Tuesday, September 21, 2021

My Experience with Column Chromatography.

Column chromatography (Silica or alumina) is one of the conventional methods, globally accepted for purifying of different class of organic compounds. As everyone is aware of, it includes glass column, silica or alumina stationary phase, eluting solvent mixture with different polarity. I have some interesting experience with this purification technique in my professional career, that I am going to share in this write-up.

Although my first experience with column chromatography was in my master course, but that was just for training/education purpose, where in I had little chance to learn or experience much.

Till now, I worked in almost seven professional research laboratories and among them, six laboratories I worked were pure organic synthesis labs (Including academic and industrial). Every time I joined the new laboratory, I have to face new challenge as the method followed in each lab for this technique was totally different. In the first laboratory (Bharavi), where I first got the professional experience, the method used was, for 1 g crude material 10 g silica was standard and if the spots are very near on TLC, for 1 g crude material 20-30 g silica. But the particle size of silica usually used was 60-120 mesh. Based on the quantity of silica used, column width and length was considered giving enough space for solvent above silica bed. My second job at NCL, Pune was again different from first one. Here the diameter of column was main factor. For 1-2 g crude, column dia should be 2-3 cm and length approximately 30 cm. For 5 g and above, the dia should be 10 cm, etc. Here again, the silica particle size was 60-120 mesh. Then I moved to Japan for PhD course at Nishino Laboratory at Kyushu Institute of technology, headed by Prof. Norikazu Nishino. He was typical Japanese Professor, very particular about the techniques and methods. He made a rule that, we have to use formula of volume of cylinder to measure the amount of silica, where in diameter and heights were variables based on quantity of crude material. So, we used to measure the silica quantity in ML in conical flask based on calculation. Here also for normal separation 20 cm height and for critical separation 30-40 cm height. Diameter again was same as in NCL, method. Here since the compounds were amino acid and peptide based polar compounds, dichloromethane and methanol were usual solvents, but silica particle size was fixed as 230-400 mesh. After finishing PhD from Japan, I moved to USA to work as postdoc in Holton laboratory at Florida State University. Here, like many US laboratories, Prof. Holton made an SOP of Flash column chromatography to purify the compounds. Obviously, the solvent selection was based on polarity of molecule (Hexane/Ethyl acetate or DCM/Methanol). Flash here means, silica particle size should be 230-400 mesh and slurry should be made in solvent mixture which give 0.2 Rf value for desired spot. Once the crude is made slurry by adsorbing on silica, it is loaded on stationary bed and then pressure is applied from top using nitrogen, so that the column should complete maximum in one hour. After moving to second postdoc at Kyushu Institute of Japan again to work in Hayase laboratory. In this lab, I had some freedom to follow my own method, as I was the senior organic chemist there. We here were working mostly on planar conjugated dyes, so there was possibility of forming aggregates, hence separation was tedious. I mixed up all my previous experiences and adopted my own method by using 230-400 mesh silica particle size and 30 cm length column, using DCM/Methanol solvent mixture (Polar compounds), but only difference is, I failed to make slurry for these dyes in silica, so I used to dissolve the crude in minimum DCM and load on stationary bed and drain. I also used to apply pressure if needed using nitrogen gas. Having spent in those previous labs, I returned back to India and started my industrial career in reputed MNC, Sigma-Aldrich (Now Merck), I again have to face new method of column technique which was as per SOP. In industries, following SOP is mandatory and its matter of compliance. Here, although the methods were somewhat matching some or other previously learnt methods, but difference here was, we use to use 250 ml, 500 ml, 1 lire and 2 liter columns volume based on the quantity of crude material and height was normally 30 cm. Since most of the compounds were moderately polar, dealing with hexane and ethyl acetate was routine business. Rarely we used to use DCM/methanol solvent mixture (Particularly for acids, amides etc). Although majority of us used 60-120 mesh particle size silica, but there were some fascinate people with lots of patience, who used to use 230-400 mesh particle size silica, with pressure applying from top by nitrogen gas.

Column chromatography, theoretically works on same principle (Adsorption and polarity), but every lab I joined gave me different experience, due to different technique practiced in that particular lab. In one lab, if silica is measured in grams, in other lab it was measured in ML. Height of the stationary phase was dependent on space between spots on TLC. If one lab followed gravity column, others followed pressure column to save time. Whatever may be the technique practiced, the purpose was same, that is purifying the compound to achieve highest purity.

To conclude with, what I can say is, column chromatography although looks simple, but there is no fixed method followed globally. It is a lab specific method, and purely depends on individual skill set. Every lab follows that particular skill set, that is comfortable to purify the compound. Not only column chromatography, there are many such techniques followed in organic synthesis labs, which as purely skill based, which makes organic chemistry interesting experimental science.

Friday, June 4, 2021

Total Synthesis: A topic of choice for PhD

The doctor of philosophy, in short PhD, is the highest academic degree considered globally, which involves completion of a set of tasks as per the regulations of particular University. To begin with, choosing a right topic for your PhD dissertation is one of the fundamental tasks. The topic one chooses should be unique, different and realistic, having tremendous research scope for one’s future career. Usually it is advisable to go through previous research records of that particular research group such as theses, research reports or publications and frame a research topic that is continuation of unsolved or partially completed previous research problem. There is also chance that the supervisor may design some interesting topic for you, that may or may not relates to his/her ongoing funded research project. Overall, it is critical step on PhD course.

When it comes to Organic chemistry, there are multiple career options post PhD. So the choice of a research topic should be in such a way that, it should be a foundation for diverse career options, giving wholesome training of 4-5 years to improve skillsets and theoretical knowledge of the graduate student. In that sense, Total synthesis of natural products can be considered as the great choice of topic. As it is known that total synthesis of natural products is a complete synthesis of natural products which are known to be complex molecules bearing chiral centers and diverse functional groups. Considering a natural product molecule and working on its total or partial synthesis not only gives the knowledge about retrosynthesis, but also it gives exposure to handling various reagents, catalysts, bond formation/bond breaking reactions, functional group transformations and also gaining experience in performing several named reactions. Starting from designing a synthetic route on a paper to setting a reaction to isolating and purifying the product, there are n-number of important steps and techniques that one needed to get trained, if he/she wants to make career in organic chemistry. In other words, natural product synthesis is the plethora of knowledge as per as organic synthesis is considered. Therefore, when one comes out after finishing the PhD course in this core topic, he/she will gain a complete training package of both theoretical and practical aspects of synthetic organic chemistry, which is basic need for both academic as well as industrial career. Having obtained with this basic training, one can easily move to different applied research areas of organic chemistry, if one desires to go for Postdoc or as faculty or as industrial chemist.

Saturday, December 5, 2020

Industrial jobs: Understanding the needs and nature of work

Career hunt is one big nightmare after academic training. May it be MSc or PhD or Postdoc or any related training course, at the end of every academic course, the question triggers our mind is, “I am done with it, now what is next??” 

Fortunately, chemistry is one subject, where in there are multiple options, when it comes to choosing career after completing academic course. I am sure many of you are near to the ending your PhD and are in same ambiguity about future. After PhD, some of you may be planning for a Postdoc training. Again, there may be multiple reasons to choose postdoc job. It may either be as need for academic job or for added exposure to become independent researcher or just because you didn’t get an industrial job, so thought of doing postdoc and then trying for moving to Industry. Some may be planning to join academia after PhD. Some of you after 4-5 years of rigorous training with acquired skills in your PhD and now must have decided that, you are fit enough for industrial job, so deliberately trying an industrial position. Same ambiguity will surpass your mind even when you are concluding your Postdoc career. If everything goes well, you may end-up in an academic position, for which you spent 2-3 years of time as postdoc. But if that didn’t happen then again you will start thinking what to do and one option that may drag your attention is Industrial job. Now you are more trained than MScs or PhDs, because you have spent some extra years as an independent researcher, you worked on the problems that you proposed, independently wrote papers, presented your work in conferences. So, definitely you will think, now I am more experienced and good asset for an industry, I can independently handle projects/teams and etc etc. 

Excellent!! All that you thought is perfectly fine. Now, let me share some of my own views, which may be helpful, if you are stepping towards for industrial job. Again, there is nothing compulsory that what I am telling is ultimate truth. 

You may be an MSc or a PhD or a Postdoc, gained enough experience/training in your academic course and now trying for industrial job. All that you gained is fine and perfectly acceptable, but my friends, when you step into an industrial job, you are again a fresher as per the requirements of this job, because industrial job is a different ball game. There are hell number of things that are completely different from what you learnt in academia. The very first difference I can quote is the TARGET. In academia, it is either your supervisor or the scrutiny or you yourself may set the target to work on it and it is lead time is flexible based on circumstances. But in industry the biggest challenge is, it is the Customer, who gives you the Target, with tight lead time. You have no other option, than to commit to the target and to meet it in given lead time without any fail. Because, your customer who gives you target has options and those options may be your competitors, so you have threat of losing the business to your competitors. You will hear many new terms such as times lines, lead times, KPIs (Key performance indicators), KRA (Key result areas), commitments, deliveries, performance and many more. There will be hell number of documentation processes and filings, quote makings, managing enquiries, client interactions, modes of reports writing, presentation of results at inter/intra department or at client levels. 

Basically, industrial jobs are skill-based professions and your performance is evaluated based on how efficiently you reach the target in given time, maintaining timelines through proper planning. Your role as a team player and sometimes as individual contributor will be monitored in any project you are working. Therefore, all that you acquired in academic course will not be enough to be considered, hence you need a training again after joining as a beginner to become familiar with the nature of industrial job and also to understand the roles/responsibilities. You may be from premier university/institute, worked with big named Professor, published great papers, but as I told, it is the skill based job, you may confront with the situation, where you have to report to one of your colleague, joined several years before you, having more skills or experience, but less graduate than you. Your number of papers, conference presentations or novelty of your research work hardly matters in industry. You may have worked in particular research area, but here there is nothing like specific and you will be given projects from various areas having different applications. Overall, let you be junior, senior, team player, individual contributor, manager, boss, but as a whole this is a Team game, where everyone has to work as a team in broad sense for fulfilling customer needs, revenue generation and overall growth of business. That’s how your job and companies growth prosper to next level year by year. 

The journey of life takes many turns and many times we fail to notice. We dream of something and something else happens, that is what life is all about. In today's competitive climate, when the secure jobs are lacking, to be successful is all about having the strong drive to push forward even when you are struggling. There is nothing wrong in choosing Industrial profession. Like many jobs, industry is also a great and challenging place to work with passion and learning. There are huge opportunities to grow professionally and financially. 

As a concluding remark, your PhD is simply a training course to make you a professional researcher. It opens up the gate for the research career. In broad sense all these PhDs, Postdocs are simply stages coming in the huge canopy of research profession. You may aim for academic career or industrial life, but for both options PhD is the first stage. Postdoc training is necessary when you opt for academic career. Otherwise it is not helpful in anyway, if you seriously think of moving to industrial job. Postdoc will simply delay your professional growth in industry. At the same time, I can not deny that recently for few industrial jobs such as discovery CROs postdoc experience is being considered as an added asset. There are also complaints regarding industries asking experience. This is definitely a debatable topic, but if experience is really a need, you still can opt for trainee positions in many industries at lower wages for couples of years and thus can acquire industrial experience certification for permeant positions in Industry. It’s your life and you have to make decision. Therefore, choose the path smartly and understand the path completely, before making any decision.

Sunday, June 28, 2020

Modern and traditional medicines.

Modern Drug discovery has very much advanced with many new techniques to ease the process. With the evolve of computational chemistry, it became easier to simulate structures of drug target proteins and their binding affinities with small molecules and thus helping to design new library of molecules. X-ray crystallographic studies are yielding the structures of target proteins and their active sites. Sequencing the genetic codes of micro-organisms such as viruses, giving the information about microorganism’s DNA/RNAs and related proteins. Based on these techniques, process of target validation, new molecules library design, their synthesis in thousands of numbers and finally are screened for their inhibitory activity against target protein through in-vitro and in-vivo methods. Among thousands of screened molecules, few may hit as lead compounds for animal study. Then phase clinical trials, ADME, FDA approval and finally commercialisation. 

Now, if we trace back the history of drug discovery process, when there were no such modern techniques, majority of new drugs discovered were the bio-active molecules isolated from crude plant extracts, algae, fungi etc. whom scientists either discovered through serendipity or by thorough screening of crude plant extracts, which were given to patients in traditional medicine system. Until Quinine alkaloid was discovered as bio-active molecule present in Cinchona bark extract, this extract only was given as medicine for treating Malaria. The extracts of Taxus brevifolia plant were believed having anti-cancer activity, until people discovered the bio-active molecule Taxol was main content of this extract, which has potential to arrest mitotic cell division in tumor cells. The anti-inflammatory drug Aspirin was once isolated from Spiraea ulmaria herb. Penicillin, the first antibiotic drug, which ruled the world for decades, was first extracted from a Fungi.

Historically, every country, culture and civilisation in some or other way had practised traditional therapeutic system by using crude extracts of many plants and their parts by trial and error base over generations. Let it be European traditional medicine, Chinese herbal treatments, Persi-Arabic Unani medicinal practice, homeopathy Or our Ayurveda, all these systems were dependent on herbal resources.

Agreed that Ayurvedic medicinal practices does not fit into modern drug discovery processes, as this method lacks data to establish drug-target interaction and many more, but at the same time one cannot ignore that those herbal medicines made from crude extracts of many medicinal plants do have the biological activities. We never know, there may be treasure of bio-active molecules present in those medicines/extracts. Therefore, a thorough investigation of those extracts/medicines to dig out what bio-active molecule is present in them, which is responsible for pharmacological property. Some countable number of natural product chemists such as Prof. Sukhadev, have worked in this line. Still more and more efforts should be made to do research on these Indian traditional medicines to discover many hidden novel molecules that in future may be cure for many diseases.

Wednesday, October 3, 2018

Are the breakthroughs in fundamental chemistry being recognized??

The Royal Swedish Academy of Sciences announced award of NobelPrize in Chemistry-2018 with one half to Prof. Frances H. Arnold for her discovery on "Directed evolution of enzymes" and the other half jointly to Prof. George P. Smith and Sir Gregory P. Winter on the "Phage display of peptides and antibodies". As usual it was disappointing to not that none of them were from fundamental chemistry field.

Since last 4-5 years we are seeing a trend that the Nobel committee is giving more preference to multidisciplinary research outcomes over hardcore chemistry. But at the same time, we also can not agree to the fact that there were no breakthroughs in fundamental chemistry in fast decade, which can be taken into account for the highest academic award (Nobel prize) nominations....…

I simply don’t understand………
  • Why Holton-Nicolaou-Danishefsky combination didn’t get recognition by scientific community for their work on the famous anticancer drug Taxol and its Total synthesis.
  • How come people didn’t see the groundbreaking research on Organic_dye sensitization of Nanoporous TiO2 semiconductors by Gratzel-Honda-Fujishima combination.
  • What made the intellects to not to nominate the invention of Flow_Chemistry and its industrial applications.
  • Why the great discovery of versatile Metallo-organic stable pigments such as Porphyrins and Phthalocyanines didn’t get recognition at global level for their enormous applications in wide variety of areas such as Photo dynamic therapy (PDT), material science, molecular imaging etc.
I still can list out some more of them and these were definitely the globally recognizable breakthroughs that opened the plethora of doors…Surely there is something missing among scientific community in chemistry discipline to honor and appreciate such breakthroughs........I am simply ambiguous to know what is that reason that is rendering the scientific community to appreciate the research outcomes from their own subject of interest.......

The question is left to readers......


Thursday, October 5, 2017

Nobel Prize to Organic Chemistry: Decreasing Frequency

Today, on 4th October 2017, the Royal Swedish Academy of Sciences announced the Nobel Prize for Chemistry. I was eagerly waiting to see any name from Organic chemistry field, but got disappointed as this year also no prize for hardcore Organic chemistry.

The Nobel Prize in Chemistry 2017 was awarded to Prof. Jacques Dubochet (University of Lausanne, Switzerland), Prof. Joachim Frank (Columbia University, New York) and Prof. Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, U.K.) for their extraordinary contribution to the developing of Cryo-Electron Microscopy for the high-resolution structure determination of biomolecules in solution. Many congratulations to all of them for their hard work and recognition and also felt happy to read more about Cry-Electron Microscopy technique.

If we trace back. since last seven years, no one from pure Organic Chemistry area got Nobel Prize. Recent one in the year 2010 for Palladium chemistry in Organic synthesis for Heck/Negishi/Suzuki and prior to that one in the year 2005 for Alkene metathesis to Chauvin/Grubbs/Schrock team and in 2001 for Chirally catalysed hydrogenation reactions to Sharpless/Noyori/Knowles team. This simply means, the frequency of getting Nobel prize in Organic chemistry is reducing, although there being many deserving Organic chemists worldwide. One reason could be, the current research trend of organic synthesis area is not matching with changing selection criteria of this highest scientific award.

We Organic chemists may claim of being the only applied discipline among other disciplines of Science, producing huge number of molecules having vast applications from biotech, pharma to material science areas. We have many deserving Giants in Organic chemistry field, who are famous for Total synthesis of complex natural products, new reactions/method development, synthesis of novel applied molecules etc etc., but when we see research areas of award recipients in recent past, it brings the feeling that we are far away from current day trend and it is a kind of warning too.

Just simply making new chemistry or molecules is not enough. There seems to be an immediate need for changing the trend and research focus. Today, the research outcomes that have INTERDISCIPLINARY FLAVOR, bearing significance to solving the REAL WORLD PROBLEMS are having more recognition in Scientific society.....




Monday, October 2, 2017

On The 10th Anniversary Of My PhD Degree Award Day.

On Sept. 30, 2017 exactly 10 years passed I got the PhD degree awarded at Kyushu Institute of Technology, Japan. In other words it is the 10th anniversary of my PhD degree. I celebrated that special day on social media and in that excitement I wrote a refreshing mail to my supervisor. As he is now 70 years old retired Professor, spending most of his time at home, easily available for interaction, replied quickly with happiness and full of regards wishing better future. It is very special day as it was one great milestone of my life.

Yes! It was my dream and ambition to pursue the highest academic degree, the PhD in Organic chemistry discipline. I could have taken some gap to pass CSIR-JRF exam and directly enter the course, but situations were not in favor of me. Therefore, I chose to work after M.Sc. While continuing my job, I kept on chasing my dream for which I gave a big fight. I knocked many doors, wrote mails, contacted many people, begging for admission to doctoral course. Later I got entry to NCL Pune, for which I must thank some of my friends/well wishers. Here again one more hurdle came, as the administration cancelled the policy of applying for SRF after working as RA for 1-2 years and made CSIR-JRF as compulsory requirement. Then, I had only one option left is to try for PhD abroad, which many of my colleagues were trying. I too followed the same process by taking guidance of my reporting scientists at NCL, Pune. On one fine day, I got admission for PhD at Kyushu Institute of Technology, Japan under the supervision of Prof. Norikazu Nishino. On 3rd October, I flied to Japan and started my dream course. Those three years of PhD course were hardest in my life. I worked very hard as it is culture in Japan. I still remember those sleepless nights, the toughest boss and his hard training. Published some papers and also presented my work in some conferences at Europe (Poland) and Tokyo, Japan. Finally after successfully defending my thesis work, I got awarded the PhD degree. That’s how I achieved my GOAL and I have to thank many of my friends and family who directly and indirectly helped and supported me in many ways.

Like a usual doctorate, I too carried out two Postdocs for more than five years. The first Postdoc was at Florida State University, USA, spending two years in the laboratory wherein Taxol synthesis was made a history. For second Postdoc, I again moved back to KyuTech, Japan to work for three years in the emerging area of solar cell research.

Having spent almost eight and half years in academia in abroad, acquiring vast experience in various research fields of interest, I decided to return back to my home land India. I dreamt of a career where in I will have enough freedom and flexibility to do what I want to do. As there is a saying that, “Sometimes reality becomes the strangest fantasy of all”, I found getting into my desired job was not so easy. Huge competition, need for papers published in top-tier journals, less number of openings and many more. For time being I dropped the idea of joining academia and thought of opting for other alternative paths where my training/skills can be explored. Finally the destiny brought me to the Industrial world and I started my career in the corporate organization as Scientist, nature of job being custom synthesis and contract research.

Industrial jobs are totally different from academic jobs. Here you don’t need multiyear Postdoc experience or more number of publications etc. Industrial jobs mainly need how skilled/trained you are to reach the target in given time. Maintaining timelines, meeting targets, planning, results and more importantly how efficient you are as a team player and as individual contributor are the crucial requirements in any industrial jobs.

Now when I look back and ask myself, what was purpose behind doing PhD, I usually get confused what to answer. I am also unable to answer, whether I really explored all the experience and trainings to bring them to reality. The journey of life takes many turns and many times we fail to notice those turns. We dream of something and something else happens, but that doesn’t mean one has to give up ones passion, the goals, and the ambitions. In today's competitive climate, when the secure jobs are lacking, to be successful is all about having the strong drive to push forward even when you are struggling.

I always receive many mails from future aspirants asking for guidance for joining PhD course and also information about Postdoc jobs. To all of you I can tell only one thing that, PhD is not a degree, it is a training course to make you a professional researcher. It opens up the gate for the research career. In broad sense all these PhDs, Postdocs are simply stages coming in the huge canopy of research profession. You may aim for academic career or industrial life, but for both options PhD is the first stage and without PhD further journey will not continue. Postdoc training is necessary when you opt for academic career otherwise it is not helpful in anyway. Also moving to industrial job after Postdoc will simply delay your professional growth in industry.