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ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

ATOMIC STRUCTURE

The purpose of these first 2 lectures is to revisit chemistry concepts that are important to Biophysics.

Electron Orbitals and the Periodic table

Molecular Bonding from the perspectives of valence bond theory and molecular orbital theory

Intermolecular Forces

Electron orbitals and the periodic table

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 ATOMIC STRUCTURE The purpose of these

In the simplistic planetary model (Bohr) of the atom, electrons orbit the nucleus, but if this actually happened, they should lose energy in a dying burst of electromagnetic radiation and crash into the nucleus. This is because the negatively charged electron is inherently attracted to the positively charged nucleus, and crashing into it represents a lower energy, and therefore more favorable state. But they do not crash.

The paradox is removed by the quantum model of the atom.

In quantum theory, the energy of an electron is only allowed to be gained or lost in discrete chunks called quanta. No 'burst' of energy is allowed, only discrete jumps between energy states. This makes the allowed energy levels in an atom like the discrete steps of a staircase, rather than a continuous gentle slope. Furthermore, transitions are only allowed to unoccupied energy states (this is called the Pauli exclusion principle). Hence, energies higher than the lowest energy state are stable, because there is nowhere unoccupied further down the staircase of energy for the electrons to fall to.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

However, this still leaves the 'ground state' (the lowest energy state). Why is this stable? Equivalently, why is the ground state not collapsing on the nucleus?

To account for this, we invoke Heisenberg's uncertainty principle (important maxim of quantum theory), which states that an electron's position (say x) and momentum (correspondingly p x ) cannot be simultaneously known with certainty. One way we can tell where an electron is in space is by hitting it with light waves. However, the more precisely we need to know the position of the electron, the smaller the wavelength of light we will need: a dinghy will leave an obvious, observable shadow behind short-wavelength water waves, but a long-wavelength tsunami will not even notice it's there. Mathematically, the uncertainty principle can be expressed as

Δx Δp x ½ h/2π,

where Δx = { <x 2 > <x> 2 } 1/2 and <A > expresses the average of A. Similarly for p x .

Also, λ = h p, or equivalently, E = m c 2 = h ν (de Broglie's and Planck's relationships), where λ is wavelength, ν frequency, E energy, p momentum, h Planck's constant, m mass, c speed of light)

So, short wavelengths carry more energy: X-rays (short wavelength) are more energetic than radio waves (long wavelength). These energetic light waves will kick the electron sufficiently to change its movement, so although we know exactly where the electron is, we will have no idea in which direction it is now traveling.

Mathematically, as Δx0, Δpx and <p x 2 >

From the above, we can see that if an electron tries to get nearer the nucleus, its position will become more certain. Hence its velocity must become less certain, and therefore higher on average. This means its energy of motion is higher, and therefore there is no net energy advantage in crashing into the nucleus, because the increase in kinetic energy would exceed any loss in potential energy. Hence the ground state is also stable.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Quantum physics states that all particles have wave-like properties (like wavelength) and that all waves have particle-like properties (like momentum). In fact, all subatomic particles can be thought of as a sort of hybrid between a wave and a particle. For example, electrons, previously considered as particles (i.e. tiny billiard balls), also have wave-like properties. Schrödinger's equation describes the electron probability ψ. For a time- independent potential V(x), separation of variables {ψ(x, t) = Ψ (x) ×T(t) } gives 2 equations: i h =E T and h 2 /2m 2 Ψ + V(x) Ψ = E Ψ. E is the total energy of the electron (kinetic plus potential). The second equation is the time-independent Schrödinger equation which can be regarded as a wave equation.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Quantum physics states that all partic

So in an atom, the electron probability waves form 'standing waves', much like those you get when you pluck a guitar string. In a similar way to a guitar string, the atom allows various modes of vibration of the standing wave. Similarly to beating a drum, one needs nodes and nodal lines in 2-D (2 numbers) and 3 numbers in 3-D.

Schrödinger's equation describes these modes of vibration, and the solutions are generally graphically displayed as orbitals, which are the space domains where there's a better than 99% chance of finding an electron. There are many sorts of orbitals. The various orbitals available to an atom are described by 4 quantum numbers, which can take certain values to create differently sized and shaped orbital of various energies. The first 3 quantum numbers correspond to the various eigefunctions of time-independent Schrödinger equation which can be solved by separation of variable in spherical coordinates Ψ (x) = R n (r) ×Φ l (φ) ×Θ m (θ) ). The angular portion of the solution (Θ and Φ) are the spherical harmonics (refer to http://mathworld.wolfram.com/SphericalHarmonic.html).

Principal (n).

Angular Momentum (l).

Magnetic (m l ).

Spin (m r ) because electrons can “spin” counter- or clock-wise (values +½ or ½ )

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Quantum physics states that all partic

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The principal quantum number (n) corresponds to the appropriate radial function R n (r) (Laguerre polynomials) and describes the order of the

Largest energy differences ('shells'). For the hydrogen atom, there are n 2 wave functions with the same energy (degenerate)

o

     

E n = - 2 π 2 μ e q e 4 /(h 2 n 2 ) Size of orbital.

Numbered 1, 2, 3, 4, 5, etc (although the shells it describes are often lettered K, L, M, etc.).

Low numbers are closest to the nucleus, and have the lowest energies.

Higher values of n indicate larger orbitals

The angular momentum quantum number (l) corresponds to the appropriate polar function Φ l (φ) (Legendre polynomials) and describes the:

Small energy differences ('subshells') due to angular momentum of the electron

Shape of orbital (number of lobes).

Given letters inspired from spectroscopy: s (sharp), p (principal), d (diffuse), f (fine), g, h, i, etc.

The blocks of the periodic table are named after the azimuthal quantum number of the orbitals being filled

(alkali metals are the s-block, the nonmetals are in the p-block, the tran sition metals are the d-block, the footnote is the f-block). The values of l run from 0 to n 1, where n is the principal quantum number of the shell in question.

An s orbital is just shorthand for l = 0, a p orbital is shorthand for l = 1, a d orbital l = 2, an f orbital l = 3, etc. This also means that (for example) the n = 3 shell can only contain subshells with l = 0, 1 or 2, i.e. only s, p and d orbitals.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

http://www.orbitals.com/orb/index.html

NOTATION: n=1 1s n=2, l=1 2p n=3, l=3 3d n=4, l=4 4f
NOTATION:
n=1 1s
n=2, l=1 2p
n=3, l=3
3d
n=4, l=4
4f

The orbitals in the same row differ in their angular momentum quantum numbers: s orbitals are spherical and have just one lobe. p orbitals have two lobes, and a 'node' between the lobes where the electrons do not spend much time. Consequently, 2p orbitals have higher energy than 2s orbitals, because the electron spends a little longer distant from the nucleus. d and f orbitals have increasing numbers of lobes. In fact, d and f orbitals can have even more bizarre shapes than this…

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

(http://winter.group.shef.ac.uk/orbitron/)

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 ( http://winter.group.sh ef.ac.uk/orbitron/) Th <a href=e sha pe of the five 3 d orbitals. From left to right: (top row) 3 d a nd 3 d (bottom row) 3 d , 3 d , and 3 d . For each, the yel low zones are where the wave functions have negative values an d the blue zones denote positive values. Th e sha pe of the seven 4 f orbitals (cubic set). From left to right: (to p row ) 4 f , 4 f , 4 f , (middle row) 4 f , 4 f , 4 f , and (bottom row) 4 f . For each, the copper zones are where the wave fun ction s have negative values and the gold zones denote positive values. " id="pdf-obj-5-11" src="pdf-obj-5-11.jpg">

The shape of the five 3d orbitals. From left to right: (top row) 3d x 2 -y 2 and 3d z 2 (bottom row) 3d xy , 3d xz , and 3d yz . For each, the yellow zones are where the wave functions have negative values and the blue zones denote positive values.

The shape of the seven 4f orbitals (cubic set). From left to right:

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 ( http://winter.group.sh ef.ac.uk/orbitron/) Th <a href=e sha pe of the five 3 d orbitals. From left to right: (top row) 3 d a nd 3 d (bottom row) 3 d , 3 d , and 3 d . For each, the yel low zones are where the wave functions have negative values an d the blue zones denote positive values. Th e sha pe of the seven 4 f orbitals (cubic set). From left to right: (to p row ) 4 f , 4 f , 4 f , (middle row) 4 f , 4 f , 4 f , and (bottom row) 4 f . For each, the copper zones are where the wave fun ction s have negative values and the gold zones denote positive values. " id="pdf-obj-5-57" src="pdf-obj-5-57.jpg">

(top row) 4f y 3 , 4f x 3 , 4f z 3 , (middle row) 4f x(z 2 -y 2 ) , 4f y(z 2 -x 2 ) , 4f z(x 2 -y 2 ) , and (bottom row) 4f xyz . For each, the copper zones are where the wave functions have negative values and the gold zones denote positive values.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The magnetic quantum number (m l ) corresponds to the appropriate azimuthal function Θ m (θ) (sines and cosines) and describes:

No energy differences at all (the orbitals are degenerate).

Orientation of the orbitals in space.

Named after the directions they point in (sort of) x, y, z, etc.

Can also be given numbers ranging from 0, ±1, ±2, ±3 … ±l. Hence

the three sorts of p orbitals, p x , p y and p z have m l of -1, 0 and +1 respectively. This restriction is called Space Quantization

Consequently, there's only one sort of s orbital (because l = 0), but:

o

3 sorts of p

o

5 sorts of d

o

7 sorts of f

o

9 sorts of g …

http://winter.group.shef.ac.uk/orbitron/

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 The magnetic quantum number (m )
√ 6 + 2 √ 6 + 1 m l 0 √ 6 - 1 √
√ 6
+ 2
√ 6
+ 1
m
l
0
√ 6
- 1
√ 6
-2
√ 6

Example of Space Quantization:

The 5 (that is 2 l +1) allowed orientations of the angular momentum with l=2. The length of each vector is {l( l +1)} 1/2 = 6

The 2p x , 2p y and 2p z orbitals all have the same energy, but different orientations in space.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Summary of Orbitals:

n=1 shell One s-orbital: 1s n=2 shell One s-orbital: 2s Three p-orbitals: 2p x 2p y 2p z

o

o

o

n=3 shell One s-orbital: 3s Three p-orbitals: 3p x , 3p , 3p z Five d-orbitals: 3d xy , 3d xz , 3d yz , 3d x 2 y 2 , 3d z n=4 shell One s-orbital: 4s Three p-orbitals: 4p x , 4p y , 4p z

o

o

o

y

o

o

o

o

Five d-orbitals: 4d

xy

, 4d xz , 4d

yz

, 4d x

2

Seven f-orbitals: 4f z 3 , 4f xz 2 4f z(x

2

2

2

y

, 4d z

2

2

y 4f xy 2 , 4f xyz , 4f x(x 2 3y 2 ) , 4f y(3x y )

) ,

2

2

The final quantum number is the spin quantum number (m r ). Each orbital (e.g. a 2p x ) can hold two electrons.

The Pauli exclusion principle states that no two electrons in a single atom can have the same quantum numbers, hence they must differ in their spin quantum number, which takes the values +½ or -½. Two electrons in the same orbital have paired (opposite) spins. Th e number of electrons a set of degenerate orbitals can contain is therefore just 2 for an s orbital, 6 for a set of p orbitals (3p x 3p y 3p z can hold 2 electrons each), 10 for a set of five d orbitals, 14 for a set of f, etc.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The Periodic Table is a list of the elements by their atomic number (i.e. by the number of electrons a neutral atom of the element possesses). Hence, as we traverse the periodic table, we are filling up electron orbitals from lowest energy to highest energy. We can write electronic configurations for atoms based on the arrangement of their electrons. We just need to write the (non-degenerate) orbitals out in energy order, then fill them up, writing the number of electrons each set of orbitals contains as a superscript

Hydrogen (1 electron) has the electronic configuration 1s 1

Boron (5 electrons) has the electronic configuration 1s 2 2s 2 2p 1

Sodium (11 electrons) has the electronic configuration 1s 2 2s 2 2p 6 2s 1

How does this relate to the periodic table? p - block Elements s- block Essential to
How does this relate to the periodic table?
p - block
Elements
s- block
Essential to
d- block
Biological
Species
f- block
ELECTRONEGATIVITY

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Properties of elements exhibit periodic behavior as we traverse the table: el ements in a vertical group, like the halogens (F, Cl, Br, I) and alkali metals (Li, Na, K, Rb) have similar properties. The reason for this is that their outermost orbitals have a similar electronic configuration: the alkali metals all have s 1 and the halogens all have s 2 p 5 in their outermost shell. Elements with similar electronic configurations have similar properties.

As we move across the horizontal periods, we are filling up electron orbitals from the lowest energy (nearest to nucleus) to the highest (furthest out). The electrons actually fill in the order below:

1s 2s 2p 3s 3p 4s 3d 4p 5s 4d 5p 6s 4f 5d 6p 7s 5f 6d 7p 8s …

So, the only rules for filling up energy levels are that they fill from the lowest energy upwards, and that electrons only pair if there's no orbital of the same energy available (Hund's rule). Looking at the periodic table, and the filling order, we can easily see that the following orbitals are filled by the elements listed:

1s : H He.

2s : Li Be.

2p : B C N O F Ne.

3s : Na Mg.

3p : Al Si P S Cl Ar.

4s : K Ca.

3d : Sc - Zn.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Properties of elements exhibit periodic be

And so on: f-orbitals are filled in the f-block lanthanides/actinides (the footnote at the bottom of most periodic tables).

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Molecular bonding

The previous section described how electrons fill up atomic orbitals, and how this relates to periodicity. What happens when there is more than one nucleus present? In short, how do electrons arrange themselves in molecules, and how do they form chemical bonds?

The short answer is that it's extremely difficult to work out!

However, many models have been proposed, each with their advantages and disadvantages. The simplest is the valence bond theory of the chemical bond. In this theory, we only consider the outermost s and p valency electrons as being responsible for most of the chemistry of an atom (or at least the ones biochemists are interested in). Having a completely full or empty octet of these outermost electrons is a favorable low-energy state. Noble gases already have this configuration, and are therefore unreactive, but other elements 'try' to completely fill or empty their outermost octet of electrons by losing, gaining or sharing them.

In iodine chloride, we can see that both Cl and I are one electron short of an octet. Hence they can share electrons and form a covalent bond between the two molecules, allowing both to have 8 electrons in their outermost orbitals, I-Cl. Note that both I and Cl have three pairs each of electrons not involved in the bond itself. These are termed lone pairs, and contribute to the shape of the molecule as we will see. The two electrons that are shared form a single covalent bond. Other molecules may share more than one pair of electrons between two atoms: in oxygen molecules (O 2 ), a double bond is formed (O=O), sharing four electrons in total, and in nitrogen (N 2 ) six electrons are shared to form a triple bond NN).

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Molecular bonding The previous section described

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

However, rather than sharing electrons, some atoms find it easier to lose or steal them. The metallic elements are termed electropositive. This means that they are more likely to lose electrons (and become positive cations) than gain them. For example, the alkali metals (Li, Na, K, Rb, Cs, FR) each have 1 electron in their outermost s orbital. They can lose them to form cations (K + , Na + ). This leaves them with a full octet at the next shell down. Metallic character increases towards the bottom left of the periodic table i.e. francium is the most electropositive, and therefore most metallic, metal.

On the other hand, the electronegative nonmetals are more likely to gain electrons and become negatively charged anions. For example, the halogens (F, Cl, Br, I, At) have 7 electrons in their outermost s and p orbitals. They can gain one more to form anions (Cl , I ). This gives them a full outer octet. Nonmetallic character increases towards the top right of the periodic table, i.e. the most nonmetallic nonmetal is fluorine.

The valency of an atom can be determined by the number of electrons it has in its outermost orbitals. As a general rule, for elements in the s and p blocks, those with 1 or 7 electrons in the outermost shell have valency one (i.e. can form just one bond), since they are only one electron away from a completely full or empty outer octet. Those with 2 or 6 electrons have valency 2, those with 3 or 5 have valency 3, and those with 4 have valency 4. The noble gases (Ne, Ar, Kr, Xe, Rn) have valency 0, since they already have full outer octets. There are numerous exceptions though, the most important being hydrogen. Hydrogen has valency one because the n = 1 shell can contain only two electrons: there is no 'octet' of s and p orbitals to fill, only a doublet of a single s orbital. The transition metals (the d block) can generally have more than one valency, since there are various energetically favourable arrangements using their partially filled s, p and d orbitals for bonding.

Different types of bond form depending on the character of the elements involved. Ionic bonds are formed between elements of very different electronegativities. For example, fluorine desperat ely 'wants' an electron, and cesium is 'desparate' to lose an electron, and therefore they will readily react to form ions:

F 2 + 2Cs 2F + 2Cs +

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The bond between the F and Cs + ions is called an ionic bond, and is typical in compounds formed between a metal and a nonmetal.

Metallic bonds are formed between two metals, and indeed, between atoms of a single metallic element. They are somewhat like covalent bonds (as in iodine fluoride), in that the electrons ar e shared between the metal atoms, but rather than a 1:1 sharing, all the valency electrons are shared between all the atoms, forming a sort of 'electron gas' between the metal atoms, and accounting for the electrical conductivity of metals. These sorts of bond are not very important in biophysics…

Covalent bonds are formed when electrons ar e shared between two atoms, as in the iodine fluoride above. If two nonmetals react to form a compound, they usually form a covalent bond, because nonmetals have similar electronegativities. However, a 'perfect' covalent bond is only formed between the atoms of the same element, e.g. in Cl 2 . All other covalent bonds have a slight ionic character, called polarity, and such bonds are called polar covalent. In IF, the chlorine is rather more electronegative than the iodine, and hence the electrons will spend slightly longer around the chlorine than the iodine. This gives the chlorine a slight negative charge (δ-), and the iodine a slight positive charge (δ+). Various weak bonds can be formed between such polar molecules. The most important in biochemistry is the hydrogen bond (covered in detail later).

An important consequence of polarity is the concept of oxidation number. The oxidation number of an atom in a molecule is basically the charge that the atom would have if the molecule were broken up into the ions that the atoms might 'like' to be. For example, the O-H bond in water is very polar: H is slightly positive (and valency 1), and O slightly negative (and valency 2). Hence, the oxidation numbers are -2 for the oxygen, and +1 for the hydrogens, because if we could break H 2 O into the ions it might 'like' to be, we'd get H + O 2 H + . In fact, in almost all biochemical compounds, H has an oxidation number of +1, and O an oxidation number of -2. Other elements have more variable oxidation numbers, but a few simple rules will get you by in most cases:

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The sum of the oxidation numbers in the molecule must add to the charge on the molecule or ion (zero if it is

uncharged). The electronegativity series for the common biochemical elements goes (most negative) F > O > Cl > N > S

> C > H > P > Fe > Mg > Ca > Na > K > Fr (least negative). An element in combination with itself has oxidation number 0, hence Cl in Cl 2 has oxidation number 0, as

there's no polarity in the Cl-Cl bond. Oxygen almost always has oxidation number 2, except in e.g. OF 2 (where it's +2, because F is more

electronegative), and in peroxides H 2 O 2 (where it's 1, because the oxygen is half in combination with itself). Hydrogen almost always has oxidation number +1, except in e.g. H 2 (0) and NaH (1).

Transition element compounds are usually named by their oxidation numbers in Roman numerals. Iron (III) chloride is FeCl 3 , iron (II) oxide is FeO.

From these rules, you can work out that the oxidation number of N in NH 3 is 3, that of S in SO 4 2 is +6, N in NO 3 is +5, Fe in Fe +2 is +2, etc.

The valence bond theory of covalent bonds is somewhat simplistic, and more quantum mechanical treatments of molecular bonding try to apply the same sort of reasoning to molecular bonds as to atomic orbitals. In the most refined treatment, molecular orbital theory, the valence electrons (in fact, all the electrons) are shared in molecular orbitals. However, somewhere between valence bond theory and full blown molecular orbital theory, we come across the concept of hybridisation, which is used to account for the shap es of covalent mole cules. The valence orbitals (outermost s and p orbitals) are hybridised (mathematically mixed) before bonding, converting some of the dissimilar s and p orbitals into identical hybrid sp n orbitals.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

sp hybrids are formed by mixing the outermost s and all three outermost p orbitals to form four sp 3 hybrids. The furthest these four [negatively charged, and therefore repulsive] orbitals can get from each other is the corners of a tetrahedron (109°).

3

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 sp hybrids are formed by mixing
ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 sp hybrids are formed by mixing

sp 3 hybrid orbitals. The top four images show the four sp 3 hybrids. These particular sp hybrids are combinations of 2s and three 2p functions. The bottom shows the relative positions of these four hybrids superimposed. Note that in each case, the nucleus is embedded in the minor lobe. Each is the same as the other but one is rotated by 109.5° relative to the other. It is appropriate to invoke sp 3 hybrid orbitals in molecules such as TiCl 4 or CH 4 where the Cl-Ti-Cl and H-C-H angles are 109.5°.

3

Any hybrid orbitals containing one electron can overlap with orbitals on other atoms to form bonds. For example, hydrogen has an s orbitals containing just one electron. An sp 3 hybridised carbon atom has four sp 3 hybrids each containing a single electron:

Hydrogen 1s 1 : one electron available for bonding

Carbon (unhybridised) 1s 2 2s 2 2p x 1 2p

y

1 2p z 0 : only two unpaired electrons available for bonding.

Carbon (hybridised) 1s 1 (2sp 3 ) 1 1 (2sp 3 ) 2 1 (2sp 3 ) 3 1 (2sp 3 ) 4 1 : four unpaired electrons available

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The overlap and pairing of the s orbitals of four hydrogen atoms with the sp 3 hybrids on a carbon forms four covalent bonds in the methane molecule CH 4 .

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 The overlap and pairing of the
ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 The overlap and pairing of the

Overlap four s orbitals from four hydrogens (blue) with four sp3 hybrids on carbon leads to formation of bonds, each containing one electron from the carbon and one from the hydrogen: these are represented by up and down pointing arrows, showing the pairing of the electron spins.

The hybridisation also accounts for the shape of molecules like methane (tetrahedral), ammonia (trigonal pyramid), water (V-shaped), and hydrogen fluoride (linear). Note that the orbitals not involved in bonding to hydrogen are still hybridised, but end up as lone pairs of electrons (symbolised by the two dots in the diagram to the right).

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

2

sp hybrids are formed when only one s and two p orbitals are involved. This leaves one remaining p orbital, which may be involved in forming a double bond. The furthest these orbitals can get from one another is a trigonal bipyramid, with the sp hybrids arranged at 120° to each other in a plane. This is characteristic of molecules with double bonds.

2

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 2 sp hybrids are formed when
ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 2 sp hybrids are formed when

sp 2 hybrids. The top three images show the three sp 2 hybrids. These particular sp 2 hybrids are combinations of 2s and two 2p functions. The bottom shows the relative positions of these three hybrids superimposed. It is appropriate to invoke sp hybrid orbitals in molecules such as BF 3 or H 2 C=CH 2 (ethene) where the F-B-F and H-C-C angles are ~ 120°

2

Three sp 2 hybrids in lilac, with two lobes of the remaining p orbital in orange.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Finally, sp hybrids are formed using just one s and one p orbital. Two sp hybrids are formed from them, and the two p-orbitals remaining may contribute to a triple bond. These arrange themselves at the corners of an octahedron, with th e two sp hybrids diametrically opposite one another. sp hybridisation is characteristic of the triple bond.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Finally, sp hybrids are formed using

sp hybrid orbitals. The top two images show the two sp hybrids at a slight angle. These particular sp hybrids are combinations of 2s and 2p functions. The bottom shows the relative positions of these two hybrids superimposed. There are two sp hybrid orbitals. Each is the same as the other but one is rotated by 180° relative to the other. It is appropriate to invoke sp hybrid orbitals in molecules such as BeH 2 or HCCH (ethyne) where the H-Be-H and H-C-C angles are 180°.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Finally, sp hybrids are formed using

Two sp hybrids in pale-blue, with four lobes of the two remaining p orbitals in orange.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Ethane (top) has only sigma bonds,

Ethane (top) has only sigma bonds, ethene (middle) and ethyne (bottom) have pi bonds too.

The formation of bonds involves the overlap of hybrid orbitals with the orbitals of other atoms, as we saw with methane. However, two sorts of bond can result from different sorts of overlap. When s and/or hybrid orbitals overlap 'end-on', sigma bonds (σ) are formed:

these have a single area of electron density between the nuclei of the two atoms whose orbitals are overlapping.

In the diagrams to the left, σ bonds are shown as simple lines. However, p orbitals can overlap sideways too: when this happens (as in ethene and ethyne), two lobes of electron density are formed between the atoms. This is termed a pi bond (π). From the diagram, you can see that the double bond in ethene is composed of one σ plus one π bond, and the triple bond in ethyne is one σ plus two π.

In class, we will present discuss examples (Pt- catalysis) where these π bonds are important.

(There are also δ and φ bonds that describe the various ways d and f orbitals can overlap.)

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Rotation is possible about a σ bond, but not (at room temperatures) about a π bond, which causes geometric isomery.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Rotation is possible about a σatur es) about a π bond, which causes geometric isomery. 2s σ and σ * bonds . Bonding and anti-bonding interac tion of nitrogen 2s orbitals on two nitrogen atoms as they approach. The two dots represent the N nuclei. The rather strange looking inne r structures are the radial nodes of the two 2 s orbitals. (http://winter.group.shef.ac.uk/orbitron/MOs/N2/2s2s-sigma /index.html) 2p π bond Bonding interaction of nitrogen 2 p orbitals on two nitrogen atoms as they approach. ( http://winter.group.shef.ac. uk/orbitron/MOs/N2/2px2px- pi/index.html ) " id="pdf-obj-19-16" src="pdf-obj-19-16.jpg">
ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Rotation is possible about a σatur es) about a π bond, which causes geometric isomery. 2s σ and σ * bonds . Bonding and anti-bonding interac tion of nitrogen 2s orbitals on two nitrogen atoms as they approach. The two dots represent the N nuclei. The rather strange looking inne r structures are the radial nodes of the two 2 s orbitals. (http://winter.group.shef.ac.uk/orbitron/MOs/N2/2s2s-sigma /index.html) 2p π bond Bonding interaction of nitrogen 2 p orbitals on two nitrogen atoms as they approach. ( http://winter.group.shef.ac. uk/orbitron/MOs/N2/2px2px- pi/index.html ) " id="pdf-obj-19-18" src="pdf-obj-19-18.jpg">

2s σ and σ* bonds. Bonding and anti-bonding interaction of nitrogen 2s orbitals on two nitrogen atoms as they approach. The two dots represent the N nuclei. The rather strange looking inner structures are the radial nodes of the two 2s orbitals. (http://winter.group.shef.ac.uk/orbitron/MOs/N2/2s2s-sigma /index.html)

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Rotation is possible about a σatur es) about a π bond, which causes geometric isomery. 2s σ and σ * bonds . Bonding and anti-bonding interac tion of nitrogen 2s orbitals on two nitrogen atoms as they approach. The two dots represent the N nuclei. The rather strange looking inne r structures are the radial nodes of the two 2 s orbitals. (http://winter.group.shef.ac.uk/orbitron/MOs/N2/2s2s-sigma /index.html) 2p π bond Bonding interaction of nitrogen 2 p orbitals on two nitrogen atoms as they approach. ( http://winter.group.shef.ac. uk/orbitron/MOs/N2/2px2px- pi/index.html ) " id="pdf-obj-19-35" src="pdf-obj-19-35.jpg">

2p π bond Bonding interaction of nitrogen 2p x orbitals on two nitrogen atoms as they approach.

(http://winter.group.shef.ac.uk/orbitron/MOs/N2/2px2px-

pi/index.html)

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Full blown molecular orbital theory is

Full blown molecular orbital theory is even more complex than this.

Example: formation of a bond between two oxygen atoms.

To consider the bond formation in this molecule, we mathematically add and subtract orbitals of similar energy and orientation to form molecular orbitals.

Oxygen has the electronic configuration 1s 2 2s 2 2p 4 .

When two oxygen atoms are brought together, orbitals of similar energy and orientation can be combined to form molecular orbitals, as shown in the diagram to the left.

On the left and right, we can see the atomic orbitals of two oxygen atoms, replete with their electrons, When we bring them close enough together to form a bond, they co mbine to form the molecular orbitals shown in the middle, which are then filled with electrons as usual (low est energy first, only pair if we must). So how do we predict the shape and number of the molecular orbitals?

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

It's actually much easier than you might think.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 It's actually much easier than you

s orbitals can only overlap 'end-on'. If we mathematically add these orbitals together, we get a sigma bonding orbital (bottom), if we subtract them, we get a sigma antibonding orbital (top). Hence, in out molecule of dioxygen, we have one σ 1s and one σ 1s * orbital from the overlap of the 1s orbitals, and likewise, a σ 2s σ * 2s from the overlap of the 2s orbitals.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

p orbitals can overlap in two ways: if we bring two oxygen atoms together, you can see that one orientation of p orbitals (say p x for the sake of argument) will meet 'end on', whereas the other two pairs, p y p z will meet 'sideways on'. The first direction will form a sigma bond/antibond pair and the sideways overlap will form a pi bond, as we saw with the hybridisation theory earlier, and a pi antibonding orbital too:

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 p orbitals can overlap in two
ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 p orbitals can overlap in two

p x orbitals overlap end-on, forming a σ 2px orbital and a σ 2px * antibonding orbital.

p y orbitals overlap sideways on forming a π 2py orbital and a π 2py * antibonding orbital.

The same applies to the 2p z orbitals.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

The exact order of molecular orbital energies in the dioxygen molecule is somewhat difficult to discern, as hybridisation of the s and p orbitals (as we saw earlier) has some influence over this. However, the diagram earlier shows the actual order, and it is a simple (!) matter to determine that the electronic structure of dioxygen is:

(σ 1s ) 2 (σ 1s * ) 2 (σ 2s ) 2 (σ 2s * ) 2 (σ 2px ) 2 (π 2py ) 4 (π 2py * ) 2 (σ 2px * ) 0

The bond-order of any molecule is the number of electrons in bonding (unstarred) orbitals minus those in antibonding (starred) orbitals divided by two.

It's easy to see that for dioxygen, this is ( 10 6 ) 2 = 2 (a double bond).

If the bond order is greater than zero, the bond will form, showing that dioxygen is a real molecule. On the other hand, the equivalent for dihelium would be:

(σ 1s ) 2 (σ 1s * ) 2 Here the bond order is zero, and that's why He 2 doesn't exist.

Similarly for Ne 2 : The number of electrons in bonding and antibonding orbitals is the same:

(σ 1s ) 2 (σ 1s * ) 2 (σ 2s ) 2 (σ 2s * ) 2 (σ 2p x) 2 (π 2p y) 4 (π 2p y * ) 4 (σ 2p x * ) 2 .

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

Intermolecular bonds

Intramolecular bonds, such as we have been describing up until now, form within molecules.

Intermolecular bonds are those formed between different molecules or atoms. They come in two main sorts:

the hydrogen bond, very important in biology's favorite solvent, water

Van Der Waals' forces.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 Intermolecular bonds Intramolecular bonds, such as

Chemically, water is hydrogen oxide, H 2 O.

The oxygen atom is sp 3 hybridised, forming two sigma bonds to two hydrogen atoms, and leaving two orbitals containing just lone pairs of electrons.

Oxygen is highly electronegative, hence the water molecule is very polar, with δ− on the oxygen and δ+ on the hydrogens. The negative charge is partially localised in the lone pairs, which repel each other just enough to squash the H-O-H bond angle to slightly less than the 109.5° you get in a symmetrical molecule like methane.

The slight positive charge on the hydrogen atoms is attracted to the slight negative charge on the oxygen atoms in other water molecules. The attraction is called a hydrogen bond and is extremely important for stabilizing the structure of many biological macromolecules (e.g. DNA, RNA, proteins, cellulose).

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 In water, the hydrogen-bond donor is

In water, the hydrogen-bond donor is the H bonded to the electronegative O and the acceptor is the lone pair of another O. Note that the hydrogen bond is about twice as long (0.18 nm) as the covalent O-H bond (0.1 nm).

However, other acceptors and donors exist:

Other donors : H bonded to N, F, Cl.

Other acceptors : lone pairs on N, F, Cl.

So NH 3 (ammonia) is also H-bonded in the liquid state, but more weakly than water (the reason it is a gas at STP), because nitrogen is less electronegative than oxygen, and hence the polarity of the N-H bond is less pronounced. Hydrogen bonds also form in ice, and since this holds the ice in a more open structure than in liquid water, it is actually less dense than water, and it floats.

ME 498 Physics of Biological Systems –Spring 2007

Lectures 1-2

There is another sort of weak intermolecular force besides the H-bond

This is the Van Der Waals' force, which comes in three varieties:

Dipole dipole interactions: between other partial charges on polar molecules.

Dipole induced dipole interactions: between a polar molecule and a non-polar molecule which has developed

a dipole in response (like a piece of non-ma gnetic iron is attracted to a magnet). London dispersion forces: between non-polar molecules which by chance occasionally have an imbalance of charge, and are fleetingly polar.

ME 498 Physics of Biological Systems –Spring 2007 Lectures 1-2 There is another sort of weak

The Van Der Waals' radius of an atom is the 'size' of an atom. There is a weak attractive force between any two atoms, up to a point. If you squash atoms/molecules more closely than this they will begin to repel each other. The VDW radius is the size of the molecule just on the cusp between attraction and repulsion.

Hydrophobic forces (the way that fats seem to attract one another and hence form a layer on top of water) are often attributed to Van der Waals' force between lipids.

NOT TRUE. The forces are far too weak. In fact, lipids force water to be more ordered around them, and ordered states, like high energy states, are unfavorable, hence the association of lipids is favored because less water is forced to be ordered, not because of the very weak attraction between alkyl chains.