Graduation has not stopped James McConnell '07 (East Setauket, NY) from continuing his research in the lab of Winslow Professor of Chemistry George Shields and Co-Director of the Center for Molecular Design Karl Kirschner. McConnell, a chemistry and math double major, plans to spend part of this summer continuing to work on his thesis project, which he began last summer, until someone else is able to take over where he left off. In the meantime, he will be able to collect more data and work in a lab he describes as "very positive."
McConnell's research involves force field development via the molecular partition function. The force fields he's working with, however, are "not the force fields from Star Trek." Rather, a force field can been seen as a set of equations that describes how molecules, which can be modeled as acting like balls attached to each other by springs, behave thermodynamically. Previous research has generated force fields using potential energy and enthalpy, but no one has yet been able to create force fields based on free energy. In order to accomplish this task, McConnell has been utilizing statistical thermodynamics and computational chemistry. Although his methods and results seem very promising, McConnell admits that "obtaining an actual force field is far away."
McConnell begins his experiments by modeling a molecule of interest. Next, he uses a program called Gaussian to optimize the molecule so that it is in the lowest energy state and to obtain thermodynamic information about it. Another program called stat thermo is then used to take the optimized structure of the molecule and extend it to a population of molecules. Since the other programs did not give him the amount of information or control he needed for his research, McConnell created a program called powerThermo that uses the data from Gaussian and stat thermo to determine the thermodynamic contributions of each part of the molecule. In other words, he is able to add X amount of free energy to his model of the molecule every time he sees a particular component, such as a certain type of bond. With these calculations, McConnell tries to generalize the free energy contributions of arbitrary molecules since free energy is "a more accurate portrayal of how molecules behave in the real world."
Although the project is currently focused on extracting and predicting thermodynamic information, in the future it will hopefully be able to apply its results to the force field equations. Force field development has many potential applications because it provides "a new tool in the [computational chemistry] toolbox." Researchers could use force fields as a new method of investigating some of the biggest problems in chemistry, such as predicting the way in which a protein will fold or designing drugs.
McConnell graduated summa cum laude with honors in both math and chemistry. He was also inducted into Phi Beta Kappa and Sigma Xi. While at Hamilton, he was a member of the College Republicans and the Chess Club. In the fall, McConnell will attend law school at Cornell University to study patent law. Although this may seem like an unusual choice for a science major, McConnell thinks of it as a "continuation rather than an abandonment" of the sciences because patent law will allow him to meet many different scientists and learn about their research. More importantly, however, it will allow him "to assist scientists in protecting and advancing the fruits of research."
-- by Nick Berry '09
McConnell's research involves force field development via the molecular partition function. The force fields he's working with, however, are "not the force fields from Star Trek." Rather, a force field can been seen as a set of equations that describes how molecules, which can be modeled as acting like balls attached to each other by springs, behave thermodynamically. Previous research has generated force fields using potential energy and enthalpy, but no one has yet been able to create force fields based on free energy. In order to accomplish this task, McConnell has been utilizing statistical thermodynamics and computational chemistry. Although his methods and results seem very promising, McConnell admits that "obtaining an actual force field is far away."
McConnell begins his experiments by modeling a molecule of interest. Next, he uses a program called Gaussian to optimize the molecule so that it is in the lowest energy state and to obtain thermodynamic information about it. Another program called stat thermo is then used to take the optimized structure of the molecule and extend it to a population of molecules. Since the other programs did not give him the amount of information or control he needed for his research, McConnell created a program called powerThermo that uses the data from Gaussian and stat thermo to determine the thermodynamic contributions of each part of the molecule. In other words, he is able to add X amount of free energy to his model of the molecule every time he sees a particular component, such as a certain type of bond. With these calculations, McConnell tries to generalize the free energy contributions of arbitrary molecules since free energy is "a more accurate portrayal of how molecules behave in the real world."
Although the project is currently focused on extracting and predicting thermodynamic information, in the future it will hopefully be able to apply its results to the force field equations. Force field development has many potential applications because it provides "a new tool in the [computational chemistry] toolbox." Researchers could use force fields as a new method of investigating some of the biggest problems in chemistry, such as predicting the way in which a protein will fold or designing drugs.
McConnell graduated summa cum laude with honors in both math and chemistry. He was also inducted into Phi Beta Kappa and Sigma Xi. While at Hamilton, he was a member of the College Republicans and the Chess Club. In the fall, McConnell will attend law school at Cornell University to study patent law. Although this may seem like an unusual choice for a science major, McConnell thinks of it as a "continuation rather than an abandonment" of the sciences because patent law will allow him to meet many different scientists and learn about their research. More importantly, however, it will allow him "to assist scientists in protecting and advancing the fruits of research."
-- by Nick Berry '09
