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Biodegradation Not Predicted

This includes

Chemicals whose Biodegradation Should Not be Predicted

There are a number of chemical classes that should not be investigated using the current version of the Pathway Prediction System (PPS). Important classes of chemicals whose biodegradation should not be predicted are listed below. This is not an exhaustive list.

This list is based on a similar list developed for the PBT System by the Environmental Science Center under contract to the Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency.

Return to Top Readily Degraded and Selected Other Compounds

PPS predictions will terminate when they reach certain small, readily degraded compounds. If one of these is entered, its biodegradation will not be predicted, and, if possible, the user will be given a link to a KEGG pathway that includes this compound. These compounds also include dead-end compounds that are not degraded and accumulate in the environment. A list of termination compounds in the current system is available.

The PPS will not display many small molecules with few or no carbon atoms, and certain common enzyme cofactors and derivates, produced in a prediction. This limits the list of predicted compounds to the more important ones. A list of filtered molecules in the current system is available. If one of these is entered, its biodegradation will not be predicted.

Return to Top Inorganic Chemicals

The rules used for the PPS were designed and developed for organic chemicals. Results for inorganic chemicals will be unreliable and their biodegradation should not be predicted using the PPS. This class of chemicals includes all chemicals that do not contain carbon. It includes neutral species such as titanium dioxide (TiO2) and inorganic salts, such as sodium chloride (NaCl) or potassium permanganate (KMnO4). This class of chemicals also includes organo-metallic chemicals (chemicals that contain carbon bonded to a metal species). An overview of microbial interactions with inorganic elements is available in the Biochemical Periodic Tables.

If a chemical contains any of the elements in the following table, its biodegradation should not be predicted:
He
Li Be B Ne
Mg Al Si Ar
Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr

Return to Top High Molecular Weight Compounds

Polymers and chemicals with a molecular weight greater than 1,000 should not have their biodegradation predicted as the PPS was not developed for these types of compounds. However, many polymers may be made up of dimers, trimers, and oligomers that have a molecular weight of less than 1,000. These smaller molecules may contain the same components as the larger polymers, and, therefore, could be run through the PPS. The results should be interpreted with due caution, however, as the biodegradation characteristics of chemicals with a molecular weight of >1,000 are likely to be significantly different from that of much smaller compounds, even if they have similar structures. This is due at least in part to the greatly reduced bioavailability of high molecular weight compounds.

Return to Top Chemicals with Unknown or Variable Composition

The PPS was developed for discrete organic chemicals. That is, organic chemicals that can be represented by a single, precisely known chemical structure. If the compound has a variable composition, (such as oligomers, natural fats, or a product mixture that changes composition depending on environmental conditions), a representative structure may be entered. However, in that case, it is possible that PPS results do not reflect the true nature of the biodegradation products.

Return to Top Mixtures

Mixtures cannot be run through the PPS because it uses a single, discrete chemical structure as its input. If the chemical whose biodegradation you want to predict is a mixture of discrete organic substances, then each substance can be run through the PPS separately. Results should be interpreted with caution, as the biodegradation pathways predicted for substances separately will possibly be very different if they were degraded together.

Return to Top Highly Fluorinated Compounds

Many highly fluorinated chemicals (those that have more fluorines than non-fluorine atoms bonded to carbon), including fully fluorinated organics (those that have all hydrogens on carbon replaced with fluorine), possess biodegradation properties that are vastly different than their non-substituted analogs. The rules used by the PPS do not accurately predict the unique characteristics of these materials. All per- and highly- fluorinated chemicals should not have their biodegradation predicted.





A fully fluorinated compound where all the hydrogens bonded to carbon have been replaced with a fluorine




A hydrochlorofluorocarbon (HCFC), an example of a highly fluorinated compound

Reactions the EAWAG-PPS does not predict

Some known environmental reactions are not predicted, primary because they are not biodegradation reactions. Also, some reactions are too difficult to predict. Important classes of these reactions are listed below. This is not an exhaustive list.
  • Detoxification reactions. These include, but are not limited to, conjugation with xylose, glucuronate and sulfate.

  • Dimerizations. These include, but are not limited to, disulfides formed from sulfide (-SH) groups, or azo compounds formed from primary amide (-NH2) groups.

  • Methylation of hydroxyl groups.

  • Acetylation of primary amines.

  • Formation of intramolecular rings.

  • Hydroxylation of aliphatic carbon atoms at positions where pure cultures of organisms that metabolize similar compounds do not hydroxylate, though environmental non-specific monooxygenases may.