CHEM10009 Study Guide - Final Guide: Trigonal Planar Molecular Geometry, Biogeochemical Cycle, Acid Rain
11 Jun 2018
School
Department
Course
Professor
Sulfur
Essential for life
-
Present in many proteins and the amino acids cysteine and methionine
-
Cys and Met
Oxidation state of S is -2
Sulfur in -2 ox state also in metalloproteins coordinated to metal ions
§
○
Geometry at S is tetrahedral in cys and met - sp3 hybridisation
○
-
Oxidation of sulfur containing compounds
Energetically favourable
○
Form SO2 (bent) and SO3 (trigonal planar)
○
-
SO2 dissolves in water -> produces weak diprotic acid H2SO3
-
SO3 dissolves in water -> produces strong diprotic acid H2SO4
-
Acid rain
Normal rain water is slightly acidic - dissolved CO2, SO2, and NO2
Products formed in burning fossil fuels - S in coal
§
○
Consequences
Lower pH of natural waters -> kills aquatic life, plants, fish
§
Toxic metals released from sediment
§
Corrosion of structures/buildings may occur
§
Marble, limestone CaCO3 react with acid
§
Structures degrade
§
○
-
Biogeochemical cycle of sulfur
SO4 2- is soluble + oxidised nutrient form of S in nature
Eg. Na+ salts are water soluble
§
○
SO4 2- is absorbed by cells, incorporated into cys and met and then into
proteins
○
-
Production of Me2S by Plankton
Produce a zwitterion from met for osmotic and cryo-protection which
decomposes upon cell death
○
Me2S is a soluble gas
Carrier of S in atmosphere
§
Strong odour!! Smell of the sea
§
○
-
Nitrogen
Element exists in nature as N2
-
Main gas in atmosphere
-
Very stable with strong triple bond
-
Simple N containing compounds often thermodynamically UNSTABLE +
decompose to stable N2
-
Eg. NaN3 in air bags
-
Nitrogen fixation
N2 - very unreactive -> difficult to incorporate into livings sytems
○
N fixation carried out by nitrogenase enzyme - N2 -> NH3
○
Nitrogen in lower oxidation states in living systems
○
Nitrogen must be SOLUBLE for nitrogen fixation to occur
○
NH3 - life: proteins, nucleic acids
○
-
-
Hydrides
Ammonia - NH3
Pyramidal
§
Sp3 hybridisation
§
Acts as base
§
Ox state N: -3
§
○
Hydrazine N2H4
Ox state N: -2
§
Sp 3
§
Strong H bonding -> high bp
§
○
-
Oxides of nitrogen
N2O - linear
○
NO - radical
○
NO2 - bent radical
○
N2O4 - planar dimer
○
-
Oxyacids and oxyanions of Nitrogen
HNO2 is unstable + weak acid
○
HNO3 - strong acid
Produced by redox
§
3NO2 + H2O -> 2HNO3 + NO
§
○
-
HNO2 and HNO3
-
-
NO2- and NO3- ions produced by deprotonation of acids
-
Biological roles of NO
NO = radical
○
Regulatory molecule
Nerve function (neurotransmission)
§
Regulation of blood pressure
Dilation of blood vessels □
§
Blood clotting
NO inhibits blood clotting - exploited by mosquitoes (saliva
contain NO-producing chemicals
□
§
Protection of nasal sinuses
§
○
Toxicity
Excess NO is toxic to humans + attacks lungs
§
○
-
Environmental Impacts of NO
Internal combustion engine
Endothermic reaction so favoured by high T in car/plane engines
Also increase in rate with temperature□
§
Catalytic converter (exhaust) - reverse reaction but not efficiency
< 100%
§
○
Atmosphere
○
-
Upper atmosphere
NO2 diffuses to upper atmosphere
○
NO produced which catalyzes ozone depletion
○
-
Lower atmosphere
NO2 catalyzes formation of O3 in photochemical reaction
○
-
O3 reacts with hydrocarbons
○
Various components constitute photochemical smog
○
Net result of Nox pollution
O3 produced in lower atmosphere -> production of photochemical smog
○
O3 lost in upper atmosphere - degradation of ozone layer which absorbs
UV rays damaging to life
○
-
Phosphorous
Essential for life
-
Biominerals
Bones and teeth
○
-
Present in
DNA and RNA (phosphodiester link)
○
Energy carriers ATP and ADP
○
-
Exists naturally as minerals
-
Hydride of Phosphorous
Phosphine, PH3
Analogous to NH3, but much weaker base
§
Pyramidal
§
Gas + finds use as a fumigant (insects) for stored grains
§
○
-
Elemental phosphorous
Number of allotropes
○
White phosphorous (P4)
Tetrahedral molecule
§
Most reactive
§
Highly strained structure
§
Reactions with oxygen -> oxides
Relieves strain □
§
○
-
Phosphoric acid (H3PO4)
H3PO4 is weak tripotic acid
○
-
H3PO4 dissociates H+ in multiple steps
§
Ka decreases as anionic charge increase - increasingly harder to
remove H+
□
H3PO4 undergoes polymerisation reactions
○
non-spontaneous reaction and to proceed requires energy supplied
by heating
§
Phosphate polyanions
Polyphoshproic acids react with base -> polyanions
○
-
Na+ 5 (P3O10)5- used in detergents
Polyanion attracts Mg2+ and Ca2+ strongly, softening water
§
○
S, O, P notes
Monday, 28 May 2018
9:27 pm
Sulfur
Essential for life
-
Present in many proteins and the amino acids cysteine and methionine
-
Cys and Met
Oxidation state of S is -2
Sulfur in -2 ox state also in metalloproteins coordinated to metal ions
§
○
Geometry at S is tetrahedral in cys and met - sp3 hybridisation
○
-
Oxidation of sulfur containing compounds
Energetically favourable
○
Form SO2 (bent) and SO3 (trigonal planar)
○
-
SO2 dissolves in water -> produces weak diprotic acid H2SO3
-
SO3 dissolves in water -> produces strong diprotic acid H2SO4
-
Acid rain
Normal rain water is slightly acidic - dissolved CO2, SO2, and NO2
Products formed in burning fossil fuels - S in coal
§
○
Consequences
Lower pH of natural waters -> kills aquatic life, plants, fish
§
Toxic metals released from sediment
§
Corrosion of structures/buildings may occur
§
Marble, limestone CaCO3 react with acid
§
Structures degrade
§
○
-
Biogeochemical cycle of sulfur
SO4 2- is soluble + oxidised nutrient form of S in nature
Eg. Na+ salts are water soluble
§
○
SO4 2- is absorbed by cells, incorporated into cys and met and then into
proteins
○
-
Production of Me2S by Plankton
Produce a zwitterion from met for osmotic and cryo-protection which
decomposes upon cell death
○
Me2S is a soluble gas
Carrier of S in atmosphere
§
Strong odour!! Smell of the sea
§
○
-
Nitrogen
Element exists in nature as N2
-
Main gas in atmosphere
-
Very stable with strong triple bond
-
Simple N containing compounds often thermodynamically UNSTABLE +
decompose to stable N2
-
Eg. NaN3 in air bags
-
Nitrogen fixation
N2 - very unreactive -> difficult to incorporate into livings sytems
○
N fixation carried out by nitrogenase enzyme - N2 -> NH3
○
Nitrogen in lower oxidation states in living systems
○
Nitrogen must be SOLUBLE for nitrogen fixation to occur
○
NH3 - life: proteins, nucleic acids
○
-
-
Hydrides
Ammonia - NH3
Pyramidal
§
Sp3 hybridisation
§
Acts as base
§
Ox state N: -3
§
○
Hydrazine N2H4
Ox state N: -2
§
Sp 3
§
Strong H bonding -> high bp
§
○
-
Oxides of nitrogen
N2O - linear
○
NO - radical
○
NO2 - bent radical
○
N2O4 - planar dimer
○
-
Oxyacids and oxyanions of Nitrogen
HNO2 is unstable + weak acid
○
HNO3 - strong acid
Produced by redox
§
3NO2 + H2O -> 2HNO3 + NO
§
○
-
HNO2 and HNO3
-
-
NO2- and NO3- ions produced by deprotonation of acids
-
Biological roles of NO
NO = radical
○
Regulatory molecule
Nerve function (neurotransmission)
§
Regulation of blood pressure
Dilation of blood vessels □
§
Blood clotting
NO inhibits blood clotting - exploited by mosquitoes (saliva
contain NO-producing chemicals
□
§
Protection of nasal sinuses
§
○
Toxicity
Excess NO is toxic to humans + attacks lungs
§
○
-
Environmental Impacts of NO
Internal combustion engine
Endothermic reaction so favoured by high T in car/plane engines
Also increase in rate with temperature□
§
Catalytic converter (exhaust) - reverse reaction but not efficiency
< 100%
§
○
Atmosphere
○
-
Upper atmosphere
NO2 diffuses to upper atmosphere
○
NO produced which catalyzes ozone depletion
○
-
Lower atmosphere
NO2 catalyzes formation of O3 in photochemical reaction
○
-
O3 reacts with hydrocarbons
○
Various components constitute photochemical smog
○
Net result of Nox pollution
O3 produced in lower atmosphere -> production of photochemical smog
○
O3 lost in upper atmosphere - degradation of ozone layer which absorbs
UV rays damaging to life
○
-
Phosphorous
Essential for life
-
Biominerals
Bones and teeth
○
-
Present in
DNA and RNA (phosphodiester link)
○
Energy carriers ATP and ADP
○
-
Exists naturally as minerals
-
Hydride of Phosphorous
Phosphine, PH3
Analogous to NH3, but much weaker base
§
Pyramidal
§
Gas + finds use as a fumigant (insects) for stored grains
§
○
-
Elemental phosphorous
Number of allotropes
○
White phosphorous (P4)
Tetrahedral molecule
§
Most reactive
§
Highly strained structure
§
Reactions with oxygen -> oxides
Relieves strain □
§
○
-
Phosphoric acid (H3PO4)
H3PO4 is weak tripotic acid
○
-
H3PO4 dissociates H+ in multiple steps
§
Ka decreases as anionic charge increase - increasingly harder to
remove H+
□
H3PO4 undergoes polymerisation reactions
○
non-spontaneous reaction and to proceed requires energy supplied
by heating
§
Phosphate polyanions
Polyphoshproic acids react with base -> polyanions
○
-
Na+ 5 (P3O10)5- used in detergents
Polyanion attracts Mg2+ and Ca2+ strongly, softening water
§
○
S, O, P notes
Monday, 28 May 2018
9:27 pm
Sulfur
Essential for life
-
Present in many proteins and the amino acids cysteine and methionine
-
Cys and Met
Oxidation state of S is -2
Sulfur in -2 ox state also in metalloproteins coordinated to metal ions
§
○
Geometry at S is tetrahedral in cys and met - sp3 hybridisation
○
-
Oxidation of sulfur containing compounds
Energetically favourable
○
Form SO2 (bent) and SO3 (trigonal planar)
○
-
SO2 dissolves in water -> produces weak diprotic acid H2SO3
-
SO3 dissolves in water -> produces strong diprotic acid H2SO4
-
Acid rain
Normal rain water is slightly acidic - dissolved CO2, SO2, and NO2
Products formed in burning fossil fuels - S in coal
§
○
Consequences
Lower pH of natural waters -> kills aquatic life, plants, fish
§
Toxic metals released from sediment
§
Corrosion of structures/buildings may occur
§
Marble, limestone CaCO3 react with acid
§
Structures degrade
§
○
-
Biogeochemical cycle of sulfur
SO4 2- is soluble + oxidised nutrient form of S in nature
Eg. Na+ salts are water soluble
§
○
SO4 2- is absorbed by cells, incorporated into cys and met and then into
proteins
○
-
Production of Me2S by Plankton
Produce a zwitterion from met for osmotic and cryo-protection which
decomposes upon cell death
○
Me2S is a soluble gas
Carrier of S in atmosphere
§
Strong odour!! Smell of the sea
§
○
-
Nitrogen
Element exists in nature as N2
-
Main gas in atmosphere
-
Very stable with strong triple bond
-
Simple N containing compounds often thermodynamically UNSTABLE +
decompose to stable N2
-
Eg. NaN3 in air bags
-
Nitrogen fixation
N2 - very unreactive -> difficult to incorporate into livings sytems
○
N fixation carried out by nitrogenase enzyme - N2 -> NH3
○
Nitrogen in lower oxidation states in living systems
○
Nitrogen must be SOLUBLE for nitrogen fixation to occur
○
NH3 - life: proteins, nucleic acids
○
-
-
Hydrides
Ammonia - NH3
Pyramidal
§
Sp3 hybridisation
§
Acts as base
§
Ox state N: -3
§
○
Hydrazine N2H4
Ox state N: -2
§
Sp 3
§
Strong H bonding -> high bp
§
○
-
Oxides of nitrogen
N2O - linear
○
NO - radical
○
NO2 - bent radical
○
N2O4 - planar dimer
○
-
Oxyacids and oxyanions of Nitrogen
HNO2 is unstable + weak acid
○
HNO3 - strong acid
Produced by redox
§
3NO2 + H2O -> 2HNO3 + NO
§
○
-
HNO2 and HNO3
-
-
NO2- and NO3- ions produced by deprotonation of acids
-
Biological roles of NO
NO = radical
○
Regulatory molecule
Nerve function (neurotransmission)
§
Regulation of blood pressure
Dilation of blood vessels □
§
Blood clotting
NO inhibits blood clotting - exploited by mosquitoes (saliva
contain NO-producing chemicals
□
§
Protection of nasal sinuses
§
○
Toxicity
Excess NO is toxic to humans + attacks lungs
§
○
-
Environmental Impacts of NO
Internal combustion engine
Endothermic reaction so favoured by high T in car/plane engines
Also increase in rate with temperature□
§
Catalytic converter (exhaust) - reverse reaction but not efficiency
< 100%
§
○
Atmosphere
○
-
Upper atmosphere
NO2 diffuses to upper atmosphere
○
NO produced which catalyzes ozone depletion
○
-
Lower atmosphere
NO2 catalyzes formation of O3 in photochemical reaction
○
-
O3 reacts with hydrocarbons
○
Various components constitute photochemical smog
○
Net result of Nox pollution
O3 produced in lower atmosphere -> production of photochemical smog
○
O3 lost in upper atmosphere - degradation of ozone layer which absorbs
UV rays damaging to life
○
-
Phosphorous
Essential for life
-
Biominerals
Bones and teeth
○
-
Present in
DNA and RNA (phosphodiester link)
○
Energy carriers ATP and ADP
○
-
Exists naturally as minerals
-
Hydride of Phosphorous
Phosphine, PH3
Analogous to NH3, but much weaker base
§
Pyramidal
§
Gas + finds use as a fumigant (insects) for stored grains
§
○
-
Elemental phosphorous
Number of allotropes
○
White phosphorous (P4)
Tetrahedral molecule
§
Most reactive
§
Highly strained structure
§
Reactions with oxygen -> oxides
Relieves strain □
§
○
-
Phosphoric acid (H3PO4)
H3PO4 is weak tripotic acid
○
-
H3PO4 dissociates H+ in multiple steps
§
Ka decreases as anionic charge increase - increasingly harder to
remove H+
□
H3PO4 undergoes polymerisation reactions
○
non-spontaneous reaction and to proceed requires energy supplied
by heating
§
Phosphate polyanions
Polyphoshproic acids react with base -> polyanions
○
-
Na+ 5 (P3O10)5- used in detergents
Polyanion attracts Mg2+ and Ca2+ strongly, softening water
§
○
S, O, P notes
Monday, 28 May 2018 9:27 pm
Document Summary
Present in many proteins and the amino acids cysteine and methionine. Sulfur in -2 ox state also in metalloproteins coordinated to metal ions. Geometry at s is tetrahedral in cys and met - sp3 hybridisation. So2 dissolves in water -> produces weak diprotic acid h2so3. So3 dissolves in water -> produces strong diprotic acid h2so4. Normal rain water is slightly acidic - dissolved co2, so2, and no2. Products formed in burning fossil fuels - s in coal. Lower ph of natural waters -> kills aquatic life, plants, fish. So4 2- is soluble + oxidised nutrient form of s in nature. So4 2- is absorbed by cells, incorporated into cys and met and then into proteins. Produce a zwitterion from met for osmotic and cryo-protection which decomposes upon cell death. Simple n containing compounds often thermodynamically unstable + decompose to stable n2. N2 - very unreactive -> difficult to incorporate into livings sytems.
