Chemistry and Biochemistry

KATHLEEN P. HOWARD, Professor
ROBERT S. PALEY, Professor and Chair
PAUL R. RABLEN, Professor
THOMAS A. STEPHENSON, Professor 4
STEPHEN T. MILLER, Associate Professor
LILIYA A. YATSUNYK, Associate Professor 3
JESSICA L. SARVER, Visiting Assistant Professor
KEVIN D. WELCH, Visiting Assistant Professor
VIRGINIA M. HECK, Senior Lecturer
MARIA G. NEWPORT, Lecturer
CAROLINE A. BURKHARD, Laboratory Instructor
DONNA T. HALLEY, Laboratory Instructor
LORI P. SONNTAG, Laboratory Instructor
IAN MCGARVEY, Scientific Instrumentation Specialist
CATHERINE CINQUINA, Administrative Assistant
3 Absent on leave, 2014–2015.
4 Absent on administrative leave, 2014–2015.

The objective of the Chemistry and Biochemistry Department is to offer effective training in the fundamental principles and basic techniques of the science and to provide interested students with the opportunity for advanced work in the main sub-disciplines of modern chemistry.

The department offers a course major, honors major, course minor, and honors minor in chemistry. In addition, the department offers the following special majors: in collaboration with the Biology Department, a course major and an honors major in biochemistry; and in collaboration with the Physics and Astronomy Department, a course major and an honors major in chemical physics. We offer teacher certification in chemistry through a program approved by the state of Pennsylvania. For further information about the relevant set of requirements, please refer to the Educational Studies section.

The Academic Program

Course Sequence Recommendations

Students planning a major in chemistry or biochemistry should complete Chemistry 010/010 HN and 022 during their first year at Swarthmore. During the sophomore year students can take 032 and 038 or 044 and 055 if the physics and mathematics requirements for physical chemistry have been completed. In addition, students planning a major in Biochemistry should complete Biology 001 in their first two years at Swarthmore.

In the last two years, chemistry and biochemistry majors have some flexibility about the sequencing of the remaining requirements for the major. However, students should note that completion of Chemistry 010/010 HN, 022 and one semester of a 40-level or 50-level course constitute a minimum set of prerequisites for enrollment in any Chemistry and Biochemistry Department 100-level seminar. In addition, individual seminars carry additional prerequisites so students should plan ahead accordingly.

Course Major in Chemistry

The course major in chemistry consists of eight required core courses, as well as their mathematics and physics prerequisites, plus a 100-level elective seminar. All majors must complete the senior comprehensive requirement, as described in a later section.

Requirements

CHEM 010/010 HN    CHEM 022

CHEM 032                  CHEM 038

CHEM 044                  CHEM 055

CHEM 056                  CHEM 057

One 100-level seminar

Ancillary Requirements (prerequisites for physical chemistry):

PHYS 003 and PHYS 004/004L (or 007,008)

MATH 034 (or equivalent)

Acceptance Criteria

All applications are reviewed by the entire department. We consider grades in all college-level courses in chemistry, biology, mathematics, and physics. Decisions will not normally be made until two chemistry courses are completed and significant progress has been made towards meeting the physics and mathematics prerequisite requirements for enrollment in physical chemistry. An element in a student’s acceptance as a major is our considered judgment of the student’s potential for satisfactory performance in advanced course work and fulfillment of the comprehensive requirement.

Course Minor in Chemistry

Requirements

The course minor in chemistry has the following requirements:

  1. The minor consists of five chemistry credits, plus any prerequisites necessary. The chemistry credits must include 010/010 HN, 022, and 044 and two additional credits, at least one of which must be numbered 050 or higher. Chemistry 001 and research credits (094, 096, 180) may not be used to fulfill the requirements for the minor.
  2. At least four of the five credits must be earned at Swarthmore College.
  3. The minor will not be titled anything other than “chemistry.” For example, there will be no minor in “organic chemistry” or “physical chemistry,” etc.

Acceptance Criteria

Applications are reviewed by the entire department, and decisions are made on the basis of the considered judgment of the faculty.

Honors Major in Chemistry

Requirements

An Honors preparation in Chemistry consists of three seminars - two in Chemistry (see item 1, below) and one in a minor - and a research thesis (see item 2, below). If, after following the procedures for applying for research in the department, an on-campus research mentor cannot be found, an Honors candidate should consult with the department's class adviser to explore alternate means of meeting the requirement.

1.  Honors chemistry majors must take at least two seminars (instead of only one required for the course major). These seminars (and their associated prerequisites) will serve as two of the honors preparations in the major.

2.  Honors chemistry majors are expected to write a senior research thesis under the supervision of an on-campus research mentor. The thesis represents the third honors preparation. Preparation for a Research Thesis within an Honors Program consists of enrollment in two credits of Chemistry 180 during the senior year. Except under extraordinary circumstances, students presenting a thesis for external examination will also spend the summer between their junior and senior years on campus initiating their research project.

The Honors Exams for Majors and Preparations

The fields offered by the Chemistry and Biochemistry Department for examination by external examiners as part of the Honors Program are the topics of the 100-level seminars. The department will offer at least two of these preparations (seminars) during each academic year.

All fields in chemistry (except the Research Thesis) will be examined in three hour written examinations prepared by External Examiners. The Honors Research Thesis will be examined orally by the External Examiner chosen in that field. Honors oral exams for other preparations will be conducted by individual Examiners as well.

Acceptance Criteria

Applications are reviewed by the entire department, and decisions are made on the basis of the considered judgment of the faculty. To be admitted as a major in the Honors Program, a student must present a minimum of two courses in chemistry taken at Swarthmore College. In addition, the department looks for indications that the student will participate actively in seminars and can successfully work in an independent manner. To be eligible, no grade in the department may be below a B- and the GPA in chemistry courses should be 3.0 or higher. A student previously accepted into the Honors Program but not maintaining this GPA in chemistry courses might be, by department decision, asked to withdraw from the Honors Program.

Honors Minor in Chemistry

Requirements

The honors minor in chemistry parallels the course minor, except that the program for an honors minor must include a seminar. The seminar serves as the basis of the honors preparation.

The Honors Exam for Minors and Preparations

All of the fields available to majors are available for students wishing to minor in chemistry, with the exception of the Research Thesis. All minors must meet the same prerequisite requirements for seminars established by the Chemistry and Biochemistry Department majors.

Acceptance Criteria

Applications are reviewed by the entire department, and decisions are made on the basis of the considered judgment of the faculty. To be admitted as a minor in the Honors Program in chemistry, a student must present a minimum of two courses in chemistry taken at Swarthmore College. In addition, the department looks for indications that the student will participate actively in seminars and can successfully work in an independent manner. To be eligible, no grade in the department may be below a B- and the GPA in chemistry courses should be 3.0 or higher. A student previously accepted into the Honors Program but not maintaining this GPA in chemistry courses might be, by department decision, asked to withdraw from the Honors Program.

Special Major in Biochemistry

The biochemistry major combines work in both the Chemistry and Biochemistry Department and the Biology Department. The requirements for a biochemistry major include all the requirements for a chemistry major plus additional course work in biology.

Requirements

CHEM 010/010 HN    CHEM 022

CHEM 032                  CHEM 038

CHEM 044                  CHEM 055

CHEM 056                  CHEM 057

One biochemically related 100-level seminar in the Chemistry and Biochemistry Dept. (CHEM 106, 108 or 110)

Ancillary Requirements (prerequisites for physical chemistry):

PHYS 003 and PHYS 004/004L (or 007,008)

MATH 034 (or equivalent)

Biochemistry majors must also complete either (1) a biochemically related sophomore-level Biology course (with lab) and a biochemically related advanced Biology seminar (with lab) or (2) two biochemically related, sophomore-level biology courses (with labs).

Biochemistry-related courses offered in the Biology Department include: BIOL 010 (Genetics), BIOL 011 (Epigenetics), BIOL 014 (Cell Biology), BIOL 016 (Microbiology), BIOL 017 (Microbial Pathogenesis and the Immune Response), BIOL 020 (Animal Physiology), BIOL 022 (Neurobiology), BIOL 024 (Developmental Biology) and BIOL 025 (Plant Biology). Please note the biology prerequisites for these courses and plan accordingly.

Biochemistry-related seminars offered in the Biology Department include: BIOL 110 (Human Genetics), BIOL 111 (Developmental Genetics), BIOL 114 (Symbiotic Interactions), BIOL 115 (Plant Developmental Biology), BIOL 116 (Microbial Processes and Biotechnology), BIOL 120 (Sleep and Circadian Rhythms), BIOL 123 (Learning and Memory), and BIOL 124 (Hormones and Behavior). Please note the biology prerequisites for these courses and plan accordingly.

Acceptance Criteria

Acceptance criteria are the same as for chemistry majors.

Requirements for Honors Major in Biochemistry

The honors biochemistry major has the same set of requirements as the course biochemistry major, plus the requirement of four honors preparations in at least two departments must also be met, as follows:

  1. Topics in Bioinorganic Chemistry (CHEM 106) or Biochemistry (CHEM 108) or Biophysical Chemistry (CHEM 110).
  2. One biochemically oriented preparation from the Biology Department.
  3. A two-credit biochemically oriented Research Thesis carried out under the supervision of faculty from the Chemistry and/or Biology Departments.
  4. One additional preparation chosen from the Chemistry and Biochemistry Department or from biochemically related preparations offered by either the biology or psychology departments.

Special Major in Chemical Physics

The chemical physics major combines course work in chemistry and physics at the introductory and intermediate levels, along with some advanced work in physical chemistry and physics, for a total of between 10 and 12 credits. Laboratory work at the advanced level in either chemistry or physics is required; math courses in linear algebra and multivariable calculus are prerequisites for this work.

Requirements

In preparation for a major in chemical physics, students must complete by the end of the sophomore year: (1) CHEM 010/010 HN and 022; (2) PHYS 005, 007, 008 (PHYS 003, 004 can substitute, but the 005, 007, 008 sequence is strongly recommended); (3) further work appropriate to the major in either CHEM (044, 055, 056, and/or 057) or PHYS (014 and 050); (4) MATH 034. A chemical physics major will ordinarily include both semesters of physical chemistry (CHEM 044 and 055). A student may satisfy the requirement for laboratory work at the advanced level by completing a research thesis (CHEM 096 or 180), but in the absence of a research thesis, the major must include CHEM 057 or PHYS 082 in order to satisfy the requirement.

Example of a special major in chemical physics: CHEM 022, 044, 055, 056, 057, 105; PHYS 007, 008, 014, 050, 111, 113.

Acceptance Criteria

Acceptance criteria are the same as for chemistry majors, except that the faculty of both the chemistry and biochemistry and physics and astronomy departments are actively involved in the decision.

Requirements for Honors Major in Chemical Physics

The honors chemical physics major has the same set of requirements as the course chemical physics major, plus the requirement of four Honors Preparations in at least two departments must also be met, as follows:

  1. One preparation (seminar) chosen from the Chemistry and Biochemistry Department.
  2. One preparation (seminar) chosen from the Physics and Astronomy Department.
  3. A two-credit Research Thesis carried out under the supervision of faculty from the Chemistry and/or Physics Departments.
  4. One additional preparation chosen from the Chemistry and Biochemistry Department or from the Physics and Astronomy Department.

Comprehensive Requirements

Chemistry

The senior comprehensive requirement consists of two components.

The first component revolves around the department’s Colloquium Series. During the academic year, speakers from other institutions visit our campus and present colloquia about their research. Each speaker recommends a small amount of published background material, which students and faculty read in preparation for the visit. These materials also serve as the basis for a “preview session,” during which a small group of students presents background and context for the speaker’s research. All senior majors are required to (1) attend the preview sessions, (2) review the suggested readings, (3) participate as a presenter in at least one preview session during the year, and (4) attend the actual colloquium presentations.

The department offers two routes for satisfying the second component of the comprehensive requirement:

  1. Completion of a two-credit research thesis. The thesis must be based on research carried out during the senior year and, in most cases, the preceding summer as well. Honors majors must choose this option. Senior majors who do not write a research thesis must take a series of short exams administered throughout the academic year. These exams are based on the presentations made by speakers in the department’s Colloquium Series and the literature readings that the speakers suggest. The following regulations will govern the exams:
    1. The department will administer a minimum of 7 exams during each academic year.
    2. An exam will generally be administered during the week following a speaker’s presentation.
    3. The exams will be designed such that prepared students should be able to answer the question(s) in 60 minutes or less.
    4. Satisfactory performance on any 4 of the exams constitutes completion of this component of the comprehensive requirement.

Finally, all students must attend at least one safety training session before the beginning of the senior year. These are offered one time per semester during the academic year and one time during the summer research session.

Biochemistry

The comprehensive requirement for biochemistry majors is the same as for chemistry majors.

Chemical Physics

The comprehensive requirement for chemical physics majors is the same as for chemistry majors. Occasionally, however, and on a case-by-case basis, the department is willing to negotiate a “hybrid” colloquium series for students completing a chemical physics special major. In consultation with both departments (chemistry and biochemistry and physics and astronomy), the student may draw up a list of colloquia pertinent to the special major and taken partly from the colloquium series of each department, and then participate in only these colloquia. However, in no event will the total number of talks for the year amount to fewer than the number of colloquia scheduled for the Chemistry and Biochemistry series.

Advanced Placement/International Baccalaureate Credit

Students with a score of 5 on the Chemistry AP exam (taken their junior year in high school or later) or a score of 6 or 7 on the Higher Chemistry IB exam can place into Foundations of Chemical Principles – Honors (Chemistry 010 HN). Students can use the Chemistry Placement Exam to place into Chemistry 010 HN in the absence of an AP/IB score.

Transfer Credit

It is sometimes possible to receive Swarthmore credit for chemistry courses taken at other colleges and universities, provided that they were taken after the student matriculated at Swarthmore. If you wish to take a chemistry course on another campus and to receive Swarthmore credit for doing so, it is essential that you follow the proper procedure and that you plan in advance. It is also important to realize that not all courses will be eligible for credit. See the department website for details.

Off-Campus Study

The Chemistry and Biochemistry Department is eager to accommodate the study abroad aspirations of chemistry and biochemistry majors. However, substantial advance planning is required and interested students are encouraged to plan their Sophomore Plan carefully and consult with their academic adviser.

Research

The Chemistry and Biochemistry Department offers opportunities for students to engage in collaborative research with faculty members. Each fall semester, the department hosts a series of short presentations by faculty members, outlining the research projects available. This meeting, normally held in November, serves as the starting point for student participation in research during the following summer and/or academic year.

Academic Year Opportunities

The Department of Chemistry and Biochemistry offers three ways for students to engage in supervised research for academic credit, during the academic year:

  1. CHEM 094 (research project). Students may enroll in this course for either a half credit or a full credit. A half credit implies a time commitment of 5–7 hours per week, while a full credit implies a time commitment of 10–15 hours per week.
  2. CHEM 096 (research thesis). A full year (two credits) of CHEM 096 corresponds to a research thesis for course majors.
  3. CHEM 180 (honors research thesis). A full year (two credits) of CHEM 180 corresponds to a research thesis for honors majors.

All students who enroll for at least one full credit of research during an academic year are required to participate in the department’s Colloquium Series and present a poster sometime during the academic year.

Research Conducted in Other Departments

Students writing a research thesis as part of their plan to satisfy the comprehensive requirement in a chemistry, biochemistry, or chemical physics major (see above) sometimes elect to carry out their research with a faculty member in an allied department, such as biology, physics and astronomy, or engineering. In general, such students have two options for how to register for courses corresponding to the thesis:

Option 1:   Use the appropriate chemistry courses (two credits of CHEM 096 for a course thesis, or two credits of CHEM 180 for an honors thesis).

Option 2:   Use the course designations appropriate to the department in which the research is conducted. For research conducted with a biology faculty member, for instance, a student might enroll in one credit of BIOL 180 and one credit of BIOL 199 over the course of the senior year. The thesis must ultimately consist of at least two full credits.

American Chemical Society Certification

Certification by the American Chemical Society (ACS) requires a second seminar and a research thesis through a full year of CHEM 096 or 180 (in addition to the minimum chemistry major).

Courses

CHEM 001. Chemistry in Context: Applying Chemistry to Society

This course covers a series of real-world issues with significant chemical content. Topics will be drawn from areas such as environmental chemistry, energy sources, materials, and human health. The course seeks to develop in students the ability to make informed decisions about issues that intersect with technology. Students may not receive credit for CHEM 001 if they have previously received credit for CHEM 010 or CHEM 010 HN.
One laboratory period every second week.
Natural sciences and engineering practicum.
Eligible for ENVS program.
1 credit.
Not offered 2014–2015.

CHEM 010. Foundations of Chemical Principles

Building upon a student’s high school introduction to chemistry, a study of the general concepts and basic principles of chemistry, including atomic and molecular structure, bonding theory, molecular interactions, and the role of energy in chemical reactions. Applications will be drawn from current issues in fields such as environmental, biological, polymer, and transition metal chemistry. CHEM 010 is the normal point of entry for the chemistry and biochemistry curriculum.
One laboratory period weekly.
Natural sciences and engineering practicum.
1 credit.
Fall 2014. Sarver, Welch.

CHEM 010 HN. Foundations of Chemical Principles - Honors

Topics will be drawn from the CHEM 010 curriculum but discussed in greater detail and with a higher degree of mathematical rigor. Special emphasis will be placed on the correlation of molecular structure and reactivity, with examples drawn from such fields as biological, transition metal, organic, polymer, and environmental chemistry. Some familiarity with elementary calculus concepts will be assumed.
Can only be taken as either a first or second year student.
One laboratory period weekly.
Prerequisite: Strong performance on the Departmental Placement Exam.
Natural sciences and engineering practicum.
1 credit.
Fall 2014. Rablen.

CHEM 022. Organic Chemistry I

An introduction to the chemistry of some of the more important classes of organic compounds; nomenclature, structure, physical and spectroscopic properties; methods of preparation; and reactions of aliphatic and aromatic hydrocarbons, halides, and monofunctional oxygen compounds, with an emphasis on ionic reaction mechanisms.
One laboratory period weekly.
Prerequisite: CHEM 010 or CHEM 010 HN.
Natural sciences and engineering practicum.
1 credit.
Spring 2015. Rablen.

CHEM 032. Organic Chemistry II

A continuation of CHEM 022 with emphasis on more advanced aspects of the chemistry of monofunctional and polyfunctional organic compounds, multistep methods of synthesis, and an introduction to bio-organic chemistry.
One laboratory period weekly.
Prerequisite: CHEM 022.
Natural sciences and engineering practicum.
1 credit.
Fall 2014. Paley.

CHEM 038. Biological Chemistry

An introduction to the chemistry of living systems: protein conformation, principles of biochemical preparation techniques, enzyme mechanisms and kinetics, bioenergetics, intermediary metabolism, and molecular genetics.
One laboratory period weekly.
Prerequisite: CHEM 032.
Natural sciences and engineering practicum.
1 credit.
Spring 2015. Miller.

CHEM 044. Physical Chemistry: Atoms, Molecules and Spectroscopy

A quantitative approach to the description of structure in chemical and biochemical systems. Topics will include introductory quantum mechanics, atomic/molecular structure, a range of spectroscopic methods and statistical mechanics. Systems of interest will range from gas-phase single molecules to condensed-phase macromolecular assemblies.
One laboratory period weekly.
Prerequisites: CHEM 010/010 HN; CHEM 022; MATH 25 (or equivalent); and PHYS 003 and 004 (or 003, 004L, or 007, 008). Prior enrollment in MATH 034 (or equivalent) is recommended.
Natural sciences and engineering practicum.
1 credit.
Fall 2014. Howard.

CHEM 055. Physical Chemistry: Energy and Change

A quantitative approach to the role that energy and entropy play in chemical and biochemical systems. Topics include states of matter, the laws of thermodynamics, chemical equilibria, electrochemistry, the thermodynamics of solutions and phases and chemical kinetics/dynamics. Examples will be drawn from both real and ideal systems in chemistry and biochemistry.
Prerequisites: CHEM 010/010 HN; PHYS 003, 004 (or 003, 004L or 007, 008) and MATH 034 (or equivalent).
1 credit.
Spring 2015. Sarver.

CHEM 056. Inorganic Chemistry

A study of the structure, bonding, and reactivity of inorganic compounds with emphasis on the transition metals. Included in the syllabus are discussions of crystal and ligand field theories, organometallic chemistry, and bioinorganic chemistry.
Prerequisites: Four prior semesters of college chemistry.
1 credit.
Spring 2015. Welch.

CHEM 057. Advanced Integrated Experimental Chemistry

Integrated experimental projects incorporating analytical, inorganic, physical, and biochemistry methods. In the absence of extenuating circumstances, it is strongly recommended that this course be taken as a junior.
Prerequisites: CHEM 044; CHEM 056 must have already been completed or taken as a co-requisite.
Natural sciences and engineering practicum.
1 credit.
Spring 2015. Howard, Welch.

Seminars

Students should note that completion of CHEM 010/010 HN, 022, and one semester of a 40-level or 50-level course constitute a minimum set of prerequisites for enrollment in any Chemistry and Biochemistry Department seminar. In unusual circumstances, the department will consider whether completion of work of comparable sophistication in another department can substitute for the requirement that a 40-level or 50-level chemistry course be completed prior to enrollment in a seminar. Individual seminars carry additional prerequisites, as listed here.

CHEM 102. Topics in Organic Chemistry

This course will address selected advanced topics of current interest in the field of synthetic organic chemistry. Material will largely be drawn from the current research literature and will likely include such topics as the applications of stoichiometric and catalytic organometallic chemistry, the control of relative and absolute stereochemistry, the use of “organocatalysts,” and carbohydrates. The total synthesis of architecturally challenging natural products will serve to highlight the application of these technologies.
Additional prerequisites: CHEM 032 and CHEM 044, 055 or 056.
1 credit.
Spring 2015. Paley.

CHEM 105. Quantum Chemistry and Spectroscopy

Advanced consideration of topics in quantum mechanics including the harmonic oscillator, angular momentum, perturbation theory, and electron spin. These concepts, along with molecular symmetry and group theory, will be applied to the study of atomic and molecular spectroscopy.
Additional prerequisites: CHEM 044, MATH 34 (or equivalent). Some familiarity with linear algebra will be useful.
1 credit.
Not offered 2014–2015.

CHEM 106. Topics in Bioinorganic Chemistry

This seminar will start with a brief review of the basic principles of inorganic and biological chemistry as well as an overview of relevant biophysical techniques. Materials will be drawn largely from the primary literature. Students will be challenged to read and evaluate scientific papers critically. The main topics of this course will have to do with the function and coordination of metals in biological systems: important cofactors and metal clusters that carry out catalysis and electron transfer reactions, metal homeostasis, metals in medicine, and the importance of inorganic model compounds to understand the function of biological systems.
Additional prerequisites: CHEM 038 and CHEM 056.
1 credit.
Not offered 2014–2015.

CHEM 108. Topics in Biochemistry

Physical methods used to study high-resolution biomacromolecular structure will be discussed, using examples from the primary literature. Techniques used to measure the forces stabilizing intramolecular and intermolecular interactions and their application to proteins will be included.
Additional prerequisites: CHEM 038, CHEM 044 or 055.
1 credit.
Fall 2014. Miller.

CHEM 110. Topics in Biophysical Chemistry

An introduction to the interdisciplinary field of biophysical chemistry in which biological systems are explored using the quantitative perspective of the physical scientist.
Additional prerequisites: CHEM 038, CHEM 044 or 055.
1 credit.
Not offered 2014–2015.

Student Research

All students who enroll in one or more research courses during the academic year are required to participate in the department’s colloquium series and present the results of their work at a poster session during the academic year.

CHEM 094. Research Project

This course provides the opportunity for qualified students to participate in research with individual faculty members. Students who propose to take this course should consult with the faculty during the preceding semester concerning areas under study. This course may be elected more than once. Students may enroll in this course for either a half credit or a full credit. A half credit implies a time commitment of 5–7 hours per week, while a full credit implies a time commitment of 10–15 hours per week.
0.5 or 1 credit.
Each semester. Staff.

CHEM 096. Research Thesis

Chemistry and biochemistry majors will be provided with an option of writing a senior research thesis as part of their comprehensive requirement. Thesis students are strongly urged to participate in on-campus research during the summer between their junior and senior years. A minimum of 2 credits of CHEM 096 must be taken during the last three semesters of the student’s residence at Swarthmore.
1 credit.
Each semester. Staff.

CHEM 180. Honors Research Thesis

An opportunity for students in the External Examination Program to participate in research with individual faculty members. The thesis topic must be chosen in consultation with a member of the faculty and approved early in the semester preceding the one in which the work is to be done. A minimum of 2 credits of CHEM 180 must be taken during the last three semesters of the student’s residence at Swarthmore.
1 credit.
Each semester. Staff.