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Chemistry

(For 2014–2015 academic year)

Professors Geier, Nolen, Rowlett, Shen
Associate Professors Chianese, Gogel, Popescu, E. Woods (Chair)
Assistant Professor Keith
Laboratory Instructors Chanatry, Jue
Lecturer Hough
Postdoctoral Fellows Ezeh, Suhanovsky

A major in chemistry or biochemistry is suitable for students who wish to prepare for careers in the chemical profession or in the related fields of life, health, or earth sciences. Many graduates go on to post-graduate programs in biochemistry, chemistry, chemical physics, pharmacology, medicine, dentistry, or veterinary medicine. Recent chemistry and biochemistry students have also pursued careers in law, business, teaching, and other fields.

Major Program in Chemistry

The major program consists of the following requirements:
a. Courses and Labs
General Chemistry (CHEM 101/101L and 102/102L)
Organic Chemistry (CHEM 263/263L and 264/264L)
Physical Chemistry (CHEM 333 and 334)
Instrumental Methods (CHEM 371 and laboratory course CHEM 381)
Molecular Spectroscopy (laboratory course CHEM 382)
Advanced Chemistry Research (CHEM 481, 482) Chemistry majors who participate in Colgate’s NIH Study Group in the fall of their senior year are exempted from CHEM 481.
At least one CHEM 380-series integrated laboratory course: CHEM 384, 385, or 387
At least two course credits one of which must be a full-semester course from:

Full-semester courses: CHEM 212/212L or 214, 353; and
Half-semester courses: CHEM 413, 415, 431, 432, 452, 454, 461, 464, 468, 477

CHEM 111/111L, a one-term course designed for the well-prepared first-year student, may be substituted for CHEM 101/101L and 102/102L and allows an early entry into 212/212L. Independent Studies (291, 391, 491) may not normally be substituted for one of the courses listed above, but if it can be demonstrated that such a course provides sufficient breadth at the advanced level, the department will consider a petition for substitution. An overall GPA of at least 2.00 is required for the chemistry courses (and associated labs) chosen to meet major requirements.

b. Additional Requirements
MATH 111 and 112
PHYS 111 and 112, or PHYS 131 and 232, or PHYS 232 and 233, and required labs

Junior and senior majors are expected to attend a weekly seminar series at which students, faculty, and guests present topics from the current literature and their own research.

c. Recommendations

Students wishing to earn an American Chemical Society certified bachelor’s degree in chemistry are required to take CHEM 212/212L, CHEM 353, and two 400-level courses.

Colgate’s chemistry department has an active summer research program, and there are numerous summer research opportunities at university, government, and private labs around the country. It is recommended that chemistry and biochemistry majors participate in a full-time research experience before they graduate, in addition to the required year of senior research (CHEM 481/482).


Those who wish to major in chemistry normally take CHEM 101/101L and 102/102L (or 111/111L and 212/212L) and MATH 111 and 112 in the first year. The usual sophomore courses are CHEM 263/263L and 264/264L, plus PHYS 111/111L and PHYS 112/112L or PHYS 131/131L and PHYS 232/232L. Students taking PHYS 232/232L and PHYS 233/233L can begin that sequence in the spring of their first or sophomore year. Juniors take CHEM 333 and 371/381 in the fall, and CHEM 334 with 382 in the spring. One additional CHEM 380-series integrated laboratory course is usually taken during the junior year. Seniors take CHEM 481, 482 during their senior year, along with at least two other upper-level chemistry course credits through a combination of full-semester or half-semester courses.

Minor Program in Chemistry

The minor requires the successful completion of CHEM 101/101L and 102/102L or 111/111L, 263/263L and 264/264L, and two additional course credits obtained from other full-semester or half-semester chemistry course(s) at the 200, 300, or 400 level. The stated prerequisites for these courses must be met, and a GPA of at least 2.00 is required in the chemistry courses chosen to meet minor requirements. Successful completion of MATH 111 and 112, and PHYS 111 and 112, or PHYS 131 and PHYS 232, or PHYS 232 and PHYS 233, and associated labs is required.

Major Program in Biochemistry

a. Course and Labs
General Chemistry (CHEM 101/101L and 102/102L) or Chemical Principles (CHEM 111/111L)
Organic Chemistry (CHEM 263/263L and 264/264L)
Molecules, Cells, and Genes (BIOL 182/182L, formerly BIOL 212/212L)
Physical Chemistry for the Life Sciences (CHEM 336), or with approval of the department chair, CHEM 333 or CHEM 334
Proteins and Nucleic Acids (CHEM 353)
Biophysical Chemistry Methods integrated laboratory course (CHEM 385)
Molecular Biology (BIOL 204)
Advanced Chemistry Research (CHEM 481, 482). Biochemistry majors who participate in Colgate’s NIH Study Group in the fall of their senior year are exempted from CHEM 481.
Either Instrumental Methods (CHEM 371) or Inorganic Chemistry (CHEM 212 or 214)
At least one CHEM 380-series integrated laboratory course: CHEM 381, 382, or 384
At least one course credit from the half-semester courses: CHEM 452, 454, or 468

Independent Studies (291, 391, 491) may not normally be substituted for one of the courses listed above, but if it can be demonstrated that such a course provides sufficient breadth at the advanced level, the department will consider a petition for substitution. An overall GPA of at least 2.00 is required for the chemistry and biology courses (and associated labs) chosen to meet major requirements.

b. Additional Requirements
MATH 111 and 112
PHYS 111 and 112, or PHYS 131 and PHYS 232, or PHYS 232 and PHYS 233, and required labs

Junior and senior majors are expected to attend a weekly seminar series at which students, faculty, and guests present topics from the current literature and their own research.

c. Recommendations

Those who wish to major in biochemistry normally take CHEM 101/101L and 102/102L (or 111/111L) and MATH 111 and 112 in the first year. The standard sophomore courses are CHEM 263/263L and 264/264L, plus the year of introductory physics or BIOL 182/182L (formerly BIOL 212/212L). Typically, juniors will take CHEM 353 and 385 in the fall or spring semester, and CHEM 336 in the spring semester. Students can elect to take either CHEM 371/381 in the fall term or CHEM 214 and a CHEM 380-series integrated laboratory course CHEM 381, 382, or 384 in the spring semester. Seniors take CHEM 481, 482 along with one course credit from CHEM 452, 454, or 468.

No minor program in biochemistry is offered.

Teacher Certification

The Department of Educational Studies offers a teacher education program for majors in chemistry who are interested in pursuing a career in elementary or secondary school teaching. Please refer to “Educational Studies.”

Honors and High Honors in Chemistry

Honors in chemistry may be awarded to majors who accumulate an overall GPA of at least 3.00 and a combined GPA of at least 3.00 in all chemistry, mathematics, and physics courses taken; complete approved honors projects; and present the results of their projects in both a written thesis and an oral defense to the department. The decision to award honors, high honors, or neither is based on the quality of the honors project, the quality of its presentation and defense, and other evidence of distinction.

Honors and High Honors in Biochemistry

Honors in biochemistry may be awarded on the same basis as honors in chemistry, except that a student must have at least an overall GPA of 3.00 and a combined GPA of at least 3.00 in all chemistry, biology, physics, and mathematics courses taken.

Awards

See Honors and Awards: Chemistry in "Chapter VI."

Advanced Placement and Pre-matriculation Credit

Students may replace the normal, two-semester, introductory chemistry sequence (CHEM 101 and 102) with a one-semester course (CHEM 111) if they meet one of the following minimum criteria: a score of 4 on the advanced placement (AP) chemistry exam, a score of 6 or 7 on the higher level international baccalaureate (IB) chemistry exam, a score of 650 on the SAT II chemistry exam, or a grade of A or B on the British A-level exam. Students choosing this course are eligible to take CHEM 212 in the spring of their first year, providing an early start into the chemistry major. Exceptionally well-prepared students from other pre-matriculation programs should consult with the department chair regarding advanced standing.

Students may also receive course credit for an AP score of 4 or 5. Those who enroll in CHEM 111 receive an AP credit for CHEM 101. Students who choose not to take any introductory chemistry courses may receive one credit toward graduation for an AP score of 4 (CHEM 101) or two credits for an AP score of 5 (CHEM 101 and 102). The department discourages the latter choice for students who plan to take 200 or higher level chemistry courses.

In consultation with the department chair, students may receive placement into CHEM 102 with a grade of A or B on the British A-level exam. No credit is awarded for CHEM 101; such students will simply gain entrance into CHEM 102. However, it is generally preferable for such students to enroll in CHEM 111 when possible.

Transfer students generally receive credit for satisfactorily completed chemistry courses taken at other colleges that correspond to courses at Colgate. The department considers such transfer credits individually, and students should provide information about the courses (syllabi, catalogue statements, lab notebooks, textbooks, etc.) to the department chair for consideration. These arrangements should be made well before beginning classes at Colgate.

Transfer Credit

Matriculated Colgate students may receive credit for chemistry courses taken at other colleges, either during a term away from Colgate or during the summer. Summer courses must meet several criteria established by the department concerning the course content, the length of the course, and the number and length of class and laboratory meetings. Students considering transferring credit to Colgate for a summer chemistry course should obtain a copy of the department’s criteria for an acceptable course, discuss the course with the department chair, and receive approval before taking the summer course. Final acceptance of the transfer credit is contingent upon satisfactory performance on an equivalency exam; the department administers this exam prior to the drop/add period for the fall term immediately following the summer course.

Summer Research Opportunities

The Department of Chemistry offers a rich summer research program in many fields of chemistry and biochemistry. Students receive stipends, and campus housing is available at reduced rates.

Study Groups

Colgate sponsors several off-campus study groups especially appropriate for majors in chemistry and biochemistry, including the following:
Australia II Study Group at the University of Wollongong
National Institutes of Health Study Group in Bethesda, Maryland
Wales Study Group at Cardiff University
For more information, consult with the department chair and see "Off-Campus Study Programs"; in Chapter VI.

Course Offerings

CHEM courses count toward the Natural Sciences and Mathematics area of inquiry requirement, unless otherwise noted.

All credit-bearing laboratories carry 0.25 course credits unless noted otherwise. Please see the “Academic Credit” section in Chapter VI for additional information and restrictions. Students wishing to retake a course that has a lab component must consult with the department chair before attempting to enroll.

In accordance with state requirements and common sense, personal protective equipment including eye protection meeting federal specifications must be worn in all laboratories.

100 The Chemistry of Altered and Natural Environments
Staff
To grapple with the complex environmental questions faced by modern society, the science that explains the phenomenon we observe must be understood. From endocrine disruptors to the ozone hole, global warming to plastics, and nuclear technology to acid rain, chemical principles allow one to understand, predict, and potentially mitigate the consequences of environmental changes in our modern age. This course provides an introduction to chemical principles and their application toward environmental issues. It focuses on those principles that are crucial in understanding environments and present-day environmental challenges. This course is designed for students who are interested in environmental science and environmental studies. There is no prior chemical knowledge expected, and there are no prerequisites. This course is not part of the CHEM 101/102 sequence of general chemistry, and students who have already taken CHEM 101/102 or CHEM 111 are ineligible for CHEM 100. Students who have taken CORE 102S are also ineligible for CHEM 100. Students who have taken CHEM 100 may take CHEM 101/102.

101/101L, 102/102L General Chemistry (I, II)
Staff
A two-term sequence that introduces chemical principles that apply to all areas of chem-istry. The first term (CHEM 101) deals with molecular and reaction stoichiometry, gases, the first law of thermodynamics, the electronic structure of atoms, the periodic table, chemical bonding and molecular geometry, intermolecular forces, and the properties of solutions. The second term (CHEM 102) covers transition metal complexes, chemical kinetics, nuclear chemistry, equilibria, acids and bases (with emphasis on equilibrium studies), the second law of thermodynamics, electrochemistry, and some descriptive chemistry of the more common elements. The required 0.25 credit-bearing laboratory courses CHEM 101L/102L must be taken concurrently with CHEM 101/102 and may not be taken as stand-alone courses. Completion of CHEM 101/101L with lecture and lab grades of C– or higher is a prerequisite for CHEM 102/102L. Students with either grade lower than a C– require instructor permission. CHEM 101/101L is offered in the fall only; CHEM 102/102L, in the spring only. Credit for CHEM101/101L does not depend on completion of CHEM 102/102L.

111/111L Chemical Principles
Staff
A one-term course designed for the well-prepared first-year student. CHEM 111 covers many of the same fundamentals covered in CHEM 101 and 102, but treats those ideas in greater depth. Enrollment requires a score of 4 or 5 on the AP exam, an A or B on A-level exam in chemistry, a score of 6 or 7 on the higher level IB chemistry exam, or a 650 or higher on the SAT II Chemistry Exam. Students enrolled in CHEM 111 who meet the standards by the AP exam may receive only one advanced placement credit for general chemistry. The required 0.25 credit-bearing laboratory course CHEM 111L must be taken concurrently with CHEM 111 and may not be taken as a stand-alone course. CHEM 111 (or CHEM 101-102) serves as a prerequisite for CHEM 263, 264 (Organic Chemistry), or CHEM 333, 334 (Physical Chemistry). Offered in the fall only.

212/212L Inorganic Chemistry
A. Chianese
An introduction to structure, bonding, and reactivity across the periodic table. The course begins by comparing the valence-bond and molecular-orbital models of bonding for small covalent compounds. Then, the solid state is explored, focusing on how bond-ing in ionic compounds, metals, and network-covalent compounds affects their behavior as materials. Additional topics include bonding in transition-metal complexes, reactivity in solution, and the use of physical methods such as spectroscopy and crystallography to elucidate elements of structure and reactivity. The required 0.25 credit-bearing laboratory course CHEM 212L must be taken concurrently with CHEM 212 and may not be taken as a stand-alone course. Pre- or co-requisite: CHEM 102 or CHEM 111. Offered in the spring only.

214 Inorganic Chemistry
A. Chianese
An introduction to structure, bonding, and reactivity across the periodic table. The course begins by comparing the valence-bond and molecular-orbital models of bonding for small covalent compounds. Then, the solid state is explored, focusing on how bond-ing in ionic compounds, metals, and network-covalent compounds affects their behavior as materials. Additional topics include bonding in transition-metal complexes, reactivity in solution, and the use of physical methods such as spectroscopy and crystallography to elucidate elements of structure and reactivity. Registration for CHEM 214 is limited to juniors and seniors who have not taken CHEM 212. Prerequisite: CHEM 102 or CHEM 111. Offered in the spring only.

263/263L, 264/264L Organic Chemistry (I, II)
R. Geier, P. Jue, E. Nolen
A study of the properties, reactions, and syntheses of representative organic com-pounds. Theories of structure and bonding, and mechanisms of organic reactions are emphasized. The characterization of molecular structure using spectroscopic and spectrometric tools is developed. Organic molecules of biological significance are used to illustrate many key principles. The laboratory affords hands-on experience in the synthesis, purification, and characterization of representative organic compounds using modern analytical instrumentation. The required 0.25 credit-bearing laboratory courses CHEM 263L/264L must be taken concurrently with CHEM 263/264 and may not be taken as stand-alone courses. Prerequisite: CHEM 102/102L or CHEM 111/111L with lecture and lab grades of C– or higher. Completion of CHEM 263/263L with lecture and lab grades of C– or higher is a prerequisite for CHEM 264/264L. Students with either grade lower than a C– require instructor permission. CHEM 263/263L is offered in the fall; CHEM 264/264L, in the spring.

333 Physical Chemistry I

Q. Shen, E. Woods
Introduction to quantum mechanics, fundamentals of chemical bonding, spectroscopy and methods of molecular structure determination, statistical thermodynamics, and mis-cellaneous topics. Prerequisites: CHEM 102 or 111, MATH 112, and PHYS 112 or PHYS 232, or permission of instructor. Offered in the fall only.

334 Physical Chemistry II

Q. Shen, E. Woods
Fundamentals of physical chemistry, particularly those most commonly applied in related fields such as organic, biological, and geological chemistry: classical thermodynamics of ideal and real systems, electrochemistry, and chemical kinetics. Prerequisite: CHEM 333 or permission of instructor. Offered in the spring only.

336 Physical Chemistry for the Life Sciences
Q. Shen, E. Woods
This physical chemistry course is designed for students interested in majoring in bio-chemistry or biology. The topics discussed include thermodynamics, chemical kinetics, electrochemistry, quantum chemistry, chemical bonding, and spectroscopy. The course introduces the basic concepts of physical chemistry within the context of biological systems and emphasizes how physical chemistry provides insight into modern biochemical and biological problems. Prerequisite: CHEM 264 and MATH 112. Pre- or co-requisite: PHYS 112 or PHYS 232, or permission of instructor. Offered in the spring only.

353 Proteins and Nucleic Acids
G. Gogel, R. Rowlett
A survey of biological polymers and of the physical and chemical methods of biopolymer research. Focuses on amino acids; protein structure; the function of proteins as cell structural materials and catalysts; and the structure, function, and chemistry of nucleic acids. Prerequisite: CHEM 264. Typically offered in the fall and spring.

371 Instrumental Methods

R. Rowlett
An introduction to the theory, practice, and applications of modern instrumental methods of chemical analysis. The theoretical background and principles of operation of modern chemical research instrumentation are examined. The required 0.25 credit-bearing laboratory course CHEM 381 must be taken concurrently with CHEM 371. Corequisite: CHEM 381. Prerequisite: CHEM 264 or permission of instructor. Offered in the fall only.

381 Practical Quantitative Analysis
A. Chianese, R. Geier, K. Pangallo, R. Rowlett
This half-semester 0.25-credit integrated laboratory course, to be taken concurrently with CHEM 371 and may not be taken as a stand-alone course. The laboratory experi-ments emphasize care, calibration, operation, and application of analytical instruments to real-life samples. Students solve quantitative problems from the fields of food, environmental and medicinal chemistry. Corequisite: CHEM 371. Prerequisite: CHEM 264 or permission of instructor. Offered in the fall only.

382 Molecular Spectroscopy
Q. Shen, E. Woods
This half-semester, 0.25-credit laboratory-based course explores the relationship between a molecule’s structure and its discrete energy levels. The students measure these energy levels through a variety of spectroscopies including infrared absorption, ultraviolet-visible absorption, fluorescence, Raman scattering, and NMR. Prerequisite: CHEM 333 or CHEM 336. Offered in the spring only.

384 Molecular Dynamics
Q. Shen, E. Woods
This half-semester, 0.25-credit laboratory-based course explores the effect of molecular motion and intermolecular forces on both the microscopic and bulk properties of matter. The topics investigated include viscosity, surface tension, isomerization kinetics, and re-laxation phenomena. Corequisite: CHEM 334 or CHEM 336. Offered in the spring only.

385 Biophysical Chemistry Methods
G. Gogel, R. Rowlett
This half-semester, 0.25-credit integrated laboratory course is designed to be an introduction to modern methods of biophysical chemistry and a bridge to independent re-search in biological chemistry. Specifically, this course includes techniques of protein purification from heterologous overexpression or natural sources. This course also focuses on modern methods of protein characterization, including electrophoresis, spectroscopy, enzyme kinetics, dynamic light scattering, and/or X-ray crystallography. Prerequisite: CHEM 264. Offered in the fall and spring.

387 Special Topics: Structure and Analysis

A. Chianese, K. Pangallo
This half-semester, 0.25-credit integrated laboratory course offers an in-depth study of quantitative and structural analysis. Students complete an independent project employing techniques that may include advanced NMR (selective decoupling, variable-temperature, NOESY), mass spectrometry including MALDI and MS/MS, chromatographic separations, and small molecule X-ray crystallography. Prerequisite: CHEM 381 or permission of instructor. Offered in the fall only.

413 Molecular Symmetry
A. Chianese
This half-semester 0.50-credit course provides an introduction to the use of group theory to describe the symmetry of molecules, and to aid in understanding their structure, bonding, and spectroscopy. The focus is on small molecules in the main group and transition-metal complexes. Prerequisite: CHEM 212 or CHEM 214 or permission of instructor. Offered in alternate years.

415 Organometallic Chemistry
A. Chianese
This half-semester 0.50-credit course is a survey of the organometallic chemistry of the transition elements, focusing on synthesis, bonding, structure, elementary reactions, and application to homogeneous catalysis. Prerequisites: CHEM 212 or CHEM 214, and CHEM 264, or permission of instructor. Offered in alternate years.

431 Molecular Modeling and Simulation
Q. Shen, E. Woods
This half-semester 0.50-credit course introduces modern simulation techniques in computational chemistry, including ab initio calculations and molecular dynamics simulations. Students learn the underlying theory of these methods at a basic level while getting hands-on experience studying chemical systems of their choice, from isolated molecules to aqueous biomolecules. Prerequisite: CHEM 333 or 336 or permission of instructor. Offered in alternate years.

432 Introduction to Statistical Thermodynamics
Q. Shen, E. Woods
This half-semester 0.50-credit course starts with a review of pertinent statistics, quantum chemistry and spectroscopy topics. The concepts of ensemble, partition function and their relationship with ideal gas thermodynamic quantities like internal energy, entropy, Gibbs energy, equilibrium constant, and other macroscopic observations are dis-cussed. Prerequisite: CHEM 334 or permission of instructor. Offered in alternate years.

452 Metabolic Chemistry
R. Geier, G. Gogel, E. Nolen, R. Rowlett
This half-semester 0.50-credit course is dedicated to exploring the chemical themes and mechanisms of biological metabolism. Specifically, the metabolism of lipids, carbohydrates, amino acids, and nucleotides are investigated. Prerequisite: CHEM 264. Offered in the fall only.

454 Bioenergetics
G. Gogel, R. Rowlett
This half-semester 0.50-credit biochemistry course covers the energy processes in living systems. The major focus of the course is mammalian biochemistry and cellular respiration in the mitochondria, but bacterial biochemistry and photosynthesis are also dis-cussed. Prerequisite: CHEM 264. Offered in the spring only.

461 Organic Reaction Mechanisms
R. Geier, E. Nolen
In this half-semester 0.50-credit course, a detailed study of organic reaction mechanisms is presented. Key mechanistic pathways are examined. Proposal of plausible mechanisms for organic reactions, experiments used to gain insight into reaction mechanisms, and the importance of mechanistic insight toward the practical application of organic reactions are considered. Classic organic reactions as well as recent examples from the primary literature are discussed. Prerequisite: CHEM 264. Offered in alternate years.

464 Organic Synthesis
R. Geier, E. Nolen
In this half-semester 0.50-credit course, a detailed study of the synthesis of organic compounds is presented. Particular attention is given to functional group compatibility, diastereoselectivity and enantioselectivity, recent developments in organic reactions, as well as reaction catalysis. The primary literature is examined with an eye to better understand the design of the synthetic approach. Prerequisite: CHEM 264. Offered in alternate years.

468 Medicinal Chemistry
R. Geier, G. Gogel, E. Nolen, R. Rowlett
In this half-semester 0.50-credit course, the basic principles of the drug discovery pro-cess are explored. Topics include traditional and novel approaches, mode of action, quantitative structure activity relationships, absorption, distribution, metabolism, and inactivation of medicinal agents. In addition, major drug classes are presented along with specific case studies for each category. Prerequisite: CHEM 264. Offered annually.

477 Environmental Chemistry
Staff
This half-semester 0.50-credit course uses a firm grounding in chemistry to seek answers to the complex environmental questions faced by modern society. The scientific literature is used to explore a variety of topics, such as: legacy and emerging contaminants, natural cycles and their anthropogenic perturbations, and energy production. Pre-requisite: CHEM 264 or permission of instructor. Offered in alternate years.

481, 482 Advanced Chemistry Research
Staff
Original research projects designed for student collaboration with faculty members pro-vide a variety of laboratory experiences. The purpose is to build on and consolidate the student’s previous experiences in literature searching, project design, use of modern in-strumentation for data acquisition and analysis, problem solution, and oral and written communication of results. The 0.50-credit CHEM 481 is generally taken in the fall semester, and the 0.50-credit CHEM 482 is taken in the spring semester. A minimum of eight hours of laboratory work per week are required, during each of two terms. Each student gives an oral presentation of his or her project at the weekly chemistry department seminar and submits written end-of-term reports. In the spring term, a student who is a candidate for a degree with honors submits and defends a thesis in lieu of a written report. Open to senior chemistry or biochemistry majors only.

291, 391, 491 Independent Study
Staff
Independent studies are designed for students who wish to pursue problems or studies not adequately covered by formal course work. Prerequisite: permission of the chemistry department.