🧪 Metal Biogeochemical Cycling
Chapter 1 - General Characteristics of Metals & Metalloids
1.1 Terminology: Why "Heavy Metals" Is a Weak Term
🎯 EXAM-STYLE: Why is "heavy metals" scientifically ambiguous?
No single agreed definition - the label changes meaning depending on which property is used, and each property
picks out a DIFFERENT set of elements:
● Density-based: > 3.5 g/cm3 OR > 7 g/cm3 (two competing thresholds in use)
● Atomic weight-based: > 23 (e.g. Na) OR > 40 (e.g. Ca)
● Atomic number-based: > 20 (Ca) OR 21-92 (Sc-U) - excludes alkali & alkaline-earth metals
● Toxicity-based: includes Pb, Cd, Hg + metalloids like As, Se, Te, and even Ti, Hf, Bi (not chemically "heavy")
● Hodson (2004): term should be abandoned - inconsistent definition, misleading implications, poor scientific
precision
Preferred alternative terminology
Term Meaning / Threshold Why used
Chemically accurate; includes metalloids (As,
Elements -
Se) that "metal" excludes
Trace elements < 100 ug/g Concentration-based, unambiguous
Can still be essential or highly toxic despite
Ultratrace elements < 10 ng/g
minute amounts
Not ideal either - ALL metals (even essential
"Toxic metals" - ones, e.g. Cu, Zn) become toxic above their
optimal concentration
Essential vs. Non-Essential Elements
Category Definition Examples
Required for normal biological function. Deficiency Major: H, C, N, O
leads to physiological/structural abnormalities. Minor (macronutrients): Mg, P, S, Cl, K
Essential
Optimal range: too little = deficiency, too much = Trace essential: F, Si, V, Cr, Mn, Fe, Co,
toxicity. Ni, Cu, Zn, Se, Mo
No known biological function; usually associated
Non-essential Cd, Pb, Hg
with toxicity.
1.2 Classification of Metals
Basis Groups Key points
Alkali: +1 cations, highly reactive. Alkaline earth:
Alkali (Gr.1) - Alkaline earth (Gr.2) - +2 cations, less reactive, important bio+geo
Periodic table Transition metals - Metalloids - Rare roles (Ca, Mg). Transition: d-block, variable
earth/Lanthanides - Actinides oxidation states. Trans-uranium = atomic
number > 92.
, Basis Groups Key points
Explains periodic table structure & type of
Electronic structure s-block - p-block - d-block - f-block
chemical bonding formed
Metals: lose e- easily -> cations; metallic bonding
(delocalised e-, high conductivity) or ionic
bonding with non-metals. Metalloids (B, Si, Ge,
Bonding behaviour Metals vs. Metalloids
As, Sb, Te, Po): intermediate
electronegativity/ionization energy, some are
semiconductors.
1.3 HSAB Theory (Hard-Soft Acid-Base) - High-Yield for Exam
Lewis acid-base theory: acid = electron-pair acceptor (all cations; species with incomplete octets e.g. BF3, AlF3); base =
electron-pair donor. Limitation: doesn't predict reaction direction/stability - HSAB fixes this.
🎯 EXAM METHOD: Predict whether a reaction occurs & whether the complex is stable
● Step 1 - Classify each species (acid = metal, base = ligand) as HARD, SOFT, or BORDERLINE using the tables
below.
● Step 2 - Apply the matching rule:
Hard acid + Hard base -> ionic bonding -> REACTION FAVOURABLE, STABLE product
Soft acid + Soft base -> covalent bonding -> REACTION FAVOURABLE, STABLE product (most stable overall)
Hard + Soft (mismatch) -> polar covalent -> LESS STABLE, reaction not favoured
● Step 3 - Conclude: the system shifts toward the combination that pairs hard-with-hard or soft-with-soft.
Classification table (learn this cold)
Characteristics Examples
Small ionic radius (<90 pm) - high +charge - empty
H+, Li+, Na+, K+, Ba2+, Ca2+, Mg2+,
Hard acids valence orbitals - low electronegativity (0.7-1.6) - weakly
Al3+, Ti4+, Cr3+/6+
polarizable - prefer OXYGEN donors
Large radius (>90 pm) - low/partial +charge - filled
Ag+, Au+, Tl+, Cu+, Cd2+, Hg+, Hg2+,
Soft acids valence orbitals - easily polarized/distorted - form
CH3Hg+, Pt2+, Pd2+
covalent bonds - prefer SULFUR donors
Borderline acids Mixed properties Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Pb2+
Small radius - high electronegativity (3.0-4.0) - highly OH-, F-, Cl-, NH3, CO3(2-), PO4(3-),
Hard bases
solvated SO4(2-), NO3-, CH3COO-
Large radius (>170 pm) - high polarizability - easily
Soft bases I-, H-, S2-, HS-, CN-, SCN-, R-SH
oxidized
Borderline
Mixed properties Br-, N3-, N2, aniline, pyridine, NO2-
bases
Worked exercises - the exact exam format (3 cases)
Reaction Classification Verdict
Reaction possible - STABLE
Al3+ + F- -> AlF3 Hard acid + Hard base
(ionic)
Reaction possible - STABLE,
Hg2+ + SCN- -> Hg(SCN)2 Soft acid + Soft base (binds through S)
complex forms through sulfur
, Reaction Classification Verdict
Reaction NOT favoured - no
Al3+ + S2O3(2-) -> ? Hard acid + Soft base (mismatch)
stable compound formed
Other classic HSAB reasoning examples
● AsF3 + PI3 -> AsI3 + PF3 - As is softer than P, and I- is softer than F- -> softer species preferentially pair ->
reaction proceeds.
● MgS + BaO -> MgO + BaS - Mg2+ is harder than Ba2+, O2- is harder than S2- -> harder acid binds harder base
-> reaction proceeds.
Applications (frequently asked as "explain why...")
Application Explanation
Soft & borderline acids (Ag+, Hg+, Hg2+, Fe2+, Cu2+, Zn2+, Pb2+) precipitate as
Precipitation reactions
METAL SULFIDES because S2- is a soft base - soft-soft match.
Predicts substitution direction, e.g. Hg2+ prefers softer Br- over harder F- -
Coordination chemistry / ligand
reflected in Keq (ligand exchange with HBr vs HF differ by ~17 orders of
exchange
magnitude).
Toxicants act as SOFT electrophiles (Lewis acids); key biological targets are SOFT
nucleophiles - thiols (cysteine), amines (lysine). Cytotoxicity occurs when
Toxicology
toxicant & target hardness/softness match -> stable adduct impairs cell
function.
Hardness/softness of the metal ion predicts solubility trends in different ligand
Solubility prediction
environments.
🎯 Worked number check - Cu+ vs Mg2+ binding to cysteine (-SH, soft donor)
Mg2+ (hard acid) + cysteine -SH (soft base): K1 < 10^4 -> poor match, weak binding
Mn2+ (hard acid): K1 = 10^4.1 -> still weak
Cu+ (soft acid) + cysteine -SH (soft base): K1 = 10^19.2 -> extremely strong match
-> Explains why copper binds strongly to proteins, and why thiol-containing biomolecules are the major targets of
soft-metal toxicity.
1.4 Complexation & Chelation - High-Yield for Exam
A metal complex = a central metal ion (Lewis acid) surrounded by ligands (Lewis bases) that donate electron pairs.
Example: Cu2+ + 6H2O -> [Cu(H2O)6]2+. Ligands can be replaced stepwise by stronger ligands (substitution reaction).
🎯 EXAM: What is chelation, and how does it differ from a metal complex?
Metal complex (general term): ANY central metal ion bonded to surrounding ligands - the ligand can be
MONODENTATE (one donor atom, e.g. NH3, H2O). No ring is necessarily formed.
Chelation (specific case of complexation): occurs when a POLYDENTATE ligand (2 or more donor atoms, e.g.
bidentate ethylenediamine, hexadentate EDTA) binds the SAME metal ion at more than one point, forming a closed
RING structure.
● Key distinction: every chelate IS a complex, but not every complex is a chelate - chelation specifically
requires ring formation via a multidentate ligand.
Denticity of ligands
, Type Donor atoms Example Note
Monodentate 1 NH3, H2O No ring formed - standard complex
Bidentate 2 Ethylenediamine ("en") Forms a chelate ring
Wraps metal completely -> highly
Hexadentate 6 EDTA
stable complexes
Ring stability
● 4-membered rings -> unstable / strained (e.g. carbonato complex)
● 5- and 6-membered rings -> stable, less ring strain
The chelate effect - why chelates are MORE stable (exam favourite: entropy argument)
Complex log K
[Cu(NH3)2(H2O)4]2+ (2 monodentate NH3) 7.86
[Cu(H2O)4(en)]2+ (1 bidentate en, same donor atom type = N) 10.6
Same donor atom type (N), yet the chelate is far more stable. Reason: replacing 2 separate H2O ligands with 1 bidentate
ligand releases an extra free water molecule -> net increase in number of dissolved particles -> entropy (delta-S)
increases -> more thermodynamically favourable (more negative delta-G). EDTA (hexadentate) pushes this furthest:
[Cu(H2O)6]2+ + EDTA4- <=> [Cu(EDTA)]2- + 6H2O, log K = 18.8.
Stability constants - stepwise vs. overall
Type Meaning Trend
Kn DECREASES with each step -
Equilibrium constant for each single ligand substitution
Stepwise (Kn) increasing steric hindrance &
step (e.g. Cu2+ + NH3 ligands added one at a time)
charge redistribution
Overall / cumulative Represents total stability of the
beta4 = K1 x K2 x K3 x K4
(beta) FULLY substituted complex
Hydrated metal ions as acids (links section 1.3-1.4 to later redox/solubility chapters)
● Coordinated water molecules polarize O-H bonds -> hydrated metal ion behaves as a weak Bronsted acid:
[Fe(H2O)6]3+ + H2O <=> [Fe(H2O)5(OH)]2+ + H3O+ (solution pH approx. 1.5).
● Further deprotonation (2nd, 3rd H+) -> eventually forms neutral, insoluble Fe(OH)3(s), which precipitates.
● Environmental controls on solubility: Low pH / low Eh -> higher solubility. High pH -> hydroxide precipitation.
Competing ligands (sulfide, carbonate) can outcompete OH- for the metal.
1.5 Composition of Natural Waters (background / quick reference)
Water type Key control / value
Geology (storage capacity, mineral contact) - Porosity (void space = storage) -
Groundwater
Permeability (flow rate, contact time, dissolution)
Freshwater Salinity < 0.5 g/L (rivers, lakes)
Seawater Salinity approx. 35 g/L dissolved salts
Estuarine water Mixture, salinity gradient between the two (covered in Ch. 3)
Major seawater constituents (% by weight) - "Chloride and sodium dominate seawater chemistry"
Chapter 1 - General Characteristics of Metals & Metalloids
1.1 Terminology: Why "Heavy Metals" Is a Weak Term
🎯 EXAM-STYLE: Why is "heavy metals" scientifically ambiguous?
No single agreed definition - the label changes meaning depending on which property is used, and each property
picks out a DIFFERENT set of elements:
● Density-based: > 3.5 g/cm3 OR > 7 g/cm3 (two competing thresholds in use)
● Atomic weight-based: > 23 (e.g. Na) OR > 40 (e.g. Ca)
● Atomic number-based: > 20 (Ca) OR 21-92 (Sc-U) - excludes alkali & alkaline-earth metals
● Toxicity-based: includes Pb, Cd, Hg + metalloids like As, Se, Te, and even Ti, Hf, Bi (not chemically "heavy")
● Hodson (2004): term should be abandoned - inconsistent definition, misleading implications, poor scientific
precision
Preferred alternative terminology
Term Meaning / Threshold Why used
Chemically accurate; includes metalloids (As,
Elements -
Se) that "metal" excludes
Trace elements < 100 ug/g Concentration-based, unambiguous
Can still be essential or highly toxic despite
Ultratrace elements < 10 ng/g
minute amounts
Not ideal either - ALL metals (even essential
"Toxic metals" - ones, e.g. Cu, Zn) become toxic above their
optimal concentration
Essential vs. Non-Essential Elements
Category Definition Examples
Required for normal biological function. Deficiency Major: H, C, N, O
leads to physiological/structural abnormalities. Minor (macronutrients): Mg, P, S, Cl, K
Essential
Optimal range: too little = deficiency, too much = Trace essential: F, Si, V, Cr, Mn, Fe, Co,
toxicity. Ni, Cu, Zn, Se, Mo
No known biological function; usually associated
Non-essential Cd, Pb, Hg
with toxicity.
1.2 Classification of Metals
Basis Groups Key points
Alkali: +1 cations, highly reactive. Alkaline earth:
Alkali (Gr.1) - Alkaline earth (Gr.2) - +2 cations, less reactive, important bio+geo
Periodic table Transition metals - Metalloids - Rare roles (Ca, Mg). Transition: d-block, variable
earth/Lanthanides - Actinides oxidation states. Trans-uranium = atomic
number > 92.
, Basis Groups Key points
Explains periodic table structure & type of
Electronic structure s-block - p-block - d-block - f-block
chemical bonding formed
Metals: lose e- easily -> cations; metallic bonding
(delocalised e-, high conductivity) or ionic
bonding with non-metals. Metalloids (B, Si, Ge,
Bonding behaviour Metals vs. Metalloids
As, Sb, Te, Po): intermediate
electronegativity/ionization energy, some are
semiconductors.
1.3 HSAB Theory (Hard-Soft Acid-Base) - High-Yield for Exam
Lewis acid-base theory: acid = electron-pair acceptor (all cations; species with incomplete octets e.g. BF3, AlF3); base =
electron-pair donor. Limitation: doesn't predict reaction direction/stability - HSAB fixes this.
🎯 EXAM METHOD: Predict whether a reaction occurs & whether the complex is stable
● Step 1 - Classify each species (acid = metal, base = ligand) as HARD, SOFT, or BORDERLINE using the tables
below.
● Step 2 - Apply the matching rule:
Hard acid + Hard base -> ionic bonding -> REACTION FAVOURABLE, STABLE product
Soft acid + Soft base -> covalent bonding -> REACTION FAVOURABLE, STABLE product (most stable overall)
Hard + Soft (mismatch) -> polar covalent -> LESS STABLE, reaction not favoured
● Step 3 - Conclude: the system shifts toward the combination that pairs hard-with-hard or soft-with-soft.
Classification table (learn this cold)
Characteristics Examples
Small ionic radius (<90 pm) - high +charge - empty
H+, Li+, Na+, K+, Ba2+, Ca2+, Mg2+,
Hard acids valence orbitals - low electronegativity (0.7-1.6) - weakly
Al3+, Ti4+, Cr3+/6+
polarizable - prefer OXYGEN donors
Large radius (>90 pm) - low/partial +charge - filled
Ag+, Au+, Tl+, Cu+, Cd2+, Hg+, Hg2+,
Soft acids valence orbitals - easily polarized/distorted - form
CH3Hg+, Pt2+, Pd2+
covalent bonds - prefer SULFUR donors
Borderline acids Mixed properties Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Pb2+
Small radius - high electronegativity (3.0-4.0) - highly OH-, F-, Cl-, NH3, CO3(2-), PO4(3-),
Hard bases
solvated SO4(2-), NO3-, CH3COO-
Large radius (>170 pm) - high polarizability - easily
Soft bases I-, H-, S2-, HS-, CN-, SCN-, R-SH
oxidized
Borderline
Mixed properties Br-, N3-, N2, aniline, pyridine, NO2-
bases
Worked exercises - the exact exam format (3 cases)
Reaction Classification Verdict
Reaction possible - STABLE
Al3+ + F- -> AlF3 Hard acid + Hard base
(ionic)
Reaction possible - STABLE,
Hg2+ + SCN- -> Hg(SCN)2 Soft acid + Soft base (binds through S)
complex forms through sulfur
, Reaction Classification Verdict
Reaction NOT favoured - no
Al3+ + S2O3(2-) -> ? Hard acid + Soft base (mismatch)
stable compound formed
Other classic HSAB reasoning examples
● AsF3 + PI3 -> AsI3 + PF3 - As is softer than P, and I- is softer than F- -> softer species preferentially pair ->
reaction proceeds.
● MgS + BaO -> MgO + BaS - Mg2+ is harder than Ba2+, O2- is harder than S2- -> harder acid binds harder base
-> reaction proceeds.
Applications (frequently asked as "explain why...")
Application Explanation
Soft & borderline acids (Ag+, Hg+, Hg2+, Fe2+, Cu2+, Zn2+, Pb2+) precipitate as
Precipitation reactions
METAL SULFIDES because S2- is a soft base - soft-soft match.
Predicts substitution direction, e.g. Hg2+ prefers softer Br- over harder F- -
Coordination chemistry / ligand
reflected in Keq (ligand exchange with HBr vs HF differ by ~17 orders of
exchange
magnitude).
Toxicants act as SOFT electrophiles (Lewis acids); key biological targets are SOFT
nucleophiles - thiols (cysteine), amines (lysine). Cytotoxicity occurs when
Toxicology
toxicant & target hardness/softness match -> stable adduct impairs cell
function.
Hardness/softness of the metal ion predicts solubility trends in different ligand
Solubility prediction
environments.
🎯 Worked number check - Cu+ vs Mg2+ binding to cysteine (-SH, soft donor)
Mg2+ (hard acid) + cysteine -SH (soft base): K1 < 10^4 -> poor match, weak binding
Mn2+ (hard acid): K1 = 10^4.1 -> still weak
Cu+ (soft acid) + cysteine -SH (soft base): K1 = 10^19.2 -> extremely strong match
-> Explains why copper binds strongly to proteins, and why thiol-containing biomolecules are the major targets of
soft-metal toxicity.
1.4 Complexation & Chelation - High-Yield for Exam
A metal complex = a central metal ion (Lewis acid) surrounded by ligands (Lewis bases) that donate electron pairs.
Example: Cu2+ + 6H2O -> [Cu(H2O)6]2+. Ligands can be replaced stepwise by stronger ligands (substitution reaction).
🎯 EXAM: What is chelation, and how does it differ from a metal complex?
Metal complex (general term): ANY central metal ion bonded to surrounding ligands - the ligand can be
MONODENTATE (one donor atom, e.g. NH3, H2O). No ring is necessarily formed.
Chelation (specific case of complexation): occurs when a POLYDENTATE ligand (2 or more donor atoms, e.g.
bidentate ethylenediamine, hexadentate EDTA) binds the SAME metal ion at more than one point, forming a closed
RING structure.
● Key distinction: every chelate IS a complex, but not every complex is a chelate - chelation specifically
requires ring formation via a multidentate ligand.
Denticity of ligands
, Type Donor atoms Example Note
Monodentate 1 NH3, H2O No ring formed - standard complex
Bidentate 2 Ethylenediamine ("en") Forms a chelate ring
Wraps metal completely -> highly
Hexadentate 6 EDTA
stable complexes
Ring stability
● 4-membered rings -> unstable / strained (e.g. carbonato complex)
● 5- and 6-membered rings -> stable, less ring strain
The chelate effect - why chelates are MORE stable (exam favourite: entropy argument)
Complex log K
[Cu(NH3)2(H2O)4]2+ (2 monodentate NH3) 7.86
[Cu(H2O)4(en)]2+ (1 bidentate en, same donor atom type = N) 10.6
Same donor atom type (N), yet the chelate is far more stable. Reason: replacing 2 separate H2O ligands with 1 bidentate
ligand releases an extra free water molecule -> net increase in number of dissolved particles -> entropy (delta-S)
increases -> more thermodynamically favourable (more negative delta-G). EDTA (hexadentate) pushes this furthest:
[Cu(H2O)6]2+ + EDTA4- <=> [Cu(EDTA)]2- + 6H2O, log K = 18.8.
Stability constants - stepwise vs. overall
Type Meaning Trend
Kn DECREASES with each step -
Equilibrium constant for each single ligand substitution
Stepwise (Kn) increasing steric hindrance &
step (e.g. Cu2+ + NH3 ligands added one at a time)
charge redistribution
Overall / cumulative Represents total stability of the
beta4 = K1 x K2 x K3 x K4
(beta) FULLY substituted complex
Hydrated metal ions as acids (links section 1.3-1.4 to later redox/solubility chapters)
● Coordinated water molecules polarize O-H bonds -> hydrated metal ion behaves as a weak Bronsted acid:
[Fe(H2O)6]3+ + H2O <=> [Fe(H2O)5(OH)]2+ + H3O+ (solution pH approx. 1.5).
● Further deprotonation (2nd, 3rd H+) -> eventually forms neutral, insoluble Fe(OH)3(s), which precipitates.
● Environmental controls on solubility: Low pH / low Eh -> higher solubility. High pH -> hydroxide precipitation.
Competing ligands (sulfide, carbonate) can outcompete OH- for the metal.
1.5 Composition of Natural Waters (background / quick reference)
Water type Key control / value
Geology (storage capacity, mineral contact) - Porosity (void space = storage) -
Groundwater
Permeability (flow rate, contact time, dissolution)
Freshwater Salinity < 0.5 g/L (rivers, lakes)
Seawater Salinity approx. 35 g/L dissolved salts
Estuarine water Mixture, salinity gradient between the two (covered in Ch. 3)
Major seawater constituents (% by weight) - "Chloride and sodium dominate seawater chemistry"
