“If, in some cataclysm, all scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words?

“I believe it is the atomic hypothesis (or atomic fact, or whatever you wish to call it) that all things are made of atoms — little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another.

“In that one sentence you will see an enormous amount of information about the world, if just a little imagination and thinking are applied.”

- Richard Feynman

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Chapter 3 3

Chapter 3 – Models of Structure to Explain Properties

Matter occurs in bulk in a number of forms. We have looked at the idea that matter is found in solid, liquid, and gaseous states. We have also classified matter as homogeneous and heterogeneous. But there are other models that we can develop for describing substances.

In particular, we can classify substances on the basis of their physical properties, their interaction with electromagnetic radiation, their chemical constituents, and other methods.

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Consider sodium chloride:- it is optically transparent to visible light.- it can grow regular crystals with stepped structures but it also dissolves in water.- it can be fractured to give smooth, straight edges.

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What do these observations tell us?

Chemists use such information about the nature of the bulk substance to infer information about the underlying structure of the material.

This process of trying to imagine what it is about a substance that leads to the observed properties is called “modelling” and the imagined arrangement of atoms is called a “model”.

We now know what many of these models are – because chemistry has been exploring matter for hundreds of years. However, it is useful to remember that when we don’t know what a compound is or why it has certain properties, we need to construct a model.

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Q3.1 Sodium chloride crystals fracture to give smooth, flat surfaces because:

a)Atoms are really small so it is hard to see bumps of surface.

b)Sodium and Chloride ions have opposite charges.c) Ionic lattices have planes of atoms.d)Being transparent makes sodium chloride a “glass”.

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Most substances can be placed in one of four models:

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Covalent Network Solids

One of the more uncommon forms of matter, in terms of the number of unique compounds, but one of the most common in terms of quantity, as silica is a network solid.

Diamond and graphite are the classic examples given in most textbooks.

Network solids depend upon covalent bonding between the atoms in the network.

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Covalent network solids are modelled as three-dimensional networks of atoms, in which each atom is bound to other atoms, forming a network of covalent bonds. This model can rationalize their high melting point (need to break the bonds to melt), lack of electrical conductivity (the atoms are neutral), and hardness (long range structure makes it difficult to cleave the lattice).

The formula of a covalent network compound tells us the relative numbers of atoms of each element in the lattice.

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Q3.2 Each carbon atom in a diamond lattice is surrounded in a tetrahedron by four other carbon atoms. As a result, the lattice is:

a) triangular b) square c) cubic d) hexagonal

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Ionic Substances

Many minerals are ionic compounds, which facilitates their dissolution leading to erosion and weathering. Indeed, ionic compounds are some of the most common forms of matter.

Typically, they have a (1) high melting point, (2) do not conduct electricity in solid form but do when molten or in solution, and (3) are hard and brittle.

The ions are arranged in a 3-D network called an “ionic lattice”.

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What and why are ions?

Book says: “Ions are atoms or groups of atoms that as a result of processes during chemical reactions have different numbers of protons and electrons.”

A good definition but could lead to confusion…. the number of protons can never change during a chemical reaction! The number of protons can not become “different” during a chemical reaction. But the number of electrons does not necessarily equal the number of protons after a reaction – and that is the better definition of an ion – “… as a result of processes during a chemical reaction that leads to the number of electrons being different from the number of protons in the nucleus.”

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Cations: more protons than electrons results in an overall positive charge.Anions: more electrons than protons results in an overall negative charge.

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The periodic table tells us a lot about what ions are formed.

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The term “species” – in chemistry – is applied to any atom, molecule, ion, or any atomic group of these that can exist as an independent entity and has its own characteristic behaviour.

Ions are different species with different characteristics compared to the atoms from which they are obtained.For example, sodium and sodium ions – one is a flammable metal, the other a condiment.

We should be careful in our use of language and not refer to “Na+” not as “sodium” but the “sodium ion”. However, we rarely are careful…

(and nomenclature doesn’t help….)

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Q3.3 What is the name of Na3PO4?

a) Sodium phosphate b) Trisodium phosphatec) Sodium phosphite d) Trisodium phosphite

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Polyatomic ions:

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Like network solids, the chemical formula for ionic compounds reflects the relative number of “atoms” – in this case, “ions” (either mono-atomic or poly-atomic).

The ratio of ions is a reflection of their charges, since the overall charge of the formula must balance out to zero.

The molar mass of an ionic compound is the sum of the molar masses of ions, taking the relative number of ions into account.

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Metals and Metallic Substances

Few metals are found in nature – gold, copper, iron. Most are found in the form of ores – lead, aluminum, nickel –and must be refined through chemical processes.

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Our model for metallic solids is much more fluid than for either network solids or ionic compounds.

Metals consist of an ordered lattice of nuclei and core electrons, suspended in a sea of delocalized valence electrons. The forces bonding the atoms is the electrostatic attraction between the nuclei and the sea of electrons – it is called “metallic bonding”.

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Q3.4 The fluid nature of the electrons within a metallic solid results in which of the following properties?

a) malleabilityb) ductilityc) thermal conductiond) shininesse) all of the above.

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“A common mistake that people make when trying to design something completely foolproof is to underestimate the ingenuity of complete fools.”

- Douglas Adams

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Molecular Substances

The vast majority of known substances fall within the category of “molecular substances”. Roughly speaking, there are 10 million identified compounds and 90% of them are molecular species (and of these, 90% are “organic compounds”).

Consider, for example, that proteins are molecular substances and that there are roughly 100,000 different proteins in the human body alone, it is not hard to realize the importance of molecular substances – particularly to life as we know it.

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Molecular substances are characterized by:

- low melting and boiling points (“low” being a relative term) – many molecular substances occur as gases (oxygen, hydrogen) or liquids (water, ethanol) at ordinary temperatures

- generally being incapable of conducting electricity (although this is not strictly true as there are many molecular species that are conducting)

- typically being soft and/or malleable (easily scratched and deformed – although, again, this isn’t always the case….)

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Our model for molecular substances has the atoms held together by covalent bonds. Literally, if the outer electrons of an atom are called “the valence shell”, then “covalent” means “sharing the valence electrons”.

In each molecule, of a molecular substance, the number of atoms and their connectivity is exactly the same.

For example, all molecules of water consist of one oxygen atom and two hydrogen atoms – hence, H2O.

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It is important to realize that for molecular compounds, it is not just the number of atoms in the molecular formula but the way that they are arranged that matters.

Both ethanol and dimethyl ether have a molecular formula of C2H6O but very different arrangements and very different properties:

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The bonds holding atoms together in molecules are formed from the sharing of electrons between atoms.

You will likely have seen such bonds before represented by a line between two atoms with each line containing a pair of electrons.

That is, “H-H” is a representation of the covalent bond that binds two hydrogen atoms together.

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For Hydrogen, which has only one electron in its outer shell, it is not really that hard to see how the electrons come together giving a pair and a covalent bond.

For Cl2, the Cl-Cl bond is still formed from a single pair of electrons (sortof) with one electron coming from each chlorine while the remaining electrons aren’t involved.

Note that each chlorine retains its “17 electrons” but also shares electrons to get a total of “18 electrons”.

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The power of the molecular model to explain compoundshas been critical to the development of modern chemistry and other sciences (i.e. molecular biology).

But to explain molecular solids, we have to explain why molecules would form a solid – since covalent bonds are entirely within a molecule. That is, covalent interactions are “intramolecular”.

In the case of molecular solids – such as wax, sugar crystals, or ice cubes – there are “intermolecular” interactions which include hydrogen bonding, dipole-dipole interactions, and even simple Van der Waals interactions. More on these later (Chapter 6).

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But to preview a bit, and because it is consistent with our discussion of molecular solids, ice is a molecular solid generated from water molecules. The structure of ice crystals is consequence of the molecule structure.

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To recap:- molecular solids are composed of discrete molecules- the composition of all molecules for a substance is the

same – each molecule has the same number of atoms of each type connected in the same fashion

- within molecules, the atoms are held together by covalent bonds

- covalent bonds consist of a pair of electrons shared between two atoms

- each atom retains its original complement of electrons- within a solid, the molecules interact through some form

of intermolecular interaction, which are weaker than covalent bonds or other forms of bonding

- molecular structure can result in the properties of the solid

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A simple covalent bond, involving only a single pair of electrons, is a “single bond” (i.e. H-Cl).Covalent bonds can be made by more than one pair of electrons. Two pairs of electrons results in a “double bond” (i.e. O=O). Three pairs results in a “triple bond” (i.e. C N).

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So, how do we know all this?

The answer is that the model has been developed over the last century by many different scientists and has evolved through false starts and blind leads, to give us our present model which is self-consistent and provides insights into the way that molecules interact with each other.

That is, the “atomic hypothesis” leads to a “molecular hypothesis” (and an “ionic hypothesis”) and the whole picture holds together.

However, at a practical level, through spectroscopy.

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Composition and Formula by Mass Spectrometry

One of the major advances in science over the past half century is in our ability to identify chemical compounds. We can identify trace molecules at increasing smaller concentrations, as the Case Study in Chapter 3 points out – where we can now detect picograms of a drug such as cocaine – but also with determining what compounds are present, as the Case Study in Chapter 2 illustrated.

Mass spectrometry (MS), Infrared Spectroscopy (IR), and Nuclear Magnetic Resonance Spectroscopy (NMR) are routine analyses for any unidentified or new compound and are usually sufficient to characterize a compound.

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We have already discussed how MS can distinguish isotopes for an element but it can also be used to determine the composition of a molecule.

Electron Impact (EI) oxidizes a molecule within the source of the spectrometer – essentially:

M(g) M+(g) + e-

The resulting molecular ion can be analyzed for its “mass-to-charge” ratio (m/z) effectively determining its molecular weight. And that is sometimes enough to determine its molecular formula.

As a trivial example, only 1H216O has an m/z of 18.

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High Resolution Mass Spectroscopy takes this one step further as it is able to measure exact masses to seven significant figures! This allows us to actually differentiate between different molecular formulas.

Consider a gas that has a molecular weight of “28”. Two gases fit the bill – carbon monoxide (CO) and nitrogen (N2). Which is it?

Note that both carbon monoxide and nitrogen consist of several “isotopologues” which are molecules with the same composition but different isotopes of an element.

For CO: 12C16O, 12C18O, 13C16O, 13C18OFor N2: 14N14N, 14N15N, 15N15N

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Two things should be apparent:

1) The number of peaks for the two will be different – and have a different pattern. For CO, there will be peaks with m/z of “28”, “29”, “30”, and “31” while for N2, there will be peaks at m/z “28”, “29”, and “30”. This might be sufficient to distinguish between the gases … but probably not.

2) The exact masses of 12C16O and 14N14N (the most abundant isotopologues by far) are not the same. For 12C16O, the exact mass is m/z 27.99491 whereas for 14N14N, the exact mass is m/z 28.00614.

If the measured mass is 27.99542, then it is likely “CO”.

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Tables of exact isotope masses exist, along with possible molecular formulas (in handout with problem set).

Acetone has a chemical formula of C3H6O. It’s most abundant isotopologue, 12C3

1H616O, has an exact mass of:

M(C3H6O) = 3 x 12.00000 + 6 x 1.00783 + 1 x 15.99491= 58.04189

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On the other hand, butane has a formula of C4H10, which gives an exact mass of:

M(C4H10) = 4 x 12.00000 + 10 x 1.00783= 58.0783

So we could use High Resolution Mass Spectroscopy to differentiate between the two molecules. A mass spectrum giving 58.04213 would be more consistent with acetone than butane.

Note that if we simple add up the weighted averages for the atomic weights from the periodic table, we would get58.0791g/mol and 58.1222 g/mol, (their molar mass) respectively. That is because the MS deals with individual isotopes not averages.

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“An experiment is a question that science poses to Nature, and a measurement is the recording of Nature’s answer.”

- Max Planck, Scientific Autobiography and Other Papers, 1949

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Determining Connectivity in Molecules

High-Res MS can lead us to the correct molecular formula but that doesn’t necessarily give us the correct molecule.

An exact mass of 58.04213 can lead us to a formula of C3H6O but that doesn’t necessarily mean that it is acetone because there are more than one constitutional or structural isomers.

So, how do we decide between them?Connectivity and fragmentation.

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When a molecule is ionized within the injection system of a Mass Spectrometer, it can fragment into pieces. The fragmentation is characteristic for the structure of the molecule.

For example, consider the molecule “chloroethane”:

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Chapter 3 47

Acetone

Propanal

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Infrared Spectroscopy is another method of determining the connectivity and structure of molecules.

The infrared region of the electromagnetic spectrum is a region “below the red” end of the visible spectrum.

In this region, radiation interacts with vibrational motion in molecules.

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Chapter 3 50

Vibrational motion of molecules can be visualized for simple molecules such as water (H2O) or methane (CH4).

methane (CH4)

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Organic compounds, in particular, can be characterized based on their functional groups

What is a functional group?There are a number of ways to think of functional groups. The books says “commonly recurring connectivity patterns in portions of molecular compounds”. That is, a common functional group is a carbonyl group which consists of a C=O double bond. Alcohols are C-OH or carbon-oxygen bonded by a single bond and with a hydrogen attached to the oxygen. Note that this is analogous to water, H-O-H.

Another way to think of a functional group is that it is a reactive portion of an organic molecule.

Another way to think is that it is a big part of organic nomenclature which we will be discussing in Chapter 4.

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In Infrared Spectroscopy, we can identify functional groups within the infrared spectrum by their characteristic absorptions.

The spectrum consists of a plot of energy, as measured by wavenumbers, versus absorbance:

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Chapter 3 57

cocaine

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Chapter 3 59

nicotine

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Chapter 3 61

sucrose

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“Science is a way of thinking much more that it is a body of knowledge.”

- Carl Sagan, Broca’s Brain, 1986