Quantum chemistry

Department of Chemistry, University of Pittsburgh
Ph.D., Chemistry, Northwestern University, 2004
Summary:

Our group develops new materials, as well as microscale and nanoscale functional devices literally from the bottom up. We focus on building electronic materials from molecular subunits, both organic and inorganic, using a variety of techniques to rationally design the desired properties. This encompasses chemical synthesis, characterization (both physical and chemical), combined with theoretical modeling and simulation.

Our group combines experimental and computational investigations to gain deep understanding of organic electronic materials.  The bottom line is to efficiently design novel molecular materials with improved properties.  Below are three areas we are currently studying in our lab.

1. Designer defects

2. Single-molecule piezoelectric springs

3. Organic solar cells

 

Most Cited Publications
  1. "Open Babel: An open chemical toolbox," Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison, Journal of Cheminformatics 3, 33 (2011)
  2. "Avogadro: an advanced semantic chemical editor, visualization, and analysis platform," Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison, Journal of Cheminformatics 4, 17 (2012)
  3. "Building Blocks for N-Type Molecular and Polymeric Electronics. Perfluoroalkyl- versus Alkyl-Functionalized Oligothiophenes (nTs; n = 2−6). Systematic Synthesis, Spectroscopy, Electrochemistry, and Solid-State Organization," Antonio Facchetti, Myung-Han Yoon, Charlotte L. Stern, Geoffrey R. Hutchison, Mark A. Ratner, and Tobin J. Marks, J. Am. Chem. Soc., 126, 13480 (2004)
  4. "Hopping Transport in Conductive Heterocyclic Oligomers:  Reorganization Energies and Substituent Effects," Geoffrey R. Hutchison, Mark A. Ratner, and Tobin J. Marks, J. Am. Chem. Soc. 127, 2339 (2005)
  5. "The Blue Obelisk - interoperability in chemical informatics," R Guha, MT Howard, GR Hutchison, P Murray-Rust, H Rzepa, C Steinbeck, J Wegner, and EL Willighagen.  Journal of chemical information and modeling 46.3 (2006)
Recent Publications
  1. "Fast, efficient fragment-based coordinate generation for Open Babel," Yoshikawa, Naruki, and Geoffrey R. Hutchison. Journal of cheminformatics 11, no. 1 (2019): 49.
  2. "Bayesian Optimization for Conformer Generation." Chan, Lucian, Geoffrey Hutchison, and Garrett Morris. (2018).
  3. "Polarizable Drude Model with s-type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields," Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, Carl Caleman, Geoffrey R. Hutchison, and David van der Spoel, ChemRxiv (2018).
  4. "A sobering assessment of small-molecule force field methods for low energy conformer predictions," IIana Y. Kanal, John A. Keith, Geoffrey R. Hutchison,International Journal of Quantum Chemistry (2017)
  5. "Interplay Among Sequence, Folding Propensity, and BioPiezoelectric Response in Short Peptides and Peptoids," Christopher W Marvin, Haley M. Grimm, Nathaniel C. Miller, W. Seth Horne, and Geoffrey R Hutchison, J. Phys. Chem. B (2017)
Department of Chemistry, University of Pittsburgh
Ph.D., Theoretical and Computational Chemistry, University of Tübingen, Germany, 2008
Summary:

The Lambrecht lab develops and applys electronic structure approaches to help guide discoveries in catalysis, spectroscopy, and materials chemistry. They develop electronic structure and embedding methods that yield an accurate and computationally feasible description of chemical reactions in solvent or solid environments. In cooperation with experiment, they aim at gaining insights into the thermodynamics, kinetics and spectral signatures along catalytic pathways. Another focus is to provide rationales for the improvement of catalysts. They are working on decomposition methods that allow us to extract correlations between electronic structure descriptors for ligands and solvents and thus ultimately allow to make recommendations for more active catalyst systems. Their research areas include:

  • Developing reduced-scaling first principles approaches for expedited predictions of molecular and materials properties: The aim is to enable calculations on larger systems than conventionally possible, which allows for more realistic chemical models. The scaling reduction is achieved by screening approaches exploiting the fact that some interactions between electrons (such as dispersion or vdW forces) are short-ranged and can therefore be neglected if the distance is big enough. Other approaches developed in the lab involve sparse matrix techniques, multi-scale approaches, as well as tensor decompositions.
  • Energy decomposition approaches to split infrared and other spectral signatures into chemically meaningful contributions and to facilitate force field development.
  • Simulating paramagnetic resonance spectra to identify the structures of metal binding sites in biological systems.
  • Metal nanoparticles (optical excitation and catalysis).
Most Cited Publications
  1. "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package," Y Shao, Z Gan, E Epifanovsky, ATB Gilbert, M Wormit, J Kussmann, ..., Daniel S Lambrecht, ..., Molecular Physics 113, 184 (2015)
  2. "Current status of the AMOEBA polarizable force field," Jay W Ponder, Chuanjie Wu, Pengyu Ren, Vijay S Pande, John D Chodera, Michael J Schnieders, Imran Haque, David L Mobley, Daniel S Lambrecht, Robert A DiStasio Jr, Martin Head-Gordon, Gary NI Clark, Margaret E Johnson, Teresa Head-Gordon, J. Phys. Chem. B 114, 2549 (2010)
  3. "Linear-scaling atomic orbital-based second-order Møller–Plesset perturbation theory by rigorous integral screening criteria" B Doser, DS Lambrecht, J Kussmann, C Ochsenfeld, J. Chem. Phys. 130, 064107 (2009)
  4. "Rigorous integral screening for electron correlation methods," DS Lambrecht, B Doser, C Ochsenfeld, J. Chem. Phys. 123, 184102 (2005)
  5. "Linear-scaling methods in quantum chemistry," C Ochsenfeld, J Kussmann, D S Lambrecht, Reviews in computational chemistry 23, 1 (2007)
Recent Publications
  1. "Generalizing energy decomposition analysis to response properties to inform expedited predictive models." Lambrecht, Daniel S. Computational and Theoretical Chemistry (2018).
  2. "A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions." Lambrecht, Daniel, and Eric Berquist. (2018).
  3. "Ligand−Substrate Dispersion Facilitates the Copper-Catalyzed Hydroamination of Unactivated Olefins", Gang Lu, Richard Y. Liu, Yang Yang, Cheng Fang, Daniel S. Lambrecht, Stephen L. Buchwald, and Peng Liu, J. Am. Chem. Soc., 139, 16548 (2017)
  4. "First-principles derived descriptors for rational design of functional molecular materials." Berquist, Eric, and Daniel Lambrecht. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 254. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, 2017.
  5. "Polymerization of silyl ketenes using alkoxide initiators: a combined computational and experimental study," Yuanhui Xiang, Daniel J. Burrill, Krista K. Bullard, Benjamin J. Albrecht, Lauren E. Tragesser, John McCaffrey, Daniel S. Lambrecht and Emily Pentzer, Polym. Chem. 8, 5381 (2017) 
Department of Chemical and Petroleum Engineering, University of Pittsburgh
Ph.D., Chemistry, California Institute of Technology, 2007
Summary:

The Keith group applies and develops computational chemistry to study and discover solutions to problems at the interface of engineering and basic science.  They are currently focused on modeling chemical reaction mechanisms and the atomic scale of materials to help develop renewable energy and sustainability technologies.

The group uses quantum chemistry-based multiscale modeling to predict and study the atomic scale of materials and chemical reactions. With electronic structure and atomistic methods, they can investigate fundamental reaction steps at different time- and length-scales that would otherwise be difficult or impossible to investigate with experiment. 

Notably, their studies are entirely carried out in silico (on a computer) and almost entirely free from artificial biases that are present when using experimental inputs. Whether doing so alone or in collaboration with experimentalists, the group provides deep perspective on the atomic-scale of catalytic environments to understand how they work and how to further improve them.

The 'ground-up' multiscale modeling approach uses appropriate levels of quantum chemistry (QC) theory (typically on up to ca. 200 atoms) to model reaction energiesbarrier heightspKas, and standard redox potentials. Using data obtained from QC theory, they can also develop analytic reactive forcefields, which are capable of modeling reaction dynamics on systems on the order of 100,000 atoms. Reactive forcefield data in turn can be used to generate rate constant libraries for kinetic Monte Carlo (kMC) simulations to model larger time-scale and length-scale phenomena such a nanoparticle/material growth and ripening.

Most Cited Publications
  1. "Water Oxidation on Pure and Doped Hematite (0001) Surfaces: Prediction of Co and Ni as Effective Dopants for Electrocatalysis," Peilin Liao, John A. Keith, and Emily A. Carter, J. Am. Chem. Soc. 134, 13296 (2012)
  2. "The Mechanism of the Wacker Reaction: A Tale of Two Hydroxypalladations," John A. Keith, Patrick M. Henry, Angew. Chem. Int. Ed. 48, 9038 (2009)
  3. "Theoretical Investigations of the Oxygen Reduction Reaction on Pt(111)," John A. Keith, Gregory Jerkiewicz, Timo Jacob, ChemPhysChem 11, 2779 (2010)
  4. "Elucidation of the selectivity of proton-dependent electrocatalytic CO2 reduction by fac-Re (bpy)(CO) 3CI," JA Keith, KA Grice, CP Kubiak, and EA Carter.  Journal of the American Chemical Society 135.42 (2013)
  5. "Theoretical Studies of Potential-Dependent and Competing Mechanisms of the Electrocatalytic Oxygen Reduction Reaction on Pt(111)," John A. Keith, Timo Jacob, Angew. Chem. Int. Ed. 49, 9521 (2010)
Recent Publications
  1. "Machine Learning Guided Approach for Studying Solvation Environments,"  Y Basdogan, MC Groenenboom, E Henderson, S De, S Rempe, and J KeithChemRxiv (2019)
  2. "Free Standing Nanoporous Palladium Alloys as CO Poisoning Tolerant Electrocatalysts for the Electrochemical Reduction of CO2 to Formate," S Chatterjee, CD Griego, J Hart, Y Li, M Taheri, J Keith, and J Snyder.  ACS Catalysis 9.6 (2019)
  3. "Benchmarking Computational Alchemy for Carbide, Nitride, and Oxide Catalysts." Griego, Charles D., Karthikeyan Saravanan, and John A. Keith. Advanced Theory and Simulations (2018): 1800142.
  4. "Mechanism of Isobutylene Polymerization: Quantum Chemical Insight into AlCl3/H2O‑Catalyzed Reactions," Minh Nguyen Vo, Yasemin Basdogan, Bridget S. Derksen, Nico Proust, G. Adam Cox, Cliff Kowall, John A. Keith, and J. Karl Johnson, ACS Catal., 8, 8006 (2018)
  5. "Oligomer Hydrate Crystallization Improves Carbon Nanotube Memory," Michael T. Chido, Peter Koronaios, Karthikeyan Saravanan, Alexander P. Adams, Steven J. Geib, Qiang Zhu, Hari B Sunkara, Sachin S. Velankar, Robert M. Enick, John A. Keith, and Alexander Star, Chemistry of Materials (2018).
Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Computational and Theoretical Organic Chemistry, UCLA, 1990
Summary:

Our research program is driven by significant problems in organic, biochemistry, and physical chemistry. Our research in chemical theory and computation is fully integrated in strong collaboration with successful experimental chemists. We have a full range on interests, starting with the development of fundamental ideas on the theory of chemical bonding, and how this information can be used to understand the fundamentals of Lewis acidity and basicity, organic reaction catalysis, organometallic structures, and the bonding and reactions at surfaces. In the field of biochemistry, we investigate the energetics and mechanisms of phosphoryl transfer reactions, and design new antimicrobial agents to light the increasing risk of drug resistant bacterial fungal infections.

Selected Publications: 
  • "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  • "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  • "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)
  • "Hyperconjugation-Mediated Solvent Effects in Phosphoanhydride Bonds," Jean C. Summerton, Jeffrey D. Evanseck, and Michael S. Chapman, J. Phys. Chem. A 116 10209 (2012)
Most Cited Publications
  1. "All-atom empirical potential for molecular modeling and dynamics studies of proteins," A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B. 102, no. 18 (1998)
  2. "Transition structures of hydrocarbon pericyclic reactions," Houk, Kendall N., Yi Li, Jeffrey D. EvanseckAngewandte Chemie International Edition 31, no. 6 (1992)
  3. "Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin," Caves, Leo SD, Jeffrey D. Evanseck, Martin Karplus.,  Protein Science 7, no. 3 (1998)
  4. "Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study," Rovira, Carme, Brita Schulze, Markus Eichinger, Jeffrey D. Evanseck, Michele Parrinello,  Biophysical journal 81, no. 1 (2001)
  5. "Density functional theory study of aqueous-phase rate acceleration and endo/exo selectivity of the butadiene and acrolein Diels-Alder reaction," Kong, S., Evanseck, J.D., Journal of the American Chemical Society 122, no. 42 (2000)
Recent Publications
  1. "Chemistry REU Leadership Group: Support for the Chemistry Undergraduate Research Community"  Watkins, L.M., Evanseck, J.DACS Symposium Series 1295, pp. 73-83
  2. "Evolution of an AwESOME Chapter"  Cooper, E., Shaik, S., Bautista, D., (...), Gawalt, E.S., Evanseck, J.D. ACS Symposium Series 1278, pp. 55-71
  3. "Metalated nitriles: SNi′ cyclizations with a propargylic electrophile," Ping Lu, Venkata S. Pakkala, Jeffrey D. Evanseck, Fraser F. Fleming, Tetrahedron Letters 56, 3216 (2015)
  4. "Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate," Sarah E. Kochanek, Traci M. Clymer, Venkata S. Pakkala, Sebastien P. Hebert, Kyle Reeping, Steven M. Firestine, and Jeffrey D. Evanseck, J. Phys. Chem. B 119, 1184 (2015)
  5. "Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites," Jean C. Summerton, Gregory M. Martin, Jeffrey D. Evanseck, Michael S. Chapman, PLOS One 9, e108310 (2014)

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