Chemistry

Tammy J. Dwyer, Ph.D., Chair
James P. Bolender, Ph.D.
Christopher J. A. Daley, Ph.D.
David O. De Haan, Ph.D.
Robert N. Dutnall, Ph.D.
Thomas R. Herrinton, Ph.D.
Peter M. Iovine, Ph.D.
Jeremy S. Kua, Ph.D.
Mitchell R. Malachowski, Ph.D.
Kimberly I. Matulef, Ph.D.
Stephen A. Mills, Ph.D.
Deborah C. Tahmassebi, Ph.D.

Chemistry is the study of matter and energy and the changes they undergo. It plays a key role in understanding the natural universe and in the scientific and technological revolution that has shaped modern society. Biochemistry is the study of the chemical nature and processes that occur in biological systems.

The programs offered in Chemistry and Biochemistry provide a strong foundation in the principles and practices of modern chemistry and biochemistry within the framework of a liberal arts education. The majors are designed to give students both the theoretical bases of the disciplines and extensive hands-on experience testing theories in the laboratory. We also offer courses that fulfill the physical sciences portion of the Core Curriculum requirements. These courses are designed to acquaint students majoring outside the natural sciences with the basic principles and methods of modern science, and with the history and development of scientific thought.

The American Chemical Society (ACS), a national organization that develops and administers guidelines defining high quality undergraduate chemistry programs, has approved USD’s Chemistry curriculum. This allows Chemistry majors the option of enhancing their career choices by earning an ACS-certified degree.

The department is distinguished by its dedication to undergraduate research and teaching. All full-time faculty members have active research programs in which undergraduates can fully participate. These activities lead, in many cases, to new discoveries and publications in major scientific journals with students as co-authors.

Students have the opportunity to work with state-of-the-art instruments in classes and research. This instrumentation includes Varian Inova 500 MHz and Mercury 400 MHz NMR spectrometers, a laser facility, three JASCO infrared spectrometers, two fluorescence spectrophotometers (PTI and JASCO), two mass spectrometers interfaced with capillary gas chromatographs (Hewlett-Packard and ThermoFinnigan), a JASCO circular dichroism spectropolarimeter, a microwave reactor system and two high-performance liquid chromatography work stations (JASCO and Varian). In addition, the department has a molecular modeling facility with 12 PC desktop and 12 Unix/Linux workstations, and a server complete with molecular modeling software, and an eighteen dual-processor Xeon cluster for computational chemistry.

A major in chemistry or biochemistry prepares a student for a variety of different career possibilities. Professional chemists and biochemists may select careers in areas such as basic or applied research, production and marketing, consulting, testing and analysis, administration, management, business enterprise, and teaching. They are employed in the chemical, pharmaceutical, petroleum, energy, engineering, and “high-technology” industries; by government laboratories and agencies working on health, energy, and the environment; in consulting firms; and by educational institutions at all levels. Undergraduate training in chemistry provides a solid foundation for many other areas such as medicine, dentistry, veterinary medicine, pharmacy, oceanography, geochemistry, chemical engineering, forensics, environmental studies, molecular biology, and law.

Two programs of study are available, differing in their focus:

The Chemistry Major

The Chemistry Major is designed to qualify students for admission to graduate school in chemistry; positions as chemists; admission to medical, dental, and pharmacy schools; or secondary teaching.

Preparation for the Major
CHEM 151, 152, 151L, 152L, 220; MATH 150, 151; PHYS 270, 271.

The Major
The 32 units of upper-division work must include Chem 301, 302, 301L, 302L, 311, 312, 331, 396W, 440, 489, one elective, and two of the following advanced laboratories: CHEM 421, 423, 425, and 427. Electives may be chosen from other chemistry courses for which prerequisites have been met. CHEM 496 may not be applied toward the 32 unit requirement. Those planning for graduate work in chemistry are recommended to complete the ACS-certified degree and to take additional upper division electives in chemistry, mathematics or physics depending on the area of interest. To obtain an ACS-certified bachelor’s degree in chemistry, chemistry majors must complete Chem 423, 425, and either 421 or 427.

The Biochemistry Major

The Biochemistry major is designed to prepare students for graduate work in biochemistry, molecular biology, pharmacology, pharmaceutical and clinical chemistry; positions as biochemists; admission to medical, dental, and pharmacy schools; or secondary teaching.

Preparation for the Major
CHEM 151, 152, 151L, 152L; MATH 150, 151: PHYS 270, 271; BIOL 190, 225, 225L.

The Major
The 33 units of upper-division work must include Biol 300, 300L; Chem 301, 302, 301L, 302L, 311, 314, 331, 335, 396W, 489, one elective, and one of the following advanced laboratories: Chem 421, 423, 425, or 427. Electives may be chosen from other chemistry courses for which prerequisites have been met or Biol 342, 376, 382, 480, 482 or 484. Chem 496 may not be applied toward the 33 unit requirement. Those planning for graduate work are recommended to take additional upper division electives in chemistry, biochemistry or biology depending on the area of interest.

The Chemistry Minor

Minimum requirements for a minor in chemistry are: Chem 151, 152, 151L, 152L and ten units of upper-division chemistry including either CHEM 311 or 331. Students taking the minor to enhance employment possibilities in biotechnology, pharmaceutical industry or pharmacy school are advised to take Chem 220.

Major Field Test Graduation Requirement
As a part of the department’s assessment program, each graduating senior is required to take the major field test in chemistry (Chem 489). A student who fails to take the major field test will be restricted from graduating.

Other Programs

Several professional options are open to the chemistry major in addition to the pursuit of a career in chemistry or biochemistry. The department offers special programs in the following areas (students interested in greater detail should consult the department chair):

Pre-Medicine/Pre-Dentistry/Pre-Pharmacy
The liberal arts curriculum provides an excellent background for graduate education in the health professions. Students planning to apply for admission to medical, dental or pharmacy schools may elect to major in any of the academic disciplines within the college, but in most cases it is advantageous to major in one of the sciences. Students may select either the chemistry or biochemistry major as preparation. The specific science courses recommended for undergraduates differ for different professional schools but should include Biol 221, 221L and 225, 225L and any additional science courses recommended by the department’s pre-medical advisor.

Chemistry Courses (CHEM)

101 Chemistry and Society / 3 UNITS
A course designed for the non-science major that focuses on the major ideas of modern chemistry and the role that chemistry plays in a technological society. The evolution of our understanding of atomic and molecular structure and chemical reactivity will be examined as examples of the scientific method and the very human nature of the scientific endeavor. The role of modern chemistry in both the creation and the solution of societal problems will also receive considerable attention. The problems examined, which may vary in different sections, include: the energy crisis, air and water pollution, global warming, nutrition and food additives, household chemicals, pesticides and agrochemicals, and nuclear power. Two lectures weekly. (every semester)

103 DNA Science and Technology / 3 UNITS
A course designed for the non-science major that covers the discovery of DNA as the genetic material, the simplicity of the three-dimensional structure of DNA and the many implications to be drawn from this structure. It explores the concepts involved in recombinant DNA technology and its applications to the pharmaceutical industry, agriculture, forensics, gene therapy and AIDS research. Two lectures weekly. Chem 101 and 111 are not prerequisites. (every semester)

105 Physical Science for K-8 Teachers / 3 UNITS
A laboratory/lecture/discussion class designed to lead students toward an understanding of selected topics in chemistry and physics. The course topics are selected to satisfy the physical science specifications of the science content standards for California Public Schools (K-12) and is intended for liberal studies majors. Two two-hour laboratory sessions per week. (fall semester)

111 Chemistry and Society with Laboratory / 3 UNITS
A course designed for the non-science major that focuses on the major ideas of modern chemistry and the role that chemistry plays in a technological society. The lecture content is similar to that in Chem 101 (above); however, this course includes a laboratory that will satisfy the general education requirement for a laboratory course in the natural sciences. Two lectures and one laboratory/discussion weekly. (spring semester)

151-152 General Chemistry / 3-3 UNITS
A two semester lecture course which introduces the fundamental principles of modern chemistry. These principles, which include atomic and molecular structure, periodicity, reactivity, stoichiometry, equilibrium, kinetics, thermodynamics, bonding, acid-base chemistry, redox chemistry, and states of matter, will be used in and expanded upon in more advanced courses. Three lectures weekly. Prerequisite: Math 115 or a passing score on the Math Level 1 Placement Exam. Co-requisite: Chem 151L, 152L (every year)

152H Honors General Chemistry / 3 UNITS
An honors course which parallels Chem 152. The topics are covered in greater depth than in Chem 152, and additional applications of chemistry are included. Three lectures weekly. Prerequisite: Chem 151/151L and consent of instructor. (spring semester)

151L-152L General Chemistry Laboratory / 1-1 UNITS
A laboratory course which introduces the concepts and techniques of experimental chemistry. Chem 151L has one laboratory period that meets bi-weekly. Chem 152L has one laboratory period that meets every week. Prerequisite: concurrent registration in Chem 151-152 or consent of instructor. (every year)

220 Analytical Chemistry / 4 UNITS
An introduction to the principles and practices of analytical chemistry with an emphasis on quantitative methods. Classical methods such as titrimetric and volumetric analyses as well as basic instrumental methods involving spectroscopy, electrochemistry, and chromatography will be performed. Some experiments will be of the project type. Two laboratory periods weekly. Prerequisites: Chem 151, 152 and Chem 151L, 152L. (fall semester)

301-302 Organic Chemistry / 3-3 UNITS
A two-semester introduction to basic organic chemistry. The relationship of structure and bonding in organic compounds to reactivity will be emphasized. Reactions will be discussed from mechanistic and synthetic perspectives. Three lectures weekly. Prerequisite: Chem 151, 152. (every year)

301L-302L Organic Chemistry Laboratory / 1-1 UNITS
This course is designed to follow the material presented in Chem 301, 302. Microscale experimental techniques will be emphasized. Experiments include: recrystallization, distillation, extraction, chromatography, spectroscopy, kinetics, multi-step syntheses, and structure determination. One laboratory period weekly. Prerequisite: Chem 151L, 152L and concurrent registration in Chem 301-302.

311 Physical Chemistry / 3 UNITS
This course covers modern physical chemistry, including atomic and molecular structure, and spectroscopy. Three lectures weekly. Prerequisites: Chem 151-152, Math 151, and Phys 270, or consent of instructor. Corequisite: Phys 271. (fall semester)

312 Physical Chemistry / 3 UNITS
This course focuses on the classical principles of thermodynamics, kinetics, and statistical mechanics. Three lectures weekly. Prerequisite: Chem 311 or consent of instructor. (spring semester)

314 Biophysical Chemistry / 3 UNITS
This course will apply the principles of thermodynamics, equilibria and kinetics toward biological systems. The course will begin with a description of the first, second and third laws of thermodynamics with special attention toward their application to proteins, nucleic acids and membranes. The course will then examine equilibrium phenomena and the associated thermodynamics. These principles will be applied toward the design and evaluation of inhibitors and drugs. In the final third of the course, principles of kinetics will be examined. Measurement of rate constants for complex biological processes including non-Michaelis-Menten enzyme kinetics, ligand binding off and on rates and ribozyme catalysis. Three lectures weekly. Prerequisites: Chem 151-152, Biol 225, Phys 270, and Math 151. Chem 311 and Chem 331 are strongly recommended. (spring semester)

331 Biochemistry / 3 UNITS
The structure, function, and metabolism of biomolecules. Structure and function of proteins, carbohydrates, lipids, nucleic acids, and important accessory molecules (cofactors and metal ions) are covered, as well as enzyme kinetics and mechanism, thermodynamics, metabolism, and the regulation of metabolism. Three lectures weekly. Prerequisite: CHEM 301, 302/301L, 302L. (every semester)

335 Biochemistry Laboratory / 3 UNITS
An advanced laboratory course that focuses on techniques for the preparation and quantitative analysis of proteins and other biomolecules. Experiments will include preparation of buffers, production and purification of proteins, and analysis of protein structure and function. Two laboratory periods weekly. Corequisite: CHEM 331. Biol 300L is strongly recommended. (every semester)

345 Bio-Inorganic Chemistry / 3 UNITS
A survey of the roles of metallobiomolecules in organisms. The functions, structure, and modes of metal coordination of the more significant molecules are examined in detail and compared to those of model compounds. The standard physical techniques used in studying these complexes are discussed. Particular emphasis is given to the role of the metal ion(s) and how their inorganic properties affect the activity of the biological compound. Three lectures weekly. Prerequisites: CHEM 302. (may not be offered every year)

355 Environmental Chemistry / 3 UNITS
A survey of the natural environment from a chemist’s point of view and the evaluation of chemicals from an environmental point of view. This course is concerned with the chemistry of air, water, soil and the biosphere in both pristine and polluted states. Pollution prevention and mitigation schemes are considered. Lab experiments include local fieldwork. Two 3-hour laboratory periods weekly. Prerequisites: CHEM 301/301L. (may not be offered every year)

360 Physical-Organic Chemistry / 3 UNITS
Applications of modern theoretical concepts to the chemical and physical properties of organic compounds. Among the topics covered are: linear free-energy relationships; acidity functions; mechanisms of nucleophilic and electrophilic substitutions; additions and eliminations; radical reactions; and pericyclic reactions. Three lectures weekly. Prerequisite: Chem 302L and 311. (May not be offered every year)

380 NMR Methods / 3 UNITS
An introduction to concepts and methods in nuclear magnetic resonance (NMR) spectroscopy. Theory of NMR will be developed and applied to the design of one-dimensional and two-dimensional experimental pulse sequences. The laboratory will emphasize instrumental operation, data acquisition and processing, and practical applications of NMR methods to scientific problems. Two lectures and two-three-hour laboratory periods weekly. Prerequisite: Math 150, Chem 301, 301L. (may not be offered every year)

396W Methods of Chemical Research / 3 UNITS
Introduction to the principles, methods, and communication of chemical research. Lab work includes general and advanced techniques with considerable hands-on use of modern instruments, proper record-keeping, data management, and consideration of laboratory safety. Techniques for searching the chemical literature are included. This course fulfills the upper-division writing requirement. Students will write and edit a report in a format suitable for journal publication. One lecture and eight hours of laboratory research weekly. Prerequisite: consent of instructor. (every semester)

421W Organic/Physical Experimental Chemistry / 3 UNITS
An advanced laboratory course with experiments and projects that integrate principles and methods in analytical, organic, and physical chemistry, with considerable emphasis on instrumental methods. This course fulfills the upper-division writing requirement. Two laboratory periods weekly. Prerequisite: CHEM 220 or Biol 300L, CHEM 301, 302/301L, 302L, and CHEM 311. (fall semester, may not always be offered as a “W” course)

423W Inorganic/Physical Experimental Chemistry /3 UNITS
An advanced laboratory course which integrates techniques and concepts from inorganic and physical chemistry plus, to a lesser extent, analytical chemistry. A wide variety of classical and modern methods of experimental chemistry, including both wet chemical and instrumental methods, will be used in experiments which show the interrelationships between these three areas of chemistry. Also, instruction in the proper methods of recording and reporting chemical experiments and practice in those methods will be included. This course fulfills the upper-division writing requirement. Two laboratory periods weekly. Prerequisites: CHEM 220 or Biol 300L, CHEM311 and CHEM 312 (may be taken concurrently). Chem 440 is strongly recommended. (spring semester, may not always be offered as a “W” course)

425W Instrumental Analysis / 3 UNITS
A survey of contemporary instrumental methods of chemical analysis, with emphasis on spectroscopic, electrochemical, and separation techniques. The theory, design, and operation of specific instruments will be discussed. Experiments and projects utilizing FTIR, NMR, GC- and LC-MS, HPLC, voltammetry, absorption, emission and fluorescence will be selected. This course fulfills the upper-division writing requirement. Two laboratory periods weekly. Prerequisites: Chem 220 or Biol 300L, Chem 302L, and Chem 311. (fall semester, may not always be offered as a “W” course)

427W Biophysical Chemistry Laboratory / 3 UNITS
An advanced laboratory course in which spectroscopic techniques are applied to biological problems in order to extract thermodynamic, kinetic and structural information. This information will then be correlated to function of the biomolecule. The techniques to be explored may include UV-Vis, CD, FTIR, NMR, MS, fluorescence spectroscopy and the computational methods necessary for data analysis. The fundamental principles and special considerations of their application to enzymes, proteins, DNA and other biomolecules will be presented in lecture and carried out in the laboratory. This course fulfills the upper-division writing requirement. Two laboratory periods weekly. Prerequisites: Chem 220 or Biol 300L, Chem 301, 302, 301L, 302L. Corequisities: Chem 311 and Chem 331 or consent of instructor. (spring semester, may not always be offered as a “W” course)

440 Inorganic Chemistry / 3 UNITS
The principles of inorganic chemistry, such as atomic and molecular structure, bonding, acid-base theory, and crystal field theory, are examined. Utilizing these principles, the chemistry of the elements of the periodic table is discussed, including the kinetics and mechanisms of reactions. The various fields within inorganic chemistry, including solid-state, coordination and organometallic chemistry are introduced. Three lectures weekly. Prerequisites: CHEM 302 and
CHEM 311. (can be taken concurrently) (fall semester)

489 Major Field Test in Chemistry / 0 Units
As a part of the department’s assessment program, each graduating senior is required to take the major field test in chemistry. A student who fails to take the major field test will be restricted from graduating. (every May)

493 Special Topics in Biochemistry / 1-4 UNITS
From time to time, courses will be given on special topics in chemistry based primarily upon the expertise of faculty. Possible topics include protein structure and function, enzyme-catalyzed reactions, nucleic acid chemistry, and membranes. May be repeated for credit when the topic changes. Prerequisite: consent of instructor (may not be offered every year).

494 Special Topics in Chemistry / 1-4 UNITS
From time to time, courses will be given on special topics in chemistry based primarily upon the expertise of faculty. Possible topics include computational chemistry, photochemistry, polymers, medicinal chemistry, and organometallic chemistry. May be repeated for credit when the topic changes. Prerequisite: consent of instructor. (may not be offered every year)

495 Seminar / 1 UNIT
Techniques of oral communication in chemistry. Each student will give a seminar on a topic of interest. One hour each week. (every year)

496 Undergraduate Research / 1-3 UNITS
A research problem in experimental or theoretical chemistry under the supervision of an individual faculty member. Projects involve literature searching, on and off campus research, and oral and written reports. The course is taught on a pass/fail basis only. Prerequisite: consent of instructor (may not be offered every year).