Petroleum Engineering

The importance of chemical principles

The following content is provided under a Creative

Commons license.

Your support will help MIT OpenCourseWare continue to

offer high quality educational resources for free.

To make a donation, or view additional materials from

hundreds of MIT courses, visit MIT OpenCourseWare at

ocw.mit.edu.

PROFESSOR: Welcome to 5.111, and today what we're going to

do is introduce you to the course and the people teaching

the course.

And we're also going to let you know that you were going

to be part of the great web exercise that is OCW,

OpenCourseWare.

So, this course is being videotaped this year, and this

is the announcement that I have to make.

So, the videotape is in the back, and if you want to come

up front and participate in the class, you know that

you'll be videotaped -- if you want to hide your face or

whatever, you can do that but please pay attention to the

lectures anyway.

So, this course will be available on the OCW site in

the future, I'm not sure exactly what that date is

going to be.

So, today we're going to introduce the chemistry

topics, which we will cover in 5.111, and give you general

information, practical information about the course

number of points you need, when the exams are, that kind

of thing, policies, and introduce you to

the teaching staff.

I am, again, Professor Cathy Drennan, and I'm one of the

lecturers in this course.

So, because this is MIT, we're going to start to quiz.

OK, not a quiz for points or anything, don't freak out, but

I do want you to tell me who these people are.

So, what about this person?

That's me -- this is my college yearbook photo.

OK, what about this person over here?

STUDENT: You?

PROFESSOR: It's not me again.

Not Elizabeth Taylor.

It is Lisa Kudrow, known as Phoebe on "Friends." So, we

both went to college at the same time, we

went to the same college.

Does anybody know what college that was?

STUDENT: Vassar.

PROFESSOR: Vassar College, very good.

And we graduated the same year -- now no one has to say what

year that was, even if you know, but we did

graduate the same year.

All right.

So, given what you know about us, what do you think Lisa

went to college to study?

STUDENT: Computer?

PROFESSOR: Computers?

No.

STUDENT: Theatre?

PROFESSOR: Theatre?

Surprisingly, no.

STUDENT: Nuclear Engineering?

PROFESSOR: Nuclear Engineering at Vassar, no for

a variety of reasons.

Any other guesses?

STUDENT: English?

PROFESSOR: English, no.

Biology --

I heard it.

Biology.

What do you think I went to college to study?

STUDENT: Theatre.

PROFESSOR: Theatre, correct!

And/or I hadn't made up my mind exactly --

biopsychology or drama.

So, biopsychology was what they called sort of brain and

cognitive sciences in those days.

So, those were the two things I was thinking about.

What do you think Lisa ended up majoring in college?

STUDENT: Biopsychology.

PROFESSOR: Not biopsychology.

STUDENT: Biology.

PROFESSOR: Biology, yes.

What do you think I majored in college?

This should be a bit easier.

STUDENT: Chemistry.

PROFESSOR: Chemistry, And, of course, our professions,

actress and chemistry professor.

So, let me ask what happened here?

My understanding about Lisa Kudrow is that she came from a

Hollywood family.

She went to college and said here's my opportunity to study

the thing that I find most interesting, and that was

biology, and then she went back and participated in the

family business, which was of course the acting profession.

For me, what happened?

Well, I have to say, I did not like chemistry in high school,

so I did not think about going to college to study chemistry.

So, why did I not like chemistry in high school?

I think it was because of images such as this one.

You spend a lot of time talking about the transition

between alchemy and modern chemistry.

I wasn't very interested in that kind of thing, and

there's nothing in these photographs that really

appealed to me personally.

I mean, Avogadro --

I'm fond of his number, and he is, in fact, an interesting,

if not frightening looking man -- this just didn't

connect with me.

But then I got to college and they said, "Well, if you're

thinking about anything bio -- biopsychology, biology -- you

have to take chemistry." And I said to my advisor, "No, no.

I have taken chemistry in high school, and I can assure you

that chemistry has no relevance whatsoever to the

life sciences." And they said, "Well, I'm sorry you feel that

way, it's incorrect, and you have to take it anyway."

So, I, like some of you in this room, took freshman

chemistry, because we had to, not because we wanted to.

And I, like hopefully some of you in this room, discovered

that chemistry was actually a lot of fun, and that the

chemistry I got in college was pretty much nothing like the

chemistry I had seen in high school.

So, let me introduce you to some of the topics we are

going to be covering in chemistry this semester.

So, there's more detail on your syllabus -- a detail of

what we'll cover every day, but these are the kind of

basic things that were covering, and you don't need

to write this down, you'll become familiar with it as the

semester goes on.

We start out with some really basic principles.

So, up here, atomic theory, periodic table, bonding,

structures and molecules.

And there will be a little bit of history in there, but this

is mostly modern chemistry and represents the basic

properties of matter, and it's basic properties of all

matter, including living matter, which was what really

interested me, that connection between chemistry and biology.

So, then we go to thermodynamics and chemical

equilibrium, and this is really about chemical

reactions -- weather a reaction will go, will it be

spontaneous, if there an equilibrium, what direction

will the reaction be shifted in.

And then, of course, not just whether the reaction will

occur but, how fast it occurs is really important.

So, that's kinetics -- how fast a reaction will go, and

from the perspective of someone who's a biochemist,

I'm interested in kinetics and enzyme kinetics, and thinking

about molecules that catalyze reactions in the body.

And then, there's acid base equilibrium, and also

oxidation reduction reactions, and what is true is that most

reactions that occur are either catalyzed by either

some kind of acid base catalysis or involve some kind

of oxidation reduction reaction, and so, this sort of

represents a lot of the basic way reactions go -- now,

whether that's a reaction in your body or a reaction in a

test tube -- it doesn't matter, a lot of the same

principles are involved.

And then, we also cover transition metals, which is

something that you often don't see in high school.

And transition metals, those all medals in the middle of

your periodic table, have some really unique properties,

which are exploited again in reactions that occur in your

body, and also are utilized in industry, for example, so

we'll talk about some of those unique properties.

And if we put all of that together, we get the real

fundamentals that you need to go on and study -- any kind of

curriculum that involves chemistry.

So, these are all the fundamentals that are involved

in chemistry that relate to physical chemistry, organic

chemistry, inorganic chemistry, biological

chemistry, and are a solid foundation for studying any

kind of life science.

So, I congratulate you of being here in this class, this

is really good solid foundation for whatever you go

on to do, here at MIT.

So, normally at this point, we do actually start class with a

little bit of history from alchemy to modern chemistry,

but I decided to skip that this year.

If you are interested in that, it's never required on any

test, it never has been, but if you're interested in that

there is an OCW lecture, which you can listen to that's an

excellent lecture by Professor Sylvia Ceyer on that.

But today instead, I thought I would give you some examples

of modern chemistry -- why people now need to know

chemistry, what they're doing with chemistry, what is

chemistry research here at MIT, and how does it utilize

these basic principles, which we'll be talking

about in the course.

So, I'll start with my colleague,

Professor Joanne Stubbe.

She studies molecules, in particular she studies

biological molecules.

And, so one of the things she's very interested in is

how this anti-cancer drug, gemcitabine,

works in the body.

So, it inhibits an enzyme, and she's interested in knowing

how that really works.

So, enzymes are made up of amino acids, you have long

chains of amino acids that form together into a protein

molecules, protein molecules in your body often act as

enzymes, catalyzing reactions.

So, she is interested in how this molecule, gemcitabine,

inhibits an enzyme.

So, to do those studies, she needs to know a lot of the

stuff on this list.

Of course, she needs to know the basic principles, but

she's also talking about it an enzyme, so she needs to know

about enzyme catalysis.

She needs to know this enzyme works by both acid base

chemistry, and oxidation reduction.

It has two irons that are involved in doing the

chemistry, so it includes transition metals.

She thinks about how things bind, how the natural

reactants binds, how the inhibitor binds, and so she

needs to know what happens to the chemical equilibrium, she

needs to know about the thermodynamics of those

binding events, and, of course, everything, all the

basic principles, are required here.

So, to do this biochemistry research, she needs to know

all of these things, and she has really made tremendous

progress in understanding how gemcitabine works, and it is

not so toxic, so it's a really good thing to have in

chemotherapy.

So, in addition to studying molecules, chemists often want

to make molecules, such as Tim Jamison,

who's an organic chemist.

So, you will hear, probably, hopefully, in this

presidential debate about the environment and about why

saving the environment is important.

And one of the things you often hear about in this

discussion is about our oceans and about rainforests, and

part of the reason why people want to protect those areas is

because you find a lot of natural

products in those regions.

So, a natural product is something that is made by

nature, and often natural products, whether it comes

from a plant or a marine organism have some really

good, useful properties.

And so, one particular compound has anti-tumor

properties.

So, again, along this line of cancer research.

So, Tim Jamison's lab figured out how to make this thing.

And often that's really important, because you can't

get enough of the organism that naturally makes it, to be

able to grind that organism up and have enough that you can

actually use as a medicine.

So, you have to make more of it, because nature doesn't

make enough.

So, it's very important to figure out how to do that.

So, in doing that, Tim Jamison's lab needs a lot of

these things.

So, he needs a lot of knowledge of bonding, he wants

to form bonds in making this.

He needs to know about the structures of the molecules,

because if the structure is wrong it's not going to work.

And often, if you want to make a lot of it, you have to think

about the thermodynamics of the system, how fast the

reactions will go and kinetics, and then whether

they'll go, the thermodynamics, and sometimes

then you need to adjust the reactions, maybe use a

transition metal to make it go better.

So, these are all the things that Tim Jamison needs to know

to do organic chemistry.

So, you'll be learning in this class a great preparation for

512, which is organic chemistry.

In addition to studying molecules and making

molecules, some chemists want to detect molecules, and a

chemist who likes to detect molecules is Tim Swager.

So, Tim Swager's lab has designed sensors that detect

vapors, and so they will detect TNT, for example.

And so, he has put this chemistry to use in this

robotic arm and they call it Fido, because often dogs are

the creatures that have to go out and detect these things,

and it's not a great job if you're a dog to be sent out to

see whether there was an explosive and discover yes,

there was, a little bit too late.

So, this is a much nicer way to detect chemicals with this

robotic arm, and here's a picture of it in use in Iraq.

So, in doing this, if you go down to kind of a basic

principles that Tim needed to know about, oxidation

reduction was really key in developing this technology, so

we'll talk about that.

So, my final example is from Alan Davidson's lab, and Alan

is an inorganic chemist -- he loved those transition metals

and they're unique properties, and he designed this compound,

it's called Cardiolite, and it's used in heart imaging.

So, many people have relatives they know of that have had to

have their heart imaged -- heart disease is a major

problem in the United States, and there's a good chance that

they had Cardiolite given to them to help in

that imaging process.

So, this again, takes advantage of those great

unique properties of transition metals, which we'll

talk about in this course.

So, again, all together, this is the basis for modern

chemistry, and examples I just gave you, are some of the

things that modern chemists are working on -- some of the

issues that our country faces and our world faces, and how

chemistry is involved in that.

So, not only will you have the fundamental knowledge to go on

and take more courses in chemistry, you will also have

the fundamental knowledge to go on and do undergraduate

research here, and here are some of the 5.111

undergraduate researchers that have come through my lab, in

particular, from this class.

So, it's a really nice solid foundation.

So, I want to encourage you to set some of your likes and

dislikes from high school aside when you come to MIT,

because at MIT you often see disciplines taught and

emphasize a very different fashion than

what you've seen before.

And you may discover that the thing you came here to study

is not the thing that you really want

to study after all.

One other thing that I'll say to you is that I said these

words at one point, it's true, I said, when I was in high

school, I said, "I hate chemistry." And now, I do

chemistry every day and will for the rest my life.

I love chemistry now.

Be very careful what you say.

Have any of you made that statement

about hating a subject?

Tell me later what it is you're going to be doing for

the rest of your life.

So, at MIT things are very different, and keep an open

mind, explore new areas -- take advantage of being at

this amazing place for science and technology and you may

surprise yourself in what you really enjoy learning about.

So, that's a little bit about the chemistry that we're going

to cover in this class, and now I'm going to talk a little

bit about some of the policies and procedures.

But first I need to introduce my co-instructor for this

class, and let me just put up her picture, you'll

see her in a minute.

So, Dr. Beth Vogel Taylor.

So, all chemistry courses are team taught, so you have a

different lecturer for the first half than the second

half, and Dr. Taylor will be doing most of the first half

lectures, and I'll be doing most of

the second half lectures.

So, Dr. Taylor will take you from atomic theory through

thermodynamics, and I'll start up with chemical equilibrium,

talk to about kinetics, acid base, oxidation reduction and

transition metals.

So, you will have both of us as lecturers in this class.

Now, in the past, sometimes students have found this whole

thing a little frustrating, that they just get used to one

lecture style, and then all of a sudden there's another

lecture style, and that can be true.

I mean sometimes the styles of the two professors couldn't be

more different -- think McCain/Palin, odd couples.

Sometimes they're more similar, and when I first,

about a year and a half ago, got to know Dr. Taylor, we

sort of realized that we had very similar styles, and we

got very excited about the idea that we could teach

together, so that there would be much more continuity

throughout the semester.

And so, Dr. Taylor had been teaching the first half of the

material in the Spring, and I had been teaching the second

half of the material in the Fall, and we thought wouldn't

it be great if we got together and taught in the Fall.

So, this was actually, for a variety of reasons, a very

complicated thing to request and do, and so we started a

campaign and campaigned for a year and a half that we should

be allowed to do this course together, and finally just a

few weeks ago in August -- we really didn't know up until

almost when this course started -- that

permission was granted.

So, I have to say, I am very excited now to introduce you

to Dr. Taylor, who I would be teaching with this semester --

limited engagement -- who will tell you about some of the

course policies.

PROFESSOR: Okay, so before we get to some of these course

policies, I think I'll tell you a little bit about my path

to chemistry as well.

Professor Drennan explained that not everyone that ends up

as a chemist started off that way on their first class

freshman year, for example, in chemistry.

And in fact, if you talk to a lot of chemists, if you talk

to some of the graduate students, maybe your TA,

you'll find that that phrase, "I hate chemistry," has maybe

been uttered by more than one us at some point in our lives

before we realized, and once it happens you don't go back,

that actually you love chemistry and it's hard to

even remember a point where you didn't see all of these

connections that it provided for you.

To give a little background of where I was, sitting where

maybe you are today on the first day of chemistry, when I

left high school, I had no interest in chemistry

whatsoever.

And I have only one strong memory from high school

chemistry, and that memory is shown right here, and that is

the common ions.

Did you guys have to learn the common ions?

Does anyone have that in their brain somewhere for ready use?

I don't, in fact, so it's actually okay if you don't

know all your common ions, if you missed that part.

This is the strongest memory I have, and I remembered a) that

I didn't learn them, and that was really bad because it kept

coming up, but the other thing I remember is that I had no

idea why they were important.

I didn't really understand what any of

these molecules were.

I certainly didn't understand how they even connected really

to chemical reactions, much less other disciplines that I

was interested in.

I couldn't have told you, for example, if we look at a

phosphate group, that that's going to be incredibly

important in DNA, that it's also an incredibly important

group when you're dealing with proteins and whether you're

turning the function of a protein on or off.

So really, I just had no context for the chemistry.

So, when I started in college, that wasn't even an option for

me and I was interested in a lot of things,

chemistry not being one.

But one that I was very interested in was biology, and

the reason was we did a lot of cool labs in high school, I

loved doing the dissections -- it was very interesting to me

to think about how different organs worked, how the heart

could be a pump, how the lungs worked.

And then when we got to more of a cellular level, it was

even more interesting to see that we could actually

understand how our body worked as low of a level as thinking

about cells.

And so, that was a clear major for me to pick --

I actually also was considering English and ended

up being a minor in English.

But, I think what most of you, actually having come to MIT,

have probably realized is sometimes it's nice to major

in a science, because you can't just pick up a reaction

and do it in your kitchen on the weekend, where as you can

sometimes join a book group and do that.

So, it's kind of nice to major in the thing that you're going

to get to have the opportunity to do for the

rest of your life.

So, I actually also started pre-med.

Is anyone else pre-med here?

Okay, so a pretty good showing.

So maybe you can relate to some of the reasons I wanted

to be pretty pre-med -- part of it was the interest in the

science and the biology.

Also, I wanted to help people -- it seemed like a really

clear way that I could have a career that was challenging

and involved in science, but also helping others.

So, it seemed like a good start for me, pre-med/bio, and

I signed up for my bio class --

I found out, as Professor Drennan did, that I had to

take chemistry as well.

I wasn't as upset, I was sort of a neutral chemistry person

at this point, but I thought it was pretty smart to get it

over with on the first semester, so

that's what I did.

And my plan was going along fine until something happened,

and what happened was that chemistry was just way more

interesting than I anticipated.

So, my perfect pre-med/bio plan was getting a little

shaken right from the start, and the reason that it was

getting taken was because I would learn this new principal

in chemistry and because I was taking bio with the same time,

I could see the connections.

And at one point I realized, "Oh, my gosh, chemistry is

just biology, it's just looking at one level deeper."

So actually, all of my interest in biology was

quickly transferred to saying, "Wow, now I can think about

things on the molecular level." And one of the

molecules that caught my attention first, and I can't

remember if this was freshman or sophomore year in high

school, was the first time I actually took meaning in

looking at a chemical structure, and that was with

the structure of penicillin here, and I know that all of

you are familiar with penicillin, whether or not you

know the structure or not, but the most important part of

this structure is the four-membered ring here, the

beta-lactam, and this was the first time I thought I could

actually understand how a molecule worked because I knew

something about chemistry.

So, for example with penicillin what it does is it

inhibits an enzyme that builds the cell wall in bacteria, the

bacterial cell wall, and if I thought about what I'd learned

in chemistry -- some of you know this from high school,

some of you will be very familiar with this soon, is

that this carbon here, for example, is

bonded to three things.

Does anyone know what angle those would like to be at?

120.

They want to get as far away from each other possible, the

ideal angle is 120.

But what we have here is a four-membered ring, so what

angle does that have to be, that bond?

90 degrees.

So, we have a problem here if we're thinking about keeping

things at the lowest energy, so there's a lot of ring

strain in the system.

And I was incredibly excited that I could look at that and

realize it and say "Wow, that's why it's so reactive,

that's why it's such a good medication," because when it

comes into contact with these bacterial cell wall building

enzyme, the enzyme can actually react with this

four-membered ring and open up the ring and

relieve that ring strain.

So, now the angles can open up all the way to 120 if it wants

to, and there's no way it's going to form that ring again,

right, because it's not going to back to those 90 degree

angles, if it can help it.

So now, the enzyme is locked up with the penicillin

molecule, no more bacterial cell wall being built, and the

penicillin has effectively killed the bacteria.

So, that, for me, was kind of the first connection that what

went, "Woah, wait a second, I want to be thinking about

these molecules all the way down to the level of

individual atoms." So, at this point, kept the pre-med, just

switched the major to chemistry.

The next problem came up when I went and

took organic chemistry.

So, if you're dead set on staying with bio, maybe, I

guess you have to take organic, so this might happen

to you, just to warn you.

We started looking at all sorts of other kinds of

molecules that became very interesting to me.

I especially love thinking about vitamins and drugs,

because I do have that interest in

medicine and human health.

These are actually all examples that we'll talk about

in freshman chemistry at some point, as an example of a

connection between a chemical principle we learn, and what

we can know about how it functions.

But what happened here was I thought "Oh, my gosh, now I

could actually, using my chemical knowledge, think

about synthesizing these molecules, or maybe coming up

with new ways to synthesize them better or synthesize

different molecules.

And the real clincher was when I started doing some

undergraduate research.

Any potential UROPs out there -- anyone planning to do a

research at some point?

Excellent.

Okay.

So, just to be warned, you might fall in love with the

subject you do your UROP in.

This is one of our summer students from this past

summer, who is also premed.

She's continuing to be pre-med, which is fantastic.

That didn't happen to me -- once I got into the lab, I

didn't want to leave.

So, I thought, "You know what, I think I'll change the

medical school plans and now I'm going to go all the way --

chemistry major, chemistry grad school." And the reason I

was able to do that and keep with what my original

intentions were was to have a career that was the

fulfilling, in terms of helping people and being

engaged in science, is all of a sudden I realized, as

chemists, we can think about better ways to build molecules

that are important for making medications.

Another thing we can do is we can use our chemistry to

understand biological systems, so we can help illucinate

pathways, maybe, that are implicated in disease.

So, the combination of these two things had made my

decision and I ended up coming here for graduate school,

actually, and working in Professor Imperiali's lab

doing bio-organic chemistry, which means that I synthesize

molecules, which I loved, and used them to

study biological systems.

So, really I'm pretty happy with what I've gotten to do,

and I just want to say we're not trying to convert all of

them you pre-med people, by any means.

My roommate for many years was going to medical school as I

was going to graduate school, and we found we had so many

interesting conversations about chemistry -- her from

the context of practicing and using medications and talking

about how they worked on a molecular level, and me

talking about my research.