2011.10.06.. TÁMOP – 4.1.2-08/2/A/KMR-2009-0006 1

Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**

Consortium leader

PÁZMÁNY PÉTER CATHOLIC UNIVERSITYConsortium members

SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER

The Project has been realised with the support of the European Union and has been co-financed by the European Social Fund ***

**Molekuláris bionika és Infobionika Szakok tananyagának komplex fejlesztése konzorciumi keretben

***A projekt az Európai Unió támogatásával, az Európai Szociális Alap társfinanszírozásával valósul meg.

PÁZMÁNY PÉTER

CATHOLIC UNIVERSITYSEMMELWEIS

UNIVERSITY

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WORLD OF MOLECULES

CASE STUDIES

(Molekulák világa)

(Esettanulmányok)

KRISTÓF IVÁN

semmelweis-egyetem.hu

1. Chemical equilibria• equilibria in gases• acid-base equilibria

2. Acid-base theories• Arrhenius theory• Brønsted-Lowry theory• Lewis theory• Pearson theory (HSAB)

3. Superacids and superbases

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World of Molecules: Case studies

Previously - Chemical equilibria, acid – base theories

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World of Molecules: Case studies

Previously - Law of mass action (1867)• can be derived from the equality of the forward and backward

reaction rates• the product of the equilibrium concentrations of the reaction

products raised to a power according to their stoichiometic constant divided by the product of the equilibrium concentrations of the reactants raised to their respective stoichiometic power is constant (K) in equilibrium.

• (under the same conditions: pressure, Volume, Temperature )• e.g. for the above reaction (H2 + I2 2 HI)

[ ][ ] [ ] constant

22

2

=⋅

=IH

HIK

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World of Molecules: Case studies

Previously - Le Châtelier - Braun's principle - example

http://commons.wikimedia.org/wiki/File:NO2-N2O4.jpg

the equilibrium reaction of 2 NO2 N2O4

left: hot, more NO2right: cold, more N2O4

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World of Molecules: Case studies

• in case of a general acid, the dissociation reaction is • HA H+ + A-

• the acid dissociation equilibrium constant can be written

• in case of a general base, the dissociation reaction is • BOH B+ + OH-

• the base dissociation equilibrium constant can be written

Previously - Acid and base dissociation constants

[ ] [ ][ ] ( )aaa KpKHA

AHK log , −=⋅

=−+

[ ] [ ][ ] ( )bbb KpKBOH

OHBK log , −=⋅

=−+

1. Hydrogen,2. Oxygen,3. Carbon,4. Nitrogen,5. Sulphur,6. Sodium, 7. Silicon,8. Boron, 9. ...2011.10.06. TÁMOP – 4.1.2-08/2/A/KMR-2009-0006 7

Table of Contentssemmelweis-egyetem.hu

World of Molecules: Case studies

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World of Molecules: Case studies

http://en.wikipedia.org/wiki/Periodic_table

metalliclattice

metallic lattice

atomic lattice

metalliclattice

Lattice structure of elements

World of Molecules: Case studies

• solely in elemental form• noble gases

• both in elemental and compound form• gold (Au), oxygen (O), carbon (C)

• only in compound form• most of the chemical elements,

e.g. sodium (Na), fluorine (F), ...

Different abundances of elements in• the Universe• crust or atmosphere of the Earth• in Humans

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Natural abundance of chemical elements

World of Molecules: Case studies

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http://commons.wikimedia.org/wiki/File:ElementsAbundance.svg

Abundance of chemical elements in the Universe

World of Molecules: Case studies

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http://commons.wikimedia.org/wiki/File:Elemental_abundances.svg

Abundance of chemical elements in the crust of the Earth

World of Molecules: Case studies

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http://en.wikipedia.org/wiki/Abundance_of_the_chemical_elements

Abundance of chemical elements in Humans

World of Molecules: Case studies

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Hydrogen and its compounds

http://en.wikipedia.org/wiki/File:Hydrogenglow.jpg

World of Molecules: Case studies

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Hydrogen and its compounds

• electron structure: 1s1

• its elemental form is H2 diatomic molecule (on Earth)• compound forms

• in inorganic compounds with covalent bond, e.g. H2O• in hydrides (where H has a higher electronegativity in the

compound) e.g. LiH, NaH• in ionic form in polar solvents

(e.g. H+ or H3O+, cf. acid-base theories)• in organic compounds with covalent bond, e.g. CH4

World of Molecules: Case studies

common reactions• with halogenides (intense)

• F2, Cl2, I2, ...

• with oxygen (explosion like)• with the elements of the N group

(aka group 15 or V)• N2 + 3 H2 2NH3

• PH3, AsH3, SbH3, ...

• ionic form in water• 2H2O H3O+ + OH-

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Hydrogen and its compounds

World of Molecules: Case studies

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Hydrogen and its compounds

Production• lab: Zn + acid, Al + base• industrial:

CH4 + H2O → CO + 3H2C + H2O → CO + H2

• electrolysis of water

Applications• organic chemistry, • petrol industry,• ...

http://en.wikipedia.org/wiki/File:Shuttle_Main_Engine_Test_Firing_cropped_edited_and_reduced.jpg

World of Molecules: Case studies

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Oxygen and its compounds

http://de.wikipedia.org/w/index.php?title=Datei:Liquid_Oxygen.gif | http://en.wikipedia.org/wiki/File:Stilles_Mineralwasser.jpg

liquid oxygenmost common compound of oxygen: water

World of Molecules: Case studies

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Oxygen and its compounds

• electron structure: 1s22s22p4

• its elemental form is diatomic or triatomic molecule (O2 or O3)

• compound forms• forms oxides with most elements• in inorganic form with covalent bond (e.g. minerals)• in organic compounds with covalent bonds,

(e.g. CH3COOH, CH3CH2OH, ...)mostly as part of a functional group

• essential for biomolecules due to Hydrogen bonds

World of Molecules: Case studies

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Oxygen and its compounds

Production• fractional distillation of

liquid air• electrolysis of water• photosynthesis

Applications• metallurgy, • polymerchemistry,• welding,• ...

http://en.wikipedia.org/wiki/File:Clabecq_JPG01.jpg

World of Molecules: Case studies

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Oxygen cycle

http://en.wikipedia.org/wiki/File:Oxygen_Cycle.jpg

World of Molecules: Case studies

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Carbon and its compounds

http://en.wikipedia.org/wiki/File:C60-Fulleren-kristallin.JPG

World of Molecules: Case studies

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Carbon and its compounds

• electron structure: 1s22s22p2

• its elemental form is solid, its allotropes: graphite, diamond, fullerene, graphene

• compound forms• in inorganic compounds mostly with CO2, CO and CN-

groups• essential part of organic compounds• in organometallic compounds

(carbon to metal bond)

World of Molecules: Case studies

graphite diamondsoft material one of the hardest materials known

lubricant abrasiveelectric conductor electric insulatorthermal insulator good thermal conductor

opaque transparentcrystallizes in hexagonal lattice cubic crystal lattices

very anisotropic material isotropic material

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Main allotropes of carbon

comparison table of the two main allotropes of carbon

World of Molecules: Case studies

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Carbon and its compounds

Production• purified from elemental

source

Applications• petrochemical industry,• oil refineries,• composite materials (e.g.

carbon fiber),• pigment in inks (laser toner),• metallurgy,• abrasive and grinding tools

(carbides), ...http://en.wikipedia.org/wiki/File:Charcoal_sticks_051907.jpg

World of Molecules: Case studies

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Carbon and its compounds

Research applications(synthetic production)• Fullerene (ball like structures)

• drug delivery, …

• Carbon nanotubes (tube likestructures)

• Electronics,• Surface chemistry,• Electrode surface enhancements,

eg. ultracapacitors,• Solar cells,…

• Graphene (single layer of carbon)

• Electronics, … http://commons.wikimedia.org/wiki/File:Types_of_Carbon_Nanotubes.png

World of Molecules: Case studies

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Carbon cycle

http://en.wikipedia.org/wiki/File:Carbon_cycle-cute_diagram.svg

World of Molecules: Case studies

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Nitrogen and its compounds

http://en.wikipedia.org/wiki/File:Nitrogen-glow.jpg

World of Molecules: Case studies

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Nitrogen and its compounds

• electron structure: 1s22s22p3

• its elemental form is N2 diatomic molecule • compound forms

• in inorganic compounds mostly with NH3 and NOx groups

• in organic compounds in fuctional groups (e.g. amino, amide, nitro, nitroso,...)

• essential for most biological molecules• due to the ability of forming Hydrogen bonds

World of Molecules: Case studies

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Nitrogen and its compounds

Production• fractional distillation of

liquid air

Applications• inert gas atmosphere,• coolant liquid,• fertilizers,• explosives and

propellants,• ...

http://en.wikipedia.org/wiki/File:Liquidnitrogen.jpg

liquid nitrogen

World of Molecules: Case studies

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Nitrogen cycle

http://commons.wikimedia.org/wiki/File:Nitrogen_Cycle.svg

World of Molecules: Case studies

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Sulfur and its compounds

http://en.wikipedia.org/wiki/File:Sulfur.jpg

World of Molecules: Case studies

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Sulfur and its compounds

• electron structure: 1s2 2s2 2p6 3s2 3p4

• its elemental form is amorphous (S8), but has 30 different allotropes

• compound forms• in inorganic compounds as sulfide (S2-),

and its oxides - mostly sulfate (SO42-)

• in organic compounds part of 2 amino acids (cysteine, methionine), thus essential part of proteins: determines secondary structure with disulfide bonds

• also as merkaptans (smell of gas)

World of Molecules: Case studies

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Sulfur and its compounds

Production• as a mineral• conversion from H2S or

petroleum• biological methods

Applications• strong acid, • vulcanization of rubber,• fertilizers,• fungicide, pesticide, ...

http://en.wikipedia.org/wiki/File:Lapis_lazuli_block.jpg

lapis lazulisemi-preciousstone

World of Molecules: Case studies

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Sodium and its compounds

http://en.wikipedia.org/wiki/File:Nametal.JPG.jpg

World of Molecules: Case studies

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Sodium and its compounds

• electron structure: 1s2 2s2 2p6 3s1

• its does not occur in elemental form (too reactive)• compound forms

• mostly in inorganic minerals (hydroxide, carbonate, hydrogen carbonate, nitrate, phosphate, sulphate, borax, ...)

• ionic form in solutions or crystals• plays a crucial role in the salt balance of organisms

through the intracellular and extracellular ion levels

World of Molecules: Case studies

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Sodium and its compounds

Production• Na2CO3 (l) + 2 C (s) →

2 Na (g) + 3 CO (g)

• NaCl electrolysis

Applications• strong base, • in alloys to enchance

certain properties,• salt balance of

organisms, ...http://commons.wikimedia.org/wiki/File:Flametest--Na.swn.jpg

World of Molecules: Case studies

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Silicon and its compounds

http://en.wikipedia.org/wiki/File:SiliconCroda.jpg

World of Molecules: Case studies

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Silicon and its compounds

• electron structure: 1s2 2s2 2p6 3s2 3p2

• its does not occur in elemental form• compound forms

• mostly in inorganic silicates, constituent of sand (SiO2)most abundant element in the crust after oxygen

• can hardly be found in bioorganisms• can have similar structure as carbon

used in synthetic plastic substances

World of Molecules: Case studies

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Silicon and its compounds

Production• metallurgic grade (98%)

SiO2 + C → Si + CO2SiO2 + 2 C → Si + 2 CO

• pure (99,9%)molten salt electrolysis

Applications• semiconductor industry, • alloys (Al-Si), • silicones (Si-O bonds), ...

http://en.wikipedia.org/wiki/File:Polycrystalline_silicon_rod.jpg

polycrystalline silicon rod

World of Molecules: Case studies

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Boron and its compounds

http://en.wikipedia.org/wiki/File:Boron_mNACTEC.jpg

World of Molecules: Case studies

• electron structure: 1s2 2s2 2p1

• in elemental form has many allotropesamorphous, α-, β-, γ-, and tetragonal boron

• compound forms• mostly in inorganic

minerals, salt, borates

Production• reduction of B2O3

• from diborane (B2H6)

Applications• semiconductor industry, • boroncarbide production

for armors (B4C), • as abrasives,• in neodymium magnets, • ...

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Boron and its compounds

World of Molecules: Case studies

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Potassium and its compounds

http://en.wikipedia.org/wiki/File:Potassium.JPG

World of Molecules: Case studies

• electron structure: 1s2 2s2 2p6 3s2 3p6 4s1

• its does not occur in elemental form (too reactive)

• compound forms• mostly in inorganic

minerals, salt, hydroxides

• ionic form in crystals

Production• molten salt electrolysis

of KCl• electrolysis of KOH

Applications• strong base, • KNO3 fertilizer,• crucial role in the salt

balance of organisms,• ...

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Potassium and its compounds

World of Molecules: Case studies

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Chlorine and its compounds

http://commons.wikimedia.org/wiki/File:Chlor_1a.jpg | http://de.wikipedia.org/w/index.php?title=Datei:Rock_salt_crystal.jpg

World of Molecules: Case studies

• electron structure: 1s2 2s2 2p6 3s2 3p5

• its elemental form is uncommon (Cl2 gas)

• compound forms• mostly in inorganic salts,• oxides,• ionic form in crystals,• ...

Production• molten salt electrolysis:

2NaCl + 2H2O → Cl2 + H2 + 2 NaOH

• lab: 4HCl + MnO2 → MnCl2 + 2H2O + Cl2

Applications• disinfectant,• water treatment, • oxidizing agent,...

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Chlorine and its compounds

1. States of matter2. Gas state3. Gas laws4. Liquid state5. Properties of liquids, surface forces6. Solid state7. Crystal lattices8. Plasma state2011.10.06. TÁMOP – 4.1.2-08/2/A/KMR-2009-0006 46

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World of Molecules: Case studies

Next – States of matter