WORLD OF MOLECULES

(1)

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

Consortium leader

PÁZMÁNY PÉTER CATHOLIC UNIVERSITY

Consortium 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 UNIVERSITY SEMMELWEIS

UNIVERSITY

(2)

WORLD OF MOLECULES

CASE STUDIES

(Molekulák világa)

(Esettanulmányok)

KRISTÓF IVÁN

semmelweis-egyetem.hu

(3)

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

World of Molecules: Case studies

Previously - Chemical equilibria, acid – base theories

(4)

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)

[ ] [ ] [ ]

₂ ₂ ^constant

2

⋅ =

= H I

K HI

(5)

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 NO₂ right: cold, more N₂O₄

(6)

• 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

[ ] [ ]

[ ]

^a

^{( )}

^a

a pK K

HA A

K = H ⁺ ⋅ ⁻ , = −log

[ ] [ ]

[ ]

^b

^{( )}

^b

b pK K

BOH OH

K = B⁺ ⋅ ⁻ , = −log

(7)

1. Hydrogen, 2. Oxygen, 3. Carbon, 4. Nitrogen, 5. Sulphur, 6. Sodium, 7. Silicon, 8. Boron, 9. ...

Lattice structure of elements

(9)

• 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

Natural abundance of chemical elements

(10)

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

Abundance of chemical elements in the Universe

(11)

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

Abundance of chemical elements in the crust of the Earth

(12)

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

Abundance of chemical elements in Humans

(13)

Hydrogen and its compounds

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

(14)

• electron structure: 1s

¹

• its elemental form is H

₂

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

(15)

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^-

(16)

Production

• lab: Zn + acid, Al + base

• industrial:

CH₄ + H₂O → CO + 3H₂ C + 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

(17)

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 oxygen most common compound

of oxygen: water

(18)

• electron structure: 1s

²

2s

²

2p

⁴

• its elemental form is diatomic or triatomic molecule (O

₂

or O

₃

)

• 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

(19)

Production

• fractional distillation of liquid air

• electrolysis of water

• photosynthesis

Applications

• metallurgy,

• polymerchemistry,

• welding,

• ...

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

(20)

Oxygen cycle

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

(21)

Carbon and its compounds

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

(22)

Carbon and its compounds

• electron structure: 1s

²

2s

²

2p

²

• 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)

(23)

graphite diamond

soft material one of the hardest materials known

lubricant abrasive

electric conductor electric insulator

thermal insulator good thermal conductor

opaque transparent

crystallizes in hexagonal lattice cubic crystal lattices very anisotropic material isotropic material

Main allotropes of carbon

comparison table of the two main allotropes of carbon

(24)

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

(25)

Carbon and its compounds Research applications

(synthetic production)

• Fullerene (ball like structures)

• drug delivery, …

• Carbon nanotubes (tube like structures)

• 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

(26)

Carbon cycle

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

(27)

Nitrogen and its compounds

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

(28)

• electron structure: 1s

²

2s

²

2p

³

• its elemental form is N

₂

diatomic molecule

• compound forms

• in inorganic compounds mostly with NH₃ and NO_x 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

(29)

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

(30)

Nitrogen cycle

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

(31)

Sulfur and its compounds

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

(32)

• electron structure: 1s

²

2s

²

2p

⁶

3s

²

3p

⁴

• its elemental form is amorphous (S

₈

), but has 30 different allotropes

• compound forms

• in inorganic compounds as sulfide (S^2-), and its oxides - mostly sulfate (SO₄^2-)

• 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)

(33)

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 lazuli semi-precious stone

(34)

Sodium and its compounds

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

(35)

• electron structure: 1s

²

2s

²

2p

⁶

3s

¹

• 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

(36)

Production

• Na₂CO_{3 (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

(37)

Silicon and its compounds

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

(38)

• electron structure: 1s

²

2s

²

2p

⁶

3s

²

3p

²

• 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

(39)

Production

• metallurgic grade (98%) SiO₂ + C → Si + CO₂ SiO₂ + 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

(40)

Boron and its compounds

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

(41)

• electron structure:

1s

²

2s

²

2p

¹

• in elemental form has many allotropes

amorphous, 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,

• ...

Boron and its compounds

(42)

Potassium and its compounds

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

(43)

• electron structure:

1s

²

2s

²

2p

⁶

3s

²

3p

⁶

4s

¹

• 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,

• ...

Potassium and its compounds

(44)

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

(45)

• electron structure:

1s

²

2s

²

2p

⁶

3s

²

3p

⁵

• its elemental form is uncommon (Cl

₂

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,...

Chlorine and its compounds

(46)

WORLD OF MOLECULES

WORLD OF MOLECULES

1. Chemical equilibria

2. Acid-base theories

3. Superacids and superbases

Previously - Chemical equilibria, acid – base theories

Previously - Law of mass action (1867)

[ ] [ ] [ ]

Previously - Le Châtelier - Braun's principle - example

Previously - Acid and base dissociation constants

[ ] [ ]

[ ]

( )

[ ] [ ]

[ ]

( )

1. Hydrogen, 2. Oxygen, 3. Carbon, 4. Nitrogen, 5. Sulphur, 6. Sodium, 7. Silicon, 8. Boron, 9. ...

Table of Contents

Lattice structure of elements

Natural abundance of chemical elements

Abundance of chemical elements in the Universe

• electron structure: 1s

• its elemental form is H

diatomic molecule (on Earth)

• compound forms

common reactions

Production

Applications

• electron structure: 1s

2s

2p

• its elemental form is diatomic or triatomic molecule (O

or O

)

• compound forms

Production

Applications

• electron structure: 1s

2s

2p

• its elemental form is solid, its allotropes:

graphite, diamond, fullerene, graphene

• compound forms

• electron structure: 1s

2s

2p

• its elemental form is N

diatomic molecule

• compound forms

• essential for most biological molecules

• due to the ability of forming Hydrogen bonds

Production

Applications

• electron structure: 1s

2s

2p

3s

3p

• its elemental form is amorphous (S

), but has 30 different allotropes

• compound forms

Production

Applications

• electron structure: 1s

2s

2p

3s

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

• compound forms

Production

Applications

• electron structure: 1s

2s

2p

3s

3p

• its does not occur in elemental form

• compound forms

Production

Applications

^{( )}

^{( )}