ChemistryBen-Gurion University of the Negev Beer-Sheva, Israel

A Message from the Chairman

Ben-Gurion University of the Negev is the youngest, but the most dynamic university in Israel and the Chemistry Department is one of the reasons for the success of BGU. Over the years, the department has acquired a reputation for combining rigorous academic training for its students, with an accommodating atmosphere and personal treatment. Students feel that BGU is the most attractive university in Israel, and the chemistry students routinely rank their experiences very positively. Both undergraduate and graduate students view the time they spent in the department with fondness. This year we have had a great influx of new students in our first year; thus we have reached the sum of 200 undergraduate students, 86 of them freshmen. We also count with 130 graduate students, among them 63 PhD students and 30 Postdoctoral researchers; this accounts for a 16% rise over the total numbers last year.

Chemistry, as the science of change, is a broad field with important connections to virtually every other scientific discipline. For this reason, chemistry is often referred to as the central science. Consequently, research in the Department of Chemistry at Ben-Gurion University of the Negev reflects both the breadth and depth of the chemical sciences, spanning disciplines as disparate as low-temperature quantum physics, nanoscience, biological physics, chemical biology, as well as the classical fields of organic, inorganic, computational chemistry and physical chemistry.

The Department of Chemistry at Ben-Gurion University is the youngest chemistry department in Israel. Currently, the Department is undergoing a period of rapid change. Fifteen outstanding young scientists have joined the ranks of our faculty during the past 10 years alone, making our Department one of the most vibrant and exciting Chemistry Centers in Israel. According to the outstanding recent results, the Department has the potential to emerge as the leading Chemistry Department in Israel, and become one of the premier Chemistry Departments in the world. Just to cite a few examples, Prof. Ashraf Brik has received two very prestigious awards this past year: The 2013 Tetrahedron Young Scientist Award for Bioorganic and Medicinal Chemistry, the first time ever an Israeli scientist receives this prestigious prize! Ashraf also received the inaugural 2012 Teva Award for Excellence in Memory of Eli Hurvitz, another great honor for the Department and the University. We have three young scientists in the department, Prof. Michael Meijler, Prof. Gonen Ashkenasy and Prof. Taleb Mokari that have received the ERC Young Researcher Starting Grant, making our department the most successful chemistry department in Israel in this regard. Department faculty members have also received a variety of prestigious awards, including the Alon Fellowship, Krill Prize and the Toronto Prize. Furthermore, Department faculty are increasingly successful in obtaining funding from many of the major Israeli and international funding agencies, such as the Israel Science Foundation (ISF), the U.S. - Israel Binational Science Foundation (BSF), the Human Frontiers Science Program (HFSP),the German-Israeli Science Foundation (GIF), The Deutsch-Israelische Projectkooperation (DIP) and the various European FP7 grant programs. The quantity and quality of scientific papers being published by department members during the past few years certainly indicates a bright future ahead.

We also care deeply to strengthen and expand our ties with the surrounding community. New collaborative programs with the Chemical Industry around the Negev region and the recent “Marie Curie” Academic Chemistry Program for Outstanding High School Students of the Negev are proof that our faculty does not wish to be isolated in an academic “ivory tower”, but we are open towards our community and towards our ultimate goal to spread the passion of science and chemistry to the younger generation. The “Marie Curie” program is currently running in its first year with 35 outstanding high school pupils carefully selected by their respective school principals from Beer-Sheva, Dimona, Kiryat Gat and Yeruham. This program is supported by the City of Beer-Sheva, Keren Rashi and Makhteshim-Agan Industries. We are certain that these seeds that we are planting today will flourish to become the leading chemists and scientists of Israel in the future.

No doubt one can “feel the energy” of the chemistry department at BGU. This brochure is summarizing and highlighting the achievements of our active members, and we hope that it will aid in connecting you to our department. Sincerely,

Prof. N. Gabriel Lemcoff, Chemistry Department Chairman, December 2013

Overview of Research in the Department

Research in the Department of Chemistry at Ben-Gurion University of the Negev spans the traditional areas of Organic Chemistry, Inorganic Chemistry, and Physical Chemistry, as well as the newer interdisciplinary fields of Chemical Biology, Nanoscience and Technology, and Systems Chemistry.

Organic Chemistry research in the Department deals with topics ranging from catalysis, total synthesis of novel compounds, to analysis of molecular structure and reaction mechanisms, and improving the methods by which spectroscopic data is used to obtain valuable information. Some of the research has potential pharmaceutical applications, while other research may contribute toward the development of “clean energy” technologies.

Inorganic Chemistry research in the Department deals with topics such as novel organometallic catalysts and coordination complexes and the analysis of inorganic reaction mechanisms. Research in this area is being carried out by a dedicated and highly prolific group of scientists.

Physical and Biophysical Chemistry research in the Department deals with a broad range of topics, from the fundamental and high-precision analysis of hydrogen bonding and proton transfer in water, to highly theoretical work on the statistical mechanics of chemical reaction mechanisms. Of considerable strength is the focus in the Biophysical sub-group on membrane biophysics, as the Department has gained a strong reputation in this field in recent years.

Chemical Biology is a rapidly developing area within the Department. Within this sub-discipline, researchers are applying the principles and tools of chemistry to study important unresolved questions in biology with molecular precision. Specific projects aim at understanding and manipulating peptide chemistry, protein-protein and protein-ligand interactions and communication between bacterial species and between prokaryotes and eukaryotes. Ultimately, through a greater understanding of important biological pathways, novel compounds with pharmaceutical applications may be obtained.

Nanoscience and Technology is one of the newer and rapidly expanding sub-disciplines within the Department. Research in this area is also fairly broad, and overlaps with a number of the areas described above. In particular, research in Nanoscience and Technology in the Department cover topics such as the development of bio-mimetic compounds that may function as sensors in biological environments, the development of novel approaches for constructing photovoltaic cells that may be used in the generation of solar power, as well as more theoretical topics in atomic, molecular, and optical physics, such as the analysis of cold atom traps and the quantum mechanics of Bose-Einstein Condensates..

Finally, Systems Chemistry is another inter-disciplinary area that has attracted the attention of Department scientists in recent years. Whereas Systems Biology seeks to model the dynamics and behavior of entire biological systems and networks, Systems Chemistry seeks to uncover the chemical principles underlying the behavior of these networks, since, in the end, biological networks may be viewed as complex reaction networks involving numerous complex bio-molecules. Department research output and impact is rising steadily, and is published in a broad array of high-impact scientific journals, including some of the most prestigious journals, such as Nature, Science, PNAS, JACS, Angewante Chemie, and Physical Review Letters. Department faculty have also received a variety of prestigious awards, including the Alon Fellowship and the Toronto Prize. Furthermore, Department faculty are increasingly successful in obtaining funding from many of the major Israeli and international funding agencies, such as the Israel Science Foundation (ISF), the U.S. - Israel Binational Science Foundation (BSF), the Human Frontiers Science Program (HFSP), and the various European FP7 grant programs. The following part of this brochure contains more detailed information about the individual researchers in our department.

Department of Chemistry, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel. Phone: +972-8-646-1641 Fax: +972-8-647-2943. http://www.bgu.ac.il/chem/eng; E-mail: chemsec@bgu.ac.il

Dr. Eyal Arbely – Senior Lecturer

Synthetic Biology, Bioorganic Chemistry, Chemical Biology

Research in the Arbely group is devoted to the development and utilization of methods for genetic code expansion. The translation mechanism has been evolved over hundreds of millions of years to translate 64 triple-nucleotide codons, each encoding either one of the canonical 20/22 amino acids, or the termination of translation. Yet, this machinery is far from exploiting its full potential – proteins with expanded chemistry can be ribosomally synthesized by site-specific incorporation of non-proteinogenic amino acids, using the amber stop codon (UAG) and an orthogonal aminoacyl-tRNA synthetase/tRNA pair. We are using different methods for ribosomal expression of chemically and structurally modified proteins for basic biochemical or biophysical research and as a platform for developing peptide-based bioactive molecules.

Recent selected publications: · Arbely, E., Torres-Kolbus, J., Deiters, A. and Chin J.W. Photocontrol of Tyrosine Phosphorylation in Mammalian

Cells via Genetic Encoding of Photocaged Tyrosine. J. Am. Chem. Soc. 134(29), 11912-11915, (2012)· Arbely, E., Natan, E., Brandt T., Allen, M.D., Veprintsev, D.B., Robinson, C.V., Chin J.W., Joerger, A.C. and Fersht,

A.R. Acetylation of Lysine 120 of p53 Endows DNA Binding Specificity at Effective Physiological Salt Concentration. Proc. Natl. Acad. Sci. 108:8251-8256 (2011)

· Arbely, E., Rutherford, J.T., Sharpe, D.T., Ferguson, N. and Fersht, A.R. Downhill versus Barrier-Limited Folding of BBL 1: Energetic and Structural Perturbation Effects upon Protonation of a Histidine of Unusually Low pKa. J. Mol. Bio. 387(4), 986–992 (2009)

· Arkin, I.T., Xu, H., Jensen, Ø M., Arbely, E., Bennett, E.R., Bowers, K.J., Chow, E., Dror, R.O., Eastwood, M.P., Flitman-Tene R., Gregersen, B.A., Klepeis, J.L., Kolossváry, I., Shan, Y. and Shaw D.E. Mechanism of Na+/H+ Antiporting. Science 317(5839), 799–803 (2007)

· Arbely, E. and Arkin, I.T. Experimental Measurement of The Strength of a Cα–H···O Bond in a Lipid Bilayer. J. Am. Chem. Soc. 126(17), 5362–5363, (2004)

Dr. Gonen Ashkenasy - Associate Professor

Laboratory of Artificial Functional Peptides and Proteins

Research Interests - The Systems Chemistry of Peptide Networks The main research effort in our lab is devoted to the design and synthesis of multi-component chemical systems, termed as Molecular Networks, and for analysis of their dynamic self-organization. This study within the new field of Systems Chemistry is inspired by the complexity in structure and function observed within natural cells. We use peptides and proteins as the active components in these studies, and thus the observed structure-function relationships are further interpreted for understanding fundamental processes, such as protein folding as well as protein interactions with small molecules and bio-macromolecules.

Our findings can be used for understanding the organizational principles of biological systems, to shine light on plausible scenarios in early molecular evolution and the Origins of Life, and to develop devices of nanotechnology and biotechnology importance.

Selected publications:· B. Rubinov, N. Wagner, H. Rapaport, G. Ashkenasy, “Self Replicating Amphiphilic ß-Sheet Peptides”, Angew.

Chem. Int. Ed. 2009, 121, 6811-6814.· N. Wagner, E. Tannenbaum, G. Ashkenasy, “Second-Order Catalytic Quasispecies Model Yields Discontinuous

Mean Fitness at the Error Threshold”, Phys. Rev. Lett. 2010, 104, 188101/1-188101/4.· M. Samiappan, S. Alasibi, R. Cohen-Luria, A. Shanzer, G. Ashkenasy “Allosteric Effects in Coiled-Coil Proteins

Folding and Lanthanide-Ion Binding” Chem. Commun. 2012, 48, 9577-9579.· B. Rubinov, N. Wagner, M. Matmor, O. Regev, N. Ashkenasy, G. Ashkenasy “Transient Fibril Structures Facilitating

Non-Enzymatic Self-Replication” ACS nano, 2012, 6, 7893-7901.· Z. Dadon, M. Samiappan, A. Shahar, R. Zarivach, G. Ashkenasy “A High-Resolution Structure that Provides Insight

into Coiled-Coil Thiodepsipeptide Dynamic Chemistry” Angew. Chem. Int. Ed. 2013, 52, 9944-9947.

The current research includes the following topics:• Self-organization of replication networks• Peptide fibrils self-assembly and self-replication• Molecular computation• Protein-based functional elements in molecular electronics• Total synthesis of repeat proteins

Dr. Yehuda Band – Professor, Snow Chair in Nanotechnology

Atomic, Molecular, and Optical Physics, Theoretical Chemical Physics

Professor Band’s research interests include collision theory, light scattering, nonlinear optics, electro-optics and quantum-optics, laser physics and chemistry, electronic transport properties of matter, molecular dissociation, and thermodynamics. His foremost expertise is in quantum scattering and the interaction of light with matter. He has worked on photodissociation of molecules, transport of electrons in small electronic devices, ultra-cold collision phenomena in laser-cooled atom traps, Bose-Einstein condensation, quantum-degenerate fermionic systems, coherent matter waves, thermodynamics of processes occurring in finite time with finite rates, the relationship of absorption and emission in multilevel systems, application of the birefringence of solid-state laser media to laser line narrowing, light-induced population transfer in molecules, nonlinear optical properties of atoms and molecules, pulse compression and mode-locking of lasers, second harmonic generation, three-wave and four-wave mixing of light and matter waves, stimulated Raman processes, pulse compression in fiber Raman lasers, self-focusing of light, and optical and matter-wave solitons. Dr. Band’s research accomplishments include the following: He helped develop the theoretical analysis and the methods to calculate state-to-state photodissociation cross sections, angular distributions, branching ratios for diatomic molecules to open shell atoms. In studies of the quantum aspects of electronic conductance, he calculated the quantized electronic conductance and the magneto-conductance of mesoscopic devices. He and his colleagues proposed a method for copiously producing ultracold ground electronic state molecules by two-photon processes during collisions of ultracold atoms in a laser trap, and another method of producing even colder molecules using a Raman photoassociation process from an atomic Bose-Einstein condensate, and developed the quantum mechanical description of output coupling of macroscopic coherent matter waves from a Bose-Einstein Condensate via a radio-frequency field in the pulsed and cw limits for both strong and weak field coupling. He explained the experimental efficiency observed in the conversion of ultracold Fermi gases to molecules as the external magnetic field is tuned near a Feshbach resonance. He and his colleagues suggested an experiment that would be the first demonstration of nonlinear atom wave optics; an experimental group at NIST successfully carried out the experiment. He explained the spectral consequences that result from using birefringent media with broadband gain inside laser cavities containing polarizing elements. He formulated the dynamics and carry out calculations of nonlinear harmonic generation for multi-mode optical fields, and was instrumental in predicting novel propagation phenomena of intense short optical pulses in dispersive optical media, including pulse tilting in non-isotropic media, optical soliton propagation in the higher order nonlinear Schrodinger equation, and temporal and spatial pulse splitting in Kerr type optical media. He developed optimal-control techniques for quantum computing with atoms in optical lattices.

Dr. Band is the author of two books, Y. B. Band, Light and Matter: Electromagnetism, Optics, Spectroscopy and Lasers, (John Wiley, 2006), and Y. B. Band and Y. Avishai, Quantum Mechanics, with Applications to Nanotechnology and Quantum Information Science, (Elsevier, 2012).

Selected publications:· R. S. Tasgal and Y. B. Band, “Continuous wave solutions in spinor Bose-Einstein condensates”, Phys. Rev. A87,

023626 (2013).· P. Szańkowski, M. Trippenbach and Y. B. Band, “Spin decoherence due to Fluctuating Fields”, Phys. Rev. E87,

052112 (2013).· Y. B. Band, “Electric Dipole Moment in a Stochastic Electric Field”, Phys. Rev. E88, 022127 (2013).· Y. Avishai, Y. B. Band and M. Trippenbach, “Feshbach Resonance in a Simple Tight-Binding Model”, Phys. Rev.

Lett. 111, 155301 (2013).· Y. B. Band and Y. Ben-Shimol, “Molecules with an Induced Dipole Moment in a Stochastic Electric Field”, submitted

to Phys. Rev. E 88, 042149 (2013).

Dr. Maya Bar Sadan – Senior Lecturer

Nano-materials, Physical Chemistry, Electron microscopy

Chemistry at the atomic scaleRevealing nanoparticles in 3D: Nanoparticles are extensively researched for decades. However, most of their characterization was made by ensemble techniques, where enormous amounts of particles contribute to an average signal. The result is smearing of the information achieved from a single nanoparticle, many times hindering recognizing reaction paths. We focus on the characterization of nanoparticles in 3D at the atomic scale, to allow following chemical reactions, understand their mechanisms and offer direct connection between structure and properties. Novel phenomena in 2D layers: Few-layer MoS2 crystals attract a significant attention recently due to their exotic physical properties and for their promise as platform for future electronic, spintronic and optoelectronic technologies. The scientific community has started exploring other transition metal dichalcogenide (TMD) thin layers such as MoSe2 and WS2 as well. Although pure materials provide rich chemistry, to fully utilize their potential as well as for the purpose of uncovering new fundamental phenomena, we pursue their alloying and doping in order to manipulate their electronic and magnetic properties.

Selected publications:· Bar-Sadan, M.; Barthel, J.; Shtrikman, H.; Houben, L., Direct Imaging of Single Au Atoms Within GaAs Nanowires.

Nano Letters 2012, 12 (5), 2352-2356.· Bar-Sadan, M.; Houben, L.; Wolf, S. G.; Enyashin, A.; Seifert, G.; Tenne, R.; Urban, K., Toward atomic-scale bright-

field electron tomography for the study of fullerene-like nanostructures. Nano Letters 2008, 8 (3), 891-896.· Bar-Sadan, M.; Houben, L.; Enyashin, A. N.; Seifert, G.; Tenne, R., Atom by atom: HRTEM insights into inorganic

nanotubes and fullerene-like structures. Proceedings of the National Academy of Sciences of the United States of America 2008, 105 (41), 15643-15648.

· Chuntonov, L.; Bar-Sadan, M.; Houben, L.; Haran, G., Correlating Electron Tomography and Plasmon Spectroscopy of Single Noble Metal Core–Shell Nanoparticles. Nano Letters 2011, 12 (1), 145-150.

· Macdonald, J. E.; Bar-Sadan, M.; Houben, L.; Popov, I.; Banin, U., Hybrid nanoscale inorganic cages. Nature materials 2010, 9 (10), 810-815.

Dr. James Y. Becker – Professor Emeritus

Organic electrochemistry; Electrochemistry in Ionic liquids; Fluorescent sensors

The unifying theme in the Becker group is organic electrochemistry, with a focus on synthesis and mechanism.

Currently the group is studying:- Electrochemical properties of organo-silicon compounds, mainly cyclic, multiply-bonded and low-valent compounds. Recently we have utilized the anodic oxidation of a-silylacetic acids to generate disilylethane derivatives in good yields.- Electro-organic synthesis, For example the functionalizion of unsaturated and aromatic compounds by anodic oxidation of various anions (e.g., azides, thiocyanates). - Electro-catalysis by utilizing inorganic, organometallic and organic compounds, as mediators for organic and inorganic reactions, mostly in homogeneous non-aqueous solutions - Electrochemistry in Ionic Liquids.- Electro-catalytic oxidation of alcohols in the presence of organic mediators such as triarylamines and TEMPO;- Electro-catalytic reduction of molecular oxygen in the presence of metalo-porphyrins- Spectral and electrochemical properties of organic and organometallic chemical sensors for metal ion sensing.- Feasibility studies of various electrochemical projects for industry.

Recent Selected publications:· Alex Shtelman and James Y. Becker, “Electrochemical synthesis of 1,2-disilylethanes from alpha-silylacetic acids”,

J. Org. Chem., 2011, 76 (11), 4710-4714. [Highlighted by Prof. Douglass F. Taber in his Highlight column on “Carbon-Carbon Bond Formation”: www.organic-chemistry.org/Highlights/2012/12March.shtm].

· Anna Gitkis and James Y. Becker, “One-pot anodic thiocyanation of aromatic compounds”, Electrochim. Acta, 2010, 55, 5854–5859.

· Tatiana Golub and James Y. Becker, “Electrochemical oxidation of amides of type Ph2CHCONHAr”, Org. Biomol. Chem. (OBC), 2012, 10, 3906-3912.

· Libi Brakha and James Y. Becker, “Anodic oxidation of α-silylacetic acids (R2R’)SiCH2COOH): Effects of anode material, current density and concentration on competing decarboxylation and desilylation processes”, Electrochim. Acta, 2012, 77, 143-149.

· Efrat Korin, Beny Cohen,Yong-Dong Liu, Cheng-Chu Zeng, Alexander. I. Shames and James Y. Becker, “Examining the binding mechanism of 3,4-dihydro-3-(2-oxo-2-phenylethylidene)-quinoxalin-2(1H)-one to Cu2+”, J. Coord. Chem., 2013, 66:13, 2351-2366.

Dr. Joel Bernstein – Professor Emeritus

Crystal engineering and crystal growth and structure

Research Interests: Over the past five years our research efforts have continued in the area of polymorphism of molecular crystals, carrying out screens for crystal forms preparing and characterizing a variety of polymorphic systems. In this period we have also undertaken a rather intensive program in crystal engineering - attained through the tools of supramolecular chemistry, an understanding and use of the interactions between molecules. This project was undertaken to explore the possibility of utilizing a specific hydrogen-bonding motif as the basis for a strategy for the design and preparation of co-crystals of organic molecules. We have made significant progress in developing a successful strategy for the controlled preparation of co-crystals with a pre-designed structure by recognizing and utilizing specific intermolecular interactions. In particular, we investigated the utility of using the previously unrecognized and unutilized hydrogen-bonding motif, defined in graph set notation )8(2

4R

, as a supramolecular synthon for the generation of co-crystals. These studies involved a statistical analysis using the Cambridge Structural Database, high level molecular orbital calculations verified the relative stability of this intramolecular motif, and a proof-of-concept experiment on prototypical model compounds led to the designed product.Many subsequent experiments, designed to exploit the principles demonstrated by the proof-of-concept experiment were successful, while other serendipidously produced previous unknown crystal forms. In particular, we have produced a variety of co-crystals with this motif, including co-crystals of amino acids, co-crystals between cyclic ethers and ureas, polymorphic co-crystals, co-crystals with a number pharmaceutically important compounds. We have also produced a large variety of new polymorphic systems, including four polymorphs of benzidene, two new hydrates of oxalic acid, and three polymorphs of phenyl carbamate.

Recent Selected Publications:· I. Goldberg and J. Bernstein; “Disruption of Hexagonal Networks of Trimesic Acid (Benzene-1,3,5-Tricarboxylic

Acid, TMA) by Acetic Acid”, Chem. Comm., (2007), 132-134.· N. Belman, J.N. Israelachvili, Y. Li, C.R. Safinia, J. Bernstein and Y. Golana; ”Structure and Reactivity of Alkylamine

Surfactants: Relevance to Nanoscale Synthesis and Assembly” Nano Letters, (2009) 9, 2088-2093.· N. Belman, J.N. Israelachvili, Y. Li, C.R. Safinya, J. Bernstein and Y. Golan; “The Temperature-Dependent Structure

of Alkylamines and Their Corresponding Alkylamine-Alkylcarbamates” J. Am. Chem. Soc (2009), 131, 9108-9113.· P. Naumov, W. M. Rabeh, J. Bernstein, N. Yasuda; “The elusive crystal structure of the neuraminidase inhibitor

Tamiflu (oseltamivir phosphate): Molecular details of action” Chem. Comm. (2013) 49, 1948-1950· A. J. Cruz-Cabeza, and J. Bernstein; “Conformational Polymorphism” Chem. Rev. (2014), in press

Dr. Ashraf Brik – Professor

Bioorganic Chemistry, Chemical Biology, Chemical Protein Synthesis

Research in the Brik group focuses on chemical and semisynthesis of posttranslationally modified proteins to study the role of these modifications at the molecular level. Posttranslational modifications play an important role in regulating protein structure and function in health and disease. Ubiquitylation is one example for such a modification wherein both the extent (polyubiquitylation vs mono-ubiquitylation) and the sequence position of this modification dictates the function and fate of the ubiquitylated protein. In the ubiquitylation process three distinct enzymes, known as the E1-E3 system, collaborate to achieve a site-specific tagging of the lysine residue(s) in the target protein. This condensation step generates an isopeptide linkage between the -NH2 of the lysine residue and the activated C-terminal glycine of ubiquitin (Ub). The overwhelming majority of studies in the field rely on the in vitro enzymatic reconstitution of this complex posttranslational modification for the protein of interest. However, this process is often challenged by the heterogeneity of the modified protein, the isolation of the specific ligase (E3) and obtaining reasonable quantities of the ubiquitinated protein. We have recently reported the developments of highly efficient and site-specific peptide and protein ubiquitination utilizing thiolysine. Moreover, we were able to achieve the chemical synthesis of ubiquitin thioester as a key intermediate in the ubiquitination process. This battery of chemical tools allowed for the first semi-synthesis of homogeneous ubiquitinated alpha-synuclein to support the ongoing efforts aiming at studying the effect of ubiquitination in health and disease. In addition, the total chemical synthesis of all Lys-linked di-ubiquitin chains as well as the K48-linked tetra-ubiquitin, composed of 304 amino acids, was also achieved. More recently, the synthesis of ubiquitinated peptides linked to mono-, di-, tri, and tetra-ubiquitin (K48 and K63) was also made possible, which enabled us to examine the behavior of these novel bioconjugates with several deubiquitinases. We have also expanded these approaches to target different deubiquitinases in the ubiquitin system to shed light on their role in health and disease, and ultimately, for drug development.

Recent Selected publications:• “Highly Efficient and Chemoselective Peptide Ubiquitylation”: K. S. A. Kumar, M. Haj-Yahya, D. Olschewski, H.A.

Lashuel, A. Brik, Angew. Chem. Int. Ed. 2009, 48, 8090–8094. • “Total Chemical Synthesis of Di-ubiquitin Chains”: K. S. A. Kumar, L. Spasser, S. Bavikar, L.A. Erlich, A. Brik Angew.

Chem. Int. Ed. 2010, 49, 9126–9131. • “Total Chemical Synthesis of a 304 Amino Acid K48-Linked Tetraubiquitin Protein “: K. S. A. Kumar, S. N. Bavikar,

L. Spasser, T. Moyal, S. Ohayon, and A. Brik, Angew. Chem. Int. Ed. 2011, 50, 6137–6141. • “Targeting Deubiquitinases Enabled by Chemical Synthesis of Proteins”: S. Ohayon, L. Spasser, A. Aharoni, A. Brik,

J.Am.Chem.Soc. 2012, 134, 3281-3289. • “Synthesis of tetra-ubiquitinated α-Synuclein reveals novel insights into the roles of ubiquitin chain in regulating its

pathophysiology”: M. Haj-Yahya, B. Fauvet, Y. Herman-Bachinsky, M. Hejjaoui, S. N. Bavikar, S. V. Karthikeyan, A. Ciechanover, H. A. Lashuel, A. Brik, Proc.Natl Acad. Sci. USA 2013, doi:10.1073/pnas.1315654110.

Dr. Yonatan Dubi – Senior lecturer

Theoretical nano-science

Research in the Dubi group is devoted to the theoretical study of charge and energy transport in nano-scale systems such as single-molecule junctions, self-assembled monolayers, nano-particles and DNA-based structures. Current focus is on understanding the basic mechanisms that contribute or inhibit energy conversion such as thermo-electricity and photo-voltaic conversion in molecular junctions. Special emphasis is placed on quantum mechanical processes and their competition with classical processes. The group develops both the models and the theoretical tools needed to address the models, including a wide variety of numerical and analytical methods. Other interests include superconductivity and correlated electron systems and quantum effects in photosynthesis.

Recent Selected publications:• Y. Dubi, Dynamical coupling and negative differential resistance from interactions across the molecule-electrode

interface in molecular junctions, J. Chem. Phys. 139, 154710 (2013) .• Y. Dubi, Origin of thermoelectric response fluctuations in molecular junctions, New Journal of Physics, New J. Phys.

15 105004 (2013).• K. Velizhanin, C.-C. Chen, Y. Dubi and M. P. Zwolak, Tunable thermal switching via DNA-based nano-devices,

Nanotechnology 24, 095704 (2013).• J.-X. Zhu, J.-P. Julien, Y. Dubi and A. V. Balatsky, Local Electronic Structure and Fano Interference on Tunneling into

a Kondo Hole System, Phys. Rev. Lett. 108 1̧86401 (2012).• Y. Dubi and M. Di Ventra, Colloquium: Heat flow and thermoelectricity in atomic and molecular junctions, Review

of Modern Physics, 83, 131 (2011).

Dr. Leah Gheber – Senior Lecturer

Biophysical chemistry, molecular motors, dynamics of the cytoskeleton, mitotic cell division

Research Interests:Mitotic chromosome segregation is a process by which duplicated genomic information is transferred from mother to daughter cells. This essential process is accomplished by the spindle, a highly dynamic, microtubule-based structure, which in each mitotic cycle, undergoes a well-programmed set of morphological changes. Compromised spindle integrity is one of the key factors for chromosome mis-segregation, which in turn may lead to genetic disease, cell death and cancer. Recent evidence indicate that molecular nano-motors from the Kinesin superfamily, which bind and move along microtubules by hydrolyzing ATP, play central roles in mediating spindle dynamics.

Specifically, our research focuses on the study of Kinesin-5 mitotic motor proteins, whose function is essential for chromosome segregation during mitotic cell division. Our objective is to explore the mechanisms by which Kinesin-5 motors perform their multiple mitotic functions by combining biophysical, biochemical, cell biology and genetics approaches such as single-molecule fluorescence motility assays and live-cell microscopy. Until recently, Kinesin-5 motors were believed to perform their essential mitotic functions as slow, processive MT plus-end directed motors. However, we have recently shown that the Saccharomyces cerevisiae Kinesin-5 homologs Cin8 and Kip1 are bi-directional motors. In vitro, individual Cin8 and Kip1 molecules could be switched by ionic conditions from rapid and processive minus-end to slow plus-end motion on single MTs. Deletion of the uniquely large insert in loop 8 of Cin8 induced bias towards minus-end motility and affected the ionic-strength dependent directional switching of Cin8 in vitro. In vivo, the deletion mutant exhibited reduced midzone-directed motility and efficiency to support spindle elongation, indicating the importance of directionality control for the function of Cin8.

In our current and future research we examine the structural and regulatory elements that control the directionality of Kinesin-5 motors in vivo and in vitro.

Recent Selected publications:· V .Fridman ,A .Gerson-Gurwitz ,N .Movshovich ,M .Kupiec and L .Gheber. (2009) Midzone organization restricts

interpolar microtubule plus-end dynamics during spindle elongation. EMBO Reports 10(4):387-93· R. Avunie-Masala, N. Movshovich, Y. Nissenkorn, A. Gerson-Gurwitz, V. Fridman, M. Kõivomägi, M. Loog, M.A. Hoyt,

A. Zaritsky and L. Gheber. (2011) Phospho-regulation of Kinesin-5 function during anaphase spindle elongation. Journal of Cell Science 15;124(6):873-8

· Gerson-Gurwitz, C. Thiede, N. Movshovich, V. Fridman, M. Podolskaya, T. Danieli, S. Lakämper, D.R. Klopfenstein, C.F. Schmidt and L. Gheber (2011) Directionality of individual kinesin-5 Cin8 motors is modulated by loop 8, ionic strength and microtubule geometry. EMBO Journal 18;30(24):4942-54

· Thiede, V. Fridman, A. Gerson-Gurwitz, L. Gheber* and C. F. Schmidt* (2012) Regulation of bi-directional movement of single kinesin-5 Cin8 molecules. Bio-Architecture 2, 70-74. *Joint corresponding authorship

· V. Fridman, A. Gerson-Gurwitz, O. Shapira, N. Movshovich, S. Lakämper, C.F. Schmidt, and L. Gheber (2013) Kinesin-5 Kip1 is a bi-directional motor that stabilizes microtubules and tracks their plus-ends in vivo. Journal of Cell Science 126(18):4147-59

Dr. Sarina Grinberg - Senior Researcher

Synthetic Organic Chemistry

Research Interests:Mitotic chromosome segregation is a process by which duplicated genomic information is transferred from mother to daughter cells. This essential process is accomplished by the spindle, a highly dynamic, microtubule-based structure, which in each mitotic cycle, undergoes a well-programmed set of morphological changes. Compromised spindle integrity is one of the key factors for chromosome mis-segregation, which in turn may lead to genetic disease, cell death and cancer. Recent evidence indicate that molecular nano-motors from the Kinesin superfamily, which bind and move along microtubules by hydrolyzing ATP, play central roles in mediating spindle dynamics.

Specifically, our research focuses on the study of Kinesin-5 mitotic motor proteins, whose function is essential for chromosome segregation during mitotic cell division. Our objective is to explore the mechanisms by which Kinesin-5 motors perform their multiple mitotic functions by combining biophysical, biochemical, cell biology and genetics approaches such as single-molecule fluorescence motility assays and live-cell microscopy. Until recently, Kinesin-5 motors were believed to perform their essential mitotic functions as slow, processive MT plus-end directed motors. However, we have recently shown that the Saccharomyces cerevisiae Kinesin-5 homologs Cin8 and Kip1 are bi-directional motors. In vitro, individual Cin8 and Kip1 molecules could be switched by ionic conditions from rapid and processive minus-end to slow plus-end motion on single MTs. Deletion of the uniquely large insert in loop 8 of Cin8 induced bias towards minus-end motility and affected the ionic-strength dependent directional switching of Cin8 in vitro. In vivo, the deletion mutant exhibited reduced midzone-directed motility and efficiency to support spindle elongation, indicating the importance of directionality control for the function of Cin8.

In our current and future research we examine the structural and regulatory elements that control the directionality of Kinesin-5 motors in vivo and in vitro.

Recent Selected publications:· V .Fridman ,A .Gerson-Gurwitz ,N .Movshovich ,M .Kupiec and L .Gheber. (2009) Midzone organization restricts

interpolar microtubule plus-end dynamics during spindle elongation. EMBO Reports 10(4):387-93· R. Avunie-Masala, N. Movshovich, Y. Nissenkorn, A. Gerson-Gurwitz, V. Fridman, M. Kõivomägi, M. Loog, M.A. Hoyt,

A. Zaritsky and L. Gheber. (2011) Phospho-regulation of Kinesin-5 function during anaphase spindle elongation. Journal of Cell Science 15;124(6):873-8

· Gerson-Gurwitz, C. Thiede, N. Movshovich, V. Fridman, M. Podolskaya, T. Danieli, S. Lakämper, D.R. Klopfenstein, C.F. Schmidt and L. Gheber (2011) Directionality of individual kinesin-5 Cin8 motors is modulated by loop 8, ionic strength and microtubule geometry. EMBO Journal 18;30(24):4942-54

· Thiede, V. Fridman, A. Gerson-Gurwitz, L. Gheber* and C. F. Schmidt* (2012) Regulation of bi-directional movement of single kinesin-5 Cin8 molecules. Bio-Architecture 2, 70-74. *Joint corresponding authorship

· V. Fridman, A. Gerson-Gurwitz, O. Shapira, N. Movshovich, S. Lakämper, C.F. Schmidt, and L. Gheber (2013) Kinesin-5 Kip1 is a bi-directional motor that stabilizes microtubules and tracks their plus-ends in vivo. Journal of Cell Science 126(18):4147-59

Nanovesicles from bolaamphiphilic compounds for targeted drug delivery

One important aspect of our research is the design of amphiphilic compounds that form nanoparticles for targeted drug delivery. The novel amphiphilic compounds that we synthesized are bolaamphiphiles - amphiphiles with two head groups connected by a long hydrophobic chain. The assembly of these bolaamphiphiles into nanoparticles is due to secondary interactions between functional groups, which are part of the amphiphilic design. In the course of our research, we identified bolaamphphiles with certain chemical moieties (i.e., head groups, alkyl chain lengths, internal polar or H-bonding groups and alkyl pendants, etc.) that provide the nanoparticles they form with good stability, high encapsulation capacity, ability to cross biological barriers, targeting to specific organs within the body and controlled release of encapsulated drugs. This multifunctionality is what is needed for nanoparticles that are used in targeted drug delivery. Our bolaamphiphiles are new oleochemicals obtained from functional oils (vernonia oil, castor and jojoba oil, etc) as starting materials. The vesicles obtained from these bola lipids are capable of delivering small molecules, peptides, proteins and polynucleotides to target organs in experimental animals. We are continuing the development of nanoparticles for the delivery of pharmaceuticals and proteins for the treatment of disorders of the central nervous system, such as brain tumors and neuro-degenerative diseases.

Recent Selected Publications· G. Dakwar, I. Abu Hammad, M. Popov, C. Linder, S. Grinberg, E. Heldman, D. Stepensky “Delivery of proteins to

the brain by bolaamphiphilic nano-sized vesicles” J. Controlled Release, 2012, 60, 315-321. · T. Kim, K. Afonin, M. Viard, A. Koyfman, S. Sparks, E. Heldman, S. Grinberg, C. Linder, R. Blumenthal and B.

Shapiro “In silico, in vitro and in vivo studies indicate the potential use of bolaamphiphiles for therapeutic siRNA delivery” Nature Therap Nuc Acids 2013, 2(3): e80.

· Y. Kaufman, S. Grinberg, C. Linder, E. Heldman, J. Gilron J, V. Freger “Fusion of bolaamphiphile micelles: a method to prepare stable supported biomimetic membranes” Langmuir, 2013. 29, 1152-1161.

· L. Philosof-Mazor, G.R. Dakwar, M. Popov, S. Kolusheva, A. Shames, C. Linder, S. Greenberg, E. Heldman, D. Stepensky, R. Jelinek. “Bolaamphiphilic vesicles encapsulating iron oxide nanoparticles: New vehicles for magnetically targeted drug delivery” Int J Pharm., 2013, 241-249.

· M. Popov, I. Abu Hammad, T. Bachar, S. Grinberg, C. Linder, D. Stepensky, E. Heldman “Delivery of analgesic peptides to the brain by nano-sized bolaamphiphilic vesicles made of monolayer membranes” Eur J Pharm Biopharm., 2013, Available online 18 June 2013.

Dr. Jacob Hormodaly – Researcher rank A +

Inorganic chemistry, glass and solid state chemistry

Our group is involved in R& D of glasses and solid state chemistry, thick film materials and technology, coatings for thermosolar applications & Ag-metallizations for solar cells. The main theme is chemistry of materials where glass compositions and inorganic materials are synthesized, characterized and applied to various projects which are detailed below.

Research interests & projects:Glass chemistry: Synthesis and characterizations of inorganic oxide glasses for thick film compositions (conductor, resistor, sensor, dielectric and overglaze); bonding ,joining and strengthening of sapphire windows and domes & glass compositions for solar applications.

Solid state chemistry: Synthesis and characterizations of Ru-based resistor and thermistors materials such as pyrochlores, perovskites and spinels. Recent efforts are to synthesis and characterized spinels of Ru with very small particles sizes. Synthesis and application of spinels peroskites and othr structures for thermosolar applications. Some of the materials synthesized can be used as catalysts.

In the last 5 years, the main efforts were devoted to the development of coatings for thermosolar applications. Compositions with very high absorbptance (≥96% in the solar range 300nm-2500nm) stability at 650°C and compatibility with various steels were developed for companies. The current efforts are to scale up selected compositions and test them in commercial solar tower. Some of the technology developed was published in a patent applications and other aspects of it will be published in the patent literature only.

Selected publications:· J. Hormadaly, “ COATINGS FOR SOLAR APPLICATIONS” (WO2012127468), 25/3/2012· Dyamant ,I ;Korin ,E ;Hormadaly, J. Characteristics of La2CaB10O19 crystallization from glass. J. of Non Crystalline

Solids , 2010, 356(35-36), 1784-1790.· J .Hormadaly, US Patent 7,435,695 Oct.14,2008, Lead-free phosphate glasses.· Dyamant, I; Korin, E; Hormadaly, J. Thermal and some physical properties of glasses in the La2O3-CaO-B2O3

ternary system. J. Non-Crystalline Solids, 2008, 354 (27): 3135-3141.· Kimmel, G; On, H; Itzhak, D; Hormadaly, J. Crystal structure of Nd2-xMxRu2O7-y (M=Cu, Ag) pyrochlores by X-ray

powder diffraction. Powder Diffraction 2007, 22 (3): 231-235.· Busana, MG; Prudenziati, M; Hormadaly, J. Microstructure development and electrical properties of RuO2-based

lead-free thick film resistors. J. Mat. Electr.,2006, 17 (11): 951-962.

Dr. Raz Jelinek - Professor

Nanotechnology, Biophysical Chemistry, Two-dimensional nanostructures, Biomimetic cellular membranes

The research carried out in the laboratory of Dr. R. Jelinek aims at exploiting biomimetic chemistry approaches for both understanding important biological processes, as well as developing novel nanostructures. The inspiration and focus of the Jelinek laboratory has been the cellular membrane. In particular, Dr. Jelinek has introduced unique chromatic lipid/polymer molecular assemblies, including small vesicles, giant vesicles, Langmuir monolayers, and polymer-labelled cells, which both mimic cellular membranes as well as provide convenient biosensing platforms. These systems have been shown to exhibit wide-ranging scientific and biotechnological applications based upon the interconnection between the bio-mimetic surface [the lipid assembly] and the colorimetric/fluorescent reporter [the polymer domains]. Recently, The Jelinek laboratory has discovered new “lithography-less” approaches for construction of two-dimension nanostructures, utilizing biomimetic lipid templates at the air/water interface.

Figure: Self-assembled Au nanoparticle electrodes at the air/water interface

Selected publications:· “Self-Assembled Transparent Conductive Electrodes from Au Nanoparticles in Surfactant Monolayer Templates” A.

Morag, L. Philosof-Mazor, R. Volinsky, E. Mentovich, S. Richter, R. Jelinek Advanced Materials, 2011, 23, 4327-4331.· “Biofilm formation on chromatic sol-gel/polydiacetylene films” Margarita Geyzer, Sofiya Kolusheva, Hadas Ganin,

Michael Meijler, Raz Jelinek ChemPlusChem, 2012, 77, 752-757. IF: 3.34· “Array-based disease diagnostics using lipid/polydiacetylene vesicles encapsulated in a sol-gel matrix” S. Kolusheva,

R. Yossef, M. Katz, R. Volinsky, M. Welt, U. Hadad, V. Drory, M. Kliger, E. Rubin, A. Porgador, Raz Jelinek Analytical Chemistry, 2012, 84, 5925–5931. IF: 5.88

· “Patterned transparent conductive Au films through direct reduction of gold thiocyanate” Ahiud Morag, Natalya Froumin, Dimitry Mogiliansky, Vladimir Ezersky, Edith Beilis, Shachar Richter, Raz Jelinek Advanced Functional Materials, 2013, 23, 5663-5668. IF: 10.2

· ”Lipid Bilayers Significantly Modulate Cross-Fibrillation of Two Distinct Amyloidogenic Peptides” Noga Gal, Ahiud Morag, Sofiya Kolusheva, Roland Winter, Meytal Landau, Raz Jelinek Journal of the American Chemical Society, 2013, 135, 13582-13589 IF: 10.7

Dr. N. Gabriel Lemcoff – Associate Professor

Organometallic Chemistry, Polymers, Organic Chemistry

Synthesis, Characterization, Properties and Development of Novel Catalysts and Polymers

The advancement of polymer science embraces the invention of molecular constructs that provide functional applications. As a result, the development of novel methodologies for the production of polymers and complex macromolecular architectures and the design of new macromolecular catalysts stand out as appealing goals enthusiastically pursued by the chemical community. Our group’s research is mainly devoted to the synthesis, characterization, development and analysis of novel macromolecular compounds, such as polymers and dendrimers, and new catalysts and reactions to produce them. Recently, we have become interested in the development of latent ruthenium based catalysts. Our achievements in the area were the synthesis of the first thermoswitchable, as well as photoswitchable olefin metathesis systems. We also recognized the importance of the cis-trans isomerism in these catalysts and studied it in detail. Also in the area of olefin metathesis we were the first to develop bimetallic catalysts that could produce cyclodimers with high selectivity. In addition we like to ‘play’ with the dynamic properties of macromolecules, such as symmetric fractal dendrimers, to develop new selective catalytic methodologies. Thus, we developed “chameleon” dendrimers that take advantage of the molecules in their surrounding media to change their catalytic properties. A very recent area of research in our group is the development of what we have dubbed “organometallic nanoparticles”. These macromolecular constructs are prepared by catching metals with pi-electron rich polymers; inducing single chain collapse that leads to well-defined catalytically active nanoparticles.

Selected publications:· Ben-Asuly A.; Tzur E.; Diesendruck C.; Sigalov M., Goldberg I.; Lemcoff N.G. “A Thermally Switchable Latent

Ruthenium Olefin Metathesis Catalyst” Organometallics, 2008, 27, 811-813. · Tzur, E.; Ben-Asuly, A.; Diesendruck, C.E.; Goldberg, I. and Lemcoff, N.G. “Homodinuclear Ruthenium Catalysts for

Dimer Ring-Closing Metathesis”, Angewandte Chemie Int. Ed., 2008, 34, 6422-6425.· Ben-Asuly, A.; Aharoni, A.; Diesendruck, C. E.; Vidavsky, Y.; Goldberg, I.; Straub, B. F. and Lemcoff, N. G.;

“Photoactivation of Ruthenium Olefin Metathesis Initiators”, Organometallics, 2009, 28, 4652–4655.· Shema-Mizrachi, M.; Pavan, G. M.; Levin, E.; Danani, A. and Lemcoff, N. G. “Catalytic Chameleon Dendrimers”,

Journal of the American Chemical Society, 2011, 14359–14367.· Mavila, S.; Diesendruck, C.E.; Linde, S.; Amir, L.; Shikler, R.; Lemcoff, N.G. “Polycyclooctadiene complexes of

rhodium(I): direct access to organometallic nanoparticles”, Angewandte Chemie Int. Ed., 2013, 52, 5767-5770.

Dr. David Lukatsky – Senior Lecturer

Theoretical Biophysical Chemistry, BiophysicsDesign principles of protein-protein recognition, promiscuity and plasticity versus specificity

The main focus of the research activity of the Dr. Lukatsky’s laboratory is the problem of specificity and design principles of protein-protein and protein-DNA interactions, and principles of biomolecular recognition in general. The main finding of the last academic year was the discovery of the genetic code for nonspecific protein-DNA interactions. In particular, we predicted that genomic DNA of eukaryotic organisms encodes its intrinsic propensity for nonspecific binding to transcription factors (TFs), and other DNA-binding proteins. Using extensive bioinformatics analysis, we verified that the predicted effect is operational in the yeast S. cerevisiae genome. We showed that nonspecific protein-DNA binding significantly influences TF-DNA binding preferences and nucleosome occupancy in yeast. We are currently analyzing the consequences of the predicted effect in the worm and fly genomes.

Selected publications:· Afek, A.; Lukatsky, D.B. Positive and Negative Design for Nonconsensus Protein-DNA Binding Affinity in the Vicinity

of Functional Binding Sites, Biophys. J. 105(7), 1653-1660 (2013). · Afek, A.; Lukatsky, D.B. Genome-Wide Organization of Eukaryotic Pre-initiation Complex is Influenced by

Nonconsensus Protein-DNA Binding, Biophys. J. 104(5), 1107-1115 (2013).· Afek, A.; Lukatsky, D.B. Nonspecific Protein-DNA Binding is Widespread in the Yeast Genome, Biophys. J. 102(8),

1881-1888 (2012). · Elkin, M.; Andre, I.; Lukatsky, D.B. Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions,

J. Stat. Phys. 146(4), 870-877 (2012). · A. Afek, I. Sela, N. Musa-Lempel, and D. B. Lukatsky, Nonspecific Transcription Factor-DNA Binding Influences

Nucleosome Occupancy in Yeast, Biophys. J. 101(10), 2465-2475 (2011).

Dr. Michael M. Meijler – Associate Professor

Synthetic Bioorganic Chemistry, Chemical Biology, Quorum Sensing

Bacterial Intra- and Interspecies CommunicationQuorum Sensing: An important focus of our research is the study of bacterial intra- and interspecies signaling molecules. Cell-to-cell communication is used by single-cell organisms to coordinate their behavior and function in such a way that they can adapt to changing environments and possibly compete with multicellular organisms. Chemical communication amongst bacteria has been termed “quorum sensing” (QS). Examples of QS-controlled behaviors are biofilm formation, virulence factor expression, antibiotic production and bioluminescence. These processes are beneficial to a bacterial population only when they are carried out in a coordinated fashion. Quorum sensing systems exist in both gram-positive and -negative bacteria and a variety of oligopeptides and N-acylhomoserine lactones have been identified as QS molecules. We will attempt to clarify the role of various QS molecules in bacterial signaling through synthesis and evaluation of QS molecules and potential antagonists and we will develop methodologies to study a wide variety of newly discovered and undiscovered QS molecules. Currently, as part of two different studies to design QS antagonists of Pseudomoas aeruginosa, we have synthesized several highly active covalent and non-covalent QS inhibitors.

Bacterial-Eukaryotic Interkingdom Signaling: Recent reports have shown that several QS molecules can also have a direct effect on eukaryotes. My group currently examines the hypothesis that diverse eukaryotic species have developed mechanisms to react to the presence of specific bacterial QS molecules in a receptor mediated fashion, with focused experiments that are designed to provide greater insight into the primary molecular mechanism of QS molecule induced effects on mammals, fungi and nematodes. More specifically, we aim to identify receptors that are highly specific for the P. aeruginosa QSM 3-oxo-C12-AHL, as no receptor has been identified yet. We are currently developing an integrated platform that will enable the discovery of unknown receptors for small hydrophobic bioactive compounds.

Selected publications:· Covalent Inhibition of Bacterial Quorum Sensing, N. Amara, R. Mashiach, D. Amara, P. Krief, S. A. Spieser, M. J.

Bottomley, A. Aharoni, M. M. Meijler (2009). J. Am. Chem. Soc. 131, 10610-9· Synthesis and validation of a probe to identify quorum sensing receptors, L. Dubinsky, L. M. Jarosz, N. Amara, P.

Krief, V. Kravchenko, B. P. Krom, M. M. Meijler (2009). Chem. Commun. 47, 7378-80· Live cell labeling of native intracellular bacterial receptors using aniline-catalyzed oxime ligation, J. Rayo, N. Amara,

P. Krief, M. M. Meijler (2011). J. Am. Chem. Soc. 133, 7469-75· Vibrio cholerae Autoinducer CAI-1 Interferes with Pseudomonas aeruginosa Quorum Sensing and Inhibits its

Growth, H. Ganin, Y. Danin-Poleg, Y. Kashi, M. M. Meijler (2012). ACS Chem. Biol. 7, 659-665.· Species selective diazirine positioning in tag-free photoactive quorum sensing probes, L. Dubinsky, A. Delago, N.

Amara, P. Krief, J. Rayo, T. Zor, V. V. Kravchenko, M. M. Meijler: Chem. Commun., 49, 5826-5828 (2013)

Dr. Dan Meyerstein – Professor Emeritus

Inorganic chemistry, chemistry of transition metals

My main interest is in the study of fast redox reactions involving transition metal complexes with uncommon oxidation states and especially reactions of radicals with transition metal complexes. Topics are selected due to the role of these reactions, or similar reactions, in catalytic and or bioinorganic processes. These studies led to the study of properties of transient complexes with metal-carbon σ-bonds in aqueous solutions, a field in which our group is a leading group in the world. Recently this led to the study of the reactions of radicals with metal powders and metal nano-particles immersed in aqueous solutions a topic that is of importance in catalytic, electrochemical, photochemical and environmental processes. This is a new field that has not been studied in depth up to date. These studies led us also to study the mechanism of reactions of peroxides including the Fenton Reaction, a reaction of crucial importance in biology and medicine as well as in catalysis. Recently the reactions of NO, a stable radical of key importance in biology and medicine are studied. Naturally these studies require from time to time the synthesis of new ligands which will induce desired properties to the transition metal ions used.

Selected publications:· A. Burg, A. ; Wolfer, Y.; Kornweitz,H.; Shenar-Jackson, J.; Masarwa, A.; Meyerstein, D. The Cu(I) catalyzed

Meerwein reaction in aqueous solutions proceeds via a radical mechanism. The effect of several ligands. Dalton Trans., 2013, 42, 4985-4993.

· Ittah, E.; Shamir, D.; Zilbermann, I.; Maimon, E.; Yardeni, G.; Shames, A. I.; Meyerstein, D. Pyrophosphate as stabilizer of Ni(III) ions in aqueous solutions. Inorg. Chim. Acta, 2013, 405, 72-76.

· Gaisin, Z.; Gellermann, G.; Meyerstein, D. Pentaglycine-NiII complex: From kinetics to structure Eur. J. Inorg. Chem., 2013, 3191-3194.

· Popivker, Zilbermann, I.; Maimon, E.; Cohen, H.; Meyerstein, D. The “Fenton Like” reaction of MoO43- involves two H2O molecules. Dalton Trans., 2013, 42, 16666-16668.

· Attia, S.; Shames, A.; Zilbermann, I.; Goobes, G.; Maimon, E.; Meyerstein, D. Covalent binding of a nickel macrocyclic complex to a silica support: towards an electron exchange column Dalton Trans., 2014, 43, 103-110.

Dr. Yifat Miller – Senior Lecturer

Computational Biophysical chemistry, Computational Chemistry

Our research activity mainly focuses in self-assembly of peptides and proton transfer in biological and chemical systems. Our computational laboratory conducts fundamental and applied research at the interface of computational structural biology, biomaterial and bionanotechnology, with the goal to better understanding of biophysicochemical interactions in the self-assembly of peptides for practical applications in biomaterials and medicine.

Our main research interests:1. Molecular design of 3D-structures of amyloids and cross-amyloids that are related to Alzheimer’s disease, Parkinson

and type 2 diabetes.2. Molecular design of metal-binding sites in amyloids and in cross-amyloids.3. Metal binding sites in proteins.4. In silico design of novel self-assembling peptides for bionanotechnology applications.5. Proton transfer in Green Fluorescence Protein.6. Proton transfer mechanisms in chemical systems.

Interactions of Aß-mutated tau oligomers, Design of self-assembled peptides, Raz and Miller, PLOS ONE, 2013 Raz et al. Chem. Comm. 2013

Recent Selected publications:· Raz Y. and Miller, Y.: Interactions between Aß and mutated tau lead to polymorphism and induce aggregation of

Aβ-mutated tau oligomeric complexes. PLOS ONE, 8(8) 2013: e73303. doi:10.1371/journal.pone.0073303.· Simkovitch R., Huppert A., Huppert D., Remington S.J. and Miller Y.: Proton Transfer in Wild-Type GFP and S205V

Mutant is Reduced by Conformational Changes of Residues in the Proton-Wire. J. Phys. Chem. B, 2013, 117, 11921-31. · Raz Y., Rubinov, B., Matmor M., Rapaport, H., Ashkenasy, G., and Miller, Y: Effects of mutations in de novo designed

synthetic amphiphilic β-sheet peptides on self-assembly of fibrils. Chem. Comm. 2013, 49, 6561-6563.· Miller, Y., Ma, B., and Nussinov, R.: The unique Alzheimer’s β-amyloid triangular fibril has a cavity along the fibril

axis under physiological conditions. J. Am. Chem. Soc. 2011, 133, 2742-2748.· Miller, Y., Ma, B., and Nussinov, R.: Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic

states. Proc. Natl. Acad. Sci. USA, 2010, 107: 9490-9495.

Dr. Taleb Mokari – Associate Professor

Nanochemistry, Nanomaterials, Photovoltaics, Renewable Energy

Synthesis, characterization and application of nanostructuresThe primary focus of our research activity is development of novel nanostructures for optical, electrical, biological and

energy application. Our Laboratory studies the science of optimally preparing and characterizing metal, semiconductor, magnetic, insulating inorganic nanostructures, and multi-component nanostructures with various interfaces, including nanocrystals, nanotubes and nanowires with controlled size, shape, and composition. The synthesis of 1-dimensional nanostructures is conducted by gas- and solution-phase, where we develop our own approaches to achieve new nanomaterails and a better control of the synthesis parameters. The research encompasses the design and synthesis of precursors, the study of microscopic elementary processes in nanostructure nucleation and growth, and the use of nanostructures in functional, multi-component devices.

The applications our group focuses on are catalysis and solar energy conversion USING nanomaterial composite systems. As catalysts, nanomaterials could improve product selectivity, thereby reducing chemical waste and produce cleaner fuels. As energy conversion materials, they could lower the final cost per kWh to the end user. From precursor design to impact on the environment, we examine the possible contributions nanomaterials could have on our world. Selected research topics:* Developing novel approaches to synthesize nanostructures with a special focus on large scale synthesis. * Synthesis of metal, metal-oxide and semiconductor nanoparticles* Shape and composition control of nanostructures* Synthesis of nanowires and other structures using gas phase techniques* Synthesis of multi-component nanostructures and assembly * Nanostructures-based composites for solar energy applications (Photovotaic and photoelectrochemical cells)* Hybrid nanocatalysis* Studying the impact of nanocrystals on the environment* Structural, chemical, optical, and electrical characterization of inorganic nanostructures

Selected Publications:· Habas, S. E.; Yang, P.; Mokari, T. “Selective Growth of Metal and Binary Metal Tips on CdS Nanorods” J. Am.

Chem. Soc., 2008, 130, 3294. · Yuhas, B. D.; Habas, S. E.; Fakra, S.; Mokari, T. “Probing compositional Variation within Hybrid Nanostructures”

ACS Nano, 2009, 3, 3369. · Diab, M.; Moshofsky, B.; Jen-La Plante, I.; Mokari, T.; “A facile one-step approach for the synthesis and assembly

of copper and copper-oxide nanocrystals” J. Mater. Chem., 2011, 21, 11626.· Rawalekar, S.; Mokari, T.; “Rational Design of Hybrid Nanostructures for Advanced Photocatalysis” Adv. Energy

Mater. 2013., 3, 12. · Jen-La Plante, I.; Mokari, T.; “Harnessing Thermal Expansion Mismatch to Form Hollow Nanoparticles” Small,

2013, 9, 56.

Dr. Eyal Nir – Senior Lecturer

Biophysical Chemistry, Experimental Chemical Physics

General· Established in 2009, our group specializes in developing single-molecule fluorescence techniques (SMF), and

utilize them to study the structure, dynamics, interaction, activity and function of natural and artificial large molecules and molecular complexes, with a special interest in DNA nanotechnology and protein-DNA interaction.

· DNA Nanotechnology - Motors: We constructed a bipedal autonomous DNA-motor with a coordinate activity between the two motor legs and monitored its activity using SMF techniques. The measurements are done in-situ which enables monitoring the motor’s progress and structural dynamics without disturbing its activity. Our kinetic measurements of the motor’s assembly and activity indicate that it takes dozens of seconds to complete reactions, rather than hours, if components are properly designed. The motor successfully completes more than 15 steps and we are now working on increasing the stepping efficiency, speed and walking range. Kinetic measurements indicate that it is possible to significantly improve this kind of motors, such that they will have far higher efficiency and speed.

· DNA Dynamics: The structural dynamics of hairpins containing various loop and stamp sequences are studied when they freely-diffusing and when immobilized to a surface. Together, these two complementary methods enable measuring hairpin dynamics with a typical time spanning over several orders of magnitude (dozens of microsecond to many minutes). For the first time, the hairpins opening and closing rates are accurately and directly measured.

· Nucleosome Core Particles (NCP): NCP are responsible for tightly packing chromosomal DNA and they form an obstacle for regulatory proteins, polymerases, repair and remodeling proteins, all of which require access to DNA for their functionality. The local mechanical properties of DNA, believed to be sequence dependent, are known to play a significant role in formation of a stable NCP. Thus, a good understanding of DNA-related processes and their regulatory functions must include the understanding of affinities between the various nucleosome components, NCP association/dissociation mechanisms and NCP dynamics, and DNA interaction with DNA-binding-proteins, all of the above, in relation to DNA sequence.

Recent Selected publications:· Tsukanov, R.; Tomov, T. E.; Masoud, R.; Drory, H.; Plavner, N.; Liber, M.; Nir, E. Detailed study of DNA hairpin

dynamics using single-molecule fluorescence assisted by DNA origami. J. Phys. Chem. B 2013, 117 (40), 11932-42. · Toma E. Tomov, Roman Tsukanov, Miran Liber, Rula Masoud, Noa Plavner, and Eyal Nir (2013) Rational Design of

DNA Motors: Fuel Optimization through Single-Molecule Fluorescence. JACS 135 11935-11941 · Rula Masoud, Roman Tsukanov, Toma E. Tomov, Noa Plavner, Miran Liber and Eyal Nir (2012) Studying the Structural

Dynamics of Bipedal DNA Motors with Single-Molecule Fluorescence Spectroscopy. ACS Nano 6(7) 6272-6283· Tomov, T.E., Tsukanov, R., Masoud, R., Liber, M., Plavner, N., & Nir, E (2012). Disentangling subpopulations in single-

molecule FRET and ALEX experiments with photon distribution analysis. Biophysical Journal 102(5), 1163-1173 · Kovchegov, Y., Meredith, N. & Nir, E. (2010). Occupation times and Bessel densities. Statistics & Probability

Letters 80, 104-110.

Dr. Doron Pappo – Senior Lecturer

Synthetic Organic Chemistry

Synthetic MethodologiesOur group is focusing on the development of novel methods for the rapid construction of phenol based material through efficient, low-cost and environmental friendly techniques. The phenol group is a common moiety in many complex and important molecules found, both in nature, as such hormones, vitamins and food antioxidants, and in man-made materials, such as plastics and herbicides. Therefore, it is important to develop techniques that will enable the design of phenol-based materials through selective transformations on the phenol’s carbon-framework. Recently we have developed a chemo-, regio- and stereoselective FeCl3/1,10-phenanthroline-catalyzed cross dehydrogenative coupling (CDC) reaction between phenols and a-substituted b-ketoesters.The reaction creates a new quaternary carbon center within a polycyclic hemiacetal or polycyclic spirolactone architecture.

Natural products synthesis Natural product synthesis serves as an arena for examining the true values of novel methods, in a ‘real-life’ situation, where high selectivity and efficiency are essential. Moreover, the value of any method is measured by its expression in syntheses of complex molecules. Part of our research is to synthesize phenolic alkaloids based on our in-house methodology. We are focusing on the synthesis of several bioactive phytochemicals. One of them is lachnanthospirone, which its central core was prepared in a single operation via a possible biomimetic approach.

Selected publications:· Iron Catalyzed Oxidative Coupling of Phenols and Alkenes. Kshirsagar, U. A.; Regev, C.; Parnes, R.; Pappo, D. Org.

Lett., 2013, 15, 3174-3177.· Aerobic Iron-Based Cross Dehydrogenative Coupling Enables Efficient Diversity-Oriented Synthesis of Coumestrol-

Based Selective Estrogen Receptor Modulators. Kshirsagar, U. A.; Parnes, R.; Goldshtein, H.; Ofir, R.; Zarivach, R.; Pappo, D. Chem. Eur. J., 2013, 19(40), 13575-13583.

· Ligand Controlled Iron-Catalyzed Coupling of a-Substituted b-Ketoesters with Phenols. Parnes, R.; Kshirsagar, U. A.; Werbeloff, A.; Regev, C.; Pappo, D. Org. Lett., 2012, 14(13), 3324-3327.

· Deca-heterosubstituted corannulenes. Pogoreltsev, A.; Solel, E.; Pappo, D.; Keinan, E. Chem. Commun., 2012, 48, 5425-5427.

· A Chiral Pool Based Synthesis of Platensimycin. Nicolaou, K.C.; Pappo, D.; Tsang, K.Y.; Gibe, R.; Chen, Y.-K.D. Angew. Chem. Int. Ed., 2008, 47(5), 944-946.

n

O

n= 1-2n

O

C O2R 1

H

n

O

O

O

R 2

nC O2R 1

OHO

F eC l3 (10 mol %)phenanthroline (5 mol %)

tB uOOtB u (2.5 equiv)70 �C

HO

H

R 2

HOR 2

C O2R 1

R 2

21 examplesup to 95% yield

+

R 1 = alkyl groupsR 2 = E WG , E DG

O

OO

O

OO

OHO

P hOMeHO

P hO

C O2Me

OH

+

F eC l3 (10 mol %)L 2 (5 mol %)

DT B P (2.5 equiv)DC E , 70 �C

5 h

lachnanthospirone

43%

Dr. Abraham Parola – The Carol and Barry Kaye Proefessor in Applied Science

Biophysical chemistry, membrane biophysics, hydrophobic interactions

The common denominator of research in the Parola group is the unraveling of the role of hydrophobic interactions in membranal and non-membranal protein function and regulation, signal transduction, cell cycle and proliferation, cell differentiation and intercellular interactions. Our biophysical approach is based primarily on the utilization of time and phase resolved fluorescence anisotropy methods. Novel techniques and fluorescent probes were designed for these purposes.

We were among the first to point out the heterogeneity of membrane dynamic behavior which could not be described by the simple fluid mosaic model of Singer & Nicholson and proceeded towards the notion of membrane domains and hydrophobic mismatching as the more adequate description. This was supported by studies with both normal vs. transformed cells as well as proteins reconstituted in model membranes. A direct linkage between a sequence of molecular signaling events and membrane dynamics was reported for the first time. Membrane dynamic alterations were correlated with a number of physiological functions (e.g., malignant cell transformation and platelet aggregation, lymphocyte activation and differentiation, bacterial cell cycle and biomotility as well as magnetic field effects on cell proliferation) which may lay the ground for a detailed description of the forces involved. Unraveling the role of hydrophobic interactions in supramolecular structures (e.g., protein-protein interaction and drug targeting) provides insight into the role of quaternary structure in enzyme function and the design of antiangiogenic drugs, respectively.

Cell death – apoptosis, necrosis and autophagy have recently become a major research of ours. Questions regarding the mechanism of cytochrome c release from mitochondria, the role of cardiolipin in necrosis, the mechanism of inhibition of necrosis by humanin and the molecular mechanism of autophagy are now explored.

Diagnostic applications are made on the development of non-invasive methods for the determination of fetal lung maturity and towards the determination of drugs in body fluids without added reagents a nd the determination of poisons in water resources for homeland security.

Recent Selected publications:· Almog, O.; Kogan, A.; Leeuw, M.; Gdalevsky, G. Y.; Cohen-Luria, R.; Parola, A. H. Structural insights into cold

inactivation of tryptophanase and cold adaptation of subtilisin S41, Biopolymers 2008, 89, 354. · Aranovich; Gdalevsky, G. Y; Cohen-Luria, R.; Fishov, I.; Parola, A. H. Membrane-catalyzed nucleotide exchange

on DnaA. Effect of surface molecular crowding, J Biol Chem 2006, 281, 12526. · Avraham, H.; Ohana, E.; Maymon, E.; Cohen-Luria, R.; Molcho, J.; Parola, A. H. Intrinsic fluorescence polarization

of amniotic fluid: II. Toward a noninvasive method for the determination of fetal lung maturity, Photochem Photobiol 2006, 82, 1591.

· "Conformational Changes and Loose Packing Promote E. coli Tryptophanase Cold Lability". Anna" Kogan, Garik Y. Gdalevsky, Rivka Cohen-Luria, Yehuda Goldgur, Robert S. Phillips, Abraham H. Parola*,and Orna Almog*. BMC Struct Biol Oct 8; 9 (1):65 (2009)

· "Detection of Poisons, Pollutants, Narcotics, and Drugs in Water Using Excitation-Emission Spectroscopy Without Added Reagents” Shlomo Mark, Yehoshua Kalisky and Abraham H. Parola Water Quality, Exposure and Health manuscript number WQEH-D-13-00034R3 in press (2014)

Dr. Ehud Pines – ProfessorPhysical chemistry, experimental chemical physics, biophysical chemistry

Water chemistry is the essence of Life on Earth and acid-base chemistry is one of the most fundamental chemical processes in nature. Combining the two has made one of the most important and enduring questions in chemistry and biology continuously puzzling experts and laymen alike. Prof. Pines has made remarkable progress in this continuously demanding and highly competitive research field with a bottom-up strategy and with an attitude of a long-distance runner: he has studied the fundamentals of proton solvation and proton transfer from a mechanistic point of view using novel experimental techniques, each time incrementally increasing our knowledge of these very complex and convoluted processes. In 2003 Prof. Pines teamed up with Dr. Erik Nibbering from the Max-Born Institute in Berlin and conducted several ground-breaking experiments in acid-base chemistry. The study heavily relied on research done in Prof. Pines Labs for the past 15 years and utilized the much improved experimental setup at MBI for measuring vibrational spectroscopy with ultra-short laser pulses. The early stage of the study was published in the prestigious Science magazine and was chosen by the Chemical and Engineering News journal (C&E News) in its end-of- the- year issue as one of the 3 most important papers in physical chemistry appearing in 2003. Improving on this early observation a second publication in Science in 2005 revealed for the first time the spectroscopic signature of the solvated proton in the IR region of the spectrum with extremely high time-resolution. By using novel experimental techniques, hydrogen ions could be “captured in the act” in the form of H3O+ while being transmitted from acid to base by water molecules in a sequential fashion. This important finding may well become relevant for technological applications, e.g., in fuel cells. Prof. Pines has advanced on these ground-breaking experimental observations and published a generalized model for acid-base reaction in aqueous solutions. The model extends the classic kinetic model for acid-base reactions in solution which successfully served the chemistry community for the past 60 years. Prof. Pines currently continues with the study of carbonic acid and received for that end a prestigious grant from NIH. He also investigates proton solvation by water, hydrogen bonding interactions and the mechanism by which water transfer the proton, the so called Grotthuss mechanism.

The direct proton transfer reaction can be represented in a different way that shows the sequential desolvation and solvation pathways as well as the possible proton shuttling channels.

Recent Selected publications:· Adamczyk, K.; Prémont-Schwarz, M.; Pines, D.; Pines E.; Nibbering. E. T. J. Real-time observation of carbonic

acid formation in aqueous solution Science, 2009, 326, 1690.· Mohammed, F.; Pines, D.; Nibbering E.T.J.; Pines, E. Base-induced solvent switches in acid-base reactions.

Angewandte Chemie-International Edition, 2007. 46, 1458. · Mohammed ,O.F ;.Pines ,D ;.Dreyer J ;.Pines E.; Nibbering, E.T.J. Sequential proton transfer through water bridges

in acid-base reactions. Science, 2005. 310(5745): p. 83-86. · Rini ,M ;.Pines ,D ;.Magnes ,B.Z ;.Pines E ;.Nibbering ,E.T.J. Bimodal proton transfer in acid-base reactions in

water. Journal of Chemical Physics, 2004. 121(19): p. 9593. · Rini ,M ;.Magnes ,B.Z ;.Pines E.; Nibbering, E.T.J. Real-time observation of bimodal proton transfer in acid-base

pairs in water. Science, 2003. 301,(5631): p. 349.

Dr. Micha Polak – Professor

Theoretical-Computational Nano-Science - Alloy Nano-Particle Surfaces & Small-System Chemical-Equilibrium

The effects of surface bond-energy variations on surface compositional structures: This work introduced two novelties concerning alloy surface phenomena and their modeling. The first involves the idea to extract the coordination dependence of bond-energies from density functional theory (DFT) computed surface energy anisotropy. In particular, polynomial functions are fitted to DFT data for energies of pure Pt, Pd, Rh and Ir surfaces. The second novel aspect was revealed when using the bond-energy variations as input in alloy surface statistical-mechanical computations, based on our free-energy concentration expansion method (FCEM). It concerns the finding that preferential elemental bond strengthening can lead to quite unique segregation characteristics: (i) Strongly oscillatory Pt segregation profile in Pt-Rh(111), in very good agreement with experimental data; (ii) The remarkable reversal to Pt segregation at certain surface sites in Pt-Pd 923-atom cuboctahedron nano-particles (NPs); (iii) For low Pt content Pt-Ir 923-atom cuboctahedron NPs the occurrence of several smoothly varying atomic exchange processes between surface sites, which are reflected as distinct Schottky-type peaks in the configurational heat-capacity curve (see Fig.1) and the sharp core-separation nanophase transition for high Pt content. Compared to other approaches, our method is highly transparent, yielding better insight into the origin of surface segregation phenomena in alloy bulk and NPs.

Nanochemical Equilibrium Involving a Small Number of Molecules: These most recent studies explore theoretically novel features of the chemical equilibrium state in a nano-confined reaction mixture, which are closely relevant to several newly developed routes for the synthesis of organic molecules, inorganic NPs, etc. Canonical-ensemble based formulation and computations predict for the equilibrated closed small systems significant deviations from the (macroscopic) thermodynamic limit (TL). The nanoconfinement entropic effects on chemical equilibrium (NCECE) include the enhancement of the equilibrium constant (or extent) of the exothermic reactions. The NCECE effect stabilizes nucleotide dimerization observed within self-assembled molecular cages. Likewise, the NCECE effect is pertinent to a longstanding issue in astrochemistry, namely the extra deuteration commonly observed for molecules reacting on interstellar dust grain surfaces (Fig.2).

Fig.1 Fig.2

Selected publications: · Polak M.; Rubinovich, L. Prediction of intercluster separation and Schottky-type heat-capacity contribution in

surface-segregated binary and ternary alloy nanocluster systems, Phys. Rev. B 71, 125426 (2005). · Polak M.; Rubinovich, L. Nanochemical Equilibrium Involving a Small Number of Molecules: A Prediction of a

Distinct Confinement Effect, Nano Letters 8, 3543-3547 (2008). · Rubinovich L.; Polak, M. “Prediction of distinct surface segregation effects due to coordination-dependent bond-

energy variations in alloy nanoclusters”, Phys. Rev. B 80 045404 (2009). · Barcaro, G.; Fortunelli, A.; Polak M.; Rubinovich, L. “Patchy Multishell Segregation in Pd-Pt Alloy Nanoparticles”,

Nano Letters 11, 1766-1769 (2011). · Polak M.; Rubinovich, L. “Remarkable Nanoconfinement Effects on Chemical Equilibrium Manifested in Nucleotide

Dimerization and H-D Exchange Reactions”, Phys. Chem. Chem. Phys. 13, 16728-16734 (2011).

Dr. Addy Pross – Professor

Origin-of-life, molecular evolution, physico-chemical principles of biological

complexification

Chemistry and biology are closely related sciences yet the chemistry-biology interface remains problematic. Our research program involves the development of a kinetic theory of replicating systems that will attempt to help bridge the chemistry-biology gap. In earlier work we have demonstrated that there are two distinct kinds of stability in nature – thermodynamic stability associated with “regular” chemical systems, and dynamic kinetic stability, associated specifically with replicating systems. We propose building on those earlier ideas in order to help relate animate to inanimate, to uncover the physicochemical principles that were responsible for the emergence of life, and help uncover the chemical roots of Darwinian Theory, specifically, the relation between emergence and evolution. Possible strategies toward the synthesis of simple living systems are being investigated.

A book detailing this topic for a more general audience is now in preparation with Oxford University Press. Publication date: September 2012.

http://ukcatalogue.oup.com/product/9780199641017.do#.T8x0irAkh8E

Selected publications:· Pross, A. Toward a general theory of evolution: Extending Darwinian theory to inanimate matter. J. Systems Chem.

2, 1, 2011. · Pross, A. Dynamic Kinetic Stability as a Conceptual Bridge Linking Chemistry to Biology Current Organic Chemistry,

Special issue on “Prebiotic Chemistry”. 17, 1702-3, 2013.· Pross, A. The evolutionary origin of biological function and complexity, J. Mol. Evol. 76, 185-191, 2013.· Pascal, R.; Pross, A.; Sutherland, J.D. Towards an evolutionary theory of the origin of life based on kinetics and

thermodynamics. Open Biol 3: 130156, 2013. http://dx.doi.org/10.1098/rsob.130156· Pross, A.; Pascal, R. The origin of life: what we know, what we can know, and what we will never know, Open Biol.

3, 120190, 2013.

Dr. Boris Tsukerblat – Professor

Molecular magnetism, spectroscopy, group theory

I. Molecular magnetism: exchange interactions in molecule-based materials and single-molecule magnets, mixed valence and double exchange: The research is focused on the exchange coupled magnetic ions and single molecule magnets (SMM), which exhibit magnetic bistability and quantum tunneling of magnetization. This is expected to allows to use them as the memory storage of molecular size. (1) Elaboration of the general approach to the problem of the orbitally-dependent exchange, applications (metal ions with unquenched orbital angular momenta). Magnetic anisotropy in SMM, magnetic bistability in Mn5 based SMMs, barrier for the reversal of magnetization in the octanuclear Re(II)4 Mn(II)4 SMM. (2) Microscopic theory of mixed valency (MV) and double exchange, approach to the evaluation of the energy pattern and magnetic properties of polynuclear MV metal clusters (iron-sulfur clusters, reduced Keggin and Wells-Dawson polyoxoanions. (3) Spin-frustrated systems: famous nanoscopic V15 cluster. Discovery of quantum oscillations in a molecular magnet

II. Vibronic interactions and Jahn-Teller (JT) effect in molecules and crystals. Spectroscopy of transition metal complexes and impurity centers in doped crystals: The theory of polarization dichroism spectra in JT centers based on the moments method was developed which is shown to provide an efficient tool for the study of the JT effect. Laser materials: Cr(III) ion in ruby (multiphonon bands, zero-phonon lines, non-radiative transitions) and rare-earth ions in crystals. A pseudo-JT dynamic vibronic model for excited states of CdIn2S4 –Cr(III) and CdSe-Cr(II) crystals widely used as the infrared tunable lasers.

III. Group theory as applied to molecular magnetism and Jahn-Teller effect: A general group-theoretical approach was developed for the analysis of spin-orbital multiplets of polynuclear multielectron exchange clusters. On the basis of the group-theoretical method “accidental” degeneracies of spin states in the Heisenberg-Dirac-Van-Vleck model are investigated and the theory of non-Heisenberg exchange interactions was developed on the basis of the irreducible tensor operators approach.

Selected publications:· Bertaina, S.; Gambarelli, S.; Mitra, T.; Tsukerblat, B.; Müller, A.; Barbara, B. Quantum oscillations in a molecular

magnet, Nature, 453 (2008) 203-206.· Tsukerblat, B.; Palii, A.; Clemente-Juan, J.M.; Gaita-Ariño, A.; Coronado, E. A Symmetry Adapted Approach to

the Dynamic Jahn-Teller Problem: Application to Mixed-Valence Polyoxometalate Clusters with Keggin Structure , International Journal of Quantum Chemistry, 112 (2012) 2849–2980 (cover image).

· Palii, A.; Tsukerblat, B.; Klokishner, S.; Dunbar, K.; Clemente-Juan, J. M.; Coronado, E. Beyond the spin model: Exchange coupling in molecular magnets with unquenched orbital angular momenta, Chem. Soc. Reviews, 40 (2011) 3130–3156 (invited critical rev.,cover image).

· Kögerler, P.; Tsukerblat, B.; Müller, A. Structure-Related Frustrated Magnetism of Nanosized Polyoxometalates: Aesthetic Beauty and Properties in Harmony, Dalton Transactions, 39 (2010) 21–36 (invited perspective review article, cover image).

· Palii, A.; Bosch-Serrano, C.; Clemente-Juan, J. M.; Coronado, E.; Tsukerblat, B. Microscopic Approach to Dissipative Electron Transfer Dynamics in Mixed Valence Dimers: Solid State Problem, J. Chem. Phys.,139 (2013) 044304-11.

Dr. Amichay Vardi – Associate Professor

Theoretical Atomic, Molecular, and Optical Physics, Quantum Physics, Nonlinear Physics

Quantum Atom Optics We theoretically study the dynamics of quantum gases. Near absolute zero temperature, the behavior of dilute gases of atoms, molecules, and excitations is highly quantum mechanical. The quantum statistics of the constituent particles is manifest in striking collective effects. Bosonic particles form Bose-Einstein condensates, whose behavior is similar to that of light-waves in nonlinear media, leading to the notion of nonlinear and quantum atom optics. By contrast, quantum gases of fermions show collective behavior characterized by Pauli exclusion. We currently investigate the utilization of Bose-Einstein condensates to study fundamental questions concerning the emergence of irreversible macroscopic thermodynamics from the reversible microscopic quantum dynamics. We aim to construct minimal models for demonstrating quantum thermalization via chaotic ergodization and to formulate new rules for mesoscopic thermodynamics. Other recent research projects include the discovery of anisotropic solitons in Bose-Einstein condensates of dipolar particles, the stabilization of coherent matter-wave states in driven atom interferometers via a Kapitza inverted pendulum effect and a many-body quantum Zeno effect, the optimization of atom interferometry below the standard quantum limit, phase-space tomography via temporal fluctuations, and the discovery of interferometric signatures of chaos in bosonic Josephson junctions.

Selected publications:· Tikhonenkov, I.; Vardi, A.; Anglin, J. R.; Cohen, D. Minimal Focker-Planck theory for the thermalization of mesoscopic

subsystems, Phys. Rev. Lett. 110, 050401 (2013).· Khripkov, C.; Cohen, D.; Vardi, A. Coherence dynamics of kicked Bose-Hubbard dimers: Interferometric signatures

of chaos, Phys. Rev. E 87, 012910 (2013)· Boukobza, E.; Moore, M. G.; Cohen, D.; Vardi, A. Nonlinear phase dynamics in a driven bosonic Josephson

junction, Phys. Rev. Lett. 104 , 240402 (2010)· Boukobza, E.; Chuchem, M.; Cohen D.; Vardi, A. Phase-diffusion dynamics in weakly-coupled Bose-Einstein

condensates, Phys. Rev. Lett. 102, 180403 (2009)· Tikhonenkov, B.; Malomed, A.; Vardi, A.; Anisotropic solitons in dipolar Bose-Einstein condensates, Phys. Rev. Lett.

100, 090406 (2008).

Metal-oxide cluster science. Numerous intellectually substantive phenomena and societally important issues can be addressed using metal-oxygen cluster anions (polyoxometalates, or POMs), and much of Weinstock’s work involves their use as physicochemical probes of molecular processes and as well-defined components of supramolecular and nano-scale assemblies. POMs are prepared from early-transition metals (e.g., V, Mo, and W) in their highest oxidation states (d0, and sometimes d1). Many POMs possess extensive and reversible redox chemistries, and as a class, their compositions and structures, which control the physicochemical properties that impart functionality, can be rationally modified at the atomic level. Functional systems are prepared through incorporation of reactive elements, such as additional transition-metal ions, by control over the nanoscale metal-oxide architectures of larger POM frameworks, and by use of POM clusters as components of supramolecular and nanoscale assemblies. In this context, Weinstock’s work addresses topics in three areas: 1) inorganic synthesis and reaction mechanisms (including electron transfer), 2) supramolecular chemistry, and 3) nanoscience.

Small (1.2 nm diameter) one-electron reduced heteropolyanions, a-Xn+W12O40(9-n)– (Xn+ = Al3+, Si4+, P5+) are used

to investigate fundamental steps in the reduction of O2 in water. The findings suggest that concerted proton-electron transfer (CPET) pathways, with the hydronium ion as the proton donor, may prove a general feature of sufficiently endergonic reductions of O2 by otherwise “outer-sphere” complexes (or electrode reactions) at sufficiently low pH values in water. In supramolecular chemistry, a porous and water-soluble 2.9-nm diameter oxomolybate macro-ion is used to address fundamental issues pertinent to host/guest and supramolecular chemistry: 1) the size-restricted passage of molecules through subnanometer-scale apertures of open-framework structures, 2) hydrophobically and H-bond driven self-assembly, and 3) catalysis in nanoconfined domains. In nanoscience, metal oxide cluster-anions form monolayers on planar surfaces, stabilize metal nanoparticles in solution, and serve as structural components of hollow, single-walled vesicles. Until recently, each of these classes of superstructures was viewed as fundamentally distinct. Moreover, electrostaticallystabilized POM ligands shells are being used to design entirely new types of protecting-shell structures that rationally control the assembly and reactions of gold nanoparticles in water.

Recent journal covers highlighting work from the Weinstock laboratory

Selected publications· Grego, A.; Müller, A.; Weinstock, I. A. “Stepwise-Resolved Thermodynamics of Hydrophobic Self-Assembly”

Angew. Chem. Int. Ed. 2013, 52, 8358 –8362.· Zeiri, O.; Wang, Y.; Neyman, A.; Stellacci, F.; Weinstock, I. A., Ligand-Shell-Directed Assembly and Depolymerization

of Patchy Nanoparticles. Angew. Chem. Int. Ed. 2013, 52, 968-972.· Wang, Y.; Zeiri, O.; Sharet, S.; Weinstock, I. A. “Role of Alkali-Metal Cation Size in the Self-Assembly of

Polyoxometalate-Monolayer Shells on Gold Nanoparticles “ Inorg. Chem. 2012, 51, 7436-7438. · Snir, O.; Wang, Y.; Tuckerman, M. E.; Geletii, Y.V.; Weinstock, I. A. “Concerted Proton-Electron Transfer (CPET) to

Dioxygen in Water” J. Am. Chem. Soc. 2010, 132, 11678-11691.· Ziv, A.; Grego, A.; Kopilevich, S.; Zeiri, L.; Miro, P.; Bo, C.; Müller, A.; Weinstock, I. A. “Flexible Pores of a Metal-

Oxide-Based Capsule Permit Entry of Comparatively Larger Organic Guests” J. Am. Chem. Soc. 2009, 131, 6380-6382.

Dr. Ira A. Weinstock – The Irene Evens Professor of Inorganic Chemistry

Inorganic chemistry: Metal-oxygen clusters, inorganic reaction mechanisms,supramolecular chemistry, nanoscience