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Chemistry 1(Vet) – CHEM1405

Welcome: Bachelor of Veterinary Science

This Week: Atomic Structure and the Periodic Table

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This Week: Atomic Structure and the Periodic Table Overview of CHEM1405, administrative matters Resources and study in chemistry Atomic structure Periodic Table

Assistance in Chemistry

Dr Adrian V George

Room 224

adrian.george@sydney.edu.au

Assistance administrative

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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

Assistance in Chemistry

Formal:

Lectures

Laboratories

Informal:

Study groups

Duty tutor

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Plan your study time from the start Plan your study time from the start –– now!now!

On-line:

eLearning

ChemCAL

Self-help problems

Off-line:

Problem sets

Textbooks

Lecture notes

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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 (htt //fi t h d d / h 1405/ )

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Resource Page (http://firstyear.chem.usyd.edu.au/chem1405/ )

ChemCAL (http://chemcal.chem.usyd.edu.au/)

Text book: Blackman et al. Chemistry

Course information

Laboratory Work

Start in week 2, attendance a requirement of the course

Assessment

15 % laboratory assessment

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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

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)

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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

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Atomic nomenclature

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Atomic Number - The number of protons.

Mass Number - The number of protons + neutrons.

Isotopes – different no of neutrons, same no of protons eg 12C, 13C.

Relative Atomic Mass

Based on a standard that the mass of 12C is exactly 12.

A mole is the same number as the number of 12C atoms in exactly 12 grams of 12C atoms.

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The number "12 grams" is chosen to coincide with the defined atomic mass of one 12C atom, 12 amu.

1 mole = 6.022 x 1023.

The relative mass of a single atom can be measured by a mass spectrometer.

Mass Spectrometer

–70 eV accelerating plates

ion beam

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+ + + + + ++

+

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+

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Mass Spectrometer

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ion beam

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+ +

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+

+

magnetic field

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++ +

Mass Spectrometer

The mass spectrometer measures relative mass of a single atom related to the mass of a single atom of 12C.

20 elements occur in nature as single isotopes: Be F Na Al P Sc Mn Co As Y Nb Rh I Cs Pr Tb

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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 (23Na) 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.

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

E.g. Chromium

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51.9405 x 83.79% = 43.5252.9407 x 9.50% = 5.0353.9389 x 2.36% = 1.27

Total = 51.99

The atomic mass of chromium is 51.99.

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The relative molar mass of a substance is the sum of its constituent atoms or ions

e.g. sodium chloride, NaClrelative molar mass = 22.99 + 35.45 = 58.34

Molar mass

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e.g. glucose, C6H12O6

relative molar mass = (6 x 12.01) + (12 x 1.008) + (6 x 16.00) = 180.16

e.g. sodium lactate, C3H5O3Narelative molar mass = (3 x 12.01) + (5 x 1.008)

+ (3 x 16.00) + 22.99 = 112.06

Atomic Theory

Light of different colour has a different wavelength

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-Ray UVX-Ray Microwave and Radio frequency

Infrared

400 500 600 700 nm

Wavelength:short long

Colour:blue red

Energy:high low

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

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Suggests the process emitting light in the atom is quantised

The electron in the atom may possess only certain energies

Continuous spectrum

Atomic spectrum

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Bohr Atom

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Other Elements

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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

Quantum Mechanical Model

Light has a dual nature and the de Broglie equation relates wavelength to momentum

= h/mv Schrödinger Equation

E

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= 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

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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

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an electron orbital is described by four coordinates. The coordinates of the orbital are given by quantum

numbers.

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.

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energy the orbital.

n = 1 n = 2 n = 3

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

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l = 0 l = 1

l = 0 "s"l = 1 "p"l = 2 "d"l = 3 "f"

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Magnetic Quantum Number, ml

ml = -l, -(l -1) … 0 … (l -1), l Describes the orientation of the orbital e.g. if l = 0; ml = 0 (s orbital)

if l = 1; ml = -1, 0, +1 (px, py, pz orbitals)

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y

if l = 2; ml = -2, -1, 0, +1, +2 (dxy, dyz, dxz, dx2-y2, dz2)

Spin Quantum Number, ms

ms = + 1/2 , - 1/2

Describes the spin of the electron. Each orbital, uniquely described by n, l and ml may contain a

maximum of two electrons, one spin +1/2, the other spin -1/2 .

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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

Question:

Complete the table

Shell, n = 1 2 3 4

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,

Sub-shell, l = 0 0, 1

Description s s, p

Maximum no. of 2 2, 6

electrons in sub-shellTotal electrons 2 8

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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

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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.

Polyelectronic Atoms The orbital energy of a polyelectronic atom

increases:

1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s <4f <5d …

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Question: complete the table

Element No of electrons Electron configurationH 1 1s1

He 2 1s2

Li 3 1s2 2s1

B 5 1s2 2s22p1

C 6

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C 6O 8Ne 10Al 13Ca 20 [Ar] 4s2

Sc 21Cr 24 [Ar] 4s1 3d5

Fe 26Cu 29 [Ar] 4s1 3d10

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Periodic TableThe vertical columns are called Groups.The horizontal rows are called Periods.

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The Group number = The number of Valence electrons (electrons in the outer shell).

The Period number = The number of occupied energy shells.

Periodic Table & ElectronsThe orbital energy of a polyelectronic atom increases1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s <4f <5d …

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Periodic Table & Quantum No

Principal Quantum Non = 1

n = 2

n = 3

n 4

Angular Momentum Quantum No

l = 0 s-block; l = 1 p-block; l = 2 d-block

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n = 4

n = 5

n = 6

n = 7

Magnetic Quantum No: 1 s-orbital; 3 p-orbitals; 5 d-orbitals

Spin Quantum No: 2 electrons in each orbital

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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.

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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.

Biological Periodic Table

This Lecture: Periodic Table Overview of the ‘Biological’ Periodic Table Ions Inorganic nomenclature

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Periodic Table & Properties

Metals Non-metalsSemi-metals or metalloids

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Metals and non-metals

Metals show:

•malleability and ductility. •good conduction of electricity and heat.•luminous surface appearance. f i i l h d i

Non-metals are typically:

•brittle solids or gases (there is one liquid, bromine). •have poor thermal and electrical conductivity. f ti l h d i ll d

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•form positively charged ions called cations.

•form negatively charged ions called anions.

Essential and Toxic Metals

All elements, just like all substances, are toxic at sufficiently high doses.

The difference between these types of elements is demonstrated in the following curves showing the relationship between concentration

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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.

Well Healthy Dead Concentration Concentration Essential Trace Element Toxic Metal

and the health of an organism.

Essential and Toxic Metals

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

1 HYDROGEN

H 1.008

2 HELIUM

He 4.003

3 LITHIUM

Li 6.941

4 BERYLLIUM

Be 9.012

5 BORON

B 10.81

6 CARBON

C 12.01

7 NITROGEN

N 14.01

8 OXYGEN

O 16.00

9 FLUORINE

F 19.00

10 NEON

Ne 20.18

11 SODIUM Na

22.99

12 MAGNESIUM

Mg 24.31

13 ALUMINIUM

Al 26.98

14 SILICON

Si 28.09

15 PHOSPHORUS

P 30.97

16 SULFUR

S 32.07

17 CHLORINE

Cl 35.45

18 ARGON

Ar 39.95

19 POTASSIUM

K 39.10

20 CALCIUM

Ca 40.08

21 SCANDIUM

Sc 44.96

22 TITANIUM

Ti 47.88

23 VANADIUM

V 50.94

24 CHROMIUM

Cr 52.00

25 MANGANESE

Mn 54.94

26 IRON

Fe 55.85

27 COBALT

Co 58.93

28 NICKEL

Ni 58.69

29 COPPER

Cu 63.55

30 ZINC

Zn 65.39

31 GALLIUM

Ga 69.72

32 GERMANIUM

Ge 72.59

33 ARSENIC

As 74.92

34 SELENIUM

Se 78.96

35 BROMINE

Br 79.90

36 KRYPTON

Kr 83.80

37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

Essential

Toxic

Medicinal

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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 pblocks of the fifth and sixth periods.

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Rb 85.47

38 STRONTIUM

Sr 87.62

39 YTTRIUM

Y 88.91

40 ZIRCONIUM

Zr 91.22

41 NIOBIUM

Nb 92.91

42 MOLYBDENUM

Mo 95.94

43 TECHNETIUM

Tc [98.91]

44 RUTHENIUM

Ru 101.07

45 RHODIUM

Rh 102.91

46 PALLADIUM

Pd 106.4

47 SILVER

Ag 107.87

48CADMIUM

Cd 112.40

49 INDIUM

In 114.82

50 TIN

Sn 118.69

51 ANTIMONY

Sb 121.75

52 TELLURIUM

Te 127.60

53 IODINE

I 126.90

54 XENON

Xe 131.30

55 CAESIUM

Cs 132.91

56 BARIUM

Ba 137.34

57-71 72 HAFNIUM

Hf 178.49

73 TANTALUM

Ta 180.95

74 TUNGSTEN

W 183.85

75 RHENIUM

Re 186.2

76 OSMIUM

Os 190.2

77 IRIDIUM

Ir 192.22

78 PLATINUM

Pt 195.09

79 GOLD

Au 196.97

80 MERCURY

Hg 200.59

81 THALLIUM

Tl 204.37

82 LEAD

Pb 207.2

83 BISMUTH

Bi 208.98

84 POLONIUM

Po [210.0]

85 ASTATINE

At [210.0]

86 RADON

Rn [222.0]

87 FRANCIUM

Fr [223.0]

88 RADIUM

Ra [226.0]

89-103 104 RUTHERFORDIUM

Rf [261]

105 DUBNIUM

Db [262]

106 SEABORGIUM

Sg [266]

107 BOHRIUM

Bh [262]

108 HASSIUM

Hs [265]

109 MEITNERIUM

Mt [266]

Medicinal

Archaea

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•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.

Reasons?

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g p y

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.

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

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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.

Bulk Elements

Bulk Elements

Biochemical Function

Calcium Bone and Teeth ca 1kg

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Chlorine Electrolyte

Magnesium Bone, some enzymes ca 25g

Phosphorous Bone, Nucleic acids

Sodium Extracellular cation - water electrolyte balance

Potassium Intracellular cation

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Trace ElementsTrace Elements Biochemical Function

Fluorine Bone and Teeth

Iodine Thyroid hormone production Chromium Utilisation of blood glucose Vanadium Co-factor of nitrate reductase Manganese Co-factor for enzymes

Iron Iron proteins, such as heme, ferritins

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Cobalt Vitamin B12 Nickel Cofactor of urease

Copper cytochrome oxidase Zinc Enzymes eg alcohol dehydrogenase

Molybdenum aldehyde oxidase Selenium Glutathione peroxidase

Arsenic Not known Silicon Connective tissue and Bone Tin Formation of bone

Toxicity & Health Effects Of Chromium

Claims:•May reduce weight and increase muscle.•May help diabetes and lower cholesterol. •Regulates blood sugar.

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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 Fe2+ and dissolved sulfides. Cr(III) is considered to be an essential nutrient.

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 H2AsO4- 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 k f b d i ht

Arsenic

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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 the bladder, kidney, liver and lung.

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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-

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F R 89

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Fr Ra 89-105

Group 1: M+ cations

Eg Na 1s2 2s2 2p6 3s1

Na+ 1s2 2s2 2p6

Group 2: M2+ cations

Eg Ca [Ar] 4s2

Ca2+ [Ar]

Group 17: X- anions

Eg Cl 1s2 2s2 2p6 3s2 3p5

Cl- 1s2 2s2 2p6 3s2 3p6

d-block: variable oxidation state

Eg Fe [Ar] 4s2 3d6

Fe2+ [Ar] 3d6

Fe3+ [Ar] 3d5

Down a group, more metallic, O.No two units apart. Eg As(III) or As(V)

Size

Atomic size related to electron configuration

Cations are always smaller than the atoms

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smaller than the atoms from which they formed

Anions are always larger than the atoms from which they formed

Ionisation Energy

Ionisation energy is always positive

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

d d h

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It depends on the strength with which the outermost electron is held by the nucleus

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Naming Ionic CompoundsIons can be either monatomic or polyatomic.Ionic compounds contain cations and anions in a ratio that maintains electrical neutrality.

cation anion Formula Name

Ba2+ NO3- Ba(NO3)2 barium nitrate

Complete

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K+ PO43- potassium phosphate

Ag+ O2- silver oxide

Cd2+ S2- cadmium sulfide

K+ MnO4- potassium permanganate

Na+ HCO3- sodium hydrogencarbonate

Fe2+ SO42- iron(II) sulfate

Fe3+ SO42- iron(III) sulfate

Complete the formula

Questions

1. What is the formula and name of the compound formed between barium and phosphate (PO4

3-)?

d h f ll f d

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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: S2-, Cl-, Ar, K+, Ca2+