Stochastic Synthesis of Natural Organic Matter

Steve Cabaniss, UNMGreg Madey, Patricia Maurice, Yingping Huang, Xiaorong Xiang, UNDLaura Leff, Ola Olapade KSUBob Wetzel, UNCJerry Leenheer, Bob Wershaw USGS

ASLO 2004 - Savannah, GAJune 2004

NOM Questions:

• How is NOM produced & transformed in the environment?

• What is its structure and reactivity?

• Can we quantify NOM effects on ecosystems & pollutants?

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

Simulating NOM Synthesis Probabilistic Reaction Kinetics

For first or pseudo-first order reaction

P = k’ ΔtP = probability that a molecule will react

with a short time interval Δt

k’ = first or pseudo-first order rate constant

units of time-1

Based on individual molecules

Stochastic Algorithm:Advantages

• Computation time increases as # molecules, not # possible molecules

• Flexible integration with transport

• Product structures, properties not pre-determined

Stochastic synthesis: Data model

Pseudo-Molecule

Elemental Functional Structural

Composition

CalculatedChemical Properties

and Reactivity

LocationOriginState

Stochastic synthesis: Environmental Parameters

Physical:Temperature

Light IntensityDuration

Chemical:Water

pH[O2]

Biological:Bacterial DensityOxidase ActivityProtease Activity

Decarboxylase Activity

Model reactions transform structure

Ester Hydrolysis

Ester Condensation

Amide Hydrolysis

Dehydration

Microbial uptake

R C

O

O R

H+ or OH-

R

O

OH

+ HO R+ O

HH

O

HH

R

OH

R

H H+

R R

+

R C

O

NH

R

R

O

OH

+ H2N R+ O

HH

Enzyme

R C

O

O R

H+

R

O

OH

+ HO R + O

HH

+ NOMNOM

Set Environmental Parameters

Specify Starting Molecules

Set time = 0 and calculate initial reaction probabilities (all molecules)

For each molecule, test: Does a reaction occur? Yes

No

Transform molecule

Calculate new propertiesand reaction probabilities

When all molecules tested: Calculate and store aggregate properties (at specific times)

Increment time step.Simulation complete?

No

Yes

DONE

Stochastic Synthesis:Algorithm

Hydrolysis and consumption of a protein

pH 7.0, 0.1 mM O2, 24.8 oC, dark

Standard enzyme activities and

bacterial density

1000 molecules,

1000 hour simulation

HN

NH

HN

NH

HN

NH2

O

O

O

O

O

O

CH3

H3C

CH3

H2C OH

HO

O

etc.

0

1000

2000

3000

4000

5000

6000

7000

8000

0 200 400 600 800 1000 1200

Time (hours)

# M

ole

cu

les

# molecules

Mn

Simulation of protein hydrolysis and consumptionTriplicate runs, random seed = 1, 2, 3

0

500000

1000000

1500000

2000000

2500000

3000000

0 200 400 600 800 1000 1200

Time (hours)

Ma

ss

C C

on

su

me

d

Simulation of protein hydrolysis and consumptionTriplicate runs, random seed = 1, 2, 3

0

500

1000

1500

2000

2500

3000

0 200 400 600 800 1000 1200

Time (hours)

Rea

ctio

n C

ou

nt

Hydrolysis

Consumption

Simulation of protein hydrolysis and consumptionTriplicate runs, random seed 1, 2, 3

Can we convert terpenes, tanninsand flavonoids in soil into NOM ?

2000 molecules each

Atmospheric O2 (0.3 mM) Acidic pH (5.0)

High oxidase activity (0.1) ~5.5 months

Bacterial density 0.01 dark

H3C

CH3 CH3

CH3

O OH

HO O

O

OH

OH

OH

HO

HO

OH

O

O

OH

OH

OHO

abietic acid

meta-digallic acid

fustin

0

200

400

600

800

1000

1200

1400

1600

0 1000 2000 3000 4000 5000

Time (hours)

MW

Mw

Mn

Evolution of NOM from small natural products in oxic soilFinal Mn = 612 amu, Mw = 1374 amu

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0 1000 2000 3000 4000 5000

Time (hours)

Ele

me

nta

l Co

mp

os

itio

n

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

0.2

C

O

H

Evolution of NOM from small natural products in oxic soilFinal composition 54% C, 41% O, 5% H

050100150200250300350400450500

0 1000 2000 3000 4000 5000

Time (hours)

Eq

uiv

alen

t W

eig

ht

0

0.1

0.2

0.3

0.4

0.5

0.6

Aro

ma

tic

ity

Eq. Wt.

Aro.

Evolution of NOM from small natural products in oxic soilFinal Eq. Wt. = 247 amu, 11% aromatic C

0

100

200

300

400

500

600

0 1000 2000 3000 4000 5000 6000

Time (hours)

Re

ac

tio

n C

ou

nt

0

5

10

15

20

25

30

Oxidations

Consumption

Condensations

Evolution of NOM from small natural products in oxic soil

Oxic soil incubation

of small natural products

increases Mw by 4X, acidity 2X, O content 30%

decreases aromaticity 57% 11%

oxidations enable consumption, condensation

Final composition similar to fulvic acid:

54% C, 41% O, 5% H

Mn = 612 amu, Mw = 1374 amu

Eq. Wt. = 247 amu, 11% ‘aromaticity’

How is this conversion to NOM affected by lowering the O2 and oxidase levels?

2000 molecules each

Reduced O2 (0.1 mM) Acidic pH (4.0)

Low oxidase activity (0.03) ~5.5 months

Bacterial density 0.01 dark

H3C

CH3 CH3

CH3

O OH

HO O

O

OH

OH

OH

HO

HO

OH

O

O

OH

OH

OHO

abietic acid

meta-digallic acid

fustin

0

200

400

600

800

1000

1200

1400

0 1000 2000 3000 4000 5000

Time (hours)

MW

Mw

Mn

Evolution of NOM from small natural products in low-O2 soilFinal Mn = 528 amu, Mw = 1246 amu

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0 1000 2000 3000 4000 5000

Time (hours)

Ele

men

tal

Co

mp

osi

tio

n

0.05

0.055

0.06

0.065

0.07

0.075

0.08C

O

H

Evolution of NOM from small natural products in low O2 soilFinal composition 67% C, 26% O, 7% H

0

200

400

600

800

1000

1200

0 1000 2000 3000 4000 5000

Time (hours)

Eq

uiv

ale

nt

We

igh

t

0

0.1

0.2

0.3

0.4

0.5

0.6

% A

rom

ati

c

Eq. Wt.

% Aromatic

Evolution of NOM from small natural products in low O2 soilFinal Eq. Wt. = 1075 amu, 37% aromatic C

0

10

20

30

40

50

60

70

80

90

100

0 1000 2000 3000 4000 5000

Time (hours)

Re

ac

tio

n C

ou

nt Consumption

Oxidation

Condensation

Evolution of NOM from small natural products in low O2 soilConsumption ~30% lower, oxidation 7X lower,

condensation 30X lower than in oxic soil.

Low O2 soil incubationof small natural products

increases Mw by 4X, H content 25% decreases aromaticity 57% 37%

Final composition more reduced, higher UV , less charged (soluble) than fulvic acid:67% C, 26% O, 7% HMn = 612 amu, Mw = 1374 amuEq. Wt. = 1075 amu, 37% ‘aromaticity’

Trial: Can we convert lignin and protein molecules into NOM ?

Atmospheric O2 (0.3 mM) Moderate light (2x10-8 E cm-2 hr-

1)

Neutral pH (7.0) 24.8 oC

Lower enzyme activity (0.01) Moderate bacterial density (0.02)

4 months reaction time 400 molecules lignin and protein

O

HO

O

H3C

O

H3C

O

O

CH3

O

etc.

lignin fragment

0

1000

2000

3000

4000

5000

6000

7000

0 1000 2000 3000 4000

Time (hours)

MW

Mw

Mn

Evolution of NOM from lignin and protein in surface waterFinal Mn = 902 amu, Mw = 1337 amu(Mass distribution is log normal.)

Evolution of NOM from lignin and protein in surface waterFinal composition 45% C, 48% O, 5.2% H, 1.8% N

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0 1000 2000 3000 4000

Time (hours)

MW

0

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0.08

ON

C

0

500

1000

1500

2000

2500

0 1000 2000 3000 4000

Time (hours)

MW

0

0.1

0.2

0.3

0.4

0.5

0.6

Eq. Wt.

Aromaticity

Evolution of NOM from lignin and protein in surface waterFinal composition Eq. Wt. = 772 amu, 15% aromatic C

0

50

100

150

200

250

0 1000 2000 3000 4000 5000

Time (hours)

Re

ac

tio

n C

ou

nts

0

200

400

600

800

1000

1200

C=C OxidationsC-OH Oxidation

Aldehyde Oxidation

Evolution of NOM from lignin and protein in surface water

Surface water degradation of biopolymers

Decreases Mn by 6X, aromatic C by 3X

Increases acidity 3X, O content 100%

Final composition similar to ‘hydrophilic’ NOM:

45% C, 48% O, 5% H, 1.8% N

Mn = 902 amu, Mw = 1337 amu

Eq. Wt. = 772 amu, 15% ‘aromaticity’

Stochastic synthesis

•Produces heterogeneous mixtures of ‘legal’ molecular structures

•Bulk composition (elemental %, acidity, aromaticity, MW) similar to NOM

•Both condensation and lysis pathways of NOM evolution are viable

Next Steps-

• Property prediction algorithms– pKa, Kow, KCu-L

– UV, IR, nmr spectra

• Spatial and temporal controls– Diurnal and seasonal changes– ‘continuous reactor’– Spatial modeling of soils, streams

• Data mining capabilities

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.

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)