Chemistry

Department of Chemistry, University of Pittsburgh
Ph.D. in Chemistry: Cornell University,1997
Summary:

Saxena Group is focused on developing Fourier Transform electron spin resonance and its application to otherwise inaccessible problems in biophysics. The coupling of electron spin angular momentum to its environment—as revealed by the ESR spectrum—provides rich information about the electronic, structural and dynamical properties of the molecule. Saxena group creates the methods that measure the precise distance between two units in a protein, in order to determine their folding patterns and conformational dynamics. These ESR Spectroscopic Rulers— based on multiple quantum coherences and double resonance experiments—are unique in that they resolve distances in the 1-16 nm length scale even on bulk amorphous materials. Much of this work is based on the use of first-principles theory to develop new experimental protocols and to analyze experimental results.

His group continues to develop applications of these spectroscopic rulers that range from capturing the essence of structural changes - such as misfolding - in proteins, to measuring the atomic-level details of ion-permeation in a ligand gated ion-channel. The main projects of his group include:

  • Pulsed ESR methods to measure distance constraints in systems containing paramagnetic metals
  • Measurement of structural and dynamical determinants of the protein-DNA interactions and functional dynamics in pentameric ligand gated ion-channels.
  • Application of the spectroscopic ruler to measure and predict global structures of nanostructured materials.
  • Role of metals in aggregation of Amyloid-β peptide.
Most Cited Publications
  1. "Nonlinear-least-squares analysis of slow-motion EPR spectra in one and two dimensions using a modified Levenberg–Marquardt algorithm." David E Budil, Sanghyuk Lee, Sunil Saxena, Jack H Freed. Journal of Magnetic Resonance, Series A.
  2. "Amplification of xenon NMR and MRI by remote detection." Adam J Moulé, Megan M Spence, Song-I Han, Juliette A Seeley, Kimberly L Pierce, Sunil Saxena, Alexander Pines. Proceedings of the National Academy of Sciences.
  3. "Double quantum two-dimensional Fourier transform electron spin resonance: Distance measurements." Sunil Saxena, Jack H Freed. Chemical physics letters.
  4. "Theory of double quantum two-dimensional electron spin resonance with application to distance measurements." Sunil Saxena, Jack H Freed. The Journal of chemical physics.
  5. "Direct Evidence That All Three Histidine Residues Coordinate to Cu(II) in Amyloid-β1−16." Byong-kyu Shin, Sunil Saxena. Biochemistry.
Recent Publications
  1. "19F Paramagnetic Relaxation-Based NMR for Quaternary Structural Restraints of Ion Channels." Vasyl Bondarenko, Marta M Wells, Qiang Chen, Kevin C Singewald, Sunil Saxena, Yan Xu, Pei Tang. ACS chemical biology.
  2. "Effects of MnO2 of different structures on activation of peroxymonosulfate for bisphenol A degradation under acidic conditions." Jianzhi Huang, Yifan Dai, Kevin Singewald, Chung-Chiun Liu, Sunil Saxena, Huichun Zhang. Chemical Engineering Journal.
  3. "Designing Open Metal Sites in Metal–Organic Frameworks for Paraffin/Olefin Separations." Mona H Mohamed, Yahui Yang, Lin Li, Sen Zhang, Jonathan P Ruffley, Austin Gamble Jarvi, Sunil Saxena, Götz Veser, J Karl Johnson, Nathaniel L Rosi. Journal of the American Chemical Society.
  4. "An Undergraduate Experiment To Explore Cu (II) Coordination Environment in Multihistidine Compounds through Electron Spin Resonance Spectroscopy." Eugene P Wagner, Kai C Gronborg, Shreya Ghosh, Sunil Saxena. Journal of Chemical Education.
  5. "Innentitelbild: EPR Spectroscopy Detects Various Active State Conformations of the Transcriptional Regulator CueR (Angew. Chem. 10/2019)." Hila Sameach, Shreya Ghosh, Lada Gevorkyan‐Airapetov, Sunil Saxena, Sharon Ruthstein. Angewandte Chemie.

Molecular Phenotypes of Structurally Homologous ETS Transcriptions Factors

Speaker(s): 
Gregory Poon
Dates: 
Thursday, September 28, 2017 - 4:30pm

 ETS transcription factors comprise an evolutionarily related family of genetic regulators that are ubiquitous in animals and control a myriad of physiologically critical processes. ETS proteins are united by a highly conserved DNA-binding domain, with overlapping target DNA preferences on the one hand, but are functionally diverse and non-redundant on the other. This so-called ìspecificity conundrumî besets not only our understanding of ETS homologs but also the structure-activity relationships of eukaryotic transcription factors in general. Translationally, it hampers efforts to develop...

Chemical Theory, Models and Computational Methods (CTMC)

  • By Aude Marjolin
  • 29 August 2016

The program supports the discovery and development of theoretical and computational methods or models to address a range of chemical challenges, with emphasis on emerging areas of chemical research. Proposals that focuson established theoretical or computational approaches should involve innovative additions or modifications that substantially broaden their applicability.

Areas of interest include, but are not limited to, electronic structure, quantum reaction dynamics, statistical mechanics, molecular dynamics, and simulation and modeling techniques for molecular systems and systems in condensed phases. Areas of application span the full range of chemical systems from small molecules to mesoscopic aggregates, including single molecules, biological systems and materials in condensed phases.

Department of Chemistry, University of Pittsburgh
Ph.D., Physical Chemistry, University of Wisconsin-Madison, 2013
Summary:

In the Laaser Lab, we are interested in developing a physical understanding of how changes at the molecular level translate to the macroscopic properties of responsive polymeric materials. For example, how does a change in charge spacing affect the interactions between charged polymers, and at what point do the polymers stop behaving like isolated chains in solution and start behaving like part of a bulk material? How do orientational changes in single polymer chains propagate through a material to achieve macroscopic ordering? And how do polymeric networks transduce force, to achieve things like mechanochemical responses?

We explore these questions by a number of optical and spectroscopic methods, such as light scattering and Raman and infrared spectroscopy, along with classical materials characterization methods like rheology and electron microscopy. Together, these methods allow us to develop new understanding of the structure and dynamic properties of responsive polymeric materials, and offer students the opportunity to gain broad experience in both physical chemistry and polymer science.

Most Cited Publications
  1. "Adding a dimension to the infrared spectra of interfaces using heterodyne detected 2D sum-frequency generation (HD 2D SFG) spectroscopy," Wei Xiong, Jennifer E. Laaser, Randy D. Mehlenbacher, and Martin T. Zanni, PNAS 108, 20902 (2011)
  2. "Time-Domain SFG Spectroscopy Using Mid-IR Pulse Shaping: Practical and Intrinsic Advantages," Jennifer E. Laaser, Wei Xiong, and Martin T. Zanni, J. Phys. Chem. B 115, 2536 (2011)
  3. "Transient 2D IR Spectroscopy of Charge Injection in Dye-Sensitized Nanocrystalline Thin Films," Wei Xiong, Jennifer E. Laaser, Peerasak Paoprasert, Ryan A. Franking, Robert J. Hamers, Padma Gopalanand Martin T. Zanni, J. Am. Chem. Soc. 131,18040 (2009)
  4. "Two-Dimensional Sum-Frequency Generation Reveals Structure and Dynamics of a Surface-Bound Peptide," Jennifer E. Laaser, David R. Skoff, Jia-Jung Ho, Yongho Joo, Arnaldo L. Serrano, Jay D. Steinkruger, Padma Gopalan, Samuel H. Gellman, and Martin T. Zanni, J. Am. Chem. Soc. 136, 95 (2014)
  5. "Bridge-Dependent Interfacial Electron Transfer from Rhenium−Bipyridine Complexes to TiO2 Nanocrystalline Thin Films," Peerasak Paoprasert, Jennifer E. Laaser, Wei Xiong, Ryan A. Franking, Robert J. Hamers, Martin T. Zanni, J. R. Schmidt and Padma Gopalan, J. Phys. Chem. C 114, 9898 (2010)
Recent Publications
  1. "Charge-Density-Dominated Phase Behavior and Viscoelasticity of Polyelectrolyte Complex Coacervates," J Huang, FJ Morin, and JE LaaserMacromolecules (2019)
  2. "Charge Density-and Hydrophobicity-Dependent Dynamics of Polyelectrolyte Complex Coacervates,"  J Laaser and J Huang.  APS Meeting Abstracts (2019)
  3. "19F Magnetic Resonance Imaging of Injectable Polymeric Implants with Multiresponsive Behavior." Sedlacek, Ondrej, Daniel Jirak, Andrea Galisova, Eliezer Jager, Jennifer E. Laaser, Timothy P. Lodge, Petr Stepanek, and Martin Hruby. Chemistry of Materials 30, no. 15 (2018): 4892-4896.
  4. "Composition-dependent dynamics in polyelectrolyte complex coacervates." Laaser, Jennifer, Frances Morin, and Jun Huang. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 255. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, 2018.
  5. "Charge Density-Dependent Phase Behavior and Rheology of Polyelectrolyte Complex Coacervates." Morin, Frances, and Jennifer Laaser. Bulletin of the American Physical Society (2018).

ACS Launches Chemistry Preprint Server

  • By Aude Marjolin
  • 15 August 2016

Authors can deposit draft chemistry papers in online archive before publication. The American Chemical Society announced today that it will create a preprint server for chemistry research to promote sharing of early scientific results.

Preprint servers allow researchers to publish draft papers or preliminary data online to get feedback from the larger research community before a paper goes through a journal’s more formal peer review process. “A preprint server dedicated to chemists will help speed the dissemination of research results, solicit valuable feedback, and foster international collaboration,” says Kevin Davies, a vice president in ACS’s Publications Division who is spearheading the effort.

ACS is currently seeking collaborators to join in development of the server, which is tentatively called ChemRxiv. The joint undertaking between two of ACS’s divisions—CAS and Publications—is expected to launch in the next few months.

Intermolecular Potentials from the Iterated Stockholder Atoms Approach

Speaker(s): 
Alston Misquitta
Dates: 
Friday, July 8, 2016 - 2:00pm

The Iterated Stockholder Atom (ISA) algorithm [1] is proving to be one of the most interesting methods for atoms‐in‐a‐molecule (AIM): it leads to a unique definition of the atoms which are guaranteed to be maximally spherical while allowing for the effects of charge movement as a result of chemical bonding. Through a basis‐space, or BS‐ISA, algorithm [2] we are able to calculate the ISA solution at the basis‐set...

Nanostructure-Controlled Heterogeneous Catalysts with Superior Catalytic Properties

Speaker(s): 
Wenyu Huang
Dates: 
Thursday, April 7, 2016 - 4:00pm to 5:30pm

Dr. Huang received a B.S. in Chemistry from Nanjing University, China in 2000. After receiving an M.S. in 2002 also from Nanjing University, he started his Ph.D. research with Professor Mostafa A. El-Sayed at Georgia Institute of Technology and received his Ph.D. in 2007. Dr. Huang then began postdoctoral research with Professor Gabor A. Somorjai at University of California,...

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.

Ken Jordan Organizes Session at the ACS Spring 2016 Meeting

  • By Aude Marjolin
  • 11 February 2016

The 251st American Chemical Society national meeting and exposition will be held from March 13-17, 2016 at San Diego, CA. The theme this year is "Computers in Chemistry", and PQI faculty Ken Jordan is co-organizing a session entitled Metastable Electronic States: Recent Advances In Theory and Experiment

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