Professor of Chemistry Emeritus
University of Alaska Fairbanks
John and Sue at John's retirement party (May 2012).
Computational chemistry and biochemistry. Properties and spectroscopy
of hydrogen bonded complexes. Computational approaches to cyclodextrins.
Applications of computational chemistry in undergraduate instruction.
Computational Chemistry. My
research students and I have undertaken several computational
studies based on student projects in undergraduate classes.
These take advantage of the excellent computational chemistry facilities in the
Department of Chemistry and Biochemistry, which maintains several servers
running a WebMO website, and
at UAF's Arctic Region Supercomputing Center,
whose Pacman cluster runs Gaussian and other programs. One ongoing project concerns the
properties of a carboxylic acid "dimer", a complex of formic acid and
trifluoroacetic acid whose gas-phase vibrational spectrum was obtained in
our lab. These so-called bidentate complexes contain a cyclic array of hydrogen
bonds and donor-accepter interactions like those found in DNA base pairs. One
question that still needs
to be answered is, Do the hydrogens in this complex exchange between the acids
faster or slower compared to symmetric carboxylic acid complexes? And how is hydrogen
transfer in this complex affected by rotation of the CF3
group? Does it speed up hydrogen transfer or slow it down?
Non-covalent interactions like these play a significant role in determining the
chemical and biochemical properties of small molecules in the atmosphere.
Accurate prediction of
the energy content, vibrational and rotational spectra, and geometry of small
molecule-target complexes are now possible using
high-level computational chemistry methods. Currently I am applying these methods to complexes of sulfur dioxide, a biologically active molecule produced
in large amounts by fossil fuel combustion and volcanic emissions.
Click here for a list of: relevant
I have done a fair amount of enzymological and structural research on the
bacterial vitamin B6-dependent enzyme dialkylglycine decarboxylase (E.C.
184.108.40.206). I started
this project in 1976 as a post-doctoral student in Marion
O'Leary's lab at the University of Wisconsin-Madison, and continued it at the
University of Alaska Fairbanks. Initially I used protein extracts from
Burkholderia cepacia that had been produced at the Fermentation Lab of the
Department of Biochemistry in Madison. Later, in Fairbanks, we cloned and
manually sequenced a 4.1-kb region of the B. cepacia
genome, which allowed us to produce and purify the recombinant enzyme from small
E. coli cultures. The insert contained the structural gene for dialkylglycine decarboxylase
and a gene encoding a LysR-type cis-acting transcriptional
regulatory protein (dgdR). This work resulted in publications in Biochemistry, Journal of Molecular Biology,
Journal of Biological Chemistry, Biochemical and Biophysical Research
Communications, Tetrahedron Letters, Journal of Chromatography,
and others. Hans Jansonius and Michael Toney of the Biozentrum of the University
of Basel played crucial roles solving the x-ray crystal structure
of the enzyme. Michael is now at the University of California-Davis Department
of Chemistry. In my lab about 50 graduate, undergraduate, and high school
students have contributed to various aspects of this research. Two U.S.
patents, 5,210,025 and 5,356,796, were issued to cover expression and possible
use of the genes.
Since I retired, I am no
longer teaching. During the period 1979-2011, I taught General Chemistry (105X
and 106X), Organic Chemistry (321, 322, and 324), Molecular Modeling (623),
Enzymology and Bioorganic Chemistry (622), and
Protein Structure and Function (654).
Department of Chemistry and Biochemistry
University of Alaska
900 Yukon Drive
Fairbanks, AK 99775-6160