stochastic synthesis of natural organic matter
DESCRIPTION
Stochastic Synthesis of Natural Organic Matter. Steve Cabaniss, UNM Greg Madey, Patricia Maurice, Yingping Huang, ND Laura Leff, Ola Olapade KSU Bob Wetzel, UNC Jerry Leenheer, Bob Wershaw USGS. Fall 2002. What is NOM? Sources:. Plant and animal decay products - PowerPoint PPT PresentationTRANSCRIPT
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Stochastic Synthesis of Natural Organic MatterSteve Cabaniss, UNMGreg Madey, Patricia Maurice, Yingping Huang, NDLaura Leff, Ola Olapade KSUBob Wetzel, UNCJerry Leenheer, Bob Wershaw USGS
Fall 2002
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What is NOM? Sources: • Plant and animal decay products
– Terrestrial- woody and herbaceous plants– Aquatic- algae and macrophytes
• Structures– cellulose, lignins, tannins, cutin– proteins, lipids, sugars
OOHOHOHOOHOHOOHOHOOOOHHOOHOHOHOOHOetc.
OOOHOHOHHOOHQuercetin
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What is NOM? Composition
45-55 Wt% Carbon
35-45 Wt% Oxygen
3-5 Wt% Hydrogen
1-4 Wt% Nitrogen
Traces P, S
MW 200-20,000 amu
Equiv. Wt. 200-400 amu
10-35% aromatic C
OOHOHOOHOOHOOHOOHOOHOOHOOOOHOOHOOOOHLeenheer, et al., 1998possible fulvic acid
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What is NOM?
A mixture of degradation and repolymerization productsfrom aquatic and terrestrial organismswhich is heterogeneous with respectto structure and reactivity.
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NOM + O2 H2O2
+ OH·
+ O2-
NOM Interactions with sunlight
Photosensitizer
Light attenuation
Fe(III)-NOM Fe(II) + NOM + CO2
+ etc.
Direct photoredox
Abs
Wavelength
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NOM Interactions with mineral surfaces
Hemi-micelleformation
Fe(II)
Fe(III)
Reductive dissolution
Adsorption Acid or complexingdissolution
Al
e-
Adsorbed NOM coatings impart negative charge and create a hydrophobic microenvironment
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NOM Interactions with microbes
Ingestion:Energy andNutrients
e- e-
Electron shuttle
Cu2+
Cu
Metal ion complexationand de-toxification
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NOM Interactions with pollutants+
Binding to dissolved NOM increases pollutant mobility
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NOM in water treatment
+ HOClCHCl3 + CHCl2Br + CCl3COOHand other chlorinated by-products
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Why study NOM?
Natural ecosystem functions Nutrition, buffering, light attenuation
Effects on pollutants Radionuclides, metals, organics
Water treatment DBP’s, membrane fouling, Fe solubility
Carbon cycling & climate change
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NOM Questions:
• How is NOM produced & transformed in the environment?
• What is its structure and reactivity?
• Can we quantify NOM effects on ecosystems & pollutants?
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Environmental Synthesis of Natural Organic Matter
NOMHumic substances& small organics
NOMHumic substances& small organics
CO2CO2
Cellulose
Lignins
Proteins
Cutins
Lipids
Tannins
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
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Simulating NOM Synthesis Deterministic Reaction Kinetics
For a pseudo-first order reaction
R = dC/dt =k’ CR = rate (change in molarity per unit time)
C = concentration (moles per liter)
k’ = pseudo-first order rate constant
(units of time-1)
Based on macroscopic concentrations
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Deterministic Reaction Kinetics:Solve a system of ODE’s
• Begin with initial Ci for each of N compounds, kj for each of M reactions
• Apply Runge-Kutta or predictor-corrector methods to calculate Ci for each time step (use Stiff solvers as needed)
• Repeat for desired length of simulation, obtaining results as Ci versus time
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Problem w/ ODE approach:Size and Computation Time
• Assuming N > 200 (different molecules)
• Assume M = 20 x N (20 reactions per molecule)
• Total set of >4000 very stiff ODE’s is impractical (transport eqns not included)
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Problem w/ODE Approach:Knowledge Base
• Structures of participating molecules unknown
• Pertinent reactions unknown
• Rate constants kj unknown
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Simulating NOM Synthesis Probabilistic Reaction Kinetics
For a pseudo-first order reaction
P = k’ ΔtP = probability that a molecule will react
with a short time interval Δt
k’ = pseudo-first order rate constant
units of time-1
Based on individual molecules
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Stochastic algorithm: Initialization
• Create initial pseudo-molecules (objects)– Composition (protein, lignin, cellulose, tannin)– Location (top of soil column, stream input)– Input function (batch mode, continuous
addition, pulsed addition)
• Create environment– specify pH, light, enzyme activity, bacterial
density, humidity, To, flow regime
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Stochastic Algorithm: Reaction Progress
• Chemical reaction: For each time-slice, each pseudo-molecule– determine which reaction (if any) occurs– modify structure, reaction probabilities
• Transport: For each time-slice, each pseudo-molecule– Determine mobility– Modify location, reaction probabilities
• Repeat, warehousing ‘snapshots’ of pseudo-molecules and aggregate statistics
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Stochastic Algorithm:Advantages
• Computation time increases as # molecules, not # possible molecules
• Flexible integration with transport
• Product structures, properties not pre-determined
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Stochastic synthesis: Data model
Pseudo-Molecule
Elemental Functional Structural
Composition
CalculatedChemical Properties
and Reactivity
LocationOriginState
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Average Lignin Molecule:Oligomer of 40 coniferyl alcohol subunits
Numbers of atoms Numbers of functional groups400 Carbon 40 Total ring structures322 Hydrogen 40 Phenyl rings81 Oxygen 1 Alcohol
1 Phenol118 Ether linkages
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Model reactions transform structure
Ester Hydrolysis
Ester Condensation
Amide Hydrolysis
Dehydration
Microbial uptake
RCOORH+ or OH-ROOH+HOR+OHH
OHHROHRHH+RR+
RCONHRROOH+H2NR+OHHEnzyme
RCOORH+ROOH+HOR+OHH
+ NOMNOM
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Reaction Probabilities:P calculated from
Molecular structure
Environment (pH, light intensity, etc.)
Proximity of near molecules
State (adsorbed, micellar, etc.)
Length of time step, Δt
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Example: Ester Hydrolysis
P = (# Esters) A e-Ea/RT (1 + b[H+] + c[OH-])
Where A = Arrhenius constant
Ea = activation energy
R = gas constant
T = temperature, Kelvins
b = acid catalyzed pathway
c = base catalyzed pathway
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Property prediction
EnvironmentalLight absorbanceMolecular weightAcid content & pKa BioavailabilityKow
Metal binding K
AnalyticalElemental %Titration curvesIR SpectraNMR spectra
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Property Calculation Methods
• Trivial- MW, elemental composition, Equivalent weight
• Simple QSAR- pKa, Kow
• Interesting– Bioavailability– Light absorption– Metal binding
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Presentation and Analysis
• Spatial mapping of molecules
• Results stored in Oracle database
• Remote query via WWW interface
• Standard graphs of reaction frequency, molecular properties versus time
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Trial: Can we convert lignin oligomer (MW ~6000) in “NOM” ?
Atmospheric O2 No light
Neutral pH No surfaces
Moderate enzyme activity No transport
27 months reaction time
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Num
ber
of M
olec
ules
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% Carbon
% Oxygen
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Mw
Mn
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% Carbon
% Oxygen
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Mw
Mn
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Lignin -> NOM conversion
• Elemental composition similar to whole water NOM
• Average MW within range for aquatic NOM, soil NOM respectively
• Aromaticity lower than normal
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Stochastic synthesisPreliminary tests
•Chromatography-like NOM movement in soils and sub-surface
•Log-normal distribution of NOM molecular weights
•Rapid consumption of proteins
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Current development
• Expanding reaction set
• Determination of reaction probabilities
• Best method of spatial mapping – Discrete grid vs Continuous space
• Remote query capability
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Next Steps-
• Property prediction algorithms
• Data mining capabilities
• Comparison with lab and field results
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Stochastic Synthesis of NOM
NOMHumic substances& small organics
NOMHumic substances& small organics
CO2CO2
Cellulose
Lignins
Proteins
Cutins
Lipids
Tannins
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
Goal: A widely available, testable, mechanistic model of NOM evolution in the environment.
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Financial Support
NSF Division of Environmental Biology and Information Technology Research Program
Collaborating Scientists
Steve Cabaniss (UNM) Greg Madey (ND)
Jerry Leenheer (USGS) Bob Wetzel (UNC)
Bob Wershaw (USGS) Patricia Maurice (ND)
Laura Leff (KSU)