Chair’s Column
New Dean
New Tenure-Track Faculty
Faculty Transitions
In Memoriam
JUST Fellows Program
Post Doctoral Fellowship
Alumni Highlight
Faculty Research Highlights
Development Award
New External Grants
Research Publications in 2008

University of San Diego
Department of Chemistry and Biochemistry

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

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Chair’s Column

 What an awesome year we have had!  I continue to be awed by the accomplishments of our extraordinary department and its members.  We have captured some of the exceptional happenings over the past year in this issue of The Spin.  The department continues to experience growth, welcoming new faculty members, new staff members, a new JUST Fellow, and preparing to graduate 40 majors this year!  Department faculty were quite successful in obtaining external research grants in 2008, bringing in over $1 million in new funding as well as publishing 10 papers with student co-authors.  We remain steadfast in our commitment to provide an unparalleled undergraduate education in chemistry and biochemistry and have recently modified our curricula to require a research experience for all majors.  The strengths, quality and promise of our faculty and students to build a vibrant and rich scientific community resulted in a partnership between USD and Research Corporation in support of departmental goals and initiatives, you can read more about this below.   The list of achievements goes on and on, and we take great pride in being able to share them with all of you.

Lastly, I encourage you to keep up with department news at our website  We especially enjoy hearing from alumni and we hope you will consider adding/updating your profile on our alumni page at

Warmest regards,

USD Welcomes Dr. Mary Boyd as Dean of the College (and she's a chemist!)

Dr. Mary K. Boyd was appointed as Dean of the College of Arts and Science and faculty member in Chemistry and Biochemistry effective August 1, 2008.  Dean Boyd came to us from her position as Professor and Chair, Department of Chemistry at Georgia Southern University where she served since 2005.  Prior to GSU, Dean Boyd was Professor of Chemistry at Loyola University Chicago where she taught Organic Chemistry, Photochemistry and Structure Determination and was awarded the Sujack Award for Teaching Excellence. 

Dean Boyd received her B.Sc. from University of Toronto, her Ph.D. in mechanistic organic photochemistry at the University of Toronto, followed by postdoctoral research at SUNY Stony Brook in physical organic chemistry. Dr. Boyd’s research has focused on the development of photocleavable protecting groups for nucleotide synthesis, with application in DNA chip synthesis. Dean Boyd is a chemistry councilor for the Council of Undergraduate Research, and serves on the American Chemical Society Committee on Minority Affairs and Executive Committee of the Division of Organic Chemistry. She has served as Secretary and Advisory Board member of the Inter-American Photochemical Society and on the ACS Women Chemists Committee.  Dean Boyd enjoys spending time with her husband John, two young children (Patrick and Maura), and gardening.

New Tenure-Track Faculty Members:

Dr. Kimberly Matulef joined USD in August 2008, from Stanford University, where she researched membrane proteins. She was attracted to USD’s Chemistry & Biochemistry department because she shares the department’s vision of excellence in both teaching and research. She was very impressed with the enthusiasm of both students and faculty and decided to join the team. She will continue to study membrane proteins involved in transporting chloride ions across cellular membranes in her lab at USD.  These proteins play critical roles in the brain, muscles, kidneys, and bones. Her research takes an interdisciplinary approach to understanding how these proteins function using: genomics, molecular biology, protein purification, and electrophysiology.  This research interest stemmed from a course taken at Brandeis University during her undergraduate years.

This Spring, Dr. Matulef is teaching Biophysical Chemistry lecture and lab courses.  She enjoys making these courses an interactive experience for students by using pictures on Power Point. In her research lab, Dr. Matulef is working with her very first undergraduate student at USD.  However, she is hoping to recruit one or two more students before summer.  In addition to moving to San Diego from the Bay Area, 2008 was most exciting for Dr. Matulef and husband, Chris McClain, an engineer at LinQuest Corporation.  They entered the action-packed “world of parenting” with the birth of their son, Max McLain, on September 25th.  They are enjoying all of his smiles and laughs; and are looking forward to showing him all of the children’s activities San Diego has to offer.

New Staff Members:

Sharon Ferguson joined the department in June 2008 as Laboratory Technician.  She prepares labs for Biochemistry as well as for a few Biology classes.  As a San Diego native with a B.S. in Biology (SDSU), she has experience working in laboratories from academic to medical to industry.  This experience includes 7 years at the Scripps Research Institute’s Molecular Biology Department. Sharon enjoys the challenges of science and looks forward to working with both faculty and students. In her other life, Sharon loves to travel, spend time with her beautiful Border collie “Blitz” (who has gone on many road trips), and teach dance at Dance for 2 Studio.

Tammy Gillespie joined the department as Chemistry Assistant in July 2008. She is involved with purchasing chemicals & supplies for the department. Along with budgeting and grant administration duties, she also interacts with other departments throughout the University to keep an open line of communication. Originally from Ohio, Tammy moved to San Diego 14 years ago. After a winter with 60 below zero temperatures, she thought a move to San Diego was the best solution. Tammy can be contacted at

Mrs. Alnelis Rodríguez joined the department as Laboratory Technician for the General and Analytical Chemistry courses in July 2008. She obtained her B.S. in Chemistry from University of Puerto Rico in May 2006 and completed several graduate courses before moving to California with her husband Roberto, an active duty member of the US Marine Corps. Alnelis loves local weather and attractions, photography, cooking and traveling.  In this picture, she was at Hoover Dam in Las Vegas, NV during Dr. Martin Luther King, Jr. holiday weekend.

Faculty Transitions: Dr. Leigh A. Plesniak

Our friend and colleague Leigh Plesniak retired as Professor of Chemistry at the end of the 2007-2008 academic year.  Dr. Plesniak was a faculty member at the University of San Diego for 13 years beginning her initial appointment in January 1995.  During that time she was an intellectually challenging teacher, led a highly productive research program involving numerous undergraduates and made enormous contributions to the Department that will have lasting impacts. Dr. Plesniak helped invigorate the discipline of biochemistry at USD by leading the charge and development of a rigorous biochemistry major.  She spearheaded large instrumentation grants in support of teaching and research (most notably the NSF-MRI award that funded our two high-field NMRs - see her pictured triumphantly on top of boxes the day the systems were delivered!) Dr. Plesniak developed a model undergraduate research program with on-going, external federal funding and top-quality publications featuring important contributions from USD students.  In her 13 years at USD, Dr. Plesniak's contributions comprise 12 publications (6 with undergraduate co-authors and 2 in education-related journals), raising nearly $1.1 million in funding (both individually and collaboratively, $400K in support of her research program, over $650K in instrumentation grants and $32K for student support initiatives), numerous invited seminars, session chairs and she is a founding member of the Educational Committee of the Protein Society.

Dr. Plesniak will enjoy spending more time with her family (husband Eric, son Kevin and daughter Nina) while continuing collaborative work with colleagues at USD, UCSD and the Burnham Institute. Dr. Plesniak's tremendous contributions to chemistry and biochemistry at USD have helped foster the strong reputation of the Department and she will be missed.

In Memoriam: Myrna Louise Stoflet

Myrna Louise Stoflet (USD Chemistry 1962) died in Mill Valley, July 11, 2008 at the age of 67.  She was retired from the San Francisco Unified School District where she taught science and math at Lincoln H.S., John O’Connell HS and Ben Franklin Middle School. Ms. Stoflet generously funded the Luisa and Harold Stoflet Scholarship for minority science women students at USD.   She lived a rich, caring life of service, but never forgot to love and laugh. 

Training Future Faculty:

JUST Fellowship Program

Dr. Kristopher Koudelka is USD’s second JUST Fellow (Joint USD-Scripps Training for Future Faculty).  His current research, in the lab of Dr. Marianne Manchester at The Scripps Research Institute, centers on the mammalian cell entry of a plant virus based nanoparticle and its derivatives.  These genetically or chemically modified plant viruses can then be used as vascular imaging agents, vaccines, antitoxins, and/or drug delivery vehicles.  At USD he team-taught general chemistry with Dr. Kua in the Fall and is teaching DNA Science and Technology this Spring.  His goals through both teaching and research are to help students build a solid foundation in science so they can attain their aspirations.

Post Doctoral Fellowship Program

Dr. Andrew Korich is a postdoctoral fellow that has joined the laboratory of Dr. Peter Iovine.  Dr. Korich received his B.S. in Environmental Science from Saint Michael’s College and his Ph.D. in Organic Chemistry from the University of Vermont in 2008.  His graduate work focused on preparing shape persistent macrocycles as advanced intermediates towards a rational synthesis of single walled carbon nanotubes.  At USD Dr. Korich will be preparing a series of polyester dendrons and examining how the size of these dendrons impacts the formation of the boroxine core.  Dr. Korich has had strong ties to undergraduate research throughout his educational career.  He has participated in several NSF REU programs including the Theoretically Interesting Molecules Consortium.  As a graduate student, he has mentored several undergraduates most of which have continued on to graduate school.  Dr. Korich is excited to continue working with undergraduates both in the classroom and laboratory settings. In Fall 2009 he will teach an Organic Chemistry Lab.

Alumni Highlight:

Alumni Highlight: Martha Medina ’00 Enjoying a Career in Industry

1. Can you provide an outline of events and timeline of your life and career since graduation from USD and leading up to where you are now? Feel free to include personal and professional details, but we leave that up to you.

Upon graduating from USD I worked at a Biotechnology firm in Mexico then in August 2000, I began graduate school in the Chemistry Department at Arizona State University.  I published three articles during my time at ASU, all in the area of proteomics with filamentous fungus.  I gave invited talks at international conferences in Mexico and Denmark and presented posters in many other conferences.  I earned my Ph.D. in Biochemistry in August 2004 and the title of my dissertation was "Proteomic Analysis of Differentially Expressed Secreted Proteins from Aspergillus flavus."  This work also led to an invitation to write a chapter in a Springer Protocols book, which was just published last year.
After ASU I traveled around the world through Mexico, Switzerland, France, Spain, Japan and Guinea in West Africa.  During this time, I was recruited by Procter & Gamble as a Scientist in the Beauty Technology Development Division, working on in vitro skin and hair projects, particularly leading the Hair In Vitro Project to address using alternative means to test hair care ingredients.  After almost 3 years in Cincinnati, I returned to Arizona and took an academic professional position at the Biodesign Institute at Arizona State University working on Clinical Population Proteomics projects to understand protein microheterogeneity in disease-state populations, particularly in cardiovascular disease, among others.
Since January 2008, I have been R&D Manager position at a small company, Innovative Brands, in Phoenix.  I am the only Ph.D. in the company with a scientific background; I lead all aspects of R&D, new product development, Quality Assurance and Control, cost savings initiatives, Consumer Relations, and Technology Transfer among many other responsibilities.  I am currently working on development of new products to launch in 2010 and 2011.

On the personal side, I continue to enjoy traveling, running three half-marathons and a triathlon in the past three years and I began teaching kickboxing last year and am loving it!

2. How did your USD education prepare you for success in your career?

Making the decision to go to USD for my undergraduate degree was the best decision I ever made.  USD was a place where teachers cared about you as a student, as an individual, and as a future professional.  The classes were great because they were small and you could get all the attention you needed.  Having the opportunity to do research in such a tight knit environment was the perfect way to gain competence and gain knowledge ahead of many of my peers in graduate school. 

3.  When/how did you decide on a career in the chemical industry?

I remember the moment I decided to switch from being a biology major to a chemistry major like it was yesterday.  It was during Dr. Leigh Plesniak’s Biochemistry class, when she was teaching about chemical bonds between amino acids, helices, beta sheets, and trying to explain why hair was straight or curly; why when dry it was different than when wet; and the difference between chemical, more permanent changes in hair and non-chemical, heat induced changes.  She showed us pictures of the enzyme xylanase, and I fell in love with it all!  It sounds corny, but from then on I knew I wanted to keep studying biochemistry! 

4. Can you describe a typical day in your professional life?

There is no "typical day" as every day is different and challenging.  Most days start at the office at 6 am and finish at 5 pm.  Since our products are made on the east coast and Canada, I am usually 2 or 3 hours behind and always trying to catch up! I often have to look at product process documents and approve them, make sure our products are being made correctly and to our specifications, and that any issues with quality of the products are taken care of correctly.  This also includes looking into consumer complaints.  I also work on new product formulas.  I work very closely with our marketing folks to understand what the consumer wants and needs, and then guide and direct the development efforts through our partners.  This aspect is the most interesting in my job.  I spend my time in a cubicle (rather than a lab) that is usually filled to the brim with product samples I’ve requested, lots of new ingredient documents and technical information.  I visit our plants and observe/monitor pilots of our new products, and solve any production issues we might have.

5. What stands out for you about your time as a student at USD that prepared you the most for your career/present position?

At USD I had the opportunity to lead a research project at an early stage in my career and gain recognition through a published article - that was great preparation for graduate school.  I was also a resident assistant at USD so my days were very full and tiring and I had to learn how to be extremely efficient in order to do everything and do it well.  This, I think, is what allowed me to finish my Ph.D. in 4 years followed by the terrific positions I've held since then.  One of my strengths is being efficient; without it, I would never have enough hours in my day!

6. What advice do you have for current USD student considering graduate school and a similar career path?

My advice is to get involved.  Find a professor whose research interests you and ask if you can participate in their research; ask how you can contribute.   One of the things that always surprised me was seeing other graduate students in biochemistry not know how to make a buffer!! They had gotten through the classes and learned from books but when it came time to begin doing research, they had a terrible time getting in the lab and being productive.  I will never forget the day I was invited to give my Ph.D. dissertation seminar at USD in 2004.  Dr. Plesniak introduced me and she said something that will stay with me forever, and that made me truly proud of all my hard work and thankful I had the opportunity to do research with her.  She said that the work I did with her transformed her research and the work we did led to her accomplishments as a scholar.  That truly was one of the best compliments I have ever received and will cherish always.

7. What do you value the most about your USD education?

I value most the time that mentors, teachers, professors, and administrators were willing to spend with me, always willing to help to make me a better person, a better professional, to be better prepared for what I would eventually encounter in the world.  I value the friendships and the relationships that have remained with me and I will always be proud to say that I am a University of San Diego alumnus. 


Faculty Research Highlights:

Bolender Research Update

Over the past 18 months Erica Hewitt (Chem ’09) has continued the work begun by Brie Simon (Chem’07) on LaF3 based nanocrystals.  Erica has worked collaboratively, with myself and Dr. Julia Shaffer, to incorporate these nanocrystals into various sol-gels and determine the feasibility of using these sol-gel monoliths as heavy metal sensors.  Erica presented her work at the Western Regional Meeting of the American Chemical Society in Las Vegas.  Recently, Lauren Schopp (Chem ’09) joined this project to alter the capping group on these nanocrystals to enhance their luminescence.  This project is a collaboration with Dr. Christopher Daley.

Our environmental work has tripled in the past year.  Dr. Boudrias and I have traveled with students to Magdalena Bay, BCS Mexico; Falmouth Bay, Jamaica; and Mbarara, Uganda.  Ashley Parks (Biochem ’08) and Raffaela Abbriano (Bio ’08) traveled to all three of these locations as part of their research.  Both completed their Honors Theses in the Spring of 2008.  Ashley’s work focused on various biomarker proteins in the common white clam as indicators of anthropogenic impact.  Her work included a long-term seasonal study of these biomarkers and a short-term transplantation study to examine immediate impacts. 

The work in Uganda is a hybrid between scholarship and service for the Bolender Group.  We travel to Mbarara (southwestern region near Rwanda and Congo) to assist Dr. Anita Hunter of the School of Nursing and the Archdiocese of Mbarara in supporting a children’s hospital.  The Holy Innocents Children’s Hospital officially opens in January 2009 and will be the only general care children’s hospital in Uganda.  We became part of the team when Dr. Hunter realized that the hospital could potentially impact the Rwizi River with human and medical waste.  Ashley, Raffaela, and I traveled to Mbarara in January 2008 to conduct preconstruction water quality analysis.  In January 2009, I will travel with Ashley Cobb (Biochem ’10), Denise Do (Biochem ’10), Erica Hewitt, and Joel Burke (MARS Graduate Student) to continue this study, and expand it to include the Ugandan National Mountain Gorilla Park in Bwindi.  Joining us on this trip is Meredith Mann (nee Troy, Class of 2003).  She will be working with Dr. Hunter and two resident pediatricians from TUORO in training the doctors and nurses in pediatric care.  The blog addresses of our trips are listed below:

Daley Research Update

The Daley research group welcomed its first undergraduate members, April Stanley, Jessica Cryder, and Ryan Haywood last spring.  They worked over the summer and we made some great strides.  First, on the funding front, our group was awarded a National Science Foundation Research at Undergraduate Institutions three-year grant totaling $306,000 to investigate the novel iron and cobalt containing nitrile hydratase enzymes.  This project is the longest standing in the Daley group and now it can be fully explored owing to the generous support.  Some of the funds from the award (and matching funds from USD) will be used to purchase six new inert atmosphere dual-manifold systems that are to be installed in ST496.  We are excited about this as it will have the dual result of helping expand our research capability and favorably impacting the upper-division laboratory classes as the next generation of upper-division students will able to learn and perform more advanced air-sensitive experiments.  On the research front, some of our highlights included April’s synthesis of a nitrile hydratase analogue, Ryan’s isolation of a crucial platinum compound, and Jessica’s breakthrough isolation and characterization of a new chiral ligand.  The latter ligand is from our other research focus: the development of new ligands for use in asymmetric catalysis.  These results will be published this year with each student being a co-author on the appropriate paper.  As of January 2009, Ryan left upon graduation but we welcomed Kyle Cordova as our newest member who will pick up where Ryan’s project left off.  We hope to get 2-3 more group members by the summer as well (so if you are looking!).

DeHaan Research Update

From summer 2008 to summer 2009, Professor David De Haan is on sabbatical at the University of Colorado; working with Professors Maggie Tolbert and Jose Jimenez to explore the atmospheric chemistry of glyoxal using aerosol mass spectrometers.

Dutnall Research Update

The Dutnall research group is continuing its studies of proteins involved in packaging DNA in cells. One of our projects is to understand the relationship between the structure and function of a histone acetyltransferase enzyme (Hat1) that is involved in gene regulation. During the Fall ’07 and Spring ’08 semesters, Devin Crane created an extensive database of Hat1 sequences from many organisms and analyzed these along with available Hat1 structures. We are using this ‘bioinformatics’ approach to identify features of the Hat1 protein that may be important for its function. Our goal is to test our hypotheses by determining the effect of mutating selected amino acids on Hat1 enzyme activity (using biochemical and biophysical methods) and correlating this with effects of the mutations on Hat1 biological function (using cellular and genetic methods). Over the summer, Devin set up a fluorescence-based assay for Hat1 activity that we can use in future studies. Ryan Brennan, who has begun work to create expression plasmids for several Hat1 mutants, joined him in Fall ‘08. Ryan will continue this Spring and Summer to express and purify these mutants so that we can assay their biochemical activity.

Dwyer Research Update

The Dwyer research group made terrific progress on determining solution structures of DNA duplexes containing non-natural, non-hydrogen bonding base pairs in collaboration with Debbie Tahmassebi’s group.  In March 2008, we published our first paper on this work (“Solution Structure of a DNA Duplex Containing a Guanine-Difluorotoluene Pair: A Wobble Pair Without Hydrogen Bonding?" Dwyer, Tammy; Tahmassebi, Deborah; Pfaff, Danielle; Clarke, Kristine; Geierstanger, Bernhard; Parr, Timothy; Cole, Joanna; J. Am. Chem. Soc., 2008, 130 (14), 4869-4878.)  In March 2008, Danielle Pfaff (Biochemistry, 2008) and I presented our work at a Gordon Conference entitled “DNA Damage, Mutation and Cancer” in Ventura, CA.  What a great experience for Danielle (who did a marvelous job co-presenting a poster with me!) and our work was extremely well received.  Danielle is now a super-star graduate student in biochemistry at Western Washington University – congratulations Danielle!  During summer 2008, Debbie Tahmassebi and I worked with two amazing students (Alyssa Rothwell-Navapanich and Shannen Cravens, picture here) who fully assigned and analyzed the NMR spectra for two DNA duplexes with the drug actinomycin bound to each.  In Fall 2008, Shannen and Alyssa began computational modeling of these complexes using molecular dynamics simulations and we hope to wrap up this work during summer 2009.  In addition, Shannon Ippoliti began working with me to determine the NMR solution structure of a DNA duplex containing a novel base pair designed by Floyd Romesberg’s group at the Scripps Research Institution.  Shannon and I hope to put the finishing touches on this structure in Spring 2009.

Iovine Research Update

In February 2008 Dr. Iovine received the NSF CAREER award. The award will provide $475,000 in funding over five years in support of Dr. Iovine’s research and teaching.  In conjunction with the grant, Dr. Iovine and his students will develop a class of materials known as dendrimers.  One objective of the grant is to use “sticky-ended” dendrimers to chemically modify a renewable material termed lignin.  By chemically decorating the renewable material with dendrimers, Dr. Iovine hopes to create novel natural-synthetic hybrid materials that can be used as plastic alternatives.  Beyond the research, the NSF CAREER award will allow Dr. Iovine and USD’s office of Community Service Learning to engage local educators and students by supporting a scientific outreach program. 

Since the last edition of the Spin, several Iovine group members have graduated.  Erik Raaum and Jared Forrester currently work for Axikin Pharmaceuticals here in San Diego.  After spending a year in Poland, in conjunction with his prestigious Fulbright scholarship, Sasha Neuwelt is attending a M.D./Ph.D. program at the University of Colorado.  Jason Loera spent a year traveling and learning Spanish but plans to attend medical school in the fall of 2009.  After working at Solamatrix for two years, Matt Fletcher (’06) will attend law school in the fall 2009.  Cole Klick returns to his Minnesota homeland and is currently attending the University of Minnesota Medical School.  Jeremy Oria works for BioBlocks, Inc here in San Diego.  Travis Scudday is attending Creighton Medical School in Nebraska. 

The summer of 2008 was exceptionally busy.  Three students conducted research in the Iovine lab:  Ben Streifel, Chris Hincke, and Caitlin Stevens.  Kristy Clarke, a chemistry teacher at Dana Point High School and USD alumnus, also made significant contributions to the summer research effort.  Dr. Iovine enjoyed a sabbatical traveled to the Costa Brava Spain and Philadelphia to present research talks.    

The list of Iovine research group alumni continues to grow.  Since the fall of 2002, over fourteen undergraduate students have worked in the Iovine research lab.  It is my hope that each of you are enjoying your post-USD years and that you will find some time to visit in the near future.   I would love to hear from all of you, send me an email or give me a call.

Kua Research Update

2008 has been a productive year for research. Our entry into aerosol chemistry began with our computational study of glyoxal dimer formation, in collaboration with the De Haan group, published in the Journal of Physical Chemistry. Sean Hanley ('08) was a co-author on this paper and worked on both computational and experimental aspects. We collaborated with the Iovine group on the first rational synthesis of heterotrimeric arylboroxines - published in Dalton Transactions. A full computational paper was subsequently published in the Journal of Physical Chemistry. Charles Gyselbrecht ('10) was a co-author on both papers. Lorenzo Bautista ('11) is extending this work by studying the detailed enthalpic versus entropic contributions comparing homotrimeric and heterotrimeric arylboroxines. Lorenzo also successfully obtained a summer research award from the ACS Petroleum Research Fund to work on parameterizing a force field for covalent organic frameworks. Kelly Nesseth ('09) obtained a SURE fellowship and laid the groundwork for this project this past summer.

The aerosol chemistry work has now been extended by Hadley Krizner ('10).  Hadley has recently completed similar calculations for methylglyoxal. Hadley is in the midst of writing up a manuscript to be submitted by February 2009. Hadley is also working on elucidating the reaction mechanism of glyoxal and amines forming imidazoles. Calvin Schneider ('09) has almost finished parameterizing a titanium-benzene force field and is starting to run several molecular dynamics simulations. Rommel Rico ('10) used his programming skills and a SURE fellowship this summer to write a Monte Carlo script for ion self-assembly. Rowena Daly ('09) is analyzing simulations of the antimony trichloride and dioxane system. Keaton Tomlin ('08) contributed to early parameterization of the force field. We are awaiting some final results before submitting the mostly-written manuscript. This work is in collaboration with Prof. Arnold Rheingold from UCSD and Prof. Adri van Duin from Pennsylvania State University!

Malachowski Research Update

As synthetic organic chemists, we love to make new compounds.  We have now moved our research efforts away from synthesizing models for biological molecules to making compounds called Metal-Organic Frameworks (MOFs).  We continue to spend our time synthesizing and characterizing large numbers (sometimes) of new organic compounds and then we make metal complexes from them.  Feverishly working on this project have been Stephanie Kishbaugh, Michelle Grau, Randy Yale, Alex Dru, Kristina Khazeni, Karey Kowalski, and Keri Oyadomari.  We have been successful in the preparation of some of the targets and we have been able to obtain a nice series of crystal structures that confirm the structures of our compounds.  Much work remains to be done and all of these students will be back in the spring, 2009 to advance this project.  We are in the process of writing up some of our results for publication and expect the papers to see the light of day in 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 2008.  I have run many workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities.  It is clear that getting students involved in research is one of the most powerful educational practices in which they can engage.  The positive outcomes go well beyond any presentations they may give or any work they may publish.  Recently, the chemistry and biochemistry department added a new requirement that all of our majors need to perform a research project and we already are very pleased at what we are seeing.

Mills Research Update

The Mills research group is making progress along two fronts in trying to understand the role of metals in proteins. Joseph Schneider, Julia Becherer and Shayna Herskovic have successfully cloned the genes for Fur proteins from 3 species of bacteria. We are working on expressing and purifying these proteins to determine how tightly they bind different metals. In July 2008, Shayna presented their progress with Fur at the Protein Society meeting in San Diego. Her poster was selected for an oral presentation. Julie and Shayna completed their time in the group this fall and we wish them both well in their next pursuits. This fall, Jourdain Artz joined them on this project. Jamie Custodio will also join the group this spring. On the other front, Laura Murphy worked very hard to build a new expression system for the copper amine oxidase from yeast that we are studying but was unsuccessful. She graduated in May 2008 and went on to vet school. We hope she enjoys her time there. Kaitlyn Dang has taken over the project and is taking it in a new direction. With all the troubles Laura had, we have set the new expression system aside for the time being. Instead, we are collaborating with another lab to provide us with the amine oxidase from pea seedlings. Kaitlyn will be studying the role of copper in this protein. This spring, Michelle Dominguez will join her on this project.

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 2008.  I have run many workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities.  It is clear that getting students involved in research is one of the most powerful educational practices in which they can engage.  The positive outcomes go well beyond any presentations they may give or any work they may publish.  Recently, the chemistry and biochemistry department added a new requirement that all of our majors need to perform a research project and we already are very pleased at what we are seeing.

Tahmassebi Research Update

Research in the Tahmassebi lab is moving forward on several fronts.  Dr. Dwyer and I continue to collaborate to study the structures and drug-binding properties of DNA containing non-natural nucleosides. Earlier this year, we published a manuscript in the Journal of the American Chemical Society based on earlier work completed by alumni Kristy Clarke ’02, Danielle Pfaff ’08, Timothy Parr ’07 and Joanna Cole ’07.  Sophomores Shannen Cravens and Alyssa Navapanich have been working since last spring on the continuation of this project.  Their work is now focused on the 2D-NMR assignments of a DNA-drug complex and using that data for molecular dynamics calculations. 

For Will Porterfield, a few years of hard synthetic work in the lab culminated in a manuscript that is currently in press in Bioorganic and Medicinal Chemistry Letters.  With the help of other talented undergraduate students, Taylor Hepp and April Stanley, Will was able to synthesize a novel fluorescent dideoxynucleoside called tC.  This molecule has potential applications as a fluorescent probe for studying the dynamics of DNA Polymerase and other enzymes.   He plans to present his results on campus in a department senior seminar and an honors senior seminar this spring.

Finally, Ben Huebner and Chrissy Spear have started working in my lab.  Their work is focused on the asymmetric synthesis of ruthenium tris-bipyridine-alanine complexes.  They expect to study the structure, stereochemistry and electronic properties of these complexes once the syntheses have been completed.  Of course, I continue to enjoy working with such a talented group of students.

Research Corporation Grants USD Chemistry and Biochemistry a Department Development Award

Several years of planning and hard work culminated in success as the Department was awarded $496,730 over four years from the Research Corporation.  Along with a $693,000 matching contribution from USD, Research Corporation will support systemic changes in the Chemistry/Biochemistry Department to enrich the research climate and augment research productivity.  James Gentile, President of the Research Corporation, stated in the award letter “we believe that the sciences at USD can stand out as a model for science as it will be practiced during the 21st century.”  During the first year of the project funds have been used for three new staff members, purchasing supplies to support the new research requirement for all chemistry and biochemistry majors, student and faculty travel to national conferences, a seminar series and a summer research coordinator and activities. The funding will also provide one new tenure-track faculty position in the fourth year of the grant.  Over the project period the USD contribution will increase as the direct funding from Research Corporation declines.  This very competitive award was based on documented progress of the department and plans for the future.

New External Grants Obtained by Chemistry and Biochemistry Faculty in 2008

Faculty Member(s)


Project Title

Funding Period

Total $$

Christopher Daley

National Science Foundation (RUI)

Biologically Relevant Metal-Amidato Complexes: Structural and Functional Studies



David De Haan

National Science Foundation (RUI)

Secondary Organic Aerosol Formation by Cloud Processing of a-Dicarbonyl and Amine Compounds



Peter Iovine

National Science Foundation (CAREER)

Macromolecular Materials Based on the Diverse Chemistry of Arylboronic Acids and Arylboroxines



Mitchell Malachowski

National Science Foundation (CCLI)

A Multifaceted Workshop Initiative by CUR


$19, 988

Kimberly Matulef

Research Corporation

Bacterial Chloride-Transport Proteins: Bridging the Structure-Function Gap



Total Secured


Faculty and Student Co-Authored Research Publications in 2008 (students designated by *):

  • Wallace, D.M.; *Brauner, N.; *Niceswanger, W.; Iovine, P.M. “Improved Synthesis and Chemical Modification of a β-O-4 Type Artificial Lignin Polymer,”  Polymer Preprints (American Chemical Society, Division of Polymer Chemistry), 49(2),725 (2008).
  • Kua, J.; *Gyselbrecht, C. R. "Favoring heterotrimeric boroxine formation using an internal Lewis base: A computational study.” J. Phys. Chem. A, 112(38), 9128-33 (2008).
  • Iovine, P. M.; *Gyselbrecht, C. R., *Perrtu, E. K.; *Klick, C.; *Neuwelt, A.; *Loera, J.; *DiPasquale, A. G.; Rheingold, A. L.; Kua, "Hetero-arylboroxines: The first rational synthesis, x-ray crystallographic and computational analysis," J. Dalton Trans. 3791-3794 (2008).
  • Malachowski, M. R.; Nelson, M., “Lessons from the CUR Institutes on Institutionalizing Undergraduate Research,” chapter in “Developing, Promoting and Sustaining the Undergraduate Research Experience in Psychology,” Eds. R. L. Miller and R. F. Rycek, Society for the Teaching of Psychology (2008).
  • Plesniak L.A., *Botsch K., *Leibrand M., Kelly M., Sem D., Adams J.A., and Jennings, P. "Transferred NOE and saturation transfer difference NMR studies of novobiocin binding to EnvZ suggest binding mode similar to DNA gyrase," Chemical biology & Drug Design 71(1):28 (2008).
  • Kua, J.; *Hanley, S. W.; De Haan, D. O. "Thermodynamics and kinetics of glyoxal formation: A computational study," J. Phys. Chem. A, 112, 66-72 (2008).
  • *Pfaff, D.; Clarke, K.; Geierstanger, B.H.; *Parr, T.; *Cole, J.; Tahmassebi, D.C.; Dwyer, T.J. “Solution Structure of a DNA Duplex Containing a Guanine-Difluorotoluene Pair: A Wobble Pair Without Hydrogen Bonding?"  J. Am. Chem. Soc., 130 (14), 4869-4878 (2008).
  • *Corrigan, A.L.; *Hanley, S.W.; De Haan, D.O. “Uptake of glyoxal by organic and inorganic aerosol,” Environ. Sci. Technol. 42 (12) 4428-4433 (2008).
  • Pearson, W.H.; Lin, S.; Iovine, P.M. “3-Pyridyl-tri(4-fluorophenyl)boroxine,” Acta Crystallographica Section E: Structure Reports Online, E64, o235-o235 (2008). 
  • Harned, T.; Kalous, O.; *Neuwelt, A.; *Loera, J.; Neuwelt, E.; Iovine, P.M.; Reynolds, C.P. “Sodium Thiosulfate (STS) Administered Six Hours After Cisplatin Does Not Compromise Anti-Neuroblastoma Activity,” C. Clin Cancer Res, 14, 533-540 (2008).

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