Humboldt State University ® Department of Chemistry

Richard A. Paselk

	VUB Biology	Fall 2001
Lecture Notes:: 12 September	© R. Paselk 2001

Atoms, Molecules & Chemistry

Exponential or scientific notation: It is often convenient to express numbers in exponential or scientific notation to avoid writing the huge numbers of zeros we often run into in the natural world.

• For example There are 6.02 x 10²³ particles in a mole.
• And the the concentration of hydrogen ions (H) is 10^-7M (M = moles/Liter) in pure water while the concentration of the water is about 55.5 M, (55.5 x 6.02 x 10²³ = 3.34 x 10²⁵ molecules/L) so about 2 out of every 10⁹ water molecules is dissociated.

What is Chemistry?

Chemistry is the study of matter and its transformations.

• "Classical" chemistry involves mostly electron transfers and/or interactions of charges (electron and nuclear). As we'll see only some electrons in atoms are involved - the outer or valence electrons of atoms.

What is matter? Stuff. Has mass and occupies space.

Mass: The measure of quantity for matter. Mass is the property of matter resulting in its inertia and and attraction via gravity.

• Do not confuse mass and weight. Weight is the force acting on an object due to gravity. We often interchange these terms in conversation, but they are quite different - you have the same mass whether you are weightless in space on here on Earth (taking a shuttle flight is no substitute for a diet!). To confuse us further we call the determination of mass "weighing"!

Matter has both physical properties and chemical properties. These are properties which do not depend on the quantity of substance and therefore they can be used to identify a substance (sometimes referred to as intensive properties).

• Physical properties of substances can be observed without, in principle, changing their compositions. Physical properties include mass, color, density etc. Note that physical changes such as melting, cutting, etc. do not change composition.

States of Matter. Matter can exist in three states under earth-surface conditions:

• Solid: definite shape and volume (Crystals vs. super-cooled liquids or glasses)
• Liquid: definite volume, but no defined shape - will fit to container etc.
• Gas: no definite shape or volume - will fill whatever container they are in.
  • both liquids and gases are fluids.
• Chemical properties of substances describe behaviors which lead to changes in composition. Chemical properties describe reactivity under various circumstances (does it burn in air, react with acids or bases, corrode in sea water etc.) Note that chemical changes result in different compositions (different ratios and/or types of atoms).

Conservation of Mass

A fundamental observation is that mass is unchanged in chemical processes. This observation is summarized in the

Law of Conservation of Mass: Mass is neither created nor destroyed during a chemical change. (Strictly speaking there is no measurable change.) For example, if we burn gasoline (octane) in air we will get carbon dioxide and water:

If we were to weigh (determine the mass) of the carbon and oxygen vs. the carbon dioxide and water we would find them to be identical - the masses are the same on both sides of the equation (that's why its called a chemical equation, the two sides are "equal"). Looked at another way, if you count the atoms, the numbers of each kind of atom on each side are identical - so we can also say that atoms are conserved in chemical processes.

This is really the fundamental assumption of chemistry, and thus the measurement of mass is the fundamental process underlying much of chemical work.

Elements

Another fundamental concept is that of elements. Elements are substances which cannot be broken down further into simpler substances by chemical or (non-nuclear) physical means.

Note that combinations of various elements to form compounds nearly always result in the formation of compounds with constant proportions by mass. In other words, the ratios of the elements in compounds generally reduce to small whole numbers (this does not hold in biological macromolecules because the molecule size is so large, but the ratio of elements in any particular macromolecule is still a ratio of whole numbers).

The Atom

Atoms are known to consist of three different types of particles: electrons, protons and neutrons (the common form of one very important atom, hydrogen, has only two kinds: a proton and an electron). The protons and neutrons reside in a small inner portion called the nucleus while the electrons reside in a relatively large cloud centered on the nucleus. (For hydrogen, if the nucleus were the size of a pea, the electrons would occupy a sphere about the diameter of a football field. Atoms are mostly empty space!) Important properties of these particles are listed in the table below:

Particle Charge Relative Mass Mass Electron (e-) -1 1/1840 9.11 x 10-28g Proton (p or H+) +1 ª1 1.67 x 10-24g Neutron (n) 0  ª1  1.67 x 10-24g

Some important terms which you must know are:

• Atomic number (Z) - the number of protons in the nucleus. This number is characteristic of a given element.
• Atomic mass number (A) - the sum of the protons and neutrons in a given atom (p + n).
• Atomic mass - the actual mass of an average atom in a sample. The characteristic atomic masses for Earth are shown on periodic tables.
• Atomic Mass Unit: the atomic mass unit = amu is a unit of mass for atoms. It is defined as 1/12 the mass of one atom of ¹²C, where the mass of ¹²C is defined as 12 exactly.

In the mid 1920's Werner Heisenberg and Erwin Schrödinger independently came up with models of the atom which accurately predicted the behavior of all atoms in principle.

A basic assumption of these treatments is that electrons behave like waves in some sense, and their locations in an atom are described by equations for waves. A second assumption is that of Heisenberg's Uncertainty Principle. This states that we cannot simultaneously know the position and momentum of a particle. Mathematically:

Schrödinger assumed that the electron's behavior could be described by a three dimensional standing wave. He derived an equation which described the amplitude of this wave. The simplest solution for the Schrödinger Equation for the ground state (1s) energy of a hydrogen atom is:

This equation has little real meaning. However, the square of the value of psi (Y²) tells the probability of finding an electron at any given location.

Electronic Energy Levels:

• We will designate the primary energy level, corresponding to the average radial distance of the electron from the nucleus as a shell, and give it the symbol n. The lowest possible energy level is then the ground state with n = 1.
• Shells with n > 1 may have subshells which are different geometrical patterns of electron distribution. Thus:
  • The lowest energy pattern is spherical and given the designation s.
  • The next lowest energy distribution is bi-lobed with a planar symmetry. It is given the designation p.
  • The third lowest energy distribution has diagonal planes of symmetry and is designated d.
  • The fourth lowest energy distribution is designated f. This is the highest subshell type occupied by ground state electrons in any atom, so we will not look any further (an infinite number of subshells exist in theory for excited states, but they are not important to our understanding).
• The average energies of the different subshells are the energy of the shell, thus when subshells are present the energy of the shell is split. For example, in the n=2 shell the 2s orbital becomes lower in energy than the shell, while the 2p orbital becomes higher in energy.
• The regions of electron occupancy in subshells are called orbitals.
  • For each shell there is one s orbital.
  • For each shell with n = 2 or greater there are three p orbitals: p_x, p_y, and p_z.
  • For each shell with n = 3 or greater there are five d orbitals: d_xz, d_yz, d_xy, d_{x²- y²}, and d_z²

Atomic Orbitals Supplement

Chemical Periodicity

Look at the Periodic Chart on the wall. The pattern arises due to a repetition or periodicity of chemical properties. The vertical columns of the charts are called groups, while the rows are referred to a periods.

Note the numbering of the groups. The numbers from 1 - 18 are the internationally accepted numbers. We will also use the I - VIII "American" numbering system. Note that the "tallest" columns comprise what are referred to as the "representative elements" (IA - VIIIA).

Terms:

• Period: the rows of elements showing a repeating pattern of properties (e.g. Na - Ar).
• Group: a vertical column of elements on the table sharing a family resemblance of properties (e.g. Li - Fr).
• Representative elements: the elements of the s-block and p-block (blue and green on the table below).
• Transition metal elements: the elements of the d-block (yellow in the table below).
• Inner-transition metal elements: The f-block or Lanthanides and Actinides (not shown on the table below)
• Groups:
  • IA = alkali metals;
  • IIA = Alkaline earth metals;
  • VIIA = Halogens (note the generic symbol of X standing for any halogen);
  • VIIIA = Noble gases (older = inert gases).

You should know the terminology above.

Periodic Table of the Elements  IA IIA IIIA IVA VA VIA VIIA VIIIA    H  He Li Be    B C N O F Ne Na Mg IIIB IVB VB VI VIIB VIIIB IB IIB  Al Si P S Cl Ar K Ca Sc  Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr  Rb Sr  Y Zr Nb Mo Tc Ru Rh Pd  Ag  Cd  In Sn Sb Te I  Xe  Cs  Ba Lu  Hf Ta  W Re Os Ir  Pt Au  Hg Tl  Pb Bi Po At Rn

Trends: Note the trends for

• atomic size: decreases going from left Æ right and from bottom Æ top.
  • Size goes up with atomic number for any individual group.
  • Size decreases irregularly as atomic number increases for any given period (more charge pulls electrons in to nucleus, but shielding reverses as subshells [s or p orbital sets] fill.
• ionization energy: increases from left Æ right and from bottom Æ top.
  • Ionization energy goes down with atomic number for any individual group.
  • Ionization energy increases irregularly as atomic number increases for any given period (more charge pulls electrons in to nucleus, but shielding reverses as subshells [s or p orbital sets] fill.
• electronegativity increases from left Æ right and from bottom Æ top.
• note hydrogen combining ratios (LIH, BeH₂, BH₃, CH₄, H₃N, H₂O, HF) and acid/base properties of oxides (basic for metals, acidic for non-metals)

What is the basis of the periodicity of properties?

Electrons are held in shells.

• The first shell holds only 2 electrons in what is called the 1s orbital. Thus helium has its first shell filled. There is no more room for electrons, so it can't react by picking up another electron. On the other hand, as a crude thought model, we can consider that each electron is held by both charges in the He nucleus, so they are much more tightly held than the electron in H, so He won't give up an electron either - its inert.
• The second shell is larger (its out further from the nucleus) so holds 2 electrons in a 2s orbital, but there is now room for an additional three 2p orbitals. Thus 8 electrons can be accommodated in the second shell. Note the consequences:
  • for lithium (Li) the inner two electrons of the 1s shell cancel the attraction of two of the three protons, so the outer 2s electron "sees" only a single charge. But its out further than the electrons in the 1s shell were, so its not held as strong, so Li loses its outer electron more readily than H and is more reactive.
  • for Fluorine on the other side of the chart we can think of the outer shell electrons being attracted to the nucleus by 9 - 2 = 7 charges, so the last open space in an orbital will be super attractive to an outside electron, so F will be be very reactive, but in an opposite way to Li - it wants to steal electrons instead of giving them up.
  • for neon all of the orbitals will be filled, and the electrons will be strongly attracted to the nucleus and there is no for additional electron in the ground state, so Ne will again be inert like He above it.
• The third shell is larger yet (further from the nucleus), but still crowded, so initially it can only accommodate another eight electrons.
  • Of course the electrons in the 3s orbitals are even farther out from the nucleus, so we would expect Na to be even more reactive than Li, and so on for K, Rb, etc. each giving up its outermost electron more readily than the element above it in the Periodic table.
  • On the other hand Cl will also attract electrons less than F, so it will be less reactive etc. for the halogens.
  • So we will expect the most reactive elements to be on the opposite corners of the table - lower left and upper right.

THE ELEMENTS OF LIFE

Let's look at the basic requirements of an idealized, simplest life form and ask why life should use the particular atoms and molecules we see dominating in living organisms.

The following observations may be made regarding the elements of life:

• Life is largely a phenomena of hydrogen and the second period of the Periodic Table. That is, the major component elements (red) in all known organisms are from these periods. Why these four elements? First we might observe that H, O, N, and C are the smallest elements capable of forming 1, 2, 3, and 4 bonds. Smallest is important because that means they can form the strongest covalent bonds. So these atoms are going to be capable of forming some of the most stable molecules, an important consideration for something that needs to grow and reproduce in a hostile environment. C, N, and O are also the only elements capable of forming strong multiple bonds (carbon and nitrogen can form triple bonds, all three can form double bonds). Thus we can hypothesize that these elements were chosen for their special properties, specifically strong covalent bond formation (to enable the formation of stable biomolecules), the ability of carbon to form large branched molecules, and for C, N, and O the formation of multiple bonds which provides chemical flexibility (step-wise oxidations, different hybridization geometries etc.).
• The next important elements to life occur in Period 3: P and S (orange). These are the smallest elements capable of multiple covalent bonds to H, C, O and N, and which also have available d-shells. The d-shells allow additional transition states and reaction mechanisms. P and S are particularly important in the capture, storage, and distribution of chemical energy.
• The "essential" elemental ions found in all studied species (blue), Ca (II), Mg (II), K (II), Na (I) and Cl (-) were probably chosen more on the basis of availability in the primordial oceans then for any specific properties: other ions are very similar.
• The trace elements required by all studied organisms (violet) are all used as co-catalysts and/or ligands. Thus they were probably chosen for their specific electronic structures as well as their availability on the early earth.
• A variety of other elements are required by at least a few organisms, and are shown on the table in black. The grayed elements are not known to be of biological importance, but are shown as "place-markers" to help us keep track on the Table.

VUB Biology Home

Notes

Last modified 12 September 2001

© R Paselk