avila@chem.columbia.eduRoom: Chandler 455Phone #: (212)854-8587Columbia UniversityDepartment of Chemistry

Tentative Class Schedule:WEEK DATE

T - RREADING MATERIAL ACTIVITIES / TOPIC

1 1/20 - 1/22 Chapters 1 and 2 Course introduction / Measurement2 1/27 - 1/29 Chapters 3 and 4 Matter and energy. Atoms and elements3 2/03 - 2/05 Chapters 5 and 6 Atomic Theory. Nomenclature

4 2/10 - 2/12 Chapter 7 and 8 Chemical composition. Chemical reactions5 2/17 - 2/19 Chapters 9 and 10 Stoichiometry. Atoms and the Periodic Table6 2/24 - 2/26 Chapters 11 Periodic Table. Chemical bonding

7 3/02 - 3/04 Chapter 12 Gases8 3/09 - 3/11 Chapters 1 through 11. Midterm review / MIDTERM

3/16 - 3/18 SPRING BREAK9 3/23 - 3/25 Chapter 13 Water, liquids and intermolecular forces

10 3/30 - 4/01 Chapter 14 Solutions11 4/06 - 4/08 Chapter 16 Chemical equilibrium12 4/13 - 4/15 Chapters 15 Acids, bases, and salts

13 4/20 - 4/22 Chapters 17 Oxidation and reduction14 4/27 - 4/29 Chapter 12 through 17 Oxidation and reduction. Final Review

5/04 Final Examination

What Does a Chemist Do?

• Studies the atomic composition and structural architecture of substances

• Investigates the varied interactions among substances

• Utilizes natural substances and creates artificial ones

• Comprehends the marvelous and complex chemistry of living organisms

• Provides a molecular interpretation of health and disease

Main Divisions of Chemistry

Organic Chemistry

Inorganic Chemistry

Physical Chemistry

Analytical Chemistry

Industrial Chemistry(Chemical Engineeringand Applied Chemistry)

Biochemistry

How Does S(He) do it?

Materials Chemistry

Environmental Chemistry

Forensic Chemistry

What is Organic Chemistry?

Physical Organic Chemistry

Largest area of specialization among the various fields of chemistry

Synthetic Organic Chemistry

• Pharmaceutical Chemistry

• Pulp and Paper Chemistry• Dye and Textile Chemistry

• Formulation Chemistry (paint, food, petroleum products, adhesives, etc.)

• Agricultural Chemistry

• Polymer Chemistry

Concerned with the correlation of the physical and chemicalproperties of compounds with their structural features.

We are primarilyengaged in theinvention and

development ofstereoselective catalytic reactions and the total

synthesis ofbiologically active andstructurally complex

natural products

Synthetic Organic Chemist: Professor James Leighton

Among our areas of current interestin the anticancer field are epothiloneand eleutherobin. While structurallydiverse, these two compounds seem tofunction by a taxol-like mechanism intheir ability to inhibit microtubuledisassembly.Several projects are addressed to goalsystems with immunochemicalimplications. Here we areparticularly concerned with theconstruction of a carbohydrate-basedtumor antigen vaccine.Synthetic Organic Chemist /

Bioorganic Chemist:Professor Samuel Danishefsky

In most cases this involvesinvestigating the interactionof small molecules with theirbiopolymeric receptors. Therecent dramatic advancementin isolation, purification andmicrospectroscopic methodshas made it possible forchemists to become involvedin such studies on amolecular structural basis

Natural Products’ Chemist : Professor Koji Nakanishi

We deal with structural aspects of bioactive compoundsand elucidation of their mode of action.

We view the photon as a reagent for initiating photoreactions and asa product of the deactivation of electronically excited molecules.

Physical Organic Chemist / PhotochemistMaterial Chemist:

Professor Nicholas Turro

Our group is developing a novel fieldtermed "supramolecular"photochemistry, or photochemistrybeyond the conventional intellectual andscientific constraints implied by the term"molecule". In supramolecularprocesses non-covalent bonds betweenmolecules play a role analogous to thatof covalent bonds between atoms.

What is Inorganic Chemistry?Deals with the properties of elementsranging from metals to non metals

• Organometallic Chemistry

• Bioinorganic Chemistry

• Ceramics and Glass

• Semiconductors

Organometallic Chemist / X-raySpectroscopist:

Professor Gerard Parkin

Zinc is a constituent of more than300 enzymes. The active sites ofthese enzymes feature a zinc centerattached to the protein backbone bythree or four amino acid residues,the nature of which influences thespecific function of the enzyme. Inorder to understand why differentzinc enzymes utilize different aminoacid residues at the active site, it isnecessary to understand how andwhy the chemistry of zinc ismodulated by its coordinationenvironment. Answers to thesequestions are being provided by astudy of small molecules thatresemble the enzyme-active sites.

Bio-organic Chemist : Professor Ronald Breslow

http://www.oit.doe.gov/cfm/fullarticle.cfm/id=743

In our major effort we are trying to prepare artificial enzymesthat can imitate the function of natural enzymes.

A related study involves thesynthesis of mimics ofantibodies or of biologicalreceptor sites, constructingmolecules that will bind topolypeptides with sequenceselectivity in water, usingmainly hydrophobicinteractions. These couldbe very useful in modulatingthe activity of peptidehormones, for instance.

Measures, correlates, and explains thequantitative aspects of chemical processes

What is Physical Chemistry?

• Theoretical ChemistryDevoted to Quantum and Statistical Mechanics. Theoretical chemists use

computers to solve complicated mathematical equations that simulatespecific chemical processes.

• Chemical Thermodynamics Deals with the relationship between heat, work, temperature,

and energy of Chemical systems.

• Chemical Kinetics Seeks to measure and understand the rates of chemical reactions.

Physical Chemistry

•Electrochemistry

Investigates the interrelationship between electric current and chemical change.

•Photochemistry, Spectroscopy Uses radiation energy to probe and induce change within matter.

•Surface Chemistry Examines the properties of chemical surfaces, using

instruments that can provide a chemical profile of such surfaces.

My research is concerned with structural and dynamicprocesses in condensed phase systems and biomacromolecularsystems.

Theoretical Chemist: Professor Bruce Berne

Because the systems studied areoften complex many-bodysystems, it is necessary to utilizethe powerful analytical methodsof statistical mechanics as well asstate-of-the-art methods ofcomputer simulation involvingmolecular dynamics and MonteCarlo techniques.

My research is materials,surfaces and nanocrystals,especially in relation tooptical and electronicproperties. This work caninclude theoreticalmodeling, experimentalchemical physics, andsynthetic chemistry. We tryto understand the evolutionof solid state properties frommolecular properties, and tocreate new materials withnanoscale structure by bothkinetic and thermodynamicself-assembly methods.

Materials Chemist: Professor Louis Brus

We investigate molecularcollisions that lead either tochemical reaction or to theexchange of energy betweenmolecules. In particular, wehave developed the infrareddiode laser absorption probetechnique to investigatecollisions between molecules.

Experimental Physical Chemist: Professor George Flynn

We also study the structure of moleculesadsorbed on surfaces by using theScanning Tunneling Microscope (STM).

What is Analytical Chemistry?QUALITATIVE ANALYSISDeals with the detection of elements or compounds (analytes) indifferent materials.

QUANTITATIVE ANALYSISRefers to the measurement of the actual amounts of the analyte presentin the material investigated.

Chemical and Biochemical Methods•Gravimetry

•Titrimetric Analysis

•Enzymic Analysis

•Inmunochemical Analysis

Analytical Chemistry

•Nuclear Magnetic Resonance (NMR)

•Electron Spin Resonance (ESR)

•Mass Spectrometry (MS)

•Vibrational Spectroscopy (IR, RAMAN)

•X-Ray Fluorescence Analysis (XPS)

•Electronic Spectroscopy (UV, VIS, Luminiscence)

•Atomic Spectroscopy (AA, ICP)

•Rotational Spectroscopy (Microwave, FIR)

• Atomic and Molecular Spectroscopic Methods

Analytical ChemistryChromatographic Methods (Partition equilibrium)

•Gas Chromatography (GC)

•High Performance Liquid Chromatography (HPLC)

•Gel Permeation Chromatography (GPC)

•Thin Layer Chromatography (TLC)

•Ion Chromatography

Analytical Chemistry

•Electrogravimetry

•Electrophoresis

•Conductimetry, Potentiometry

•Polarography

•Voltammetry

• Electrochemical Methods

• Thermal Methods•Thermogravimetry (TG)

•Differential Thermal Analysis (DTA)

•Differential Scanning Calorimetry (DSC)

•Thermomechanic Analysis (TMA)

We study enzyme mechanisms using NMR. A variety of experimentsallow us to probe structural details,dynamics or chemical details suchas protonation states.

Biophysical Chemist / NMR Spectroscopist: Professor Ann McDermott

In photosynthetic reactioncenters, light energy isconverted to chemicalpotential energy throughlong-range electron transferevents. A wealth ofcrystallographic, mutagenic,and spectroscopic work onthese centers still leavesimportant mechanisticquestions unanswered.

The Tools of the Trade

Periodic Table of the Elements

Ag

Na

Li

Fr

Cs

Rb

K

Be

Ca

Mg

Ra

Ba

Sr

Sc

La

Y

Ac

Ti

Hf

Zr

Rf

V

Ta

Nb

Ha

Cr

W

Mo

Sg

Mn

Re

Tc

Bh

Fe

Os

Ru

Hs

Co

Ir

Rh

Mt

Ni

Pt

Pd

Cu

Au

Zn

Hg

Cd

Ga

Al

Tl

In

Pb

Sn

Bi Po

B

Ge

Si

As

Sb Te

At

H

C N

P

O

Se

S

F

Br

Cl

I

Ne

Kr

Ar

Rn

Xe

He

Ce

Th

Pr

Pa

Nd

U

Pm

Np

Sm

Pu

Eu

Am

Gd

Cm

Tb

Bk

Dy

Cf

Ho

Es

Er

Fm

Tmi

Md

Yb

No

Lu

Lr

47

11

3

87

55

37

19

4

20

12

88

56

38

21

57

39

89

22

72

40

104

23

73

41

105

24

74

42

106

25

75

43

107

26

76

44

108

27

77

45

109

28

78

46

29

79

30

80

48

31

13

8l

49

82

50

83 84

5

32

14

33

51 52

85

1

6 7

15

8

34

16

9

35

17

53

10

36

18

86

54

2

58

90

59

91

60

92

61

93

62

94

63

95

64

96

65

97

66

98

67

99

68

100

69

101

70

102

71

103

The Tools of the Trade

Periodic Table of the Elementshttp://www.spectroscopynow.com/Spy/tools/periodic.html

Interesting Applications

The KSC-ALS Breadboard Project

• Uses biological systems to recycle material through a ALS (Advanced LifeSupport) system. Humans take in oxygen, food and water, and expelcarbon dioxide and organic waste. Plants utilize carbon dioxide, producefood, release oxygen, and purify water. Inedible plant material and humanwaste are degraded by microorganisms to recycle nutrients for plants in aprocess termed resource recovery.

• produce food

• purify their water supply and

• create oxygen from the carbon dioxide they expel.

When humans establish permanent bases on the Lunar surface ortravel to Space for exploration, they need to develop systems to:

Physico-chemical processes can perform the two latter tasks,but only biological processes can perform all three.

• A life support system that would perform these regenerative

functions, whether strictly by biological means or by a

combination of biological and physico-chemical methods, has

been called a Controlled Ecological Life Support System

(CELSS).

• Biological systems utilize plants and microorganisms to perform these life support tasks in a process termed bioregeneration.

A CELSS is a tightly controlled system, using crops to perform life supportfunctions, under the restrictions of minimizing volume, mass, energy, and labor.