Biochemistry/Molecular Biology

Some of the most active areas of research at the University of Oregon are in the fields of Biochemistry and Molecular Biology. Research in these areas has been fostered by long-standing collaboration among chemists, biologists and physicists. The common theme in this research is developing an understanding of complex biological and biochemical problems at the molecular level.

The interdisciplinary nature of the research has resulted in labs collaborating on combining traditional biochemistry, modern genetic techniques, together with sophisticated physical chemical approaches (x-ray crystallography, atomic force microscopy, etc.) as well as synthetic organic chemistry, to solve important but complex problems in the life sciences. Faculty in these areas have very close associations with the Institute of Molecular Biology and the Institute of Neuroscience.

*Professor von Hippel continues to be research active and welcome postdoctoral applications, as well as applications from undergraduates interested in research.

*Professor Keana has retired from research and teaching activities but continues to serve as a medicinal chemistry/organic chemistry consultant for several small biopharmaceutical companies and several patent law firms.

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Bioorganic/Chemical Biology 

Bioorganic Chemistry and Chemical Biology, broadly defined, are fields in which organic synthetic chemistry plays a significant role in the life sciences. These disciplines include topics such as small molecule sensing and molecular recognition, nucleic acid chemistry and biochemistry, bio-inspired catalysis, structure-function studies of therapeutics, and bioconjugates. Students focused on this area at Oregon develop a solid foundation in synthetic chemistry and also benefit from the outstanding biochemistry/molecular biology research environment at UO.

Bioorganic Chemistry and Chemical Biology research at Oregon includes work on rational synthesis of anion receptors aimed at detecting ion fluxes in biological contexts (Haley, Johnson); new approaches for RNA structure/function analysis (DeRose); novel bifunctional Pt compounds for biological target analysis (DeRose, Haley); and development of new methods for detection and delivery of biological hydrogen sulfide (Pluth).

Biophysics

Biophysical chemistry at the University of Oregon enjoys a particularly outstanding national reputation. The strength of this program stems from the extensive collaborations between research groups involved in the development and application of physical methods and research groups with expertise in molecular and cellular biology, neurobiology, biochemistry and synthetic organic chemistry. Some of the physical methods in use include scanning force microscopy, x-ray crystallography, Raman spectroscopy, calorimetry, circular dichroism, photoelectron microscopy and rapid time scale fluorescence methods. Some of the areas of active research include protein structure, dynamics of protein folding, protein-nucleic acid interactions, force measurements on single molecules and imaging of large (non-crystalline) macromolecular complexes. Because of the interdisciplinary nature of the research, biophysical chemistry faculty have very close associations with the Institute of Molecular Biology.

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Environmental Chemistry

Solving many of the environmental problems of today requires both a strong basis in the fundamental science as well as innovative research ideas. The graduate program in chemistry at the University of Oregon offers both. In Geri Richmond’s lab, researchers are investigating a variety of adsorption and exchange processes that occur at liquid and solid surfaces that have direct relevance to many important environmental processes.

In recent years, several labs have begun projects in green chemistry.

Green chemistry specifically focuses on the rational development of environmentally-benign products and processes. At the UO, research groups apply basic chemical principles to develop innovative products and processes.

Several research groups are developing products that are environmentally benign and/or have applications that are environmentally friendly. For example, new solar cell materials can be made of benign materials and be used to cleanly generate electricity. Specific areas of interest to UO research groups include:

Photoactive materials – photodegradeable plastics, and photoelectric cells (used in solar panels), (Dave Johnson). Electronic materials – nanomicroelectronics (Hutchison) and low-temperature modulated elemental reactions (Dave Johnson). Thermoelectric Materials – materials to produce electrical energy from waste heat (Dave Johnson).

To meet the goals of green chemistry, greener methods of preparing these and other new materials must also be developed. UO research groups have a strong emphasis on developing greener chemical processes including:

Design of ligands for hazardous substances—binding, separating, and sequestering of a wide range of metal ions, including toxic heavy metals, radio isotopes, and hazardous compounds (Hutchison, Doxsee, Darren Johnson); and developing nanoscale assemblies that can act as hosts for harmful molecules such as toxins and nerve agents (Darren Johnson). Green manufacturing of nanomaterials—combining green principles and nanoscience to develop new technology for microelectronics (Hutchison); developing methods for the phase- and shape-controlled synthesis of materials using benign precursors and solvents (Doxsee); developing novel microchannel reactors for efficient high-volume production of nanoparticles (Hutchison, Doxsee, Lonergan).

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Inorganic/Organometallic Chemistry

Modern inorganic chemistry is an enormously broad field that spans a profusion of fascinating subdisciplines ranging from solid-state chemistry at one extreme to solution photochemistry at the other. Although no department can claim to cover all areas of inorganic chemistry, most of the important frontier areas of inorganic research are being actively studied in our department. The links below describe Professors Dave Johnson’ and Doxsee’s  research in solid-state chemistry, Professor Page’s work on surfaces, Professor Hutchison’s work on metal nanocrystals and his work on surfaces, the Boettcher lab’s work on designing and understanding inorganic solids for solar energy harvesting and electrochemical energy storage, and Professor Jasti’s work on structure-property relationships of novel graphitic nanomaterials, Professor Pluth’s work using molecular recognition to activate small molecules for use in catalysis and sensing, and Professor Darren Johnson’s work exploring problems in coordination chemistry and organic synthesis using supramolecular chemistry as a tool.

Regardless of special area, all students receive a broad education in inorganic chemistry. Entry level graduate courses emphasize the common interdisciplinary themes of synthesis, structure, and dynamics. Subsequent special topics courses then provide in-depth specialization in the particular subdisciplines. Organometallic chemistry is likewise thoroughly covered by researchers in our department. Projects in the Doxsee lab focus on the use of organometallics in organic synthesis. The Haley lab is synthesizing organometallic compounds with unusual electronic properties. The Hendon group uses quantum mechanics and super computers to explore chemical properties arising in metal-organic frameworks and on the surfaces of catalysts. The Brozek Lab synthesizes soft materials and uses physical inorganic methods to investigate their unique redox properties for catalysis, energy capture, and electronic devices. Research in the Cook group develops new catalysts for the transformation of organic molecules. The catalysts studied are molecular organometallic complexes, as well as heterogeneous materials with well-defined active sites. They also use elements of physical organic chemistry to study the mechanisms of these transformations.

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Materials Chemistry

Materials chemistry is a relatively new discipline centered on the rational synthesis of novel functional materials using a large array of existing and new synthetic methods. The focus is on designing materials with specific useful properties, synthesizing these materials and understanding how the composition and structure of the new materials influence or determine their physical properties in order to optimize the desired properties. Many research groups within the chemistry department are involved with a broad range of materials synthesis and characterization. Topics of active research include:

Polymer Chemistry (Brozek, Guenza, Jasti, Marcus)     
Nanostructured Materials (Guenza, D.W. Johnson, Jasti, Nazin, Prell, Wong)     
Thin Film Multilayers (D.C. Johnson)     
Interfaces and Surfaces (Boettcher, Brozek, Cook, Guenza, Hendon, D.C. Johnson, Nazin, Prell, Richmond)     
Crystallization of Metastable Phases and Tectons for Materials (D.C. Johnson, D.W. Johnson)     
Solid State Materials with Thermoelectric, Superconducting or Magnetic Properties (Brozek, D.C. Johnson)     
Optical and Electronic Materials (Brozek, Haley, Jasti, Nazin, Wong)

There is a high level of interaction and collaboration between these groups and with other scientists in the multidisciplinary Materials Science Institute. Excellent facilities are available for this research, including equipment for synthesis and purification (furnaces, glove boxes, gel-phase and HPLC chromatography), structural characterization (solution-phase and solid-state NMR, UV-Vis and IR spectrometers and powder, thin film and single crystal X-ray diffractometers), compositional characterization (X-ray photoelectron spectroscopy), thermal analysis (TGA, DSC, DTA), thin film analysis (ellipsometry, contact angle goniometer, TOF-SIMS), microscopy/visualization (SEM, TEM, AFM), and property characterization (magnetic susceptibility, electron paramagnetic resonance, and equipment for measurement of electronic and thermal conductivity).

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Optics and Spectroscopy

The interest in optics and molecular spectroscopy at Oregon is unusually broad, reflecting the strong interdisciplinary emphasis of the chemistry department. Individual research programs span chemical systems from diatomic molecules to DNA and optical sources from microwaves to high-power lasers. Ongoing work includes theoretical and experimental work on spectroscopy of molecules at liquid surfaces and interfaces, spectroscopy of small molecules, studies of van der Waals clusters and molecules in solution, nonlinear optical properties of surfaces and interfaces, picosecond studies of photocarrier dynamics in photovoltaic materials and spatially-resolved spectroscopy of individual molecules and nano-scale materials.

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Organic Synthesis

The mastery of organic synthesis affords chemists with a powerful and unique skill—the ability to create new structures with new properties. The intellectual challenge of organic synthesis coupled with the potential of synthesis to help solve real world problems continues to attract generation after generation of talented young scholars to the field. Students at the University of Oregon have excellent opportunities to explore and learn both the depth and breadth of contemporary organic synthesis, as well as prepare themselves for tomorrow’s organic chemistry related careers in academia and industry.

The UO has a strong research program focusing on problems in modern synthetic organic chemistry, including: the synthesis and application of carbon-rich nanostructures (Haley, Jasti, D. W. Johnson), the design and implementation of new chemical tools for biological investigations (Pluth, DeRose, Haley), and the study of novel supramolecular phenomena (D. W. Johnson, Haley, Pluth, Jasti, Doxsee).

In addition, several interdisciplinary research problems under study at the University of Oregon also apply organic synthesis as a key component. These programs include the synthesis of hybrid organic/inorganic materials (Hutchison, D. W. Johnson, Jasti), the preparation of novel ligands for use in organometallic mechanistic studies and in catalysis design (Haley, Pluth), assembly of water-soluble structures for applications in catalysis and molecular recognition (D. W. Johnson, Jasti), and the  synthesis of functional molecules for optical and electronic applications (Haley, Page, Jasti).

All of these areas of study benefit greatly from state-of-the-art characterization facilities and support staff at the University of Oregon (see http://camcor.uoregon.edu/).

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Physical Chemistry

Physical chemistry focuses on understanding the physical basis of chemical phenomena. This goal is pursued through the concerted efforts of experimentalists and theorists. While experimentalists design and carry out laboratory investigations of chemical systems, theorists conceive and develop theoretical tools to explain and predict system properties. Physical chemistry provides the fundamental scientific tools to investigate systems of interest in a wide range of disciplines, including material science and biology.

At the University of Oregon, research in physical chemistry focuses on a variety of topics in the quantum and classical regimes.

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Polymer Chemistry

The chemistry department at the University of Oregon has the following faculty working in the area of Polymer Chemistry.

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Solid-State Chemistry

Solid-state chemistry continues to play an expanding role in an astounding array of disciplines. As the discovery of new physical phenomena has often depended on the development of new materials, the synthesis of new solid-state materials and kinetically stable composites with optimized properties is of central importance. While solid-state materials have historically been prepared through high temperature solid-state reactions, generally affording the most thermodynamically stable phases, a variety of techniques have been developed to overcome the limitations inherent in this traditional approach.

The solid-state chemistry groups at the University of Oregon have been leaders in the discovery, development, and application of the concept of reaction mechanism to the synthesis of solid-state materials, essentially recruiting for the service of extended solid-state chemistry the basic concepts long used by molecular chemists. D. C. Johnson has developed elementally modulated thin films as reactants and shown how initial film structure controls subsequent reaction pathways. Page has demonstrated the importance of following the evolution of sol-gel samples, particularly for ternary and quaternary systems, as they progress to complex oxides in order to determine processing conditions. Doxsee has pioneered “complexation-mediated crystallization”, controlling the crystallization of both molecular organic solids and extended inorganic solid-state materials through the use of chelating agents in nonaqueous solvents. The Brozek Lab uses synthetic tools of solid-state chemistry to generate reactive clusters and porous polymers that blur the distinction between dynamic liquids and rigid materials. The Hendon lab uses high performance computers to quantify electronic properties of materials for energy storage and conversion applications. All of these approaches proceed via amorphous intermediates, allowing the exploitation of nucleation, a kinetic process, as the rate limiting step in the formation of crystalline solids and thereby affording control over the structure of the final solid-state products through the control of nucleation energies.

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Statistical Mechanics of Liquids and Complex Fluids

The study of structure and dynamics of complex fluids holds the key to understanding some of the most relevant problems in chemistry, biology, and engineering. Examples of complex fluids include self-assembling molecular systems, proteins, colloids, fibers, cellular filaments, films, glasses, membranes, granular materials, but also …. ketchup and sand! 

The challenge in the study of complex fluids is the fact that these are liquids where the relevant physical processes often occur over a logarithmically varying range of characteristic length and time scales. To make the matter even more challenging, phenomena occurring at different length scales can be strongly correlated leading to the complex physical behaviors observed in nature. 

The tools to study and model these phenomena are Statistical Mechanics, and Spectroscopy. 

The effort in the study of complex fluids is the design of new experimental techniques (Marcus) and innovative theoretical approaches (Guenza) to increase the range of time and spatial scales in which complex fluid properties can be measured and modeled. 

Research at the University of Oregon in this field crosses from Physics to Chemistry to Biology and includes the study of structure, phase behavior and dynamics of systems such as membranes, macromolecules, and biological cells. 

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Surfaces and Interfaces

Some of the most important chemical and physical processes on our planet occur at a surface or interface. The surface of a medium whether it be a liquid or a solid has very special properties which are often quite distinct from the bulk substance. For example, the surface of water has a very high surface tension, allowing more dense objects to float on top of it. The surface of a semiconductor can have very different electronic properties than the bulk due to the molecular orbitals of the surface atoms which are left “dangling” as the bulk lattice is terminated. In the biochemical area, most drugs act by interaction with substances at cell surfaces and surface chemistry plays an important role in the events that govern such processes. Several research groups are involved in studies of surfaces and interfaces at the University of Oregon that examine a range of environmentally, biologically and technologically important surfaces and interfaces using a wide range of methods and techniques.

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Theoretical Chemical Physics

At the University of Oregon theoretical research spans a range of fundamental problems, from dynamics of small atoms and molecules, to properties of macromolecules in condensed systems. Theoretical methods range from purely analytical to computationally intensive. Theorists at Oregon have collaborations with a variety of experimental groups, locally and around the world. Specific areas of focus include: fundamental approaches to electron correlation in atoms; new analytical methods for description of molecular potentials; new methods for chaotic dynamics and theoretical analysis of experiments on highly excited molecules; theory of time-resolved optical measurements in condensed phases; optical control of molecular dynamics; statistical mechanics of structure and time dependent phenomena of materials such as liquid crystals, glasses, carbohydrates, polymers, and proteins; theory of random processes where fluctuations are important, including Brownian motion.

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