Graduate Study in - Chemistry - Johns Hopkins University
Graduate Study in - Chemistry - Johns Hopkins University
Graduate Study in - Chemistry - Johns Hopkins University
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<strong>Chemistry</strong><br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
www.jhu.edu/~chem
Contents<br />
2 Welcome<br />
3 Baltimore<br />
4 <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
5 Department of <strong>Chemistry</strong><br />
7 Faculty<br />
7 Kit H. Bowen<br />
8 Paul J. Dagdigian<br />
9 David E. Draper<br />
10 D. Howard Fairbrother<br />
11 David P. Goldberg<br />
12 Marc M. Greenberg<br />
13 Tamara L Hendrickson<br />
14 Kenneth D. Karl<strong>in</strong><br />
15 Thomas Lectka<br />
16 Gerald J. Meyer<br />
17 Douglas Poland<br />
18 Gary H. Posner<br />
19 Harris J. Silverstone<br />
20 Joel R. Tolman<br />
21 John P. Toscano<br />
22 Craig A. Townsend<br />
23 David R. Yarkony<br />
24 Instrumentation<br />
26 Useful Information<br />
28 Baltimore Map & Directions to Campus<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
1
Welcome<br />
Rendition of new chemistry<br />
build<strong>in</strong>g currently under<br />
construction<br />
Greet<strong>in</strong>gs and welcome to the Department of <strong>Chemistry</strong> at <strong>Johns</strong><br />
Hopk<strong>in</strong>s <strong>University</strong>. As you will see throughout this brochure,<br />
we offer an excit<strong>in</strong>g environment for graduate studies <strong>in</strong> all areas<br />
of the chemical sciences. Our department has a unique<br />
advantage <strong>in</strong> its ability to ma<strong>in</strong>ta<strong>in</strong> <strong>in</strong>ternationally recognized<br />
research programs <strong>in</strong> a wide variety of chemical discipl<strong>in</strong>es, while<br />
rema<strong>in</strong><strong>in</strong>g small enough for close student-faculty <strong>in</strong>teractions. This<br />
tradition of excellence has been carried forward from the department’s<br />
<strong>in</strong>ception as the first Ph. D. program <strong>in</strong> chemistry <strong>in</strong> America, and as you<br />
will see, is now cont<strong>in</strong>ued by an outstand<strong>in</strong>g group of scientific leaders<br />
that make up the <strong>Chemistry</strong> Department faculty. It is an excit<strong>in</strong>g time to<br />
enter our department. The <strong>Chemistry</strong> department resides <strong>in</strong> Remsen Hall,<br />
which underwent a complete renovation <strong>in</strong> the 1990’s, Dunn<strong>in</strong>g Hall, and<br />
the new state-of-the-art <strong>Chemistry</strong> build<strong>in</strong>g that is be<strong>in</strong>g constructed to<br />
accommodate department growth. The build<strong>in</strong>g will follow a Georgian<br />
style (see sketch) to blend with the Hopk<strong>in</strong>s campus. Students choos<strong>in</strong>g to<br />
do their graduate work here will benefit from cutt<strong>in</strong>g-edge research<br />
programs and facilities, while work<strong>in</strong>g <strong>in</strong> a friendly environment <strong>in</strong> which<br />
access to faculty is unrestricted.<br />
Students can work on many projects that cross the traditional<br />
l<strong>in</strong>es of chemistry, rang<strong>in</strong>g from materials chemistry and surface<br />
science to bioorganic and bio<strong>in</strong>organic chemistry. There is an<br />
extraord<strong>in</strong>ary commitment here by the faculty towards the<br />
development and growth of the graduate students; one only has to<br />
look at the many students who have graduated from the <strong>Chemistry</strong><br />
Department and gone on to successful careers <strong>in</strong> both <strong>in</strong>dustry and<br />
academia as concrete evidence of this commitment.<br />
The Department is located on the Homewood campus of <strong>Johns</strong><br />
Hopk<strong>in</strong>s <strong>University</strong>, approximately 3 miles from the Inner Harbor<br />
of downtown Baltimore. The city of Baltimore offers all of the<br />
advantages and recreational activities of a major metropolitan area,<br />
and has seen a fantastic revitalization <strong>in</strong> the downtown section and<br />
Inner Harbor <strong>in</strong> the past few years. Many other outstand<strong>in</strong>g<br />
research <strong>in</strong>stitutions are located <strong>in</strong> the Baltimore/Wash<strong>in</strong>gton D.C.<br />
area, <strong>in</strong>clud<strong>in</strong>g the National Institutes of Health (NIH) <strong>in</strong> Bethesda,<br />
Maryland, the National Institute of Standards and Technology (NIST) <strong>in</strong><br />
Gaithersburg, Maryland, the Food and Drug Adm<strong>in</strong>istration (FDA), the<br />
National Aeronautics and Space Adm<strong>in</strong>istration (NASA), the Naval<br />
Research Laboratory (NRL), the Army Research Laboratory (ARL), and<br />
the <strong>University</strong> of Maryland’s Baltimore County campus, as well as its<br />
Biotechnology Institute at College Park. This concentration of scientific<br />
research centers and programs is one of the highest <strong>in</strong> the country and<br />
gives students <strong>in</strong> the <strong>Chemistry</strong> Department the opportunity for<br />
collaborations and other <strong>in</strong>teractions, <strong>in</strong>clud<strong>in</strong>g sem<strong>in</strong>ars and meet<strong>in</strong>gs<br />
with different scientists from private <strong>in</strong>dustry, government laboratories<br />
and other academic <strong>in</strong>stitutions. If you are <strong>in</strong>terested <strong>in</strong> this type of<br />
stimulat<strong>in</strong>g environment and are committed to push<strong>in</strong>g the boundaries of<br />
the scientific frontier, we <strong>in</strong>vite you to jo<strong>in</strong> one of the country’s<br />
outstand<strong>in</strong>g chemistry departments.<br />
2 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Baltimore<br />
<strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong> is located with<strong>in</strong> the city<br />
of Baltimore, a very livable and affordable East<br />
Coast city situated between Philadelphia and<br />
Wash<strong>in</strong>gton. The <strong>Chemistry</strong> Department is housed<br />
on the Homewood campus, which lies with<strong>in</strong> a<br />
residential neighborhood about 2 miles north of the<br />
central bus<strong>in</strong>ess area.<br />
Baltimore has undergone an urban renaissance <strong>in</strong><br />
recent years. Many long established neighborhoods have<br />
experienced a significant <strong>in</strong>flux of new residents. The<br />
area around the Homewood Campus cont<strong>in</strong>ues to be an<br />
attractive neighborhood <strong>in</strong> which to live, and is<br />
typified by artistic brownstones, row houses, and newer<br />
apartment build<strong>in</strong>gs.<br />
The city offers ample recreational and cultural activities.<br />
Harborplace, located along the scenic Inner Harbor just south of the<br />
central bus<strong>in</strong>ess district, is a strik<strong>in</strong>g collection of pavilions and<br />
promenades set at the water’s edge. The National Aquarium adjo<strong>in</strong>s<br />
Harborplace on the east and has undergone a major recent expansion. To<br />
the south of Harborplace is the Maryland Science Center, which features a<br />
variety of scientific exhibits and houses a planetarium and Imax theater.<br />
To the west is the Camden Yards baseball stadium, home of the Baltimore<br />
Orioles, and Raven’s Stadium, home of the Baltimore Ravens.<br />
There are a number of major museums located with<strong>in</strong> the city.<br />
These <strong>in</strong>clude the Walters Art Museum, which possesses a large collection<br />
of antiquities, and the Baltimore Museum of Art, which houses an<br />
excellent collection of French Impressionist pa<strong>in</strong>t<strong>in</strong>g and is adjacent to the<br />
Hopk<strong>in</strong>s Homewood campus. Also located <strong>in</strong> the city is the Baltimore and<br />
Ohio Railroad Museum, which has an extensive collection of historic<br />
railway equipment, the Babe Ruth Museum, and a museum dedicated to<br />
Edgar Allen Poe (a former Baltimore resident). Baltimore is also home to<br />
several f<strong>in</strong>e musical organizations. The Baltimore Symphony Orchestra is<br />
world-renowned and offers a range of symphonic and “pop” music at the<br />
modern Joseph A. Meyerhoff concert hall. The Baltimore Opera Company<br />
performs at the renovated Lyric Theatre.<br />
Throughout the year, a variety of festivals and special events occur<br />
<strong>in</strong> Baltimore. These <strong>in</strong>clude the Preakness, which is held at Pimlico Race<br />
course and is the second leg of thoroughbred rac<strong>in</strong>g’s Triple Crown, the<br />
Baltimore Marathon, and Artscape, a citywide arts festival.<br />
Baltimore is conveniently located to other<br />
attractions <strong>in</strong> the mid-Atlantic region. Wash<strong>in</strong>gton, D.C.<br />
is less than an hour to the south by car or tra<strong>in</strong> and offers<br />
some of the best museums and cultural offer<strong>in</strong>gs <strong>in</strong> the<br />
country. Philadelphia is less than two hours north of<br />
Baltimore. With<strong>in</strong> Maryland, the Chesapeake Bay and<br />
the Atlantic shore offer water and beach<br />
activities, while the mounta<strong>in</strong>s lie two hours west of<br />
Baltimore, for ski<strong>in</strong>g <strong>in</strong> the w<strong>in</strong>ter and year-round hik<strong>in</strong>g<br />
and camp<strong>in</strong>g.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
3
<strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
Establishment<br />
<strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong> was the first American <strong>in</strong>stitution to offer and<br />
emphasize graduate education. Its history began <strong>in</strong> 1867, when at the<br />
request of <strong>Johns</strong> Hopk<strong>in</strong>s, a successful Baltimore bus<strong>in</strong>essman, two<br />
corporations were formed: <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong> and <strong>Johns</strong> Hopk<strong>in</strong>s<br />
Hospital.<br />
With this unique vision and generous private endowment, Daniel<br />
Coit Gilman opened the doors to <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong> <strong>in</strong> 1876.<br />
Throughout the years, the name <strong>Johns</strong> Hopk<strong>in</strong>s has become world<br />
renowned and synonymous with scholarly excellence, cutt<strong>in</strong>g edge<br />
scientific research, the advancement of medic<strong>in</strong>e and care of humanity.<br />
<strong>Johns</strong> Hopk<strong>in</strong>s has consistently ranked among the top universities by U.S.<br />
News and World Report.<br />
Organization<br />
<strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong> is a privately endowed, coeducational<br />
<strong>in</strong>stitution consist<strong>in</strong>g of several academic divisions. The Zanvyl Krieger<br />
School of Arts and Sciences (which <strong>in</strong>cludes the <strong>Chemistry</strong> department)<br />
and the G.W.C. Whit<strong>in</strong>g School of Eng<strong>in</strong>eer<strong>in</strong>g occupy the Homewood<br />
campus, a 200 year old estate located <strong>in</strong> a pleasant residential<br />
neighborhood <strong>in</strong> northern Baltimore. The School of Medic<strong>in</strong>e<br />
and the School of Public Health and Hygiene are located <strong>in</strong> east<br />
Baltimore adjacent to the <strong>Johns</strong> Hopk<strong>in</strong>s Hospital. A regular 20<br />
m<strong>in</strong>ute shuttle bus service connects the two campuses. The<br />
Peabody Conservatory of Music is located <strong>in</strong> the elegant Mt.<br />
Vernon neighborhood of Baltimore, between the two ma<strong>in</strong><br />
campuses and is also served by shuttle bus.<br />
Also on the Homewood campus are the Space Telescope<br />
Science Institute, which is the ground base for NASA’s Hubble<br />
Space Telescope, and the Carnegie Institution of Wash<strong>in</strong>gton, a<br />
well known molecular biology research <strong>in</strong>stitute. The Applied<br />
Physics Laboratory is located midway between Baltimore and<br />
Wash<strong>in</strong>gton, and the School of Advanced International Studies is<br />
<strong>in</strong> Wash<strong>in</strong>gton, D.C.<br />
<strong>Johns</strong> Hopk<strong>in</strong>s now has an<br />
<strong>in</strong>ternational identity with learn<strong>in</strong>g<br />
centers <strong>in</strong> Italy and Ch<strong>in</strong>a, but<br />
the city of Baltimore, and the<br />
Homewood campus, rema<strong>in</strong>s its<br />
home. No matter the season, this<br />
<strong>in</strong>comparable campus consist<strong>in</strong>g<br />
of impeccable landscap<strong>in</strong>g, marble<br />
and iron balustrades, and red<br />
brick halls, creates an air of<br />
Victorian decorum. Whatever the<br />
scholarly spirit, this campus<br />
<strong>in</strong>spires!<br />
4<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
The Department of <strong>Chemistry</strong><br />
The <strong>Graduate</strong> Program<br />
F<strong>in</strong>ancial Support<br />
Each graduate student is provided with f<strong>in</strong>ancial<br />
support <strong>in</strong> the form of full tuition and a stipend,<br />
assum<strong>in</strong>g that normal progress toward the degree is<br />
ma<strong>in</strong>ta<strong>in</strong>ed. F<strong>in</strong>ancial support is provided from a<br />
comb<strong>in</strong>ation of teach<strong>in</strong>g and research<br />
assistantships. In addition to the regular stipend,<br />
the department awards a number of fellowships<br />
(Marks Awards) to students of exemplary promise.<br />
Students are also encouraged to apply for the many<br />
national fellowships that are available.<br />
Course Requirements<br />
Eight graduate-level courses are required, and a<br />
program is tailored to the <strong>in</strong>dividual <strong>in</strong>terests and<br />
needs of each student dur<strong>in</strong>g an advis<strong>in</strong>g session<br />
with a faculty committee. Course requirements are<br />
typically completed <strong>in</strong> the first year of graduate<br />
study. <strong>Graduate</strong> courses can be taken with<strong>in</strong> the<br />
<strong>Chemistry</strong> Department or <strong>in</strong> other departments,<br />
and a current list of possible courses can be found<br />
on the <strong>Chemistry</strong> department’s web page<br />
(www.jhu.edu/~chem). Many students take<br />
selected courses <strong>in</strong> the Departments of Biology,<br />
Biophysics, Earth and Planetary Sciences, Electrical<br />
and Computer Eng<strong>in</strong>eer<strong>in</strong>g, Geography and<br />
Environmental Eng<strong>in</strong>eer<strong>in</strong>g, Materials Science and<br />
Eng<strong>in</strong>eer<strong>in</strong>g, Physics and Astronomy, as well as<br />
Pharmacology and Molecular Sciences on the<br />
Medical School campus.<br />
Select<strong>in</strong>g a Faculty Advisor<br />
The choice of a research advisor and dissertation<br />
topic occurs dur<strong>in</strong>g the first semester. To aid <strong>in</strong> this<br />
process, new graduate students at <strong>Johns</strong> Hopk<strong>in</strong>s<br />
attend a series of research sem<strong>in</strong>ars given by<br />
<strong>in</strong>dividual faculty members detail<strong>in</strong>g their<br />
current research activities. New graduate students<br />
also meet <strong>in</strong>dividually with potential faculty<br />
mentors. Most students jo<strong>in</strong> a research group and<br />
beg<strong>in</strong> their <strong>in</strong>dependent graduate work by the end<br />
of the fall semester.<br />
Oral Exam<strong>in</strong>ation<br />
To be recommended for candidacy for the Ph. D.<br />
degree <strong>in</strong> <strong>Chemistry</strong>, each student must prepare and<br />
defend a research proposal that describes his or her<br />
objectives <strong>in</strong> the planned dissertation research. This<br />
proposal should describe progress and accomplishments<br />
to date and plans for future research. The<br />
proposal is presented <strong>in</strong> writ<strong>in</strong>g to a faculty<br />
committee two weeks before the scheduled oral<br />
exam<strong>in</strong>ation. The faculty committee consists of<br />
three members of the <strong>Chemistry</strong> faculty; these faculty<br />
should also be considered as a resource for the<br />
student dur<strong>in</strong>g the rema<strong>in</strong>der of his/her studies.<br />
Students are also required to pass a universityrequired<br />
<strong>Graduate</strong> Board oral exam<strong>in</strong>ation, for<br />
which a committee of five <strong>Chemistry</strong> and outside<br />
faculty members are assembled.<br />
Research<br />
Research is at the heart of the Ph.D. program at<br />
<strong>Johns</strong> Hopk<strong>in</strong>s, and descriptions of faculty member’s<br />
research <strong>in</strong>terests are conta<strong>in</strong>ed <strong>in</strong> this<br />
brochure. Throughout the graduate program,<br />
coursework, sem<strong>in</strong>ars and presentations are<br />
designed to help students with their research<br />
activities and to prepare them for describ<strong>in</strong>g their<br />
work to a scientific audience. For each graduate<br />
student, the successful completion, publication and<br />
dissem<strong>in</strong>ation of results from one or more research<br />
projects forms the basis of the Ph. D. degree.<br />
Dissertation and Defense<br />
The f<strong>in</strong>al step towards a Ph.D. degree is the writ<strong>in</strong>g<br />
of a thesis that describes a student’s <strong>in</strong>dependent<br />
and orig<strong>in</strong>al research accomplishments. This<br />
dissertation is written <strong>in</strong> close consultation with<br />
your faculty advisor. F<strong>in</strong>ally, each student presents<br />
his or her graduate research <strong>in</strong> a departmental<br />
sem<strong>in</strong>ar and private defense before their<br />
dissertation committee.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
5
The Department of <strong>Chemistry</strong><br />
Faculty Research<br />
The Department of<br />
<strong>Chemistry</strong> at <strong>Johns</strong><br />
Hopk<strong>in</strong>s <strong>University</strong> is<br />
made up of a diverse<br />
group of faculty. In addition<br />
to the traditional<br />
areas of chemical<br />
research, many <strong>in</strong>terdiscipl<strong>in</strong>ary<br />
research <strong>in</strong>terests<br />
are present with<strong>in</strong><br />
the department, at the<br />
<strong>in</strong>terface of chemistry and fields <strong>in</strong>clud<strong>in</strong>g biology,<br />
medic<strong>in</strong>e, physics, and environmental and material<br />
sciences. Each faculty member has <strong>in</strong>cluded a brief<br />
description of their research <strong>in</strong>terests <strong>in</strong> this<br />
brochure.<br />
Several faculty members have jo<strong>in</strong>t<br />
appo<strong>in</strong>tments with other departments <strong>in</strong>clud<strong>in</strong>g<br />
Biology, Biophysics, Materials Science and<br />
Eng<strong>in</strong>eer<strong>in</strong>g, and Pharmacology and Molecular<br />
Sciences. A number of <strong>in</strong>terdiscipl<strong>in</strong>ary programs<br />
and research centers based at <strong>Johns</strong> Hopk<strong>in</strong>s<br />
<strong>in</strong>clude members of the <strong>Chemistry</strong> department.<br />
These <strong>in</strong>clude the Materials Research Science and<br />
Eng<strong>in</strong>eer<strong>in</strong>g Center on nanostructures with<br />
enhanced magneto-electronic properties, the NSFsupported<br />
environmental research program <strong>in</strong><br />
Redox-Mediated Dehalogenation <strong>Chemistry</strong>, and<br />
the Program <strong>in</strong> Molecular Biophysics.<br />
Remsen Lecture<br />
Each year, the Department of <strong>Chemistry</strong>, <strong>in</strong><br />
collaboration with the Maryland Section of the<br />
American Chemical Society, bestows a Remsen<br />
Award to a noteworthy Chemist of <strong>in</strong>ternational<br />
acclaim. The award ceremony is accompanied by a<br />
lecture given by the award recipient. The annual<br />
Remsen Award Lectures were <strong>in</strong>augurated <strong>in</strong> May,<br />
1946 by the Maryland Section of the American<br />
Chemical Society to honor Ira Remsen, Professor of<br />
<strong>Chemistry</strong> and President of the <strong>Johns</strong> Hopk<strong>in</strong>s<br />
<strong>University</strong>. The Remsen Memorial Lecturers are<br />
chemists of outstand<strong>in</strong>g achievement, <strong>in</strong> keep<strong>in</strong>g<br />
with Ira Remsen’s long and devoted career as an<br />
exponent of the highest standards <strong>in</strong><br />
teach<strong>in</strong>g and research <strong>in</strong> chemistry.<br />
Past Remsen Award Recipients <strong>in</strong>clude:<br />
2001 Dr. Ad Bax NIH<br />
2000 Dr. Alexander P<strong>in</strong>es UC-Berkeley<br />
1999 Dr. Thomas J. Meyer UNC-Chapel Hill<br />
1998 Dr. Peter B. Dervan Cal Tech<br />
1997 Dr. William H. Miller UC-Berkeley<br />
1996 Dr. David A. Evans Harvard <strong>University</strong><br />
1995 Dr. Alfred G. Redfield Brandeis <strong>University</strong><br />
1994 Dr. Edward I. Solomon Stanford <strong>University</strong><br />
1993 Dr. Christopher T. Walsh Harvard Medical School<br />
1992 Dr. William Klemperer Harvard <strong>University</strong><br />
1991 Dr. Rudolph A. Marcus Cal Tech<br />
Application and Admission<br />
No formal degree is required for admission, although enter<strong>in</strong>g students usually hold a<br />
bachelor’s or master’s degree <strong>in</strong> chemistry or a related science. All applicants for admission are required to<br />
furnish academic transcripts, three letters of recommendation, and scores of <strong>Graduate</strong> Record<br />
Exam<strong>in</strong>ations, <strong>in</strong>clud<strong>in</strong>g the Advanced <strong>Chemistry</strong> Exam<strong>in</strong>ation. An application to our graduate program is<br />
<strong>in</strong>cluded at the end of this brochure and on our web page (www.jhu.edu/~chem).<br />
For further <strong>in</strong>formation, or if you have any questions, please contact:<br />
Academic Program Coord<strong>in</strong>ator<br />
Phone: 410-516-7427<br />
Fax: 410-516-8420<br />
E-mail chem.grad.adm@jhu.edu<br />
Faculty members are also happy to answer questions about their <strong>in</strong>dividual research <strong>in</strong>terests; their e-mail<br />
addresses are <strong>in</strong>cluded <strong>in</strong> the faculty research section of this brochure.<br />
6<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Kit H. Bowen<br />
Experimental Physical <strong>Chemistry</strong>: Clusters and Nanoparticles<br />
kitbowen@jhu.edu<br />
Clusters are aggregates of atoms and/or molecules held together by the same<br />
<strong>in</strong>teratomic or <strong>in</strong>termolecular forces which are responsible for cohesion <strong>in</strong><br />
solids and liquids. Clusters are thus f<strong>in</strong>ite-size microcosms of the condensed<br />
phase, the realm <strong>in</strong> which most chemistry occurs. A major objective of Dr.<br />
Bowen’s research is to provide a molecule’s eye view of many-body, condensed<br />
phase <strong>in</strong>teractions. The study of size-specific and composition-specific clusters<br />
provides an <strong>in</strong>cisive means of address<strong>in</strong>g this fundamental and longstand<strong>in</strong>g problem<br />
<strong>in</strong> phyical chemistry.<br />
For technical reasons, clusters are best studied as negatively-charged species.<br />
Experimental methods utilized <strong>in</strong> Dr. Bowen’s group to study clusters <strong>in</strong>clude both<br />
cont<strong>in</strong>uous and pulsed negative ion photoelectron spectroscopy, mass spectrometry,<br />
and photodissociation spectroscopy. This work is <strong>in</strong>strumentally oriented, with major<br />
components of his several ion beam apparatus <strong>in</strong>clud<strong>in</strong>g both cont<strong>in</strong>uous and pulsed<br />
lasers, high vacuum systems, ion and electron optics, electronics and computers, as<br />
well as time-of-flight, quadrupole, magnetic sector, and Wien filter mass<br />
spectrometers. The tra<strong>in</strong><strong>in</strong>g <strong>in</strong> advanced <strong>in</strong>strumentation, afforded students <strong>in</strong> Dr.<br />
Bowen’s group, lays a firm foundation for careers <strong>in</strong> either physical or analytical<br />
chemistry. Experimental emphasis is also placed on design<strong>in</strong>g unique sources of<br />
cluster ions and on the preparation and characterization of nanoparticles for a variety<br />
of technological applications, such as catalysis.<br />
A particularly attractive aspect of cluster studies concerns the very wide<br />
variety of scientific problems that can be addressed, stretch<strong>in</strong>g from the edge of<br />
biology, through chemistry and condensed matter physics, to the edge of<br />
astrophysics. Us<strong>in</strong>g the versatile techniques described above, Dr. Bowen’s group is<br />
study<strong>in</strong>g the number of water molecules necessary to <strong>in</strong>duce the formation<br />
of zwitterions <strong>in</strong> am<strong>in</strong>o acids, the energetics of electron capture <strong>in</strong><br />
hydrated nucleic acid bases, the solvent-<strong>in</strong>duced stabilization of otherwise unstable<br />
organic anions, the solvation of anions by aqueous and non-aqueous solvents, the<br />
energetics and growth paths of charged atmospheric aerosols, the microscopic<br />
conditions necessary for form<strong>in</strong>g solvated electrons, the stability of color centers <strong>in</strong><br />
nanocrystals of metal compounds, the <strong>in</strong>sulator-to-metal transition <strong>in</strong> clusters of<br />
divalent metals, the electronic structure of alkali metal clusters, the prospects for<br />
magic clusters as build<strong>in</strong>g blocks of futuristic cluster-assembled materials, the nature<br />
of exotic species such as dipole bound and double Rydberg anions, the magnetism<br />
exhibited by silicon-encapsulated transition metals, and the role of nanoclusters <strong>in</strong><br />
<strong>in</strong>terstellar dust. The opportunity to be <strong>in</strong>volved <strong>in</strong> such a diversity of fields is an<br />
excit<strong>in</strong>g aspect of this work for Dr. Bowen and his research group.<br />
Ph.D., Harvard <strong>University</strong><br />
Postdoctoral, Harvard<br />
<strong>University</strong><br />
Fellow, American Physical<br />
Society<br />
Humboldt Research Awardee<br />
K + K + K + K +<br />
Selected Publications <strong>in</strong>clude:<br />
“In search of theoretically-predicted magic clusters: lithium-doped alum<strong>in</strong>um cluster anions,” O.C. Thomas, W.-J. Zheng, T.P. Lippa,<br />
S.-J. Xu, S.A. Lyapust<strong>in</strong>a, and K.H. Bowen, J. Chem. Phys. 114, 9895 (2001).<br />
“Solvent-<strong>in</strong>duced stabilization of the naphthalene anion by water molecules: A negative cluster ion photoelectron spectroscopic<br />
study”, S.A. Lyapust<strong>in</strong>a, S.-J. Xu, J.M. Nilles, and K.H. Bowen, J. Chem. Phys. 112, 6643 (2000).<br />
“Vibrationally-resolved photoelectron spectroscopy of MgO - , and ZnO - , and the low-ly<strong>in</strong>g electronic states of MgO, MgO - , and<br />
ZnO”, J.H. Kim, X. Li, L.-S. Wang, H.L. deClercq, C.A. Fancher, O.C. Thomas, and K.H. Bowen, J. Phys. Chem. A. 105, 5709<br />
(2001).<br />
K +<br />
Al - 13<br />
K + K +<br />
K + 7<br />
“Magic numbers <strong>in</strong> copper-doped alum<strong>in</strong>um cluster anions”, O.C. Thomas, W.–J. Zheng, and K.H. Bowen, J. Chem. Phys. 114,<br />
5514 (2001).<br />
The cluster-assembled ionic<br />
“molecule”, KAl 13 , the kernel of<br />
a new material<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Paul J. Dagdigian<br />
Experimental Physical <strong>Chemistry</strong><br />
Gas-Phase Collision Dynamics and Spectroscopy<br />
pjdagdigian@jhu.edu<br />
Ph. D., <strong>University</strong> of<br />
Chicago<br />
Postdoctoral, Columbia<br />
<strong>University</strong><br />
Fellow, American Physical<br />
Society<br />
We are employ<strong>in</strong>g laser fluorescence excitation and resonance-enhanced<br />
multiphoton ionization of atoms and small molecules <strong>in</strong> studies of<br />
gas-phase collisional processes, <strong>in</strong>volv<strong>in</strong>g chemical reactions,<br />
photodissociation, and nonreactive energy transfer processes. Recent<br />
work has <strong>in</strong>cluded the study of collision-<strong>in</strong>duced rotational and<br />
electronic transitions <strong>in</strong> the CN radical and the photodissociation of vibrationally<br />
excited methyl chloride.<br />
We are also <strong>in</strong>terested <strong>in</strong> understand<strong>in</strong>g the non-bond<strong>in</strong>g <strong>in</strong>teractions<br />
between light atoms, such as boron, carbon, alum<strong>in</strong>um, and silicon, with rare gases<br />
and small molecules such as H 2 . We <strong>in</strong>terrogate these <strong>in</strong>teractions through the<br />
measurement of the electronic spectra of weakly bound complexes of these species,<br />
prepared <strong>in</strong> a free-jet supersonic expansion. Such studies allow us to <strong>in</strong>fer the<br />
evolution of the chromophore of an atomic transition from that <strong>in</strong> the free atom,<br />
b<strong>in</strong>ary and higher complexes through to the atom-doped solid.<br />
There is a cont<strong>in</strong>u<strong>in</strong>g need for the development of laser diagnostics for the<br />
detection of transient species <strong>in</strong> reactive environments, as well as the detection of<br />
explosives <strong>in</strong> trace quantities. Our group is participat<strong>in</strong>g <strong>in</strong> a recently funded DoD<br />
multi-university <strong>in</strong>itiative, “Spectroscopic and Time Doma<strong>in</strong> Detection of Trace<br />
Explosives <strong>in</strong> Condensed and Vapor Phases.” We will be implement<strong>in</strong>g cavity<br />
r<strong>in</strong>g-down spectroscopy (CRDS) as one of a suite of ultrasensitive laser analytical<br />
techniques to be applied to the detection of land m<strong>in</strong>es. In our laboratory, we are also<br />
employ<strong>in</strong>g CRDS to study the spectroscopy and k<strong>in</strong>etics of transient <strong>in</strong>termediates,<br />
for example the H 2 CN radical.<br />
Selected Publications <strong>in</strong>clude:<br />
Tan, X.; Dagdigian, P. J.; and Alexander, M. H., “Electronic Spectroscopy and Excited State Dynamics of the Al–H 2 /D 2 Complex,”<br />
Faraday Discuss. 2001, 118, 387.<br />
Lei, J.; and Dagdigian, P. J., “Laser Fluorescence Excitation Spectroscopy of the CAr van der Waals Complex,” J. Chem. Phys.<br />
2000, 113, 602.<br />
Lei, J.; Teslja, A.; Nizamov, B.; and Dagdigian, P. J., “Free-Jet Electronic Spectroscopy of the PO 2 Radical,” J. Phys. Chem. A 2001,<br />
105, 7828.<br />
Nizamov, B.; Dagdigian, P. J.; and Alexander, M. H., “State-Resolved Rotationally Inelastic Collisions of Highly Rotationally Excited<br />
CN(A 2 ∏) with Helium: Influence of the Interaction Potential,” J. Chem. Phys. 2001, 115, 8393.<br />
8 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
David E. Draper<br />
Physical Biochemistry<br />
draper@jhu.edu<br />
“<br />
RNA fold<strong>in</strong>g” has become a vigorous area of research as many unexpected and<br />
important functional roles have been discovered for RNA molecules. Research<br />
<strong>in</strong> my lab is concerned with two related questions about RNA: What are the<br />
energetics of fold<strong>in</strong>g compact RNA tertiary structures How do prote<strong>in</strong>s<br />
recognize specific RNA sites and carry out specific tasks A variety of<br />
physical, biochemical, and genetic techniques are be<strong>in</strong>g used to explore several RNA<br />
systems.<br />
For a number of years, we have used ribosomal prote<strong>in</strong> - RNA complexes as<br />
systems to explore different aspects of prote<strong>in</strong> - RNA recognition and RNA fold<strong>in</strong>g.<br />
Most of our current efforts <strong>in</strong> this area concern two highly conserved regions of the<br />
ribosome that b<strong>in</strong>d elongation factor G (EF-G), which catalyzes GTP hydrolysis and<br />
translocation of the ribosome along the messenger RNA. Each region consists of a<br />
ribosomal RNA fragment and several ribosomal prote<strong>in</strong>s; assembly of these<br />
complexes and their <strong>in</strong>teractions with EF-G are be<strong>in</strong>g studied by physical methods.<br />
Mutations whose properties are known from the <strong>in</strong> vitro studies are be<strong>in</strong>g <strong>in</strong>troduced<br />
<strong>in</strong>to ribosomes <strong>in</strong> vivo, to probe the functional significance of the complexes that are<br />
be<strong>in</strong>g prepared. Initial work <strong>in</strong> this area resulted <strong>in</strong> the first crystal structure of a<br />
ribosomal prote<strong>in</strong> - RNA complex (Conn et al., 1999), which, <strong>in</strong> conjunction with<br />
solution thermodynamic studies, has yielded considerable <strong>in</strong>sight <strong>in</strong>to prote<strong>in</strong> - RNA<br />
recognition mechanisms and unexpected features of RNA tertiary fold<strong>in</strong>g. Our<br />
crystallographic efforts are be<strong>in</strong>g carried out <strong>in</strong> collaboration with Prof. Ed Lattman’s<br />
laboratory <strong>in</strong> the Biophysics Department.<br />
In the last few years we have been particularly concerned with electrostatic<br />
aspects of RNA. Fold<strong>in</strong>g of an RNA tertiary structure is opposed by the unfavorable<br />
free energy needed to br<strong>in</strong>g negatively charged phosphates <strong>in</strong>to proximity, and it has<br />
long been known that Mg 2+ is much more effective than monovalent ions at<br />
reduc<strong>in</strong>g the electrostatic free energy of RNA tertiary folds. We have recently<br />
developed a theoretical framework for describ<strong>in</strong>g cation <strong>in</strong>teractions with RNA. The<br />
model successfully accounts for the special properties of Mg 2+ , and we are mak<strong>in</strong>g<br />
direct experimental measurements of Mg 2+ - RNA <strong>in</strong>teractions to further test our<br />
predictions. In other work, we are exam<strong>in</strong><strong>in</strong>g the electrostatic component of prote<strong>in</strong> -<br />
RNA b<strong>in</strong>d<strong>in</strong>g, and aga<strong>in</strong> are mak<strong>in</strong>g measurements <strong>in</strong> simple peptide - RNA<br />
complexes to test our theoretical predictions quantitatively.<br />
Ph.D., <strong>University</strong> of<br />
Oregon<br />
Postdoctoral, <strong>University</strong><br />
of Colorado<br />
NIH Career Development<br />
Award<br />
NIH MERIT Award<br />
Selected publications <strong>in</strong>clude:<br />
Conn, G. L., Gittis, A. G., M<strong>in</strong>od, V., Lattman, E. E. & Draper, D. E. (2002). A compact RNA tertiary structure conta<strong>in</strong>s a buried<br />
backbone - K + complex. J. Mol. Biol., 318, 963-973.<br />
Misra, V. K. & Draper, D. E. (2001). A thermodynamic framework for Mg 2+ b<strong>in</strong>d<strong>in</strong>g to RNA. Proc. Natl. Acad. Sci. U S A 98, 12456-<br />
12461.<br />
Misra, V. K. & Draper, D. E. (2002). The l<strong>in</strong>kage between magnesium b<strong>in</strong>d<strong>in</strong>g and RNA fold<strong>in</strong>g. J. Mol. Biol., 317, 507-521.<br />
Gerstner, R. B., Pak, Y. & Draper, D. E. (2002). Recognition of 16S rRna by ribosomal prote<strong>in</strong> S4 from Baccillus stearothermophilus.<br />
Biochemistry 40, 7165-7133.<br />
Shiman, R. & Draper, D. E. (2000). Stabilization of RNA tertiary structure by monovalent cations. J. Mol. Biol., 302, 79-91.<br />
Draper, D. E. (1999). Themes <strong>in</strong> RNA-prote<strong>in</strong> recognition. J. Mol. Biol., 293, 255-270.<br />
Conn, G. L., Draper, D. E., Lattman, E. E. & Gittis, A. G. (1999). Crystal structure of a conserved ribosomal prote<strong>in</strong> - RNA complex.<br />
Science, 284, 1171-1174.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
9
D. Howard Fairbrother<br />
Ph.D., Northwestern<br />
<strong>University</strong><br />
Postdoctoral, <strong>University</strong><br />
of California, Berkeley<br />
NSF CAREER Award<br />
Experimental Surface <strong>Chemistry</strong><br />
Reactions at Polymer and Environmental Interfaces<br />
Materials Process<strong>in</strong>g<br />
howardf@jhu.edu<br />
Dr. Fairbrother’s research program is focused on elucidat<strong>in</strong>g the mechanisms of<br />
chemical reactions that occur on surfaces and <strong>in</strong> th<strong>in</strong> films as well as their<br />
impact on material properties. This <strong>in</strong>terest is motivated by the wide range of<br />
technologically significant processes that are mediated by surface reactions<br />
<strong>in</strong>clud<strong>in</strong>g catalysis, materials process<strong>in</strong>g as well as adhesion and friction.<br />
The modification of polymer surfaces <strong>in</strong> vacuum environments is important<br />
<strong>in</strong> a number of different situations <strong>in</strong>clud<strong>in</strong>g plasma process<strong>in</strong>g, polymer<br />
metallization and for vehicles <strong>in</strong> low earth orbits. We are explor<strong>in</strong>g the microscopic<br />
surface events that accompany polymer surface process<strong>in</strong>g (Figure 1) and their impact<br />
on <strong>in</strong>terfacial properties. For example, we have explored the modification of<br />
fluor<strong>in</strong>ated organic films dur<strong>in</strong>g X-ray irradiation and metallization as well as the<br />
reactions of oxygen free radicals with self assembled monolayers.<br />
Surface reactions are also responsible for a wide range of environmental<br />
processes <strong>in</strong>clud<strong>in</strong>g atmospheric chemistry on ice and aerosol particles and the<br />
elementary reaction steps <strong>in</strong> Fe-based organohalide remediation <strong>in</strong> groundwater.<br />
Us<strong>in</strong>g an electrochemical cell coupled to a surface analysis chamber we are study<strong>in</strong>g<br />
the liquid/solid <strong>in</strong>terface, specifically the effect of surface composition on the rate and<br />
product partition<strong>in</strong>g associated with Fe-based organohalide remediation. In related<br />
studies we are also study<strong>in</strong>g the mechanisms associated with electron beam and<br />
plasma remediation of chlorocarbons <strong>in</strong> aqueous solutions (Figure 2).<br />
Our studies utilize a wide variety of modern surface analytical tools<br />
<strong>in</strong>clud<strong>in</strong>g X-ray Photoelectron Spectroscopy (XPS), Infrared Spectroscopy, Mass<br />
Spectrometry and Atomic Force Microscopy (AFM). A number of our projects are<br />
highly collaborative <strong>in</strong> nature, <strong>in</strong>volv<strong>in</strong>g <strong>in</strong>teractions with the Department of<br />
Geography and Environmental Eng<strong>in</strong>eer<strong>in</strong>g and the Department of Materials Science<br />
and Eng<strong>in</strong>eer<strong>in</strong>g.<br />
Selected Publications:<br />
“Electron-Stimulated Chemical Reactions <strong>in</strong> Carbon Tetrachloride/Water (Ice) Films” A. J. Wagner, C. Vecitis, D. H. Fairbrother,<br />
J. Phys. Chem. B. 102 (2002) 4432.<br />
“Effect of X-ray Irradiation on the Chemical and Physical Properties of Semifluor<strong>in</strong>ated Self- Assembled Monolayer”, A. J. Wagner,<br />
S. R. Carlo, C. Vecitis, D. H. Fairbrother, Langmuir 18 (2002) 1542.<br />
“Self-Assembled Monolayers as Models for Polymeric Interfaces,” C. C. Perry, S. R. Carlo, A.<br />
J. Wagner, C. Vecitis, J. Torres, K. Kolegraf, D. H. Fairbrother (ACS Symposium Series on “Solid Surfaces and Th<strong>in</strong> Films”)<br />
“Radical Reactions with Organic Th<strong>in</strong> Films: Chemical Interaction of Atomic Oxygen with an X-ray Modified Self-Assembled<br />
Monolayer” J. Torres, C.C. Perry, S.J. Bransfield, D.H. Fairbrother, J. Phys. Chem. B., 106 (2002) 6265.<br />
Figure 1: AFM image of a PTFE<br />
(Teflon) surface dur<strong>in</strong>g Ti<br />
Deposition<br />
Figure 2: Mass Spectrum of Volatile Species Produced<br />
dur<strong>in</strong>g Electron Beam Irradiation of Ice (bottom)<br />
and a 13 CCl 4 /Ice Film (top)<br />
10 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
David P. Goldberg<br />
Inorganic <strong>Chemistry</strong><br />
Bio<strong>in</strong>organic <strong>Chemistry</strong><br />
Environmental <strong>Chemistry</strong><br />
dpg@jhu.edu<br />
Our research addresses a number of <strong>in</strong>terest<strong>in</strong>g challenges <strong>in</strong><br />
<strong>in</strong>organic/bio<strong>in</strong>organic chemistry. Currently, our group is divided <strong>in</strong>to two<br />
ma<strong>in</strong> areas. Part of our research group is <strong>in</strong>terested <strong>in</strong> the synthesis, physical<br />
properties and reactivity of new porphyr<strong>in</strong>oid compounds. We have<br />
recently discovered a method for synthesiz<strong>in</strong>g corrolaz<strong>in</strong>es, a new class of<br />
porphyr<strong>in</strong>-like compounds that are related to r<strong>in</strong>g-contracted compounds called<br />
corroles. Corroles, known for over 30 years, have a remarkable advantage over<br />
porphyr<strong>in</strong>s <strong>in</strong> stabiliz<strong>in</strong>g high-valent oxidation states (e.g. Mn V , Fe IV , Co IV , Ni III ), yet<br />
little is known about their ability to function as catalysts and/or mimics for<br />
biological systems because of the difficulties encountered <strong>in</strong> their preparation. We<br />
have synthesized Co, Ni, Cu, Mn, and Fe corrolaz<strong>in</strong>es, and are now mapp<strong>in</strong>g out a<br />
new area of metallocorrolaz<strong>in</strong>e reactivity and catalysis. Applications immediately<br />
envisioned for these complexes <strong>in</strong>clude their reactivity toward O 2 and H 2 O 2 for<br />
oxygen activation, the oxygenation/functionalization of substrates such as<br />
hydrocarbons, and their use <strong>in</strong> mediat<strong>in</strong>g the dehalogenation of environmentally<br />
significant organohalides.<br />
In another area, we are design<strong>in</strong>g and synthesiz<strong>in</strong>g small-molecule analogues<br />
of the active sites of certa<strong>in</strong> metalloprote<strong>in</strong>s. Many biological processes rely on<br />
transition metals to effect catalytic reactions. For example, peptide deformylase (PDF)<br />
relies on an unusual (His) 2 (Cys)Fe II (OH 2 ) active site for deformylation dur<strong>in</strong>g<br />
bacterial prote<strong>in</strong> synthesis. We have synthesized new N 2 S thiolate ligands to mimic the<br />
His 2 Cys coord<strong>in</strong>ation sphere found <strong>in</strong> PDF, and have prepared a family of new<br />
transition metal complexes with these ligands. Some of these complexes represent<br />
stabilized forms of <strong>in</strong>termediates postulated to exist dur<strong>in</strong>g catalysis, such as<br />
[(PATH)Zn(formate)], which was prepared from the useful synthon [(PATH)Zn(Me)].<br />
Other complexes exhibit the functional capacity to effect the hydrolysis of certa<strong>in</strong><br />
substrates (e.g. esters), and these reactions are be<strong>in</strong>g exam<strong>in</strong>ed through k<strong>in</strong>etic<br />
studies. We have recently prepared new, more elaborate ligands with imidazole<br />
donors and are explor<strong>in</strong>g their transition metal chemistry, <strong>in</strong>clud<strong>in</strong>g d<strong>in</strong>uclear,<br />
hydroxo-bridged z<strong>in</strong>c complexes that are relevant to enzymes that cleave DNA and<br />
RNA. The study of these complexes will shed light on the fundamental role of metal<br />
ions <strong>in</strong> the related biological systems, and may lead to the development of<br />
<strong>in</strong>dustrially important catalysts and novel pharmaceutical agents.<br />
Ph.D. Massachusetts<br />
Institute of Technology<br />
NIH Postdoctoral Fellow,<br />
Northwestern <strong>University</strong><br />
NSF CAREER Award<br />
Alfred P. Sloan Research<br />
Fellowship<br />
Recent publications <strong>in</strong>clude:<br />
Chang, S.; Karambelkar, V. V.; di Targiani, R. C.; Goldberg D. P. “Model Complexes of the Active Site of Peptide Deformylase: A<br />
New Family of Mononuclear N 2 S-M II Complexes,” Inorg. Chem., 2001, 40, 194-195.<br />
Ramdhanie, B.; Stern, C. L.; Goldberg. D. P. “Synthesis of the First Corrolaz<strong>in</strong>e: A New Member of the Porphyr<strong>in</strong>oid Family” J. Am.<br />
Chem. Soc., 2001, 123, 9447-9448.<br />
Chang, S.; Sommer, R.; Rhe<strong>in</strong>gold, A.; Goldberg, D. P. “A Model Complex of a Possible Intermediate <strong>in</strong> the Mechanism of Action of<br />
Peptide Deformylase: First Example of an N 2 SZn-formate Complex,” J. Chem. Soc., Chem. Commun., 2001, 2396-2397.<br />
Chang, S.; Karambelkar, V. V.; Sommer, R.; Rhe<strong>in</strong>gold, A.; Goldberg, D. P. “New Monomeric Cobalt(II) and Z<strong>in</strong>c(II) Complexes of a<br />
Mixed N,S(alkylthiolate) Ligand: Model Complexes of (His)(His)(Cys) Metalloprote<strong>in</strong> Active Sites,”Inorg. Chem. 2001, 41, 239-<br />
248.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
11
Marc M. Greenberg<br />
Organic and Bioorganic <strong>Chemistry</strong><br />
mgreenberg@jhu.edu<br />
Ph.D., Yale <strong>University</strong><br />
American Cancer Society<br />
Postdoctoral Fellow,<br />
California Institute of<br />
Technology<br />
Alfred P. Sloan Research<br />
Fellowship<br />
As the carrier of genetic <strong>in</strong>formation, it is no surprise that DNA damage and<br />
repair is important <strong>in</strong> ag<strong>in</strong>g and a variety of genetically based diseases, such<br />
as cancer. However, modified nucleic acids are becom<strong>in</strong>g <strong>in</strong>creas<strong>in</strong>gly<br />
important as diagnostic tools and therapeutic agents. The pivotal roles of<br />
DNA <strong>in</strong> chemistry and biology are <strong>in</strong>terwoven. For <strong>in</strong>stance, the reactivity of<br />
DNA with reactive oxygen species determ<strong>in</strong>es the types of structural modifications<br />
(lesions) formed. The <strong>in</strong>teraction of lesions with repair and polymerase enzymes <strong>in</strong><br />
turn determ<strong>in</strong>es their biological effects. Identify<strong>in</strong>g the location and level of DNA<br />
lesions <strong>in</strong> the genome may assist the diagnosis and treatment approach of disease.<br />
Our research group uses organic chemistry to address questions concern<strong>in</strong>g<br />
the reactivity, function, structure, and uses of nucleic acids. Examples of current<br />
projects <strong>in</strong> our group are:<br />
• determ<strong>in</strong><strong>in</strong>g how nucleic acids are oxidatively damaged by synthesiz<strong>in</strong>g molecules<br />
(e.g 1) that enable us to <strong>in</strong>dependently generate reactive <strong>in</strong>termediates at def<strong>in</strong>ed<br />
sites <strong>in</strong> DNA.<br />
• elucidat<strong>in</strong>g the effects of specific DNA lesions (e.g. 2, 3) on the function of nucleic<br />
acids, and their structural basis.<br />
• the development of methods and applications for modified oligonucleotide<br />
synthesis.<br />
To br<strong>in</strong>g these projects to fruition we synthesize novel molecules and study<br />
their behavior us<strong>in</strong>g a variety of physicochemical, biochemical, and biological<br />
techniques. Recent accomplishments by our research group <strong>in</strong> these areas <strong>in</strong>clude:<br />
• the discovery of novel pathways for DNA damage that produce tandem lesions<br />
(Scheme 1).<br />
• the discovery of the first example of irreversible <strong>in</strong>hibition of DNA repair by a DNA<br />
lesion (Scheme 2).<br />
• the first synthesis of oligonucleotides conta<strong>in</strong><strong>in</strong>g formamidopyrimid<strong>in</strong>e lesions (e.g.<br />
Fapy•dG) and determ<strong>in</strong>ation of their effects on DNA repair and polymerase<br />
enzymes.<br />
• the development of highly efficient, convergent methods for oligonucleotide<br />
conjugate synthesis.<br />
In addition to cont<strong>in</strong>u<strong>in</strong>g these research projects, the above discoveries have<br />
given rise to new projects <strong>in</strong> our group that <strong>in</strong>clude the development of novel<br />
radiosensitiz<strong>in</strong>g agents and mechanism based <strong>in</strong>hibitors of DNA repair enzymes.<br />
Selected publications <strong>in</strong>clude:<br />
Fapy•dA Induces Nucleotide Mis<strong>in</strong>corporation Translesionally by a DNA Polymerase. Delaney, M. O.; Wiederholt, C. J.; Greenberg,<br />
M. M. Angew. Chem. Int. Ed. 2002, 41, 771.<br />
Oxygen Dependent DNA Damage Amplification Involv<strong>in</strong>g 5,6-Dihydrothymid<strong>in</strong>-5-yl <strong>in</strong> a Structurally M<strong>in</strong>imal System. Tallman, K.<br />
A.; Greenberg, M. M. J. Am. Chem. Soc. 2001, 123, 5181.<br />
(3)<br />
The 2-Deoxyribonolactone Lesion Produced <strong>in</strong> DNA by Neocarz<strong>in</strong>ostat<strong>in</strong> and Other DNA Damag<strong>in</strong>g Agents Forms Cross-L<strong>in</strong>ks with<br />
the Base-Excision Repair Enzyme Endonuclease III. Hashimoto, M.; Greenberg, M. M.; Kow, Y. W.; Hwang, J.-T.; Cunn<strong>in</strong>gham, R. P.<br />
J. Am. Chem. Soc. 2001, 123, 3161.<br />
Introduc<strong>in</strong>g Structural Diversity <strong>in</strong> Oligonucleotides Via Photolabile, Convertible C5-Substituted Nucleotides. Kahl, J. D.; Greenberg,<br />
M. M. J. Am. Chem. Soc. 1999, 121, 597.<br />
Scheme 1 Scheme 2<br />
1<br />
2<br />
12<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Bioorganic <strong>Chemistry</strong> and Enzymology<br />
hendrick@jhu.edu<br />
Tamara L. Hendrickson<br />
Our research group is <strong>in</strong>terested <strong>in</strong> evaluat<strong>in</strong>g the mechanisms and<br />
consequences of complex enzymatic systems, with<strong>in</strong> the broad field of<br />
prote<strong>in</strong> translation. We use a multidiscipl<strong>in</strong>ary approach, <strong>in</strong>tegrat<strong>in</strong>g tools<br />
from biochemistry, molecular biology, enzymology and synthetic organic<br />
chemistry.<br />
Several projects focus on an <strong>in</strong>direct pathway for tRNA am<strong>in</strong>oacylation.<br />
Traditionally, it was believed that all organisms use 20 am<strong>in</strong>oacyl-tRNA synthetases<br />
(one for each encoded am<strong>in</strong>o acid) to biosynthesize a complement of<br />
am<strong>in</strong>oacyl-tRNAs. The wealth of genomic data that has become available over the<br />
past few years, however, has revealed that many bacteria and archaea thrive <strong>in</strong> the<br />
absence of glutam<strong>in</strong>yl- and/or asparag<strong>in</strong>yl-tRNA synthetase. In these cases,<br />
tRNA Gln and tRNA Asn are misacylated respectively by either glutamyl- or<br />
aspartyl-tRNA synthetase. Next, a glutam<strong>in</strong>e-dependent amidotransferase<br />
(Glu-AdT) converts the misacylated tRNA to the correct species. (Fig. 1 depicts this<br />
process for the generation of glutam<strong>in</strong>ylated-tRNA Gln .) Very little is known about<br />
Glu-Adt, its mechanism of action or the methods by which it recognizes two different<br />
tRNA substrates (tRNA Gln and tRNA Asn ). Several projects <strong>in</strong> our lab seek to address<br />
some of these issues, by evaluat<strong>in</strong>g Glu-Adt from the stomach ulcer-<strong>in</strong>duc<strong>in</strong>g<br />
pathogenic bacterium H. pylori, from human mitochondria and from the<br />
hyperthermophilic archaeon P. furiousus.<br />
The second area of <strong>in</strong>terest <strong>in</strong> the lab is the biosynthesis of glycosyl<br />
phosphatidyl<strong>in</strong>ositol (GPI) membrane anchored prote<strong>in</strong>s (Fig. 2). GPI anchor<br />
attachment converts a soluble prote<strong>in</strong> <strong>in</strong>to a membrane-associated prote<strong>in</strong>. The<br />
complexity of this system is due to the specificity with which a putative transamidase<br />
(GPI-T) aligns two large substrates, target<strong>in</strong>g the carbohydrate anchor to a particular<br />
amide bond with<strong>in</strong> the prote<strong>in</strong> substrate. GPI prote<strong>in</strong>s are found throughout<br />
eukaryotes, and are particularly abundant <strong>in</strong> some forms of parasitic protozoa,<br />
mak<strong>in</strong>g this modification a potential target for drug design. We are currently<br />
develop<strong>in</strong>g the first soluble k<strong>in</strong>etic assay for GPI-T by synthetically <strong>in</strong>corporat<strong>in</strong>g<br />
chromophoric groups <strong>in</strong>to a typical peptide substrate. The development of such an<br />
assay will enable the first detailed exam<strong>in</strong>ation of the mechanism of action of this<br />
complex enzyme.<br />
Selected publications<br />
Hendrickson, T. L., Nomanbhoy, T. K., de Crecy-Lagard, V., Schimmel, P. “Mutational Separation of Two Pathways for Edit<strong>in</strong>g by a<br />
Class I tRNA Synthetase,” Mol. Cell, 2002, 9, 353-362.<br />
Ph.D., California Institute<br />
of Technology<br />
NIH Postdoctoral Fellow,<br />
Massachusetts Institute of<br />
Technology and The<br />
Scripps Research Institute<br />
Research Corporation<br />
Innovation Award<br />
Hendrickson, T. L. “Recogniz<strong>in</strong>g the D-Loop of Transfer RNAs,” Proc. Natl. Acad. Sci., 2001, 98, 13473-13475.<br />
Dör<strong>in</strong>g, V.; Mootz, H. D.; Nangle, L. A.; Hendrickson,T. L.; de Crécy-Lagard, V.; Schimmel, P.; and Marliére, P. “Enlarg<strong>in</strong>g the Am<strong>in</strong>o<br />
Acid Set of Escherichia coli by Infiltration of the Val<strong>in</strong>e Cod<strong>in</strong>g Pathway,” 2001, 292, 501-504.<br />
Hendrickson, T. L.; Spencer, J. R.; Kato, M.; Imperiali, B. “Design and Evaluation of Potent Inhibitors of Asparag<strong>in</strong>e-L<strong>in</strong>ked Prote<strong>in</strong><br />
Glycosylation,” J. Am. Chem. Soc., 1996, 118, 7636-7637.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
13
Kenneth D. Karl<strong>in</strong><br />
Ph. D., Columbia<br />
<strong>University</strong><br />
Postdoctoral, Cambridge<br />
<strong>University</strong>, England<br />
Editor, Progress <strong>in</strong><br />
Inorganic <strong>Chemistry</strong><br />
(Wiley)<br />
Buck-Whitney Award<br />
Biological and Environmental Inorganic <strong>Chemistry</strong><br />
Synthetic Models for Heme and/or Copper Prote<strong>in</strong>s<br />
Reactions with O 2 , NOx & R-Cl; Cu-DNA & peptide <strong>in</strong>teractions<br />
karl<strong>in</strong>@jhu.edu<br />
Dr. Karl<strong>in</strong>’s bio<strong>in</strong>organic research focuses on coord<strong>in</strong>ation chemistry relevant to<br />
biological and environmental processes. Essential prote<strong>in</strong>s with active-site<br />
copper aggregates or heme (porphyr<strong>in</strong>-iron) centers react with O 2 or nitrogen<br />
oxides. Thus, we study reactions <strong>in</strong>volv<strong>in</strong>g O 2 , NO – 2 (nitrite), NO (nitric<br />
oxide), N 2 O (nitrous oxide) as well as organohalides. Metal/O 2 chemistries<br />
with organic substrates, DNA and prote<strong>in</strong>s are also under <strong>in</strong>vestigation.<br />
Our laboratory approaches <strong>in</strong>clude (a) the rational design and syntheses of<br />
ligands allow<strong>in</strong>g formation of appropriate Cu or Fe complexes, b) elucidation of<br />
structure and physical properties us<strong>in</strong>g X-ray crystallography and a variety of<br />
physical methods, and c) reactivity and k<strong>in</strong>etic-mechanistic <strong>in</strong>vestigations. The<br />
studies should provide <strong>in</strong>sights to questions of biological concern, and also may<br />
provide a rationale for the chemist to design practical reagents for O 2 -mediated<br />
oxidations, NOx-reduction catalysts, or agents which can dehalogenate R-Cl<br />
pollutants.<br />
Recent notable achievements (also see diagrams below) <strong>in</strong>clude: (a) the<br />
detailed characterization of several types of copper-dioxygen adducts, <strong>in</strong>clud<strong>in</strong>g the<br />
trans -1,2-peroxodicopper(II) complex shown below, (b) the generation of<br />
cytochrome c oxidase (heme-copper) O 2- reactivity models, with -peroxo Fe III -(O 2<br />
2–)<br />
-Cu II and -oxo Fe III -(O 2– )-Cu II species, and (c) the demonstration that <strong>in</strong> a highly specific<br />
manner, certa<strong>in</strong> ligand-Cu 2 (or Cu 3 ) complexes oxidatively cleave DNA at the<br />
junction of double and s<strong>in</strong>gle-stranded regions.<br />
Recent publications <strong>in</strong>clude:<br />
Zhang, C. X.; Liang, H.-C.; Kim, E.-i.; Gan, Q.-F.; Tyeklár, Z.; Lam, M.; Rhe<strong>in</strong>gold, A. L.; Kaderli, S.; Zuberbühler, A. D.; Karl<strong>in</strong>, K. D.,<br />
“Dioxygen Mediated oxo-transfer to an am<strong>in</strong>e and oxidative N-dealkylation chemistry with a d<strong>in</strong>uclear copper complex”, Chem.<br />
Commun., 2001, 631-632.<br />
Ghiladi, R. A.; Hatwell, K. R.; Karl<strong>in</strong>, K. D.; Huang, H.-w.; Moënne-Loccoz, P.; Krebs, C.; Marzilli, L. A.; Cotter, R. J.; Kaderli, S.;<br />
Zuberbühler, A. D. “Dioxygen Reactivity of Mononuclear Heme and Copper Components Yield<strong>in</strong>g a High-Sp<strong>in</strong> Heme-Peroxo-Cu<br />
Complex”, J. Am. Chem. Soc., 2001, 123, 6183-6184.<br />
Humphreys, K. J.; Karl<strong>in</strong>, K. D.; Rokita, S. E. “Recognition and Strand Scission at Junctions between S<strong>in</strong>gle- and Double-Stranded<br />
DNA by a Tr<strong>in</strong>uclear Copper Complex”, J. Am. Chem. Soc., 2001, 123, 5588-5589.<br />
Fellow, American<br />
Association for the<br />
Advancement of Science<br />
(AAAS)<br />
Ira Remsen Chair<br />
<strong>in</strong> <strong>Chemistry</strong><br />
14<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Thomas Lectka<br />
Organic <strong>Chemistry</strong><br />
lectka@jhu.edu<br />
The thrust of our research is towards the development of new catalytic<br />
asymmetric reactions. In particular we are <strong>in</strong>terested <strong>in</strong> chiral, all-organic<br />
molecules, and Lewis acids as catalysts, as illustrated <strong>in</strong> three projects:<br />
Project I. Catalytic, Asymmetric -Lactam and -Am<strong>in</strong>o Acid Synthesis.<br />
We have developed practical methodology for the catalytic, asymmetric synthesis<br />
of lactams <strong>in</strong> high diastereo- and enantioselectivity employ<strong>in</strong>g chiral nucleophiles<br />
as catalysts. Our reactions should provide access to a large number of ser<strong>in</strong>e protease<br />
<strong>in</strong>hibitors of prostate specific antigen, cytomegalovirus protease, elastase, thromb<strong>in</strong>,<br />
and cell metathesis. We have also recently developed a new synthesis of am<strong>in</strong>o acid<br />
derivatives through a catalytic, asymmetric process <strong>in</strong> which the chiral nucleophile<br />
benzoylqu<strong>in</strong><strong>in</strong>e (BQ) plays no less than five discrete roles. The reaction is a<br />
multistage, multicomponent reaction <strong>in</strong> which the start<strong>in</strong>g materials are <strong>in</strong>expensive.<br />
Project II. Asymmetric Catalysis on Sequentially-L<strong>in</strong>ked Columns.<br />
The all-organic nature of our catalyst systems renders them attractive to attach to a<br />
solid phase. Along those l<strong>in</strong>es, we have developed a catalytic, asymmetric process <strong>in</strong><br />
which reactions are conducted on a series of sequentially-l<strong>in</strong>ked columns packed with<br />
solid-phase based catalysts and reagents. Our goal is ultimately to produce a<br />
“synthesis mach<strong>in</strong>e” <strong>in</strong> which a complex series of transformations is conducted on the<br />
column assemblies.<br />
Project III. Catalytic, Asymmetric Halogenation.<br />
The third project we have underway concerns the development of catalytic,<br />
asymmetric halogenation reactions. Asymmetric halogenation represents a<br />
challeng<strong>in</strong>g new frontier <strong>in</strong> asymmetric synthesis.<br />
Representative Publications:<br />
“Catalytic, Enantioselective Alkylation of Im<strong>in</strong>o Esters: The Synthesis of Nonnatural Am<strong>in</strong>o Acid Derivatives” J. Am. Chem.<br />
Soc. 2002, 124, 67-77.<br />
“Asymmetric Catalysis on Sequentially-L<strong>in</strong>ked Columns” J. Am. Chem Soc. 2001, 123, 10853-10859.<br />
“Reactive Ketenes through a Carbonate/Am<strong>in</strong>e Shuttle Deprotonation Strategy: Catalytic, Enantioselective<br />
Halides” Org. Lett. 2001, 3, 2049-2051.<br />
“Catalytic, Asymmetric Halogenation” J. Am. Chem. Soc. 2001, 123, 1531-1532.<br />
“Catalytic, Asymmetric Synthesis of Lactams” J. Am. Chem. Soc. 2000, 122, 7831-7832.<br />
Brom<strong>in</strong>ation of Acid<br />
Ph.D. Cornell <strong>University</strong><br />
Postdoctoral, Universität<br />
Heidelberg<br />
NIH Postdoctoral Fellow,<br />
Harvard <strong>University</strong><br />
Alfred P. Sloan Research<br />
Fellowship<br />
Camille Dreyfus Teacher-<br />
Scholar Award<br />
DuPont ATE Award<br />
NSF CAREER Award<br />
Eli Lilly Young Investigator<br />
Grantee<br />
NIH First Award<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
15
Gerald J. Meyer<br />
Inorganic Materials <strong>Chemistry</strong><br />
Environmental <strong>Chemistry</strong><br />
meyer@jhu.edu<br />
(a)<br />
Ph.D., <strong>University</strong> of<br />
Wiscons<strong>in</strong> at Madison<br />
Postdoctoral, <strong>University</strong><br />
of North Carol<strong>in</strong>a at<br />
Chapel Hill<br />
The Meyer group research focuses on <strong>in</strong>organic chemistry with a particular<br />
emphasis on the <strong>in</strong>terface between molecules and solid-state materials. A<br />
theme of our research has been to design materials at the molecular level that<br />
have desired optical, electrical, environmental, biological, magnetic, and/or<br />
catalytic functions. Summarized below are three key research areas:<br />
We prepare solar cells, based on<br />
Nanocrystall<strong>in</strong>e Semiconductor Interfaces.<br />
nanocrystall<strong>in</strong>e semiconductors sensitized to light with <strong>in</strong>organic coord<strong>in</strong>ation<br />
compounds that efficiently convert sunlight <strong>in</strong>to electrical power. These materials<br />
also allow <strong>in</strong>terfacial electron transfer processes to be quantified <strong>in</strong> unprecedented<br />
molecular detail. Shown below, is a schematic representation of an <strong>in</strong>terface designed<br />
for fundamental photo-<strong>in</strong>duced electron transfer studies. Other ongo<strong>in</strong>g research<br />
projects with these <strong>in</strong>terfaces <strong>in</strong>clude the study of bimetallic compounds, charge<br />
transport, energy transfer, and catalysis.<br />
Magnetic Nanowire Interfaces. Nanowires with segments of different magnetic and<br />
non-magnetic materials are prepared <strong>in</strong> our labs. An example is shown below where<br />
a magnetic nickel segment has been functionalized with a fluorescent dye while a<br />
non-magnetic gold segment has not. In the visible image (a) the two wire segments<br />
appear similar while the fluorescent image (b) clearly reveals the nickel segment. The<br />
magnetic properties of the nanowire materials are under active study as part of the<br />
Hopk<strong>in</strong>s’ NSF-funded MRSEC and can be used for applications <strong>in</strong> separations, sens<strong>in</strong>g,<br />
magnetic record<strong>in</strong>g and biotechnology.<br />
Environmental Interfaces. We prepare materials that convert sunlight <strong>in</strong>to electrical<br />
power and materials that can decontam<strong>in</strong>ate water of halocarbon pollutants. This<br />
latter project is the subject of a NSF-funded ‘CRAEMS’ program that <strong>in</strong>volves<br />
<strong>in</strong>terdiscipl<strong>in</strong>ary research with five Hopk<strong>in</strong>s groups. Our approach has been to study<br />
mechanistic aspects of organohalide reaction with natural and synthetic iron<br />
porphyr<strong>in</strong>s. These studies provide <strong>in</strong>sights <strong>in</strong>to how liv<strong>in</strong>g organisms can both<br />
dehalogenate organic halocarbons and die from exposure to them.<br />
Recent Publications:<br />
Pseudo-halogens for Dye-Sensitized TiO 2 Photoelectrochemical Cells. Oskam, G.; Bergeron, B.V; Meyer, G.J.; Searson,<br />
P.C. J. Phys. Chem. B 2001, 105, 6867.<br />
Long Distance Electron Transfer Across Molecular-Nanocrystall<strong>in</strong>e Semiconductor Interfaces. Galopp<strong>in</strong>i, E.; Guo, W.;<br />
Qu, P.; Meyer, G.J. J. Am. Chem. Soc. 2001, 123, 4342.<br />
Magnetic Alignment of Fluorescent Nanowires. Tanase, M.; Bauer, L.A.; Hultgren, A.; Silevitch, D.M.; Sun, L.; Reich, D.H.;<br />
Searson, P.C.; Meyer, G.J. NanoLett. 2001, 1, 155.<br />
Proton Controlled Electron Injection from Molecular Excited States to the Empty States <strong>in</strong> Nanocrystall<strong>in</strong>e TiO 2 .<br />
Qu, P.; Meyer, G.J. Langmuir 2001, 17, 6720.<br />
(b)<br />
Crowded Cu(I) Complexes Involv<strong>in</strong>g Benzohqu<strong>in</strong>ol<strong>in</strong>e: π-Stack<strong>in</strong>g Effects and Long Lived Excited States. Riesgo,<br />
E.C.; Hu, Y.-Z.; Bouvier, F.; Thummel, R.P.; Scaltrito, D.V.; Meyer, G.J. Inorg. Chem. 2001, 40, 3413-3422.<br />
16<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Douglas Poland<br />
Theoretical <strong>Chemistry</strong><br />
Statistical Mechanics, K<strong>in</strong>etics of Cooperative Processes,<br />
Distribution Functions <strong>in</strong> Prote<strong>in</strong>s and Nucleic Acids<br />
poland@jhu.edu<br />
Early <strong>in</strong> my career I was <strong>in</strong>terested <strong>in</strong> the application of the methods of<br />
equilibrium statistical mechanics to the problem of conformational transitions<br />
(helix-coil) transitions <strong>in</strong> prote<strong>in</strong>s and nucleic acids. This work is reviewed <strong>in</strong><br />
two books: (with H.A. Scheraga) Theory of Helix-Coil Transitions <strong>in</strong> Biopolymers<br />
(Academic Press, New York, 1970) and Cooperative Equilibria <strong>in</strong> Physical<br />
Biochemistry (Oxford <strong>University</strong> Press, London, 1978). My <strong>in</strong>terests then turned to<br />
simple lattice-gas models for phase transitions. This work <strong>in</strong>volved extensive<br />
calculation of exact series expansions for thermodynamic functions for various latticegas<br />
models and the analysis of the series (search for phase-transition s<strong>in</strong>gularities). I<br />
also became <strong>in</strong>terested <strong>in</strong> the use of statistical mechanics to treat the k<strong>in</strong>etics of<br />
cooperative phenomena such as cooperative adsorption and enzyme reaction<br />
networks. The general problem <strong>in</strong> this area of study is to understand the nonl<strong>in</strong>ear<br />
equations that arise <strong>in</strong> such systems. When a system is far from equilibrium<br />
<strong>in</strong>stabilities can arise, often giv<strong>in</strong>g rise to limit cycles (oscillations <strong>in</strong> the density) or<br />
chaotic behavior.<br />
Recently my <strong>in</strong>terests have returned to biological macromolecules. In<br />
particular I have been explor<strong>in</strong>g ways to determ<strong>in</strong>e distributions functions for various<br />
molecular properties. For example, given the temperature dependence of the heat<br />
capacity one can convert this data <strong>in</strong>to a f<strong>in</strong>ite set of moments of the distribution<br />
funtion for molecular enthalpies (analog of the Maxwell-Boltzmann distribution of<br />
k<strong>in</strong>etic energies). Given a set of moments one can then use the maximum-entropy<br />
method to construct an approximate distribution function, the quality of the<br />
approximation <strong>in</strong>creas<strong>in</strong>g with the number of moments used. For many prote<strong>in</strong>s this<br />
distribution function is bimodal, <strong>in</strong>dicat<strong>in</strong>g the presence of two major species, the<br />
native and denatured form of the prote<strong>in</strong>. This same technique can be used to<br />
determ<strong>in</strong>e distribution functions for the number of ligands bound to prote<strong>in</strong>s and<br />
nucleic acid us<strong>in</strong>g data from an appropriate b<strong>in</strong>d<strong>in</strong>g isotherm.<br />
Ph.D., Cornell <strong>University</strong><br />
Postdoctoral, Cornell<br />
<strong>University</strong><br />
Selected Publications Include:<br />
Poland, D. "Maximum-Entropy Calculation of Energy Distributions", Journal of Chemical Physics, 2000, 112, 4774-4784.<br />
Poland, D. "Enthalpy Distributions <strong>in</strong> Prote<strong>in</strong>s", Biopolymers, 2001, 58, 89-105.<br />
Poland, D. "Prote<strong>in</strong>-B<strong>in</strong>d<strong>in</strong>g Polynomials", Journal of Prote<strong>in</strong> <strong>Chemistry</strong>, 2001, 20, 91-97.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
17
Gary H. Posner<br />
Organic <strong>Chemistry</strong>; Medic<strong>in</strong>al <strong>Chemistry</strong><br />
ghp@jhu.edu<br />
Professor Posner’s research deals generally with development of new synthetic<br />
methods and asymmetric synthesis of natural products, with special emphasis<br />
on design and synthesis of new compounds hav<strong>in</strong>g beneficial effects on the<br />
quality of human life (i.e., new medic<strong>in</strong>al agents). Recently, the Posner<br />
research team has prepared a promis<strong>in</strong>g analog of vitam<strong>in</strong> D 3 for treatment of<br />
the sk<strong>in</strong> disease psoriasis, a promis<strong>in</strong>g analog of the Ch<strong>in</strong>ese medic<strong>in</strong>e q<strong>in</strong>ghaosu for<br />
treatment of malaria, and some new isothiocyanates as promis<strong>in</strong>g lead compounds<br />
for prevention of cancer.<br />
Professor Posner is well known for his <strong>in</strong>volvement with organocopper<br />
chemistry as a researcher and writer. His orig<strong>in</strong>al research publications and his two<br />
review articles and one book on organocopper chemistry have helped to make this<br />
area one of the fastest develop<strong>in</strong>g ones <strong>in</strong> modern synthetic organometallic chemistry.<br />
Recent publications <strong>in</strong>clude:<br />
Posner, G.H.; Northrop, J.; Paik, I.-K.; Borstnik, K.; Dolan, P.; Kensler, T.W.; Xie, S.; Shapiro, T. A., “New Chemical and Biological<br />
Aspects of Artemis<strong>in</strong><strong>in</strong>-Derived Trioxane Dimers,” Bioorg. Med. Chem. 2002, 10, 227-232.<br />
Ph.D., Harvard <strong>University</strong><br />
Postdoctoral, <strong>University</strong><br />
of California, Berkeley<br />
<strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
Dist<strong>in</strong>guished Teach<strong>in</strong>g<br />
Award<br />
Executive Editor,<br />
Tetrahedron Reports<br />
Gardezi, S.A.; Nguyen, C.; Malloy, P.J.; Feldman, D.; Posner, G. H.; Peleg, S., “A Rationale for Treatment of Hereditary Vitam<strong>in</strong> D<br />
Resistant Rickets with Analogs of 1 -25-Dihydroxyvitam<strong>in</strong> D 3 ,” J. Biol. Chem. 2001, 276, 29148-29156.<br />
Posner, G. H.; Jeon, H.B.; Parker, M.H.; Krasav<strong>in</strong>, M.; Paik, I.-K.; Shapiro, T. A., “Antimalarial Simplified 3-Aryltrioxanes: Synthesis<br />
and Precl<strong>in</strong>ical Efficacy/Toxicity Test<strong>in</strong>g <strong>in</strong> Rodents,” J. Med. Chem., 2001, 44, 3054-3058.<br />
Posner, G.H.; Crawford, K.R.; Peleg, S.; Welsh, J.E.; Romu, S.; Gewirtz, D.A.; Gupta, M.S.; Dolan, P.; Kensler, T.W., “A Non-Calcemic<br />
Sulfone Version of The Vitam<strong>in</strong> D3 Analog Seocalcitol (EB 1089): Chemical Synthesis, Biological Evaluation, and Potency<br />
Enhancement of the Anticancer Drug Adriamyc<strong>in</strong>,” Bioorg. Med. Chem., 2001, 9, 2365-2371.<br />
Somjen, D.; Waisman, A.; Lee, J.K.; Posner, G.H.; Kaye, A.M., “A Noncalcemic Analog of 1,25-Dihydroxyvitam<strong>in</strong> D 3 (JKF)<br />
Upregulates The Induction of Creat<strong>in</strong>e K<strong>in</strong>ase B by 17-Beta-estradiol <strong>in</strong> Osteoblast-like ROS 17/2.8 Cells and <strong>in</strong> Rat Diaphysis,” J.<br />
Steroid Biochem. Mol. Biol., 2001, 77, 205-212.<br />
Szpilman, A.M.; Korsh<strong>in</strong>, E.E.; Hoos, R.; Posner, G.H.; Bachi, M.D., “Iron(II)-Induced Cleavage of Antimalarial Beta-Sulfonyl<br />
Endoperoxides. Evidence for the Generation of Potentially Cytotoxic Carbocations,” J. Org. Chem., 2001, 66, 6531-6540.<br />
O’Neill, P.M.; Miller, A.; Bishop, L.P.D.; H<strong>in</strong>dley, S.; Maggs, J.L.; Ward, S.A.; Roberts, S.M.; Sche<strong>in</strong>man, F.; Hoos, R.; Posner, G.H.;<br />
Park, B.K., “Synthesis, Antimalarial Activity, Biomimetic Iron(II) <strong>Chemistry</strong>, and the <strong>in</strong> vitro Metabolism of Novel, Potent C-10-<br />
Phenoxy Derivatives of Dihydroartemis<strong>in</strong><strong>in</strong>,” J. Med. Chem., 2001, 44, 58-68.<br />
Guyton, K.Z.; Kensler, T.W.; Posner, G.H., “Cancer Chemoprotection Us<strong>in</strong>g Natural Vitam<strong>in</strong> D 3 and Synthetic Analogs,” Annu. Rev.<br />
Pharm. Toxicol. 2001, 41, 421-442.<br />
White, M.C.; Burke, M.; Peleg, S.; Bren, H.; Posner, G.H., “Conformationally Restricted Hybrid Analogs of the Hormone 1,25-<br />
Dihydroxyvitam<strong>in</strong> D 3 : Design, Synthesis, and Biological Evaluation,” Bioorg. Med. Chem., 2001, 9, 1691-1699.<br />
Posner, G.H.; Halford, B.; Dolan, P.; Kensler, T.W.; White, J.; Jones, G., “Conceptually New Low-Calcemic Oxime Analogs of the<br />
Hormone 1-alpha, 25-Dihydroxyvitam<strong>in</strong> D3: Synthesis and Biological Test<strong>in</strong>g,” J. Med. Chem., 2002, 45, 000.<br />
Korsh<strong>in</strong>, E.K.; Hoos, R.; Szpilman, A.M., Konstant<strong>in</strong>ovski, L.; Posner, G.H.; Bachi, M.D., “An Efficient Synthesis of Bridged-Bicyclic<br />
Peroxides Structurally Related to Antimalarial Y<strong>in</strong>gzhaosu A based on Homolytic Co-Oxidation of Thiols and Monoterpenes,”<br />
Tetrahedon, 2002, 58, 2449-2469.<br />
18<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Harris J. Silverstone<br />
Theoretical <strong>Chemistry</strong><br />
hjsilverstone@jhu.edu<br />
My ma<strong>in</strong> research <strong>in</strong>terests are quantum problems that cannot be solved <strong>in</strong><br />
simple closed form, but that can be solved by <strong>in</strong>f<strong>in</strong>ite series expansions,<br />
especially divergent asymptotic expansions. Atoms <strong>in</strong> external electric and<br />
magnetic fields are prime examples. When the external field is regarded as<br />
a perturbation, the result<strong>in</strong>g series are asymptotically divergent.<br />
Divergent series are <strong>in</strong>terest<strong>in</strong>g when they are “summable.” That is, when<br />
there is a procedure for f<strong>in</strong>d<strong>in</strong>g directly from the series the mathematical function that<br />
the series represents. There is often a related, sometimes physical, quantity that is<br />
“exponentially small” and that governs the rate of divergence of the series. In the case<br />
of the electric field, the exponentially small quantity is the ionization rate. A new<br />
development is a higher-order summation technique called hyperasymptotics that<br />
uses the exponentially small subseries to sum the divergent series. The exponentially<br />
small subseries are <strong>in</strong>timately connected with the “connection formula” problem <strong>in</strong><br />
semiclassical methods <strong>in</strong> quantum mechanics, such as the JWKB method.<br />
The hyperasymptotics research is <strong>in</strong> collaboration with Professor Gabriel<br />
Álvarez of the Departamento de Física Téorica II, Universidad Complutense,<br />
Madrid, Spa<strong>in</strong>, and with Professor Christopher J. Howls of the Faculty of<br />
Mathematical Studies, <strong>University</strong> of Southampton, UK.<br />
Research now complete provided a detailed feature-by-feature analysis of the<br />
photoionization cross section of hydrogen <strong>in</strong> an electric field <strong>in</strong> terms of expansions<br />
over resonances. Extension of the expansion to <strong>in</strong>f<strong>in</strong>ite fields led to a complete<br />
understand<strong>in</strong>g of the “Bender-Wu” branch cuts of the anharmonic oscillator, a<br />
somewhat serendipitous result. Earlier work used perturbation expansions to<br />
elucidate the transition between classical, semiclassical and quantum mechanics. Still<br />
earlier work concerned electron correlation (how electrons avoid each other) <strong>in</strong> atoms<br />
and molecules, the evaluation of molecular <strong>in</strong>tegrals us<strong>in</strong>g expansions generated from<br />
Fourier-transforms, and the use of piecewise-polynomial expansions for electronic<br />
wave functions.<br />
A separate research <strong>in</strong>terest, <strong>in</strong> collaboration with Professor Betty Jean<br />
Gaffney of the Department of Biological Science, Florida State <strong>University</strong>, has been the<br />
simulation of electron magnetic resonance spectra for high-sp<strong>in</strong> iron <strong>in</strong> heme prote<strong>in</strong>s<br />
and <strong>in</strong> enzymes.<br />
Ph.D., California Institute<br />
of Technology<br />
NSF Postdoctoral Fellow,<br />
Yale <strong>University</strong><br />
Alfred P. Sloan Research<br />
Fellowship<br />
Selected publications <strong>in</strong>clude:<br />
Connection formula, hyperasymptotics, and Schröd<strong>in</strong>ger eigenvalues: dispersive hyperasymptotics and the anharmonic oscillator;<br />
Gabriel Álvarez, Christopher J. Howls, and Harris J. Silverstone <strong>in</strong> Toward the Exact WKB Analysis of Differential Equations, L<strong>in</strong>ear or<br />
Non-L<strong>in</strong>ear, edited by Christopher J. Howls, Takahiro Kawai, and Yoshitsugu Takei (Kyoto <strong>University</strong> Press, Kyoto, 2000).<br />
Large-field behavior of the LoSurdo-Stark resonances <strong>in</strong> atomic hydrogen; Gabriel Álvarez and Harris J. Silverstone;<br />
Phys. Rev. A 50, 4679-4699 (1994).<br />
Simulation methods for loop<strong>in</strong>g transitions; Betty J. Gaffney and Harris J. Silverstone; J. Magn. Reson. 134, 57-66 (1998).<br />
Anharmonic oscillator discont<strong>in</strong>uity formulae up to second-exponentially-small order; Gabriel Álvarez, Christopher J. Howls, and<br />
Harris J. Silverstone; J. Phys. A 35, 4003-4016 (2002).<br />
Dispersive hyperasymptotics and the anharmonic oscillator; Gabriel Álvarez, Christopher J. Howls, and Harris J. Silverstone;<br />
J. Phys. A 35, 4017-4042 (2002).<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
19
Joel R. Tolman<br />
Biophysical <strong>Chemistry</strong><br />
jtolman@jhu.edu<br />
Ph.D., Yale <strong>University</strong><br />
Human Frontier<br />
Postdoctoral Fellow,<br />
<strong>University</strong> of Toronto<br />
Postdoctoral, École<br />
Polytechnique Fédérale de<br />
Lausanne<br />
With<strong>in</strong> the past two decades, Nuclear Magnetic Resonance spectroscopy<br />
(NMR) has become a powerful technique for the study of<br />
macromolecular structure and dynamics <strong>in</strong> the solution state. Research<br />
<strong>in</strong> my lab will be concerned with both the development and application<br />
of novel NMR techniques for study<strong>in</strong>g the complex <strong>in</strong>teractions that<br />
underlie biological function. Of particular <strong>in</strong>terest are studies of molecular dynamics,<br />
the nature of <strong>in</strong>termolecular recognition and the quaternary organization of multidoma<strong>in</strong><br />
prote<strong>in</strong> systems.<br />
The full repertoire of multidimensional NMR methodology will be employed<br />
to study these problems, <strong>in</strong>clud<strong>in</strong>g sp<strong>in</strong> relaxation, scalar coupl<strong>in</strong>g, NOE, and<br />
hydrogen exchange experiments. However, the primary approach will be centered<br />
around recently developed techniques for the measurement of Residual Dipolar<br />
Coupl<strong>in</strong>gs (RDCs) <strong>in</strong> macromolecules. These RDCs, which are normally averaged to<br />
zero <strong>in</strong> solution, are made observable by <strong>in</strong>troduc<strong>in</strong>g a very weak degree of alignment<br />
of the biomolecule relative to the magnetic field. This alignment is typically achieved<br />
by dissolv<strong>in</strong>g the prote<strong>in</strong> or nucleic acid along with a suitable co-solute, such as<br />
bacteriophage particles. The result<strong>in</strong>g RDCs are relatively easily measured and<br />
represent an abundant source of highly precise <strong>in</strong>formation on the relative<br />
orientations of different <strong>in</strong>ternuclear ‘bonds’ with<strong>in</strong> the molecule. Intrigu<strong>in</strong>gly, RDCs<br />
also exhibit sensitivity to molecular motions on the nsec-sec timescales, dur<strong>in</strong>g which<br />
many functionally important motions occur. These motional timescales have<br />
traditionally been very difficult to access experimentally, and thus a major objective<br />
will be to develop RDC-based techniques to enable the study of these motions.<br />
One of the applications of these techniques will be to <strong>in</strong>vestigate the<br />
quaternary organization of tetrameric ubiquit<strong>in</strong>. Tetramers of the prote<strong>in</strong> ubiquit<strong>in</strong><br />
can assume a multi-faceted role <strong>in</strong> cellular signal-transduction mechanisms, which<br />
depends on how they are l<strong>in</strong>ked together. A major goal will be to ga<strong>in</strong> <strong>in</strong>sights <strong>in</strong>to<br />
the nature of this important and versatile signal through studies of its solution state<br />
conformations. In addition, efforts are ongo<strong>in</strong>g to develop methodology for the<br />
simultaneous determ<strong>in</strong>ation of both the 3-dimensional structure and a detailed<br />
description of the dynamics of a prote<strong>in</strong>. A closely related objective is to develop the<br />
capability of us<strong>in</strong>g NMR to rapidly determ<strong>in</strong>e the backbone fold of a prote<strong>in</strong> to<br />
moderate resolution, which would represent an important contribution to current<br />
structural genomics <strong>in</strong>itiatives.<br />
Selected publications <strong>in</strong>clude:<br />
Tolman, J.R., “Dipolar Coupl<strong>in</strong>gs as a Probe of Molecular Dynamics and Structure <strong>in</strong> Solution,”<br />
Curr. Op<strong>in</strong>. Struct. Biol. 2001, 11, 532-539.<br />
Al-Hashimi, H.M.; Tolman, J.R.; Majumdar, A.; Gor<strong>in</strong>, A.; and Patel, D.J., “Determ<strong>in</strong><strong>in</strong>g<br />
Stoichiometry <strong>in</strong> Homomultimeric Nucleic Acid Complexes Us<strong>in</strong>g Magnetic Field Induced Residual<br />
Dipolar Coupl<strong>in</strong>gs,” J. Am. Chem. Soc. 2001, 123, 5806-5807.<br />
Tolman, J.R.; Al-Hashimi, H.M.; Kay, L.E.; and Prestegard, J.H., “Structural and Dynamic Analysis<br />
of Residual Dipolar Coupl<strong>in</strong>g Data for Prote<strong>in</strong>s,” J. Am. Chem. Soc. 2001, 123, 1416-1424.<br />
Tolman, J.R.; Flanagan, J.M.; Kennedy, M.A.; and Prestegard, J.H., “NMR Evidence for Slow<br />
Collective Motions <strong>in</strong> Cyanometmyoglob<strong>in</strong>,” Nature Struct. Biol. 1997, 4, 292-297.<br />
20 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Organic <strong>Chemistry</strong>; Photochemistry and Photobiology;<br />
Characterization of Reactive Intermediates<br />
jtoscano@jhu.edu<br />
John P. Toscano<br />
Most photochemical reactions take place through very short-lived<br />
<strong>in</strong>termediates such as s<strong>in</strong>glet or triplet excited states, radicals, carbenes,<br />
nitrenes, and nitrenium ions. A thorough understand<strong>in</strong>g of these<br />
<strong>in</strong>termediates is not only of basic scientific concern, but also has direct<br />
relevance to many critical issues <strong>in</strong> photochemistry and photobiology. The<br />
Toscano group’s ma<strong>in</strong> research <strong>in</strong>terests <strong>in</strong>volve the application of time-resolved<br />
spectroscopic techniques to the study of these <strong>in</strong>termediates with particular emphasis<br />
on the use of newly developed methods <strong>in</strong> time-resolved <strong>in</strong>frared spectroscopy.<br />
Nitric oxide (NO), a diatomic radical known previously as a noxious<br />
environmental pollutant, is now known to be <strong>in</strong>volved <strong>in</strong> a wide range of important<br />
bioregulatory processes <strong>in</strong>clud<strong>in</strong>g neurotransmission, blood clott<strong>in</strong>g, and blood<br />
pressure control. In addition, macrophages have been shown to kill cancerous tumor<br />
cells and <strong>in</strong>tracellular parasites by releas<strong>in</strong>g large amounts of NO. Deficiencies <strong>in</strong><br />
these processes caused by a poor endogenous supply of NO are often treatable with<br />
NO-releas<strong>in</strong>g drugs. Diazeniumdiolates (1) are an <strong>in</strong>terest<strong>in</strong>g class of such drugs<br />
presently under development. Recent efforts to make diazeniumdiolates more<br />
effective pharmaceuticals have concentrated on us<strong>in</strong>g derivatives of such compounds<br />
to deliver NO specifically to a targeted site. Given the large number of biological<br />
phenomena now known to be mediated by NO, such target<strong>in</strong>g will be critical to the<br />
success of most medical applications.<br />
We have begun to develop photochemical precursors to diazeniumdiolates<br />
that can be used as effective and potentially selective NO-releas<strong>in</strong>g agents. S<strong>in</strong>ce<br />
<strong>in</strong>itial experiments <strong>in</strong> other laboratories with classical photoprotect<strong>in</strong>g groups (P)<br />
gave unexpected and disappo<strong>in</strong>t<strong>in</strong>g results, we are presently clarify<strong>in</strong>g reaction<br />
pathways so that more efficient phototriggered NO-releas<strong>in</strong>g drugs can be rationally<br />
designed. In addition, if diazeniumdiolates are to enjoy rout<strong>in</strong>e medical use, their<br />
basic photochemistry must be understood so that phototoxicity issues may be<br />
anticipated and avoided.<br />
Recent Publications Include:<br />
Toscano, J. P. “Structure and Reactivity of Organic Intermediates as Revealed by Time-Resolved IR Spectroscopy” Adv. Photochem.<br />
2001, 26, 41-91.<br />
Sr<strong>in</strong>ivasan, A.; Kebede, N.; Saavedra, J. E.; Nikolaitchik, A. V.; Brady, D. A.; Yourd, E.; Davies, K. M.; Keefer, L. K.; Toscano, J. P.<br />
“<strong>Chemistry</strong> of the Diazeniumdiolates. 3. Photoreactivity” J. Am. Chem. Soc. 2001, 123, 5465-5472.<br />
Srivastava, S.; Ruane, P. H.; Toscano, J. P.; Sullivan, M. B.; Cramer, C. J.; Chiapper<strong>in</strong>o, D.; Reed, E. C.; Falvey, D. E. “Structures of<br />
Reactive Nitrenium Ions: Time-Resolved Infrared Laser Flash Photolysis and Computational Studies of Substituted N-Methyl-N-aryl-<br />
Nitrenium Ions” J. Am. Chem. Soc. 2000, 122, 8271-8278.<br />
Wang, Y.; Toscano, J. P. “Time-resolved IR Studies of 4-Diazo-3-Isochromanone: Direct K<strong>in</strong>etic Evidence for a Non-Carbene Route to<br />
Ketene” J. Am. Chem. Soc. 2000, 122, 4512-4513.<br />
Ph.D., Yale <strong>University</strong><br />
NIH Postdoctoral Fellow,<br />
Ohio State <strong>University</strong><br />
Camille and Henry Dreyfus<br />
New Faculty Award<br />
NSF CAREER Award<br />
Camille Dreyfus Teacher-<br />
Scholar Award<br />
Alfred P. Sloan Research<br />
Fellowship<br />
“Controlled Photochemical Release of Nitric Oxide from O 2 -Benzyl Substituted Diazeniumdiolates” Ruane, P.H.; Bushan, K.M.;<br />
Pavlos, C.M.; D’Sa, R.A.; Toscano, J. P. J. Am. Chem. Soc. 2002, <strong>in</strong> press.<br />
“Solvent Dependence of the 2-Napthyl (carbomethoxy)carbene S<strong>in</strong>glet-Triplet Energy Gap” Wang, Y.; Hadad, C.M.; Toscano, J. P.<br />
J. Am. Chem. Soc. 2002, 124, 1761-1767.<br />
O<br />
R2N N<br />
+ h<br />
N<br />
O<br />
P<br />
O<br />
R2N N<br />
+<br />
N<br />
O<br />
+<br />
P<br />
H 2 O<br />
pH 7.4<br />
R 2 NH + 2 NO + OH P<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
21
Craig A. Townsend<br />
Bioorganic <strong>Chemistry</strong><br />
townsend@jhunix.hcf.jhu.edu<br />
Research programs <strong>in</strong> Dr. Townsend’s group are broadly <strong>in</strong> the area of<br />
bioorganic chemistry with specific <strong>in</strong>terests <strong>in</strong> natural product biosynthesis,<br />
the enzymology and molecular biology of secondary metabolism and<br />
molecular medic<strong>in</strong>e. Underly<strong>in</strong>g these studies are <strong>in</strong>terests <strong>in</strong> reaction<br />
mechanism and synthesis, notably biomimetic synthesis, mechanistic<br />
enzymology, prote<strong>in</strong> structure and prote<strong>in</strong> eng<strong>in</strong>eer<strong>in</strong>g, exploration of the genetic<br />
organization and over-expression of biosynthetic enzymes, and the study of and the<br />
design and synthesis of fatty acid synthase <strong>in</strong>hibitors lead<strong>in</strong>g to practical treatments<br />
<strong>in</strong> cancer, tuberculosis and obesity.<br />
Recent publications <strong>in</strong>clude:<br />
Khaleeli, N.; Li, R.-F.; Townsend, C. A. “Orig<strong>in</strong> of the -Lactam Carbons <strong>in</strong> Clavulanic Acid from an Unusual Thiam<strong>in</strong>e Pyrophosphate-<br />
Mediated Reaction,” J. Amer. Chem. Soc. 1999, 121, 9223-9224. [See ‘Perspectives’ article: Science 2000, 287, 818-819.]<br />
Challis, G. L.; Ravel, J.; Townsend, C. A. “Predictive, Structure-Based Model of Am<strong>in</strong>o Acid Recognition by Non-Ribosomal Peptide<br />
Synthetase Adenylation Doma<strong>in</strong>s,” <strong>Chemistry</strong> & Biology 2000, 7, 211-224.<br />
Ph.D., Yale <strong>University</strong><br />
Postdoctoral,<br />
Eidgenössiche<br />
Teschnische Hochschule<br />
Alfred P. Sloan Research<br />
Fellowship<br />
Camille Dreyfus - Teacher<br />
Scholar Award<br />
Loftus, T. M.; Jaworsky D.; Frehywot, G. L.; Townsend, C. A.; Ronnett, G.; Lane, M. D.; Kuhajda, F. J. “Inhibitors of Fatty Acid<br />
Synthase Induce Weight Loss: A L<strong>in</strong>k Between Fatty Acid Synthesis and Feed<strong>in</strong>g Behavior,” Science 2000, 288, 2379-2381.<br />
Jones, P. B.; Parrish, N. M.; Houston, T. A.; Stapon, A. S.; Bansal, N. P.; Dick, J. D.; Townsend, C. A. “A New Class of Anti-<br />
Tuberculosis Agents,” J. Med. Chem. 2000, 43, 3304-3314.<br />
Li. R.-F.; Stapon, A.; Blanchfield, J. T.; Townsend, C. A. “Three Unusual Reactions Mediate Carbapenem and Carbapenam<br />
Biosynthesis,” J. Amer. Chem. Soc. 2000, 122, 9296-9297.<br />
Miller, M. T.; Bachmann, B. O.; Townsend, C. A.; Rosenzweig, A. C. “Stucture of ß-Lactam Synthetase Reveals How to Synthesize<br />
Antibiotics Instead of Asparag<strong>in</strong>e,” Nature Struct. Biol. 2001, 8, 684-689.<br />
Udwary, D.W.; Casillas, L.K.; Townsend, C.A. “Synthesis of 11-Hydroxyl O-Methylsterigmatocyst<strong>in</strong> and the Role of a Cytochrome P-<br />
450 <strong>in</strong> the F<strong>in</strong>al Step of Aflatox<strong>in</strong> Biosynthesis,” J. Amer. Chem. Soc. 2002, 124, 5294-5303.<br />
Maryland Chemist of the<br />
Year (1992)<br />
ACS Arthur C. Cope<br />
Scholar Award<br />
22<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
David R. Yarkony<br />
Theoretical <strong>Chemistry</strong><br />
yarkony@jhu.edu<br />
Accord<strong>in</strong>g to the Born-Oppenheimer approximation nuclei move on a s<strong>in</strong>gle<br />
potential energy surface created by the faster mov<strong>in</strong>g electrons. This<br />
approximation is at the heart of our description of most chemical processes.<br />
From prote<strong>in</strong> fold<strong>in</strong>g to tribology to catalysis the Born Oppenheimer<br />
approximation rules. So why study nonadiabatic processes, processes <strong>in</strong><br />
which the Born-Oppenheimer approximation breaks down. The answer is simple <strong>in</strong><br />
the absence of nonadiabatic processes life on earth, as we know it would not exist.<br />
Light harvest<strong>in</strong>g, vision and essential upper atmospheric processes depend on<br />
electronically nonadiabatic steps. Of course this has been known for decades. What<br />
is unusual and excit<strong>in</strong>g is that <strong>in</strong> the last 10 years our way of th<strong>in</strong>k<strong>in</strong>g about<br />
electronically nonadiabatic processes has begun to change, and change dramatically.<br />
The chang<strong>in</strong>g face of nonadiabatic chemistry is the consequence of a reth<strong>in</strong>k<strong>in</strong>g of the<br />
role of surface <strong>in</strong>tersections (conical <strong>in</strong>tersections) of states of the same symmetry<br />
these processes. Once little more than a theoretical curiosity today conical<br />
<strong>in</strong>tersections of two states of the same symmetry are now understood to be an<br />
essential part of nonadiabatic processes. This change <strong>in</strong> paradigm can dramatically<br />
change the predicted/expected rate of a nonadiabatic process. My research group has<br />
helped lead this revolution. Over the last decade we have developed the tools for<br />
study<strong>in</strong>g conical <strong>in</strong>tersections that def<strong>in</strong>e the state of the art <strong>in</strong> this area and as a result<br />
have lead the way <strong>in</strong> advanc<strong>in</strong>g the computational description of this s<strong>in</strong>gular<br />
consequence of the separation of nuclear and electronic time scales. More recently we<br />
have attacked the problem of nonadiabatic processes <strong>in</strong>volv<strong>in</strong>g heavy atoms <strong>in</strong> which<br />
the sp<strong>in</strong>-orbit <strong>in</strong>teraction and Kramers’ degeneracy play an essential role. Our work<br />
<strong>in</strong> this area has provided the first ever location of a conical <strong>in</strong>tersection <strong>in</strong> a<br />
polyatomic molecule based on ab <strong>in</strong>itio wave functions with the sp<strong>in</strong>-orbit <strong>in</strong>teraction<br />
<strong>in</strong>cluded <strong>in</strong> the Hamiltonian.<br />
We are currently build<strong>in</strong>g on our expertise <strong>in</strong> the description of the<br />
electronic structure aspects of nonadiabatic processes by develop<strong>in</strong>g fully quantum<br />
mechanical wave packet methods to quantify the role of conical <strong>in</strong>tersections <strong>in</strong><br />
nonadiabatic dynamics.<br />
In summary, nonadiabatic chemistry is an important field with a bright new<br />
future and we expect to cont<strong>in</strong>ue to play a lead<strong>in</strong>g role <strong>in</strong> this area.<br />
Recent publications<br />
Nuclear Dynamics near conical <strong>in</strong>tersections <strong>in</strong> the adiabatic representation: I. The effects of local topography on <strong>in</strong>terstate transition: David<br />
R. Yarkony, J.Chem. Phys., 114, 2601-2613 (2001).<br />
Ph.D., <strong>University</strong> of<br />
California, Berkeley<br />
Postdoctoral,<br />
Massachusetts Institute of<br />
Technology<br />
Fellow, American Physical<br />
Society<br />
Alfred P. Sloan Research<br />
Fellowship<br />
Conical <strong>in</strong>tersections: The New Conventional Wisdom – Feature Article, D. R. Yarkony, J. Phys. Chem. A 105, 6277-6293 (2001).<br />
On the Effects of Sp<strong>in</strong>-Orbit Coupl<strong>in</strong>g on Conical Intersection Seams <strong>in</strong> Molecules with an Odd<br />
Number of Electrons. I: Locat<strong>in</strong>g the Seam; Spiridoula Matsika and David R. Yarkony, J. Chem.<br />
Phys. 115, 2038-2050 (2001).<br />
On the Effects of Sp<strong>in</strong>-Orbit Coupl<strong>in</strong>g on Conical Intersection Seams <strong>in</strong> Molecules with an Odd<br />
Number of Electrons. II: Characteriz<strong>in</strong>g the local topography of the seam; Spiridoula Matsika and<br />
David R. Yarkony, J. Chem. Phys. 115,5066-5075, (2001).<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
23
Instrumentation<br />
The department is well equipped with <strong>in</strong>strumentation to perform<br />
modern chemical research. Rout<strong>in</strong>e <strong>in</strong>strumentation is housed <strong>in</strong><br />
the Instruments Facility <strong>in</strong> Remsen Hall and is ma<strong>in</strong>ta<strong>in</strong>ed by staff<br />
with<strong>in</strong> the department. In addition, there is a large variety of<br />
custom-built equipment <strong>in</strong> <strong>in</strong>dividual research laboratories.<br />
Our nuclear magnetic resonance facilities <strong>in</strong>cludes a 500 MHz<br />
Varian Unity <strong>in</strong>strument with full three-channel, gradients capability, a<br />
Varian 400 MHz spectrometer upgraded to a Unity console, and a 300<br />
MHz Bruker AMX. The lower-field NMRs are used for more rout<strong>in</strong>e synthetic<br />
chemistry applications, while the high-field NMR is primarily dedicated<br />
to multi-dimensional analysis of prote<strong>in</strong>s and nucleic acids. In<br />
addition, the undergraduate <strong>in</strong>structional laboratories house a Varian<br />
Mercury 200 MHz spectrometer that is also available for research use.<br />
In a jo<strong>in</strong>t <strong>in</strong>itiative by the Departments of Biology, Biophysics, and<br />
<strong>Chemistry</strong>, the Krieger School of Arts and Sciences has commissioned the<br />
development of a Nuclear Magnetic Resonance Center for the study of the<br />
structure and dynamics of biological macromolecules. This facility will be<br />
constructed <strong>in</strong> connection with the new chemistry build<strong>in</strong>g, at a site<br />
bridg<strong>in</strong>g the chemistry and biology departments. The first <strong>in</strong>strument to<br />
be housed <strong>in</strong> this facility, a 600 MHz spectrometer, has recently been<br />
ordered.<br />
In addition to the NMR <strong>in</strong>itiative, the department has recently<br />
received fund<strong>in</strong>g to establish a state of the art small molecule x-ray<br />
diffraction facility. This staffed facility, used for detailed molecular level<br />
structural characterization of new organic or <strong>in</strong>organic compounds, will<br />
be available fo graduate student use.<br />
24 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Instrumentation<br />
The department has significantly upgraded its mass spectrometric<br />
<strong>in</strong>strumentation with the acquisition of the follow<strong>in</strong>g<br />
systems: (1) A Kratos laser desorption time-of-flight (MALDI-TOF) mass<br />
spectrometer with l<strong>in</strong>ear and reflectron modes, (2) A Shimadzu gas<br />
chromatograph mass spectrometer with both electron-impact and electron<br />
ionization, and (3) A Thermoquest/F<strong>in</strong>negan electrospray ionization mass<br />
spectrometer (ESI-MS), fitted with a liquid chromatograph and with the<br />
capability for multiple mass spectral analyses. These <strong>in</strong>struments<br />
compliment our VG 70S high-resolution GC-mass spectrometer, which is<br />
capable of FAB, DCI, EI, and CI spectrometry. The department also<br />
ma<strong>in</strong>ta<strong>in</strong>s a Bruker EMX 10 /2.7 EPR spectrometer (X band and low<br />
temperature)<br />
In addition to computers and workstations dispersed throughout<br />
all the <strong>in</strong>dividual research groups, a dedicated computer lab is housed <strong>in</strong><br />
Remsen Hall, with access available to all students, staff, and faculty.<br />
Many of the faculty research laboratories have purchased or<br />
constructed highly specialized <strong>in</strong>strumentation tailored to their specific<br />
research objectives. These <strong>in</strong>clude the follow<strong>in</strong>g: several molecular beam<br />
apparatus, negative ion photoelectron spectrometers, ultra-high vacuum<br />
surface analysis chambers with Auger electron and X-ray photoelectron<br />
spectrometers, an atomic-force microscope, a time-resolved <strong>in</strong>frared<br />
spectrometer, numerous laser systems (Nd:YAG, excimer, dye, optical<br />
parametric oscillator, argon ion), a phase fluorimeter, a fluorescence<br />
microscope, and nanophase material generators.<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
25
Useful Information<br />
Student Activities<br />
As <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>’s ma<strong>in</strong> campus, the<br />
Homewood Campus provides students with an<br />
environment that successfully balances academics and<br />
extracurricular activities. A strong Student Activities Office<br />
oversees and advises over 160 student groups represent<strong>in</strong>g<br />
students <strong>in</strong>volved <strong>in</strong> cultural, religious, recreation, sports,<br />
government, and special <strong>in</strong>terests. Homewood is home to the JHU<br />
<strong>Graduate</strong> Representative Organization (GRO). This graduate<br />
student group won the 2001 National Association of <strong>Graduate</strong>-<br />
Professional Students (NAGPS) award for Outstand<strong>in</strong>g National<br />
<strong>Graduate</strong> Student Organization.<br />
In addition to the various student organizations, the<br />
campus hosts other notable events, such as symposia featur<strong>in</strong>g<br />
well-known speakers, various cultural and sport<strong>in</strong>g activities, and<br />
the annual <strong>Johns</strong> Hopk<strong>in</strong>s Spr<strong>in</strong>g Fair. This popular attraction is the<br />
largest student run fair <strong>in</strong> the country with 150,000 visitors over the<br />
course of three days.<br />
Two new enhancements to campus life are the new Matt<strong>in</strong> Center for Student<br />
Arts and Activities, and a state-of-the-art Athletic Recreation Center. The Matt<strong>in</strong><br />
Center offers a substantial home for student groups and organizations, while<br />
provid<strong>in</strong>g a direct connection to the area’s cultural arts, such as the Baltimore<br />
Museum of Art, which is located adjacent to the center. The new Athletic Recreation<br />
Center is a 63,000 square foot facility hous<strong>in</strong>g a fully equipped gymnasium for<br />
students, faculty and staff.<br />
After Graduation<br />
Many of our students do postdoctoral work, and have won prestigious postdoctoral<br />
fellowships from the Sloan Foundation, American Cancer Society, NIH, and the<br />
National Research Council. In the last few years they have gone on to Universities<br />
such as Yale, Stanford, MIT, Berkeley, Caltech, the <strong>University</strong> of Chicago, and<br />
Harvard, national laboratories such as the NIH, NIST, the Air Force Hanscom<br />
Laboratory, and Brookhaven, or research laboratories at companies such as DuPont,<br />
Merck, and SmithKl<strong>in</strong>e Beecham. Some go abroad for further study; former students<br />
are currently <strong>in</strong> England, Japan, and Switzerland.<br />
Alumni of the department are scattered across the country and around the<br />
world <strong>in</strong> academic, government, and <strong>in</strong>dustrial positions. In the last few years, our<br />
graduates have taken faculty positions at the <strong>University</strong> of Ill<strong>in</strong>ois, <strong>University</strong> of<br />
California at Riverside, Ohio State <strong>University</strong>, Harvard <strong>University</strong>, Bryn Mawr<br />
College, Hood College, and many other colleges and universities. Recent graduates<br />
are now work<strong>in</strong>g for a number of pharmaceutical and chemical companies (Upjohn,<br />
Pfizer, Hoechst-Roussel, Glaxo, Bristol-Meyers Squibb, Dow, Allied, 3M, Enichem<br />
Americas, Hoechst-Celanese, to name a few). As a regular part of our colloquium<br />
schedule, we <strong>in</strong>vite former students back to describe their work and meet with<br />
graduate students.<br />
Hous<strong>in</strong>g<br />
Near the university there is a wide selection of liv<strong>in</strong>g quarters. Many graduate<br />
students, s<strong>in</strong>gle and married, take advantage of the affordable apartment build<strong>in</strong>gs<br />
adjacent to the Homewood campus. Most of the apartments <strong>in</strong> the immediate<br />
vic<strong>in</strong>ity are with<strong>in</strong> easy walk<strong>in</strong>g distance (< 0.5 miles) of the chemistry build<strong>in</strong>gs.<br />
Additional s<strong>in</strong>gle rooms and apartments are generally available <strong>in</strong> areas readily<br />
accessible by car or bus. The <strong>University</strong> ma<strong>in</strong>ta<strong>in</strong>s a hous<strong>in</strong>g office to help students<br />
f<strong>in</strong>d suitable accommodations (Hous<strong>in</strong>g Office, 3339 North Charles Street, Baltimore,<br />
MD 21218, 410-516-7960). The <strong>Chemistry</strong> department also has an <strong>in</strong>formal system <strong>in</strong><br />
place to aide students <strong>in</strong> f<strong>in</strong>d<strong>in</strong>g suitable hous<strong>in</strong>g.<br />
26 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>
Useful Information<br />
The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
FACULTY<br />
E-MAIL<br />
Zanvyl Krieger School of Arts & Sciences 410-516-8212<br />
<strong>Graduate</strong> Admissions Office - 410-516-8174<br />
Office of F<strong>in</strong>ancial Aid - 410-516-8724<br />
Kit H. Bowen<br />
Paul J. Dagdigian<br />
David E. Draper<br />
kitbowen@jhu.edu<br />
pjdagdigian@jhu.edu<br />
draper@jhu.edu<br />
Office of the Registrar - <strong>Graduate</strong> Information -<br />
410-516-8081<br />
D. Howard Fairbrother howardf@jhu.edu<br />
David P. Goldberg<br />
dpg@jhu.edu<br />
Department of <strong>Chemistry</strong><br />
Telephone - 410-516-7429<br />
Fax - 410-516-8420<br />
E-Mail - chem.grad.adm@jhu.edu<br />
Web Site - http://www.jhu.edu/~chem<br />
Research Professor<br />
JOHN P. DOERING<br />
Experimental Chemical Physics<br />
Emeritus Faculty<br />
DWAINE O. COWAN<br />
Organic and Physical <strong>Chemistry</strong><br />
ALSOPH H. CORWIN<br />
Biological Organic <strong>Chemistry</strong><br />
Marc Greenberg<br />
Tamara L Hendrickson<br />
Kenneth D. Karl<strong>in</strong><br />
Thomas Lectka<br />
Gerald J. Meyer<br />
Douglas Poland<br />
Gary H. Posner<br />
Harris J. Silverstone<br />
Joel R. Tolman<br />
John P. Toscano<br />
Craig A. Townsend<br />
David R. Yarkony<br />
mgreenberg@jhu.edu<br />
hendrick@jhu.edu<br />
karl<strong>in</strong>@jhu.edu<br />
lectka@jhu.edu<br />
meyer@jhu.edu<br />
poland@jhu.edu<br />
ghp@jhu.edu<br />
hjsilverstone@jhu.edu<br />
jtolman@jhu.edu<br />
jtoscano@jhu.edu<br />
townsend@jhu.edu<br />
yarkony@jhu.edu<br />
JOHN W. GRYDER<br />
Inorganic and Physical <strong>Chemistry</strong><br />
WALTER S. KOSKI<br />
Physical <strong>Chemistry</strong><br />
BROWN L. MURR<br />
Organic <strong>Chemistry</strong><br />
ALEX NICKON<br />
Physical-Organic and Stereochemistry<br />
DEAN W. ROBINSON<br />
Physical <strong>Chemistry</strong><br />
Jo<strong>in</strong>t Appo<strong>in</strong>tments<br />
JEREMY BERG<br />
Biophysics, School of Medic<strong>in</strong>e<br />
BLAKE HILL<br />
Biology, Kreiger School of Arts and Sciences<br />
ALBERT MILDVAN<br />
Biological <strong>Chemistry</strong>, School of Medic<strong>in</strong>e<br />
LAWRENCE PRINCIPE<br />
History of Science Medic<strong>in</strong>e and Technology/<strong>Chemistry</strong>,<br />
Kreiger School of Arts and Sciences<br />
MICHAEL YU<br />
Material Science and Eng<strong>in</strong>eer<strong>in</strong>g,<br />
Whit<strong>in</strong>g School of Eng<strong>in</strong>eer<strong>in</strong>g<br />
<strong>Graduate</strong> <strong>Study</strong> <strong>in</strong><br />
<strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong><br />
27
Baltimore Map & Directions to Campus<br />
Directions to Homewood Campus<br />
3400 North Charles Street<br />
Baltimore, Maryland 21218<br />
From I-95 (southbound) or from I-695 (the Baltimore Beltway):<br />
Take the beltway toward Towson to exit 25. Take Charles<br />
Street south for about 7 miles (when Charles Street splits<br />
a block after Loyola College and Cold Spr<strong>in</strong>g Lane, take<br />
the right fork). As you approach the university and cross<br />
<strong>University</strong> Parkway, cont<strong>in</strong>ue southbound but be sure to<br />
jog right onto the service road. After you pass the university<br />
on the right, turn right onto Art Museum Drive. Just<br />
after the Baltimore Museum of Art, bear right at the traffic<br />
island onto Wyman Park Drive. Take an almost immediate<br />
right through the university gates. A visitors' lot<br />
and park<strong>in</strong>g meters will be on the left.<br />
From I-95 (northbound):<br />
Take exit 53 onto I-395 north toward downtown<br />
Baltimore, then take the exit to Mart<strong>in</strong> Luther K<strong>in</strong>g Jr.<br />
Boulevard and follow the directions from Mart<strong>in</strong> Luther<br />
K<strong>in</strong>g Junior Boulevard below.<br />
From Maryland 295 (the Baltimore-Wash<strong>in</strong>gton Parkway):<br />
Enter<strong>in</strong>g Baltimore, the parkway becomes Russell Street.<br />
Stay on Russell Street until (with the new Baltimore<br />
Ravens stadium to your right and Oriole Park at Camden<br />
Yards loom<strong>in</strong>g before you) you reach the right-hand exit<br />
marked Mart<strong>in</strong> Luther K<strong>in</strong>g Jr. Boulevard (look carefully<br />
for this; the signs are small). This exit will put you very<br />
briefly on a service road parallel to Russell Street. Stay to<br />
the left and take the ramp marked Mart<strong>in</strong> Luther K<strong>in</strong>g Jr.<br />
Boulevard. Follow the directions (below) from Mart<strong>in</strong><br />
Luther K<strong>in</strong>g Jr. Boulevard.<br />
From Mart<strong>in</strong> Luther K<strong>in</strong>g Jr. Boulevard:<br />
Take K<strong>in</strong>g Boulevard north until it ends at Howard Street<br />
(rema<strong>in</strong> <strong>in</strong> one of the middle lanes of K<strong>in</strong>g Boulevard to<br />
avoid a premature forced right or left turn). Turn left at<br />
Howard Street and proceed about 2 miles. One block<br />
past 29th Street, turn left at the traffic island (just before<br />
the Baltimore Museum of Art) onto Wyman Park Drive.<br />
Take an almost immediate right through the university<br />
gates. A visitors' lot and park<strong>in</strong>g meters will be on the<br />
left.<br />
From the Jones Falls Expressway (I-83) southbound:<br />
Take the 28th Street exit and go left on 28th Street. Turn<br />
left on North Howard Street. One block past 29th Street,<br />
turn left at the traffic island (just before the Baltimore<br />
Museum of Art) onto Wyman Park Drive. Take an almost<br />
immediate right through the university gates. A visitors'<br />
lot and park<strong>in</strong>g meters will be on the left.<br />
From Baltimore's Penn Station:<br />
From Penn Station, you can catch the Hopk<strong>in</strong>s shuttle<br />
bus which will take you to the Homewood, Peabody, or<br />
medical campuses. There is no charge to take the shuttle.<br />
If you opt to take a taxi, the fee should be quite modest.<br />
The university is very close to the tra<strong>in</strong> station.<br />
28 <strong>Graduate</strong> <strong>Study</strong> <strong>in</strong> <strong>Chemistry</strong> at The <strong>Johns</strong> Hopk<strong>in</strong>s <strong>University</strong>