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How to Write a Research Paper

Writing a research paper is a bit more difficult that a standard high school essay. You need to site sources, use academic data and show scientific examples. Before beginning, you’ll need guidelines for how to write a research paper.

Start the Research Process

Before you begin writing the research paper, you must do your research. It is important that you understand the subject matter, formulate the ideas of your paper, create your thesis statement and learn how to speak about your given topic in an authoritative manner. You’ll be looking through online databases, encyclopedias, almanacs, periodicals, books, newspapers, government publications, reports, guides and scholarly resources. Take notes as you discover new information about your given topic. Also keep track of the references you use so you can build your bibliography later and cite your resources.

Develop Your Thesis Statement

When organizing your research paper, the thesis statement is where you explain to your readers what they can expect, present your claims, answer any questions that you were asked or explain your interpretation of the subject matter you’re researching. Therefore, the thesis statement must be strong and easy to understand. Your thesis statement must also be precise. It should answer the question you were assigned, and there should be an opportunity for your position to be opposed or disputed. The body of your manuscript should support your thesis, and it should be more than a generic fact.

Create an Outline

Many professors require outlines during the research paper writing process. You’ll find that they want outlines set up with a title page, abstract, introduction, research paper body and reference section. The title page is typically made up of the student’s name, the name of the college, the name of the class and the date of the paper. The abstract is a summary of the paper. An introduction typically consists of one or two pages and comments on the subject matter of the research paper. In the body of the research paper, you’ll be breaking it down into materials and methods, results and discussions. Your references are in your bibliography. Use a research paper example to help you with your outline if necessary.

Organize Your Notes

When writing your first draft, you’re going to have to work on organizing your notes first. During this process, you’ll be deciding which references you’ll be putting in your bibliography and which will work best as in-text citations. You’ll be working on this more as you develop your working drafts and look at more white paper examples to help guide you through the process.

Write Your Final Draft

After you’ve written a first and second draft and received corrections from your professor, it’s time to write your final copy. By now, you should have seen an example of a research paper layout and know how to put your paper together. You’ll have your title page, abstract, introduction, thesis statement, in-text citations, footnotes and bibliography complete. Be sure to check with your professor to ensure if you’re writing in APA style, or if you’re using another style guide.


research paper on synthetic organic chemistry

Pharmaceutical Analytical Chemistry: Open Access Open Access

ISSN: 2471-2698

Synthetic Organic Chemistry

Synthetic Organic Chemistry is related to the chemical science involving in the construction of specific chemical compounds from simple compounds. In synthetic organic chemistry the synthesis is implied to the aspect of a planned sequent route resulting in products with desired activity. The process permits synthesis of naturally occurring compounds with actual structure or once needed with structural variation to enhance desired characteristics. Synthetic Organic Chemistry journals emphasis the fields of Organic Chemistry, Medicinal Chemistry and Polymer Chemistry.

Related Journals of Synthetic Organic Chemistry

Organic Chemistry: Current Research, Macromolecular Research, Organic Syntheses, Contemporary Organic Synthesis, Pharmaceutical Analytical Chemistry: Open Access, Chromatography and Separation Techniques.

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research paper on synthetic organic chemistry

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Review article, synthetic organic compounds from paper industry wastes: integrated biotechnological interventions.

research paper on synthetic organic chemistry

Synthetic organic compounds (SOCs) are reported as xenobiotics compounds contaminating the environment from various sources including waste from the pulp and paper industries: Since the demand and production of paper is growing increasingly, the release of paper and pulp industrial waste consisting of SOCs is also increasing the SOCs’ pollution in natural reservoirs to create environmental pollution. In pulp and paper industries, the SOCs viz . phenol compounds, furans, dioxins, benzene compounds etc. are produced during bleaching phase of pulp treatment and they are principal components of industrial discharge. This review gives an overview of various biotechnological interventions for paper mill waste effluent management and elimination strategies. Further, the review also gives the insight overview of various ways to restrict SOCs release in natural reservoirs, its limitations and integrated approaches for SOCs bioremediation using engineered microbial approaches. Furthermore, it gives a brief overview of the sustainable remediation of SOCs via genetically modified biological agents, including bioengineering system innovation at industry level before waste discharge.


The paper and pulp industry consumes various raw materials i.e., wood, cellulose-based products, etc. The main aim of the paper and pulp industry is to produce on large scale to figure out the demand. This review insight into the environmental pollution caused by SOCs produced at various processing stages ( Table 1 ). Deforestation for wood has caused a decline in oxygen level worldwide, directly responsible for floods and droughts. Water pollution by waste discharge from pulp industries also contaminates the water bodies with dissolved organic compounds (DOCs), synthetic organic compounds (SOCs), and suspended particles ( Gupta and Gupta, 2019 ; Ramírez-García et al., 2019 ). The organic compounds reaching humans via water consumption leads to health issues, which are not immediate but show long term effects. The waste discharge also disturbs aquatic life ( Karbalaei et al., 2018 ; Gupta et al., 2019 ). The emission of harmful chemicals and gases i.e., sulfur dioxide, nitrogen oxide, carbon monoxide will cause acid rain as they are water-soluble and reaches the water bodies indirectly ( Gupta and Shukla, 2020 ). Metlymercaptans, hydrogen sulfides, and dimethyl sulfides along with volatile organic compounds (VOCs) lead to air and water pollution ( Singh and Chandra, 2019 ; Pino-Cortés et al., 2020 ). The trials for pollution prevention are in continuous use by industries (by use of alternative bleaching agents), environmentalist (by releasing norms) as well as by consumers (by recycling waste and use of sedimentation tanks). Still, these measures are not fulfilling the demand to degrade the SOCs waste from the paper and pulp industry ( Zumstein et al., 2018 ; Liu, 2020 ). In recent reports, the researchers have shown their interest in the biotechnological advancements for degrading the pollutants ( Ellouze and Sayadi, 2016 ; Tripathi et al., 2017 ; Sharma et al., 2020 ). This review covers the advancement in methodologies via engineered biological agents (mainly bacteria) that are reviewed and suggested for sustainable bioremediation of SOCs.

Table 1. Types of SOCs from the paper industry.

SOCs From Paper Industry Wastes

An ecosystem polluted and damaged by human activities with increasing intensity becomes a primarily global problem. SOCs are of xenobiotic origin in nature and thus there are difficulties involved in biotransformation ( Antizar-Ladislao and Galil, 2004 ; Kumar et al., 2019 ). Due to recalcitrant, it has ecotoxic effects on the biosphere. SOCs can be primarily produced by following compounds such as methane, ethylene, aliphatics, and aromatics. Among the above, most of the industrial important SOCs derived from the aromatics viz., ethylbenzene, xylene, benzene, and toluene ( Fang et al., 2018 ). Based on their primary uses SOCs are mainly classified such as cyclic, acyclic, aromatics, or aliphatics. SOCs contain huge categories like volatile organics carbons (VOCs), and relatively emerging organic contaminants (EOCs). VOCs primarily contain industrial re-solvents, gasolene agents, trihalomethanes, etc., while EOCs have pharmaceuticals, endocrine disrupting substances, hormones, food additives, microplastics, etc. ( Lapworth et al., 2012 ; Postigo and Barceló, 2015 ). SOCs are primarily present in wastewater treatment plants. Most of the SOCs pass througfh various photo-transformations or chemical reactions and many of them remain inert in an open environment system.

In the paper mill, SOCs are released during the pulping and papermaking process. Chlorine and its derivatives have been released and restrained as adsorbable organic halides (AOX) ( Savant et al., 2006 ), while other xenobiotic agents (resin acids, chlorinated lignins, dioxins, phenolic (tannins), and furans) are produced via pulping and paper manufacturing ( Chandra et al., 2011 ). Out of the above, polychlorinated dibenzofurans and dibenzodioxins compounds of furans and dioxins are notably resistant to degradation and are persistent in nature ( Gupta and Shukla, 2020 ). The polar phenolic polymeric compounds (tannins) are released in wastewater during the debarking process of raw wood material, which creates 50% COD of this wastewater ( Chandra et al., 2018 ). Another study revealed that the naturally occurring tricyclic diterpenes (resin acids) are released during the pulping operations, which have pathetic aqua-phobic acids and toxicity levels to aquatic animals at conc. of 200–800 μg/l in wastewater ( Duan et al., 2020 ). Mainly resin acids are produced from the pulping process containing dehydroabietic acid, abietic acid, pimaric acid, isopimaric acid, levopimaric acid, and neoabietic acid ( Yadav and Chandra, 2018 ). Out of all the resin acids, isopimaric acid is notable as highly toxic. Many SOCs are discharged into the water body during the chemical process like calendaring (coating for paper smoothness) in the paper manufacturing industry. The schematic diagram of pulp processes releasing SOCs is given in Figure 1 . The dioxins and furans are also released when chlorine reacts with some defoamers and wood preservatives like pentachlorophenol (PCP) during the pulping, washing and pulp bleaching process ( Badar and Farooqi, 2012 ). Additionally, most SOCs that are discharged from the bleaching process areditolyethane, bis (methylphenoxy) ethane, di-iso-propyl naphthalene, terphenyl, chloromethyl-phenoxy-methyl-phenyl-ethane, etc. ( Singh and Chandra, 2019 ). There are a lot of dyes used for paper printing in paper mills. At the end result, approximately 200 billion liters of dye effluents are released based on fabric type and dye used. Many researchers reported that synthetic organic dyes such as azo, phthalocyanine and anthraquinone dyes discharged as effluents in the water body and have the most toxic effect on the environment as well as human health ( Tkaczyk et al., 2020 ).

Figure 1. Schematic diagram of pulp processes releasing various SOCs.

Ways to Restrain SOCs Production as Waste

To evaluate and mitigate the hazardous effect and load of SOCs released from the pulp and paper industries into the environment, various processes such as the use of chlorine-free bleaching process, use of ecofriendly chemicals for pulping, use of enzymatic pulping, and bleaching instead of the chemical pulping and bleaching process have been used. Among these, several other advanced and more significant methods have been adopted to reduce the SOCs load into wastewater, which is discussed below.

Many researchers have adopted many significant and ecological important methods help to remove organic pollutants from the environment, viz adsorption, biodegradation, striping, hydrolysis, photolysis, etc. ( Ali et al., 2012 ). But significant results have not yet been obtained. Additionally, conventional adsorption techniques integrated with post-treatment using granular activated carbon (GAC) have been globally adopted for the removal of AOX for pulp mill wastewater. According to Osman et al. (2013) , the treatment of paper mill wastewater GAC used with a sequenced batch biofilm reactor (GACSBBR) has significant capability to remove AOX at the longest hydraulic retention time (HRT) ( Farooqi and Basheer, 2017 ). Currently, researchers have revealed that the use of biochar adsorption to mitigate organic pollutants has become an interesting field of research and hotspot. Biochar has a porous structure and contains functional groups of oxygen and minerals ( Weber and Quicker, 2018 ). To eliminate dyes, these dyes go to different types of the treatment process ( Puzyn and Mostrag, 2012 ). The biological, chemical, and physical processes can be done based on wastewater treatment stages (Primary, secondary and tertiary treatment) ( Samer, 2015 ). The removal of organic and inorganic solids takes place in the primary treatment via sedimentation, grinding, and flocculation. While in the biological treatments (secondary treatment), organic materials are used by the aerobic or anaerobic microorganisms by the means of biological oxidation and biosynthesis processes. In the tertiary treatment, the wastewater undergoes different treatment processes like advanced oxidation processes, ion exchange, adsorption and reverse osmosis processes. For example, many researchers used ferric oxide-biochar nanocomposite absorbent extracted from paper mill sludge ( Chaukura et al., 2017 ).

Another study reported/investigated that the biochar can be prepared from cardboard (BCPD), pig manure (BC-PM), and pinewood (BC-PW) for the use in adsorption of various synthetic organic dyes within several pyrolysis terms. Due to high ash content, BC-PM showed significant adsorption properties ( Lonappan et al., 2016 ). Adsorption methods are amongst those used to remove dyes in comparison with other methods ( Srivastava et al., 2018 ). During the degradation process of synthetic organic dyes, it undergoes various transformations kinetics. Some of the changes are into the more toxic agents and some of them non-toxic agents. Advanced techniques such as oxygen cooking techniques, hydrogen peroxide, and ozone treatment for the pulp bleaching process could be options for pretreatment of primary sludge wastes, which helps with the reduction of an environmental load of SOCs production. There are mostly two types of chemical pretreatment used, alkaline and acidic. Acidic pretreatment is promoted for the hemicellulose while alkaline pretreatment for the lignocellulose, which makes it more accessible to use their products ( Hendriks and Zeeman, 2009 ). However, lots of modified methods have been used for the pulping and bleaching process of the pulp mill. Bio-pulping is most suitable for the pulping process using eco-friendly enzymes and it can reduce the production of SOCs in waste materials. Some other techniques like innovation in the bleaching process can be adopted by many researchers. These techniques are elemental chlorine-free (ECF) bleaching techniques and a totally chlorine-free (TCF) bleaching technique ( Gupta et al., 2019 ).

Detection and Analysis

Gas chromatography (GC) and Gas chromatography-mass spectrometry (GC/MS) have been used to detect and analyze the SOCs effluent released from the pulp and paper industries. Some metabolites formed by degradation of AOX can be identified by using GC/MS ( Pronk et al., 2015 ). Many researchers used a multi X2500 analyzer to characterize bleaching AOX effluent. A study has stated that organic chlorides were recognized by using GC-MS incorporation with or without hot water abstraction. By these methods, AOXs were categorized into at least four main components such as macromolecular, small molecular organic chloride, chloro-phenol and chlorobenzene. Although, these methods are conventional methods and are time-consuming and expensive. Nowadays, advanced technologies like biosensors have been used, which offer an advantage over classical analytical methods due to their selectivity, sensitivity, eco-friendly, inexpensiveness and short assay time ( Yao et al., 2017 ). However, an immobilized laccase based biosensor has been used for the detection and analysis of organic compounds. Several other electrochemical biosensors such as voltammetric sensor, amperometric laccase biosensor and optical biosensors are used for the analytical analysis of various organic effluents released from industrial operations. Among these, amperometric transducer methods have been reported as widely studied and used in laccase biosensors, while presently optical biosensors have the most significant results in terms of sensitivity ( Rodríguez-Delgado et al., 2015 ). Additionally, a nanomaterial-based ( Pena-Pereira et al., 2020 ) colorimetric detector has been used for the quantitative analysis of low molecular weight gaseous VOCs ( Azzouz et al., 2019 ). Some researchers have employed high-temperature combustion to the transformation of Total organic halides (TOX) into halides and detected and quantified these halides using micro-coulometry methods. In 1977, micro-coulometry titration methods have been replaced by the more reliable ion-selective electrode (ISE) to detect the halides present in the wastes released from the paper mill ( Chen et al., 2020 ).

Limitations and Challenges

SOCs such as aromatic compounds (phenols and biphenyls), polycyclic aromatic hydrocarbons (pyrene), are generally discharged into the water bodies. Most of the SOCs found in the environment/wastewater are recalcitrant due to their complexity compared to other effluents. However, these effluents have drawn more attention to treatment systems. These compounds are highly persistent, more toxic compounds that remain over a long period and bio-accumulated into the water body. Separation and treatment of these effluents became mandatory before releasing effluents in the marine ecosystem. For this purpose, the development of efficient techniques has been an interesting area of research for a long time ( Awad et al., 2019 ). The use of conventional technologies has many disadvantages that limit the application area. The main environmental impact is the production of a huge amount of hazardous sludge that creates dumping problems and increases toxicity concentration in treated water ( Ashrafi et al., 2013 ). Traditional methods are more expensive than advanced methods. However, environmental and health costs are also affected by using this classical method. Gaseous emissions, wastewater and sludge production from effluent treatments are relatively unmonitored. In developing countries, these effluents are primarily disposed of into unsecured landfills. The hazardous agents leach out over a long period from the landfills and go directly or indirectly into the environment. Constraints are in place with the purpose of limiting these effects, which have been mandatory across industries ( Nimkar, 2017 ). However, the challenges of the reduction of SOCs production are still under investigation. Researchers have used some innovative and modified technologies for the treatment process of wastewater to help in the mitigation of hazardous compounds in the environment. Mostly SOCs are derived from the aromatic source, viz., toluene, ethylbenzene, anthracene, etc., which are persistent over the period and recalcitrant in the ecosystem because of the rigidness of their molecular structure and present thermodynamically stable aromatic ring ( Postigo and Barceló, 2015 ). The ecotoxic impacts of SOCs on the environment have been accepted and implicit. However, water scarcity, water pollution and water recycling are serious challenges globally ( Jain et al., 2020 ).

Economical Importance and Hindrance by SOCs for the Paper Industry

Pulp and paper are produced from cellulosic fibers, other plant material and synthetic materials may be used. Papers are mainly derived from wood fibers but cotton liners, bagasse, rags, etc are also used in some papers ( Bajpai, 2018 ). Pulp and paper mills waste material and used papers can be further recycled and used to create economical values. The pulp and paper mills librated a substantial amount of wastewater composed of organic material such as high cellulose, hemicellulose, lignin contents ( Kaur et al., 2020 ). Lignins are cross-linked phenolic polymers. These organic materials are suitable for the derivation of glucose and other fermentable sugars for example galactose, mannose, arabinose, and xylose. By using physical and chemical treatment methods, transformation of paper industry sludge into a glucose-rich liquid can be achieved. Enzymatic hydrolysis is a promising approach for the derivation of sugars from paper industry sludge. Other valuable products can be obtained by causing the fermentation of sugars ( Naicker et al., 2020 ). Production of biofuels such as bioethanol could be successfully achieved by the conversion of pulp and paper industry waste mainly composed of cellulose, hemicellulose, and lignin contents. These components require a series of reaction steps such as hydrolysis, hydrogeoxygenation alkylation, etc to be converted into biofuel. Lignin based biofuels can be produced by using one-pot depolymerization or by the upgrading of bio-oil from biomass decomposition. Pulp and paper industry waste conversion into biofuel is an interesting approach to manage paper industry waste and to create commercial value out of it ( Zhu et al., 2020 ). The paper industry also generated sludge composed of biomass fly ash and calcareous sludge that is commonly disposed of in landfills. Calcareous sludge can be used in the manufacturing of green geopolymeric mortars for the application in construction. These components are released during the Kraft process of lignin. Biomass fly ash was reused as an alternative source of silica and aluminum, and calcareous sludge mainly constituting of calcite, was recycled and used in GP mortars construction. The implemented Mix design was outlined to maximize the incorporation of the calcareous sludge and improve the mortar’s mechanical performance ( Saeli et al., 2020 ). To accomplish a productive re-utilization of waste generated from the paper industry, waste effluent was recycled and used to produce green-composites with high strength which depends on ultra-molecular weight polyethylene, high-density polyethylene, and low-density polyethylene. The three green-composites were developed by an extrusion and injection molding named PLC, PUC, and PHC composites. The maleic anhydride grafted polyethylene, an organic compound, was used as a compatibilizer for preparing composites. The utilization of paper mill waste avoids the environmental waste and also produces the green-composites ( Zhang et al., 2020 ). Anaerobic digestion under mesophilic condition is widely applied for the production of biogas by utilizing waste rich in suspended organic materials liberated from the paper industry. Industry waste contains a very high level of COD and BOD due to the presence of lignin, fatty acids, tannins, resin acids, and chlorinated compounds, etc. This biofilm technology is highly effective in biogas production ( Bakraoui et al., 2020 ). Biogas production can be successfully achieved by using UASB digester technology and it can be applied on a large and small scale. Anaerobic digestion of Recycled pulp and paper industry waste can be carried out at different organic loading rates and in mesophilic conditions ( Bakraoui et al., 2020 ). The amount of lignin is very important in paper manufacturing because lignin will affect the properties of the resultant paper. Lignin amount influences the tensile strength and elongation of cellulose fiber.

Effect on Ecological and Biological Health

The production of SOCs comes from mainly the pulping and bleaching stage of the pulp mill. These compounds have toxic properties, which may cause carcinogenic disease, allergic and dermatic disease ( Puzyn and Mostrag, 2012 ). The production of trichlorotrihydroxybenzenes and bromomethylpropanylbenzene in the spent bleach liquor from pulp and paper industries have mutagenicity effects on the aquatic body as well as human beings. Additionally, some other SOCs such as chlorophenols and chloroguaiacols from bleach effluents notably carcinogen, reproductive toxicity in fish, and estrogenic in humans. Further, it has acute toxicity, which prevents the ATP synthesis process and oxidative phosphorylation mechanism ( Singh and Chandra, 2019 ). Some endocrine-disrupting chemicals as residual organic compounds showed chromosomal aberration in marine animals ( Chandra et al., 2018 ). The discharge of black liquor containing SOCs into the environment causes a direct effect on flora and fauna. In a developing country, untreated wastewater released from pulp and paper industries is discharged into the water body ( Duan et al., 2020 ). They have to use this water for irrigation purposes so a lot of hazardous chemicals come into the fields and affected the crops due to changes to the soil properties, like alteration in pH values and beneficial microbes ( Nguyen et al., 2020 ). The organic compounds pass through different trophic levels in the marine ecosystem and are bio-accumulated at a different level, which can be harmful to marine animals. However, the use of biochar for the adsorption of SOCs helps to retain fertilizers in the soil, promoting soil fertility, removal of heavy metals and acids, etc. ( Shiralian, 2016 ). Based on dissipation time, SOCs can be classified into three main categories: highly persistent, moderately persistent, and low persistent. Humans are more exposed to SOCs through polluted air, water, or soil ( Bilal and Iqbal, 2019 ). SOCs combined with their precursors employ eco-toxic effects on the environment ( Figure 2 ; Jaishankar et al., 2014 ). An experiment was conducted which reported that the effect of SOCs on rainbow trout ( Oncorhynchus mykiss ) in the rivers of Chile, Canada, and Argentina was observed as stimuli for the development of secondary sexual properties and enhanced the intersex features in the young rainbow trout ( Oncorhynchus mykiss ) ( Chiang et al., 2015 ). Similarly, a study conducted in China (2018) reported that long term exposure of andostenrdione has masculinization and reproductive effects in both male and female wastern mosquitofish ( Gambusiaaffinis ) ( Hou et al., 2018 ). Another experiment demonstrated by terasaki and co-workers in 2012 stated that the effects of Dimethyldiphenylmethane and di-iso-propylnaphthalene have reproductive and tissue toxicity on marine fish ( Terasaki et al., 2012 ). The exposure of hexachlorobutadine (HCBD) in human beings has hostile effects on human health either directly or metabolically. The nephrotoxicity effects of HCBD have been observed in animal host experiments and reported as having a necrosis effect on the renal proximal tubule, up-regulation of kidney injuring molecule-1 and lipid peroxidation in renal cells ( Sadeghnia et al., 2013 ). In china, the approximately 8.0 × 10 –6 μg/kg/day of HCBD exposure dose for human and animal risk was observed which has caused skin diseases, carcinogenicity, sexual abbreviation and mutagenicity in humans as well as aquatic communities ( Zhang et al., 2014 ).

Figure 2. The overall view of SOCs affecting the ecological and biological health.

Biotechnological Interventions in Preserving Environment Through Bioremediation

The recalcitrant nature and toxicological assessment of synthetic organic compounds were not carried out at the early industrial stage. But as the industrialization sector boomed and ill-effects of various pollutants were studied then SOCs also came under scrutiny because of their presence in polluted industrial water. Since then it has become a matter of great concern to remediate these pollutants. Various biological and technological approaches have been utilized to remove SOCs from wastewater before their discharge into water bodies ( Jain et al., 2020 ).

Bioelectrochemical systems, containing electro genesis systems, electro hydro-genesis systems, microbial electrosynthesis (MES) systems ( Liu et al., 2018 ), and microbial desalination systems, are an emerging technology to remediate pollutants ( Wang et al., 2015 ; Fernando et al., 2019 ). This technology uses electricity and microorganisms to degrade pollutants into less toxic elements. Certain value added products such as biofuels (including hydrogen, butanol, and ethanol, etc.) ( Kondaveeti et al., 2019 ; Liu and Yu, 2020 ), acetates, and metals are also produced by using these techniques ( Moscoviz et al., 2016 ; Maktabifard et al., 2018 ). The relatively low energy value (0.2–0.8 V) is needed for the MEC system as compared to conventional water electrolysis ( Kadier et al., 2016 ). Rozendal and co-workers reported that approximately 7 kg COD/m 3 bioreactor volume/day could be removed by the BES which is the same as a conventional treatment system ( Rozendal et al., 2008 ). Lab scale results reported that MEC showed COD removal efficiency was observed to be about 90–97% of synthetic wastewater at different temperature profile (ranging 5–23°C) and 0.6 kWh/kg electricity. Hence, the BSE is more suitable for small and lab scale systems due to the low energy utilization with improved byproduct production which minimizes the capital cost ( Tartakovsky et al., 2018 ). But the implementation of BES with ordinary systems at industrial levels is more challenging due to the high capital cost which is required ( Santoro et al., 2017 ). Microbial fuel cells (MFCs) are efficient for the biochemical conversion of energy for a useful purpose. Dual-chamber MFC has been utilized for the management of polyaromatic hydrocarbons (PAHs) contagion from diesel. The proposed system detached 82% of PAHs and generated about 31 mW/m 2 power. MFCs with tubular single- and dual- chambers were applied to reveal ex situ and in situ management of refinery wastewater or groundwater having a blend of PAHs, containing benzene and phenanthrene ( Adelaja et al., 2017 ). Fenton reaction and the microbial consortium was evaluated for the removal of tannery dye effluent. This exceptional combination was able to remove 89.5% pollutants and led to a reduction in the COD level of 93.7% ( Shanmugam et al., 2019 ). Another advanced oxidation process of ultrafiltration and photoelectrolysis alone was found to remove total phosphorus between 90 and 97% from municipal wastewater and 44% from industrial wastewater ( Gray et al., 2020 ).

Activated carbon has been used as a suitable adsorbent for many pollutants. Superfine powdered activated carbon is found to be more suitable as an adsorbent due to its smaller size, lesser surface oxygen amount, bigger aperture diameters, and neutral pH. An increase in adsorption of planar (phenanthrene) compounds was affected more than non-planar (2-phenyl phenol) compounds ( Partlan et al., 2020 ). Activated carbon can also be used in supporting biofilms for pollutant removal. Due to the larger surface area provided by activated carbon, biomass was able to degrade xylene and other BTEX compounds efficiently and reduce the toxicity of up to 99% ( Mello et al., 2019 ). In this era of machine learning, modeling strategy to check the efficient substrates of adsorption of SOCs can help in the development of efficient adsorbents. In a study, Ghosh et al. (2019) developed a regression support model quantitative structure-property relationship (QSPR). According to this model, they have calculated the adsorption coefficient of 40 SOCs on single-walled carbon nanotubes. They found that various hydrophobic and electrostatic interactions as well as hydrogen bonding help in the adsorption of SOCs on nanotubes. The interaction studies help in the development of suitable adsorbent for SOCs removal from wastewater ( Ghosh et al., 2019 ).

Modified zeolites are also emerging as suitable adsorbents for wastewater treatment. Hashemi et al. (2019) modified a zeolite Y made from bentonite by using CTAB. Various adsorption isotherms indicated removal of 89% total organic carbon and involvement of electrostatic and hydrophobic interactions ( Hashemi et al., 2019 ). Another Fe-nano zeolite was able to absorb phenol (Ph), 2-chlorophenol (2-CP) and 2-nitrophenol (2-NP) in the amount of 138.7, 158.9, and 171.2 mg/g, respectively. This zeolite-based adsorbent was even more cost effective than activated carbon ( Tri et al., 2020 ).

Sustainable Remediation of SOCs via Genetically Modified Biological Agents

In the pulp and paper industry paper is derived from wood and produces a huge amount of waste effluents as sludge and polluted water. Toxic chemicals and recalcitrant organic compounds are found in this wastewater ( Dixit et al., 2020 ). Pulp and paper industry waste released into freshwater alters aquatic habitats and adversely impacts human health. The remediation of these organic compounds is necessary to accomplish environmental sustainability. Bioremediation of pollutants is a novel technique to make the effluents less toxic and safe for discarding the waste ( Gupta et al., 2019 ). To protect human lives, the advancement of remediation technologies for the recovery of polluted sites is of utmost importance. Sustainable remediation, which seeks to reduce concentrations to risk-based levels as well as mitigate ancillary environmental consequences such as waste generation, has recently gained significance ( Cecchin et al., 2017 ). Bioremediation requires the use of particular microorganisms to degrade organic pollutants, a reasonable and efficient approach based on microbes’ unique catabolic capacity ( Dvořák et al., 2017 ). This has led to increased efforts using innovative biotechnological methods ( Table 2 ) to develop more effective, ecologically sustainable, environmentally acceptable, and cost-effective remediation technologies ( Kumar et al., 2017 ). Various microorganisms, mainly bacteria and fungi, play an important role to degrade synthetic organic compounds. Degradation of these compounds depends upon the secretion of enzymes by microorganisms that participate in the metabolic pathways. The traditional physicochemical bioremediation methods ( in situ and ex situ ) ( Jaiswal et al., 2020 ) are inefficient for degradation and removal of new emerged compounds ( Jaiswal and Shukla, 2020 ). With the development of genetic engineering and Recombinant DNA technology many genetically modified microorganisms were constructed by using various techniques for the remediation of synthetic organic compounds ( Liu et al., 2019 ). Biodegradation of recalcitrant azo dye was successfully done by enzyme azoreductase encoded by gene azoA from Enterococcus sp. L2 into E. coli and Pseudomonas fluorescens using the expression vector PBBRMCS2. To further increase the degradation of azo dye NADH regenerate system depended on the formate dehydrogenase enzyme introduced into the host strain by the overexpression of fdh gene from Mycobacterium vacccae N10. For efficient dye decolorization processes the transcription fusion of azoA – fdh provided a simple genetic cassette for genetic engineering of an appropriate host ( Rathod et al., 2017 ). Moreover, Biodegradation of phenol and p-nitrophenol was successfully done by genetically modified Bacillus cereus strains by introducing the vgb gene from Vitrocilla stercoraria . The gene was cloned into a pUB110 multicopy plasmid. A higher degradation rate was obtained at 37°C under aerobic conditions by genetically modified bacteria compared with wild type. p-Nitrophenol degradation was obtained high by using the strain with uni-copy of vgb gene ( Vélez-Lee et al., 2016 ). Bacillus cereus and its recombinant strains are effectively used for biodegradation of phenols and p-nitrophenol under anaerobic and aerobic conditions. Different Phenolic compounds are effectively degraded by the action of Manganese peroxidase, an extracellular heme enzyme of white-rot basidiomycete Ganoderma . 1092 bp full-length cDNA of the MnP gene, designated as G. lucidum MnP (GluMnP1) , was cloned from G. lucidum and a eukaryotic expression vector, pAO815: GlMnP was constructed and transferred it into the methylotrophic yeast Pichia pastoris SMD116 by the electroporation-mediated transformation. Recombinant GluMnP1 is capable of the degradation of phenol and the degradation of four types of dyes. Great potential for the enzymatic remediation of phenolic compounds and industrial dyes was shown by the Recombinant GluMnP1. Phenol and the main oxidation degradation products including hydroquinone, pyrocatechol, and resorcinol were analyzed by using HPLC ( Xu et al., 2017 ). In another study for the remediation of the phenolic compound engineered Escherichia coli effectively used. Nine genes namely, pheA1, pheA2, catA, catB, catC, catD, pcaI, pcaJ, and pcaF were selected from different microorganisms and an oligonucleotide was synthesized. By using the modified overlap-extension PCR method, all synthesized genes were seamlessly connected with the T7 promoter and terminator to construct a gene expression cassette. All the cassettes were transformed to the host Escherichia coli strain BL221-AI and the transformant was named BL-phe/cat. The engineered Escherichia coli was effectively used for phenol degradation ( Wang et al., 2019 ). Degradation of organophosphates, carbamates, and pyrethroids was achieved by engineering Pseudomonas putida . In a study, a scarless genome-editing tool was applied for the engineering of Pseudomonas putida KT2440. The vgb and gfp genes were transferred into the chromosome. It was observed that the genetically modified strain Pseudomonas putida KTUe having genes (ΔphaC1, Δvdh, ΔalgA/algF, Δfcs, Δupp, ΔphaZ/phaC2, gfp+, mcd+, cehA+, mpd+, pytH+, vgb+) was able to decompose all the pesticides screened. Also, it was found that to sequester oxygen in the soil study with the VHb gene was responsible. Thus, this engineered Pseudomonas putida strain is a powerful approach for the degradation of pesticides ( Gong et al., 2018 ). Recent genetic editing technology is a promising approach for engineering the various microorganisms to perform remediation of pollutants ( Dangi et al., 2019 ). With the help of gene-editing techniques, modified microorganisms with maximum quality can be produced by making targeted modifications in the genome using molecular scissors involving engineered nucleases. Clustered regularly interspaced short palindromic repeat (CRISPR-Cas), zinc finger nucleases (ZFNs) and Transcription-activators like effector nucleases (TALENs) are the main gene-editing tools that have the dynamic capacity to boost bioremediation of synthetic pesticides ( Jaiswal and Shukla, 2020 ; Kumari and Chaudhary, 2020 ). The gene editing process involves self-designed guide sequences that are inserted complementary to the sequence of the gene of interest assisting break at a site, repaired by homologous recombination, insertion, or deletion of desired sequence fragments. A double-stranded (DSB) break can be created by Transcription-activators like effector nucleases in the target sequence on DNA and makes sticky ends. Likewise, zinc finger nucleases also introduce a DSB in the target sequence of the host genome. On another hand, CRISPR-Cas comprise of crRNA and trcRNA joined by gRNA. gRNA controls the Cas9 enzyme to create DSB in the desired sequences of DNA ( Jaiswal et al., 2019 ). In another study plants also play a main role in the removal of various pollutants by phytoremediation. Phytoremediation is a bioremediation form that requires plants as tools for the removal of hazardous contaminants from the environment. Phytostimulation, phytoextraction, phytoextraction, phytostabilization, and phytovolatilization are different approaches of phytoremediation for the remediation of metals/metalloids and other hazardous contaminants. A plant’s genome can be modified by utilizing CRISPR-Cas, ZFNs, and TALENs gene-editing tools ( Figure 3 ; Aminedi et al., 2020 ). Indeed, clustered regularly interspaced short palindromic repeat (CRISPR-Cas) is a revolutionary genetic engineering tool in plants that provides a pragmatic approach to synthesize advanced phenotypes ( Saxena et al., 2020 ). On another hand, progress in the development of recombinant microorganisms has created potential risks associated with the release into the open environment of such genetically engineered microorganisms (GEMs). But many attempts are being made to monitor and track genetically engineered microorganisms to address these risks. Designing genetically engineered microorganisms by employing sufficient genetic methods to contain the bacterial system will help to reduce the anticipated hazards. For example, transposition vectors are designed which are deemed to be safe in the environment. Another containment technique primarily includes the production of suicidal genetically engineered microorganisms, but the technology has yet to be applied. These advanced technologies are one of the most promising ways to mitigate the adverse effects of genetically engineered microorganisms release in the open environment ( Hussain et al., 2018 ). But certain risks could also exist and further study will then be needed to produce acceptable technical regulatory guidelines.

Figure 3. Integrated biotechnological interventions for SOCs pollution treatment.

Table 2. Advance biotechnological techniques for SOCs level reduction.

Conclusion and Future Perspective

The review shows the extent that the recent research in the field of environmental pollution by the paper and pulp industry has reached. The researchers and environmentalists concluded that SOCs pollutant levels must be declined, and have worked in the same direction. They found that the composition of various chemicals varies with the stage and methodologies applied for paper production. The detection and degradation of organic chemicals produced during paper production are enhanced by researchers using advanced techniques. Biotechnological intervention using synthetic and systems biology for producing genetically modified organisms specifically for potential degradation of SOCs came into consideration. Thus, this review covers the recent reports and methodologies used by the researcher for environmental sustainability.

Author Contributions

SJ wrote the first draft of the manuscript with contributions from GK, M, and KP. PS read and edited the final draft. All authors approved the final draft for its submission.

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The infrastructural support from the Department of Science and Technology, New Delhi, Govt. of India, through FIST grant (Grant No. 1196 SR/FST/LS-I/2017/4) and Department of Biotechnology, Government of India (Grant No. BT/PR27437/BCE/8/1433/2018) is duly acknowledged. The Junior Research Fellowship (JRF) by DBT (Grant No. BT/PR27437/BCE/8/1433/2018), Govt. of India to GK and Project Assistantship to KP, is duly acknowledged. SJ acknowledges Maharshi Dayanand University, Rohtak, India, for providing University Research Scholarship (Award letter-URS-20/2/2020-R&S/R-15/20/842). MD acknowledges the Junior Research Fellowship from CSIR, India (Award No. 09/382(0211)/2019-EMR-1).

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Keywords : synthetic organic compounds, bioremediation, xenobiotics, pollution, pulp and paper industry

Citation: Jaiswal S, Kumar Gupta G, Panchal K, Mandeep and Shukla P (2021) Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions. Front. Bioeng. Biotechnol. 8:592939. doi: 10.3389/fbioe.2020.592939

Received: 08 August 2020; Accepted: 30 November 2020; Published: 08 January 2021.

Reviewed by:

Copyright © 2021 Jaiswal, Kumar Gupta, Panchal, Mandeep and Shukla. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Pratyoosh Shukla, [email protected] ; [email protected] ;

† These authors have contributed equally to this work and share first authorship

‡ Present address: Pratyoosh Shukla, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India

This article is part of the Research Topic

Advanced Bioremediation Technologies and Processes for the Treatment of Synthetic Organic Compounds (SOCs)

Journal of Organic & Inorganic Chemistry

Synthetic organic chemistry.

Synthetic Organic Chemistry may be a Special Branch of chemical synthesis and cares with the development of organic compounds via organic reactions. Organic molecules usually contain the next level of complexness than strictly inorganic compounds, in order that the synthesis of organic compounds has developed into one among the foremost vital branches of chemistry.

Related Journals for Synthetic Organic Chemistry

Organic Chemistry: Current Research, Macromolecular Research, Organic Syntheses, Contemporary Organic Synthesis.

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section " Organic Chemistry ".

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The activity in the search for new synthetic methods continues in full progress, especially in totally enantioselective developments, using among flourishing methodologies the domino and multicomponent reactions, which lead to a more sustainable chemistry (Green Chemistry).

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Royal Society of Chemistry

Problem types in synthetic organic chemistry research: Implications for the development of curricular problems for second-year level organic chemistry instruction

Jeffrey R. Raker a and Marcy H. Towns * b a Department of Chemistry, Iowa State University, Ames, IA, USA b Department of Chemistry, Purdue University, West Lafayette, IN, USA. E-mail: [email protected]

First published on 17th January 2012

Understanding of the nature of science is key to the development of new curricular materials that mirror the practice of science. Three problem types (project level, synthetic planning, and day-to-day) in synthetic organic chemistry emerged during a thematic content analysis of the research experiences of eight practising synthetic organic chemists. Project-level problems include the overarching purpose of synthesizing target molecules. Synthetic planning problems include both the retrosynthetic analysis of target molecules and subsequent development of synthetic pathway proposals. Day-to-day problems include the ‘hurdles’ faced in research laboratories while attempting to realize proposed synthetic pathways. Recommendations are made as to how understanding of the three problem types impact undergraduate-level organic chemistry instruction.


The development of problem-solving abilities is a frequently cited and fundamental outcome of the chemistry and broader educational curriculum ( Heyworth, 1999 ; American Chemical Society, 2008 ; Zoller, 1987 ). The American Chemical Society (ACS) Committee on Professional Training has proposed that “problem solving is one of the most empowering learning experiences for science students” (2002, p. 3) . It has been argued that scientific research is fundamentally problem solving ( Bodner, 1991 ; Nersessian, 1995 ), and that through instruction on problem solving, the practice of science can be taught ( Bodner and Domin, 2000 ; Society Committee on Education, 2003 ).

Because of these goals, the authors (JRR & MHT) then set out to develop pseudo-research experiences for the lecture component of second-year organic chemistry courses through instructional problem sets, a much less resource dependent part of the chemistry curriculum than the instructional laboratory. Pseudo-research experiences seek to incorporate research type problems and situations into the context of the traditional curriculum.

Using an instructional design methodology (IDM) discussed by Jonassen and Hernandez-Serrano (2002) , the authors sought to transform the problem-solving experiences of practising organic chemists into instructional problems for undergraduate students. A preliminary component of the IDM was to establish an understanding of problem-solving experiences in synthetic organic chemistry, i.e. the nature of synthetic organic practice. This understanding was achieved through a review of the science education and organic chemistry literature, a review of graduate-level instructional textbooks and research overviews, and interviews with eight practising synthetic organic chemists (six graduate students and two postdoctoral researchers) in academia. Presentation of the results from interviews with the eight practising synthetic organic chemists is the purview of this article.

The three problem types found in synthetic research, as discussed by the eight practising synthetic organic chemist participants, will first be presented. This understanding of the practice of synthetic organic chemistry will be followed by a discussion of implications for the design and development of sophomore-level organic chemistry instructional problems.


Instructional design model, description of participants, description of interview protocols, description of think-aloud problems.

Two problems asked participants to confirm the identity of a desired product and to “prepare items necessary to discuss your work for Friday's research group meeting” based on experimental data (including proton and carbon-13 nuclear magnetic resonance spectroscopy data for both starting materials and obtained reaction products). Nuclear magnetic resonance spectroscopy is an experimental technique used to identify the types, number, and chemical environment of observed atoms.

One problem asked participants to consider two provided synthetic pathways to a given target molecule and “recommend an improved synthetic route” with the intent of “reducing the number of synthetic steps and increasing the overall selectivity and yield of the synthetic pathway.”

One problem asked participants to develop experimental procedures for a given series of compounds based on a literature-reported reaction methodology.

One problem asked participants to conduct a retrosynthetic analysis and to propose a synthetic pathway for a given biologically active target molecule. Retrosynthetic analysis is a backward thinking strategy where the researcher begins with the target molecule in mind and then “disconnects” the molecule using viable reactions until commercially available reagents remain.

Six of the participants completed two to three of these “classroom” problems. The choice, number, and order of the problems utilized for each participant was decided by the interviewer (author JRR), in the context of the interview, in response to the interview length and ability of participants to generate solutions to and reflect on the “classroom” problems. The goal of the think-aloud protocol was to generate reflection on the types of problems and the problem-solving processes of synthetic organic chemists; therefore, the process of think aloud problem selection is consistent with the goal of obtaining data-rich reflections by the participant's on their “research” problem-solving experiences. Each “classroom” problem, except one, was sampled three times; the total synthesis problem was sampled four times.

Thematic content analysis

Types of problems in research process, project-level problems.

Any molecule “that can be drawn [and] pretty much anything that has been isolated from nature can be [synthesized] with enough effort” (“Ignatius;” & cf. Deslongchamps, 1984 ). The choice of a target molecule is governed by several factors identified by the participants: chemical resources, funding sources, available laboratory equipment, synthetic difficulty, the opportunity to test a new synthetic methodology, researcher's and research team's knowledge, therapeutic potential, client requirements, etc. As chemists evolve in their skills and abilities, the complexity of target molecules and research projects increases (“Aloysuis”). Target molecule complexity was seen as a function of the open-endedness of the project-level problems; the more open-ended, the more complex the target molecule (“Xavier”). “Alberto” saw the open-endedness of the problem as a direct function of the number of possible synthetic pathways to a given target molecule; if every possible pathway was considered, an upwards of “thousands” of paths could be posited for any given target molecule.

Project-level problems give insight into the societal application of the target molecule's specific structure or functionality. In the opinion of “Aloysuis,” target molecules have most recently been limited to biologically active molecules. A review of Feature Articles from the Journal of Organic Chemistry in 2010 and 2011 shows that biologically active compounds including antibacterial, antibiotic , anticancer, antifungal, and disease inhibitors have been a key focus of synthetic organic chemistry research.

Project-level problems as discussed by the practising organic chemists were centered on total syntheses of target molecules; however, this is a limitation of the participant sample. A second category of project-level problems is ‘methodological.’ Three of the practising synthetic organic chemists mentioned this problem type; however, they stated that methodological research was not considered to be the main focus of their research initiatives. “Alberto” described methodology as…more of optimizing a, a reaction. So, you kind of create a new reaction, a new method to build up the structure. And, and, the problem is having probably poor yields or side products that you don't want, ah side products that are major. So, you try to reverse basically the ratio between the compounds. “Aloysuis” saw total synthesis and methodology problems working in tandem; “when you are working on total synthesis, without knowing, you would be working on methodology too.”

The definition of project-level problems, as reported by the participants, originates with the principal investigator, a faculty-level research advisor. The graduate student participants felt obligated to adopt the project-level problems and methods for solving those problems as directed by their research advisor. “Aloysuis”, a sixth year graduate student, and the two postdoctoral research associate participants noted that as their research careers progressed, their research advisors invited them to participate more in the definition of project-level problems and the direction necessary to solving the problems.

Synthetic planning problems

Retrosynthetic analysis, a method introduced to the organic chemistry community by E. J. Corey, was explicitly discussed by five of the eight practising organic chemist participants. Corey received the Nobel Prize in 1990 for his idea of retrosynthetic analysis (see Corey, 1988, 1991 ; Corey and Cheng, 1995 ). Retrosynthetic analysis is a process of proposing possible “disconnections” (“Robert”), the reverse of forming bonds (see Fig. 1 for an “Edmund's” example of a retrosynthetic analysis).

By making several disconnections within a target molecule, a researcher intends to disconnect the target molecule into a set of commercially available starting materials; this process may not be as easy as stated and may involve the development of new and modification of several known reaction types. The retrosynthetic analysis, with possible disconnections, becomes the foundation for proposing synthetic pathways.

If every possible disconnection were considered, the number of pathways to a given target would be extremely large. As discussed by the participants, several goals guide retrosynthetic analysis and the proposal of synthetic pathways. These goals include enantioselectivity, cost—inexpensive starting materials and reactants, efficiency—greatest yield, efficiency—shortest pathway (total number of steps), environmentally friendly ( Anastas and Warner, 1998 ), intricacy—multiple bonds/stereocenters formed in one reaction ( Fuchs, 2001 ), no unwanted products ( i.e. , side reactions), no use of protecting groups, and no waste ( i.e. , atom economy; Trost, 1991 ). As possible disconnections are considered and pathways are proposed, these goals inform and constrain the synthetic planning process.

As “Xavier” noted, once a pathway is set “then it's just a matter of getting the reactions to go.” “Xavier” is stating that at the conclusion of the planning process, the next step is to realize the planning in the laboratory through synthesis and experiment. The next section will describe the day-to-day routines in which the participants get their “reactions to go” and the problems that emerge during those routines.

Day-to-day problems

Day-to-day problems, as defined by the participants, are most typical of what would be considered a “problem” in the problem-solving literature ( Hayes, 1989 ; Wheatley, 1984 ). “Aloysuis” defined a problem as a “challenge that keeps you from going to the next step;” he also described problems as “dead ends.” “Bernadette” stated that a “problem then is anything that needs to be fixed. Not working the way it should;” she also used the term “hiccup” to describe these kinds of problems. “Xavier” described day-to-day problems as anything “unexpected” or “hurdles” to be jumped. These three participant's problem definitions mirror two commonly referenced definitions from the problem-solving literature: Hayes (1989) has stated that “whenever there is a gap between where you and now and where you want to be, and you don't know how to find a way to cross the gap, you have a problem.” And, Wheatley (1984) has stated that problem solving is “what you do, when you don't know what to do.” Elements of both of these literature definitions were found in the participant's responses.

Problems of the day-to-day type arise in the context of four routine processes: (1) The physical setup of glassware, heating and stirring apparatuses, and vessels and tools for adding reagents to the reaction vessel (“Edmund”). (2) The purification of reactants and products (“Edmund,” & “Ignatius”). (3) The characterization of products (“Bernadette,” “Edmund,” “Ignatius,” & “Xavier”). (4) Property testing of products ( e.g. , biological activity; “Alberto,” “Bernadette,” “Claudia,” “Edmund”).

Within these four routine processes, the eight participants identified seven common day-to-day problems: (1) The formation of byproducts or unexpected products. This problem often emerges during the characterization process. Under certain circumstances a single unwanted product is the only product isolated. Under other circumstances, mixtures of byproducts and the intended product are obtained. Mixtures of products often lead to re- purification and re-characterization.

(2) Impure starting materials and reactants . Participants discussed that after discovering that the expected product was not obtained that they would often refer back to the characterization of the starting materials. By following the characterization backwards, being conscious of potential byproducts, participants were able to determine whether the starting material was impure or not the compound originally thought.

(3) Insoluble starting materials , reactants , or products. When all solvent was removed from the reaction mixture, the products solidified into an insoluble product that prohibited it to be characterized by common methods ( i.e. , liquid phase nuclear magnetic resonance spectroscopy ).

(4) Instrument failure. Instruments being used in synthesis research are most commonly associated with characterization of the product; although, for those conducting their own biological activity testing, this also could include instruments used as such in that process.

(5) Reaction does not go to completion ; low yields are obtained . This was determined by comparing their obtained product yields to those reported in the literature. The second way this is determined is through monitoring the reaction and noting residual starting materials.

(6) Reaction does not produce any product . This problem type is of two forms: First, no reaction is observed; only starting materials were obtained after a given amount of time determined by the participant and research advisor. Second, a reaction occurred but labile products were obtained ( i.e. , decomposition of starting materials and products occurred); these labile products were unable to be separated and characterized. In both these cases, some variable associated with the reaction conditions led to the lack of formation of products or the decomposition of products.

(7) The reaction is not reproducible from literature accounts or previous research experience . When the reproducibility problem arose, the participant was either repeating literature procedures or their own procedures and was unable to get the reaction to occur or go to completion ( e.g. , achieve a similar yield as previously obtained).

Implications for undergraduate education

Problem-based learning “situates learning in complex problem-solving contexts. It provides students with opportunities to consider how the facts they acquire relate to a specific problem at hand” ( Hmelo-Silver, 2004, p. 261 ). The three problem types found in this study provide the context ( Jonassen, 2003 ) necessary for instructional designers to develop instructional problems centered on “authentic” problem-solving contexts ( Overton and Potter, 2008 ). The implications of each problem type on developing instructional problems will be discussed.

The analogous target, 2 , could be given as a viable multiple-step synthetic target appropriate for sophomore-level students; synthesis of target 1 is beyond the knowledge of a sophomore-level organic chemistry student. However used in a problem prompt, 1 and 2 should include a discussion on where the molecule, 1 , was discovered, the importance of synthesizing analogues in medicinal chemistry (if this has not already been presented), data on the biological activity, and references to appropriate literature articles discussing the target molecule. Some have attempted to include such societal applications in their curriculum ( Doxsee, 1990 ; Ferguson, 1980 ; Harrison, 1989 ; Kelley and Gaither, 2007 ); however, broad based adoption of this implication has not occurred in the organic chemistry curriculum.

Organic chemistry instructors give more “predict-the-product” problems than multiple-step syntheses problems ( Raker and Towns, 2010 ). Why? Because they are easier to grade? Multiple-step syntheses often have multiple correct answers that could complicate a rigid grading scheme. But, very seldom, if ever, do practising organic chemists recite their knowledge of chemical reactions as a canon of individual reactions. References materials are available to practising chemists that have a tangible organization of their knowledge ( Caruthers and Coldham, 2004 ; Gallego and Sierra, 2004 ; Li, 2003 ; Mackie et al. , 1999 ); however, each reaction unto itself is not the focus of achieving research goals. Multiple-step synthesis problems should become more of a focus in encouraging students to discover how the reactions, in combination, can and are used to synthesize complex target molecules ( Bhattacharyya and Bodner, 2005 ). Such a focus could help to alleviate the perception that learning chemistry is “an enormous and onerous chore” of memorization ( Hendrickson, 1978 ).

Day-to-Day problems

Knowledge of infrared (IR) spectroscopy , mass spectrometry (Mass Spec), and nuclear magnetic resonance (NMR) spectroscopy taught earlier in the course can then serve as a foundation for posing problems where students are to discover the formation of unexpected products or impure starting materials and reagents. For example, Fig. 2 shows a two-step reaction and final product 1 H NMR data.

A student would be asked to confirm if the product was or was not obtained. The product shown in Fig. 2 was not obtained. The spectroscopic data (and knowledge of hydrohalogentation reaction mechanisms) should lead a student to conclude that tert-pentylbenzene was the obtained product; in other words, the intended intermediate, 2-chloro-3-methyl-butane , was not obtained. (This problem has been pilot-tested with sophomore-level organic chemistry students who were able to successfully generate solutions.) This type of problem reaffirms the role data has in understanding chemical reactions while providing students with real life experiences of how the chemistry they are taught is utilized.


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Organic chemistry

Organic chemistry is the study of the synthesis, structure, reactivity and properties of the diverse group of chemical compounds primarily constructed of carbon. All life on earth is carbon-based, thus organic chemistry is also the basis of biochemistry. The ability to form compounds containing long chains of carbon atoms is the basis of polymer chemistry.

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Catalysis Catalyst: Synthetic Organic Chemistry as a Force for Good

K.C. Nicolaou is currently the Harry C. Olga K. Wiess Professor of Chemistry at Rice University. He previously served concurrently as the founding chair of the Chemistry Department at the Scripps Research Institute and a Distinguished Professor of Chemistry at the University of California, San Diego (1989–2013). His research activities focus on the discovery and development of new synthetic strategies and technologies and their applications to the total synthesis of natural and designed molecules of biological and medical importance. He is a co-author of the Classics in Total Synthesis series (I–III) and Molecules That Changed the World .

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