Middlebury

 

Jim Larrabee

Viola Ward Brinning & Elbert Calhoun Brinning Professor of Chemistry & Biochem

Email: 
Phone: work802.443.5453
Office Hours: Fall 2014: Tues/Thurs 9:30AM to 11:30AM; and by appointment
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Jim Larrabee obtained a B.S. degree from Trinity College and a Ph.D. degree from Princeton University. He worked for Exxon Research and Engineering Company as a Research Chemist before joining the Middlebury Faculty in 1986.

Research Interests

My area of research specialization is bioinorganic chemistry, which is the study of biological molecules that contain or react with metallic elements. My current research is in the application of magnetic circular dichroism (MCD) to the study of dimetallic hydrolase enzymes. Recently published studies include those  on three organo-phosphorous degrading enzymes (GpdQ, OpdA, and OPH), an N-terminal peptidase (methionine aminopeptidase), and model compound mimics of metallo-β-lactamases. Students in my research group use inorganic electronic spectroscopy (MCD, UV/VIS/NIR absorption and diffuse reflectance) and ligand field theory (angular overlap model) to help us understand the immediate coordination environment around the metal ions in these enzyme active sites. This information provides insight on the enzyme mechanism.

 

Courses


indicates offered in the current term
indicates offered in the upcoming term[s]

CHEM 0104 - General Chemistry II      

General Chemistry II
Major topics include chemical kinetics, chemical equilibrium, acid-base equilibria, chemical thermodynamics, electrochemistry, descriptive inorganic chemistry, and coordination chemistry. Lab work includes inorganic synthesis, qualitative analysis, and quantitative analysis in kinetics, acid-base and redox chemistry. (CHEM 0103 or by waiver) 3 hrs. lect., 3 hrs. lab, 1 hr. disc.

DED SCI

Spring 2011, Spring 2012, Spring 2014

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CHEM 0230 - Metals in Biology      

Metals in Biology
Life depends on the proper functioning of metalated proteins and nucleic acids. In this course we will study the structures and reactivities of metalloproteins and other metallobiomolecules. We will begin with an overview of biological inorganic chemistry that includes metal ions in proteins, metal cofactors, transport and storage of metals, and metals in medicine. We will then proceed to a variety of special topics (e.g., oxygen metabolism, nitrogen fixation, and electron transfer), depending on the specific interests of the students. The textbook will be Biological Inorganic Chemistry: Structure and Reactivity by Bertini, Gray, Stiefel, and Valentine. (CHEM 0104 or CHEM 0107).

SCI

Winter 2012, Spring 2013, Fall 2013

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CHEM 0311 - Instrumental Analysis      

Instrumental Analysis
This course introduces fundamental concepts of analytical chemistry, instrumental analysis, and scientific writing. Lecture topics include experimental design and quality control; sample collection and preparation; calibration, error, and data analysis; statistics; and the theory and operation of chemical instrumentation. Multi-week laboratory projects provide hands-on experience in qualitative and quantitative analysis using a variety of research-quality instrumentation (e.g., graphite furnace atomic absorption spectroscopy, UV/Vis spectrometry, gas chromatography mass spectrometry, circular dichroism spectroscopy, high pressure liquid chromatography). Writing workshops promote professional scientific writing skills through guided practice in writing analysis, peer review, and revision. (CHEM 0204 or CHEM 0242) 3 hr. lect., 6 hrs. lab.

CW

Fall 2011, Fall 2012, Fall 2014

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CHEM 0312 - Inorganic & Physical Chemistry      

Inorganic and Physical Chemistry Laboratory
In this course students will carry out experiments in the field of inorganic and physical chemistry and write journal-style reports based on their results. In the first half of the semester students will conduct a multi-step synthesis and characterization of a Mo-Mo complex with a quadruple bond. Students will learn inert atmosphere synthetic techniques and how to use a glove box. The synthesized Mo-Mo complex will be characterized by UV-Vis, IR, 1H and 31P NMR spectroscopies, and cyclic voltammetry. In the second half of the semester students will conduct two physical chemistry experiments. First students will carry out a kinetic study of the isomerization of the Mo-Mo (alpha to beta or beta to alpha) complex by UV-Vis spectroscopy. Finally, students will obtain the high-resolution IR spectra of acetylene and deuterated acetylene and analyze the rotation-vibration spectra using statistical and quantum mechanics to obtain structural data and interpret the peak intensities. In addition to the laboratory activities, there will be lectures on metal quadruple bonds, principles of UV-Vis , IR, 1H and 31P NMR spectroscopies, cyclic voltammetry, and statistical mechanics. (CHEM 0311, CHEM 0351, and CHEM 0355. CHEM 0355 can be taken concurrently.) 3 hrs. lect. 3 hrs. lab

Spring 2012, Spring 2013

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CHEM 0431 - Advanced Inorganic Chemistry      

Advanced Inorganic Chemistry
Atomic structure, bonding theories, and properties applicable to inorganic and organometallic compounds will be developed in depth. Specific topics will include valence bond theory, molecular orbital theory, ligand field theory, applications of group theory, and reaction mechanisms. (CHEM 0351) 3 hrs. lect.

Fall 2011, Fall 2012, Fall 2013, Fall 2014

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CHEM 0500 - Independent Study      

Independent Study Project
Individual study for qualified students. (Approval required)

Winter 2011, Spring 2011, Fall 2011, Winter 2012, Spring 2012, Fall 2012, Winter 2013, Spring 2013, Fall 2013, Winter 2014, Spring 2014, Fall 2014, Winter 2015, Spring 2015

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CHEM 0700 - Senior Research      

Senior Research
In this course students complete individual projects involving laboratory research on a topic chosen by the student and a faculty advisor. Prior to registering for CHEM 0700, a student must have discussed and agreed upon a project topic with a faculty member in the Chemistry and Biochemistry Department. Attendance at all Chemistry and Biochemistry Department seminars is expected. (Approval required; open only to seniors)

Winter 2011, Spring 2011, Fall 2011, Winter 2012, Spring 2012, Fall 2012, Winter 2013, Spring 2013, Fall 2013, Winter 2014, Spring 2014, Fall 2014, Winter 2015, Spring 2015

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CHEM 0701 - Senior Thesis      

Senior Thesis
Students who have initiated research projects in CHEM 0400 and who plan to complete a senior thesis should register for CHEM 0701. Students are required to write a thesis, give a public presentation, and defend their thesis before a committee of at least three faculty members. The final grade will be determined by the department. Attendance at all Chemistry and Biochemistry Department seminars is expected. (CHEM 0400; approval required)

Spring 2013, Fall 2013, Winter 2014, Spring 2014, Fall 2014, Winter 2015, Spring 2015

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FYSE 1328 - Elements of Murder      

The Elements of Murder
In this seminar we will study a combination of history, chemistry, factual crime, and fictional crime surrounding the darker side of some of the elements. Mercury, arsenic, antimony, lead, thallium have notorious reputations for causing accidental death and as instruments of murder. Readings will include The Elements of Murder, by John Emsley; Beethoven's Hair: An Extraordinary Historical Odyssey and a Scientific Mystery Solved by Russell Martin; The Pale Horse by Agatha Christie, and Strong Poison by Dorothy L. Sayers. We will spend some time in the lab investigating the properties of these elements. 3 hrs. sem/disc./lab

CW

Spring 2011

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INTD 1061 - Elements of Murder      

The Elements of Murder
In this course we will study a combination of history, chemistry, factual crime, and fictional crime surrounding the darker side of some of the elements. Mercury, arsenic, antimony, lead, thallium have notorious reputations for causing accidental death and as instruments of murder. Readings will include The Elements of Murder, by John Emsley; Beethoven's Hair: An Extraordinary Historical Odyssey and a Scientific Mystery Solved by Russell Martin; The Pale Horse by Agatha Christie, and Strong Poison by Dorothy L. Sayers. We will spend some time in the lab investigating the properties of these elements. (One year high school chemistry) 8 hrs. lect./disc./lab

WTR

Winter 2014

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Recent Publications

* Denotes Middlebury College undergraduate co-authors.

Pedroso, M. M.; Ely, F.; Mitic, N.; Carpenter, M. C.; Gahan, L. R.; Wilcox, D. E.; Larrabee, J. A.; Ollis, D. L.; Schenk, G. “Comparative investigation of the reaction mechanisms of the organophosphate-degrading phosphotriesterases from Agrobacterium radiobacter (OpdA) and Pseudomonas diminuta (OPH)” J. Biol. Inorgan. Chem. 2014, 19, 1263-1275, DOI: 10.1007/s00775-014-1183-9.

Daumann, L. J.; Larrabee, J. A.; Ollis, D.; Schenk, G.; Gahan, L. R. “Immobilization of the enzyme GpdQ on magnetite nanoparticles for organophosphate pesticide bioremediation” J. Inorg. Biochem. 2014, 131, 1-7, DOI: 10.1016/j.jinorgbio.2013.10.007.

Daumann, L. J.; Larrabee, J. A.; Comba, P.; Schenk, G.; Gahan, L. R. “Dinuclear cobalt(II) complexes as metallo-β-lactamase mimics” Eur. J. Inorg. Chem. 2013, 2013, 3082-3089, DOI: 10.1002/ejic.201300280.

Daumann, L. J.; Comba, P., Larrabee, J. A.; Schenk, G.; Stranger, R.; Cavigliasso, G.; Gahan, L. R. “Synthesis, magnetic properties, and phosphoesterase activity of dinuclear cobalt(II) complexes” Inorg. Chem. 2013, 52, 2029-2043, DOI: 10.1021/ic302418x.

Daumann, L. J.; McCarthy, B. Y.; Hadler, K. S.; Murray, T. P.; Tracy, P.; Gahan, L. R.; Larrabee, J. A.; Ollis, D. L.; Schenk, G. “Promiscuity comes at a price: Catalytic versatility vs efficiency in different metal ion derivatives of the potential bioremediator GpdQ” Biochim. Biophys. Acta 2013, 1834, 424-432, DOI: 10.1016/j.bbapap.2012.02.004.

Ely, F.; Hadler, K. S.; Mitić, N.; Lawrence R Gahan, L. R.; David L. Ollis, D. L.; *Plugis, N. M.; *Russo, M. T.; Larrabee, J. A.; Schenk, G. “Electronic and geometric structure of the organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA)” J. Biol. Inorg. Chem.2011, 16, 777-787, DOI: 10.1007/s00775-011-0779-6.

Hadler, K. S.; Mitić, N.; Gahan, L. R.; Ollis, D. L.; Schenk, G.; Larrabee, J. A. “Electronic structure analysis of the dinuclear metal center in the bioremediator glycerophosphodiesterase (GpdQ) from Enterobacter aerogenesInorg. Chem. 2010, 49, 2727-2734, DOI: 10.1021/ic901950c.

Larrabee, J. A.; *Johnson, W. R.; *Volwiler, A. S. “Magnetic circular dichroism study of a complex with mixed 5- and 6-coordination: A spectroscopic model for dicobalt(II) hydrolases” Inorg. Chem. 2009, 48, 8822-8829, DOI: 10.1021/ic901000d.

Hadler, K. S.; Mitić, N.; Ely, F.; Hanson, G. R.; Gahan, L. R.; Larrabee, J. A.; Ollis, D. L.; Schenk, G. “Structural flexibility enhances the reactivity of the bioremediator glycerophosphodiesterase by fine tuning its mechanism of hydrolysis” J. Am. Chem. Soc. 2009, 131, 11900-11908, DOI: 10.1021/ja903534f.

Larrabee, J. A.; *Chyun, S-A.; *Volwiler, A. S. “Magnetic circular dichroism study of a methionine aminopeptidase/fumagillin complex and dicobalt II-II and II-III model complexes” Inorg. Chem. 2008, 47, 10499-10508, DOI: 10.1021/ic8011553.

Hadler, K. S.; Tanifum, E.; Yip, S. H-C.; Mitić, N.; Guddat, L. W.; Jackson, C. J.; Gahan, L. R.; Carr, P.; Ollis, D. L.; Hengge, A. C.; Larrabee, J. A.; Schenk, G. “Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in glycerophosphodiesterase from Enterobacter aerogenesJ. Am. Chem. Soc. 2008, 130, 14129-14138, DOI: 10.1021/ja803346w.

Johansson, F. B.; Bond, A. D.; Nielsen, U. G.; Moubaraki, B.; Murray, K. S.; Berry, K. J.; Larrabee, J. A.; McKenzie, C. J. “Dicobalt II–II, II–III and III–III complexes as spectroscopic models for dicobalt enzyme active sites” Inorg. Chem. 2008, 47, 5079-5092, DOI: 10.1021/ic7020534.

Choi, S.; *Vastag, L.; *Leung, C-H.; *Beard, A. M.; *Knowles, D. E.; Larrabee, J. A. “Kinetics and mechanism of the oxidation of guanosine derivatives by Pt(IV) complexes” Inorg. Chem. 2006, 45, 10108-10114, DOI: 10.1021/ic061243g.

Larrabee, J. A.; *Leung, C-H.; *Moore, R. L.; *Thamrong-nawasawat, T.; *Wessler, B. S. H. “Magnetic circular dichroism and cobalt(II) binding equilibrium studies of Escherichia coli methionyl aminopeptidase” J. Am. Chem. Soc. 2004, 126, 12316-12324, DOI: 10.1021/ja0485006.

Larrabee, J. A.; *Thamrong-nawasawat, T.; *Mon, S. Y. “An HPLC method for the assay of methionine aminopeptidase activity: Application to the study of enzymatic inactivation” Anal. Biochem. 1999, 269, 194-198, DOI: 10.1006/abio.1998.3086.

Larrabee, J. A.; *Alessi, C. M.; *Asiedu, E. T.; *Cook, J. O.; *Hoerning, K. R.; *Klingler, L. J.; *Okin, G. S.; *Santee, S. G.; *Volkert, T. L. “Magnetic circular dichroism spectroscopy as a probe of geometric and electronic structure of cobalt(II)-substituted proteins: Ground state zero field splitting as a coordination number indicator” J. Am. Chem. Soc. 1997, 119, 4182-4196, DOI: 10.1021/ja963555w.

Recent Grants

NSF/RUI, CHE-1303852 “RUI: Magnetic circular dichroism of dicobalt(II) enzymes” 2013-2016, $201,000.

NSF/RUI, CHE-0848433 “RUI: Magnetic circular dichroism of dicobalt(II) enzymes and complexes” 2009-2013, $300,000.

NSF/MRI, CHE-0820965 “Acquisition of spectropolarimeter for circular dichroism and magnetic circular dichroism” 2008-2009, $76,748.