E. coli, the green celebrity!


Escherichia coli or more commonly known as E. coli, according to me, happens to be the celebrity of the green world when it comes to biology in green chemistry. These are the friendly bacteria that live in our guts and help digest our food. Although, some of its strain do cause problems to us. It’s time to give it some positive attention. Scientists genetically engineer E. coli and greenify a chemical reaction.

Here are a few examples of how they did it:

  1. Reduction of GO: Microbial reduction of graphene oxide by Escherichia coli: A green chemistry approach
  2. Cleaner chemistry: Transplanting metabolic pathways into E. coli
  3. Biofuels: Turning bacteria into butanol biofuel factories
  4. Turning waste into fatty acids: Genetically Modified E. coli Bacteria Turn Waste Into Fat For Fuel!
  5. Sugars into biofuels

The Presidential Green Chemistry Challenge Award Recipients included individuals/organizations who used E. coli. Here are some entries:

2012 Codexis, Inc.; Professor Yi Tang, University of California, Los Angeles LovD, an acyltransferase from E. coli engineered by directed evolution, now performs regioselective acylation in the sysnthesis of the drug simvastatin (summary)
2011 BioAmber, Inc. Genetically engineered E. coli strain licensed from the Department of Energy produces succinic acid from wheat-derived glucose on a commercial scale (summary)
2011 Genomatica Genetically engineered E. coli strain produces 1,4-butanediol by fermentation of readily available sugars (summary)
2011 BioAmber,Inc. Glucose is fermented on a commercial scale by a genetically engineered E. coli strain to make succinic acid, traditionally produced from petroleum (summary)
2011 Genomatica Readily available sugars fermented by a genetically engineered E. colistrain produce 1,4-butanediol, a large-volume chemical usually made from petroleum (summary)

The world outside our guts is far harsher for these bacteria, especially in our reaction flasks. So what are scientists doing about it? They are making hospitable environments for these little celebrities. Making safer solvents for them is one way. But is E. coli losing its shine? Time will tell.

Read more:

How yeast replaced E. coli: BioAmber phases out E.coli use

Go Planet!

I grew up watching Captain Planet and the Planeteers, an American animated environmentalist television program. I used to like the idea of doing something for planet earth. But as I grew up, I read and heard about the problems our earth is facing, the politics and most importantly how incomplete my knowledge is. In the process, I only learnt to keep an open mind.

“Believe nothing, no matter where you read it, or who said it, no matter if I have said it, unless it agrees with your own reason and your own common sense.” – Buddha

Last Edited: January 9 2018

Inherently Safer Plants – Part II

Volunteer Image Author Meditations

This blog post introduces some common terminologies related to safety, and then moves on to the intricacies of it.

Hazard: A hazard is anything that may cause harm, such as chemicals, electricity, working from ladders, an open drawer, etc.

Risk: The risk is the chance, high or low, that somebody could be harmed by these and other hazards, together with an indication of how serious the harm could be.

Safety engineering: It is an engineering discipline which assures that engineered systems provide acceptable levels of safety.

Hazard Identification Study: It is the process of identifying hazards in order to plan for, avoid, or mitigate their impacts. Hazard identification is an important step in risk assessment and risk management.

Risk assessment: It is the determination of quantitative or qualitative value of risk related to a concrete situation and a recognized threat (also called hazard). A risk assessment is simply a careful examination of what, in your work, could cause harm to people, so that you can weigh up whether you have taken enough precautions or should do more to prevent harm.

Occupational safety and health (OSH): It is a cross-disciplinary area concerned with protecting the safetyhealth and welfare of people engaged in work or employment. The goals of occupational safety and health programs include to foster a safe and healthy work environment.

Hazard analysis: It is used as the first step in a process used to assess risk. The result of a hazard analysis is the identification of different type of hazards.

Now that you know some of the terms that are frequently encountered while approaching this topic, we can move on to the intricacies of it. Before anything, analysis is must, an assessment of a risk. How is it done?

  • Step 1: Identify the hazards
  • Step 2: Decide who might be harmed and how
  • Step 3: Evaluate the risks and decide on precautions
  • Step 4: Record your findings and implement them
  • Step 5: Review your assessment and update if necessary

Follow the link to learn about the five steps to risk assessment.

HAZOP Studies (Hazard and Operability Studies):

HAZOP study is the assessment on adequacy of safety measures taken by industries vis-avis the hazards present and is primarily carried for chemical industries.

Any plant operation sometimes involve deviation from design parameters during the operation. HAZOP study is a structured methodology to identify all possible deviations of the process parameters namely temperature, pressure, composition, direction of flow etc, and all the consequences associated with each deviations. The deviation is also correlated to the safety interlocks, instrumentation and administrative procedure related to the operation.

The output of HAZOP is a list of possible deviations, their causes, consequences, safety measures and additional safety measures required to avoid consequences.


The Occupational Safety and Health Administration (OSHA) has written voluminous occupational safety and health standards and regulations that affect employers and employees in the United States. It is the employer’s legal responsibility to educate employees on all workplace safety standards and the hazards that their employees may face while on the job.

Because different countries take different approaches to ensuring occupational safety and health, areas of occupational safety and health’s needs and focus also vary between countries and regions. Read more here.

Everyone has the Right to Know, the chemicals they are working with, the environment they will be exposed to.

This topic stretches miles. One can go on reading about safety and the laws surrounding it. Last but not the least, we should not forget that we are humans, imperfect, we make mistakes. So, considering this, one also has to study something known as Behavior-based safety. Read more here.

OSH, India: http://www.oshindia.com/

Before looking at the strategies of making plants safer, lets us first see how it is traditionally done.

LOPA (Layers of protection analysis):

The various measures for prevention and mitigation of major accidents may be thought of as lines of defence’ (LODs) or ‘layers of protection’ (LOPs). These lines or layers serve to either prevent an initiating event (such as loss of cooling or overcharging of a material to a reactor, for example) from developing into an incident (typically a release of a dangerous substance), or to mitigate the consequences of an incident once it occurs. This is illustrated in figure below.

Read more about LOPA, here.

Coming to the strategies, they will be presented in order of reliability:

  • Inherent: Eliminating the hazard by using materials and process conditions which are non-hazardous. It is the most reliable way. How about creating an atmospheric pressure reaction using non-volatile solvents. This way there is no potential for over pressure. Instead of using a corrosive substance like AlCl3 as a regent in huge quantities, we can use catalytic quantities of say, scandium triflate. A scientist, Shu Kobayashi, has researched a lot on Lewis acid catalysts like metal triflates, which are non-corrosive in nature, unlike the usual lewis acid catalysts.
  • Passive: Minimizing the hazard by process equipment features which reduce either the probability or consequence of the hazard without active functioning. Designing a vessel for 4 atm when the operating condition is 1 atm or having equipment before or after the vessel to reduce the excess pressure. A reaction capable of generating 150 psig pressure in case of a runaway, in a vessel designed for 250, this way the reactor can contain the accident unless it is damaged.
  • Active: Using controls, safety interlocks and emergency shutdown systems to detect and correct process deviations (engineering controls). A reaction capable of generating 150 psig in case of a runaway in a 15 psig reactor with a 5 psig interlock that stops feeds and a rupture disk to reduce pressure, directing contents to effluent treatment. What could happen?
  • Procedural: Using operating procedures, administrative checks, emergency response, and other management approaches to prevent incidents, or to minimize the consequences (administrative controls). Consider the same 150 psig reaction, same reactor, without the interlock. The operator is instructed to monitor the pressure and shuts down feed. Mind you, there can be a human error to make it worse, hence it is the least preferred method.

Another way of looking at inherently safer process strategies is this:

  • Minimize: Use of smaller quantities of hazardous substances. (Intensification/Continuous processes)
  • Substitute: Replace a material with a less hazardous substance.
  • Moderate: Use less hazardous conditions, a less hazardous form of a material, or facilities which minimize the impact of a release of hazardous material or energy. (Attenuation or limitation)
  • Simplify: Design facilities which eliminate unnecessary complexity  and make operating errors less likely, and which are forgiving of errors which are made. (Error tolerance)

Do you remember? It is the same strategy we looked up to design safer chemicals.

Further reading:

Last Edited: January 8 2018

Inherently Safer Plants – Part I

Volunteer Image Author DarkSouls1

“What you don’t have, can’t leak!”

These are the words of Mr Trevor Kletz, ICI and LU.

If you develop, operate and control a chemical process such that bad consequences are reduced, owing to different chemistry, chemicals, conditions or simplicity, wouldn’t the safety of the plant be improved? Is this better than layers of protection? Prevention is better than cure.

The inherent safety structure consists of three parts:

  1. Hazard Identification
  2. Hazard Evaluation
  3. Inherent Safety Evolution

A hazard is a physical or chemical characteristic that has the potential for causing harm to people, the environment or property. They are characteristic of the materials, chemistry and process variables.

Let’s see some of the hazards, relating them to their intensity of destruction.

  • Acute toxicity: Chlorine is toxic by inhalation.
  • Chronic toxicity: Sulfuric acid is extremely corrosive to skin. Nuclear material can cause chronic toxicity too.
  • Flammability: Ethylene is flammable.
  • Instability: High pressure confined steam contains a lot of energy.
  • Extreme conditions: Styrene can polymerize releasing heat.

Air pollution, water pollution, ground water pollution, waste disposal are other  examples of consequences.

Representative list of types of hazards:

  1. Fires: Flash fires, Pool fires, Jet fires. For example, ammonia, multi-bond hydrocarbons
  2. Explosions: Vapor cloud explosion (VCE), Confined deflagration, Detonation, Pressure vessel rupture. For example, multi-bond hydrocarbons, epoxides, hydrides and hydrogen, metal acetylides, nitrogen compounds, oxygenated compounds of halogens, oxygenated manganese compounds, peroxides.
  3. Toxicity: Environmentally (chronic, acute, individually toxic, broadly toxic), pesticides, fungicides, herbicides, insecticides, fumigants. For example, ammonia, chlorinated hydrocarbons, cyano compounds, polychlorinated biphenyls, poly-cyclic aromatic hydrocarbons.
  4. Product: Customer injury, waste disposal

Are there other hazards associated with dangerously reactive chemicals?

Many dangerously reactive materials can also undergo dangerous reactions from direct contact with other and incompatible materials. Incompatibility hazards can be complicated. The chance of a dangerous reaction depends not just on the different combinations of chemicals involved, but it also depends on the amounts of each, the surrounding conditions such as temperature, and whether the substances are enclosed in a sealed container or not.

The SDS and the container labels should explain all of the hazards of the dangerously reactive liquids and solids that you work with.

Reactive combinations of chemicals:

  • Acids + chlorates = spontaneous ignition
  • Acids + cyanides = Toxic/flammable gas
  • Acids + fluorides = Toxic gas
  • Acids + epoxides = Heat/Polymerization
  • Alkali + nitro compounds = Easy to ignite
  • Alkali + nitroso compounds = Easy to ignite
  • Ammonium salts of alkali metals + chlorates = Explosive salts
  • Ammonium salts of alkali metals + nitrates = Explosive salts
  • Ammonium salts of alkali metals + alcohols = Flammable gas
  • Ammonium salts of alkali metals + glycols = Flammable gas
  • Ammonium salts of alkali metals + amides = Flammable gas
  • Ammonium salts of alkali metals + amines = Flammable gas
  • Ammonium salts of alkali metals + azo compounds = Flammable gas
  • Ammonium salts of alkali metals + diazo compounds = Flammable gas
  • Inorganic sulfide metals + water = Toxic/Flammable gas
  • Inorganic sulfide metals + explosives = Heat/Explosives
  • Inorganic sulfide metals + Polymerizable compounds = Polymerization

Read more:


Dangerously Reactive Liquids and Solids – Hazards

Last Edited: January 8 2018

Accepting reality

Volunteer image author Tigerlily713

Are green chemistry principles feasible? Can they be scaled to plants? Can the industries helps the environment and at the same time profit from it?

First, let’s look at the ideal process parameters. An ideal process should be green, because it not only is safe to the environment but at the same time saves a lot of money. Following are the ideal process parameters, not in an order of preference:

  1. Room temperature
  2. Atmospheric pressure
  3. No solvent use
  4. No flammability
  5. Not a viscous fluid (Why? Because if it is viscous we have to spend energy in agitating it or mixing it)
  6. Benign like water

Are there any such ideal processes? No. So how are the real processes? This is what happens in the industry:

  1. Machines are needed (Motion free process is not conceivable)
  2. Driven by electricity or some other form of energy
  3. Skilled or semi-skilled or unskilled workers (Automation may not be a complete solution)
  4. Ill-informed operators work on real processes because they are not allowed to know the intricacies of the process. For example, no worker in the Coca-Cola company knows the recipe of its cold-drink.
  5. Fierce competition for survival and growth exists
  6. “Risk is better than starvation” attitude
  7. NIMBY (Not-in-my-back-yard) attitude of manufacturers
  8. Hazard exists (Risk is part and parcel of all activities)

Now, what can we do?

  • Can all chemicals be replaced by safer chemicals?
  • Can we live without gases to avoid leaks which cannot be contained?
  • Can we avoid volatile liquids altogether?
  • Can we stop designing and operating plants irrespective of the inherent characteristic of the chemicals?

Can you live like a caveman, a nice hut, a little vegetable garden, livestock in the backyard? Will everyone do it? No. So what now? We now should accept things and adapt to them. Adapt in a way that will keep this planet sustainable, for us and other species.

What green chemistry will do for us is to deal with the existing problems and helps us create a sustainable environment, at the same time cleaning up the mess that our creations have caused. We don’t know if we are late but it is worth the try. Act in a way that also takes care of the economy because if economies fail, the nation fails, it will lead to chaos, we don’t want that.

Reading more: Principles of Green Engineering

Last edited: December 19th 2017

Toxicity generating mechanisms

Volunteer image author Miniformat65

This post assumes you are well-versed with electrophiles and nucleophiles along with basics of Biology. If not, here are some links for you that can help.

Toxicity generating mechanisms involving electrophiles:

Electrophilic substitution or those metabolized to electrophilic species are capable of reacting covalently with nucleophilic substituents of cellular macromolecules such as DNA, RNA, enzymes, proteins and others.

Nucleophilic toxic substituents

  • Thiol groups of cysteinyl residue in protein
  • S atoms of methionyl residue in protein
  • Primary amino groups of argimine and lysine residues
  • Secondary groups (histidine) in protein
  • Amino groups of purine bases in DNA or RNA
  • O atoms of purines and pyrimidines
  • P=O of RNA and DNA

Refer to this table: Nucleophilic toxic substituents. Keep the table opened in one of your tabs and read further.

These are the groups highly likely to cause such effects but the effects can be reduced or eliminated by replacing the functional group or by changing its position in the molecule. Hence, the presence of any of these substituents does not automatically mean that the substance is or will be toxic.

Example 1:

Ethyl Acrylate (Carcinogenic)


Acrylates contain alpha, beta unsaturated C=O system and undergo Michael addition. This is the reason for carcinogenic properties of acrylates. Methacrylates are better than acrylates. Incorporation of a CH3 group on to the alpha C to give ethacrylates decreases the electrophilicity (i.e. reactivity) of the beta C. Hence, methacrylates do not undergo 1,4-michael addition easily. Methacrylates have some commercial efficacy.

Example 2:

Isocyanates are used in adhesives and intermediates. The endogeneous nucleophiles in isocyanates are responsible for their toxicity. During coating, the ketoxime moiety is removed thermally thereby regenerating the isocyanate.

Example 3:

Vinyl sulfolane are:

  • highly electrophilic
  • used in textile fibre industry
  • reacts covalently with hydroxy groups of cellulose fibres
  • is made safe by converting into a sulfate ester which is not electrophilic during storage and handling. It can be regenerated again by neutralizing.

Example 4:

Structural requirements for high teratogenic potency of carboxylic acids? *

IMG-1463 (1).jpg

What aspects of this molecule can lead to teratogenic potency?

  • a free carbonyl group
  • only one hydrogen atom at C(2)
  • an alkyl substituent larger than methyl at C(2)
  • no double bonds between C(2) and C(3) or C(3) and C(4)

*Teratogenic potency is based on in vivo data.

In general we can say:

  • Ortho or meta substituents are better.
  • Reduce alkyl chain carbons.
  • Methyl is better than ethyl.

Last edited: December 19th 2017