Periodic Reporting for period 4 - ENCOPOL (Encoding information into polymers)
Reporting period: 2022-01-01 to 2022-06-30
Our society is quickly changing as a result of the new information technologies that have become available in the last decennia. Nowadays, we produce and process enormous amounts of digital data (~220 exabytes per month; 1 exabyte is 10exp18 bytes), which is expected to become even larger in the coming years. This flood of information is increasingly affecting our environment. For instance, the world data centers currently consume more energy (~420 terawatt hours) than a country such as the UK (330 terawatt hours) and, as a further example, the amount of energy that is required for doing 300 Google searches is equivalent to that of boiling 1 liter of water. It is evident that new approaches are needed to tackle the energy consumption and the problems connected with it (e.g. not enough silicon can be produced in the future to handle all digital information that has to be stored). Nature has already solved this data and energy problem during the long period of its evolution. Our brains can easily store and process some 2.5 quadrillion (10exp15) bytes, while the energy consumption is only 20 watt/ day.
In our ERC Advanced grant project ENCOPOL we are following a new approach and aim at developing technologies to write and store digital data on the level of molecules. That is, not writing onto hard discs but onto synthetic polymers in the form of chemical functions, e.g. epoxide groups. The latter groups can occur in two forms, which are each other’s mirror images, each encoding for a digit: (R,R)-epoxide = digit 1 and (S,S)-epoxide = digit 0. Our source of inspiration is the class of naturally occurring DNA polymerases, which make copies of DNA, also an information storing polymer: combinations of its 4 base pairs encompass information for the synthesis of specific proteins. The DNA polymerases are machines that glide along a DNA chain and while doing so, copy the DNA strand. Just like in nature we intend to use molecular machines, but now completely synthetic ones for the writing of chemical information onto synthetic polymers. Also the theoretical machine proposed by the mathematician Alan Turing for the construction of a computer provides a useful blueprint for the encoding of information on the molecular level. This so-called Turing machine can write, read, erase, and store information. It is composed of a tape head that moves forwards and backwards along a tape while printing the digits 1 and 0.
Our molecular machine is composed of a molecular tape head constructed from a manganese porphyrin cage molecule that can bind to a long polymer chain containing alkene double bonds and while gliding along it convert these double bonds into (R,R)- or (S,S)-epoxide functions in a controlled fashion, i.e. with the help of light. To this end a light-switchable Feringa motor is attached to the cage and the state of this switch eventually determines whether a digit 1 or 0 is printed.
In our ERC Advanced grant project ENCOPOL we are following a new approach and aim at developing technologies to write and store digital data on the level of molecules. That is, not writing onto hard discs but onto synthetic polymers in the form of chemical functions, e.g. epoxide groups. The latter groups can occur in two forms, which are each other’s mirror images, each encoding for a digit: (R,R)-epoxide = digit 1 and (S,S)-epoxide = digit 0. Our source of inspiration is the class of naturally occurring DNA polymerases, which make copies of DNA, also an information storing polymer: combinations of its 4 base pairs encompass information for the synthesis of specific proteins. The DNA polymerases are machines that glide along a DNA chain and while doing so, copy the DNA strand. Just like in nature we intend to use molecular machines, but now completely synthetic ones for the writing of chemical information onto synthetic polymers. Also the theoretical machine proposed by the mathematician Alan Turing for the construction of a computer provides a useful blueprint for the encoding of information on the molecular level. This so-called Turing machine can write, read, erase, and store information. It is composed of a tape head that moves forwards and backwards along a tape while printing the digits 1 and 0.
Our molecular machine is composed of a molecular tape head constructed from a manganese porphyrin cage molecule that can bind to a long polymer chain containing alkene double bonds and while gliding along it convert these double bonds into (R,R)- or (S,S)-epoxide functions in a controlled fashion, i.e. with the help of light. To this end a light-switchable Feringa motor is attached to the cage and the state of this switch eventually determines whether a digit 1 or 0 is printed.
In our ENCOPOL project we proposed two blue prints for an information encoding molecular machine: machine design 1.0 and machine design 2.0. With respect to the first blueprint: we managed to attach a chiral Feringa motor to a chiral porphyrin cage molecule via a spacer (chiral means that two mirror images are possible). This leads to 4 different species: two so-called diastereomers and for each of these diastereomers two so-called enantiomers. We were able to isolate each of the species separately and characterize them fully with the help of various physical techniques. They differ in the way the motor part is linked to the cage compound, some of them partly covering the opening that is present in the latter. Furthermore, we showed that the motor-porphyrin conjugates can thread onto a polymer chain and glide along it, one diastereomer moving faster than the other one. This is a first, very promising step in the direction of a molecular Turing machine that can write information. Detailed studies were performed to see what precisely happens when the motor-cage compound conjugate binds to the polymer tape and moves along it. The next step will be to combine the prepared chiral tape heads with chiral polymer tapes in order to allow the former ones to move in one particular direction along the latter ones, which is an important requirement for the encoding of information. After all, the writing should be in one direction and not a random process leading to the printing of random numbers or random words on the tape.
In machine design 2.0 the molecular tape head has a more complex architecture and consists of a two porphyrin cage compounds that are connected via a molecular linker. One cage compound provides the instructions for the writing process (again controlled by light) and the other one prints the information. The latter cage compound should be connected to a fast rotating Feringa motor, which now does not act as a switch, but as a pulling motor. In the past period we have made a series of double cage compounds and studied their behavior with respect to the binding to a polymer chain and the process of movement along the chain. Our experiments show that the double cage tape heads indeed can thread onto a polymer and move along it, which is a very positive result for the further development of this information encoding system.
In machine design 2.0 the molecular tape head has a more complex architecture and consists of a two porphyrin cage compounds that are connected via a molecular linker. One cage compound provides the instructions for the writing process (again controlled by light) and the other one prints the information. The latter cage compound should be connected to a fast rotating Feringa motor, which now does not act as a switch, but as a pulling motor. In the past period we have made a series of double cage compounds and studied their behavior with respect to the binding to a polymer chain and the process of movement along the chain. Our experiments show that the double cage tape heads indeed can thread onto a polymer and move along it, which is a very positive result for the further development of this information encoding system.
Writing and storing information onto synthetic polymers with the help of molecular machines, as proposed in our ENCOPOL project, has not been done before. We have made very important steps in realizing such an encoding process with the synthesis (up to 100 mg) of chiral tape heads composed of porphyrin cage compounds to which light switchable Feringa motors are attached. Different variants including slowly and fast rotating motors have been prepared and studied. For one system we were already able to show that the tape head can thread onto a polymer chain and move along it. We also showed that the state of the motor, which is controlled by light, has an effect on the binding of chiral low molecular weight molecules in the cage of the tape head. Further experiments will be carried out with chiral polymeric molecules. In the second part of the project we will focus on the writing process itself, i.e. answering the question whether we can write either an (R,R)- or an (S,S)-epoxide depending on the state of the Feringa motor. Furthermore, we hope to demonstrate that the Feringa motor can be used as well to pull the tape head in one particular direction along a chiral polymer tape. For this, the above-mentioned design 2.0 tape heads have to be provided with a fast rotating motor, which is a big challenge. We will also spend time on realizing the process of reading the information that is printed on the polymer chain. According to the proposal we will tackle this issue by developing a reading head composed of a zinc porphyrin cage to which a dye is attached. Energy transfer from the zinc porphyrin to the dye, which can be recorded spectroscopically, may depend on what type of epoxide is present in the cage, i.e. an (R,R)- or an (S,S)-epoxide. In the mean time we have prepared a first prototype of such a reading device and we hope to investigate soon whether it can be used for the intended purpose.