Chemistry

Department of Chemistry, University of Pittsburgh
Ph.D., Chemistry, University of Chicago, 1983
Summary:

The Chiral-Induced Spin Selectivity Effect

Waldeck’s group is examining the nature of the Chiral-Induced Spin Selectivity (CISS) effect and exploring ways in which it can be exploited technologically. As electrons move through a chiral molecule (or structure) the electron current generates an effective magnetic field, , that acts on the electrons’ intrinsic magnetic moment. Thus, a preference exists for electrons with one magnetic moment direction to pass through the chiral molecule (or structure). A thorough understanding of the properties that affect the chiral induced spin selectivity effect is important for realizing its true potential.

The chiral induced spin selectivity effect can be exploited for facilitating chemical reactions. We demonstrated that chiral materials are accompanied by a spin polarization that can be used to discriminate between triplet and singlet reaction pathways. Additionally, these studies are guiding the development of new methods for enantiomeric separation and discrimination.

Chiral nanomaterials represent a new class of materials with promising properties for applications in the fields of optoelectronics and spintronics, amongst others. This part of our group is focused on the synthesis of new chiral nanomaterials and understanding mechanistically how the chirality manifests. These studies are pointing to structure – property relationships for the rational design of new chiral materials. We are studying spin-mediated processes of chiral materials and the tantalizing phenomena that manifest. Our work is leading to technological breakthroughs in the separation of enantiomers, the miniaturization of ferromagnets, and chiral oxide spin filters.

Most Cited Publications
  1. "Photoisomerization dynamics of stilbenes." David H Waldeck. Chemical Reviews.
  2. "Noncovalent engineering of carbon nanotube surfaces by rigid, functional conjugated polymers." Jian Chen, Haiying Liu, Wayne A Weimer, Mathew D Halls, David H Waldeck, Gilbert C Walker. Journal of the American Chemical Society.
  3. "Breakdown of Kramers theory description of photochemical isomerization and the possible involvement of frequency dependent friction." Stephan P Velsko, David H Waldeck, Graham R Fleming. The Journal of Chemical Physics.
  4. "Spintronics and chirality: Spin selectivity in electron transport through chiral molecules." Ron Naaman and David H. Waldeck. Annu. Rev. Phys. Chem 66 (2015), 263-281. 
  5. "Chiral-induced spin selectivity effect." Ron Naaman and David H. Waldeck, The Journal of Physical Chemistry Letters 3 (2012), 2178-2187.
Recent Publications
  1. "Chiral Induced Spin Selectivity and Its Implications for Biological Functions" Ron Naaman, Yossi Paltiel, and David H. Waldeck. Ann. Rev. Biphysics. 51 (2022)99-114. 
  2. "Enantiospecificity of Cysteine Adsorption on a Ferromagnetic Surface: Is It Kinetically or Thermodynamically Controlled?" Yiyang Lu, Brian P. Bloom, Shangyu Qian, David H. Waldeck. J. Phys. Chem. Letters 12 (2021) 7854-7858. 
  3. "Delocalization-assisted transport through nucleic acids in molecular junctions" Jesus Baldiviezo, Caleb Clever, Edward Beall, Alexander Pearse, Yookyung Bae, Peng Zhang, Catalina Achim, David N. Beratan, and David H. Waldeck. Biochemistry 60 (2021) 1368-1378. 
  4. "The spin selectivity effect in chiral materials" David H. Waldeck, Ron Naaman, Yossi Paltiel APL Materials 9 (2021) 040902. 
  5. "Increasing the Efficiency of Water Splitting through Spin Polarization using Cobalt Oxide Thin Film Catalysts." Supriya Ghosh, Brian P. Bloom, Yiyang Lu, Daniel Lamont, and David H. Waldeck. J. Phys. Chem. C 124 (2020) 22610-22618.
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 and Biochemistry, Duquesne University
Ph.D., Chemistry, Texas A&M University, 1994
Summary:

Undergraduate and graduate students in the van Stipdonk research group use ion trap mass spectrometry, spectroscopy and theory to study a variety of chemical processes in the gas-phase. As summarized below, our current research projects can be grouped into three general areas: (a) fundamental studies of peptide ion dissociation to support application of tandem mass spectrometry (tandem MS) to peptide and protein identification in proteomics; (b) studies of the intrinsic stability and reactivity of metal ion complexes important to biology, energy production and the environment, and (c) vibrational spectroscopy of gas-phase ions using wavelength-selective infrared multiple-photon photodissociation. Besides extensive use of mass spectrometry and tandem MS, work in our laboratory involves the synthesis of model molecules and peptides, including those with isotope labels, and use of density functional theory (DFT) to predict ion structures, energies and vibrational spectra. Our work on tandem MS and peptide dissociation has been funded by the National Science Foundation (NSF). Studies of intrinsic metal ion chemistry have been supported by the U.S. Department of Energy and the Idaho National Laboratory. Work on ion spectroscopy is supported in part by the NSF, the Institue for Molecules and Materials, Radboud University Nijmegen; and the Nederlandse Organisatie voor Wetenschappelijk Onderzoek. 

Selected Publications: 
  1. "Formation of [UVOF4] by collision-induced dissociation of a [UVIO2(O2)(O2C-CF3)2] precursor," Michael Van Stipdonk, Amanda Bubas, Irena Tatosian, Evan Perez, Nevo Polonsky, Luke Metzler, Arpad Somogyi, International Journal of Mass Spectrometry 424, 58 (2018)
  2. "Equatorial coordination of uranyl: Correlating ligand charge donation with the Oyl-U-Oyl asymmetric stretch frequency," John K Gibson, Wibe A de Jong, Michael J van Stipdonk, Jonathan Martens, Giel Berden, Jos Oomens, Journal of Organometallic Chemistry (2017)
  3. "Cleaving Off Uranyl Oxygens through Chelation: A Mechanistic Study in the Gas Phase," Rebecca J Abergel, Wibe A de Jong, Gauthier J-P Deblonde, Phuong D Dau, Ilya Captain, Teresa M Eaton, Jiwen Jian, Michael J van Stipdonk, Jonathan Martens, Giel Berden, Jos Oomens, John K Gibson, Inorg. Chem., 56, 12930 (2017)
  4. "Thermodynamics and Reaction Mechanisms of Decomposition of the Simplest Protonated Tripeptide, Triglycine: A Guided Ion Beam and Computational Study," Abhigya Mookherjee, Michael J. Van Stipdonk, P. B. Armentrout, J. Am. Soc. Mass Spectrom. 28, 739 (2017)
  5. "Revealing Disparate Chemistries of Protactinium and Uranium. Synthesis of the Molecular Uranium Tetroxide Anion, UO4–," Wibe A. de Jong, Phuong D. Dau, Richard E. Wilson, Joaquim Marcalo,  Michael J. Van Stipdonk, Theodore A. Corcovilos, Giel Berden, Jonathan Martens, Jos Oomens,and John K. Gibson, Inorg. Chem., 56, 3686 (2017)
Most Cited Publications
  1. "Calcium phosphate phase identification using XPS and time-of-flight cluster SIMS." Charles C Chusuei, D Wayne Goodman, Michael J Van Stipdonk, Dina R Justes, Emile A Schweikert. Analytical chemistry.
  2. "Sequence-scrambling fragmentation pathways of protonated peptides." Christian Bleiholder, Sandra Osburn, Todd D Williams, Sándor Suhai, Michael Van Stipdonk, Alex G Harrison, Béla Paizs. Journal of the American Chemical Society.
  3. "Vibrational Characterization of Simple Peptides Using Cryogenic Infrared Photodissociation of H2-Tagged, Mass-Selected Ions." Michael Z Kamrath, Etienne Garand, Peter A Jordan, Christopher M Leavitt, Arron B Wolk, Michael J Van Stipdonk, Scott J Miller, Mark A Johnson. Journal of the American Chemical Society.
  4. "A Comparison of Desorption Yields from C+60 to Atomic and Polyatomic Projectiles at keV Energies." EA Schweikert, Michael J van Stipdonk, Ronny D Harris. Rapid communications in mass spectrometry.
  5. "Infrared spectroscopy of fragments of protonated peptides: direct evidence for macrocyclic structures of b 5 ions." Undine Erlekam, Benjamin J Bythell, Debora Scuderi, Michael Van Stipdonk, Béla Paizs, Philippe Maître. Journal of the American Chemical Society.
Recent Publications
  1. "Measurement of the asymmetric UO22+ stretching frequency for [UVIO2 (F) 3]-using IRMPD spectroscopy." Irena Tatosian, Luke Metzler, Connor Graca, Amanda Bubas, Theodore Corcovilos, Jonathan Martens, Giel Berden, Jos Oomens, Michael J Van Stipdonk. International Journal of Mass Spectrometry.
  2. "Formation and Hydrolysis of Gas‐phase [UO2(R)]+: R=CH3, CH2CH3, CH=CH2 and C6H5." Irena Tatosian, Amanda Bubas, Anna Iacovino, Susan Kline, Luke Metzler, Michael Van Stipdonk. Journal of Mass Spectrometry.
  3. "Gas-Phase Deconstruction of UO22+: Mass Spectrometry Evidence for Generation of [OUVICH]+ by Collision-Induced Dissociation of [UVIO2(C≡CH)]+." Michael J van Stipdonk, Irena J Tatosian, Anna C Iacovino, Amanda R Bubas, Luke J Metzler, Mary C Sherman, Arpad Somogyi. Journal of The American Society for Mass Spectrometry.
  4. "Computational Investigation of the Dissociation Pathways of Peptides." Mary C Sherman, Luke Metzler, Michael J Van Stipdonk. Biophysical Journal.
  5. "Isotope labeling and infrared multiple-photon photodissociation investigation of product ions generated by dissociation of [ZnNO3(CH3OH)2]+: Conversion of …." Evan Perez, Theodore A Corcovilos, John K Gibson, Jonathan Martens, Giel Berden, Jos Oomens, Michael J Van Stipdonk. European Journal of Mass Spectrometry.
Department of Chemistry, University of Pittsburgh
Ph.D., Northwestern University, 2008
Summary:

Inorganic and Materials Chemistry; Nanomaterials; Mechanochemistry; Surface and Colloid Chemistry

Whether they will be used in catalysis or artificial limbs, nanoparticle surfaces influence every aspect of their behavior. The ligand shell of a nanocrystal can determine its luminescence, its performance in a solar cell, or its clearance from the human body – to name just a few examples. In the Millstone group, we are interested in synthetically controlling this nanoparticle surface architecture – both the crystallographic and chemical composition – in order to develop new nanoparticle morphologies and reaction mechanisms that will have applications in fields ranging from catalysis to medicine.

Colloidal Nanoparticle Alloys: From bronze to steel, alloyed materials have defined the technological capabilities of their times, and like their monometallic counterparts, can experience dramatic changes in their physical properties at the nanoscale. Small, multimetallic nanoparticles (diameter = 1-5 nm) promise to provide improved catalysts for efficient use of fossil fuel resources as well as multifunctional tools in biomedical applications. However, current methods to prepare discrete, multimetallic particles afford limited tunability of particle composition, especially with respect to selectivity between alloyed, core-shell and Janus architectures. We use particle surface chemistry to control nanoparticle composition and elucidate both the synthesis and the resulting materials using a wide variety of electron microscopy and molecular characterization techniques. 

Multifunctional Nanoparticle Synthesis:  It is well known that the physical properties of nanoscale materials are highly dependent on their morphology. However, there is currently no systematic way to design and then rationally access a particular nanoparticle architecture. Elucidating these pathways would allow us to better use our current materials, and more effectively tailor new ones. Just as organic chemistry research has developed a mechanistic framework and synthetic toolbox that has produced everything from plastics to pharmaceuticals, so too must these concepts be developed for nanochemistry in order to harness the similar potential of nanomaterials. Through the discovery of nanoparticle reaction mechanisms, we work to develop a set of physical, analytical, and synthetic principles to rationally generate complex, highly-tailored nanoparticles for environmental remediation and catalysis applications.

Mechanochemistry of nanoparticles: At the nanoscale, the interplay between mechanical forces and physical properties is likely exaggerated compared to bulk materials. We are interested in understanding how mechanical forces can be used to manipulate the chemical reactivity of nanostructures. We will work to understand the response of anisotropic nanoparticles to mechanical stresses, and establish how mechanical perturbation can be used as a new type of synthetic tool in the development and application of nanomaterials.

Most Cited Publications
  1. "Observation of a quadrupole plasmon mode for a colloidal solution of gold nanoprisms." Jill E Millstone, Sungho Park, Kevin L Shuford, Lidong Qin, George C Schatz, Chad A Mirkin. Journal of the American Chemical Society.
  2. "Colloidal gold and silver triangular nanoprisms." Jill E Millstone, Sarah J Hurst, Gabriella S Metraux, Joshua I Cutler, Chad A Mirkin. small.
  3. "Rationally designed nanostructures for surface-enhanced Raman spectroscopy." Matthew J Banholzer, Jill E Millstone, Lidong Qin, Chad A Mirkin. Chemical Society Reviews.
  4. "Oligonucleotide loading determines cellular uptake of DNA-modified gold nanoparticles." David A Giljohann, Dwight S Seferos, Pinal C Patel, Jill E Millstone, Nathaniel L Rosi, Chad A Mirkin. Nano letters.
  5. "The role radius of curvature plays in thiolated oligonucleotide loading on gold nanoparticles." Haley D Hill, Jill E Millstone, Matthew J Banholzer, Chad A Mirkin. ACS nano.
Recent Publications
  1. "Zinc-Adeninate Metal–Organic Framework: A Versatile Photoluminescent Sensor for Rare Earth Elements in Aqueous Systems." Scott E Crawford, Xing Yee Gan, Peter CK Lemaire, Jill E Millstone, John P Baltrus, Paul R Ohodnicki Jr. ACS sensors.
  2. "Redefining the Experimental and Methods Sections." Jill E Millstone, Warren CW Chan, Cherie R Kagan, Luis M Liz-Marzán, Nicholas A Kotov, Paul A Mulvaney, Wolfgang J Parak, Andrey L Rogach, Paul S Weiss, Raymond E Schaak. ACS nano.
  3. "Announcing the 2019 ACS Nano Award Lecture Laureates." Holly Bunje, Jill E Millstone, Guangjun Nie, Andrew TS Wee, Tanja Weil, Sergey N Shmakov, Paul S Weiss. ACS nano.
  4. "Plasmon-Enhanced Chemical Conversion Using Copper Selenide Nanoparticles." Xing Yee Gan, Emily L Keller, Christopher L Warkentin, Scott E Crawford, Renee R Frontiera, Jill E Millstone. Nano letters.
  5. "Surface Chemistry-Mediated Near-Infrared Emission of Small Coinage Metal Nanoparticles." Scott E Crawford, Michael J Hartmann, Jill E Millstone. Accounts of chemical research.
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.
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., Physical Chemistry, University of California Berkeley, 2005
Summary:

An urgent problem in protein science is to understand ion uptake and ion recognition (selectivity) by proteins and polypeptides. This impacts proteins ranging from ion channels to ion sensors to metalloregulatory proteins to metallo-enzymes. Why and how are these bio-nanostructures so exquisitely sensitive to particular ions? How do local changes in the binding pockets lead to global conformational change? These questions have major implications for biology, and they need an answer from physical chemistry. In a separate field, that of green chemistry, there is another pressing problem to understand structural and dynamical heterogeneity in ionic liquids. What does this proposed heterogeneity imply about the solvation properties of these new "designer solvents''? Can we measure it? Can we use it to tune the solvent's properties? Better understanding the chemical physics of these systems will aid the rational design of new solvents, which in turn will have industrial consequences. There is an underlying connection between these biophysical and chemical physics questions – to really probe the mechanisms in operation, one must be able to separate static and dynamic heterogeneity. The nonliear spectroscopies developed in the Garrett-Roe lab can do exactly this. Multidimensional infrared spectroscopy can reveal structural dynamics on timescales spanning femtosecond–microseconds, and make molecular movies as reported by vibrational frequencies. These techniques will clarify

  1. The mechanism of ion selectivity in selectivity filter of an archetypal biological ion channel (KcsA).
  2. The conformational dance of guest and host in the molecular recognition of ionophores such as valinomycin.
  3. The binding of calcium ions in a biological ion sensor, EF hand, in a time- and reside-resolved way. Calcium uptake is a key step of many cellular signalling processes and is unexplored on a submicrosecond timescale.
  4. The structural and dynamical heterogeneity of ionic liquids. These fluids are a fascinating arena to move towards a deeper understanding of complex fluids.

Each of these experiments requires a combination of experimental expertise in the non-linear spectroscopy as well as skill modelling stochastic dynamics on a complex free energy landscape.

Most Cited Publications
  1. "Time- and angle-resolved two-photon photoemission studies of electron localization and solvation at interfaces," P. Szymanski1, S. Garrett-Roe, C.B. Harris, Progress in Surface Science 78, 1 (2005)
  2. "Electron Solvation in Two Dimensions," A. D. Miller, I. Bezel, K. J. Gaffney, S. Garrett-Roe, S. H. Liu, P. Szymanski, C. B. Harris, Science 297, 1163 (2002)
  3. "Intermolecular zero-quantum coherence imaging of the human brain," Rahim R. Rizi, Sangdoo Ahn, David C. Alsop, Sean Garrett-Roe, Marlene Mescher, Wolfgang Richter, Mitchell D. Schnall, John S. Leigh, Warren S. Warren, Magnetic Resonance in Medicine 43, 627 (2000)
  4. "Transient excitons at metal sufaces," Cui, X., Wang, C., Argondizzo, A., Garrett-Roe, S., Gumhalter, B., Petek, H., Nature Physics 10, no. 7 (2014)
  5. "Purely absorptive three-dimensional infrared spectroscopy," Sean Garrett-Roe and Peter Hamm, J. Chem. Phys. 130, 164510 (2009)
Recent Publications
  1. "An Ultrafast Vibrational Study of Dynamical Heterogeneity in the Protic Ionic Liquid Ethyl-ammonium Nitrate," Johnson, Clinton, Anthony W. Parker, Paul M. Donaldson, and Sean Garrett-Roe. ChemRxiv (2019).
  2. "Viscosity Dependence of the Ultrafast Vibrational Dynamics of Borohydride in NaOH Solutions: Crowding Effect on Dihydrogen Bonds," Johnson, Clinton, Kai C. Gronborg, Thomas Brinzer, Zhe Ren, and Sean Garrett-Roe. ChemRxiv (2019).
  3. "Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: III. Dynamics and Spectroscopy," Thomas Brinzer, Clyde A. Daly, Cecelia Allison, Sean Garrett-Roe, and Steven A. Corcelli, J. Phys. Chem. B (2018)
  4. "Hydrogen bond dynamics in protic ionic liquids: Ultrafast vibrational spectroscopy of SCN." Garrett-Roe, Sean. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 255. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, (2018).
  5. "POGIL activity clearinghouse: Helping authors to create, test, and distribute peer-reviewed POGIL activities." Garrett-Roe, Sean, Caryl Fish, Michael Garoutte, Melissa Reeves, Craig Teague, Robert Whitnell, Alexander Grushow, and Sally Hunnicutt. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 255. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, (2018).
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) 

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