Hutchison Group

Chris Marvin and Ilana Kanal Join

Paula Hoffmann — Fri, 10 Feb 2012 15:42:10 +0000

This February, graduate students Christopher Marvin and Ilana Kanal joined the Hutchison group. Chris comes to us from South Carolina and will be working on the piezoelectric project. Ilana has lived in Pittsburgh for awhile with her husband and four … Continue reading →

Open Babel: An Open Chemical Toolbox

Geoff Hutchison — Fri, 07 Oct 2011 15:17:32 +0000

Noel M. O’Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch, Geoffrey R. Hutchison. “Open Babel: An open chemical toolbox.” J. Cheminf. 2011 3:33. Open Access.

Background

A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.

Results

We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.

Conclusions

Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

Valerie Lentz and Terry Paske Join

Paula Hoffmann — Wed, 05 Oct 2011 15:07:58 +0000

This fall, undergraduate students Valerie Lentz and Terry Paske have joined the group. Terry will work on the single-molecule piezoelectric project focusing on AFM characterization under the direction of graduate student Xinfeng Quan. Valerie will be working on organic synthesis with the organic solar cells project.

Welcome Valerie and Terry!

Solar Cell Research Featured in Chemistry Views

Geoff Hutchison — Tue, 04 Oct 2011 19:56:18 +0000

ChemViews magazine, published by 16 European chemical societies featured a blurb on Reverse Engineering Organic Solar Cells, published recently by the Hutchison group.

Steve Owens wins 2011 Stafford Award

Geoff Hutchison — Tue, 27 Sep 2011 17:48:04 +0000

Congratulations to Steve Owens, for winning one of the 2011 Safford Awards for Excellence as a Graduate Student Teacher! Steve is now the third member of the group who has won a Safford award.

Steve was recognized for his outstanding contributions to Chem 0960 and 0970 (undergraduate general chemistry), including being “very student-oriented in every aspect of your teaching assignment” and showed “such attention to detail and care for your students, Hurd Safford would have been proud.”

Prof. Hutchison on the Radio

Geoff Hutchison — Fri, 23 Sep 2011 14:24:30 +0000

Yesterday, Prof. Hutchison was a guest on The American Entrepeneur radio show, hosted by Ron Morris. He was discussing the group’s recent research on finding optimal polymer photovoltaic materials. You can listen to the segment “Is a Solar-Powered Society Economically Feasible” online.

Optimal Photovoltaic Paper on Cover of J. Phys. Chem. C

Geoff Hutchison — Tue, 16 Aug 2011 17:56:28 +0000

Our recent paper is currently featured on the cover of the Journal of Physical Chemistry C.

J. Phys. Chem. C Cover Art

Cover description: In silico discovery of polymer photovoltaics. Rapid computational screening of conjugated polymers for organic solar cells. Using the common acceptor material, phenyl-C61-butyric acid methyl ester (PCBM), and a simple model of photovoltaic cell efficiency derived from electronic structure properties, over 90000 copolymers were generated “in silico.” A genetic algorithm was used to solve the “inverse design” of copolymers with optimal power efficiency, many with predicted efficiencies over 10%. The method rapidly finds near-optimal structures, suggesting new synthetic directions for polymer photovoltaics. Further screening methods are suggested to refine initial targets into more viable lead compounds.

Demos at the Carnegie Museum

Geoff Hutchison — Sat, 13 Aug 2011 16:34:31 +0000

The Hutchison group gave demos of solar cells and piezoelectric electric generation during the Carnegie Museum of Natural History’s “Polar Weekend,” focusing on the science of climate change.The group prepared materials demonstrating organic solar cells. While our research is on polymer devices, we used fruit juices to demonstrate dye-sensitized solar cells, and homemade piezoelectric disks attached to LEDs to highlight alternative electricity generation. If you are interested in materials developed for the demo, or in having the group demo at your school or workplace, please contact us!

Effects of Charge Localization in Bithiophene Clusters

Geoff Hutchison — Thu, 04 Aug 2011 16:35:47 +0000

Tamika A. Madison, Geoffrey R. Hutchison. “The Effects of Charge Localization on the Orbital Energies of Bithiophene Clusters.” J. Phys. Chem. C 2011 115(35) pp 17558–17563. Available Online.
Standard and constrained density functional theory calculations were used to study the degree of charge localization in positively charged bithiophene clusters. While polarization effects due to the crystalline environment are known, many charge transport models in pi-conjugated organic materials assume a highly localized picture of carriers due to the strong electron-phonon interaction. These first- principles calculations show that that the positive charge delocalizes over at least 8 molecules in 1D herringbone stacks. For such 1D clusters, positive charge is more likely to localize on “tilted€” molecules than “parallel”€ molecules due to polarization effects. For 2D clusters, while polarization effects cancel due to symmetry, positive charge is shown to affect molecular sites anisotropically. Differences in computed HOMO energies between the localized and delocalized charges are ~1-2 eV, about the same as the difference in energy computed between a singly-charged and doubly-charged stack. These results suggest that models for charge transport in organic semiconductors should be revised to account for significant charge delocalization and intermolecular interactions such as polarization.

Optimal Polymer Photovoltaics

Geoff Hutchison — Wed, 06 Jul 2011 17:53:19 +0000

Noel M. O’Boyle, Casey M. Campbell, Geoffrey R. Hutchison. “Computational Design and Selection of Optimal Organic Photovoltaic Materials.” J. Phys. Chem. C 2011 115 (32) pp 16200–16210. Available Online.
Conjugated organic polymers are key building blocks of low-cost photovoltaic materials. We have examined over 90000 copolymers using computational predictions to solve the “inverse design” of molecular structures with optimum properties for highly efficient solar cells (specifically matching optical excitation energies and excited-state energies). Our approach, which uses a genetic algorithm to search the space of synthetically accessible copolymers of six or eight monomer units, yields hundreds of candidate copolymers with predicted efficiencies over 8% (the current experimental record), including many predicted to be over 10% efficient. We discuss trends in polymer sequences and motifs found in the most frequent monomers and dimers in these highly efficient targets and derive design rules for the selection of appropriate donor and acceptor molecules. We show how additional computationally intensive filtering steps can be used, for example, to eliminate targets likely to have poor hole mobilities. Our method effectively targets optimum electronic structure and optical properties far more efficiently than time-consuming serial experiments or computational studies and can be applied to similar problems in other areas of materials science.