Quantum chemistry

Department of Physics and Astronomy, University of Pittsburgh
Ph.D. Physics, University of Science & Technology of China, 2003
Summary:

1. The wet electron structure of the H/H2O/TiO2(110) surfaces system using Density Functional Theory.

2. The excited state structure of H/H2O/TiO2(110) using delta-scf method and TDDFT.

3. The resonance of alkali atoms adsorbed on Ag and Cu surface using first-principle and model potential calculation methods.

Selected Publications: 
  1. "Plasmonic coupling at a metal/semiconductor interface," Shijing Tan, Adam Argondizzo, Jindong Ren, Liming Liu, Jin Zhao, Hrvoje Petek, Nature Photonics 11, 806 (2017)
  2. "Time-resolved photoemission study of the electronic structure and dynamics of chemisorbed alkali atoms on Ru(0001)," Shengmin Zhang, Cong Wang, Xuefeng Cui, Yanan Wang, Adam Argondizzo, Jin Zhao and Hrvoje Petek, Phys. Rev. B 93, 045401 (2016)
  3. "Temperature- and Coverage-Dependent Kinetics of Photocatalytic Reaction of Methanol on TiO2(110)-(1x1) Surface," Hao Feng, Shijing Tan, Haoqi Tang, Qijing Zheng, Yongliang Shi, Xuefeng Cui, Xiang Shao, Aidi Zhao, Jin Zhao, and Bing Wang, J. Phys. Chem. C, 120, 5503 (2016)
  4. "Nano-scale Polar-Nonpolar Oxide Heterostructures for Photocatalysis," Hongli Guo, Wissam A. Saidi, Jinlong Yang and Jin Zhao, Nanoscale 8, 6057 (2016)
Most Cited Publications
  1. "Wet Electrons at the H2O/TiO2(110)", Ken Onda, Bin Li, Jin Zhao,                                 Kenneth D. Jordan, Jinlong Yang, Hrvoje Petek, Science, 308, 1154 (2005)
  2. "Atomlike, hollow-core-bound molecular orbitals of C60 ", Min Feng, Jin Zhao, Hrvoje Petek, Science, 320, 359 (2008)
  3. "Ultrafast interfacial proton-coupled electron transfer", Bin Li, Jin Zhao, Ken Onda, Kenneth D. Jordan, Jinlong Yang, Hrvoje Petek, Science, 311, 1436 (2006). 
  4. "The electronic structure of oxygen atom vacancy and hydroxyl impurity defects on titanium (110) surface," Minato, T., Sainoo, Y., Kim, Y., (...), Yang, J., Hou, J.G. Journal of Chemical Physics 130(12) (2009)
  5. "Single C59N molecules as a molecular rectifier,"     Zhao, J., Zeng, C., Cheng, X., (...), Hou, J.G., Zhu, Q.     Physical Review Letters
    95(4) (2005)
Recent Publications
  1. “Low-Frequency Lattice Phonons in Halide Perovskites Explain High Defect Tolerance Towards Electron-Hole Recombination.” W. Chu, Q. Zheng, O. V. Prezhdo, J. Zhao and W. A. Saidi. Sci. Adv. , in press, (2019)

  2. “K Atom Promotion of O2 Chemisorption on Au(111) Surface.” J. Ren, Y. Wang, J. Zhao, S. Tan and H. Petek. J. Am. Chem. Soc. , 141, 4438, (2019)

  3. “Suppression of Electron-Hole Recombination by Intrinsic Defects in 2D Monoelemental Material.” L. Zhang, W. Chu, Q. Zheng, A. V. Benderskii, O. V. Prezhdo* and J. Zhao. J. Phys. Chem. Lett. , 10, 6151-6158, (2019)

  4. “Tailoring Exciton Dynamics of Monolayer Transition Metal Dichalcogenides by Interfacial Electron-Phonon Coupling.” Z. Nie, Y. Shi, S. Qin, Y. Wang, H. Jiang, Q. Zheng, Y. Cui, Y. Meng, F. Song, X. Wang, I. C. E. Turcu, X. Wang, Y. Xu, Y. Shi, J. Zhao, R. Zhang and F. Wang. Communications Physics , 2, 103, (2019)

  5. “Suppression and reversion of light-induced phase separation in mixed-halide perovskites by oxygen passivation.” W. Fan, Y. Shi, T. Shi, S. Chu, K. Lghodalo, W. Chen, J. Zhao, X. Li*, and Z. Xiao. ACS Energy Lett. , 4, 2052-2058, (2019)

Quantum Mechanics, Chemical Space, and Machine Learning

Speaker(s): 
O. Anatole von Lilienfeld
Dates: 
Thursday, September 29, 2016 - 4:30pm to 5:30pm

Many of the most relevant chemical properties of matter depend explicitly on atomistic details, rendering a first principles approach mandatory. Alas, even when using high-performance computers, brute force high throughput screening of compounds is beyond any capacity for all but the simplest systems and properties due to the combinatorial nature of chemical space, i.e. all compositional, constitutional, and conformational isomers. Consequently, efficient exploration algorithms need to exploit all implicit redundancies present in chemical space. I will discuss...

Department of Materials Science and Engineering, Carnegie Mellon University
Ph.D., Chemistry, Weizmann Institute of Science, 2010
Summary:

Computational Materials Science

The goal of our research is to computationally design materials with desired properties for target applications.

Through the portal of computer simulations we gain access to the vast configuration space of materials structure and composition. We can explore the uncharted territories of materials that have not been synthesized yet and predict their properties from first principles, based solely on the knowledge of their elemental composition and the laws of quantum mechanics.

To navigate the configuration space we use genetic algorithms, steered to the most promising regions by the evolutionary principle of survival of the fittest. We develop a massively parallel genetic algorithm code, GAtor, and run it on some of the world’s most powerful supercomputers. We apply our methods to study functional nano-structured interfaces in organic and hybrid solar cells, molecular crystals, layered materials, and cluster-based nanocatalysts.

Most Cited Publications
  1. "Stacking and registry effects in layered materials: the case of hexagonal boron nitride." Noa Marom, Jonathan Bernstein, Jonathan Garel, Alexandre Tkatchenko, Ernesto Joselevich, Leeor Kronik, Oded Hod. Physical review letters.
  2. "Dispersion interactions with density-functional theory: Benchmarking semi-empirical and inter-atomic pair-wise corrected density functionals." Noa Marom, Alexandre Tkatchenko, Mariana Rossi, Vivekanand V Gobre, Oded Hod, Matthias Scheffler, Leeor Kronik. Journal of Chemical Theory and Computation.
  3. "Report on the sixth blind test of organic crystal structure prediction methods." Anthony M Reilly, Richard I Cooper, Claire S Adjiman, Saswata Bhattacharya, A Daniel Boese, Jan Gerit Brandenburg, Peter J Bygrave, Rita Bylsma, Josh E Campbell, Roberto Car, David H Case, Renu Chadha, Jason C Cole, Katherine Cosburn, Herma M Cuppen, Farren Curtis, Graeme M Day, Robert A DiStasio Jr, Alexander Dzyabchenko, Bouke P Van Eijck, Dennis M Elking, Joost A Van Den Ende, Julio C Facelli, Marta B Ferraro, Laszlo Fusti-Molnar, C-A Gatsiou, Thomas S Gee, René De Gelder, Luca M Ghiringhelli, Hitoshi Goto, Stefan Grimme, Rui Guo, Detlef WM Hofmann, Johannes Hoja, Rebecca K Hylton, Luca Iuzzolino, Wojciech Jankiewicz, Daniël T De Jong, John Kendrick, Niek JJ De Klerk, H-Y Ko, Liudmila N Kuleshova, Xiayue Li, Sanjaya Lohani, Frank JJ Leusen, Albert M Lund, Jian Lv, Yanming Ma, Noa Marom, Artëm E Masunov, Patrick McCabe, David P McMahon, Hugo Meekes, Michael P Metz, Alston J Misquitta, Sharmarke Mohamed, Bartomeu Monserrat, Richard J Needs, Marcus A Neumann, Jonas Nyman, Shigeaki Obata, Harald Oberhofer, Artem R Oganov, Anita M Orendt, Gabriel I Pagola, Constantinos C Pantelides, Chris J Pickard, Rafal Podeszwa, Louise S Price, Sarah L Price, Angeles Pulido, Murray G Read, Karsten Reuter, Elia Schneider, Christoph Schober, Gregory P Shields, Pawanpreet Singh, Isaac J Sugden, Krzysztof Szalewicz, Christopher R Taylor, Alexandre Tkatchenko, Mark E Tuckerman, Francesca Vacarro, Manolis Vasileiadis, Alvaro Vazquez-Mayagoitia, Leslie Vogt, Yanchao Wang, Rona E Watson, Gilles A De Wijs, Jack Yang, Qiang Zhu, Colin R Groom. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials.
  4. "Electronic structure of copper phthalocyanine: A comparative density functional theory study." Noa Marom, Oded Hod, Gustavo E Scuseria, Leeor Kronik. The Journal of chemical physics.
  5. "Benchmark of G W methods for azabenzenes." Noa Marom, Fabio Caruso, Xinguo Ren, Oliver T Hofmann, Thomas Körzdörfer, James R Chelikowsky, Angel Rubio, Matthias Scheffler, Patrick Rinke. Physical Review B.
Recent Publications
  1. "Genarris 2.0: A Random Structure Generator for Molecular Crystals." Rithwik Tom, Timothy Rose, Imanuel Bier, Harriet O'Brien, Alvaro Vazquez-Mayagoitia, Noa Marom. arXiv preprint arXiv:1909.10629.
  2. "Anomalous pressure dependence of the electronic properties of molecular crystals explained by changes in intermolecular electronic coupling." Maituo Yu, Xiaopeng Wang, Xiong-Fei Du, Christian Kunkel, Taylor M Garcia, Stephen Monaco, Bohdan Schatschneider, Harald Oberhofer, Noa Marom. Synthetic Metals.
  3. "Phenylated Acene Derivatives as Candidates for Intermolecular Singlet Fission." Xiaopeng Wang, Xingyu Liu, Rithwik Tom, Cameron Cook, Bohdan Schatschneider, Noa Marom. The Journal of Physical Chemistry C.
  4. "Structure searching methods: general discussion." Matthew Addicoat, Claire S Adjiman, Mihails Arhangelskis, Gregory JO Beran, Jan Gerit Brandenburg, Doris E Braun, Virginia Burger, Asbjoern Burow, Christopher Collins, Andrew Cooper, Graeme M Day, Volker L Deringer, Matthew S Dyer, Alan Hare, Kim E Jelfs, Julian Keupp, Stefanos Konstantinopoulos, Yi Li, Yanming Ma, Noa Marom, David McKay, Caroline Mellot-Draznieks, Sharmarke Mohamed, Marcus Neumann, Sten Nilsson Lill, Jonas Nyman, Artem R Oganov, Sarah L Price, Susan Reutzel-Edens, Michael Ruggiero, German Sastre, Rochus Schmid, Julia Schmidt, J Christian Schön, Peter Spackman, Seiji Tsuzuki, Scott M Woodley, Shiyue Yang, Qiang Zhu. Faraday discussions.
  5. "Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion." Matthew Addicoat, Claire S Adjiman, Mihails Arhangelskis, Gregory JO Beran, David Bowskill, Jan Gerit Brandenburg, Doris E Braun, Virginia Burger, Jason Cole, Aurora J Cruz-Cabeza, Graeme M Day, Volker L Deringer, Rui Guo, Alan Hare, Julian Helfferich, Johannes Hoja, Luca Iuzzolino, Samuel Jobbins, Noa Marom, David McKay, John BO Mitchell, Sharmarke Mohamed, Marcus Neumann, Sten Nilsson Lill, Jonas Nyman, Artem R Oganov, Pablo Piaggi, Sarah L Price, Susan Reutzel-Edens, Ivo Rietveld, Michael Ruggiero, Matthew R Ryder, German Sastre, J Christian Schön, Christopher Taylor, Alexandre Tkatchenko, Seiji Tsuzuki, Joost Van Den Ende, Scott M Woodley, Grahame Woollam, Qiang Zhu. Faraday discussions.
Department of Chemical and Petroleum Engineering, University of Pittsburgh
Ph.D., Theoretical and Computational Chemistry, University of Crete, 2006
Summary:

My research expertise is interdisciplinary, blending concepts and techniques from Chemistry, Physics, Materials Science and Chemical Engineering. I use theory and computation to investigate the physicochemical properties of nanomaterials with potential applications in diverse nanotechnological areas, ranging from energy generation and storage, to materials design, nanoparticle growth, magnetism, and catalysis.

In the Computer-Aided Nano and Energy Lab (C.A.N.E.LA.), led by Prof. Mpourmpakis, we use theory and computation to investigate the physicochemical properties of nanomaterials with potential applications in diverse nanotechnological areas, ranging from green energy generation and storage to materials engineering and catalysis. Our laboratory core expertise lies on "ab-initio" electronic-structure theoretical calculations. We develop structure-activity relationships and apply multiscale tools to elucidate complex chemical processes that take place on nanomaterials. Ultimately, we design novel nanostructures with increased, molecular-level precision and tailored multifunctionality. 

Most Cited Publications
  1. "SiC nanotubes: a novel material for hydrogen storage." Giannis Mpourmpakis, George E Froudakis, George P Lithoxoos, Jannis Samios. Nano letters.
  2. "Carbon nanoscrolls: a promising material for hydrogen storage." Giannis Mpourmpakis, Emmanuel Tylianakis, George E Froudakis. Nano letters.
  3. "Correlating particle size and shape of supported Ru/γ-Al2O3 catalysts with NH3 decomposition activity." Ayman M Karim, Vinay Prasad, Giannis Mpourmpakis, William W Lonergan, Anatoly I Frenkel, Jingguang G Chen, Dionisios G Vlachos. Journal of the American Chemical Society.
  4. "Why boron nitride nanotubes are preferable to carbon nanotubes for hydrogen storage?: An ab initio theoretical study." Giannis Mpourmpakis, George E Froudakis. Catalysis today.
  5. "DFT study of furfural conversion to furan, furfuryl alcohol, and 2-methylfuran on Pd (111)." Vassili Vorotnikov, Giannis Mpourmpakis, Dionisios G Vlachos. Acs Catalysis.
Recent Publications
  1. "Identification of Stable Bimetallic Nanoclusters Via a Mathematical Optimization Framework." Xiangyu Yin, Natalie M Isenberg, Michael G Taylor, Giannis Mpourmpakis, Chrysanthos E Gounaris. 2019 AIChE Annual Meeting.
  2. "Generalized Adsorption Models on Metal Nanoparticles." James Dean, Michael G Taylor, Giannis Mpourmpakis. 2019 AIChE Annual Meeting.
  3. "Prediction of Nanoparticles Size Distribution: The Effects of Ligand Surface Coverage and Nanoparticle Size in Altering the Kinetics of Surface Growth." Saeed Mozaffari, Wenhui Li, Mudit Dixit, Giannis Mpourmpakis, Ayman M Karim. 2019 AIChE Annual Meeting.
  4. "Understanding Mixing Behavior of Bimetallic Nanoparticles through Genetic Algorithm Modeling." Michael Cowan, James Dean, Giannis Mpourmpakis. 2019 AIChE Annual Meeting.
  5. "Understanding Oligomerization Steps in Zeolite Growth Using Density Functional Theory." Emily Freeman, Jeffrey D Rimer, Giannis Mpourmpakis. 2019 AIChE Annual Meeting.
Department of Chemistry, University of Pittsburgh
Ph.D., Computational Organic Chemistry, University of California, 2010
Summary:

Reactivity and Selectivity Rules in Organic and Organometallic Reactions
We are developing computational models to quantitatively describe the origins of reactivity and selectivity in organocatalytic and transition metal-catalyzed reactions. We perform quantum mechanical calculations to explore the reaction mechanism, followed by thorough analysis on various stereoelectronic effects to predict how changes of the catalyst structure, substituents, and solvent affect rate and selectivity. We use quantitative energy decomposition methods to dissect the key interactions in the transition state and provide chemically meaningful interpretation to the computed reactivity and selectivity. We apply these computational studies to a broad range of organic and organometallic reactions, such as C–H and C–C bond activations, coupling reactions, olefin metathesis, and polymerization reactions. 

Catalyst Screening and Prediction
We are developing a multi-scale computational screening protocol which could efficiently rank the catalysts based on ligand-substrate interaction energies in the transition state. 

Applications of Computational Chemistry in Understanding Organic Chemistry
We are collaborating with experimental groups at Pitt and many other institutions to solve problems in organic chemistry using computational methods and programs. Our goal is to establish the most effective strategy to use modern computational methods and hardware to help address the grand challenges in synthetic chemistry. 

 

Most Cited Publications
  1. "Computational Explorations of Mechanisms and Ligand-Directed Selectivities of Copper-Catalyzed Ullmann-Type Reactions." Gavin O Jones, Peng Liu, KN Houk, Stephen L Buchwald. Journal of the American Chemical Society.
  2. "Suzuki− Miyaura Cross-Coupling of Aryl Carbamates and Sulfamates: Experimental and Computational Studies." Kyle W Quasdorf, Aurora Antoft-Finch, Peng Liu, Amanda L Silberstein, Anna Komaromi, Tom Blackburn, Stephen D Ramgren, KN Houk, Victor Snieckus, Neil K Garg. Journal of the American Chemical Society.
  3. "Conversion of amides to esters by the nickel-catalysed activation of amide CN bonds." Liana Hie, Noah F Fine Nathel, Tejas K Shah, Emma L Baker, Xin Hong, Yun-Fang Yang, Peng Liu, KN Houk, Neil K Garg. Nature.
  4. "Palladium-Catalyzed Meta-Selective C–H Bond Activation with a Nitrile-Containing Template: Computational Study on Mechanism and Origins of Selectivity." Yun-Fang Yang, Gui-Juan Cheng, Peng Liu, Dasheng Leow, Tian-Yu Sun, Ping Chen, Xinhao Zhang, Jin-Quan Yu, Yun-Dong Wu, KN Houk. Journal of the American Chemical Society.
  5. "Mechanism of Photoinduced Metal-Free Atom Transfer Radical Polymerization: Experimental and Computational Studies." Xiangcheng Pan, Cheng Fang, Marco Fantin, Nikhil Malhotra, Woong Young So, Linda A Peteanu, Abdirisak A Isse, Armando Gennaro, Peng Liu, Krzysztof Matyjaszewski. Journal of the American Chemical Society.
Recent Publications
  1. "Ruthenium-Catalyzed Reductive Cleavage of Unstrained Aryl─ Aryl Bonds: Reaction Development and Mechanistic Study." Jun Zhu, Peng-hao Chen, Gang Lu, Peng Liu, Guangbin Dong. Journal of the American Chemical Society.
  2. "The Thermal Rearrangement of an NHC‐Ligated 3‐Benzoborepin to an NHC‐Boranorcaradiene." Masaki Shimoi, Ilia Kevlishvili, Takashi Watanabe, Steven J Geib, Katsuhiro Maeda, Dennis P Curran, Peng Liu, Tsuyoshi Taniguchi. Angewandte Chemie.
  3. "Tuning the Reactivity of Cyclopropenes from Living Ring‐Opening Metathesis Polymerization (ROMP) to Single‐Addition and Alternating ROMP." Jessica K Su, Zexin Jin, Rui Zhang, Gang Lu, Peng Liu, Yan Xia. Angewandte Chemie.
  4. "An enzymatic platform for the asymmetric amination of primary, secondary and tertiary C (sp 3)–H bonds." Yang Yang, Inha Cho, Xiaotian Qi, Peng Liu, Frances H Arnold. Nature chemistry.
  5. "Diastereo-and Enantioselective CuH-Catalyzed Hydroamination of Strained Trisubstituted Alkenes." Sheng Feng, Hua Hao, Peng Liu, Stephen L Buchwald. ChemRxiv.
Department of Chemical and Petroleum Engineering, University of Pittsburgh
Ph.D., Chemical Engineering, Cornell University, 1992
Summary:

The Johnson group investigates problems in the broad areas of energy and the environment using atomistic simulation methods, including quantum mechanics, statistical mechanics, and machine learning. Current projects involve: (1) developing new materials in silico for proton conducting membranes capable of operating under low humidity and high temperatures; (2) developing and modeling new materials for capture and destruction of chemical warfare agents; (3) modeling adsorption and diffusion of toxic chemicals in defective metal organic framework materials; (4) applying, testing, and improving methods of correcting for density functional theory self-interaction errors.

Most Cited Publications
  1. Anastasios I. Skoulidas, David M. Ackerman, J. Karl Johnson, and David S. Sholl "Rapid Transport of Gases in Carbon Nanotubes", Physical Review Letters, 89, 185901 (2002). DOI: 10.1103/PhysRevLett.89.185901
  2. Long Pan, Michelle B. Sander, Xiaoying Huang, Jing Li, Milton Smith, Edward Bittner, Bradley Bockrath, and J. Karl Johnson, "Microporous Metal Organic Materials: Promising Candidates as Sorbent for Hydrogen Storage", Journal of the American Chemical Society, 126, 1308-1309 (2004). DOI: 10.1021/ja0392871
  3. Q. Wang and J. K. Johnson, "Molecular Simulation of Hydrogen Adsorption in Single-Walled Carbon Nanotubes and Idealized Carbon Slit Pores", Journal of Chemical Physics, 110, 577-586 (1999). Giovanni Garberoglio, Anastasios I. Skoulidas, and J. Karl Johnson, "Adsorption of gases in metal organic materials: Comparison of simulations and experiments", Journal of Physical Chemistry B, 109(27), 13094-13103 (2005). DOI: 10.1021/jp050948l
  4. Sangil Kim, Liang Chen, J. Karl Johnson, and Eva Marand, "Polysulfone and Functionalized Carbon Nanotube Mixed Matrix Membranes for Gas Separation: Theory and Experiment", Journal of Membrane Science, 294, 147-158 (2007). DOI:10.1016/j.memsci.2007.02.028
Recent Publications
  1. Siddarth Achar, Jacob Wardzala, Leonardo Bernasconi, Linfeng Zhang, J. Karl Johnson, "A Combined Deep Learning and Classical Potential Approach for Modeling Diffusion in UiO-66", Journal of Chemical Theory and Computation, 18, 3593-3606 (2022). DOI: 10.1021/acs.jctc.2c00010
  2. Kushantha Withanage, Kamal Sharkas, J. Karl Johnson, John Perdew, Juan Peralta, and Koblar Jackson, "Fermi-Löwdin Orbital Self-Interaction Correction of Adsorption Energies on Transition Metal Ions", Journal of Chemical Physics, 156, 134102 (2022). DOI: 10.1063/5.0078970
  3. Prakash Mishra, Yoh Yamamoto, J. Karl Johnson, Koblar A. Jackson, Rajendra R. Zope, Tunna Baruah, "Study of self-interaction-errors in barrier heights using locally scaled and Perdew-Zunger self-interaction methods", Journal of Chemical Physics, 156, 014306 (2022). DOI: 10.1063/5.0070893
  4. Venkata Swaroopa Datta Devulapalli, Ryan P. McDonnell, Jonathan P. Ruffley, Priyanka B. Shukla, Tian-Yi Luo, Mattheus L. De Souza, Prasenjit Das, Nathaniel L. Rosi, J. Karl Johnson, Eric Borguet, "The Identification of UiO-67 Metal Organic Framework Defects and Binding Sites through Ammonia Adsorption", ChemSusChem, 15, e202102217 (2022). DOI: 10.1002/cssc.202102217
  5. Jonathan M. Klan, Daniel K. Harper, Jonathan P. Ruffley, Xing Yee Gan, Jill E. Millstone, J. Karl Johnson "A Theoretical Study of the Impact of Vacancies and Disorder on the Electronic Properties of Cu2-xSe", Journal of Physical Chemistry C, 125, 22, 12324-12332 (2021). DOI: 10.1021/acs.jpcc.1c02147
Department of Chemistry, University of Pittsburgh
Ph.D., Chemical Physics, Harvard University, 1984
Summary:

Exact and approximate wavepacket dynamics techniques, developed in our group and elsewhere, have been utilized to investigate experimentally observable signatures of condensed phase quantum dynamics. Specific processes include resonance Raman spectra of chromophores (e.g. CS2) in solvents of various polarities, electron transfer of mixed valences transition metal complexes in polar solvents and electron stimulated desorption of adsorbates from solid surfaces. [(e.g., CO on Cu].

Theoretical issues include development of (i) numerical algorithms capable of solving the many-body time-dependent Schrodinger Equation, (ii) implementable formalism for extracting spectroscopic observables from condensed phase wavepacket simulations, and (iii) simple models (e.g., of a single particle interacting with an environment) to aid in the interpretation of experimental and simulation data.

Frontiers include (i) quantum dynamics of systems immersed in liquids and other amorphous environments, (ii) determination of Born-Oppenheimer level electronic structure "on the fly" in the course of during nuclear wavepacket dynamical evolution, (iii) accurate treatment of ele ctronuclear coupling effects, for example, in nondiabatic transition processes, and (iv) understanding the effect of applied laser fields on electron transfer reactions.  

Selected Publications: 
  • "Free energy of nanoparticle binding to multivalent polymeric substrates," Chad Gu, Rob D. Coalson, David Jasnow, and Anton Zilman, J. Phys. Chem. B 121, 6425 (2017)
  • "Precise control of polymer coated nanopores by nanoparticle additives: Insights from computational modeling," Afshin Eskandari Nasrabad, David Jasnow, Anton Zilman, and Rob D. CoalsonJournal of Chemical Physics 145, 064901 (2016)
  • "Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the nuclear pore complex," Vovk, A., Gu, C., Opferman, M.G., Kapinos, L.E., Lim, R.Y.H., Coalson, R.D., Jasnow, D., Zilman, A., eLife 5, e10785 (2016)
  • "Water and ion permeability of a claudin model: A computational study," Laghaei, R., Yu, A.S.L., Coalson, R.D.Proteins: Structure, Function and Bioinformatics 84, 305 (2016)
  • "A polymer-brush-based nanovalve controlled by nanoparticle additives: Design principles," Coalson, R.D., Eskandari Nasrabad, A., Jasnow, D., Zilman, A., J. Phys. Chem. B 119, 11858 (2015)
  • "Calculation of iron transport through human H-chain ferritin," Laghaei, R., Kowallis, W., Evans, D.G., Coalson, R.D., J. Phys. Chem. A 118, 7442 (2014)
Most Cited Publications
  1. "A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel," MG Kurnikova, RD Coalson, P Graf, A Nitzan, Biophysical Journal 76.2 (1999)
  2. "Molecular basis for cation selectivity in claudin-2–based paracellular pores: identification of an electrostatic interaction site," Alan S.L. Yu, Mary H. Cheng, Susanne Angelow, Dorothee Günzel, Sanae A. Kanzawa, Eveline E. Schneeberger, Michael Fromm, Rob D. Coalson, Journal of General Physiology 133.1 (2009)
  3. "A nonequilibrium golden rule formula for electronic state populations in nonadiabatically couples systems," RD Coalson, DG Evans, A Nitzan, Journal of Chemical Physics 101.1 (1994)
  4. "Three-dimensional Poisson-Nernst-Planck theory studies: Influence of membrane electrostatics on gramicidin A channel conductance," AE Cardenas, RD Coalson, MG Kurnikova, Biophysical Journal 79.1 (2000)
  5. "Fourier path-integral Monte Carlo methods: Partial averaging," JD Doll, RD Coalson, DL Freeman, Physical Review Letters 55.1 (1985)
Recent Publications
  1. "Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse grained simulations test simple approximate theories,"  M Ozmaian, D Jasnow, AE Nasrabad, A Zilman, and RD CoalsonJournal of Chemical Physics 148.2 (2018)
  2. "Controlling the Surface Properties of Binary Polymer Brush-Coated Colloids via Targeted Nanoparticles" Ozmaian, M., Freitas, B.A., Coalson, R.D. Journal of Physical Chemistry B
  3. “Calculating tracer currents through narrow ion channels: Beyond the independent particle model." Coalson, R.D., Jasnow, D.     Journal of Physics Condensed Matter
    30(29),294002. (2018).
  4. "Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories." Ozmaian, M., Jasnow, D., Eskandari Nasrabad, A., Zilman, A., Coalson, R.D.     Journal of Chemical Physics 148(2),024902. (2018).
  5. "Driven water/ion transport through narrow nanopores: A molecular dynamics perspective." Coalson, R.D.     Faraday Discussions 209, pp. 249-257. (2018).
  6. "Free Energy of Nanoparticle Binding to Multivalent Polymeric Substrates." Gu, C., Coalson, R.D., Jasnow, D., Zilman, A.     Journal of Physical Chemistry B 121(26), pp. 6425-6435. (2017).
Department of Chemistry, University of Pittsburgh
Ph.D., Biophysics, University of California San Francisco, 2002
Summary:

Our research is focused on the use of molecular simulations to characterize the free energy landscapes and kinetics of a variety of biological processes, including large protein conformational transitions and protein binding. We have also been developing simulation strategies for aiding the design of protein-based conformational switches. Finally, we are developers of an upcoming AMBER force field and https://westpa.github.io/westpa/, a freely available, highly scalable software implementation of weighted ensemble path sampling strategies for the simulation of rare events (e.g. protein folding and protein binding).

Our research falls into the following main areas:

1) Development of weighted ensemble path sampling strategies and software for the efficient sampling of rare events (e.g. protein folding and binding) with rigorous kinetics.

2) Application of molecular simulations to investigate the mechanisms of protein conformational transitions, binding, and assembly processes.

3) Development of molecular simulation strategies for aiding the design of protein conformational switches.

4) Development of biomolecular force fields.

Selected Publications: 
  • "Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (Review)," Zuckerman, D.M.Chong, L.T., Annual Review of Biophysics 46, 43 (2017)
  • "Path-sampling strategies for simulating rare events in biomolecular systems," Chong, L.T., Saglam, A.S., Zuckerman, D.M., Current Opinion in Structural Biology 43, 88, (2017)  
  • "Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide," Zwier, M.C., Pratt, A.J., Adelman, J.L., Kaus, J.W., Zuckerman, D.M., Chong, L.T., J. Phys. Chem. Lett 7, 3440 (2016)
  • "Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model," Debiec, K.T., Cerutti, D.S., Baker, L.R., Gronenborn, A.M., Case, D.A., Chong, L.T., J. Chem. Theory Comput. 12, 3926 (2016)
  • "Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models," Saglam, A.S., Chong, L.T., J. Phys. Chem. B 120, 117 (2016)
Most Cited Publications
  1. "Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models"  Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
  2. "The Amber biomolecular simulation programs" Case, D.A., Cheatham III, T.E., Darden, T., (...), Wang, B., Woods, R.J. Journal of Computational Chemistry 26(16), pp. 1668-1688
  3. "GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit" Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
  4. "Docking and scoring in virtual screening for drug discovery: Methods and applications" Kitchen, D.B., Decornez, H., Furr, J.R., Bajorath, J. 2004 Nature Reviews Drug Discovery
  5. "Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model" Onufriev, A., Bashford, D., Case, D.A. Proteins: Structure, Function and Genetics
Recent Publications
  1. "Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields,"  K T Debiec, A M Gronenborn, and L T Chong Journal of Physical Chemistry B 123.19 (2019)
  2. "Large enhancement of response times of a protein conformational switch by computational design,"  Alex J. DeGrave, Jeung-Hoi Ha, Stewart N. Loh & Lillian T. Chong, Nature Commnications, 9, 1013 (2018).
  3. "Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein." Debiec, K.T., Whitley, M.J., Koharudin, L.M.I., Chong, L.T., Gronenborn, A.M.     Biophysical Journal 114(4), pp. 839-855. (2018).
  4. "WESTPA 2.0 Advances in Sampling, Storage, and Analysis of Weighted Ensemble Simulations,"  AJ Pratt, D M Zuckerman, and L T ChongBiophysical Journal 114.3 (2018)
  5. "Links between the charge model and bonded parameter force constants in biomolecular force fields." Cerutti, D.S., Debiec, K.T., Case, D.A., Chong, L.T.     Journal of Chemical Physics 147(16),161730. (2017).
Department of Chemistry, Carnegie Mellon University
Ph.D., Chemistry, State University of New York at Stony Brook, 1988
Summary:

The main research goal of the Kim group is to gain theoretical understanding of condensed-phase chemical and electrochemical processes at the molecular level with proper account of solvation effects. They develop and apply analytic models and computational methods, viz., statistical mechanics theory, quantum chemistry tools and molecular dynamics simulations, to quantify solvation effects on free energetics and dynamics of chemical reactions and related spectroscopy in homogeneous and heterogeneous environments. Their primary focus is on solution systems that have important environmental, biological or energy implications. 

Our specific thrust areas include:

  • Solvation and chemical reactions in green solvents: The primary focus is on chemical reactions involving charge shift (e.g., SN1 and electron transfer reactions) and related dynamics (e.g., dielectric relaxation and vibrational energy relaxation) in environmentally benign green solvents, in particular, room-temperature ionic liquids and supercritical water.
  • Energy storage: Supercapacitors and pseudocapacitors: The main effort is directed towards quantitation of how electrode properties such as size and shape of carbon micropores and electrolyte properties, e.g., ion size, density and conductivity, control the energy and power densities of EDLCs.
  • Structure and dynamics of multi-domain proteins: The current thrust is to investigate specific bindings and interactions between domains of plasminogen using various simulation techniques.
Most Cited Publications
  1. "Mass spectrum of chiral ten-dimensional N=2 supergravity on S5,"  HJ Kim, LJ Romans, and P van Nieuwenhuizen.  Physical Rev D 32.2 (1985)
  2. "Nanoporous Carbon Supercapacitors in an Ionic Liquid: A Computer Simulation Study," Youngseon Shim and Hyung J. Kim, ACS Nano 4, 2345 (2010)
  3. "Equilibrium and nonequilibrium solvation and solute electronic structure I. Formulation," HJ Kim and JT Hynes.  Journal of Chemical Physics 93.7 (1990)
  4. "Equilibrium and nonequilibrium solvation and solute electronic structure.  III. Quantum theory," HJ Kim and JT Hynes.  Journal of Chemical Physics 96.7 (1992)
  5. "Solvation in molecular ionic liquids," Y SHim, J Duan, MY Choi, and HJ KimJournal of Chemical Physics 119.13 (2003)
Recent Publications
  1. "Vibrational spectroscopy of imidazolium-based ionic liquids: A combined MD/DFT study,"  J Liu, H Kim, NR Dhumal, and HJ KimJournal of Molecular Liquids 292 (2019)
  2. "Modeling neural circuit, blood-brain barrier, and myelination on a microfluidic 96 well plate," SR Lee, S Hyung, S Bang, Y Lee, J Ko, S Lee, HJ Kim, and NL Jeon, Biofabrication 11.3 (2019)
  3. "Gold-Paladium Nanoalloys Supported by Graphene Oxide and Lamellar TiO2 for Direct Synthesis of Hydrogen Peroxide," S Guo, S Zhang, Q Fang, H Abroshan, HJ Kim, M Haruta, and G Li.  ACS Applied Materials & Interfaces 10.47 (2018)
  4. "Theoretical Study of Alkylculfonic Acids: Force-Field Development and Molecular Dynamics Simulations."  Jiannan Liu, Nilesh R Dhumal, and Hyung J KimJournal of Phys. Chem. B 122.42 (2018)
  5. "Deconvolution of Conformational Equilibria in Methimazolium-Based Ionic Liquid Ion Pair: Infrared Spectroscopic and Computational Study." Nilesh R. Dhumal, Arsalan Mirjafari, and Hyung J KimJournal of Molecular Liquids 266 (2018)
Department of Chemistry, University of Pittsburgh
Ph.D., Physical Chemistry, Massachusetts Institute of Technology, 1974
Summary:

The Jordan group's research interests lie in several areas:

Accomodation of excess charge by water clusters: Excess electrons and protons in water are engaged in a wide range of important chemical, biological, and geochemical processes. Our group has been especially interested in understanding how these charged particles are accommodated by the water networks. Much of our work in this area is in collaboration with the Johnson group at Yale, which uses vibrational predissociation spectroscopy as a probe of the structure of the clusters. The resulting spectra tend to be highly anharmonic, providing a significant challenge to theory. Our group has been engaged in the development of model Hamiltonian approaches to characterize excess electrons in water and to understand the trends in the OH stretch spectra of protonated water clusters.

Long-range correlation effects: We are engaged in developing methods to describe long-range correlation effects in molecules, clusters, and at surfaces. This work includes extensions of the dispersion-correlated atomic potential (DCACP) procedure of Rothlesberger and co-workers, and the use of quantum Drude oscillators to describe long-range correlation effects between excess electrons and molecules and clusters.

Quantum Monte Carlo methods: The DMC method is highly parallel and can be run over tens of thousands of CPU cores enabling calculation of accurate energies for systems for which large basis set CCSD(T) calculations are not feasible. The main approximation of DMC calculations is the fixed-node approximation, which is made to maintain fermionic character of the wavefunction. Our research is focused on the development of improved nodal approximations via the use of multiconfigurational trial functions.

Sustainability: We are using computational methods to address a range of problems relevant to clean energy and sustainability. These include modeling heat transport in methane hydrate and other hydrates and elucidation of the role of water in the uptake of CO2 by clays. In these studies, we are using classical Monte Carlo and molecular dynamics simulation methods with classical force fields.

 

Most Cited Publications
  1. "Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer," K. Kim, K. D. JordanJ. Phys. Chem. 98, 10089 (1994)
  2. "Spectral Signatures of Hydrated Proton Vibrations in Water Clusters," Jeffrey M. Headrick, Eric G. Diken, Richard S. Walters, Nathan I. Hammer, Richard A. Christie, Jun Cui, Evgeniy M. Myshakin, Michael A. Duncan, Mark A. Johnson, Kenneth D. JordanScience 108, 1765 (2005)
  3. "Infrared Signature of Structures Associated with the H+(H2O)n (n = 6 to 27) Clusters," J.-W. Shin, N. I. Hammer, E. G. Diken, M. A. Johnson, R. S. Walters, T. D. Jaeger, M. A. Duncan, R. A. Christie, K. D. JordanScience 304, 1137 (2004)
  4. "Studies of the temporary anion states of unsaturated hydrocarbons by electron transmission spectroscopy," Kenneth D. Jordan, Paul D. Burrow, Acc. Chem. Res. 11, 341 (1978)
  5. "Role of water in electron-initiated processes and radical chemistry: Issues and scientific advances,"  KD Jordan et. al., Chemical Reviews 105.1 (2005)
Recent Publications
  1. "Prediction of a Non-Valence Temporary Anion State of  (NaCl)2," A Kairalapova, KD Jordan, MF Falcetta, DK Steiner, BL Sutter, and JS Gowen.  Journal Phys. Chem. B (2019)
  2. "Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface,"  J Denton, PJ Kelleher, MA Johnson, MD Baer, SM Kathmann, CJ Mundy, BA Wellen Rudd, HC Allen, TH Choi, and KD JordanProceedings of the National Academy of Sciences (2019)
  3. "Prediction of a Non-Valence Temporary Anion Shape Resonance for a Model (H 2 O) 4 System,"  A Kairalapova, KD Jordan, DN Maienshein, MC Fair, and MF Falcetta.  Journal of Physical Chemistry A 123.13 (2019)
  4. "Tag-Free and Isotopomer-Selective Vibrational Spectroscopy of the Cryogenically Cooled H9O4+ Cation with Two-Color, IR–IR Double-Resonance Photoexcitation: Isolating the Spectral Signature of a Single OH Group in the Hydronium Ion Core." Duong, Chinh H., Nan Yang, Patrick J. Kelleher, Mark A. Johnson, Ryan J. DiRisio, Anne B. McCoy, Qi Yu, Joel M. Bowman, Bryan V. Henderson, and Kenneth D. Jordan. The Journal of Physical Chemistry A (2018).
  5. "Accurate Predictions of Electron Binding Energies of Dipole-Bound Anions via Quantum Monte Carlo Methods." Hao, Hongxia, James Shee, Shiv Upadhyay, Can Ataca, Kenneth D. Jordan, and Brenda M. Rubenstein. The journal of physical chemistry letters 9, no. 21 (2018): 6185-6190.

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