I am the first natural-born American citizen in my family – everyone else is German. So growing up, my family visited Germany many times, of course, but we also lived in Mexico City, Seoul, and Madrid. When I was about ten years old, I remember boldly proclaiming that I wanted to be a ‘citizen of the world’! - and I guess, I am still working on that dream by whatever means are open to me.

What would your advice be to students considering graduate school?

The biggest change in grad school is going from taking courses to doing research full time. I was very good at courses, but less good at research, so once the courses were over, I had some serious adjusting to do. Most of my classmates, no matter how much undergraduate research experience they came in with, agreed: Graduate school was not what we expected!

I think that one of the biggest challenges to graduate students is the feeling that the supervisors hold all the power over their futures. Try not to get sucked into that negativity.  Similar to the way everyone who eats at the cafeteria complains about the food, most graduate students complain about their advisors. Generally speaking, you’re probably the one who chose them, so remember why you chose them and what you came to them for. Although they appear all-powerful over your future - - -they are actually only human, so treat them respectfully that way. (That said - - - some advisors are easier to work with than others, and it is wise to factor that into your choice!)

You worked in Dr. Pat Traylor’s lab synthesizing blue-copper protein mimics.  How did your undergraduate research experience impact your decision to pursue a Ph.D. studying enzyme kinetics at the University of Illinois at Urbana-Champaign?

A main theme to my educational choices was about getting down to how things really work. I didn’t like the “blobs” and “pac-mans” that represented proteins and enzymes in my biology textbooks, and that’s why I initially chose to major in chemistry and also why I chose to do research with enzymes. My work in Traylor’s lab influenced my decision to distance myself from synthesis and move closer to the enzymes themselves. For my graduate thesis, I had to synthesize many molecules – but always in the service of an enzymatic investigation.

The larger scope of my grad school research was about investigating the molecular basis for the evolution of enzymes. In my thesis I was able to uncover a molecular evolutionary step from a ubiquitous ancestral enzyme to its more modern pollutant-induced progeny. I feel pretty satisfied with how close I’ve been able to get to “how things really work” along the path of chemistry.

Following your Ph.D. you completed two different post-docs – one at the University of Auckland, New Zealand and a second in industry back in San Diego. What was the most important outcome from these two very different experiences?

The main outcome was that I really wanted to find an industrial position that would give me the chance to be an integral part of the organization. I had never really envisioned myself as an academic professor, so when I returned from my time in New Zealand, I looked into industry. I was able to land an industrial postdoc at a company whose technology was very exciting to me. However, the nature of my work was tangential to the main momentum of the company, and it made me want to have a more integral role in my next position. That’s why I was really glad when I was able to obtain my latest position at Codexis.

For the past several years you have been working as a Team Leader in the Analytical Biochemistry group of Codexis Laboratories in Singapore. You moved into that position after a few years as a Scientist in the same group.  What are the pros and cons of working in Singapore?

It’s a smaller place, so, professionally speaking, I have been presented with opportunities which I wouldn’t have gotten in the US at this stage of my career.  It has been educational for me to be able to get my first taste of management here. 

I could talk about the challenge of working with cultures that are foreign to me; however, I do not expect that to be a challenge unique to working in Singapore. For example, my company’s home office in the Bay Area is probably as culturally diverse as the Singapore office! I do believe the experience of living and working in an area where my home culture is not the dominant culture is invaluable. I hope it has made me a more a sensitive and patient colleague.

It is fun to live in Singapore – the daily logistics are quite easy, but the cultural experiences are rich. Singapore has four major languages and cultural influences (Chinese, Indian, Malaysian and English), so there is always something new to see, taste, hear, experience!

Also, except for the fact that it is very far from home, you can’t beat the geographical position. Changi Airport is even better than its reputation would lead you to believe – and the excellent connections to Asia present amazing options for weekend trips. I spent many weekends in Bali last year, and just last weekend I was in Chiang Mai. It’s incredible!

The major con is that when you want to go back home, you have to quit your job, because it is very hard (though not impossible!) to land a job in the States while you’re not on the continent. However, that con is directly attached to another pro: I’ll take the opportunity to go on an epic 6-week SCUBA diving trip in the Coral Triangle before returning to the States.

Have you enjoyed the transition into what appears to be a more administrative position?

I’ll say this much: the learning never ends. Where in grad school I made the transition from course work to full time research project work, in industry I’ve made the transition from solo-project work to teamwork. And now as a manager, I’ve been able to get a better view of what it takes to coordinate the resources and efforts of a larger group of people. I enjoy that I no longer only analyze my own data – I have to assimilate the work of a larger group of people and decide what it means for the direction of a project.

Research is now required for all chemistry and biochemistry majors at USD. When you were an undergraduate student, there was no such requirement. What made you decide to get involved in undergraduate research? Were there other students working in the lab with you at the same time? If yes, do you remember who they were and what they went on to do after graduation?

When I was an undergraduate, I wanted to be one of the “big kids” who were doing research as soon as possible. At that time, Molly Welp and Vincent DeTuri were the big kids.

I started research in Pat Traylor’s lab just before the summer of 1995. I worked with Joseph Pezzato. We would listen to the classic rock station and entertain ourselves by participating in their radio quizzes, though we never won anything. We also used to console ourselves, when our synthetic yields disappointed us, with cookies from the candy machine upstairs, which we would eat in the sunshine on the grass outside of the basement.

What are a few of your fondest memories from the department and USD?

I was the student who “lived” in the chemistry basement from 1993 to 1996. My classmates and professors used to ask if I got my mail delivered there. I started work-study with Debbie Finocchio in the second semester of my freshman year, and then I started TAing as soon as possible after that, followed by RAing in the Traylor lab. Also, I tested out of several General Education requirements (foreign language and logic), which enabled me to take every upper level chemistry class that was offered during my junior and senior years. I was pretty serious about the chemistry. I did, however, find a moment to learn how to SCUBA dive back then, and I even went on a dive trip to Mexico with the Oceans Club. That was a highlight. But mostly, I spent my time at USD in the chemistry basement.

I think my favorite memories are: surviving Dr. Traylor’s famous organic chemistry course; work study parties with Debbie Finocchio; afternoon gossip sessions in Renate Valois’s office; Dr. Traylor thinking I was ridiculous because I chose version B of the Chemistry degree (The one with the “emphasis in Biochemistry”) for the express purpose of avoiding Calculus 3; being forbidden to enroll in Logic by Dr. Traylor who insisted that I test out of it (Thank you Dr. Traylor! I studied about two hours for a whole semester of credit! Good deal!)…

Jamie Lucia Jamie Lucia graduated cum laude with a BA in Chemistry in 2001. While at USD, she was on the Women's Basketball team and was a Trustee Scholar, completed the Honors Program and was a member of the West Coast Conference All-Academic Team. After graduation, she did graduate coursework at the University of Colorado, Boulder in the Optical Science and Engineering Program, before moving back to San Diego, where she worked at Arena Pharmaceuticals as a research chemist until 2003. She then earned a JD from The George Washington University Law School in Washington, DC. She started as an Associate in the Washington, DC office of Ropes & Gray in 2006, and is now an Associate in the firm's New York office, where she has been since the end of 2009. Her work focuses on patent litigation in a variety of fields, including pharmaceuticals, computer science, mechanical engineering and business methods.

You are working at a law firm in the middle of New York City. What is your daily life like at a law firm?

Patent litigation is a very team oriented profession. I am part of a large group of patent litigation attorneys at Ropes & Gray, and I work with many of them on a day-to-day basis, including attorneys in our offices all over the country and across the world. The teams that I work on collaborate on strategy and meet regularly to discuss case progress. Then the individual team members, including myself, prepare briefs, reports, and other work product that consistent with team strategy.

What are some of the challenges working in such a large city?

Of all the cities that I have called home, New York City is the easiest city to live in. The subway makes my commute very easy and very short. I get from my apartment to my office within 20 minutes. The energy in New York City on a daily basis is inspiring. There is truly never a dull moment. For people who haven’t ever lived in the city, the size of the living spaces would probably be a shock, but it makes you learn to live with only what you truly need, so it is a very clean, minimalist way of living.

How much do you use your background in chemistry in your current work?

A large portion of the work I do is for pharmaceutical clients, and the technology can be very challenging. We staff our cases with attorneys that have backgrounds that complement the specific technology at issue, so I am able to frequently call on my chemistry background when I am staffed on pharmaceutical cases. Ultimately, as attorneys, we need to be able to present highly technical information to a judge and a jury in a manner that they will understand. In doing so, it is helpful to have some working knowledge of the relevant technology. It is professionally very rewarding to be able to use my chemistry background to improve the quality of my work as a lawyer.

Following your graduation from USD, it took you a while to decide to pursue a career in law. How did you eventually make that decision?
Being a lawyer wasn’t even on my radar until I worked at Arena Pharmaceuticals as a research chemist. In that role, I frequently met with the in-house attorneys that were responsible for the company’s intellectual property. One day, I simply asked the attorney to explain his job to me and to explain how he was able to use a science background in a seemingly unrelated profession. As soon as her explained it to me, I knew that it was something that would fit my personality quite well. Within a few short months of that conversation, I was preparing to take the LSAT and had applied to law schools on both the east and west coasts.

What experiences along the way helped you to figure out what you did and did not want in a career?

I am truly a scientist at heart, but it took me some time to realize that I wasn’t the type of person that would be happy working in a lab on a daily basis. I really wanted to find a profession that would allow me to interact with more people, but that would get me out of the lab and into a professional setting. During law school I was a summer associate at the firm where I now work, and it gave me the opportunity to experience what it would be like to be a patent litigator. Patent litigation turned out to be the perfect fit for me because I am challenged on a daily basis. The best part of this line of work is that we have to navigate complex scientific issues while maximizing our client’s likelihood of success from a legal perspective.

You had quite a breadth of experiences as an undergraduate student at USD. How did those experiences prepare you for your current career?

My participation on the Women’s Basketball team at USD and my experiences as a chemistry major have been exceedingly valuable to my career. Balancing basketball and my chemistry major while at USD helped me develop my time management skills. I am now in my 6th year as a patent litigation attorney and I continue to draw on those skills on a daily basis.

Did some of these experiences end up being more or less important to you than you had originally thought they would be?

I am actually surprised at how helpful many of the classes I took while completing my chemistry major have been in my current profession. The wide range of scientific subjects, including the analytical courses and physics courses that I took at USD, provided me with a strong scientific base from which I now draw. That wide range makes it possible for me to work on cases that aren’t strictly within my expertise because it makes more subject areas more accessible to me.

What are some of your most memorable experiences from USD?

My entire time at USD is something that I treasure. I feel very lucky to have been able to be a member of the Women’s Basketball team. I am so glad that I was able to participate in athletics at that level, and still be able to complete a chemistry major at USD. Every year at about this time, when March Madness kicks off, I am reminded of my junior year when we went to the NCAA tournament. I remember that during that year, I had to ride my bike between the chemistry building and the JCP and sports center just to make it on time to all of my classes, labs and practices, because it was too far to walk in the short amount of time I had in between each obligation. Of course, the beautiful views made those frantic rides a little easier to handle. Looking back on it now, I wouldn’t change a thing. My time at USD and the people that helped me navigate those years were key ingredients for my successes today.

Jim Meyer Jim Meyer graduated with a B.A. in Chemistry in 1998. He started working with Biosite, Inc. just after he graduated. While the company has changed from Biosite to Inverness Medical and now to Alere, Jim has stayed through all of the transitions. Jim started out as a Research Associate I in 1999. Having completed an M.B.A at UCLA in 2006, he is now a Heath Systems Executive managing nine Account Executives and Consultants responsible for direct sales in the Northwest Region.

While you have been at the same company for approximately 14 years, your job description and career focus have changed dramatically over time. Between the years of 1999 and 2004, you transitioned from Research Associate I up through a Supervisor position. Then, you made a big change by moving to a position as an Analyst. What made you decide to transition out of a lab-based position?

My studies at USD were research focused and I did consider (was encouraged by my great USD professors!) to pursue graduate studies in Chem/Biochem. I was eager to start working in the San Diego Biotech Industry and through some USD networking with Dr. Dwyer I got a job with a good company that really promoted the growth of its employees. Working in the development lab and seeing the commercialization of products for the healthcare market really opened my eyes to the business side of science and I liked what I saw. I started to explore career options that were business focused but also leveraged my science background and sales and marketing was my best fit.

Did you pursue an MBA with this transition in mind or did the job change become available to you after you completed the degree? Would such a transition been possible without completing an MBA?

After researching the best path for my career transition I found that an MBA opened up the most opportunities and would build a solid business foundation for me to use throughout my career. I think it is possible to transition without an MBA, especially if you have taken business classes during undergrad but the MBA, like other advanced degrees does more than train you for a job. Hiring managers look favorably on education, not only for what you know but as a representation of the time and effort you are willing to put into advancing your knowledge.

Would a student be able to start out as an analyst with a background in science and business? Are there advantages to spending time as a research associate first?

Yes, I believe there are many types of positions in the biotech industry outside of the lab for newly graduated students such as the analyst position. In my role today, there are significant advantages in having spent time as a research associate first. To best represent my products I need a thorough understanding of their technical, clinical, and operational benefits.  A research associate gains a in depth understanding of the principles of biochemistry and how they are applied to the specific products being developed, whether it be diagnostics, pharmaceuticals, or medical devices.

With sales responsibilities across the Northwest, does your job require significant travel?    If yes, do you enjoy the travel aspects of your position?

I am typically on the road, by car or plane 4 days a week visiting hospitals and meeting with physicians, nurses, laboratorians, and hospital administrators. I enjoy it because I like to meet new people and constantly get to see new places. Also, as a field based employee, I work from a home office so there is more flexibility in creating my own schedule.

In 2011, you received a Champions Club invitation based on your 1st place ranking overall among 10 health systems executives. What do you feel has allowed you to be so successful?

Sales is like any other job in that the harder you work and the more effort you put in to it the more likely you are to be successful. I try to work intelligently and use all of the tools I have been prepared with through my studies and prior work experience. I’m fortunate to have found a job that I’m passionate about which makes work easier and fun. 

What experiences at USD stand out as most valuable to you now that you reflect back? What do you wish you would have spent more time on?

Working in the research labs of Sister Shaffer and Dr. Dwyer really helped me connect chemistry to the real world. The focus on solving real world problems like childhood leukemia and the effectiveness of drug therapy, inspired me to want to be involved and contribute to the great things going on in the biotechnology industry. I wish I had considered taking more courses outside of my major like business or political science, possibly seeking a minor in one of these areas. I’ve seen a lot of great career options with backgrounds combining Science degrees with Business and Law that seem very interesting.

It Takes a Village Back to top

With an increase in majors and students taking chemistry and biochemistry courses, the roles that our staff, course directors and instrument specialist play in supporting academics, research and instrumentation in the department is extremely important to our success. While their work is often behind the scènes, we would come to a screeching halt without them all.

It Takes a Village

Post-Doc Updates Back to top

NamandjÉ Bumpus

For Dr. Bumpus, getting started as a faculty member at Johns Hopkins University School of Medicine beginning in July 2010 has been very exciting! The lab currently consists of 2 undergrads, a PhD student, a post-baccalaureate student and a research technician. The laboratory has already produced publications including one where an undergraduate student is the first author. The lab has been focusing on investigating the metabolism and toxicology of antiretrovirals used to treat HIV and has obtained funding thus far from the Pharmaceutical Researchers and Manufacturers of America (PhRMA) Foundation and Roche. The students in the lab have had the opportunity to present research in the laboratory at both national and international conferences through poster and oral presentations. Dr. Bumpus has enjoyed classroom teaching as well and was well prepared for this because of her experience at the University of San Diego.

Dr. Bumpus (right) and her students
Dr. Bumpus (right) and her students

Ola Ghoneim

After successfully finishing her Joint University of San Diego-Scripps Teaching program (JUST) fellowship in 2008, Dr. Ghoneim was appointed as an Assistant Professor of Medicinal Chemistry, Qatar University (QU). QU is located in Doha, Qatar, which is a small, fast developing country in the Arabian/Persian gulf. She joined the newly developed Pharmacy Program, that offers dual degrees BSc and PharmD in Pharmacy. The program was shortly converted into the first College of Pharmacy in the country, followed by, achieving the Canadian Accreditation from the Canadian Council for Accreditation of Pharmacy Programs (CCAPP) as the only international accredited pharmacy program outside Canada. The three years she spent at Qatar University were a life learning experience for her. They were challenging, yet enjoyable years. During her time at QU, Dr. Ghoneim was responsible for solo teaching medicinal chemistry courses (PHAR200 and PHAR201), and team teaching other pharmacy courses such as pharmacology, pharmaceutical biotechnology and directed studies, and critical thinking skills in Pharmacy. At QU, she was also able to independently develop several grant applications. She was successfully awarded a half million dollar grant by Qatar’s main funding agency; Qatar National Research Fund under its national priorities research program and was selected among the 93 successful awarded proposal with 20% success rate. In addition to, other smaller undergraduate students research experience grants. Her research interest is focused on designing and synthesis series of single chemical entities with dual pharmacological profile as selective serotonin reuptake inhibitors and serotonin 5-HT1B/1D antagonists as potential therapeutic avenue for treating repetitive behaviors in Autism Spectrum Disorder. The outcome of these grants resulted in 3 publications in 2011/2012. During her last months at QU, she was appointed an acting chair of Pharmaceutical Sciences Department where she served for 5 months. She also enjoyed being the leader of a cultural exchange program between Qatar University and Peace College in Raleigh, NC. She was the students' chaperon for two international trips to Raleigh, NC and the head of the host team hosting Peace students in Doha, Qatar. Moreover, she established an international potluck event at QU, which is now an annual event, where our unity in diversity (One family…One world!) is celebrated. At the end of academic year 2011, and after graduating our first College of Pharmacy graduates, Dr. Ghoneim moved back to the US, where she was appointed as an Assistant Professor at the newly established accelerated PharmD program at Saint Joseph College-School of Pharmacy.

Dr. Ghoneim and her students
Dr. Ghoneim (center back with bright pink top, multi-colored head scarf and giant smile) and her students.

Andrew Korich

Andrew Korich is finishing his first year as an Assistant Professor at Grand Valley State University, located near Grand Rapids, MI. In addition to teaching organic chemistry, Dr. Korich has begun conducting research with two undergraduates. His research focuses on developing a bottom up approach towards developing novel materials. Hw is looking forward continuing this work with his students over summer. He is also excited about his up-and-coming wedding in July.

Andrew Korich

Kris Koudelka

After completion of the Joint USD-Scripps Training for Future Faculty Members (JUST) Fellowship in 2010, Kris Koudelka obtained a tenure-track position at Carthage College in Kenosha, Wisconsin.  He enjoys the small classes sizes there and the community the faculty and students have built together.  Within the chemistry department he teaches biochemistry, general chemistry, and senior thesis.  He also has a joint appointment in the biology department through which he teaches genetics.  His research with undergraduates focuses on the chemical modification of a common virus that infects bacteria.  His group specifically tailors these viruses to deliver therapeutic drugs across the blood brain barrier or to cancerous sites in the body.  In addition to his daughter Kylie, he and his wife have recently welcomed a son, Mason.

Kris Koudelka and his classmates Kris Koudelka and his family

Faculty News Back to top

The University of San Diego, Dean Mary Boyd Primary Investigator, recently received $600,000 from NSF’s ADVANCE program to support “Advancement of Female Faculty: Institutional climate, Recruitment and Mentoring (AFFIRM).” AFFIRM aims to strengthen USD’s recruiting efforts of female faculty, especially those of color, in science, technology, engineering and mathematics (STEM). AFFIRM will help USD become a model for comprehensive or predominantly undergraduate institutions that want to increase their diversity and provide a supportive environment for female faculty. AFFIRM initiatives include developing and implementing pro-active recruitment strategies, as well as workshops to foster the professional development of female STEM faculty, and to establish a comprehensive mentoring program. AFFIRM will also use a campus survey to measure perceptions of institutional factors related to hiring and advancement, and use interactive theatre to engage faculty and administration in a campus-wide dialogue on issues affecting female faculty, particularly faculty of color.

The best sunsets are in Baja…                                     (A restrospective by Dr. James Bolender)

Twelve years ago, I made my first trip to Puerto San Carlos with Dr. Michel Boudrias of Marine and Environmental Studies and Dr. Richard Malatesta, the academic dean at the School for Field Studies. To say that trip was eventful would be an understatement. In the span of three days, I nearly vomited walking past the cannery for the first time, saw the autoclaves vent in an area we were walking an hour before (which explained the dead birds that looked partially cooked), saw our panguero (boat driver) mouth siphon gasoline from one 55 gallon container to the gas can for the boat…with a lit cigarette in his hand, and departed a taxi near the Tijuana-San Diego border only to see a gentleman twirling a revolver on his “trigger finger.” Luckily, I eventually saw the red plug in the barrel of the pistol, but that didn’t stop the sudden adrenaline rush. After reading what I just wrote, it is hard to believe I went back 25 more times.

The Center for Coastal Studies in Puerto San Carlos closed in May of 2011 due to a lack of enrollment. Mexico is not seen as a true study abroad location, and the drug violence in many of the border cities gives most undergraduates pause when choosing a study abroad location. With its closure, it most likely brought to an end our long-term projects in Magdalena Bay.

In the twelve years we worked in Mag Bay, our main project was evaluating the impact of Conservera Cal-Mex on the bay. Along the way, Dr. Boudrias and I mentored over 30 students on individual research projects that ranged from the benthic community structure of the area (the critters that live in the sand) to heavy metals and protein biomarkers in clams and crabs. From these projects came 15 Honors Theses. If Dr. Boudrias and I have one fault, it is not putting these projects into scientific papers quickly enough. However, our sabbatical leaves coincide this year and we are putting a dent into this backlog as I write this.

While the science is great, the biggest thing I take from these past 12 years is the passion of the people who worked with us, many of who fell in love with Mag Bay. The students who experienced Mag Bay worked hard, amazingly hard. Fifteen-hour days were not uncommon. The uncommon days were when we only had 6 or 8 hours of work to do during the day. In those 26 trips, I don’t ever recall a complaint about the work to be done.

This coming summer will be the first summer since 2003 that I won’t spend at least two weeks on the peninsula. I know that I will miss seeing my friends made – Poncho, Gustavo, Chelaco, Julio, Conde, and Lilia to name a few. It was wonderful when they referred to us as the “good gringos.” But as chapters draw to a close, other opportunities open. It was this trial by fire that took a lab based physical chemist to a reasonably competent environmental chemist, and opened opportunities for me in Uganda and now Kenya. My field season this year will take Dr. Malatesta and I to the School for Field Studies center in southeastern Kenya to collect preliminary data for a long term project assisting the communities in the Maasai-Mara area, near Kilamanjaro, with accessibility to clean water. This project in collaboration with SFS and Drs. Boudrias, Yin, and O’Shea of Marine and Environmental Sciences will provide a scientific assessment of the water shed near Amboseli National Park to be coupled with the human side of water quality issues. While I am sad to see our work in Baja come to an end, there are exciting opportunities ahead.

Statistics for 12 years of Baja:

  • 26 trips
  • Miles traveled along the Baja peninsula – approximately 50,000 (air and car)
  • Traffic “violations” – 2
  • Mordidas (bribes) paid – 2
  • Pollution in the Sand students - 70
  • Most student trips – 10 – tied by Ashley Parks and Jennifer Schollee
  • Student research experiences – 36
  • Graduate degrees received or in progress for former Baja students:
    6 Medical or Dental
    5 Masters
    6 PhD’s
    1 Law
  • Armando’s tacos consumed – hundreds…

Baja California

Instrumentation News Back to top

Knowing the 3-dimensional structure of a molecule is a key piece of information that can help us understand its function and reactivity. One of the most powerful methods for determining structures at atomic resolution is X-ray crystallography. In this method a crystal of the molecule is generated (sometimes easy, more often not easy at all!) and subjected to a high intensity beam of X-rays. Some of the X-rays are scattered by electrons in the atoms of the molecule, leading to a diffraction pattern that can be recorded by a detector. The angles and intensities at which the X-rays are diffracted depend on the symmetrical arrangement of molecules in the crystal, and the arrangement of atoms in each molecule. With suitable diffraction data, and some powerful computational methods, the X-ray diffraction pattern can be used to calculate the arrangement of atoms in the crystal and hence the structure of the molecule.

The USD Chemistry & Biochemistry Department is one of a select few undergraduate chemistry departments in the nation to house an X-ray diffraction instrument. In December 2011, with funding obtained from the National Science Foundation, we obtained a Bruker-AXS Smart APEX II Duo X-ray diffractometer with dual (molybdenum & copper) sealed X-ray sources, an extremely sensitive CCD X-ray detector, and variable temperature capabilities for cooling crystals (Figure 1). The two X-ray sources will allow structures ranging in size from a few atoms to the size of proteins to be analyzed. We can also do powder diffraction studies for materials chemistry. Crystals are mounted on thin glass fibers or in thin loops, which are positioned in the X-ray beam. Since the crystal will scatter X-rays in all directions, the angle of the detector can be changed and the crystal can be rotated during the experiment so that all of the diffracted X-rays can be recorded. A full data set can be collected in a few hours or days depending on the molecule being analysed and the quality of the crystal. We have already used the system to solve the structure of the protein lysozyme, using crystals grown by students in Biochem lab (Figure 2).

The X-ray diffraction system is located in SCST148 and is available to our Department faculty and student researchers who have received the necessary safety and practical training. It will also be used by collaborators from other institutions in the San Diego area for research and teaching purposes. Undergraduate students at USD will be able to gain valuable hands-on experience with X-Ray diffraction in a series of teaching labs: Chem 421 (Organic Physical Experimental Lab), Chem 423 (Inorganic Physical Experimental Lab), and Chem 427 (Biophysical Chemistry laboratory) starting this spring 2012.  Many undergraduate students can then go on to use this instrument for their research projects. Undergraduate students have thus an opportunity to enhance their understanding of how X-Ray diffraction works, solve molecular structures, and realize its powerful potential for understanding molecular structure and function.

Bruker X-ray diffraction system in ST148
The Bruker X-ray diffraction system in ST148

X-ray diffraction image from crystals of lysozyme protein
Determination of the structure of lysozyme with the Bruker X-ray diffraction system. Left panel shows an X-ray diffraction image obtained from crystals of the lysozyme protein. The right panel shows the electron density map (blue) calculated from the diffracted X-ray intensities. This map is used to locate atoms and build a chemical model of the structure (yellow lines).

Faculty Awards/ranking Back to top

Henry Dreyfus Teacher-Scholar Award – Jeremy Kua

Dr. Kua was one of six recipients nationally to receive the award that support the research and teaching of young faculty in the chemical sciences.  The award is based on excellent teaching and research with undergraduate students.

University Professorship – Tammy Dwyer

Dr. Dwyer has been awarded a 2012-2013 University Professorship. The University Professorship is the highest academic honor bestowed university-wide and is given in recognition of outstanding scholarly achievements in teaching and research.

Research Corporation Cottrell Science Program

University of San Diego ranks No. 8 amongst primarily undergraduate institutions with greater than 5,000 students who have received awards from the Research Corporation Cottrell Science program.  Faculty in the Departments of Chemistry and Biochemistry and Department of Physics at USD have been awarded eight grants in the past 10 years. Considering the far fewer faculty at USD as compared to the institutions who ranked above us, our research is certainly ranked excellent on a national level.

Faculty Research Updates Back to top

Check out the large group of students and faculty engaged in summer research in the department last summer – quite the crowd!

Students and Faculty engaged in summer research summer 2011

Benz Group

Recent news in the Benz lab includes the graduation of our first group member, Karen Cesafsky (’11), who accepted a position at Millenium Laboratories, and has plans to apply to graduate school next year. Congratulations Karen! Karen’s undergraduate work was recently accepted for publication in the Journal of Chemical Education. This project involved the development of an undergraduate laboratory experiment which employs the use of magnetic levitation to investigate solid phase reaction kinetics.

Benz Group

Top image (L to R): Tran Le, Lauren Benz, Aileen Park, Michael Chau, Victoria Park
Lower images (L to R): Karen Cesafsky, Tran Le, Jenelle Corey, Michelle Mezher

Last summer we were awarded a Cottrell College Science Award from Research Corporation for $35,000 for the preparation and investigation of nanoporous films. We are interested in these films for their potential use in gas storage, as well as their interesting chemical properties. Tran Le (’13) has broken initial ground on this project, successfully preparing our first films.

Aileen Park (’14), Jenelle Corey (’13), and Michelle Mezher (’13) continue to make strides in their research related to the removal of organosulfur compounds present in petroleum. Such compounds are problematic since they lead to environmental pollution when petroleum is burned. Their work will be presented at this year’s Creative Collaborations in April, as well as at the American Chemical Society’s National meeting in March. We recently welcomed Victoria Park (’13) to the group! Victoria has been involved in our most recent efforts involving the use of X-ray photoelectron spectroscopy in the elucidation of desulfurization mechanisms.

Finally, Michael Chau (‘13), our newest group member, has been working on a joint project between the Benz lab and the Ngo lab in Engineering. He is investigating the degradation of composite materials prepared by Dr. Truc Ngo’s group using spectroscopic techniques.

Clark Group

Clark GroupThe focus of the Clark research group is on the development of organometallic catalysts to perform synthetically valuable organic reactions. The specific focus of the research group is on developing metal-catalyzed reactions that incorporate boron substituents into organic compounds. One project involves the copper-catalyzed addition of diboron reagents to carbonyls and is funded by the National Institutes of Health. The second project uses an iridium catalyst to convert a C–H bond to a C–B bond using an amine on the substrate to selectively direct the reaction. This project has a pending proposal to the National Science Foundation.

The Clark research lab has been set-up and is now fully functional. In July, Dr. Clark brought three Western Washington University students to USD for the summer to join two USD students (Marissa Ringgold, ’14 and Peter Cannamela, ’14) in the research lab. A post-doctoral research associate, Andrew Roering, was also hired to help initiate the research program. Three additional USD students (Jessica Capaldi, ’13, Wendy Guan, ’14 and Randall Clendenen, ’14) have joined the Clark research group and will be involved in full-time research over the upcoming summer. Four abstracts, with USD student co-authors, will be presented at the ACS national meeting in San Diego this spring.

Daley Group

Daley Group

Left-to-right: Dr. Daley, Daniel Huh, Lauren Bernier, Jessica Rodriguez, and Amber Vitalo at the 242nd ACS National Meeting in Denver, CO

The 2011 Daley Group consisted of Lauren Bernier, Hillary Hawkins, Daniel Huh, Danielle McCourt, Emily Prieto, Jessica Rodriguez, and Amber Vitalo. This new year of 2012, we will have another big turnover as Amber Vitalo and Emily Prieto have already departed via graduation, and Lauren Bernier, Danielle McCourt, and Jessica Rodriguez are slated to graduate this spring! It is anticipated that the Daley Group will shrink to 3-4 members over the upcoming summer but it will hopefully grow again next fall. Before we get to next year, below is a recap of the Daley Group’s efforts since the last Spin.

On the research front, we published our first major paper (Journal of Biological Inorganic Chemistry 2011, 16, 937-947) on the synthesis and characterization of Dr. Daley’s beloved nitrile hydratase analogue. This was the first project developed in the Daley Group and all those students who worked so hard on it have finally been rewarded with a nice publication. Specifically, Dr. Daley wants to recognize Lauren Schopp, Amber Vitalo, and April Stanley of USD along with Jennifer Angelosante, Breia Lewis, and Rebecca Swanson of Western Washington University for their tremendous work on the project. We hope that this will be the first of a series of papers to be published on this project with contributions from Daniel Huh’s diamidato-bis(phosphine) metal complex studies, Jessica Rodriguez’s Co-NHase oxidation studies, and Amber Vitalo’s new serine based ligand system. Dr. Daley was also a PI on the successful grant acquisition of a single crystal X-ray diffractometer (see announcement in this Spin) and the group is very anxious to learn and perform crystallography in house!

The Daley Group had several poster, and one oral, presentations at the 242nd ACS National Meeting that was held in Denver, Colorado (August 2011). Each student (pictured above) did an excellent job with their presentations and to treat ourselves for our hard work, we ate at 1515 Market Grill. It was an appropriate spot where liquid nitrogen was used for Dan’s meal and there were pipettes used to deliver various sauces, etc. for other dishes – all in all a chemistry geek delight!

Outside of lab, Dr. Daley and Mrs. Dr. Daley welcomed their second child, and first son, Owen into the world in September 2011. While the timing of the birth was not ideal being a week earlier than expected and early-semester, the Daleys have had nothing but smiles on their faces. Furthermore, that his half-birthday falls on St. Patrick’s Day gives Dad a glow in his Irish heart.

De Haan Group

Left-to-right: Summer 2011 Crew: Nazin Sedehi, Dr. Lelia Hawkins, Brenna Espelien, Michelle Powelson, and Dr. De Haan

The De Haan group has been busy analyzing reactions between compounds found in clouds and aerosol, looking for the fastest and “brownest” reactions possible in the atmosphere, funded by a new grant from the National Science Foundation. Such reactions cause clouds and aerosol to absorb light, rather than just reflect it, which can impact the global climate. Ashley Torkelson and Eric Czer have been following up on a discovery made by Alec Rynaski: that glyoxal and sulfur dioxide, both present in clouds, can react under the right conditions to produce a black substance, which he identified as a benzoquinone. Ashley and Eric are using fluorimetry and liquid chromatography to quantify benzoquinone formation under cloud-like conditions. Nazin Sedehi, Kevin Forey and Kat Millage have been studying the pH and temperature dependence of reaction rates using overnight NMR runs. Kevin has also been finishing up electrospray mass spectrometry studies of insanely fast aldehyde – protein reactions. (Proteins are present in clouds and aerosol, too!) Brenna Espelien and Michelle Powelson, meanwhile, have been using fluorimetry and UV-Vis spectroscopy to determine which reactions brown the fastest, and whether the reactions produce material that fluoresces at the same wavelengths as atmospheric aerosol. Nazin, Brenna, and Michelle all traveled to Orlando, Florida with Dr. De Haan in October to present their research projects at the annual meeting of the American Association for Aerosol Research. In August, Lelia Hawkins joined the faculty at Harvey Mudd College, but not before showing that our reaction products absorb water slowly – just like atmospheric aerosol – an effect not previously observed in lab studies.

Dutnall Group

My research lab studies the Hat1 acetyltransferase complex. This complex is involved in depositing histone proteins onto DNA to help package the enormous amount of genetic material inside the cell nucleus. It is also involved in regulating gene expression and DNA repair. The Hat1 complex consists of at least five proteins (Hat1, Hat2, Hif1 and two histones called H3 and H4). The Hat1 protein chemically modifies histones while Hat2 and Hif1 are histone binding proteins. Our overall goal is to assemble and characterizing the entire complex so that we can understand the molecular mechanisms by which it modifies histones and how it contributes to regulating gene expression and DNA repair.

Our work is currently focused on the Hif1 protein. Hif1 binds histones and can deposit them onto DNA and we are trying to understand the molecular basis for these activities. We can make the protein in bacteria and show that it binds histones. We know that the protein is a dimer (two identical copies of the protein stably associate) and we have mapped the region of the protein necessary for dimer formation. We are also mapping the region of the protein required for histone binding. We are also trying to crystallize the Hif1 protein so that we can determine the structure of the protein via X-ray crystallography, using our newly acquired X-ray diffraction system.

I currently have four students working in my lab on this project. This last year we said goodbye to Elyssa Pickle, who worked with Dr. Lorraine Pillus at UCSD last summer as part of the USD Bridges to Doctoral Programs and is currently working at DiscoverRx, a San Diego Biotech company, and Allison Bigeh who completed her degree requirements at the end of Fall ‘11 and will graduate in May ’12. Michael Bagley continues to work in the lab and has been joined by Nessa Seangmany, a PURE student who started in summer ’11, Stephen Szabo and Lani May Centeno. Allison, Michael and Nessa will be presenting the results of their work as a poster at the American Society of Biochemistry and Molecular Biology National Meeting that will be held in San Diego this April.

You can read more about my research and follow more news at my lab website:

Dwyer Group

The Dwyer research group saw a lot of progress and change in 2011. Spring 2011 was a productive time and three students (Shannen Cravens, Alyssa Navapanich and Hannah Sadler) traveled to the ACS National Meeting in Anaheim with me and Debbie Tahmassebi to present a poster on our work with the non-natural, non-hydrogen bonding guanine mimic that we call “H”.  In May, Shannen and Alyssa (two long-time members of our group) graduated and moved on to great things. Shannen is a graduate student in Molecular Biophysics at Johns Hopkins University and Alyssa is a rising start at a local biotech firm, Pharmatek. Hannah graduated in December and will begin law school in fall 2012. We are putting the finishing touches on a manuscript, “NMR and Computational Analyses of the Conformational Preferences in a DNA Duplex Containing the Guanine Mimic 4-fluoro-6-methylbenzimidazole”, describing the work of these remarkable women. Our group has also continued to collaborate with Floyd Romesberg at the Scripps Research Institute. We solved the solution structure of another DNA duplex containing a non-natural base pair that is replicated nearly as well as an A-T base pair. That work was recently accepted for publication in Nature Chemical Biology. Progress on the General Chemistry e-text I am co-authoring (along with Charlie Grisham of University of Virginia) is coming along nicely and we are hoping for a 2014 release.

Dwyer Group

Iovine Group

First, I wanted to say a big hello to all the Iovine lab alumni out there. So many of you are doing great things; it is always great to hear from you.

Graduation will hit us hard this year. Long time lab members Amanda Walker and Kristiana Lehn will leave the group in May. Amanda began research in the summer of 2009 while Kristiana joined the group in the summer of 2010. Both Amanda and Kristiana have developed an entirely new class of amphiphilic lignin-based material that has great promise in a variety of application areas. This project has certainly been challenging but it has also forced us to learn new areas and to explore new measurements. Amanda is off to graduate school in the fall and Kristiana will travel in advance of medical school.  Lab members Austin Apramian and Andrew Fleming also graduate this spring with plans to attend medical school.

Summer 2012 approaches and I anticipate having a full lab. This summer marks the first funding year of the “Theoretically Interesting Molecules NSF Consortium” ( The consortium is funded by NSF and consists of USD, Northern Kentucky University, Trinity University, Colby College, Grand Valley State University, and Macalester College. The program provides summer funding for two students along with funds supporting extensive travel to present research results.

We are making excellent progress on our starch-based materials project. It is our goal to present this body of work, for the first time, at the Philadelphia ACS meeting. Stay tuned! A new research group website is on the horizon so please send me some updated information and recent pics.

Kua Group

The Kua research group is moving into Origin of Life research, thanks to funding from a Dreyfus Teacher-Scholar Award received by Dr. Kua in Fall 2011. Dr. Kua had a very productive sabbatical visiting several labs related to origin of life research and was able to present "Primordial Ocean Chemistry and the RNA World" at the triennial ISSOL meeting in Montpellier, France, this past summer. The work has since been published in the journal Origin of Life and Evolution of the Biospheres. The formaldehyde molecule is the theme of our research group this year! Christopher Lee ('12) has taken on a computational study of the formose reaction - the oligomerization of formaldehyde into sugars. Lily Marucci ('13) is working on understanding the co-oligomerization reactions involving formaldehyde and amines. Dr. Kua has been working on formaldehyde oligomerization to form polyethers and cyclic oxanes. Dr. Kua will be giving a talk at the San Diego ACS national meeting on his work, and chairing a session in origin of life chemistry. Chris will be presenting a poster. In other news, work by Hadley Krizner ('10) on understanding the reaction of glyoxal and amines was published in the Journal of Physical Chemistry A in 2011. The computational work done by Lorenzo Bautista ('11) has been written up as part of a manuscript involving a collaboration with Dr. Arnie Rheingold's group at UCSD and then plan is to submit this work later this spring to a special issue of the journal Polyhedron celebrating Alfred Werner and his contributions to inorganic chemistry.

Malachowski Group

Dr. Malachowski was on sabbatical leave during the 2010-2011 academic year. During that time he traveled extensively going to conferences, giving talks on various campuses and offering workshops to campuses interested in doing more undergraduate research. He also has continued to pursue his work on the impact of undergraduate research on students and student learning and published a series of articles and chapters in books on this topic during 2011. A good deal of this time was taken up by running workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities. This work accelerated as he 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. During 2011, the first workshops for state systems (Wisconsin and California) were offered along with one for the Council on Public Liberal Arts Colleges where 23 universities sent teams. In 2012, these workshops will be offered for the City University of New York campuses, the Great Lakes Academic Consortium and for the state of Pennsylvania system. It is amazing how undergraduate research has taken hold at US universities of all kinds and we are proud of how far along our chemistry department is in this area and in our ability to provide national leadership for these efforts.

Dr. Malachowski’s work on binding dipyrromethenes to metal ions continues and he now has a large collection of beautiful complexes formed with copper, cobalt and iron. Growing crystals continues to be a large part of the group’s efforts and they now have hundreds of solutions set up that they are hoping are now leading to crystal growth. They recently submitted a manuscript to the Journal of the Chemical Society, Dalton Transactions that detailed some of their most recent results. 

Matulef Group

This was the Matulef lab’s most productive year yet! Last summer Sabrina Phillips (‘12) finished up her work characterizing the small molecule inhibitor of the E. coli CLC antiporter called CLC-ec1 using lipid bilayer recordings, a technique that allows us to precisely control the voltage across a membrane to measure the activity of the protein. She found that this inhibitor, OADS, is the highest affinity small-molecule inhibitor known for CLC-ec1, and her work led to the surprising discovery that the ability of OADS to inhibit this antiporter depends on the lipid composition of the membrane. After finishing this work last June, Sabrina joined forces with Luis Rodriguez (’11) in July to characterize a novel bacterial homolog called CLC-b. This work led to some surprising discoveries regarding the requirements for chloride and proton transport. Intriguingly, CLC-b lacks several amino acids thought to coordinate the chloride binding sites, but nevertheless transports chloride. It also lacks a glutamate residue thought to be part of the proton permeation pathway, yet it transports protons. Both of these studies were presented at the Biophysical Society Annual Meeting in February and we are currently writing them up for publication. In addition, Michelle Hustedt (’13) spent last summer working towards characterizing the function of the first eukaryotic CLC of known structure. It was a great summer!

Mills Group

The Mills group has been working to understand how the copper amine oxidases react with oxygen. This year, we have worked with three different copper amine oxidases – Pea seedling amine oxidase (PSAO), E. coli amine oxidase (ECAO), and Bovine serum amine oxidase (BSAO). We are evaluating the role of copper in these enzymes by replacing it with cobalt and examining the affect of metal substitution on catalysis. Our results with PSAO showed that this enzyme does not work well with cobalt in the active site. We presented our results at the American Chemical Society national meeting in Anaheim last March and published a paper describing these results in the Journal of Biological Inorganic Chemistry. Dayn Sommer and Alex Bitsimis worked on this project. While finishing the study of PSAO, we turned our attention to ECAO. Eunah Choi developed conditions to express this protein. Last summer, Dayn and Alex purified ECAO and began our studies of this protein. Courtney Chow has joined Dayn working to replace the copper with cobalt and evaluate its affect. We have also begun to look at BSAO. The first part of this is to purify the protein. Dayn has been working with Courtney and Eunah to obtain enough BSAO to study. Eunah graduated in December. Dayn will graduate in May. We have also been examining the metal binding properties of the Ferric Uptake regulators from several different bacteria. Megumi Sugawara presented our results on this project at the ACS meeting last March. Megumi graduated in May.

Courtney Chow and Dayn Sommer Megumi Sugawara

Courtney Chow and Dayn Sommer

Megumi Sugawara

Tahmassebi Group

This past year was very productive as we moved from the synthesis to measurement phase of a project. In Summer 2010, Raymond Sullivan and Kristy Clarke scaled up a synthesis designed by alum Will Porterfield to make a large amount of a fluorescent dideoxynucleoside. A collaborator of ours then incorporated the fluorophore into DNA. In Summer 2011, Raymond, Holly Keene (both below), Hannah Sadler and Shannen Cravens (see Hannah and Shannen pictured above) studied the structure and properties of a couple of oligos containing the fluorophore. In addition, Hannah and Shannen worked on a manuscript to describe results using a non-natural nucleoside "H" – work described above in Dwyer research). Raymond will be presenting the results of his synthesis and Hannah's structural analysis at Creative Collaborations this spring. In addition, I plan to present this work at a conference this summer and the manuscript is in preparation to publish the results. Shannen also got some promising initial results that will launch the application phase of the project.

Hollie Keene and Raymond Sullivan

Recent Faculty Publications - *undergraduate co-authors Back to top

R. V. Gough, J. J. Turley,* S. E. Wood,* G. R. Ferrell,* K. E. Cordova,* D. O. De Haan, C. P. McKay, O. B. Toon, M. A. Tolbert, “Can rapid loss, high variability of Martian methane be explained by surface H2O2?” Planet. Space Sci., doi:10.1016/j.pss.2010.09.018

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. 107 (15) 6687-6692 (2010), doi: 10.1073/pnas.0912121107

Korich, Andrew L.; Iovine, Peter M. “Boroxine Chemistry and Applications: A Perspective” Dalton Trans., 2010, 39, 1423-1431. DOI: 10.1039/b917043j

Korich, Andrew L.; Walker, Amanda*; Stevens, Caitlin*; Hincke, Christopher*.; Iovine, Peter M. “Synthesis, Characterization, and Star Polymer Formation of Boronic Acid End-Functionalized Polycaprolactone”  J. Polym. Sci. Part A: Polym. Chem. 2010, 48 (24), 5767-5774.

Malachowski, Mitchell R. “Is CUR Helping Diminish the Importance of Teaching at Predominately Undergraduate Institutions?” Council on Undergraduate Research Quarterly, 31, 32-36, 2010.

Leigh A. Plesniak, Bridget Salzameda, Holly Hinderberger*, Elizabeth Regan*, James Kahn*, Stephen A. Mills, Peter Teriete, Yong Yao, Patricia Jennings, Francesca Marassi & Joseph A. Adams, “Structure and Activity of CPNGRC: A Modified CD13/APN Peptidic Homing Motif” (2010) Chemical Biology and Drug Design, published online 30 March 2010.

Query, I. P.; Squier, P. A.; Larson, E. M.; Isley, N. A.; Clark, T. B.“Alkoxide_Catalyzed Reduction of Ketones with Pinacolborane” J. Org. Chem. 2011, 76, 6452-6456.

“Enabling Bifunctionality and Hemilability of N-Heteroaryl NHC Complexes”, Specht, Z.; Cortes-Llamas, S.; Tran, H.; van Niekerk, C.; Rancudo, K.; Golen, J.; Moore, C.; Rheingold, A.; Dwyer, T.J.; Grotjahn, D., Chemistry - A European Journal, 17, 6606-6609 (2011).

Korich, Andrew L.; Fleming, Andrew B.*; Walker, Amanda R. *; Wang, Jifu; Tang, Chuanbing; Iovine, Peter M. “Chemical Modification of Organosolv Lignin Using Boronic Acid-Containing Reagents“ Available Online 22 November 2011. Polymer, 2011.

Wang, Jifu; Yao, Kejian; Korich, Andrew L.; Li, Shigeng; Ma, Shuguo; Ploehn, Harry J.; Iovine, Peter M.; Wang, Chunpeng; Chu, Fuxiang; Tang, Chuanbing. “Combining Renewable Gum Rosin and Lignin: Towards Hydrophobic Polymer Composites by Controlled,Polymerization“ J. Polym. Sci. Part A: Polym. Chem. 2011, 49 (17), 3728-3738. DOI: 10.1002/pola.24809.

Kang, Youn K.; Iovine, Peter M.; Therien, Michael J. “Electron Transfer Reactions of Rigid, Cofacially Compressed, π-Stacked Porphyrin-Bridge-Quinone Systems“ Coord. Chem. Rev. 2011, 255 (7-8), 804-824.

Stephen A. Mills, Doreen E. Brown, Dayn Sommer*, Alexandra Bitsimis*, Kaitlyn Dang*, Jennifer Nguyen*, David M. Dooley, “Cobalt Substitution Supports an Inner-Sphere Electron Transfer Mechanism for Oxygen Reduction in PSAO” (2011) J. Biol. Inorg. Chem. DOI 10.1007/s00775-011-0872-x. Published online 19 Jan 2012.