Justification
The narrative of the young chemist is a first of its kind approach to the organic chemistry laboratory. The idea for writing this narrative was born from the observation that many sophomore level organic chemistry students were not reading the pre-lab material before coming to lab. I wanted to create something that would pique the interest of my students so that they would look forward to reading the weekly experimental handouts. The narrative of the young chemist is broken up into nine installments and each installment is related to the technique that is to be learned for that week. The serial nature of the stories is critical because the students do in fact anticipate the weekly experimental handouts, and they are reading the experimental handouts in preparation for the lab. The interesting thing about this narrative is that students who are actually enrolled in the organic chemistry course strongly relate to the young chemist. Organic chemistry students understand firsthand how the journey through this course is challenging and that they must persevere and endure even in the face of great trials. However, as is noted in the narrative of the young chemist, he was never alone; a mentor was always there to teach and to encourage the young chemist when the road seemed impassable. Similarly, organic chemistry students have faculty who will encourage them to keep pressing on and will offer assistance when appropriate.
Description
The narrative of the young chemist describes the journey that is traveled by an ambitious young student who desires to learn classical and modern techniques germane to the field of organic chemistry. The story begins with the young chemist learning how to recrystallize an organic solid and then covers a range of techniques that include extraction, distillation, and column chromatography. Along the young chemist’s journey he meets individuals such as Extractor, Distiller, and Purifier who become the young chemist’s mentors. The antagonist of the narrative is Examiner who takes pleasure in trying to derail the young chemist’s journey. Throughout the young chemist’s journey he experiences great joy when a new technique is learned or an “exam” is passed, but he is also stung by the harsh reality of isolation and loss. However, hope is ever-present even when it would appear that the Examiner has won; the young chemist relies on the knowledge that his mentors have taught him while knowing that his mentors are never too far from him.
The Journey of the Young Chemist
Chapter 1
As the aspiring young chemist embarks on his journey through organic chemistry to discover the principles and time-honored traditions of the discipline, he knows that recrystallization is the first technique that he must master. Recrystallization is the purification of a solid organic compound and it is an extremely powerful and artistic technique. The young chemist will need to determine the optimal recrystallization solvent system and the appropriate amount of that solvent system in order to successfully complete this technique. Throughout the ages it has been taught that too little solvent will prevent the material from being purified, and too much solvent will prevent the precious organic solid from being recovered. Recrystallization will not only challenge the young chemist to develop chemical intuition, but it will be the first chemical tool in his “synthetic toolbox.” Mastery of recrystallization will enable the young chemist to tackle the myriad trials that await him on his arduous journey.
Chapter 2
With the recent completion of recrystallization still in his memory, the young chemist presses on with singular focus to gain knowledge from those who have developed synthetic tools and techniques. Upon entering the city of Ordo ab Chao, the young chemist is reminded of the stories told about a man called Extractor. It was said in these tales of old that this man could pull the essence from matter; that molecules would abandon the shelter of organic matter to be held in the hands of Extractor. As the young chemist approaches the outskirts of the city, he spies a figure that resembles nothing more than a mere shadow sitting by an old fire. The naïve young chemist marches boldly over to the shadowy figure and holds out his hand to introduce himself. As the ancient hand of the figure, hidden by darkness, touches the hand of the young chemist, visions appear before his minds’ eye that display molecules crying out from green mosses, sea sponges, mold residing on tree bark, cave-dwelling microorganisms, and seeds. Still recovering from the shock of this recent event, the young chemist is confident that this wraithlike figure holds great secrets of old science. Then all of a sudden, the young chemist is filled with great trepidation as he realizes that the hand he now holds belongs to Extractor. Before the young chemist could force words from his mouth, the figure behind the darkness expunged the tension by saying, “Sit young Master, there is much to learn.” Extractor told the young chemist that interesting molecules have been hidden throughout nature. He told of molecules isolated from mold that can cure infection, and of molecules extracted from the venom of snails that can paralyze and kill grown men. The young chemist asked how he knew about these molecules, and Extractor told him that he had developed a technique, fittingly known as extraction, that could extricate molecules from biological sources. Extractor told the young chemist that he would teach him how to perform an extraction because he knows that the young chemist will need this technique as he continues on his journey. Command of extraction will provide the young chemist with another tool for his “synthetic toolbox” and it will allow him to address the difficulties that certainly await him on the road ahead.
Chapter 3
As the young chemist considers his recent encounter with Extractor and the powerful techniques that he has now added to his “synthetic toolbox” he sets off for the Opscurum Spelaea where the townspeople say lives a reclusive man that can manipulate matter in the liquid state. Standing at the mouth of the first cave the young chemist lights his torch and begins the rapid decline into the bowels of the Earth. After a long, arduous walk the tunnel eventually led to a central area where the smell of harsh, volatile gases and extreme heat nearly overtook the young chemist. As he looked closer, he noticed a large alembic that sat atop an even larger copper cucurbit that was positioned above an open magma pit. The narrow mouth of the alembic was carefully placed over a relatively small receiving flask that contained a clear and colorless liquid. As the young chemist comprehended the entire space he failed to notice the figure that had been lurking behind him. When the figure was within arms length of the young chemist, he placed a hand on his shoulder, which made the young chemist recoil in fear. To pacify the young chemist, the figure made it clear that he was not a threat and that he had been waiting for him for some time now. “Who are you and how could you be waiting for me?” snapped the young chemist. A few moments later the figure simply stated, “My name is Distiller and I have heard that you are on a journey to discover the secrets of those who have developed techniques for the manipulation of matter. I know that you have learned how to separate complex mixtures and purify organic solids. I also know why you are here and what you desire to learn from me.” With all pretenses rapidly fading away, the young chemist asked Distiller if he would teach him how to identify an unknown liquid and how to separate a mixture of liquids. Distiller agreed and immediately turned towards the magma pit in the center of the cave, and then informed the young chemist that he would be learning how to distill organic liquids. The addition of distillation to the young chemist’s “synthetic toolbox” will equip him with a very powerful technique for identifying and isolating components from a mixture of liquids.
Chapter 4
Now that the young chemist has learned how to utilize simple distillation as a means of determining the identity of an unknown liquid and separating volatile organic liquids from non-volatile species, he is ready for his second lesson on distillation. Distiller tells the young chemist that there are times when the components of a mixture of organic liquids will have very similar boiling points and it will be impossible to use simple distillation to perform the separation. He explained that the number of vaporization-condensation cycles that occur during a simple distillation are not enough to efficiently separate these components. Therefore, to increase the number of vaporization-condensation cycles, the surface area between the cucurbit and the alembic must be increased so that the two components can be efficiently separated. As the young chemist listened, Distiller walked over to a cabinet at the far end of the cave and pulled out a tall, tubular column that he subsequently placed between the cucurbit and alembic utilized during the recent simple distillation. He then poured a complex mixture of volatile liquids into the cucurbit and then positioned the entire apparatus over the magma pit. “As you shall soon see for yourself young Master, the components within this mixture will separate as they move up the fractionating column, and each of the components will be collected as pure species,” stated Distiller. The addition of fractional distillation to the young chemist’s “synthetic toolbox” will allow him to efficiently separate a complex mixture of volatile organic liquids.
Chapter 5
As the young chemist considers the new techniques that he has learned to manipulate matter in the liquid state, he is confident that he will be able to separate all mixtures of miscible volatile organic liquids. While the young chemist reflects on his recent successes, Distiller suggests that it is time to learn the third and final lesson on distillation. “What could I possibly learn about distillation that I don’t already know?” questioned the young chemist. Distiller laughed at the young chemist’s naivety and stated, “Along your journey you have been told that molecules have been hidden throughout nature, and that many of those molecules possess interesting properties. I have perfected a technique, developed by the Ancients, that can manipulate these organic molecules and separate them from their natural sources.” With his curiosity piqued, the young chemist asked Distiller to teach him this new technique. Distiller agreed and said, “Inside this spearmint leaf is a molecule called carvone, and I would be hard pressed to isolate this molecule through a means other than this new technique. If I heated the leaves alone and tried to distill carvone it would burn and decompose. To avoid this disastrous end, you must employ steam distillation because it will coax the molecule from its shelter in the leaf and co-distill with water at 100ºC, which is much lower than the actual boiling point of pure carvone (231ºC).” As the young chemist took all of this information in, Distiller emptied a sack filled with spearmint leaves into his very large cucurbit and added two buckets of water. The cucurbit was then positioned over the magma pit and the generation of steam quickly started and the young chemist waited with great anticipation to observe the isolation of carvone from the spearmint leaves. The addition of steam distillation to the young chemist’s “synthetic toolbox” will allow him to gently separate high boiling liquids from non-volatile sources.
Chapter 6
With his recent successes in learning how to manipulate matter in the liquid state the young chemist confidently marched from the mouth of Distiller’s cave and set off on his journey. The young chemist headed north to the Land of Purgatio, which meant that he must travel through Eremus and then Lustrum. The young chemist knew that his knowledge and skills to survive would be challenged as he ventured through these barren and deadly lands. The sun was still rising in the sky as he entered Eremus and all confusion as to why this particular name was given to the land was removed. Heaps of mangled metal and trash were scattered throughout the landscape and hot, noxious gases escaped with great force from massive holes in the Earth. Many hours had passed as he journeyed through this tormented land, when suddenly the landscape changed and the young chemist feared for his life. The ground crunched beneath his feet, the sun beat down upon his head, and the young chemist was confident that a drop of water would not be found for one hundred miles…at least. Eremus was going to attempt to claim his life, but the young chemist pressed on with singular focus. Miles into his trek across Eremus the young chemist spotted what appeared to be an abandoned shed that was as isolated as it was disheveled. The young chemist approached the shed with great caution and looked for traces of recent traffic around the shed. To his delight the young chemist found nothing so he pushed open the door of the shed and was relieved as he stepped out from under the penetrating rays of the sun and into the cool shade of the shed. The young chemist’s relief was short-lived as he heard the click of the lock behind him, multiple candles were lit at once and he saw a cloaked figure standing across the room. The cloaked figure stood nine feet tall, had large bony fingers and eyes that were black as the darkest of nights. The young chemist shouted, “Who are you?” and waited for a response. He repeated this two more times until the cloaked figure let out a ghastly groan and stated, “I am Examiner.” He then gasped for air as he continued, “Here in this abandoned shed in the heart of Eremus your journey now ends.” The young chemist, certain that his life would soon end, begged Examiner not to kill him. As Examiner approached the young chemist, the door of the shed burst open and in walked Extractor with Distiller behind him. Extractor grabbed the young chemist by the shoulder to pull him out of Examiner’s reach and then stated with authority in his voice, “Examiner, have you forgotten the duties of your job or are you ready to vacate this position?” The presence of Extractor in the ever-decreasing space of the shed changed Examiner’s entire demeanor; he was no longer able to stand nine feet tall because he evidently feared Extractor. “My purpose is to test the abilities of young minds as they develop into mature chemists. I have heard how this young chemist has excelled in all that he has been taught, but he is too young to be here. I will not be made a fool by some child who clearly wants to flaunt his tricks!” said Examiner with poison in his voice. “Listen very carefully Examiner, you will test his abilities while Extractor and I observe the examination process,” stated Distiller sternly. Distiller and Extractor took the young chemist aside and informed him about Examiner’s test. “You have already proven to us that you are capable young Master, but Examiner is cunning. I am sure that you will be required to perform an extraction and a distillation during your examination, but first he will require you to transform matter,” explained Distiller. Extractor continued, “You must be able to perform a substitution reaction where an alcohol is converted to its corresponding bromo-compound. Although we cannot help you throughout the examination process young Master, Distiller and I will remain right here.” As the young chemist approached the dilapidated table in the middle of the shed, he shot a glance at Examiner and then took a seat at the table. Examiner then exclaimed, “If you are unsuccessful in performing this elementary test young chemist your journey will come to an abrupt end.” As the young chemist begins his first examination, he will need to remember all of the information and techniques that he has learned throughout his journey. He must employ all of the tools that he has added to his “synthetic toolbox” if he wishes to complete this trial.
Chapter 7
Overjoyed by the successful completion of Examiner’s test, the young chemist jumped up from his chair at the table and quickly moved towards Distiller and Extractor to celebrate his outstanding accomplishment. The excitement of the young chemist had sickened Examiner, which prompted him to quickly exit the shed and head north. Distiller and Extractor patted the young chemist on the shoulder and Extractor proclaimed, “You have mastered all of the techniques that you have been taught, and you possess the makings of a skilled chemist! We never doubted your skills for one moment young Master.” Distiller continued, “There will be challenges ahead, but we are certain that there is nothing that you cannot accomplish. A second exam awaits you in Lustrum, which will test your ability to perform an elimination reaction. You must once again apply all of the knowledge that you have gained over these past many weeks to this second exam. We will meet again young Master, but until then…take care.” Distiller gave the young chemist two canteens filled with water and told him to drink sparingly because it would be just enough water to get him to Lustrum. The young chemist said his goodbyes to Distiller and Extractor, and with haste he left the abandoned shed in the heart of Eremus. The young chemist had walked for many hours and was beginning to think that he would not reach Lustrum alive when all of a sudden he noticed what appeared to be green clouds sitting on the horizon. As he continued on his journey north, it became abundantly clear that the “green clouds” were not clouds at all, but were actually the Towering Timbers of Lustrum. The young chemist finally reached the border that separated Eremus from Lustrum and was speechless at the sight of these magnificent giants that towered over the land. He breached the border and made his way into the cool, damp shelter of Lustrum. It had not been more than an hour into his journey through Lustrum when the young chemist realized that something or someone was following him. Not regarding the presence of his newly discovered “companion” the young chemist pressed on through Lustrum. A few moments later, the young chemist heard an alarming crack that jarred him to his core. A quick glance over his shoulder allowed him to identify the source of the noise and to then escape the imminent harm that was about to befall him; one of the giants of Lustrum had broken in half and was intent on making the forest the young chemist’s final resting place. The young chemist was understandably shaken by this recent event, but as he surveyed the aftermath of the fallen tree he was filled with an overwhelming sense of terror. The two ends of the fractured tree possessed no jagged edges or splinters; the tree had been cut cleanly through from one side to the other. The young chemist, now filled with a sudden sense of impending danger, began to run. After running for some time, the young chemist stumbled upon a tiny house in the middle of Lustrum, and upon further inspection he observed that the house was actually the stump of a large tree that had been carved out and fashioned into a modest dwelling place. Furthermore, the roof of the house was covered in a thick, green moss that blanketed the stump in a comforting manner, and in the middle of the roof was a stone chimney that exhaled a steady stream of white smoke. The young chemist, weary from his recent examination and subsequent journey that nearly took his life, decided to march into the house created from the stump of a giant tree. He sat down at the table in the center of the house and laid his head down to rest. Moments later, the young chemist was abruptly woken from his sleep when the door was forcefully flung open and Examiner made his way into the house. “So this is how the little genius spends his free time?” spat Examiner. “Well, I have a very busy schedule and you have an exam! You will not have your friends to support you this time chemist, and when you fail my exam I will make sure to let them know how poorly you performed,” continued Examiner. With the little energy that the young chemist had left he forced out the words, “I have been trained by the best and they are certain that I am made for greatness Examiner! I have studied and I have studied some more, and I am confident that I will pass your second exam. I am very tired Examiner so if you insist on testing me now, then please let’s begin.” With that, Examiner threw down the exam and hissed, “Good luck, you’ll need it.” As the young chemist begins his second examination, he will need to remember all of the information and techniques that he has learned throughout his journey. He must employ all of the tools that he has added to his “synthetic toolbox” if he wishes to complete this trial.
Chapter 8
With the successful completion of the second exam behind him, the young chemist quickly exited the tiny house in the center of Lustrum to put distance between himself and Examiner. Examiner had actually attempted to strike the young chemist as he completed his exam, so he was fairly certain that staying in the house would be problematic. The young chemist headed north toward the Land of Purgatio, which was his final destination in his journey to discover the secrets of those who have developed synthetic tools and techniques. He had traveled for many hours when all of a sudden the trees came to an abrupt end, and the brilliant white sand of Purgatio was all that he could see for miles. He stepped out onto the sand and continued his journey north in hopes of reaching the gates to the city before nightfall. As the sun sank beneath the horizon, the young chemist approached the city and was in awe of its beauty and splendor. The gates and every other structure in the city were white as bone, and the city appeared to glow as the moonlight reflected off of the buildings. Walking through the gates to the city the young chemist recalled a story that Extractor had told him about a powerful woman who lived in the Land of Purgatio that could purify all states of matter. The woman had developed a technique to purify impure liquids and solids by passing them through sand of Purgatio. Energized by the thought of learning this final technique the young chemist headed to the center of the city to look for signs of this woman. As he approached the center of the city a woman clothed in a sharp white suit grabbed his arm and told him to follow her. While being led by the arm to an unknown location the young chemist looked at his captor and observed that she was tall with sharp features and had brilliant white hair that was cut short. After a twenty minute walk to the outskirts of the city the woman released the young chemist’s arm and then told him that she had been waiting for him. “I just received the news of your recent examination and I am convinced that you are the next great chemist. No one has passed Examiner’s tests without making a single mistake, and most have had to retake the exam,” exclaimed the woman in white. “Who are you? How could you possibly know that I recently took Examiner’s tests?” questioned the young chemist. “My name is Purifier and your reputation precedes you young Master. I also know why you are here and I will certainly teach you the purification technique that I developed years ago,” stated Purifier. With introductions made, Purifier pulled a bottle from her jacket that contained a black oil; she then informed the young chemist that the oil was a complex mixture of organic compounds and would be impossible to purify using fractional distillation because the components of the mixture had identical boiling points. She set the bottle on the ground and then pulled what appeared to be a long, hollow glass cylinder from her jacket, which she proceeded to fill with sand that she had scooped up from the ground. She poured the black oil on top of the white sand in the glass cylinder, and then added a clear liquid to the cylinder that caused the black oil to travel down the column of white sand. “As the oil passes through the sand of Purgatio, the components will separate from each other based on their specific interactions with the sand. The sand is very polar young chemist; therefore, very polar compounds travel slowly down the cylinder while non-polar compounds move very quickly. The separation and purification of the mixture results as the components interact with the sand and the liquid that carries the components through the sand,” explained Purifier. The addition of this purification technique, known as column chromatography, to the young chemist’s “synthetic toolbox” will allow him to purify mixtures of organic compounds that exist in all states of matter.
Chapter 9
“He is dead,” cried Purifier. It was over in an instant; no one in the room, save Extractor, even saw Examiner pull the pouch of dark powder from his pocket.
One hour earlier, the young chemist was celebrating the successful completion of his first chromatographic separation utilizing column chromatography. Purifier was extremely proud of the young chemist and told him that she had never seen anyone perform such a perfect separation of such a complex mixture. “I stand in awe of you young Master. Most of us have only ever perfected one technique, while you have mastered every technique that you have been taught. Extractor taught you how to isolate organic molecules from complex mixtures, while Distiller taught you how to manipulate matter in the liquid state. Extractor is very proud of you young Master and he has been watching over you since he first met you in the city of Ordo ab Chao. He has regularly updated Distiller and me on your progress throughout your journey and he was the reason why we both expected your visits,” stated Purifier plainly. As the young chemist was about to respond, Distiller and Extractor walked through the front door of Purifier’s home. “My old friend, it has been too long,” stated Extractor as he embraced Purifier. “And how are you young Master? I hear that you have successfully completed Purifier’s chromatographic technique. I am very proud of you and of how much you have accomplished in such a short period of time,” exclaimed Extractor. The young chemist thanked Extractor and then began telling him about his journey since Eremus. “Examiner actually tried to strike me after I completed my examination in Lustrum. I really don’t think that I should be alone with him; I strongly believe that he will attempt to kill me,” explained the young chemist. “Well, you will have to see Examiner one more time young Master, because you have one more examination. The examination will be a chemoselective reduction of an aldehyde in the presence of an ester using a novel reducing agent. You will need to employ an extraction to separate the organic product from the inorganic reagents and then determine whether you need to utilize column chromatography to purify the organic product,” explained Distiller. Not one moment later, Examiner walked through the door of Purifier’s home. “If it is not the terrible young chemist and his mentors that so vigilantly protect him,” hissed Examiner and then continued, “I will not stay here longer than I need to; therefore, your exam will commence now.” The young chemist furiously worked through Examiner’s final trial and was sure that this would be the exam that he would be unable to pass. He envisioned the look of disappointment on the faces of Extractor, Distiller and Purifier once it was determined that he had failed his exam. These thoughts were quickly dispelled as Extractor stated, “No matter what the outcome of this exam is young Master you have already demonstrated to us that you possess greatness. You have nothing to prove to me or to the others. We are immensely proud of you.” With that the young chemist’s spirits were lifted and he pressed on with such intense focus that all of a sudden he realized that he was finishing up the final steps of the examination. Examiner shouted in anger as he scanned the young chemist’s results. He was absolutely livid that the young chemist had gotten a perfect score on his most difficult exam. Enraged by the recent events, Examiner practically ran from Purifier’s home. He knew that he would be unable to do anything to the young chemist while his three mentors protected him. Overcome with excitement and the reality of finishing his months-long journey, the young chemist broke down in tears as he fell to the floor. Purifier got to him first and held him in her arms. Distiller sat down beside them and said to the young chemist, “You completed your journey young Master, and we are so proud of you. You finished with such grace and humility. You certainly are made for greatness.” Extractor then looked down at the young chemist and said, “I am very proud of you young Master. It seems like only yesterday that we met on the outskirts of Ordo ab Chao and you were so unsure of your abilities. Although you had your doubts, I knew that you would complete your journey and become a truly skilled chemist. No matter where you go from here young Master, we will always be with you. We will be with you until your journey’s end.” As the newly minted skilled young chemist recovered from the emotions of his recent accomplishments, Extractor spied the cloak of Examiner waving in the doorway of Purifier’s home. Before Extractor could say a word, Examiner burst into Purifier’s home and threw a pouch filled with a dark powder at the skilled young chemist.
Examiner had already fled as Extractor lay lifeless on the floor of Purifier’s home. The black powder was actually Deathdust, and its intended target was the skilled young chemist; however, Extractor intercepted the deadly poison as he used his body to shield the skilled young chemist from its deadly purpose. The moment the pouch hit Extractor, the powder burst into the air and with deadly precision found Extractor’s lungs. He breathed his last breath before his head hit the ground. It was over in an instant.
“No, no!!” cried the skilled young chemist as he leapt towards Extractor. He fell down at the side of Extractor’s body and wept, for he knew that his mentor and friend was gone. He was never coming back. With tears streaming down her face, Purifier confirmed what Distiller and the skilled chemist already knew, “He is dead.” Enraged by the death of Extractor, the skilled young chemist stormed out of Purifier’s home to chase after the monster that had killed his mentor. As he exited Purifier’s home he tripped over a very large object that spanned the width of the front door. To the skilled young chemist’s surprise, Examiner’s lifeless body was discovered to be the obstacle at the foot of Purifier’s doorstep. Apparently, the Deathdust not only found Extractor’s lungs, it also found Examiner’s lungs when he threw the pouch in the direction of the skilled young chemist. “Come here young Master. You have been through enough today with the loss of Extractor,” stated Distiller plainly. Purifier continued by saying, “We will be leaving tonight after we have taken care of Extractor’s body.” That night the skilled young chemist and his two mentors embarked on a new journey and left their grief in the Land of Purgatio. For many years, they remained together and developed new synthetic techniques that gained extensive utility in the discipline. Eventually, the skilled young chemist parted ways with Distiller and Purifier to live the rest of his days in the city of Ordo ab Chao; the city where he first met Extractor and where his adventure as an organic chemist began. Some say that the skilled young chemist is patiently waiting for a “young chemist” to begin her journey into the field of organic chemistry so that he might mentor her as she travels along this arduous road in pursuit of the secrets of those that have developed new and novel synthetic tools and techniques.