Assistance in Chemistry

Chemistry 1(Vet) CHEM1405 Welcome: Bachelor of Veterinary Science This Week: Atomic Structure and the Periodic Table Overview of CHEM1405, administrative matters Resources and study in chemistry Atomic structure Periodic Table 1 Assistance in Chemistry Dr Adrian V George Room 224 adrian.george@sydney.edu.au Assistance - administrative First Year Enquiry Office (10 am - 3.15 pm) E-mail: firstyear@chem.usyd.edu.au Assistance - Course Work Duty Tutor Room (Monday Friday, 1-2, back of Lab D) Chem1405 discussion board 2 Assistance in Chemistry Formal: Lectures Laboratories Informal: Study groups Duty tutor On-line: elearning ChemCAL Self-help problems Off-line: Problem sets Textbooks Lecture notes Plan your study time from the start now! 3 1

Assistance in Chemistry Information and Resources First Year Chemistry web site (http://firstyear.chem.usyd.edu.au/) elearning (learn-on-line.usyd.edu.au ) (NB change of address from notes) Resource Page (http://firstyear.chem.usyd.edu.au/chem1405/ t h d d / h ) ChemCAL (http://chemcal.chem.usyd.edu.au/) Text book: Blackman et al. Chemistry 4 Course information Laboratory Work Start in week 2, attendance a requirement of the course Assessment 15 % laboratory assessment 15 % tutorial quizzes (Week 6, 9, 12) 10 % organic spectroscopy assignment 60 % 3 hour exam at the end of semester Staff-Student Liaison Committee 5 Recap: Atomic Structure 1803 J Dalton provided evidence for fundamental indivisible particles - atoms 1897 J J Thomson studied cathode rays - electrons 1909 R A Millikan measured the charge of an electron (1.6 x 10-19 C) 1909 E Rutherford proposed an atom be composed of a small positive nucleus surrounded by a lot of space occupied by the electrons 1920s N Bohr electrons occupy orbits of defined energy 6 2

Atomic nomenclature Atomic Number - The number of protons. Mass Number - The number of protons + neutrons. Isotopes different no of neutrons, same no of protons eg 12 C, 13 C. 7 Relative Atomic Mass Based on a standard that the mass of 12 C is exactly 12. A mole is the same number as the number of 12 C atoms in exactly 12 grams of 12 C atoms. The number "12 grams" is chosen to coincide with the defined atomic mass of one 12 C atom, 12 amu. 1 mole = 6.022 x 10 23. The relative mass of a single atom can be measured by a mass spectrometer. 8 Mass Spectrometer 70 ev accelerating plates + + + + + + + + + + + + + + + ion beam 9 3

Mass Spectrometer ion beam magnetic field + + + + + + + + + + + + + 10 Mass Spectrometer The mass spectrometer measures relative mass of a single atom related to the mass of a single atom of 12 C. 20 elements occur in nature as single isotopes: Be, F, Na, Al, P, Sc, Mn, Co, As, Y, Nb, Rh, I, Cs, Pr, Tb, Ho, Tm, Au, Bi. Their atomic masses are shown on the periodic table. Thus, the atomic mass of a sodium atom ( 23 Na) is 22.9898 amu. The remaining elements are each mixtures of several isotopes. The atomic mass being a weighted average of the naturally occurring atomic masses. 11 E.g. Chromium The atomic weight of chromium is obtained by multiplying each isotopic mass by its fractional abundance and then summing: 49.9461 x 4.35% = 2.17 51.9405 x 83.79% = 43.52 52.9407 x 9.50% = 5.03 53.9389 x 2.36% = 1.27 Total = 51.99 The atomic mass of chromium is 51.99. 12 4

Molar mass The relative molar mass of a substance is the sum of its constituent atoms or ions e.g. sodium chloride, NaCl relative molar mass = 22.99 + 35.45 = 58.34 e.g. glucose, C 6 H 12 O 6 relative molar mass = (6 x 12.01) + (12 x 1.008) + (6 x 16.00) = 180.16 e.g. sodium lactate, C 3 H 5 O 3 Na relative molar mass = (3 x 12.01) + (5 x 1.008) + (3 x 16.00) + 22.99 = 112.06 13 Atomic Theory Light of different colour has a different wavelength Wavelength: short long Colour: blue red Energy: high low -Ray 400 500 600 700 nm X-Ray UV Infrared Microwave and Radio frequency 14 Atomic Spectrum of Hydrogen Light emitted from a hydrogen arc lamp is composed of only a few lines: Only light of certain energy is emitted The pattern of lines is unique to hydrogen Atomic spectrum Continuous spectrum Suggests the process emitting light in the atom is quantised The electron in the atom may possess only certain energies 15 5

Bohr Atom 16 Other Elements Atomic emission spectrum is a characteristic of the element Bohr model of the atom works well for H but not for other elements (see http://onsager.bd.psu.edu/~jircitano/periodic4.html) Quantum mechanics gives a better description 17 Quantum Mechanical Model Light has a dual nature and the de Broglie equation relates wavelength to momentum = h/mv Schrödinger Equation = E This can only be solved if various boundary conditions are applied. That is, the waves must be standing waves that are continuous single valued multiples of a whole number of half wavelengths 18 6

Quantum Mechanical Model There are then discrete solutions that represent the energy of each electron orbital. A point in 3-D space may be described by three coordinates; an electron orbital is described by four coordinates. The coordinates of the orbital are given by quantum numbers. 19 Principal Quantum Number, n n = 1, 2, 3 Describes the size and extent of the orbital. The larger the value of n, the bigger & the higher energy the orbital. n = 1 n = 2 n = 3 20 Angular Momentum Quantum No, l l = 0, 1, 2 (n -1) Describes the shape of the orbital e.g. if n = 2; l = 0 or 1 l = 0 l = 1 l = 2 l = 3 "s" "p" "d" "f" l = 0 l = 1 21 7

Magnetic Quantum Number, m l m l = -l, -(l -1) 0 (l -1), l Describes the orientation of the orbital e.g. if l = 0; m l = 0 (s orbital) if l = 1; m l = -1, 0, +1 (p x, p y, p z orbitals) if l = 2; m l = -2, -1, 0, +1, +2 (d xy, d yz, d xz, d x2 -y 2, d z 2) 22 Spin Quantum Number, m s m s = + 1 / 2, - 1 / 2 Describes the spin of the electron. Each orbital, uniquely described by n, l and m l may contain a maximum of two electrons, one spin + 1 / 2, the other spin - 1 / 2. Why is this important? Relates to a thorough understanding of the periodic table Size of atom/ion related to metal toxicity Relates to type of bonds (σ or ) formed in compounds Shape essential for design of selective drugs 23 Question: Complete the table Shell, n = 1 2 3 4 Sub-shell, l = 0 0, 1 Description s s, p Maximum no. of 2 2, 6 electrons in sub-shell Total electrons 2 8 24 8

Polyelectronic Atoms When determining the ground state electron configuration, there are three rules: Pauli exclusion principle - no two electrons can have an identical set of four quantum numbers. i.e. there are a maximum of 2 electrons in any one orbital. Aufban principle - fill up low energy orbitals before high energy ones. Hund s rule - orbitals with the same energy (i.e. the same sub-shell) have the maximum number of unpaired electrons. 25 Polyelectronic Atoms The orbital energy of a polyelectronic atom increases: 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s <4f <5d 26 Question: complete the table Element No of electrons Electron configuration H 1 1s 1 He 2 1s 2 Li 3 1s 2 2s 1 B 5 1s 2 2s 2 2p 1 C 6 O 8 Ne 10 Al 13 Ca 20 [Ar] 4s 2 Sc 21 Cr 24 [Ar] 4s 1 3d 5 Fe 26 Cu 29 [Ar] 4s 1 3d 10 27 9

Periodic Table The vertical columns are called Groups. The horizontal rows are called Periods. The Group number = The number of Valence electrons (electrons in the outer shell). The Period number = The number of occupied energy shells. 28 Periodic Table & Electrons The orbital energy of a polyelectronic atom increases 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s <4f <5d 29 Periodic Table & Quantum No Principal Quantum No n = 1 n = 2 n = 3 n = 4 n = 5 n = 6 n = 7 Angular Momentum Quantum No l = 0 s-block; l = 1 p-block; l = 2 d-block Magnetic Quantum No: Spin Quantum No: 1 s-orbital; 3 p-orbitals; 5 d-orbitals 2 electrons in each orbital 30 10

Summary You should now be able to Recognise how relative atomic masses are derived. Calculate relative molar mass for any substance. Understand the difference between a Bohr model and quantum mechanical model of an atom. Understand the relationship between the four quantum numbers and electron configuration. Determine the electron configuration of an element from its position in the Periodic Table. Recognise whether an element is a metal, non-metal or semi-metal from its position in the Periodic Table. 31 Biological Periodic Table This Lecture: Periodic Table Overview of the Biological Periodic Table Ions Inorganic nomenclature 32 Periodic Table & Properties Metals Semi-metals or metalloids Non-metals 33 11

HYDROGEN LITHIUM SODIUM RUBIDIUM CAESIUM BERYLLIUM MAGNESIUM STRONTIUM BARIUM YTTRIUM ZIRCONIUM HAFNIUM NIOBIUM TANTALUM MOLYBDENUM TUNGSTEN TECHNETIUM RHENIUM RUTHENIUM OSMIUM RHODIUM IRIDIUM PALLADIUM PLATINUM SILVER GOLD CADMIUM MERCURY BORON ALUMINIUM INDIUM THALLIUM CARBON SILICON TIN LEAD NITROGEN PHOSPHORUS ANTIMONY BISMUTH OXYGEN SULFUR TELLURIUM POLONIUM FLUORINE CHLORINE IODINE ASTATINE HELIUM NEON ARGON XENON RADON Metals and non-metals Metals show: malleability and ductility. good conduction of electricity and heat. luminous surface appearance. form positively i charged ions called cations. Non-metals are typically: brittle solids or gases (there is one liquid, bromine). have poor thermal and electrical conductivity. form negatively charged ions called anions. 34 Essential and Toxic Metals All elements, just like all substances, are toxic at sufficiently high doses. Some metallic elements are essential trace elements needed by the body to maintain good health, others are of no benefit to a healthy body and are toxic at even very low concentrations. The difference between these types of elements is demonstrated in the following curves showing the relationship between concentration and the health of an organism. Well Healthy Dead Concentration Essential Trace Element Concentration Toxic Metal 35 Essential and Toxic Metals 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 1 H 1.008 3 Li 6.941 11 Na 22.99 19 POTASSIUM 4 Be 9.012 12 Mg 24.31 20 CALCIUM 21 SCANDIUM 22 TITANIUM 23 VANADIUM 24 CHROMIUM 25 MANGANESE 26 IRON 27 COBALT K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 39.10 40.08 44.96 47.88 50.94 52.00 54.94 55.85 58.93 58.69 63.55 65.39 69.72 72.59 74.92 78.96 79.90 83.80 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 85.47 87.62 88.91 91.22 92.91 95.94 [98.91] 101.07 102.91 106.4 107.87 112.40 114.82 118.69 121.75 127.60 126.90 131.30 55 56 57-71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Cs 132.91 87 FRANCIUM Fr [223.0] Ba 137.34 88 RADIUM Ra [226.0] Hf 178.49 89-103 104 RUTHERFORDIUM Rf [261] Ta 180.95 105 DUBNIUM Db [262] W 183.85 106 SEABORGIUM Sg [266] Re 186.2 107 BOHRIUM Bh [262] Os 190.2 108 HASSIUM Hs [265] Ir 192.22 109 MEITNERIUM Mt [266] 28 NICKEL Pt 195.09 29 COPPER Au 196.97 30 ZINC Hg 200.59 5 B 10.81 13 Al 26.98 31 GALLIUM Tl 204.37 6 C 12.01 14 Si 28.09 32 GERMANIUM Pb 207.2 7 N 14.01 15 P 30.97 33 ARSENIC Bi 208.98 8 O 16.00 16 S 32.07 34 SELENIUM Po [210.0] 9 F 19.00 17 Cl 35.45 35 BROMINE At [210.0] 2 He 4.003 10 Ne 20.18 18 Ar 39.95 36 KRYPTON Rn [222.0] Essential Toxic Medicinal Medicinal Archaea Nearly all of the trace essential elements are from the first row of the d block. Most of the highly toxic elements are from the late d and early p blocks of the fifth and sixth periods. 36 12

Reasons? Nature has made use of the more abundant elements. Toxic elements from inert bonds (in general) and the toxic elements don t bind well to the O and N donor ligands preferred by nature. An important aspect of abundance is availability. For example, Al is one of the most abundant elements but is toxic. It is not bioavailable because of the insolubility of the forms it is found in nature. Increased use of Al is making it much more bioavailable but our bodies have evolved only limited ability to deal with it. 37 Biological Roles for Metals Trace Element: A chemical element required by an organism in only a trace amount. Typically require less than 3 mg/day intake. Bulk elements - Essential elements with typical intakes of greater than 100 mg/day. Enzyme: A protein specialised to catalyse a specific metabolic reaction. Cofactor: A small-molecular-weight substance required for the action of an enzyme. 38 Bulk Elements Bulk Elements Calcium Chlorine Magnesium Phosphorous Sodium Potassium Biochemical Function Bone and Teeth ca 1kg Electrolyte Bone, some enzymes ca 25g Bone, Nucleic acids Extracellular cation - water electrolyte balance Intracellular cation 39 13

Trace Elements Trace Elements Fluorine Iodine Chromium Vanadium Manganese Iron Cobalt Nickel Copper Zinc Molybdenum Selenium Arsenic Silicon Tin Biochemical Function Bone and Teeth Thyroid hormone production Utilisation of blood glucose Co-factor of nitrate reductase Co-factor for enzymes Iron proteins, such as heme, ferritins Vitamin B12 Cofactor of urease cytochrome oxidase Enzymes eg alcohol dehydrogenase aldehyde oxidase Glutathione peroxidase Not known Connective tissue and Bone Formation of bone 40 Toxicity & Health Effects Of Chromium Claims: May reduce weight and increase muscle. May help diabetes and lower cholesterol. Regulates blood sugar. Cr(VI) is classified as "Carcinogenic to Humans". Cr(VI) compounds are soluble in water thus may have a harmful effect on the environment. Cr(VI) is readily reduced by Fe 2+ and dissolved sulfides. Cr(III) is considered to be an essential nutrient. 41 Arsenic As(III) combines with -SH groups and interferes with the function of a number of enzymes. As(V) is considerably less toxic than As(III). Forms H 2 AsO 4- which is chemically similar to phosphate and can interfere with phosphate metabolism. The lethal dose to humans is estimated at 1 to 4 mg of arsenic per kg of body weight. Long-term exposure to low concentrations of arsenic has been reported to cause skin cancer and it may carry risk of various internal organ cancers. Other effects of high exposure levels include nausea, vomiting and diarrhoea; decreased production of red and white blood cells; abnormal heart rhythms; blood vessel damage; and a "pins" and "needles" sensation in hands and feet. Arsenic is carcinogenic. Breathing it increases the risk of lung cancer. Ingesting it increases the risk of skin cancer and tumours of 42 the bladder, kidney, liver and lung. 14

Ions and Oxidation States H He Li Be B C N O F Ne Na Mg 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 57-71 Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra 89-105 Down a group, more metallic, d-block: variable O.No two units oxidation state apart. Eg As(III) or As(V) Group 2: M 2+ cations Eg Ca [Ar] 4s 2 Ca 2+ [Ar] Group 1: M + cations Eg Na 1s 2 2s 2 2p 6 3s 1 Na + 1s 2 2s 2 2p 6 Eg Fe [Ar] 4s 2 3d 6 Fe 2+ [Ar] 3d 6 Fe 3+ [Ar] 3d 5 Group 17: X - anions Eg Cl 1s 2 2s 2 2p 6 3s 2 3p 5 Cl - 1s 2 2s 2 2p 6 3s 2 3p 6 43 Size Atomic size related to electron configuration Cations are always smaller than the atoms from which they formed Anions are always larger than the atoms from which they formed 44 Ionisation Energy Ionisation energy is always positive M(g) M + (g) + e - It depends d on the strength with which the outermost electron is held by the nucleus 45 15

Naming Ionic Compounds Ions can be either monatomic or polyatomic. Ionic compounds contain cations and anions in a ratio that maintains electrical neutrality. cation anion Formula Name Ba 2+ NO3 - Ba(NO3)2 barium nitrate K + PO4 3- potassium phosphate Ag + O 2- silver oxide Cd 2+ S 2- cadmium sulfide Complete the formula K + MnO4 - potassium permanganate Na + HCO3 - sodium hydrogencarbonate Fe 2+ SO4 2- iron(ii) sulfate Fe 3+ SO4 2- iron(iii) sulfate 46 Questions 1. What is the formula and name of the compound formed between barium and phosphate (PO 4 3- )? 2. Order the following atoms in terms of increasing radius: Ar, Li, Na, P, Sb 3. Order the following species in terms of increasing radius: S 2-, Cl -, Ar, K +, Ca 2+ 47 16