# Acid-Base Reactions

Comment:
Typical time scale about 1s to 1 hour; log K=-7.82 at T-25, I=0.


# General Comments

Subject:
Gibbs free energy for organic matter reactions

Comment:
The values of free energy changes for organic matter reactions are reported per mole of CH2O.


Comment:
1)This field contains abbreviations for the models in which the given reaction is used. 
2)  LSSE-Toy reaction set is a set of 7 equations used in a preliminary (Phase-I) model developed by the LSSE group at the University of Ottawa.
3) LSSE-Mega is the model currently being developed in the LSSE group at the University of Ottawa.


Comment:
Ferric iron oxyhydroxide phases (e.g. goethite FeOOH and ferrihydrite Fe(OH)3) are occasionally used interchangeably in the reaction and alternative reaction fields.


Comment:
Values for pe (w) apply to the electron activity for unit activities of oxidant and reductant in neutral water, at pH = 7.0 for 25 C.
Values of pe (=log K) are for the relative electron activity when all other species are at unit activity.

Author:
SK (based on Stumm-Morgan-96 and Davison-93)


Comment:
Commonly used abbreviations and symbols are summarized in the form Abbreviations and Symbols.


Comment:
The reaction ID is a unique reference number that identifies the reactions. It is assigned at the time the reaction is entered into the database and cannot be changed. If, for some reason, the reaction is subsequently removed from the database, its ID number is lost and cannot be used any more. For that reason, some reaction IDs are missing, e.g. there are no reactions number 1 or 2.


Comment:
As this database is intended as a collection of kinetic data, and is a work in progress, it may lack many reactions that describe equilibrium between various solid and liquid species, as well as equilibrium speciation reactions for aqueous species. The user is encouraged to look up such reactions in one of the programs/databases designed specifically for equilibrium thermodynamic calculations (MINTEQ, PHREEQC, etc.). A non-exhaustive list of equilibrium reactions alone with stability constants can be found, for example, in Appelo-Postma-93.


# Half Reaction List

Comment:
Carbon oxidation state in OM is 0.
Eh=-0.471; deltaG0=-181.65 kJ/mol.


Half Reaction:
MnOOH  +  3 H+  +  e-  =  Mn2+  +  2 H2O


Half Reaction:
FeOOH  +  3 H+  +  e-  =  Fe2+  +  2 H2O


Comment:
Eh=-0.503; Carbon oxidation state in oxidized OM is +2; deltaG0=-97.05 kJ/mol.


Comment:
Eh=-0.374; Carbon oxidation state in oxidized OM is -2; deltaG0=-216.68  kJ/mol.


Comment:
Eh=-0.238; Carbon oxidation state in oxidized OM is -4; deltaG0=-184.02 kJ/mol.


Comment:
Eh=-0.182; Carbon oxidation state in oxidized OM is -2; deltaG0=-35.03 kJ/mol.


Comment:
Eh=-0.006; Carbon oxidation state in oxidized OM is -4; deltaG0=-2.37 kJ/mol.


Comment:
Eh=-0.279; Carbon oxidation state in oxidized OM is -3/+3; deltaG0=--215.03 kJ/mol.


Comment:
Eh=-0.280; Carbon oxidation state in oxidized OM is -3/-2/+3; deltaG0=--378.25 kJ/mol.


Half Reaction:
HCO3-  +  CH3COO-  +  7 H+  +  6 e-  =  CH3CH2COO-  +  4 H2O

Comment:
Eh=-0.282; Carbon oxidation state in oxidized OM is -3/-2/+3; deltaG0=-163.22 kJ/mol.


# Half Reactions

Comment:
with acid-base reaction
CO2 (aq)  +  H2O  =  HCO3-  +  H+


Comment:
with acid-base reaction
H2O  =  OH-  +  H+


Comment:
with acid-base reaction
NH4+  =  NH3  +  H+


Comment:
with acid-base reaction
H2S  =  HS-  +  H+


Comment:
with acid-base reaction H2S  =  HS-  +  H+


# Reactions

Reaction:
CH3COO-  +  4 NO3  =  CO2  +  HCO3-  +  H2O  +  4 NO2-

Comments:
G0 is -16.03 kcal/electron equivalent (McCarty-72)


Comments:
In Kallio-Kauppi-90, deposition and dissolution of SO2 produced more H+ in the studies basins than direct deposition of H+.


Comments:
Winters-Buckley-86 postulate that Fe exists in aqueous FeSi3(OH)8 form and when its solubility is exceeded Fe(OH)3 or FeSiO3 can precipitate.


Description:
Ammonium oxidation with nitrite in an anammox process

Comments:
This process occurs anaerobically.
-------------
The reaction was suggested to be a significant (up to 50%) sourse of N2 in ocean sediments (Dalsgaard et al -2003).
--------
In laboratory sediment incubations, up to 65% of produced N2 was due to this reaction (Dalsgaard-Thamsdrup-2002).

Rate comment:
Rysgaard et al -2004 quantified the rates of N2 production by anammox reaction in Arctic sediments. Anammox accounted for 1-92 micromol N/m^2/yr (1-35 % of total N2 production). For one site, optimum temperature for anammox was 12 C, response was psychrophilic.


Comments:
Schwertmannite forms in acid mine lakes (pH about 2-4). At low pH and high SO4 concentration, this mineral forms instead of goethite.


Reaction:
CH2O  +  H3PO4  +  Fe  (or Al)  = humic-metal-phosphate complex


Description:
Uptake / release of phosphate by bacteria or algae

Comments:
One needs to distinguish between the uptake of P into bacterial storage pools and the incorporation of P into bacterial biomass in the process of bacterial growth. In the latter case, other components, e.g. oxygen, may be also needed for consumption.
-----------------------
Microbial P uptake/release may be redox-sensitive. Microorganisms can release a large proportion of their P in a matter of hours under anoxic conditions (Shapiro-67). The process is completely reversible upon aeration.

Rate comment:
Rate = k [PO4] [algae] / (K + [PO4]) (Reichert-Wehrli-2004)
-------------
Release can occur on a time scale of hours. Uptake rate changes 2-2.5 times per 10 degrees of temperature change (Shapiro-67).
--------------
The uptake rate can also depend on the concentration of oxygen (Omlin et al -2001a).


Reaction:
algae biomass = F(H3PO4, NO3, O2, etc.);
Microbial populations = F(H3PO4, NO3, O2, etc.);

Description:
Growth / death of algal biomass and
microbial populations

Comments:
Omlin et al -2001a model algal growth with variable stoichiometry with respect to phosphorus, to reflect P limitation (in the water column).
----------------------
Cordeiro et al -73 simulate seasonal variations in algal concentrations by modeling microbial population dynamics.

Rate comment:
Monod-type expression is used in Omlin et al -2001a.
---------------
Monod expressions do not represent the dynamics of microbial cell growth and the multiplication of factors does not give the growth rate for multiple limiting nutrients (Cordeiro et al -73).


Description:
Oxidation of nitrite (NO2) to nitrate (NO3) by MnO2

Comments:
This reaction is suggested to oxidize NO2 in the absence of O2.

Rate comment:
The reaction is first order in each reactant with a second order rate
constant k= 493 1/(M min) at 21.5 C and pH 5.0  (Luther-Popp-2002). 
------------------
The reaction rate decreases with increasing pH and decreasing temperature (Luther-Popp-2002).
-----------------
The reaction is associative and diffusion controlled, occurring via an inner-sphere mechanism  (Luther-Popp-2002). The reaction is proton assisted and slows down at pH ≥5.5. In natural waters, i.e. at higher pH, the reaction may proceed via microbial mediation.


Description:
Conversion between reactive and refractory Fe(III) fractions.

Comments:
Fraction (a) is available for both bacterial and abiotic reactions, fraction (b) is available only for inorganic reaction.
Such a reaction is justified by observations that a larger pool of FeOOH is typically available for reduction by H2S than for bacterial reduction (Berg et al -2003).


Description:
Conversion between reactive and refractory MnO2  fractions.

Comments:
Fraction (a) is available for both bacterial and abiotic reactions, fraction (b) is available only for inorganic reaction.


Comments:
Most analytical methods cannot distinguish Mn(III) from a mixture of Mn(II) and Mn(IV).
-----------------------
Mn(III) can form complexes with sulfide, carboxylic acid, etc.
-------------------
Mn(III)-oxides are metastable phases that result from the oxidation of Mn2+ (mostly abiotic) (Anschutz et al -2005). Mn(IV) oxides can result from aging of Mn(III) oxyhydroxides.


Rate comment:
Gallon et al -2004 estimated the precipitatino rate constant k= (0.16-8)x10^(-20) mol/cm^3/s.


Comments:
See also reaction 33.
-----------------
Mn(III) is both a reductant and an oxidant. It can be reduced to Mn(II) or oxidized to Mn(IV). 
----------------
It is typically found in aquatuc environments with large suboxic layers (e.g. Black Sea).
----------------
Mn(III) can comprise close to 100% of dissolved Mn pool between the oxygen penetration depth and the depth where the concentration of H2S becomes substantial
-------------------
Mn(III) is probably found exclusively in complexes with organic ligands.


Comments:
C106H263O110N16P1 is the average composition of organic matter in plankton. In freshwater, stoichiometric coefficients for C, N, P can fluctuate seasonally, e.g. C:P varies from 100 to 600 (Reichert-Wehrli-2004).
---------------------
Decreases pH due to the release of CO2.
----------------------
The reaction is opposite of photosynthesis
-----------------
Dittrich et al -2004 consider that OM degradation releases HS- into the porewater as well.
-------------------
Mangini et al -2001 relate the historical evolution of the position of the redox boundary to the peaks in profiles of Mn and U. They chart the oxygen penetration depth as a function of interface O2 concentration and OM loading.
-----------------
Jung et al -97 estimate the burn-down depths for sapropels under varying oxic conditions and perform model sensitivity analysis.
----------------
Gehlen et al -97 and Glud et al. -2003 demonstrate how oxygen profile in the sediment can be affected by episodic organic matter depositions, bottom water oxygen concentration variations, and bioirrigation.
------------
Temporal variations in the amount of deposited OM can cause redox boundary migrations, especially large in OM-poor sediments, and generate peaks in the profiles of redox-sensitive elements (Mn, Fe, etc.) on a time scale of several years or decades (Katsev et al -2006).

Rate comment:
1) Monod-type expressions are typically used. Overall OM decomposition (by all mechanisms) is frequently approximated by first-order kinetics. Overall reaction rate constant (for OM degradation by all pathways) varies from 10^(-7) to 10^3 1/yr. Middelburg-89 suggests that overall rate constant k varies with time as log k =-0.95 log t – 0.81 in marine sediments.
--------------------- 
2) In a Monod-type expression R~C/Clim, Clim is reported 0.63-62 microM (Van Cappellen-Wang-96). In an expression R= k C/(C+K), Dittrich et al -2004 use K=0.02 mM. Boudreau-96 uses K=0.008 mM.
---------------------
3) Oxygen reduction rate, in marine sediments, is estimated 1-1200 micromoles/cm^2/yr and varies with depth (Reeburgh-83).


Description:
Degradation of OM by denitrification  (NO3– as  oxidant), dissimilatory nitrate reduction.

Comments:
The reaction occurs when concentration of O2 is lowered to less than 5%  of its value for fully aerated water, typically  in the top few cm of sediment.
--------------------------
G0 is shown per mole of CH2O
-------------------------
pe at standard conditions is approximately 11.
-------------------
The reaction is believed to be the only quantitatively important process that converts fixed N to gasous N2. Thumdrup-Dalsgaard-2002 report that anaerobic ammonium oxidation coupled to nitrate reduction is also important.

Rate comment:
see comment (1) to reaction 3.
---------------------------
In a Monod-type expression R~C/Clim, NO3lim is reported 1.6-35 microM (Van Cappellen-Wang-96).  In an expression of the type R= k C/(C+K), Dittrich et al -2004 use K=0.05 mM. Luff-Moll-2004 use 0.02 mM.
---------------------------
Denitrification rate is estimated in marine sediments 1-300 mM/yr or 0.5-2.5 micromole/cm^2/yr. 
Total denitriﬁcation rates ranged from 1.8 to 3.3 micromol N /m^2/h in Wang et al -2003..


Description:
Degradation of OM by Mn reduction  (Mn oxide as the oxidant), dissimilatory Mn reduction.

Comments:
MnO2 compounds become more stable with age (Fosssing et al -2004). It therefore makes sense to consider two pools: easily degradable and refractory.
--------------
Recycling of Mn across the redox boundary may result in each atom being reduced and oxidized several hundred times before being permanently burried (Canfield et al -93).
----------------
Mangini-Eisenhauer-91 write this reaction with formation of MnCO3 as the reduced Mn phase (see alt. reaction).
--------------
Vertical migrations of the sediment redox boundary and the associated precipitation/dissolution of Mn may result in the formation of peaks in the solid Mn profile (Katsev et al -2006; Mangini et al -2001; Burdige-2005; Burdige-93; Thomson et al -96). Thus, such peaks may be (non-uniquely) related to paleo-records.

Rate comment:
see comment (1) to reaction 3.
-------------------------
In a Monod-type expression R~C/Clim, MnO2lim is reported 74 micromol/dm^3 (Van Cappellen-Wang-96).  In an expression R= k C/(C+K), Dittrich et al -2004 use K=0.005 mmol/g. Luff-Moll-2004 use Monod constant 10 mM. 
----------
Fe(OH)3 or FeOOH compounds become more stable with age (Fosssing et al -2004). It therefore makes sense to consider two pools: easily degradable and refractory.
---------------
Silverberg-Sundby-90 estimated overall Mn dissolution rate constant 250 1/yr. and precipitation rate constant 50000 1/yr (non-differentiating between solid Mn phases).
---------------
In experiments with turbidites of Chaillou et al -2005, a small peak in Mn oxide disappeared in 7 days after the environment became anoxic following the deposition of a new turbidite layer.


Reaction:
CH2O  +   4 FeOOH(s)   +   7 CO2   +   H2O    =    4 Fe2+   +   8 HCO3–

Description:
Degradation of OM by Fe reduction  (Fe oxyhydroxide as the oxidant, causes dissolution of HFO)

Comments:
The exact position in sediment is not known. There is evidence in deap-sea sediments (Froelich-79) that it occurs after Mn reduction.
-----------------------------
For alternative reaction with organic carbon:  Important in groundwaters. In surface water, mass of available oxyhydroxide is usually too small. Fe2+ may remain in solution, precipitate as FeCO3, or participate in sulfate reduction.
---------------------------
Microbial catalysis dominates Fe(III) oxide reduction in nonsulfidogenic environments. Variations in particle size, surface area and solubility lead to a continuum of Fe(III) oxide reactivity.
----------------------
Fe(OH)3 or FeOOH compounds become more stable with age (Fosssing et al -2004). It therefore makes sense to consider two pools: easily degradable and refractory.
---------------------
Electron-shuttling compounds and/or Fe(III) chelators may alleviate the need for the Fe(III) reducers to establish direct contact with Fe(III) oxides (Nevin-Lovley-2002).
--------------------
Recycling of Fe across the redox boundary may result in each atom being reduced and oxidized several hundres times before being permanently burried (Canfield et al -93).

Rate comment:
1) see comment (1) to reaction 3.
-----------------------
2) In a Monod-type expression R~C/Clim, Fe(OH)3lim is reported 200 micromol/dm^3 (Van Cappellen-Wang-96).  In an expression of the type R= k C/(C+K), Dittrich et al -2004 use K=0.3 mmol/g.  Luff-Moll-2004 use Monod constant 10 mM. 
-----------------------
3) Roden-2003 and Roden-Wetzel-2002 provide reaction rates for various amounts and compositions of iron oxides and bacterial populations. Typical rates of Fe(III) reduction are 5*10^(-9) mol/m^2/min or 1 mmol/L/d. Typical time scale for Fe(III) reduction in sediments is 2-20 days.
-----------------------
4) Study of Roden-Wetzel-2002 has shown that microbial Fe(III) reduction rate is first order with respect to amorphous Fe(III) oxide concentration in a wetland sediment. This is consistent with surface-area controlled mineral transformation.
------------------------
5) The amount of Fe(II) in porewater affects the kinetics of Fe(III) reductive dissolution through surface complexation.
---------------------------
6) Transformations between degradable and refractory fractions may need to be considered (Fosing et al -2004)
--------------------------
Gallon et al -2003 estimated rate constant for reductive Fe dissolution in a lake sediment as 0.2+-0.05 cm3/mol/s.

Redox:
Characteristic Eh 200-250 mV. Reeburgh-83 gives 60 mV.


Description:
Degradation of OM by sulfate reduction  (SO42– as terminal electron acceptor or oxidant)

Comments:
This reaction is often a dominant pathway of OM degradation in marine sediments.  The hydrogen sulfide produced reacts with iron to form insoluable sulfides (e.g., greigite, mackinwite, FeS, pyrite). This constitutes a main sink of S from the oceans.  The produced ammonia and dissolved phosphate diffuse up and are recycled to the water, constituting a main mechanism of nutrient regeneration in the oceans.
----------------------------------
If pH>7, HS- forms rather than H2S. If pH<6, CO2 forms rather than HCO3-.
-------------------------------
Occurs after denitrification, typically in the first meter of the sediment. Sulfate reduction is energetically less favorable than manganese and iron reduction.
----------------------------
In freshwater sediments, sulfate reduction can precede iron reduction (Postma-Jakobsen-1996)
----------------------------
Large populations of sulfate reducers and the associated high rates of sulfate reduction have been reported in oxic zones of sediments (Wieringa et al. -2000).

Rate comment:
see comment (1) to reaction 3.
-----------------------------
In a Monod-type expression R~C/Clim, SO4lim is reported 0.001-1 mM (Van Cappellen-Wang-96).  In an expression of the type R= k C/(C+K), Dittrich et al -2004 use K=0.005 mM. Boudreau-96 uses K=1.0 mM.
--------------------------
Typical rates in marine sediments 7-41 molC/m^2/yr (Henrichs-93) or 1-80 mM/yr (Reeburgh-83). Nedwell-82 gives 0.21-6.0 mM/day for interdidal sediments, 0.005 to 0.58 for coastal, and 0.0001 to 0.04 for deep sea.
--------------------
Pallud-Van Cappellen-2005 report half-saturation constant Clim in the range 0.1-0.3 mM in freshwater and marine sites, and 0.4-0.9 mM at a brackish site.
---------------------
Based on the work in pure cultures, it has been proposed that freshwater SRB exhibit a greater affinity for sulfate than their marine counterparts, and that Clim values are one or two orders of magnitude lower in freshwater (Ingvorsen-Jorgensen -84). However, Pallud-Van Cappellen-2005 demonstrate in flow-through experiments that in Clim have similar values with no dependence on salinity.


Description:
Methane consumption (anoxic or anaerobic oxidation)

Comments:
The reaction occurs in a narrow depth interval, at the bottom of the sulfate reduction zone. For this reason (primarily), the anaerobic methane oxidation has been linked with sulfate reduction.
So far, nobody can explain which bacteria catalyzes this reaction (Schink-97). 
In freshwater, this reaction is virtually absent, presumably due to the absence of sulfate reducers (Reeburgh-80).

Rate comment:
Rate=k[CH4][SO42-]
For alternative reaction 1, rate constant is 10^4 1/(M yr) (Van Cappellen-Wang-96) Rate constant is estimated (constrained to be about 10^4) in marine environment.
--------------------------------------
Rate constant 1x10^10 1/(M yr) is used in Van Cappellen-Wang-95.
--------------------------------------
Reeburgh-80 gives methane oxidation rates about 1 to 3 mM/yr.
-----------------------------------------
Reeburgh-83 gives the rate of anaerobic methane oxidation in the water column about 0.01 micromol/yr.
---------------------------
Luff-Wallmann-2003 estimate depth-integrated rate of 870 umol/cm2/yr in a sediment subjected to a large (869 umol/cm2/yr) inflow of methane from below.


Alternative:
C6H12O6   =    3 CH4   +   3 CO2;
Sequence: 2CH2O + 2 H2O = 2 CO2 + 8 (H), then 8 (H) + CO2 = CH4 + 2 H2O.;
CH3COOH (acetic acid) = CH4 + CO2;
(CH2O)x(NH3)y(H3PO4)z   +   (y-2z) H2O    =   x/2 CH4  +  (x-2y+4z)/2 CO2  +  (y-2z) HCO3-   +  y NH4+  +  z HPO42-

Comments:
1. Typically occurs below the depth where sulfur disappears, below 1m. In lakes it is important because of the low sulfur concentrations. In marine sediments, methanogenesis was observed to be responsible for 20% of total OM decomposition (Henrichs-93).
--------------------------------------
2. Equilibrium pe is about -4.
----------------------------------------
3. Schink-97 discusses many intermediate reaction steps, their energetics, various methanogenic bacterial cultures and their cooperations.

Rate comment:
1) see comment (1) to reaction 3.
---------------------------------
2) Typical rates in marine sediments 0.5-10 molC/m^2/yr (Henrichs-93).


Reaction:
CH3CH2CH2COO- (butyrate)   +   2 H2O    =    2 CH3COO-(acetate)   + 2  H+   +  2  H2

Alternative:
2 CH3CH2CH2COO- (butyrate)   +   2 H+  +  2 H2O    =    5 CH4  +  3 CO2

Description:
Degradation of OM by fermentation,
acetate production and eventually methanogenesis

Comments:
Coupled with e.g. reaction 64, overall reaction (alternative) yields methane and G0=-177 kJ/mol per 2 mols of butyrate.


Reaction:
C7H5O2- (benzoate)   +   7 H2O   +    =    3 CH3COO-(acetate)   +   HCO3–   +   3 H+   +   3 H2


Reaction:
2 CH3CH2CH2COO- (butyrate)   +   HCO3–   +   H2O    =    4 CH3COO- (acetate)   +   H+   +   CH4


Reaction:
4 C7H5O2- (benzoate)   +   19 H2O    =    12 CH3COO- (acetate)   +   HCO3–   +   9 H+   +   3 CH4


Description:
Degradation of OM by fermentation, methanogenic H2 consumption


Description:
Precipitation of OML or of metal-complexed OML (M-OML)

Comments:
This occurs (in the forward, left to right direction) when the pH is lowered and consumes H+, thereby buffering (increasing) the pH.


Alternative:
Fe2+   +   CO2   +   H2O     =     FeOOH(s)   +   CH2O

Description:
Photosynthesis of OM using Fe2+ as electron donner and producing HFO


Description:
Precipitation of hydrous ferric oxide (HFO) from aqueous Fe3+

Comments:
This occurs (in the forward, left to right direction) when the pH is increased and acts to lower the pH.
----------------------------------
Log K = 3.0-5.0 for ferrihydrite, log K = -1.0 for goethite (Stumm-Morgan-96).
----------------------------------
For the general reaction, solid phases range from Fe2O3 to FeOOH*xH2O.
-------------------------------
At low pH (<4-5), solid Fe(OH)3 slowly transforms to Fe(OH)2+ and FeOH2+ that are the dominant species (Byrne-Kester-76).
---------------------------
The reaction takes place at pH as low as 3, it is easily reversible, and may serve both as source and as sink of Fe3+.


Description:
Precipitation of hydrous ferric oxide (HFO) by oxidation of aqueous Fe2+

Comments:
1) This occurs (in the forward, left to right direction) when the pH is increased and acts to lower the pH.
------------------------------
2) The reaction is accelerated by the reaction product HFO and by the addition of HFO.
------------------------
3) Gunnars et al -2002 studied the morphology of the resulting Fe(III) aggregates and their relations to P cyclnig and the binding of Ca.
---------------------------------
4) The presence of dissoved OM may significantly affect the rate of reaction (Rose-Waite-2002). Up to 99% of dissolved Fe(III) is complexed to organics.

Rate comment:
Rate=k[Fe2+][O2]. Rate constant  1.4x10^8 1/(M yr) is quoted in Van Cappellen-Wang-96 as independent (measured) parameter for the alternative reaction in marine environment.  . 
Rate constant value 2x10^9 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (as well as in marine ones).

Millero et al -87 give expressions for the rate constant in seawater as a function of temperature, salinity, and pH.
----------------------
Tamura et al -76 give for constant pH and O2 concentration -d[Fe2+]/dt = (k+k' [Fe(III)]) [Fe2+], where k' for the heterogeneous reaction is determined by ks0 [O2] K/ [H+], K being the equilibrium constant for the adsorption of Fe2+ on HFO. Oxidation is accelerated by Fe(III) oxyhydroxides. See also Tamura et al -80.
-----------------------
The rate is strongly influenced by pH (Stumm-Lee-61). An increase by 1 pH increases k by 100.
Experimental rate law R=k[O2][Fe2+][H+]^(-2)
------------------------
At pH 7.5, half-life is 3.4min (Davison-Zhang-96).
At pH 8 half life is about 1s, at pH 7 - several min, at pH 6 - several hours (Pankow-Morgan-81)


Description:
Precipitation of hydrous ferric oxide (HFO) by oxidation of aqueous Fe2+ using Mn-oxide as an oxidant

Comments:
Fe2O3 may perhaps form instead of Fe(OH)3 (Davison-93, p153).

Rate comment:
Rate constant 3x10^6 1/(M yr) is estimated in Van Cappellen-Wang-96 for the alternative reaction in marine environments (constrained <10^9). Rate is assumed Rate=k[MnO2][Fe2+]
Rate value 1x10^6 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (2x10^8 in shelf sea).
------------------------------
Hunter et al -98 use 10^3 1/(M yr) in groundwater.
-----------------
Berg et al -2003 use 7.5x10^(-11) 1/(microM sec) = 2.4x10^3 1/(M yr).
-------------
Luff-Moll-2004 use 10^4 1/(M yr).


Description:
Formation of HFO by oxidation of FeCO3 (siderite) and denitrification

Comments:
Quantitative importance is not yet clear (Schulz-Zabel-2000).


Description:
Precipitation of FeS (Fe2+ sulphide)
(reversible)

Comments:
Rickard-Morse-2005 provide a comprehensive review of iron sulfide formation.
--------------------------------
Reverse reaction, combined with reaction 98, gives the alternative reaction 98.
---------------------------------
A competing mechanism of FeS formation is represented by reactions 193 and 194.
----------------------------
(Murray-95) report solubility product in a lake pKsp = 2.6 - 3.75
pK = 2.95 - 5.25 (Stumm-Morgan-96)
For Ksp = [Fe2+][HS-]/[H+], Morse et al -87 give Ksp = (1.14+-0.23)x10^(-3) for amorphous FeS, and Ksp=(2.86+-0.57_x10^(-4) for mackinawite.
Davison-91 gives equilibrium constants for a variety of FeS compounds (mackinawate, greigite, etc.).
Hunter et al -98 use for main reaction log K = -15.5 while citing Stumm-Morgan-96 logK=-16.85.
------------------------
The reaction may be important in phosphorus cycling in lake sediments, it binds reduced Fe under anoxic conditions and allows P to remain in solution.

Rate comment:
Rate constant 1.5x10^(-5) mol/(g yr) is fitted from the model in Van Cappellen-Wang-96 for the alternative precipitation reaction. Fitted constant for the dissolution reaction: k=1x10^(-3) 1/yr.
Rate constant 1x10^(-6) 1/(M yr) is used in Van Cappellen-Wang-95.
-----------------------
Blodau-Peiffer-2003 consider this reaction fast and  equilibrium.
------------------------
Hunter et al -98 use 6x10^(-5) mol/dm^3/yr for precipitation and 10^(-4) 1/yr for dissolution in ground water while quoting 4x10^(-6)-3.2x10^(-4) and 10^(-3), respectively.
---------------------
For dissolution reaction (Morse et al -87): at pH <4.3, activation energy is 6.8 kcal/mol. The reaction rate is d[H2S]/dt=k*A*H/v where A is surface are of FeS and v is molecular volume.
-----------------------
 Rickard-95 reports an observed law -d[H2S]/dt=k[H2S], where k=90 1/s. The rate law is consistent with Eigen-Wilkins model, in which the rate is d[FeS]/dt = -d[H2S]/dt = k[Fe2+][H2S]. The theoretical value for k is log k=7+-1 l/mol/s.
-------------------------
Dittrich et al -2004 obtain k=0.001 mol/l/d by fitting a model.


Comments:
Alt. reaction (1) corresponds to complete oxidation. G0 is shown for alt. reaction (1).
------------
Canfield et al -93 hypothesise that this reaction accounted for most of the MnO2 consuption in their marine sediment.


Description:
Formation of pyrite (FeS2) from FeS, (from elemental S or polysulphides)

Comments:
In the Reaction field, "x" refers to the number of sulphur atoms participating in the reaction.
----------------------
While the alt. reaction implies reaction between two solids, actual dissolution of FeS has to occur to enhance reactivity.
---------------------------------
FeS is a general name for a variety of compounds with compositions close to FeS, see e.g. alt. reaction.
--------------------
Rickard-Morse-2005: S(0) is actually S8 at ambient temperatures, and the reaction as written represents a ninth order process. Collision of 9 molecules is highly unlikely. However, a virtually infinite number of reactions may be written to describe pyrite formation in the natural environment, depending on what the observer chooses to use as
reactants and products. The kinetics is equally applicable and true for all these various overall reactions, since
they refer to the rate-controlling molecular step.

Rate comment:
Fossing et al -2004 give 3.0x10^(-12) cm^3/nmol/s for second-order reaction (alt. 1).


Reaction:
8 H2O   +   FeS2(s)   +   14 Fe3+ (-OML)    =    2 SO42–   +   15 Fe2+ (-OML)   +   16 H+, where the (-OML) are optional.

Description:
Oxidative dissolution of pyrite (FeS2) by Fe3+

Comments:
Fe3+ reacts with pyrite faster than O2 and may be an important oxidant, especially below the oxic layer, since it remains adsorbed onto the surface of FeS2.
Decreases pH


Comments:
See also oxidation reaction 83.
1. The kinetics of homogeneous reaction is very slow (Diem and Stumm 1984).
-----------------------------------
2. G0 is indicated for the alternative reaction (2).
------------------------------
3. This reaction may follow reaction 32 in effective oxidation of ammonia to N2 by oxigen  (Anschutz et al -2000).
-----------------------------
4. The reaction is thermodynamically favored at pH>4
-----------------------------
5. In reality, oxygenation product range from MnO1.3 to MnO1.5 at circumneutral pH.

Catalyst:
manganese oxidizers / manganese reducers

Rate comment:
Rate = k[Mn2+][O2]. Rate constant is 10^7-2x10^9 1/(M yr) (Wang-Van Cappellen-96).
The reaction is typically insignificant compared to the heterogeneous reaction 51.
Characteristic time scale is several years.
-------------------------
Hunter et al -98 use k=10^7 1/(M yr) in groundwater while quoting another reported value 2x10^9 1/(M yr).
-----------------------
Hoffmann-81 gives k=9.1x10^(-2) 1/(M s)= 3x10^6 (1/(M yr).
The reaction rate is strongly pH dependent (accelerates with rising pH).
-------------------
Morgan-2005 reviews the kinetics of Mn(II) oxidation in a variety of enviroments.


Description:
Reductive (anoxic) dissolution of Mn-oxide by nitrification

Comments:
Also sometimes called the “anammox” reaction: anaerobic ammonium oxidation
-----------
see also reaction 32 and reaction 82
---------------
Thamsdrup-Dalsgaard-2000 reported that no oxidation of NH4 took place in their MnO2-rich sediment.
--------
Hulth et al -99 find positive correlation between nitrification rate and sulfate reduction rate.
-------------
Hulth et al -99 suggest that anoxic nitrate production during Mn reduction indicates that nitrification and
denitrification can occur simultaneously in subsurface sediments, without vertical stratification.
------------
Hulth et al -99 suggest that this reaction was more active than the direct production of N2 (reaction 32).

Rate comment:
Hulth et al -99 report that NO3 production is increased in presence of MnO2. Assuming that the observed increase was caused entirely by this reaction, and assuming a second-order kinetics R=k[MnO2][NH4], I estimate the reaction rate constant k=10^5 - 10^6 g/(yr mol). This is likely to be the upper limit for the k value.
----------------
Hulth et al -99 report that the rate of NO3 production was proportional to the amount of MnO2.
---------------
Chaillou et al -2005 observed production of NO3- in anaerobic turbidites in presence of Mn. The appearance of the peak was noted after 7 days of the experiment.


Description:
Reductive (anoxic) dissolution of Mn-oxide by N2 production

Comments:
see also reaction 31 and reaction 82.
--------------
Effectively short-circuits the nitrification-denitrification cycle (Luther et al -97) by producing N2 directly.
---------------------
This reaction may be followed by reaction 30 in effective oxidation of ammonia to N2 by oxigen (Anschutz et al -2000).
-------------------
Thamsdrup-Dalsgaard-2000 reported that no oxidation of NH4 took place in their MnO2-rich sediment.
--------------
Hulth et al -99 suggest that this reaction (direct production of N2 from NH4) ) is less active than reaction 31, which is a step in the overall anoxic N2 production.
---------------
Depending on the assumed form of MnO2, this reaction is not thermodynamically favorable except in zones of relatively high NO3- and pH (Hulth et al -99).


Description:
Dissolution of Mn-oxide by sulfide oxidation, Mn reduction

Comments:
1. Coupled with reaction 68, gives the net reaction S0  +  3 MnO2  +  2 H2O  =  SO42-  +  3 Mn2+  +  4 OH- (cyclic reoxidation of H2S with MnO2). Involves S0-disproportionating bacteria. (Schippers-Jorgensen-2001)
---------------------------
2.  In Wang-Van Cappellen-96, this reaction is accountable for less than 5% of all rectants/products and may be ignored.

Rate comment:
Rate=k TS [MnO2] where TS=[H2S]+[HS-]. Rate constant is 2x10^4 1/(M yr) (Van Cappellen-Wang-96)
Rate constant is estimated (constrained <10^8) for the alternative reaction 1 in marine environments. 
Rate value 1x10^4 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments.
Luff-Moll-2004 used k=10^4 1/(M yr)
-------------------------
Hunter et al -98 use 2x10^4 in groundwater.


Comments:
see also reaction 49
----------------
The reaction occurs under anoxic conditions
---------------
Mucci-2004 studied dissolution of natural ordered kutnahorite (Mn1.14 Ca0.82 Mg0.04 Fe0.012 (CO3 )2 ) and a  disordered, calcian rhodochrosite (Mn1.16 Ca0.78 Mg0.06 (CO3 )2 ) precipitated in the laboratory. Both solids dissolved congruently in distilled water in an open system and yielded identical long-term equilibration or extrapolated ion activity products, IAPpkt =[a (Ca2+)^x a(Mn2+)^(1-x) a(CO32-)]^2 = 1.7(+-0.12)x10^(-21) or pIAP = 20.77 (+-0.03). This value is believed to be the thermodynamic solubility product of pseudokutnahorite.
-----------
Equilibrium constant for metastable pseudokutnahorite is about 11 times greater than for its ordered counterpart. (Mucci-2004)
------------
Phases of different stoichiometry may form in response to large variations of the [Mn2+]:[Ca2+] ratio in solution (Mucci-2004). The nature (i.e.,mineralogy) and composition of manganese-rich carbonate phases that may form under suboxic/anoxic conditions in marine sediments are dictated by the porewater [Mn2+]:[Ca2+] ratio, the abundance of calcite surfaces and reaction kinetics.
--------------------
The presence of minor amounts of Mg may signiﬁcantly in ﬂuence the order –disorder relations in the kutnahorite structure (Peacor et al.,1987).
------------------
McBeath et al.(1998) propose that within the compositional range 0.186<x <0.734, the Ca_x Mn_(1-x) CO3 system is thermodynamically stable.Their evaluations of the excess Gibbs free energy of mixing for this system at 25 C indicate
increased stability at x=0.45, corresponding nearly to the ideal kutnahorite composition.
-------------------
The presence of phosphate may inhibit precipitation of carbonate minerals (refs in Mucci-2004).
------------------
In paleorecords, there is evidence (Gingele-Kasten-94) that manganese carbonate peaks occur at deglaciation phases (decreased supply of organic matter) though the total manganese contents are nearly constant.

Rate comment:
Rate constant for precipitation reaction is 1x10^(-4) mol/(g yr) (constrained <10^(-2)) (Van Cappellen-Wang-96).
-------------------------------
For dissolution: k=2.5x10^(-1)  1/yr (constrained 10^(-2)-10^3) (Van Cappellen-Wang-96).

Rate law:
Rate = k(Omega/K-1),
Omega=[Mn2+][Co32-]/x, K=eq.const.
----------
dissol Rate = [MnCO3](1-Omega/K)


Reaction:
Ca2+   +   2 HCO3–    =    CaCO3(s)   +   CO2   +   H2O

Alternative:
1. Three general mechanisms:
Ca2+  +  HCO3-  =  CaCO3(s)  +  H+;
Ca2+  +  2 HCO3-  =  CaCO3(s)  +  H2CO3;
Ca2+  +  HCO3-  +  OH-  =  CaCO3(s)  +  H2O;
2. Ca2+  +  CO32-  =  CaCO3(s)

Comments:
The reaction is reversible
---------------------------
G0 is given for the alternative reaction 2. Log K=-8 at T=25 C and log K = 10 at T=5C..
For alternative reaction 2, deltaH0 = -2.297 kcal/mol, log K = -8.480 (Stumm-Morgan-96)
-------------------------------------
Analytical expression for temperature dependence for alt. (2) (Appelo-Postma-93) is logK = -171.9-0.0779*T +  2839.3/T + 71.595 log T.
--------------------
Plummer et al -78 study calcite dissolution reactions in great detail.
-------------------
Reaction is pH-dependent. Dissolution occurs mainly at pH<7 (Plummer et al -78).

Rate comment:
R = k (1-[Ca2+][CO32-]/K)^n, where n is about 4.5 for calcite and 4.2 for aragonite. K is weakly constrained (Schulz-Zabel-2000)
---------------------------------
PWP model (Plummer et al 1978):
R=k1 [H+]  + k2 [H2CO3]  +  k3 [H2O]  -  k4 [Ca2+][HCO3-]
R is in mol/(cm s).
--------------------------------
Hunter et al -98 use 6x10^(-5) mol/l/yr for precipitation and 5x10^(-4) 1/yr for dissolution in groundwater (from numerical arguments).
-------------------------
Dissolution rates as function of pH and partial CO2 pressure are given in Plummer et al -78.
-----------------------
Luff-Wallmann-2003 use k=5 1/yr for aragonite dissolution and 10 mmol/cm3/yr for calcite precipitation.


Description:
Degradation of OM by Fe reduction  (Fe oxide as the oxidant)

Comments:
The exact position in sediment is not known.


Comments:
This is an approximate net reaction in natural waters. C106H263O110N16P1 is the average composition of organic matter in plankton.


Reaction:
C (organic) +  NO3-  +  H2O  +  H+   = 2 CO2  +  NH3


Description:
Ammonium ion formation (acid-base reaction)

Comments:
Reversible.
Causes rise in pH. 
The initial ammonia is typically released by microbial processes.

Rate comment:
should be fast as it is an acid-base reaction


Description:
Nitrate production by ammonium ion oxidation (nitrification)

Catalyst:
Nitrosomonas, Nitrosococcus (alt. 2-1)
Nitrobacter (alt. 2-2)

Rate comment:
Rate=k[NH4+][O2]. Rate constant 5x10^6 1/(M yr) is estimated (constrained to be about 10^7) in marine environment (Van Cappellen-Wang-96).
Rate constant value 2x10^7 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (1.5x10^7 in shelf sea). 
------------------------
Hunter et al -98 use 5x10^6 in groundwater.
-----------------------------
Wijsman et al -2002 use reaction rate constant 20 1/day and use Monod-type kinetics.
------------
Monod-type expression is used in Omlin et al -2001a.


Comments:
1. The reaction has many intermediate steps
--------------------------
2. G0 is shown for the alternative reaction 1.
--------------------------
3. In Wang-Van Cappellen-96, this reaction is accountable for less than 5% of all rectants/products and may be ignored.

Rate comment:
Rate=k TS [O2]. Rate constant1.6x10^5 1/(M yr) is estimated (constrained >1.6x10^5) in marine environment (Van Cappellen-Wang-96).
Rate value 6x10^8 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (same as in shelf sea).
-----------------------------
In Boudreau-91, rate 10^(15) 1/(M a) is estimated from the model.
----------------------------
Morse et al -87 give half-oxidation time 10 to 1000 min, depending on O2 concentration. Pseudo-first order rate constant for H2S oxidation increases with pH from 6 to 8.5, decreases from 8.5 to 9, and increases to about pH 11. 
----------------------------
Hunter et al -98 use 1.6x10^5 in groundwater.
--------------------------
Hoffmann-81gives k=1.0x10^(-1) 1/(M s) = 3x10^6 1/(M yr).


Comments:
Alt. reaction shows the complete oxidation to HFO. G0 is indicated for the alt. reaction.

Rate comment:
Rate=k[FeS][O2].
Rate constant 3x10^5 1/(M yr) is fitted from the model in marine environment (Van Cappellen-Wang-96).
Rate 2x10^7 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (2.2x10^7 in shelf sea).
Rate constant 2.4x10^7 1/ (M yr) is used in Luff-Moll-2004.
--------------------
Hunter et al -98 use 6x10^4 in groundwater while quoting literature values 3x10^5-2x10^7.


Rate comment:
Rate=k[CH4][O2]
Rate constant 10^10 1/(M yr) is fitted from the model in marine environment (Van Cappellen-Wang-96).
Rate 1x10^10 1/(M yr) is used in Van Cappellen-Wang-95 in lacustrine environments (same as in shelf sea).
------------------------------
Di Toro et al -96 fit k=6*10^6 1/(M yr).
-----------------------
Reeburgh-83 gives aerobic methane oxidation rate 0.1-3.4mM/yr.
-------------------------------
Mayer et al -2002 give an assumed value of 1.0x10^(-9) mol /L/s.


Reaction:
Mn2+  +  2 HCO3-  =  MnCO3(s)  +  CO2  +  H2O

Description:
Mn precipitation due to carbonic acid (rhodochrosite formation)

Comments:
see also reaction 34
----------------------
For the alt. Reaction: Log K=-10.
For alt.reaction LogK = -10.39 to -11.13 (Stumm-Morgan-96).
pK = 2.60 (Davison -93) for alt. Reaction

Rate comment:
Rate constant is 1x10^(-6) M/yr ( Wang-Van Cappellen-96).
Value 2x10^(-4) and a range <10^(-2) mol/(g yr) are given in Wang-Van Cappellen-96 in marine sediments for forward precipitation reaction and 10^(-2) - 10^(3)  1/yr for reverse reaction.
-----------------------
Hunter et al -98 use 10^(-4) mol/l/yr for precipitation and 10^(-4) 1/yr for dissolution while quoting literature on 4x10^(-6) - 5x10^(-3) for precipitation and  10^(-2)-10^3 for dissolution.

Rate law:
Rate = k(Omega/K-1),
Omega=[Mn2+][CO32-], K=eq.const.
----------
dissol Rate = [MnCO3](1-Omega/K)


Reaction:
Fe2+  +  2 HCO3-  =  FeCO3(s)  +  CO2  +  H2O

Description:
Fe precipitation (siderite) due to carbonic acid

Comments:
For alt. reaction 1,  pK = 10.2 - 10.7.
For crystalline siderite, deltaH0 = -2.48 kkal / mol (Stumm-Morgan-96).
G0 is specified for alt. dissolution reaction.
-----------
Siderite and vivianite may be in thermodynamic equilibrium with each other and PO4 and CO32- in sediment (Bray et al -73).

Rate comment:
Rate constant is 1x10^(-6) M/yr (Van Cappellen-Wang-95)
Value 4x10^(-3) mol/(g yr) and range <10^(-2) are used in Wang-Van Cappellen-96 for forward reaction and 5x10^(-1) 1/yr (range >10^(-2)) for the reverse reaction.
------------------------
Hunter et al -98 use 5x10^(-5) mol/l/yr for precipitation and 5x10^(-5) 1/yr for dissolution in groundwater while quoting literature <10^(-1) for precipitation and >10^(-2) for dissolution.
-----------------------
Wersin et al -91 estimate maximum precipitation rate 3 microgramm/g(DW)/yr. Because of kinetic limitations, there were no siderite in their sediment.
-----------------------
Duckworth-Martin-2004 measured the anoxic dissolution rate 10^(-8.65) mol/m^2/s for 5.5<pH<12. Uder oxic conditions, dissolution rate decreases.

Rate law:
Rate = k(Omega/K-1),
Omega=[Fe2+][CO32-], K=eq.const.
----------
dissol Rate = [FeCO3](1-Omega/K)


Description:
Heterogeneous Mn oxidation and  precipitation

Comments:
Similar to reaction 30.  In Van Cappellen-Wang-95 reaction 30 (homogeneous oxidation) is not used because of the very slow kinetics.

Rate comment:
1. Rate=k[S-Mn+][O2]. Rate constant is 5x10^6 1/(M yr) (Van Cappellen-Wang-96) for the alternative reaction. (Range 8x10^5 - 2x10^7 is given in Wang-Van Cappellen-96).
Rate value 2x10^9 1/(M yr) is used in Van Cappellen-Wang-95  in a lacustrine environment (as well as in marine).
--------------------------
2. In Wilson-80, different expression is used. Rate=k0[Mn2+]+k[Mn2+][MnOx]. Dependence on pH is calculated.
-----------------------
Pankow-Morgan-81 also use this expression. MnO2 which is formed, because of its adsorptive properties, accelerates the removal of Mn2+ thus providing an autocatalytic effect.
-----------------------
3) Characteristic time scale for a bacteria-assisted reaction is from days to months. Inorganic reaction time scale is about 1 day at pH 9.
---------------------------------
The rate should strongly depend on pH (compare to reaction 20 for Fe)


Description:
Heterogeneous Fe oxidation and precipitation

Comments:
1) Compare with reaction 20. In Van Cappellen-Wang-95, both this reaction and the  reaction 20 are used.
--------------------------------
2) The reaction becomes more favorable as pH increases (Luther et al -97, may refer to the homogeneous reaction 20)
----------------------------------
3) The reaction may be catalyzed by bacteria.

Rate comment:
Rate is assumed Rate=k[S-Fe+][O2].  The rate constant 5x10^7 1/(M yr) is estimated in Van Cappellen-Wang-96 and constrained (<10^8) in marine environment. 5x10^6 is used in Wang-Van Cappellen-96.


Description:
Fe reduction by H2S oxidation
Dissolution of HFO by HS–

Comments:
FeOH+ may form instead of Fe2+ with the formation of polysulfides (Morse et al -87).
--------------------------------
Compare to similar reaction 98 (alt.(4)) with SO4 production.
---------------------------------
S0 is a prominent oxidation product (Peiffer-94)
In diagenetic models, this reaction can create a "mass leak" if S0 is not considered as a model species (Meysman-Middelburg-2005). 
--------------------------------
This reaction may be important in phosphorus release from lake sediments as it leads to the binding of Fe as FeS and removal of HFO adsorption substrates.

Rate comment:
1. Rate=k TS [Fe(OH)3]
Rate constant 8x10^3 1/(M yr) is estimated (constrained <10^5) in marine environment in Van Cappellen-Wang-96.
-----------------------------------
2. In Van Cappellen-Wang-95, rate 1x10^4 M/yr is given for the alternative reaction 2, in lacustrine environments.
--------------------------------
3. Dissolution of metal oxides is typically surface-controlled (Peiffer et al -92). The reaction is then first order with strong pH dependence. R=k[H+]^(-2)[H2S]A; k=1.5x10^(-13) M^2/min for 5<pH<6, and R=k[H+][H2S]A; k=2x10^6 M^(-1)/min for 7<pH<8.6.
Dissolution rate increases with surface area and proton concentration.
Reaction rate constant (pseudo-first-order with respect to H2S) measured in the range 0.01-0.15 1/min (Peiffer-94).
-------------------------------------
4. Second-order reaction rate constant is estimated from model in Wijsman et al -2002 as 1x10^(-7) 1/micromolar/day.
----------------------------
5. Fossing et al -2004 use 1.0x10^(-8) 1/micromolar/s.
----------------------
Luff-Moll-2004 use 2.4x10^7 1/(M yr).


Comments:
Includes reaction 50 as a limit case x=1.

Rate comment:
Rate constant 4.5x10^(-4) mol/(g yr) for precipitation reaction (constrained <10^(-2)) (Van Cappellen-Wang-96).
For dissolution: k=2.5 10^(-1) (constrained >10^(-2)  1/yr).

Rate law:
Rate = k(Omega/K-1),
Omega=[Fe2+][CO32-]/x, K=eq.const.
----------
dissol Rate = [FeCO3](1-Omega/K)


Comments:
May be used to model local pH balance and alkalinity conservation.


Comments:
May be considered as relatively fast prossess.
------------------
Obeys a simple linear equilibrium isotherm. In Cape Lookout Bright sediments, the adsorption coefficient was determined to be 2.30 (Klump-Martens-89).
-----------------
Berg et al -2003 use K = 1.6 cm^3/g where [NH4-ads] (mol/g) = K [NH4] (mol/cm^3).

Rate comment:
The reaction is typically considered as equilibrium and described by an equilibrium constant.


Comments:
May be considered as relatively fast prossess. Adsorption capacity generally decreases with depth.
---------------
Berg et al -2003 use K = 28 cm^3/g where [Mn-ads] (mol/g) = K [Mn-dissolved] (mol/cm^3).
---------------
Canfield et al -93 speculate that, in their sediment, most of Mn2+ was adsorbed onto MnO2 for the average oxidation state >3.8.
--------------
Hulth et al -99 estimate reversible adsorption coefficients in the range 2-10 (simple ratio).
--------------
Estimates of the partition coefficients of Mn(II) in calcite range between 1.5 and 51 (refs in Mucci-2004).

Rate comment:
The reaction was considered in equilibrium and described by an equilibrium constant.


Comments:
May be considered as relatively fast prossess.  Adsorption capacity generally decreases with depth in sediment.
-------------
Berg et al -2003 use K = 268 cm^3/g where [Fe-ads] (mol/g) = K [Fe-dissolved] (mol/cm^3).


Description:
Anoxic Mn2+ oxidation with NO3- and MnO2 precipitation

Comments:
For the alternative reaction, G0=-653.
Hulth et al -99 give G0=-98.
-----------------------------------------
The reaction is favorable for pH=1 to 10 and becomes more favorable as pH increases.
------------------
compare to reaction 31.
-----------------
This reaction is invoked to explain several features in the depth profiles in Anschutz et al -2000.

Rate comment:
Rate = k[Mn2+][NO3]
For the lack of kinetic information on this reaction, second order was assumed in Boudreau et al -98.
Rate constant was k=10^4 - 10^5 1/(mM yr)
----------
Luff-Moll-2004 used rate constant 10 1/(mM yr).


Description:
Fe2+ oxidation with NO3- and HFO precipitation

Rate comment:
Rate adjusted for the model 150 l(pw)/mmol/yr (Dhakar-Burdige-96)
-------------
Archer et al -2002 use the rate that is first order in Fe2+ and zeroth order in NO3-.


Description:
Mn2+ oxidation by IO3- and MnO2 precipitation

Comments:
IO3- is found dissolved in a seawater. This may provide additional pathway to Mn2+ oxidation in addition to O2 and NO3-. The reaction provides coupling between the Mn and iodine cycles. See also reaction 87.
----------------
Oxidation of Mn2+ by IO3 may result in a gap between the depth profiles of dissolved and solid (oxidized) Mn.


Comments:
Acetic acid may stand for a variety utilizable compounds.
Hanselmann-86 gives deltaG = -53 kJ/mol.


Comments:
Schink-97 specifies G0=-36 kJ/mol.
For alt. reaction, G0=-31 kJ/mol.


Description:
Acetogenesis, H2 consumption.
Degradation of OM and CO2 fixation by fermentation with acetate production.


Reaction:
CH3CH2OH  +  H2O  =  CH3COO-  +  2 H2  +  H+

Alternative:
2 CH3CH2OH  + 2 CO2  =  2 CH3COO-  +  2  H+  +  CH4

Description:
Fermentative acetate production from ethanol and methanogenesis

Comments:
Alternative reaction yields G0=-56 kJ/mol of ethanol


Reaction:
CH3CH2COO-  +  3 H2O  =  CH3COO-  +  HCO3-  +  3 H2  +  H+

Alternative:
CH3CH2COO-  +  2 H2O  =  CH3COO-  +  CO2-  +  3 H2

Description:
Fermentative acetate production from fatty acids

Comments:
Several other reactions are listed in Schink-97

Rate comment:
The overall rates of volatile fatty acid turnover in sediments are estimated in the range 3-340 microM/hr, both in lakes and ocean (Reeburgh-83).


Description:
Disproportionation of sulfur (also called inorganic fermentation)

Comments:
It is an endergonic process under standard conditions and requires an efficient removal of the formed HS- (e.g. by reaction with Mn or Fe oxides)  to pull the reaction.
----------------------------
Coupled with reaction 33, gives the net reaction S0  +  3 MnO2  +  2 H2O  =  SO42-  +  3 Mn2+  +  4 OH- (cyclic reoxidation of H2S with MnO2). Involves S0-disproportionating bacteria. (Schippers-Jorgensen-2001)
---------------------
Disproportionation of sulfur is likely  the most important fate of elemental sulfurin sediment (Canfield-Thamdrup-96).

Rate comment:
The rate constant is 7.0x10^(-7) 1/s (Fossing et al -2004). The reaction is inhibited by its own product. It proceeds as long as the concentration of H2S remains below a certain limit.


Comments:
compare to reaction 7.
-------------------------
This reaction combines with reaction 129 to produce pyrite.

Rate comment:
MEDIA code (Meysman et al -2003(II) suggests Monod kinetics.


Description:
Incomplete sulfate reduction (to thiosulfate)


Rate comment:
Rate = k[NO3][TS]
There is no kinetic information on this reaction so the second order was assumed in Boudreau et al -98.
Rate constant was k=10^4 - 10^5 1/(mM yr)


Reaction:
Silica <=> Dissolved silica
SiO2(s)  <=>  SiO2(aq)

Comments:
For chalcedony, log K=-3.73.
log K =-3.999.

Rate comment:
Opal dissolution rate constant 100-400 1/yr was obtained by fitting the model data to observations in Carmen Basin  and San Pedro Basin. Not a steady-state value.
-----------------------
Steefel-Lichtner-98 give for chalcedony log k =-13.39 (mol/m^2/s) and surface area 5.3x10^3 m^2/m^3.


Description:
Precipitation of Fe due to phosphate
(vivianite formation)

Comments:
Log K = -32 at T=5 C.
pK = 33.5 - 36 (Davison-93)
For alternative reaction (1), log K = -32 (Stumm-Morgan-96).
Solubility product constant is pK=-234.205+12,242.6/T+92.510* log10(T) (in Al-Borno-Tomson-94).
Using this expression, at T=25C and pressure 0.969atm, Ksp= -35.767, G0=204.1kJ/mol, H0=5.05kJ/mol, S0=-667.8 J/K/mol, Cp0=-769 J/K/mol.
--------------------------
Vivianite is the most important stable ferrous orthophosphate solid phase in sediment environments under most conditions (Al-Borno-Tomson-94).
-----------------
pKsp increases with decreasing Fe:Mn ratios in sediment (Cornwell-87).
In Cornwell-97 study, saturation was reached approximately below the oxic layer.
--------------------
Vivianite in lake sediments generally occurs in eutrophic systems. It is formed primarily in anoxic, nonsulfidic sediments (otherwise Fe2+ is consumed too quickly).
-----------------------
Vivianite reacts sensitively to pH variations, including seasonally. All of sediment is frequently supersaturated with respect to vivianite (Friedl et al -97) but kinetic factors may result in very slow precipitation (Wersin et al -91).
---------------------------
 Nriagu-Dell-74 give thermodynamic data for the formation of vivianite and other iron phosphates.
---------------------
Siderite and vivianite may be in thermodynamic equilibrium with each other and PO4 and CO32- in sediment (Bray et al -73).
-------------------
Under aerobic conditions, strengite (FePO4*2H2O) typically precipitates instead of vivianite (Al-Borno -Tomson-94).

Rate comment:
Berner-80 gives R = k(C-Ceq) for diffusion-controlled precipitation, where C is the phosphorus concentration. Rate constant is k=12 1/yr. For surface-controlled precipitation, k is about 1000 times larger.
-----------------
K=3x10^(-7) mol/l/d is obtained in Dittrich et al -2004 by model fitting.
-----------------
Emerson-Widmer-78 suggest that vivianite growth is controlled by surface reaction and not by diffusion. The response time of dissolved phosphate with respect to mineral precipitation is 1-20 days.
-----------------
Observations are often made that vivianite crystals are not normally seen in fresh sediments but rather in long cores. It is often contended that nucleation and ripening takes decades.
-----------
Rate law Rate = k((Omega/K)^alpha-1) with k=1.7x10^(-9) mol/g/yr is used in Katsev et al. -2006(II), where Omega is the solubility product, K is the equilibrium constant, and alpha=1/5.

Rate law:
R = k(C-Ceq)
------
R = k((Omega/K)^alpha-1), Omega=solubility product


Comments:
Suggested as a pathway alternative to the nitrification-denitrification for the formation of N2 in sediments
------------------------
Favorable at pH=1 to 14. Becomes less favorable as pH increases.
----------------------
The reaction may also include oxidation of NH4+.


Description:
Mn reduction by NH3 with NO3- production

Comments:
Suggested as a pathway alternative to the nitrification-denitrification for the formation of N2 in sediments
------------------------
The reaction is unfavorable for pH>7.8
-----------------
compare to reaction 31


Comments:
log K = -4.5, the reaction is thermodynamically favored in the entire pH range of natural waters.
---------------------------
1. Coupled with reaction  81, gives a significant free energy gain.
---------------------
2. The reaction may follow reaction 91 thus effectively converting NH4+ into N2 by O2 (Anschutz et al -2000).
--------------------------
3. In the absence of Mn-bacteria or surface catalysts, the reaction may not proceed for several years.
----------------------
A review of Mn oxidation processes is given in Morgan-2005.

Rate comment:
In the absence of Mn-bacteria or surface catalysts, the reaction may not proceed for several years (Diem-Stumm-84).


Rate comment:
(Schippers-Jorgensen-2001) found rates to be about 1 nmol/(m^2 s) for total dissolved S and Fe.


Comments:
Fe3+ is usually dissolved
------------------------------------
This reaction is known to be a rate-limiting step in abiotic pyrite oxidation.
-------------------
The reaction can be microbially catalysed (Fowler et al -99).

Rate comment:
The reaction rate constant is k=9.6x10^(-1) 1/(M s), assuming second order kinetics at pH 7 and T=20C (Hoffmann-81). The reaction is slow.


Comments:
IO3- is found dissolved in a seawater. This may provide additional pathway to Mn2+ oxidation in addition to O2 and NO3-. Provides coupling between the Mn and iodine cycles. See also reaction 61.


Comments:
Favorable for pH<9. The resulting I2 is highly reactive and can react further with OM to produce iodinated organic molecules.


Description:
NH4+ oxidation by MnOOH with N2 production (Mn reduction)

Comments:
May be followed by reaction 83 thus effectively converting NH4+ into N2 by O2 (Anschutz et al -2000)


Description:
NH4+ oxidation by MnOOH with NO3- production  (Mn reduction)


Description:
NH4+ oxidation by Fe(OH)3 with NO3- production (Fe reduction)

Comments:
This reaction is much less likely than reaction 92. log K =3.09 at 25C. The reaction can only occur where dissolved Fe(II) is at very low concentrations.


Alternative:
2 Fe2O3 + HS-  +  5 H+  =  2 Fe2+  +  3 H2O  +  S0(s)
Sequence:
-FeOH + HS-  =  -FeS- + H2O,
-FeS-  =  Fe(II)S*,
-Fe(II)S(s)* + H2O  =  Fe(II)OH2(s)+  +  S*-,
-Fe(II)OH2(s)+  (+ H+)  =  new surface site + Fe2+

Description:
Reductive dissolution of hematite by H2S.

Comments:
The reaction is surface controlled and its kinetics depends on the concentration and type of the surface complexes.
This heterogeneous reaction is relatively fast.

Rate comment:
Dissolution rate was about -4 Mol/(m^2 h)  in Stumm-Sulzberger-92
-------------------------------
Dissolution laws and rates for different conditions are given in dos Santos-Stumm-92.


Comments:
This reaction occurs up to neutral pH. Ferric iron is then precipitated as Fe(III) hydroxide according to the overall reaction 96.


Reaction:
Fe2+ (aq)  +  2 H2O  +  light  =  gamma-FeOOH(s)  +  2 H+ (aq)  +  1/2 H2

Description:
Precipitation of ferric hydroxide due to photo-oxidation of Fe2+.


Description:
Photochemical reductive dissolution of hematite in the presence of oxalate

Comments:
Overall reaction.
Occurs in a deaerated suspension.


Description:
Fe hydroxide precipitation by SO42- reduction (alt. with FeS precipitation)

Comments:
The reaction is reversible in some conditions (Blodau-Peiffer-2003 suggest the hypothetical reverse reaction alt.(4)).
--------------------------------
Suggested to occur at the interface between the Fe(III) and sulfate reducing zones. Combined with reverse reaction 25 gives the alternative reaction with the formation of FeS.
----------------------------
The reverse reaction can be responsible for removing Fe from the Fe-phosphate cycle. The reverse reaction is also responsible for the so-called "iron curtain", i.e. prevention of H2S upward diffusion (Fossing et al -2004).  
------------------------------
The reverse reaction is included in MEDIA code.

Rate:
0.3x10^(-2) 1/micromol/yr for reverse reaction

Rate comment:
The reaction rate constant for the reverse reaction in Meysman et al -2003(II) is k=0.257x10^(-2) 1/micromol/yr.


Reaction:
CH3COCH3  +  CO2  +  H2O  =  2 CH3COO-  +  2 H+

Description:
Fermentative conversion of acetone to acetate and then to methane

Comments:
Coupled with reaction 64 gives the alternative reaction with G0=-97.6 kJ/mol


Description:
Fe reduction by FeS oxidation by Fe(OH)3

Comments:
Complete oxidation may proceed to Fe(OH)3 or FeCO3 (reactions 120 and 121)

Rate comment:
Rate is commonly assumed Rate=k[FeS][Fe(OH)3].
The reaction (in suspension) occurs on a time scale of days.


Description:
FeS precipitation by Fe2+ oxidation by S2-

Comments:
G0 is specified for dissolution reaction. 
pK = 18.31


Comments:
Compare to reaction 46.
This reaction is a step in pyrite formation. The resulting S0 reacts with FeS (obtained by reaction 25) to form FeS2 (reaction 129).


Comments:
The final oxidation product is commonly Fe(OH)3.
---------------
The reaction may be a result of direct microbial metabolism.


Description:
Nitrification by ammonium ion oxidation by HNO3

Comments:
Ammonium oxidation coupled to nitrate reduction may be important to global N cycling (Thumdrup-Dalsgaard-2002).


Comments:
Conforms to the general form of oxide dissolution in Blesa-Maroto-86. Possibly can also be written without H2 and with Fe3+ (e.g. alt.reaction) as one of the products (see reaction 1 of Blesa-Maroto-86).


Comments:
May be used as a half-reaction with FeCO3 as an intermediate product.

Rate comment:
Mayer et al -2002 give an assumed value of 1.0x10^(-9) mol/L/s.


Comments:
May be used as a half-reaction with MnCO3 as an intermediate product.
-------------

Rate comment:
Morgan-2005 gives a review of the rate constants)


Description:
MnS (alabandite) precipitation by Mn2+ oxidation by HS-

Comments:
pK = 0.40
For alt. reaction, pK=15 (also reported pK=18.96 and Keq=4*10^(-14)).
G0 is given for alt. dissolution reaction.


Comments:
compare to reaction 29 (oxidative dissolution of pyrite).


Description:
Reductive dissolution and transformation of HFO to hematite.

Comments:
This reaction is a suggestion based on the general form for a  metal oxide phase transformation suggested in Blesa-Maroto-86. Need environmental evidence that it actually occurs.


Comments:
In limnological literature, especially in early papers, the term adsorption is often misused and refers to an overall retention of P rather than true surface sorption.
----------------------
Equilibrium adsorption constant Kp is about 1.7 to 2 in anoxic sediments. In oxic conditions, K is about 20 to 50 times higher. For pure iron oxide phases, K is of the order of 1000s (Krom-Berner-80).
---------------------------------------
In Parfitt-89, the amount of adsorbed P followed the order hematite<goethite<ferrihydrite<allophane.
--------------------------------------
This reaction is expected to be important for the P cycling in sediments and water column. May affect vivianite formation. 
--------------------------
Complexation with the surface is multi-dental.
---------------------------
The adsorption process for PO4 may be much slower than adsorption of Fe2+ and Mn2+.
-----------------------------------
Data of Slomp et al -96(2) as well as many others suggest that, averaged over typical iron phases in marine sediments, P adsorbs to iron phases in ratio P:Fe=1:10 to 1:12.
------------------------
Golterman-95 suggested Freundlich isotherm for adsorption on iron oxyhydroxides Pads = 23626.10^(-0.416*pH) (2.86-(1.86 e^(-Ca)))*(P^(1/3)) where Ca is in mmol/l and P and Pads in mg/l.. The isotherm fits data well for pH>8 but is inferior to Langmuir isotherm for pH<8.
-------------------
Omlin et al -2001a consider sorption of P to OM particles settling in the hypolimneoun.
-------------------
Williams et al -70 report that noncalcareous lake sediments generally adsorb more added inorganic P than calcareous sediments. This could be related to the amount of Fe, rather than CaCO3.
------------------
Gao-Mucci-2003 report that adsorption of PO4 is decreased slightly in presence of SO4 and increased in presence of Mg2+ and Ca2+.

Rate comment:
Adsorption is a reversible two-step process. Fist step is adsorption to surface (time scale of hours), second step is diffusion into interior of particles (time scale of days) (Froelich-88).
----------------------------------
In the LSSE-Mega model equilibrium is assumed as [S-H3PO4] = Kp [H3PO4], where Kp depends on pH and [H3PO4] according to Langmuir isotherm. 
-----------------------------
Krom-Berner-80 report that equilibrium was achieved in 24h in their experiments. Desorption was more rapid that adsorption.
-----------------------
Wang et al -2003 use kinetic sorption approximation in their model. Reaction rate constant is 0.72-357 1/day
---------------------
Fossing et al -2004 use 5.0x10^(-11) 1/s for binding of phosphate with goethite.
------------------------
Wallmann-2003 considers uptake of phosphate by sediments (both sorption, precipitation, and bacterial uptake) as Rate = k[PO4][NO3]/([NO3]+Kno3), where k=55 1/yr. for deep sea and 165 1/yr for the shelf.
------------------------
Omlin et al -2001a consider sorption of P to OM particles settling in the hypolimneoun. They use: Rate = k (alpha - X_pi,s / X_s ) [H3PO4] X_s, where X_s is the concentration of dead biodegradable OM, X_pi,s is concentration of phosphate adsorbed to mineral particles associated with dead OM (Reichert-Wehrli-2004).

Rate law:
equilibrium
---------
Rate = k[PO4][NO3]/([NO3]+Kno3)
---------
Rate = k (alpha - X_pi,s / X_s ) [H3PO4] X_s


Rate comment:
For three marine coastal sites, empitical low (Canfield-Berber-87) was dCmagnetite/dt = -1.1x10^(-5)[H2S in mM]^0.5*Cmagnetite*Amagnetite, A in cm^2 per g of magnetite.


Description:
Iron liberation from biotite with kaolinite formation

Comments:
The alt. reaction gives the reverse reaction


Comments:
In chemical experiments (Schippers-Jorgensen-2001), FeS2 could not be oxidized by NO3-.
---------------------
Anaerobic microbial dissolution of FeS2 is probably insignificant in marine sediments.


Comments:
In chemical experiments (Schippers-Jorgensen-2001), FeS2 could not be oxidized by amorphous Fe(III) oxide.
---------------------
Anaerobic microbial dissolution of FeS2 is probably insignificant in marine sediments.


Comments:
In chemical experiments (Schippers-Jorgensen-2001), FeS2 could not be oxidized by amorphous Fe(III) oxide.
-------------------
Anaerobic microbial dissolution of FeS2 is probably insignificant in marine sediments.


Comments:
Reaction 100 is the first step of this overall reaction.
---------------------------
In chemical experiments (Schippers-Jorgensen-2001), FeS could not be oxidized by amorphous Fe(III) oxide..


Comments:
Reaction 100 is the first step of this overall reaction. 
----------------------
In chemical experiments (Schippers-Jorgensen-2001), FeS could not be oxidized by amorphous Fe(III) oxide.


Comments:
In chemical experiments (Schippers-Jorgensen-2001), FeS could not be oxidized by NO3-.
-----------------------
 The process is possible if microbially mediated.


Comments:
The reaction may participate in a Cd precipitation / dissolution cycle that pumps Cd deeper into the sediment (Gobeil et al -97) and involves Cd cycling across the redox boundary.
-----------------

Rate comment:
Rate=k[O2][CdS]
The rate constant k=0.001-0.01 1/d -(mgO2/L) is obtained by fitting a model to the experiments (Di Toro et al -96). 
K=0.01 is for marine sediments with typical OC and AVS concentrations, k=0.001 is for freshwater sediment with high POC and low AVS.


Rate comment:
Rate=k[Cd][FeS]. The rate constant k=10.0 1/d- mol/m^3 is obtained by fitting a model to the experiments (Di Toro et al -96).
The rate constant was the same in marine and freshwater sediments.


Description:
Adsorption of Cd2+ onto particulate organic carbon and Fe hydroxides


Comments:
pK=31.8 at T=5 C. In mixed Fe2+ - Mn2+  - PO43-  solutions, pKsp increases with increasing Fe:Mn ratios. 
-----------------------
In Cornwell-97 study, saturation was reached approximately below the oxic layer. 
-------------------------------
Reddingite is an unlikely pure mineral phase in sediments high in Fe2+. May form solid solution with vivianite.


Comments:
Hydroxyapatite is the thermodynamically most stable form of calcium phosphate.
----------------------------
Values for solubility product pK vary from 35 to 60. Calculations based on heat of formation give pK =56 at T=5 C (Kramer-67). 
----------------------------
In non-calcareous sediments, precipitation is hindered by sluggish crystallization kinetics.
---------------------------
In Great Lakes, water is undersaturated in winter and slightly oversaturated in summer (Kramer-67). In Cornwell-97 study, saturation was reached approximately below the oxic layer. An eqiulibrium diagram (ionic product vs temperature) is given in Kramer-67.


Comments:
Together with reaction 63, may participate in the iron-sulfur cycle. H2S and Fe2+ may precipitate as FeS.


Description:
Pyrite formation by FeS oxidation by H2S

Comments:
-------------------------------
pK=6.1 at T=25C.
----------------------------------
In many studies, this process is not observed and pyrite formation from aqueous solution is inhibited (see discussion in Rickard-97). In the way it is written, this reaction proceeds at measurable rates only above 100 C (Drobner et al -90).
----------------------------------
Rickard-Morse-2005 argue that solid FeS is not a precursor to pyrite formation and that pyrite is formed from aqueous solution.
---------------------------------
This process is the most rapid of the pyrite-forming processes identified thus far (Rickard-97). 
------------------
The H2S process is favored in strictly anoxic environments. With limited O2, pyrite formation by polysulfide pathway or solid state process may become more important.
---------------------------------
Produced H2 is removed by sulfate-reducing bacteria via reaction 71.

Rate comment:
dFeS2/dt = k (FeS)(H2S). The reaction rate constant k=1.03x10^(-4) L/mol/s is obtained for T=25 C (Rickard-97). At T=125 C, k=3.20x10^-3 L/mol/s. 
------------------------
Values of k for different FeS and H2S concentrations are given in Rickard-97.
---------------------------------
Up to 50% reaction is completed in 1 day.
In typical sulfidic sediments, this reaction should produce 3x10^-10 to 3x10^-5 mol FeS2 / g sed /yr.
--------------------------------
Meysman et al -2003(II) use k=17.9 1/micromol/yr.


Comments:
Suggested in Rickard-97 as a hypothetical step in reaction 129. The resulting FeOOH can then react with H2S to form pyrite.


Description:
Pyrite formation from dissolved thiosulfate


Description:
Pyrite precipitation by Fe2+ oxidation by H2S in presence of S0.

Comments:
Compare to reaction 129 and reaction 102.
----------------
In the process, FeS is first formed that later reacts with S0 to form pyrite. At pH 7 FeS does not react with S0 for weeks, at least at room temperature. The overall reaction is inhibited at higher pH.

Rate comment:
In experimental study (Rickard-75), the kinetics was observed to conform to d(FeS2)/dt = k1(FeS)^2(S)P_H2S or d(FeS2)/dt = k2(FeS)^2(S)(sumS2-){H+}  where (FeS) is the surface area of FeS in cm^2, P_H2S is partial pressure of H2S, (sumS2-) is the sum of activities of dissolved sulfide species. The apparent activation energy is 17 kcal/mole. The rate constants vary as k1= 2x10^(-20) at T=40C to 5x10^(-22) cm^6atm/ moles/liter/sec at T=5C; and k2=1x10^(-12) at T=40C to 3x10^(-14) cm^6/moles/liter/sec at T=5C.


Description:
Pyrite precipitation from remobilized Fe(III) in clays


Comments:
The reaction is a sum of bacteria-catalyzed oxidation of sulfur and iron by O2.


Comments:
This reaction participates in pyrite dissolution/oxidation cycle. It may take place on the pyrite surface or on the solution.


Description:
Pyrite oxidation by O2 to Fe sulfate (jarosite)


Comments:
log K= -4.58
G0 is given for the dissolution reaction.

Rate comment:
Hunter et al -98 use 6x10^(-5) mol/l/yr for precipitation and 5x10^(-4) 1/yr for dissolution in groundwater (from numerical arguments).
-----------------------------------
Steefel-Lichtner-98 in their groundwater calculations use log k = -8.0 (mol/m^2/s) and surface area 100 m^2/m^3.

Rate law:
R = k[Omega/K-1)
------
dissol. R = k[CaSO4](1-Omega/K)


Description:
Organic matter oxidation and iron reduction using strengite as electron acceptor.

Comments:
A hypothetical reaction examplary of a class of reactions involving Fe and P phases.

Rate comment:
In laboratory experiments, rate was 1.35*10^(-11) mmol/h/cell (Hyacynthe, pers.comm.).


Description:
Pyrite formation by direct precipitation following Fe(III) reduciton

Comments:
This effective reaction represents a mechanism of pyrite formation that does not require formation of FeS as a precursor phase.  Pyzik-Sommer-81 have shown, however, that this reaction may involve formation of a FeS precursor.
--------------------
The reaction is thought to be active in salt marsh sediments.
-------------------
compare with reaction 133.


Comments:
Stability constants for polysulfides formation (for various n) are reviewed in Rickard-Morse-2005.


Description:
Reductive precipitation of aqueous uranyl carbonate

Comments:
Eh 0.687
----------------
UO2 can accumulated within bacteria cells. This can protect it from oxidation.
-----------------
Ferrihydrite inhibits bacterial U reduction (Wielinga et al -2000).
-----------------
Bacteria can utilize oxiduzed uranium as terminal electron acceptor.

Rate comment:
In incubations of Fredrickson et al -2002, most precipitation occurred within 25 hours. Most dissolution occurred within 5 hours.
---------
Mn oxides can lower the rate of reduction (Fredrickson et al -2002).


Description:
Precipitation / dissolution of uranium (generic reaction)

Comments:
This is a general reaction form. For specific reactions, see reaction 236.
---------------------
Uranium (U(VI)) forms very stable aqueous complexes (e.g., carbonate, hydroxide), which greatly increase its solubility. The reduced state (U(IV)) generally forms phases of limited solubility such as the mineral uraninite (UO2). (Wielinga et al -2000).
The most common salts of U(IV) are uranite (UO2), pitchblende(UO2), and coffinite (USiO4).
They have much lower solubilities than salts of the uranyl ion (UO2 2+). Uranyl ion also forms strong aqueous complexes with carbonate. (Behrends-Van Cappellen-2005).
---------------------
UO2 can accumulate within bacteria cells. This can protect it from oxidation.
-----------------
Bacteria can utilize oxiduzed uranium as terminal electron acceptor.
Microorganisms that rapidly reduce U(VI) to U(IV) include both dissimilatory metal-reducing bacteria or sulfate-reducing bacteria. The enzymatic reduction of uranium by D. desulfuricans was not inhibited in the presence of sulfate (Wielinga et al -2000). Ferrihydrite inhibits bacterial U reduction (Wielinga et al -2000). The presence of goethite speeds up the reduction.
-------------------
Under suboxic conditions, U(VI), rather than Fe(III) is considered the preferred terminal electron acceptor for mictobial respiration, due to a higher energetic yield (Behrends-Van Cappellen-2005 and refs therein).
----------------
U accumulation in sediments can indicate diagenesis conditions in terms of OC flux and oxygen concentration (McManus et al -2005).
----------------
In sediments, one-third to two-thirds of the authigenic U precipitated is later regenerated, even under very low
BWO concentrations (15 uM). Bioturbation exposes U to oxidizing conditions near sediment surface,  remobilizing 
authigenic U (Zeng et al -2002).
----------------
In experiments of Behrends-Van Cappellen-2005, abiotic reduction of U(VI) by Fe(II), catalized by the hematite surface, was the dominant pathway for U reduction. It outcompeted direct enzymatic reduciton of U.
----------------
The diffusion coefficient for dissolved U in porewater: 2.7x10^(-6) cm2/s (Barnes-Cochran-93); 1.09x10^(-6) cm2/s (Mangini et al -2001).

Rate comment:
In experiments of Wielinga et al -2000, uranyl was removed from uranyl acetate within 10 h.
The presence of ferrihydrite decreased the reduction rate of U(VI).
----------------------
In incubations of Fredrickson et al -2002, most precipitation occurred within 25 hours. Most dissolution occurred within 5 hours.
----------------
In experiments of Jeon et al -2004, adsorption of dissolved U(VI) occurred in 3 days and its reduction within 20 days. Similar time scale was reported by Lee et al -2005.
---------
Mn oxides can lower the rate of reduction (Fredrickson et al -2002).
-----------
Jeon et al -2004 concluded that the rate and extent of reduction of U(VI) associated with surfaces of synthetic Fe(III) oxides (hydrous ferric oxide, goethite, and
hematite) was comparable to that observed during reduction of aqueous U(VI). In contrast, microbial reduction of U(VI) sorbed to several different natural Fe(III) oxide-containing solids was slower and less extensive compared to synthetic Fe(III) oxide systems. The reduction reaction occurred mostly at the solid-water interfaces.
-------------
Liger et al -99 suggested the rate of U reduction dU(VI)/dt = -k[S-Fe][U(VI)ads], where S-Fe is the neutral hydroxo surface complex =Fe(III)Ofe(II)OH0, U(VI)ads is the uranyl adsorbed on the hematite surface, and k=399+-25 1/(M min) = 2.1x10^13 1/(kM yr) at 25C.
---------------
In Barnes-Cochran-93, the rate of U removal from porewater was first order with respect to dissolved U concentration, and the rate constant correlated linearly with the rate of sulfate reduction.


Description:
Reductive precipitation of aqueous uranyl by hydrogen sulfide

Comments:
Experiments in which this reaciton occurred required either elevated temperature and/or high concentrations of both U and HS-. There is no evidence that inorganic U reduction occurs at in-sity concentrations of U and H2S (Barnes-Cochran-93).


Description:
Oxidation of OM coupled to Uranium reduction.

Comments:
The energy yield for this reaction is intermediate between Mn and Fe reductions.


Description:
Precipitation of mercury by hydrogen sulfide


Description:
Association of mercury with dissolved organic matter


Rate comment:
Soler-Lasaga-98: dissolution rates: at pH from 5 to 8, k=3.40x10^(-13) mol/m^2/s.; at pH <5, k=3.40x10^(-12); at pH>8, k= 2.14x10^(-11).
---------------------------
Steefel-Lichtner-98 give more rates. In groundwater calculations, they used surface area 5.7x10^5 m^2/m^3.


Comments:
see also reaction 160.
-------------------------------
Carbonate fluorapatite (CFA) is an authigenic mineral and can account for 25 to 70% of the total burial flux of reactive P, thus serving as a sink for P (results obtained in low sedimentation, continental margin environment).
-------------------------------
Ruttenberg-92 presents sequential extraction techniques for characterizing detrital and authigenic fluorapatite.
--------------
CFA is also referred to as francolite as a non-accepted name (see McArthur-85).

Rate comment:
The rate constant k=1.0x10^(-3) 1/d was obtained by fitting a model (Slomp et al -96).


Comments:
Fe3+  can reversibly precipitate as Fe(OH)3.


Reaction:
CH2O  +  2 H2AsO4 -  +  H+  =  HCO3-  +  2 H3AsO3

Description:
Decomposition of OM using dissolved As(V)

Comments:
The free energy change for this reaction is slightly more negative than for OM oxidation by Fe(OH)3.
-------------------------------
In simulations of Saunders et al -2001, dissolved As(V) was assumed to be co-mobilized with Fe2+  during Fe(III) oxide reduction according to a molar ratio 0.00075, assuming that Fe oxides contained 0.1 wt % As.


Description:
Oxic oxidation of dissolved As(III) to As(V)


Reaction:
H3AsO3  +  MnO2  +  H+  =  H2AsO4 -  +  Mn2+  + H2O


Comments:
Dissolved As may also co-precipitate with FeS.


Comments:
Together with reaction 194, serves as a pathway to FeS formation, with may compete with reaction 25.

Rate comment:
Observed rate law -d[HS-]/dt =k[HS-]^2, where k=1.3x10^7 liter/mol/s at T=25C (Rickard-95). The Eigen-Wilkins model gives  k=k'[Fe2+][HS-]^2, where log k'=12.5 liter^2/mole^2/s.


Comments:
Together with reaction 193, constitutes a pathway for FeS formation, which may compete with reaction 25 . The reaction is relatively slow.


Rate comment:
Rate=k*(C-Ceq), the rate constant k=0.01-0.1 1/yr range in marine environment is explored in Van Cappellen-Berner-88


Comments:
In the context of lake geochemnistry, may become important when evaporates are considered.


Comments:
This may be considered as a weathering reaction.


Comments:
Alt. reaction gives the reverse process. Alt. reaction (2) proceeds in the absence of alkalinity. In that case, Ca may build up in solution or precipitate as gypsum.


Description:
Dolomite weathering/dissolution by sulfuric acid


Description:
Anorthite weathering with kaolinite formation


Description:
Albite weathering with smectite formation


Description:
Biotite weathering with formation of gibbsite and goethite


Comments:
Highly acidic weathering. The reaction is important in soils, as well as it can buffer pH through consuming H+.
-----------------------------
For alt. reaction, log K=6.81

Rate comment:
Soler-Lasaga-98: dissolution rate: at pH<9, k=1.65x10^(-13) mol/m^2/s
--------------------------------
Steefel-Lichtner-98 give more rates. In groundwater calculations, they used surface area 5.7x10^6 m^2/m^3.


Reaction:
NaAlSi3O8(s)  +  4 H2O  +  4 H+  =  Na+  +  Al3+  +   3 H4SiO4(aq)

Comments:
The reaction is important in soils, as well as it can buffer pH through consuming H+.


Description:
Magnesium silicate precipitation (e.g. sepiolite, kerolite(talc), chrysotile)

Comments:
The reaction may occur in lakes at the time of extensive evaporation. It leads to removal of Mg2+ ions from water. Typically, during and after this reaction, CaCO3 precipitation occurs.


Comments:
The weathering product is a montmorillonite-like mineral.


Comments:
In MEDIA code, considered as mineralization reaction.

Rate comment:
MEDIA code (Meysman et al -2003(II)) suggests Monod kinetics.


Comments:
In MEDIA, considered as mineralization reaction


Rate comment:
MEDIA code (Meysman et al -2003(II)) suggests Monod kinetics


Comments:
In natural lake sediments, this reaction is irreversible because the dissolved PO4 diffuses up.
-----------------------------------
Dissolution of vivianite may be preceded by dissolution of strengite (see reaction 202).
----------------------------
The reaction has been suggested to contribute to P release from sediments, as it remobilizes precipitated P.

Rate comment:
Katsev et al -2006(II) use R=k[TS][viv] with k=1.0x10^7 cm3/mol/yr.


Comments:
log K = 2.04 (Schindler-67)
log K=3.21 (Cosby et al -85)


Description:
Precipitation of Ca-Mg carbonate (kutnohorite)


Reaction:
Na+  +  KAlSi3O8(s)  =  K+  +  NaAlSi3O8(s)

Description:
Equilibration of Na and K aluminum-silicates


Description:
Liberation of K+ from aluminum silicates (feldspar) -> (kaolinite)


Comments:
Al(OH)3 may be represented by several polymorphic minerals.
Log K = -16.76
Log K = 8.1 (synthetic gibbsite)
Log K = 8.77 (natural gibbsite)
Log K = 9.35 (microcrystalline gibbsite)
Log K = 10.8 (amorphous aluminum trihydroxide)
For alt. reaction, G0 = 71 kJ/mol for dissolution and pK = 12.39.
Dissolution (weathering) reaction may provide pH buffering in soils, as well as lakes.


Comments:
The composition formula and the reaction are approximate. 
----------------------------
Ferrous hydroxides are important precipitates in reducing and high pH conditions. At neutral pH, they may possible form in small areas around ferric oxides. 
Such oxides were suggested to contribute significantly to sorbing phosphate at the time of HFO reduction during anoxia.
--------------------------------
G0 is specified for alt. dissolution reaction. 
pK = 9.10


Reaction:
CH3CH3COO-  +  SO42-  =  CH3COO-  +  HS-  +  H+

Description:
Oxidation of fatty acids by sulfate-reducing bacteria

Comments:
Compare with reaction 67.
Several alternative reactions are listed in Hanselmann-86, including complete oxidation to HCO3-.


Description:
Acetate conversion by sulfur-reducing bacteria


Description:
Dissolution of ferrihydrite with formation of solid ferrous hydroxide

Comments:
G0 is for dissolution reaction.
pK = 17.75


Comments:
Siderite has higher Fe(II) solubility than vivianite and thus prevents vivianite dissolution in sediment by reaction 201. Siderite and vivianite may be in thermodynamic equilibrium with each other and PO4 and CO32- in sediment (Bray et al -73).

Rate comment:
Katsev et al -2006(II) use R = k [FeCO3][TS] with k=1.0x10^7 cm3/mol/yr.


Comments:
Hypothetical reaction was invoked to explain laboratory observations. Inorganic. The reaction can perhaps be used as an equivalent of FeOOH=PO4  +  H2S.


Comments:
Aqueous reaction. See also reaction 205.

Rate comment:
Rate 1.0x10^(-10) mol/L/s is reported in Mayer et al -2002.


Rate comment:
Mayer et al -2002 give 8x10^(-12) mol/L/s for goethite and 4x10^(-11) mol/L/s for amorphous Fe(OH)3.


Reaction:
1) CH2O  +  oxidant  =  CO2  +  ODU  +  H2O
2) ODU  +  O2  =  oxidant

Comments:
ODU = oxygen demand unit.
This approach was used in Soetaert et al -96 to simulate the effects of electron acceptors other than O2 withing explicitly considering their concentrations.
---------------------
Sequences of OM degradation reactions and intermediate organic compounds are investigated in some detail in McCarty-72.
-----------------
Dauwe-Middelburg-98 and Dauwe et al -99 suggested a Degradation Index (DI) as a proxy for OM degradation based on a Principal Component Analysis of the protein amino acid composition.
-------------
Berg et al -2003 use 3 OM pools (highly reactive, slowly reactive, and non-degradable) and argue that 2 degradable pools are necessary to reproduce their data.
--------------
Capone-Kiene-88 review the differences between microbial metabolism in freshwater and marine environements and compare the relative importance of OM oxidation pathways.
---------------
During organic matter oxidation, large organic molecules are first hydrolysed (typically by bacterial enzymes released into the porewater), then the hydrolysis products are further broken down by fermentation, and finally fermentation products (e.g., acetate, butyrate) are converted to inorganic end products. Iron and sulfate reducers utilize fermentation products for their methabolism, aerobes and denitrifiers can use hydrolysis products.
Burdige-2001 investigates the distribution of high-molecular-weight and low-molecular-weight dissolved organic compounds within the sediment porewater.
---------------
The dissolved organic fractions have much higher transport rates than solid organic fractions (porewater diffusion vs. bioturbation). Considering the dissolved fraction may be crucial to models of transient diagenesis, e.g., where organic matter arrivers to the sediment in pulses, as the downward propagation of reactive organic matter can be controled by the molecular diffusion of light substances such as acetate and butyrate. After the arrival of a OM pulse, active iron and sulfate reduction may occur even below the bioturbated sediment layer (Katsev et al. -2005).

Rate comment:
Hee et al -2001 investigated the timing of the release of hydrolysis, fermentation, and inorganic end products from anoxic sediments. Typical time scale for the the release and utilization of hydrolysis and fermentation products is 10-20 days.
-----------------
Accessibility of oxidant and reductant phases affects the kinetics of microbial OM reduction. For example, iron reducers access solid phase iron and dissolved organic fermentation products while sulfate reducers and methanogens can utilize only dissolved substances. As a result, sulfate reducers and methanogens can outcompete iron reducers in non-bioturbated sediments.


Description:
Pyrite formation from FeS in presence of sulfate

Comments:
This is a gross process that is a combination of reaction 71 and reaction 129.

Rate comment:
Fossing et al -2004 give the reaction rate constant 2.5x10^(-11) 1/s.


Description:
OM-S compounds formation by complexing of H2S with OM

Comments:
The reaction incorporates sulfur into organic matter. The reaction is typically abiotic.


Reaction:
RCH(NH3)COO-  +  1/2 O2  =  RCOCOO-  +  NH4+

Description:
Aminoacid dissociation under aerobic conditions

Comments:
The reaction is inorganic and usually slow. Amino acid decomposition is catalyzed by metal ions.


Reaction:
CH3COO-  +  2 O2  =  CO2  +  HCO3-  +  H2O

Comments:
G0 is -25.28 kcal/electron equivalent (McCarty-72)


Description:
Pyrite formation by release of Fe from FeS


Comments:
The reaction can serve as a precursor for pyrite formation, as elemental sulfur dissolves at higher pH.

Rate comment:
The first alt. reaction kinetics can be described by d(FeS)/dt = k{H+}^2(S)^(3/2)(A) where A is goethite surface area. The reaction rate constant is about 1.5x10^7 moles^(-1/2)liters^(-1/2)cm^(-2)sec^(-1).


# Abbreviations and symbols

Comment:
This abbreviation, which commonly refers to ferrihydrite, here is sometimes used  to include other iron oxyhydroxides.


Comment:
An interdisciplinary group at the University of Ottawa that maintains this dSED database. Contact: Denis G. Rancourt dgr@science.uottawa.ca; Sergei Katsev skatsev@physics.uottawa.ca.; Ivan L'Heureux ilheureu@physics.uottawa.ca.


Comment:
mesured at pH 7 if not indicated otherwise


# Minerals

Comments:
Is biogenic in magnetotactic bacteria and many other animals.


Comments:
(“vacancy ordered maghemite”)
See Barron and Torrent (GCA 66, 2002, 2801) for a first description of this new maghemite-like phase that has extra XRD Bragg peaks relative to ordinary maghemite.
   Oxidized form of magnetite.  Spinel structure.
Complete magnetite-maghemite solid solution exists


Comments:
Also referred to as hydrous ferric oxide (HFO).
Is biogenic in ferritin.
Believed to be most common diagenetic iron oxide in recent aquatic sediments.
Necessary precursor to the formation of early-diagenetic hematite. Can have different degrees of “crystallinity”, from 2 to 6 lines in its X-ray diffraction pattern.


Comments:
Usual end-product of ferrihydrite transformation in oxic environments. 
Believed to be the second most common Fe oxide in soils, after goethite.


Comments:
Possible end-product of ferrihydrite transformation.
Believed to be the most common Fe oxide in soils.
Has recently been shown by van der Zee et al. (submitted 2003) to be the predominant reactive Fe oxyhydroxide phase in marine and lacustrine sediments, in nanogoethite form.


Comments:
Also known as double layer hydroxide, green rust.
An important group of first precipitates in reducing and high pH conditions.


Comments:
Common in soils.  
Also referred to as “7Å-manganite”.  Mixed valence states of Mn.  
Structure not known.  Four-line XRD pattern:  0.727, 0.360, 0.244, 0.141 nm.  
Lines at 0.24 and 0.14 nm are common to many Mn4+ oxide phases and arise from layers of close packed O atoms containing edge-shared MnO6 octahedra.  Lines at 0.727 and 0.360 nm are the basal spacings (001, 002) resulting from octahedral sheets separated by ~0.72 nm.


Comments:
Mn analogue of HFO.  Has only two lines at 0.24 and 0.14 nm.


Comments:
(stoichiometric, most stable form of MnO2)


Comments:
Common in terrestrial and ocean-floor environments. Occurs in sedimentary lake evaporites.  
Also referred to as “10Å-manganite”.


Comments:
Occurs in deep sea ferromanganese nodules.  Expanded form of todorokite.


Comments:
Common Mn ore, as are the polymorphs groutite and feitknechtite


Comments:
Authigenic mineral believed to occur in freshwater lake sediments.  See:  Jones and Bowser, “Chapter 7: The mineralogy and related chemistry of lake sediments” in: Lakes; Chemistry, geology, physics (ed. Lerman, 1978).


Comments:
(Al trihydroxides or Al hydroxides)
Colloidal hydrolyzed Al-OH polymers and polymerized clusters that are the building blocks of crystalline Al(OH)3.


Comments:
(Al oxide-hydroxides or Al oxyhydroxides)


Comments:
Most common Al hydroxide in soils.
Gibbsite, nordstrandite, and bayerite are stacking polymorphs of each other in a close packed stacking of OH groups.  All have platy habits.
The relations between microcrystalline gibbsite and amorphous aluminum hydroxide (with same nominal stoichiometry) and their relevance to environmental aquatic systems are discussed by Nordstrom and Ball (Science, 232, 1986, 54).


Comments:
Gibbsite, nordstrandite, and bayerite are stacking polymorphs of each other in a close packed stacking of OH groups.  All have platy habits.


Comments:
Clay fraction authigenic anatase is common in soils.


Comments:
most stable and most common petrogenic silica


Comments:
disordered cristobalite is common in soils


Comments:
amorphous, hydrous.
Diatom, phytolith, and radiolaria skeletons and sponge spicules are amorphous silica (opal-A).
Opal-A has a VERY broad XRD peak at ~ 0.40 nm.  
Opal-A (from diatoms and phytoliths) can be expected in loess (e.g. 250 g/kg of silt fraction in dust off the west coast of Africa)


Comments:
(Fe2+_(3–x)Fe3+_x)[PO4]2.(OH)x .(8–x)H2O
Common sink for P in aquatic sediments.  Believed to be an important player in the Fe and P cycles.  Fe2+ can also be substituted by Ni, Mg, Co, Zn, …


Comments:
(apatite group)
End members:  fluorapatite, chlorapatite, hydroxylapatite.
Authigenic P sink in marine sediments.
Wide occurrence in all classes of rocks.  Accounts for ~950 g/kg of total P in igneous rocks.  
Common substitution:  PO4 = CO3, OH.
A main source of phosphate for fertilizer.  
Many substitutions are possible in A10[XO4]6Z2 as:
A = Ca, Sr, Mn, Pb, Mg, Ba, Zn, Cd, Fe, Cu, Na, K, Rb, U, Th, Zr, ... (+, 2+, 3+, 4+)
[XO4] = PO4, SiO4, SO4, AsO4, VO4, CrO4, BeO4, CO3F, CO3OH, BO4, ...
Z = F, OH, Cl, Br, I, ...


Comments:
Believed to be a major authigenic P sink in anoxic marine sediments.


Comments:
(apatite group)
According to Kastner (1999), francolite in marine sediments is indicative of high productivity, forms “phosphorite” nodules and crusts.  “Francolite” is not a presently accepted mineral species and it has also been referred to as carbonate fluorapatite (CFA).  See O’Brien and Veeh (1980)


Comments:
Authigenic mineral believed to occur in freshwater lake sediments.


Comments:
Often associated with the heavy fractions of soils.  
Very resistant to weathering.


Comments:
(monetite group)
Also called “anhydrous dicalcium phosphate” (DCPA).


Comments:
(variscite group)
Most widely distributed form of the variscite-strengite series.  Important in soils


Comments:
(whitlockite group)
Ca2+ is substituted by Fe2+ and Mg2+.  The other three are synthetic fertilizer components synthesized at high temperatures.


Comments:
(struvite group)
Group includes:  newberyite, phosphorrossierite, schertelite, stercorite, and hannayite, having various amounts of H2O, H, Mg, Na, K, and NH4.


Comments:
(churchite group)
Brushite is the thermodynamically favoured calcium phosphate under weakly acidic conditions (pH 4-5), according to Scudiero et al. (1999).


Comments:
(paravauxite group)
Paravauxite group minerals are generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.  In particular, many of these minerals couple Fe and Mn.


Comments:
Whiteite group minerals are generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.   In particular, many of these minerals couple Fe and Mn.


Comments:
(arthurite group)
Arthurite group minerals are generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.   In particular, some of these minerals couple Fe and Mn.


Comments:
(lazulite group)
Lazulite group minerals are generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.  In particular, some of these minerals couple Fe and Mn.


Comments:
Generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.  In particular, these minerals couple Fe and Mn.


Comments:
(solid solution pair)
Generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.  In particular, these minerals couple Fe and Mn.


Comments:
generally secondary/hydrothermal species not normally associated with surface environments but it is worth looking for them in aquatic sediments.  In particular, these minerals couple Fe and Mn.


Comments:
Also called acid volatile sulphur (AVS).
Present in anoxic layers of S-rich aquatic sediments.  
Characteristic black colour, accompanied by an odor of H2S.


Comments:
Commonly associated with basic igneous rocks.


Comments:
Most common and widespread sulfide mineral.
Fe and S sink in marine sediments, anoxic layers.
Precipitates in wet tidal flats and river deltas of costal areas.
Weathers to jarosite or gypsum in soils.


Comments:
Less stable and less common than pyrite.  Associated in clays, secondary mineral


Comments:
Common hydrothermal mineral.  Formed in the water column, associated with decaying phytoplankton, settles to bottom where it can be a productivity proxy.  Some benthic marine organisms make barite crystals.  Easily dissolved upon sulphate reduction. See Kastner (1999) for discussion of its biogeochemistry.  May form a solid solution with celestine.


Comments:
Associated with gypsumBCaSO4.2H2 but less common.


Comments:
Common mineral in sedimentary rocks.  
The most common sulfate.


Comments:
Rare, secondary.  Found as an efflorescence on mine timbers.


Comments:
Secondary coatings on ferrugineous ores.  
A weathering/oxidation product of pyrite in soils.


Comments:
Other minerals such as epsomite, hexahydrite, pentahydrite, starkeyite, kieserite, mirabilite, thenardite, loeweite, bloedite, etc. are highly solvable evaporites that can be found in certain soils and in sedimentary evaporite beds.


Comments:
Tends to be rather pure with respect to Mg and Fe but has a complete solid solution with rhodochrositeBMnCO3.  
Predominant mineral in sedimentary rocks. This mineral is common in lake sediments.
Important fraction of calcite is biogenic (shells and skeletons).
Most important use is in the manufacture of cements.


Comments:
A biogenic form of CaCO3, formed by skeletal organisms.  Dissolves more easily than calcite.
This mineral is common in lake sediments.


Comments:
Rhodochrosite-siderite-magnesite form complete solid solution series.
Alteration product of Mg-rich rocks, in presence of water.
Siderite is part of Precambrian banded iron formations and is an iron ore.
Rhodochrosite is relatively rare.  
Important mineral sink of Mn in anoxic layers of marine sediments.


Comments:
On of the three common polymorphs of serpentine.   
Main substitutions:  Mg = Fe, Ni;  Si = Al.  
The TBO mismatch causes significant curvature of the layer and associated structural consequences.
Common and widely distributed mineral.  
Usual alteration reaction:  
2Mg2SiO4 (forsterite) + 3H2O = Mg3Si2O5(OH)4 + Mg(OH)2 (brucite).
About 95 % of the production of asbestos is from chrysolite.


Comments:
One of the three common polymorphs of serpentine.   
Main substitutions:  Mg = Fe, Ni;  Si = Al.  
The TBO mismatch causes significant curvature of the layer and associated structural consequences.
Common and widely distributed mineral.  
Usual alteration reaction:  
2Mg2SiO4 (forsterite) + 3H2O = Mg3Si2O5(OH)4 + Mg(OH)2 (brucite).
About 95 % of the production of asbestos is from chrysolite.


Comments:
Fe-rich analogue of the serpentine composition.
Fairly common in unmetamorphosed Precambrian iron formations.


Comments:
Has little compositional variation.
TBO type layers, dioctahedral.  (1:1 type layer silicate)
Dickite and nacrite have different stacking polytypes and are less common.  
Common mineral, chief constituent of kaolin clay.
Found in soils, lake beds, etc.  Most common 1:1 layer silicate in soils.  A major source of ocean sediments.  (See Fig. 10-16 of Dixon and Weed, for representative XRD patterns!)
Always formed by weathering or hydrothermal alteration, of many different minerals.  
Broad aqueous stability field between gibbsite, K-mica, K-feldspar, and amorphous silica, including conditions of sea water (see Fig.10-12 of Dixon and Weed). A major deposit to lakes from rivers fed through well leached soils. 
Uses:  manufacture of brick, china, sewer pipe, etc.;  paper filler;  rubber industry;  manufacture of refractories.


Comments:
Polymorph of kaolite but can also be intercalated with water.
(1:1 type layer silicate)
Forms micro-tubes and spheroids.  
Early product of alteration/weathering but less stable than kaolinite


Comments:
Dominant clay mineral in bentonite, altered volcanic ash.
Bentonite expands to several times its original volume when paled in water.
Bentonite is used for stopping leakage in soil, rocks, and dams. 

Smectites are TBOBT type layer silicates that can be dioctahedral or trioctahedral.  They have an outstanding capacity to intercalate water molecules, resulting in significant expansions.  The dioctahedral members are montmorillonite, beidellite, and nontronite.  The trioctahedral species are:  hectorite and saponite.  Major importance in soils, sedimentary rocks, and poorly drained environments.  001 basal spacings vary from 1.0 to 2.0 nm, depending on water content.  A primary reaction of marine diagenesis is the conversion of smectite to mica or chlorite, under the elevated temperatures of burial, with most change occuring at 100oC at a depth of ~1.5 km.  Differential expansivity XRD is the main diagnostic tool, using glycerol or ethylene glycol.  
In lakes, smectites are believed to mainly arise from the soil catchment, rather than being diagenetic.


Comments:
Smectites are TBOBT type layer silicates that can be dioctahedral or trioctahedral.  They have an outstanding capacity to intercalate water molecules, resulting in significant expansions.  The dioctahedral members are montmorillonite, beidellite, and nontronite.  The trioctahedral species are:  hectorite and saponite.  Major importance in soils, sedimentary rocks, and poorly drained environments.  001 basal spacings vary from 1.0 to 2.0 nm, depending on water content.  A primary reaction of marine diagenesis is the conversion of smectite to mica or chlorite, under the elevated temperatures of burial, with most change occuring at 100oC at a depth of ~1.5 km.  Differential expansivity XRD is the main diagnostic tool, using glycerol or ethylene glycol.  
In lakes, smectites are believed to mainly arise from the soil catchment, rather than being diagenetic.


Comments:
Note:  Need to resolve the Mossbauer of nontronite and HFO...

Smectites are TBOBT type layer silicates that can be dioctahedral or trioctahedral.  They have an outstanding capacity to intercalate water molecules, resulting in significant expansions.  The dioctahedral members are montmorillonite, beidellite, and nontronite.  The trioctahedral species are:  hectorite and saponite.  Major importance in soils, sedimentary rocks, and poorly drained environments.  001 basal spacings vary from 1.0 to 2.0 nm, depending on water content.  A primary reaction of marine diagenesis is the conversion of smectite to mica or chlorite, under the elevated temperatures of burial, with most change occuring at 100oC at a depth of ~1.5 km.  Differential expansivity XRD is the main diagnostic tool, using glycerol or ethylene glycol.  
In lakes, smectites are believed to mainly arise from the soil catchment, rather than being diagenetic.


Comments:
Kastner (1999) claims saponite in marine sediments to be a diagenetic transformation product of volcanic glass.
Note:  Look into Mossbauer, in particular ferric content via OH loss…
Smectites are TBOBT type layer silicates that can be dioctahedral or trioctahedral.  They have an outstanding capacity to intercalate water molecules, resulting in significant expansions.  The dioctahedral members are montmorillonite, beidellite, and nontronite.  The trioctahedral species are:  hectorite and saponite.  Major importance in soils, sedimentary rocks, and poorly drained environments.  001 basal spacings vary from 1.0 to 2.0 nm, depending on water content.  A primary reaction of marine diagenesis is the conversion of smectite to mica or chlorite, under the elevated temperatures of burial, with most change occuring at 100oC at a depth of ~1.5 km.  Differential expansivity XRD is the main diagnostic tool, using glycerol or ethylene glycol.  
In lakes, smectites are believed to mainly arise from the soil catchment, rather than being diagenetic.


Comments:
Alkali-deficient mica, near the muscovite composition.
The illites have less Al substitution for Si than micas and contain more water.  
Often occurs with smectites.  
Smectites transform to illites by diagenetic reaction, in a process known as illitization:  
Smectite + Al3+ + K+ = Illite + Si4+  and released Ca and Na may go to form plagioclase feldspars.
Smectite + K-feldspar + ? = I/S + chlorite + quartz.
Smectites have lower layer charge, more hydrated exchangeable inter-layer cations, and a greater expansibility in water.


Comments:
Biotite-like compositions (R2+ = Fe, Mg)
Authigenic mineral found in green pellets in marine sedimentary rocks.


Comments:
Alteration product of biotite.
Talk-like structure with intercalated water.


Comments:
Low-grade metamorphism and unmetamorphosed Precambrean banded iron formations.  
Modulated structure.


Comments:
Older calcareous marine sediments with higher sedimentation rates.


Comments:
Marine sediments with low sedimentation rates and at shalow burial depths.


Comments:
Little variations from ideal formula, with some Na = K, Ca.
Primary mineral in some igneous rocks and produced by hydrothermal action.  
Borderline with feldspathoids.


Comments:
Fibrous zeolite.  Little deviation from ideal formula.


Comments:
Substitutions:  Ca = Na, K;  (Na,K)Si = CaAl.
Channel diameter = 3.9 Е (e.g., argon, 3.84 Е, enters rapidly).
Found lining cavities in basalt.


Comments:
Considerable (Na)Si = (Ca)Al substitution.
Found in cavities of basic igneous rocks.


Comments:
Formula represents a series or group of minerals.
This mineral is common in lake sediments.


Comments:
Formula represents a series or group of minerals.


Comments:
There is much evidence for such a compound, with Fe:P = 2:1, occurring in sediments and in the watercolumn.  See:  Mayer et al. (Water Res. 16, 1982, 1189);  Lienemann et al. (Aquat. Sci. 61, 1999, 133);  Buffle et al. (GCA 53, 1989, 399);  Wheat et al. (GCA 60, 1996, 3593);  Gunnars et al. (GCA 66, 2002, 745);  Rose et al. (Langmuir 13, 1997, 1827).
Indeed, there appears to be a continuum of possible P contents between this proposed end member and P-absent HFO.
In addition, it appears that Ca can be involved significantly (Buffle et al., 1989).


Comments:
In analogy with P-HFO.  Rancourt et al. (AM 86, 2001, 834) have described such compounds in some detail.


Comments:
Rancourt et al. (AM 86, 2001, 834) have described such compounds in some detail.


Comments:
Forms in acid mine lakes.
At low pH and high SO4 concentration,, this mineral forms instead of goethite.


Comments:
possible solid solution with minnesotaite


Comments:
Biscaye (1965) finds talc and/or pyrophyllite in marine sediments, with characteristic XRD reflections at d-spacings 9.5, 9.4, 9.2 Å and the 9.2 Å reflection being accompanied by 4.60 and 3.06 Å reflections.


# Mineral Classes

Name:
Amorphous, nanophase, and poorly defined materials

Description:
The materials in this group have poorly defined crystalline structure and stoichiometry because of the small particle size. However, they are extremely important because of their high reactive and sorption abilities.


Description:
Oxidation and alkaline pH can reduce availability of Mn in soils to the point of deficiency, whereas reduction under leaching acidic conditions can produce toxic levels of Mn.  Also the Mn oxyhydroxides have high sorption capacities for heavy metals.  Mn2+/Mn3+/Mn4+ substitutions are extensive:  There are continuous series of nominal compositions from MnO to MnO2.  Oxides have mostly tunnel and layer structures.


Description:
The list of phosphates is long because of the importance of P as a key nutrient in both soils and sediments.  Mn and Fe play an important role in PO4 mineralogy, thereby coupling the P, Mn, and Fe cycles in pedogenic and aquatic environments. Calcium phosphates are important biogenic minerals present in: enamel, dentine, bone, kidney stones, etc.  
Note:  Phosphorite is not a mineral but rather a common marine nodule or crust type that is P-rich and contains more than 50% carbonate fluorapatite (CFA, also called francolite).  See O’Brien and Veeh (Nature, 288, 1980, 690).


Description:
Muller et al. (1972) review the occurances of calcium-bearing minerals in the sediments of 25 lakes with pH (7.1-10.5).  They have detected aragonite, calcite, dolomite, huntite, magnesite, hydromagnesite, and nesquehonite.  Last (2001) claims that carbonate minerals are the most common endogenic (formed within the water column) minerals in many lakes.


Name:
Silicates - Layer silicates - Chlorite group

Description:
Trioctahedral TBOBT layers of ideal composition [Mg3(AlSi3)O10(OH)2]1B interleaved with Abrucite layers of ideal composition [Mg2Al(OH)6]1+.  

The general formula of chlorite is:

A5B6Z4O10(OH)8

where		A = octahedral sites = Al, Fe2+, Fe3+, Li, Mg, Mn, Ni, ...
Z = tetrahedral sites = Al, Si, Fe3+, ...

Broad solid solutions occur with incomplete trioctahedral filling.
Common rock forming minerals.


Name:
Silicates - Layer silicates - Serpentine group


Name:
Silicates - Layer silicates - Clay minerals

Description:
Includes the kaolinite and smectite groups.  Illite is included, although it is formally part of the mica group.   Alteration products and authigenic layer silicates are included.  Layer silicates relevant to soils and aquatic sediments are emphasized.
  These minerals are active sorbents but also participate in ion exchange reactions and various intercalation/deintercalation reactions.


Description:
Zeolites are among the most important authigenic silicates in deep-sea sediments, in particular clinoptilolite and phillipsite. See, for example, the description of occurrence of clinoptilolite-heulandite by Biscaye (1965).  He also detected phillipsite in one sample. May possibly form directly from alumino-silica gels (oxyhydroxides) in aquatic environments.  
Found in cavities and veins in igneous rocks but also alteration products of volcanic tuff and volcanic glass.  
Also, diagenetic alteration products of silicic tuffs in Cenozoic lacustrine deposits, especially those deposited in highly saline and alkaline waters.  

Hardness and specific gravity (density) evolve along a sequence:
class			hardness		density
quartz			7			2.65
feldspars		6			2.54B2.75
feldspathoids		5B6			2.15B2.5
zeolites		3-1/2B5-1/2		2.0B2.4

~41 natural species.  Large interconnecting spaces or channels.
Classified as:  	(1) fibrous habit, underlying chain structure
(2) platy habit, underlying sheet structure
(3) equant habit, underlying framework structure.

Can dehydrate and rehydrate continously (100B300 oC range), without structural damage, up to ~600 oC.  Used as desicants in industry.  Can readily exchange a great variety of cations.  Used to control water hardness (Na/Ca), remove toxic or radioactive heavy metals, remove ammonia from sewage and agricultural waste.  Major industrial uses in catalytic cracking and as molecular sieves.  Synthetic production (of pure and specific zeolites) is over 12,000 tons per year.


Name:
Silicates - Layer silicates - Talc-like group


