NEW YORK
NEW YORK UNIVERSITY
100 Washington Square East, Room 1001
New York, NY 10003
TEL: (212) 998-8400
FAX: (212) 260-7905
Web: chemistry.fas.nyu.edu
Email: chem.web@nyu.edu
Department of Chemistry
Michael D. Ward, Professor and Chair.
Degrees Offered: B.S, M.S, Ph.D.
Fields of Specialization: Theoretical/Physics, Biomolecular/Biophysical, Organic/Bio-organic.
See Biochemistry Section.
ARORA, PARAMJIT S. Associate Professor. B.S,
1992, University of California at Berkeley; Ph.D, 1999,
University of California at Irvine. Postdoctoral Fellow,
1999-2002, California Institute of Technology. Bioorganic Chemistry; Organic Chemistry. We are interested
in the design and synthesis of organic molecules that allow control over specific protein-protein, protein-nucleic
acid, and protein-carbohydrate interactions. TEL: (212)
998-8470 FAX: (212) 260-7905
Web: chemistry.fas.nyu.edu/object/paramjitarora.html
Email: arora@nyu.edu
Nicholas G. Angelo, Laura K. Henchey, Adam J. Waxman,
James W. Canary, Paramjit S. Arora and Donald Wink, Synthesis and characterization of aldol condensation products
from unknown aldehydes and ketones. an inquiry-based experiment in the undergraduate laboratory, J. Chem. Educ, 84,
1816-1818 (2007).
Nicholas G. Angelo and Paramjit S. Arora, Solution- and
solid-phase synthesis of triazole oligomers that display protein-like functionality, J. Org. Chem, 72, 7963-7967 (2007).
Anupam Patgiri, Andrea L. Jochim and Paramjit S. Arora,
A hydrogen bond surrogate approach for stabilization of
short peptide sequences in a-helical conformation, Acc.
Chem. Res, 41, 1289-1300 (2008).
Deyun Wang, Min Lu and Paramjit S. Arora, Inhibition of
HIV-1 fusion by hydrogen-bond-surrogate-based ␣ helices,
Angew. Chem., Int. Ed, 47, 1879-1882 (2008).
Ross Chapman, John L. Kulp, III, Anupam Patgiri, Neville
R. Kallenbach, Clay Bracken and Paramjit S. Arora, Trapping a folding intermediate of the a-helix: stabilization of the
p-helix, Biochemistry, 47, 4189-4195 (2008).
Laura Henchey, Andrea L. Jochim and Paramjit S. Arora,
Contemporary strategies for the stabilization of peptides in
the alpha-helical conformation, Curr. Opin. Chem. Biol, 12,
692-697 (2008).
Jie Liu, Deyun Wang, Qi Zheng, Min Lu and Paramjit S.
Arora, Atomic structure of a short ␣-helix stabilized by a
main chain hydrogen-bond surrogate, J. Am. Chem. Soc, 130,
4334-4337 (2008).
Kent Kirshenbaum and Paramjit S. Arora, Cross-dressing
proteins by olefin metathesis, Nat. Chem. Biol, 4, 527-528
(2008).
Deyun Wang, Nucleation and stability of hydrogen-bond
surrogate-derived alpha-helices and their applications in targeting protein-protein interactions. (D)
Nicholas G. Angelo, Design, synthesis and biological activity of 1,2,3 triazole-based beta-strand mimics. (D)
Ross N. Chapman, Design, synthesis, characterization and
applications of hydrogen bond surrogate helices. (D)
BACIC, ZLATKO (b.1954) Professor. B.S, 1977,
University of Zagreb (Croatia); Ph.D, 1981, University
of Utah. Postdoctoral Fellow, 1984, Max-Planck Institute
fur Stromungsforschung, Gottingen, W. Germany; Postdoctoral Fellow, 1985, Hebrew University of Jerusalem,
Jerusalem, Israel; Postdoctoral Fellow, 1986-1987, University of Chicago; Postdoctoral Fellow, 1988, Los Alamos National Laboratory, Los Alamos, New Mexico.
Theoretical Chemistry. Accurate theoretical description
of IR spectra and unimolecular reactions of highly rovibrationally excited floppy molecules and molecular complexes; accurate quantum treatment of the spectroscopy
and photodissociation dynamics of molecules in clusters.
Theoretical studies of molecules in highly quantum solvent environment of clusters of helium and molecular
hydrogen. TEL: (212) 998-8435 FAX: (212) 260-7905
Web: chemistry.fas.nyu.edu/object/zlatkobacic.html
Email: zlatko.bacic@nyu.edu
Minzhong Xu, Francesco Sebastianelli and Zlatko Bacic,
Hydrogen Molecule in the Small Dodecahedral Cage of a
Clathrate Hydrate: Quantum Translation-Rotation Dynamics
at Higher Excitation Energies, J. Phys. Chem. A, 111, 1276312771 (2007).
Francesco Sebastianelli, Minzhong Xu, Dalal K. Kanan
and Zlatko Bacic, One and Two Hydrogen Molecules in the
Large Cage of the Structure II Clathrate Hydrate: Quantum
Translation-Rotation Dynamics Close to the Cage Wall, J.
Phys. Chem. A, 111, 6115-6121 (2007).
Minzhong Xu and Zlatko Bacic, Wave Function Delocalization and Large-Amplitude Vibrations of Helium on Corrugated Aromatic Microsurfaces: Tetracene·He and Pentacene·He van der Waals Complexes, J. Phys. Chem. A, 111,
7653-7663 (2007).
Francesco Sebastianelli, Minzhong Xu, Yael S. Elmatad,
Jules W. Moskowitz and Zlatko Bacic, Hydrogen Molecules
in the Small Dodecahedral Cage of a Clathrate Hydrate:
Quantum Translation-Rotation Dynamics of the Confined
Molecules, J. Phys. Chem. C, 111, 2497-2504 (2007).
Minzhong Xu, Francesco Sebastianelli, Zlatko Bacic, Ronald Lawler and Nicholas J. Turro, Quantum dynamics of coupled translational and rotational motions of H2 inside C60, J.
Chem. Phys, 128, 011101/1-011101/4 (2008).
Minzhong Xu, Francesco Sebastianelli, Zlatko Bacic, Ronald Lawler and Nicholas J. Turro, H2, HD, and D2 inside C60:
Coupled translation-rotation eigenstates of the endohedral
molecules from quantum five-dimensional calculations, J.
Chem. Phys, 129, 064313/1-064313/9 (2008).
Minzhong Xu, Francesco Sebastianelli and Zlatko Bacic,
Quantum dynamics of H2, D2, and HD in the small dodecahedral cage of clathrate hydrate: Evaluating H2-water nanocage
interaction potentials by comparison of theory with inelastic
neutron scattering experiments, J. Chem. Phys, 128, 244715/
1-244715/13 (2008).
BRENNER, HENRY C. (b.1946) Associate Professor. B.S, 1968, Massachusetts Institute of Technology;
M.S, 1969, University of Chicago; Ph.D, 1972, University of Chicago. Postdoctoral Research Associate, 19721975, University of California, Berkeley. Physical
Chemistry. Optical and magnetic resonance studies of
molecular crystals and biological systems; excited state
energy transfer in solids; optically detected spin coherence techniques. TEL: (212) 998-8432 FAX: (212) 2607905
Email: henry.brenner@nyu.edu
No publication information submitted for this edition.
CANARY, JAMES W. (b.1960) Professor. B.S, 1982,
University of California, Berkeley; Ph.D, 1988, University of California, Los Angeles. NIH Postdoctoral Fellowship, 1988-1991, Columbia University. Nanochemistry; Organic Chemistry. Stereochemistry and conformational dynamics, molecular devices, molecule-based sensors and triggered materials, chiral nanoscale materials,
biomedical imaging. TEL: (212) 998-8422 FAX: (212)
995-4367
Web: www.nyu.edu/pages/canary
Email: james.canary@nyu.edu
Andrea E. Holmes, Debasis Das and James W. Canary,
Chelation-Enhanced Circular Dichroism of Tripodal Bisporphyrin Ligands, J. Am. Chem. Soc, 129, 1506-1507 (2007).
Nicholas G. Angelo, Laura K. Henchey, Adam J. Waxman,
James W. Canary, Paramjit S. Arora and Donald Wink, Synthesis and characterization of aldol condensation products
from unknown aldehydes and ketones. An inquiry-based experiment in the undergraduate laboratory, J. Chem. Educ, 84,
1816-1818 (2007).
Zhaohua Dai and James W. Canary, Tailoring tripodal ligands for zinc sensing, New J. Chem, 31, 1708-1718 (2007).
Yu Liu, Risheng Wang, Liang Ding, Ruojie Sha, Phillip S.
Lukeman and James W. Canary, Thermodynamic stability of
nylon-DNA/DNA duplexes, ChemBioChem, 9, 1641-8
(2008).
Debasis Das, Zhaohua Dai, Andrea Holmes and James W.
Canary, Exploring the scope of redox-triggered chiroptical
switches: syntheses, X-ray structures, and circular dichroism
of cobalt and nickel complexes of N,N-bis(arylmethyl)methionine derivatives, Chirality, 20, 585-591 (2008).
Yu Liu, Akinori Kuzuya, Ruojie Sha, Johan Guillaume,
Risheng Wang, James W. Canary and Nadrian C. Seeman,
Coupling Across a DNA Helical Turn Yields a Hybrid DNA/
Organic Catenane Doubly Tailed with Functional Termini, J.
Am. Chem. Soc, 130, 10882-10883 (2008).
Yu Liu, Ruojie Sha, Risheng Wang, Liang Ding, James W.
Canary and Nadrian C. Seeman, 2’,2’-Ligation demonstrates
the thermal dependence of DNA-directed positional control,
Tetrahedron, 64, 8417-8422 (2008).
Johan Guillaume, Regioselective crosslinking of DNA oligomers. (M)
Ge Ma, DNA templated synthesis of nylon-like oligomers.
(D)
Yu Liu, 2’-linked nucleic acids: New dimension of structures and properties. (D)
EVANS, JOHN SPENCER (b.1957) Professor. B.S,
1978, Northwestern University; D.D.S, 1982, University
of Illinois; Ph.D, 1993, California Institute of Technology. NIH Fellowship, 1988-1993, California Institute of
Technology; Amgen Fellowship, 1992, California Institute of Technology; Proctor and Gamble Fellowship,
1992, California Institute of Technology. Biophysics/
Biophysical Chemistry; Materials Science. Biomineralization and inorganic/organic nano-tech protein structurefunction studies. Experimental methods include NMR
spectroscopy, mass spectrometry, CD spectrometry, and
1
interfacial surface analyses (SEM, TEM, AFM, SIMS).
Our group also pursues computational chemistry and
algorithm design to study polypeptide—interfacial interactions. TEL: (212) 998-9605 FAX: (212) 995-4087
Web: chemistry.fas.nyu.edu/object/chem.faculty.evans.
interests.html
Email: jse1@nyu.edu
Sebastiano Collino and John Spencer Evans, Structural
Features That Distinguish Kinetically Distinct Biomineralization Polypeptides, Biomacromolecules, 8, 1686-1694 (2007).
Katya Delak, Sebastiano Collino and John Spencer Evans,
Expected and Unexpected Effects of Amino Acid Substitutions on Polypeptide-Directed Crystal Growth, Langmuir, 23,
11951-11955 (2007).
John L. Kulp, III, Tamiko Minamisawa, Kiyotaka Shiba,
Margaret Tejani and John Spencer Evans, Structural Properties of an Artificial Protein That Regulates the Nucleation of
Inorganic and Organic Crystals, Langmuir, 23, 3857-3863
(2007).
Urartu Ozgur Safak Seker, Brandon Wilson, Sevil Dincer,
Il Won Kim, Ersin Emre Oren, John Spencer Evans, Candan
Tamerler and Mehmet Sarikaya, Adsorption Behavior of Linear and Cyclic Genetically Engineered Platinum Binding
Peptides, Langmuir, 23, 7895-7900 (2007).
Sebastiano Collino, Ii won Kim and John Spencer Evans,
Identification and Structural Characterization of an Unusual
RING-Like Sequence within an Extracellular Biomineralization Protein, AP7, Biochemistry, 47, 3745-3755 (2008).
Sebastiano Collino, Il Won Kim and John Spencer Evans,
Identification and structural characterization of an unusual
RING-like sequence within an extracellular biomineralization protein, AP7, Biochemistry, 47, 3745-3755 (2008).
Sebastiano Collino and John Spencer Evans, The molecular specifications of a mineral modulation sequence derived
from the aragnote-promoting protein, n16, Biomacromolecules, 9, 1909-1918 (2008).
Sebastiano Collino and John Spencer Evans, Molecular
Specifications of a Mineral Modulation Sequence Derived
from the Aragonite-Promoting Protein n16, Biomacromolecules, 9, 1909-1918 (2008).
Mustafa Gungormus, Hanson Fong, Il Won Kim, John
Spencer Evans, Candan Tamerler and Mehmet Sarikaya,
Regulation of in vitro Calcium Phosphate Mineralization by
Combinatorially Selected Hydroxyapatite-Binding Peptides,
Biomacromolecules, 9, 966-973 (2008).
Mustafa Gungormus, Hanson Fong, Il Won Kim, John
Spencer Evans, Candan Tamerler and Mehmet Sarikaya,
Regulation of in vitro calcium phosphate mineralization by
combinatorially selected hydroxyapatite binding peptides,
Biomacromolecules, 9, 966-973 (2008).
John Spencer Evans, “Tuning in” to mollusk shell nacreand prismatic-associated protein terminal sequences. Implications for biomineralization and the construction of high
performance inorganic-organic composites, Chemical Reviews, 108, 4455-4462 (2008).
Il Won Kim, Jennifer Giocondi, Christine Orme, Sebastiano Collino and John Spencer Evans, Morphological transformation of calcite crystal growth by prismatic “acidic”
polypeptide sequences, Crystal Growth and Design, 8, 11541160 (2008).
Katya Delak, Jennifer Giocondi, Christine Orme and John
Spencer Evans, Modulation of crystal growth by the terminal
sequences of the prismatic associated Asprich protein, Crystal Growth and Design, 8, 4481-4486 (2008).
Marketa Hnilova, Ersin Emre Oren, Uratu Seker, Brandon
R. Wilson, Sebastiano Collino, John Spencer Evans, Candan
Tamerler and Mehmet Sarikaya, Effect of molecular conformations on adsorption behavior of gold binding peptides,
Langmuir, 24, 12440-12445 (2008).
Rebecca A. Metzler, Il Won Kim, Katya Delak, John
Spencer Evans, Dong Zhou, Elia Beniash, Fred Wilt, Mark
Abrecht, Jin-Wong Chiou, Jin Guo, Susan N. Coppersmith
and P. U. P. A. Gilbert, Probing the organic-mineral interface
(OMI) at the molecular level in model biominerals,
Langmuir, 24, 2680-2687 (2008).
Rebecca A. Metzler, Il Won Kim, Katya Delak, John
Spencer Evans, Dong Zhou, Elia Beniash, Fred Wilt, Mike
Abrecht, Jau-Wern Chiou, Jinghua Guo, Susan N. Coppersmith and P. U. P. A. Gilbert, Probing the Organic-Mineral
Interface at the Molecular Level in Model Biominerals,
Langmuir, 24, 2680-2687 (2008).
John Spencer Evans, Ram Samudrala, Tiffany Walsh, Ersin Emre Oren and Candan Tamerler, Molecular design of inorganic—binding polypeptides, MRS Bulletin, 33, 8-14
(2008).
GANS, PAUL JONATHAN (b.1933) Professor.
B.Sc, 1954, Ohio State University; Ph.D, 1959, Case Institute of Technology. Postdoctoral Fellowship, 19591962, University of Illinois. Statistical mechanics; stochastic processes; digital computer simulation of systems
of chemical interest. TEL: (212) 998-8485 FAX: (212)
260-7905
Email: gans@scholar.chem.nyu.edu
No publication information submitted for this edition.
GEACINTOV, NICHOLAS E. (b.1935) Professor.
B.S, 1957, Syracuse University and SUNY College of
Environmental Science and Forestry; M.S, 1959, Syra-
2
NEW YORK
cuse University and SUNY College of Environmental
Science and Forestry; Ph.D, 1961, Syracuse University
and SUNY College of Environmental Science and Forestry. Resident Associate, 1961-1963, Polytechnic Institute of Brooklyn; Resident Scientist, 1963-1969, New
York University. Biochemistry; Biophysics/Biophysical
Chemistry. Mechanisms of DNA damage induced by
chemical carcinogens and metabolites of conjugated estrogens. Mechanisms of DNA repair, chemical carcinogenesis, and structure-function relationships. Electron
transfer reactions and oxidative damage in nucleic acids.
TEL: (212) 998-8407 FAX: (212) 998-8421
Email: ng1@nyu.edu
Shuang Ding, Robert Shapiro, Nicholas E. Geacintov and
Suse Broyde, 4-Hydroxyequilenin-Adenine Lesions in DNA
Duplexes: Stereochemistry, Damage Site, and Structure, Biochemistry, 46, 182-191 (2007).
Lei Jia, Vladimir Shafirovich, Nicholas E. Geacintov and
Suse Broyde, Lesion Specificity in the Base Excision Repair
Enzyme hNeil1: Modeling and Dynamics Studies, Biochemistry, 46, 5305-5314 (2007).
Qian Ruan, Tongming Liu, Alexander Kolbanovskiy, Yang
Liu, Jian Ren, Milan Skorvaga, Yue Zou, Joshua Lader, Brijesh Malkani, Shantu Amin, Bennett Van Houten and Nicholas E. Geacintov, Sequence Context- and Temperature-Dependent Nucleotide Excision Repair of a Benzo[a]pyrene
Diol Epoxide-Guanine DNA Adduct Catalyzed by Thermophilic UvrABC Proteins, Biochemistry, 46, 7006-7015
(2007).
Shixiang Yan, Min Wu, Dinshaw J. Patel, Nicholas E.
Geacintov and Suse Broyde, Simulating structural and thermodynamic properties of carcinogen-damaged DNA. [Erratum to document cited in CA139:129520], Biophys. J, 92,
697 (2007).
Young Ae Lee, Byeong Hwa Yun, Seog K. Kim, Yelena
Margolin, Peter C. Dedon, Nicholas E. Geacintov and Vladimir Shafirovich, Mechanisms of oxidation of guanine in
DNA by carbonate radical anion, a decomposition product of
nitrosoperoxycarbonate, Chem.—Eur. J, 13, 4571-4581
(2007).
Vincent Mocquet, Konstantin Kropachev, Marina Kolbanovskiy, Alexander Kolbanovskiy, Angels Tapias, Yuqin
Cai, Suse Broyde, Nicholas E. Geacintov and Jean-Marc
Egly, The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions, EMBO
J, 26, 2923-2932 (2007).
Oksana M. Subach, Diana V. Maltseva, Anant Shastry,
Alexander Kolbanovskiy, Saulius Klimasauskas, Nicholas E.
Geacintov and Elizaveta S. Gromova, The stereochemistry of
benzo[a]pyrene-2’-deoxyguanosine adducts affects DNA
methylation by SssI and HhaI DNA methyltransferases,
FEBS J, 274, 2121-2134 (2007).
Byeong Hwa Yun, Young Ae Lee, Seog K. Kim, Vladimir
Kuzmin, Alexander Kolbanovskiy, Peter C. Dedon, Nicholas
E. Geacintov and Vladimir Shafirovich, Photosensitized Oxidative DNA Damage: From Hole Injection to Chemical
Product Formation and Strand Cleavage, J. Am. Chem. Soc,
129, 9321-9332 (2007).
Rebecca A. Perlow-Poehnelt, Ilya Likhterov, Lihua Wang,
David A. Scicchitano, Nicholas E. Geacintov and Suse
Broyde, Increased Flexibility Enhances Misincorporation:
Temperature effects on nucleotide incorporation opposite a
bulky carcinogen-DNA adduct by a Y-family DNA polymerase, J. Biol. Chem, 282, 1397-1408 (2007).
Yuqin Cai, Dinshaw J. Patel, Nicholas E. Geacintov and
Suse Broyde, Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair, J. Mol. Biol, 374, 292-305 (2007).
Fabian A. Rodriguez, Yuqin Cai, Chin Lin, Yijin Tang,
Alexander Kolbanovskiy, Shantu Amin, Dinshaw J. Patel,
Suse Broyde and Nicholas E. Geacintov, Exocyclic amino
groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor
groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context, Nucleic Acids Res, 35, 1555-1568
(2007).
Pingna Xu, Lida Oum, Lorena S. Beese, Nicholas E. Geacintov and Suse Broyde, Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage
and bypass in a high-fidelity DNA polymerase, Nucleic Acids
Res, 35, 4275-4288 (2007).
Pingna Xu, Lida Oum, Nicholas E. Geacintov and Suse
Broyde, Nucleotide Selectivity Opposite a Benzo[a]pyreneDerived N2-dG Adduct in a Y-Family DNA Polymerase: A
5’-Slippage Mechanism, Biochemistry, 47, 2701-2709
(2008).
Shuang Ding, Robert Shapiro, Yuqin Cai, Nicholas E.
Geacintov and Suse Broyde, Conformational Properties of
Equilenin-DNA Adducts: Stereoisomer and Base Effects,
Chem. Res. Toxicol, 21, 1064-1073 (2008).
Shuang Ding, Yan Wang, Alexander Kolbanovskiy, Alexander Durandin, Judy L. Bolton, Richard B. van Breemen,
Suse Broyde and Nicholas E. Geacintov, Determination of
Absolute Configurations of 4-Hydroxyequilenin-Cytosine
and -Adenine Adducts by Optical Rotatory Dispersion, Electronic Circular Dichroism, Density Functional Theory Calculations, and Mass Spectrometry, Chem. Res. Toxicol, 21,
1739-1748 (2008).
Conor Crean, Nicholas E. Geacintov and Vladimir Shafirovich, Pathways of Arachidonic Acid Peroxyl Radical Reactions and Product Formation with Guanine Radicals, Chem.
Res. Toxicol, 21, 358-373 (2008).
Suse Broyde, Lihua Wang, Ling Zhang, Olga Rechkoblit,
Nicholas E. Geacintov and Dinshaw J. Patel, DNA Adduct
Structure-Function Relationships: Comparing Solution with
Polymerase Structures, Chem. Res. Toxicol, 21, 45-52
(2008).
Alexandra Dimitri, Lei Jia, Vladimir Shafirovich, Nicholas
E. Geacintov, Suse Broyde and David A. Scicchitano, Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage
T7 RNA polymerase, DNA Repair, 7, 1276-1288 (2008).
Conor Crean, Nicholas E. Geacintov and Vladimir Shafirovich, Intrastrand G-U cross-links generated by the oxidation
of guanine in 5’-d(GCU) and 5’-r(GCU), Free Radical Biol.
Med, 45, 1125-1134 (2008).
Young Ae Lee, Alexander Durandin, Peter C. Dedon,
Nicholas E. Geacintov and Vladimir Shafirovich, Oxidation
of Guanine in G, GG, and GGG Sequence Contexts by Aromatic Pyrenyl Radical Cations and Carbonate Radical Anions: Relationship between Kinetics and Distribution of Alkali-Labile Lesions, J. Phys. Chem. B, 112, 1834-1844
(2008).
Conor Crean, Yuriy Uvaydov, Nicholas E. Geacintov and
Vladimir Shafirovich, Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand
cross-links between guanine and thymine bases separated by
cytosines, Nucleic Acids Res, 36, 742-755 (2008).
Suse Broyde, Lihua Wang, Olga Rechkoblit, Nicholas E.
Geacintov and Dinshaw J. Patel, Lesion processing: high-fidelity versus lesion-bypass DNA polymerases, Trends Biochem. Sci, 33, 209-219 (2008).
Fabian A. Rodriguez, Nuclear magnetic resonance solution
structure of covalent polycyclic aromatic carcinogen–DNA
adducts: Influence of base sequence context and carcinogen
topology. (D)
Lida Oum, Base-sequence effects on in vitro translesion
bypass catalyzed by A- and Y-family polymerases. (D)
Yijin Tang, Optical spectroscopic and NMR studies of covalent polycyclic aromatic hydrocarbon–DNA adducts: Influence of base sequence context and carcinogen topology. (D)
JERSCHOW, ALEXEJ (b.1971) Assistant Professor.
B.S, 1994, University of Linz, Austria; Ph.D, 1997, University of Linz, Austria. Premier Assistant, 1997-1999,
University of Lausanne; Visiting Scientist, 1999-2001,
University of California, Berkeley. Chemical Physics;
NMR Spectroscopy. NMR of quadrupolar nuclei. MR
Imaging. Method development and applications in medical imaging spectroscopy and biophysics. TEL: (212)
998-8451 FAX: (212) 260-7905
Web: www.nyu.edu/projects/jerschow
Email: alexej.jerschow@nyu.edu
Jacob M. Newman and Alexej Jerschow, Improvements in
Complex Mixture Analysis by NMR: DQF-COSY iDOSY,
Anal. Chem. (Washington, DC, U. S.), 79, 2957-2960 (2007).
Yael Elmatad, Michael Zitolo, Daniela Fera and Alexej
Jerschow, Examining gas kinetics in MATLAB, Chem. Educ,
12, 89-93 (2007).
Wen Ling and Alexej Jerschow, Relaxation-allowed nuclear magnetic resonance transitions by interference between the
quadrupolar coupling and the paramagnetic interaction, J.
Chem. Phys, 126, 064502/1-064502/6 (2007).
Eleonora Del Federico, Jacob Newman, Lindsay Tyne,
Cyndi O’Hern, Licio Isolani and Alexej Jerschow, SolidState NMR Studies of Ultramarine Pigments Discoloration,
Mater. Res. Soc. Symp. Proc, 984E (2007).
S. Chandra Shekar, Peng Rong and Alexej Jerschow, Irreducible spherical tensor analysis of quadrupolar nuclei,
Chem. Phys. Lett, 464, 235-239 (2008).
Peng Rong, Ravinder R. Regatte and Alexej Jerschow,
Clean demarcation of cartilage tissue 23Na by inversion recovery, J. Magn. Reson, 193, 207-209 (2008).
Wen Ling, Uzi Eliav, Gil Navon and Alexej Jerschow,
Chemical exchange saturation transfer by intermolecular
double-quantum coherence, J. Magn. Reson, 194, 29-32
(2008).
Wen Ling, Ravinder R. Regatte, Gil Navon and Alexej Jerschow, Assessment of glycosaminoglycan concentration in
vivo by chemical exchange-dependent saturation transfer
(gagCEST), Proc. Natl. Acad. Sci. U. S. A, 105, 2266-2270
(2008).
KAHR, BART (b.1961) Professor. A.B, 1983, Middlebury College; M.S, 1985, Princeton University; Ph.D,
1988, Princeton University. Postdoctoral Associate,
1988-1990, Yale University. Crystallography; Materials
Science. Our group studies the growth, structure, and optical properties of crystalline materials. We analyzed the
supramolecular chemistry of dyeing crystals using new
techniques in polarized light imaging. These microscopies are applied to a histochemical staining mechanisms
with the aim of introducing chiroptical contrast mechanisms into biomedical imaging. Likewise, polarimetric
imaging is to parse structures and mechanisms of formation of mesoscale polycrystalline patterns. TEL: (212)
998-8400 FAX: (212) 260-7905
Web: www.nyu.edu/fas/dept/chemistry/kahrgroup/
Email: bart.kahr@NYU.edu
Dawn E. Cohen, Jason B. Benedict, Brian Morlan, Daniel
T. Chiu and Bart Kahr, Dyeing Polymorphs: The MALDI
Host 2,5-Dihydroxybenzoic Acid, Cryst. Growth Des, 7,
492-495 (2007).
Theresa Bullard, John Freudenthal, Serine Avagyan and
Bart Kahr, Test of Cairns-Smith’s crystals-as-genes’ hypothesis, Faraday Discuss, 136, 231-245 (2007).
Werner Kaminsky, Erica Gunn, Ryan Sours and Bart Kahr,
Simultaneous false-color imaging of birefringence, extinction, and transmittance at camera speed, J. Microsc, 228,
153-164 (2007).
Christine Isborn, Kacey Claborn and Bart Kahr, The Optical Rotatory Power of Water, J. Phys. Chem. A, 111, 78007804 (2007).
Kristin L. Wustholz, Eric D. Bott, Christine M. Isborn,
Xiaosong Li, Bart Kahr and Philip J. Reid, Dispersive Kinetics from Single Molecules Oriented in Single Crystals of Potassium Acid Phthalate, J. Phys. Chem. C, 111, 9146-9156
(2007).
Kacey Claborn, Christine Isborn, Werner Kaminsky and
Bart Kahr, Optical rotation of achiral compounds, Angew.
Chem., Int. Ed, 47, 5706-5717 (2008).
Bart Kahr and Kacey Claborn, The lives of Malus and his
bicentennial law, ChemPhysChem, 9, 43-58 (2008).
Bart Kahr and John H. Freudenthal, Dendritic crystal
growth, differential circular scattering, and the origin of
biomolecular homochirality, Chirality, 20, 973-977 (2008).
Andrew L. Rohl, Massimo Moret, Werner Kaminsky, Kacey Claborn, Joshua J. McKinnon and Bart Kahr, Hirshfeld
surfaces identify inadequacies in computations of intermolecular interactions in crystals: Pentamorphic 1,8-dihydroxyanthraquinone, Cryst. Growth Des, 8, 4517-4525 (2008).
Kristin L. Wustholz, Daniel R. B. Sluss, Bart Kahr and
Philip J. Reid, Applications of single-molecule microscopy to
problems in dyed composite materials, Int. Rev. Phys. Chem,
27, 167-200 (2008).
Jason B. Benedict, John H. Freudenthal, Eva Hollis and
Bart Kahr, Orientational Dependence of Linear Dichroism
Exemplified by Dyed Spherulites, J. Am. Chem. Soc, 130,
10714-10719 (2008).
Kristin L. Wustholz, Eric D. Bott, Bart Kahr and Philip J.
Reid, Memory and Spectral Diffusion in Single-Molecule
Emission, J. Phys. Chem. C, 112, 7877-7885 (2008).
David A. Hrovat, Christine M. Isborn, Bart Kahr and Weston Thatcher Borden, Internal Dynamics and Optical Rotations Predicted for Oh- and O-Symmetric Cubanes, Org. Lett,
10, 4763-4766 (2008).
J. B. Benedict, Dyeing crystals: From 19th century phenomenology to 21st century technology. (D)
K. L. Wustholz, Single- molecule orientations and photophysics in dyed salt crystals. (D)
T. V. Bullard, Luminescence labeling and dynamics of
growth active crystal surface structures. (D)
KALLENBACH, NEVILLE R. (b.1938) Professor.
B.S, 1958, Rutgers University, New Brunswick, NJ;
Ph.D, 1961, Yale University, New Haven, CT; M.A. (honoris causa), 1971, University of Pennsylvania. NSF Fellowship, 1961-1962, University of California, San Diego; NIH Fellowship, 1962-1964, University of California, San Diego. Biophysics/Biophysical Chemistry.
Structure and function of proteins and nucleic acids.
Analysis of secondary structure in peptides and model
proteins, design and synthesis of nanoscale protein complexes and antimicrobial agents. TEL: (212) 998-8757
FAX: (212) 260-7905
Web: chemistry.fas.nyu.edu/object/nevillerkallenbach.
html
Email: nrk1@nyu.edu
Kang Chen, Zhigang Liu, Chunhui Zhou, W. Clay Bracken
and Neville R. Kallenbach, Spin relaxation enhancement
confirms dominance of extended conformations in short alanine peptides, Angew. Chem., Int. Ed, 46, 9036-9039 (2007).
Zhigang Liu, Anna Brady, Anne Young, Brian Rasimick,
Kang Chen, Chunhui Zhou and Neville R. Kallenbach,
Length effects in antimicrobial peptides of the (RC)n series,
Antimicrob. Agents Chemother, 51, 597-603 (2007).
Jie Liu, Qi Zheng, Yiqun Deng, Qunnu Li, Neville R. Kallenbach and Min Lu, Conformational specificity of the lac repressor coiled-coil tetramerization domain, Biochemistry, 46,
14951-14959 (2007).
Zhigang Liu, Anne W. Young, Po Hu, Amanda J. Rice,
Chunhui Zhou, Yingkai Zhang and Neville R. Kallenbach,
Tuning the membrane selectivity of antimicrobial peptides by
using multivalent design, ChemBioChem, 8, 2063-2065
(2007).
Yiqun Deng, Qi Zheng, Jie Liu, Chao-Sheng Cheng, Neville R. Kallenbach and Min Lu, Self-assembly of coiled-coil
tetramers in the 1.40 Å structure of a leucine-zipper mutant,
Protein Sci, 16, 323-328 (2007).
Anthony J. Bell, Seema Chauhan, Sarah A. Woodson and
Neville R. Kallenbach, Interactions of recombinant HMGB
proteins with branched RNA substrates, Biochem. Biophys.
Res. Commun, 377, 262-267 (2008).
Ross Chapman, John L. Kulp, III, Anupam Patgiri, Neville
NEW YORK
R. Kallenbach, Clay Bracken and Paramjit S. Arora, Trapping a Folding Intermediate of the ␣-Helix: Stabilization of
the ␲-Helix, Biochemistry, 47, 4189-4195 (2008).
Chunhui Zhou, Jaeki Min, Zhigang Liu, Anne Young,
Heather Deshazer, Tian Gao, Young-Tae Chang and Neville
R. Kallenbach, Synthesis and biological evaluation of novel
1,3,5-triazine derivatives as antimicrobial agents, Bioorg.
Med. Chem. Lett, 18, 1308-1311 (2008).
Yiqun Deng, Jie Liu, Qi Zheng, Qunnu Li, Neville R. Kallenbach and Min Lu, A Heterospecific Leucine Zipper Tetramer, Chem. Biol. (Cambridge, MA, U. S.), 15, 908-919
(2008).
Kang Chen, The structure and stability of polyproline II
conformation in unfolded peptides. (D)
Zhigang Liu, Novel antibacterials derived from antimicrobial peptides. (D)
A simple strategy for the creation of a recombinant lectin microarray, Mol. BioSyst, 4, 654-662 (2008).
Alexander Brennan Preston, Carbohydrate cloak disguises
HIV as normal cellular product. (M)
Lisa Alexis Alexander, Toward the directed evolution of
the FimH lectin. (M)
Luz D. Carillo, Genetically encoded FRET-based sensors
for the study of ß-O-N-acetyl-D-glucosamine dynamics. (M)
Megan Brown, Examining reciprocity between O-GlcNAc
and O-phosphate in cell signaling using reciprocal FRET
based sensors. (M)
Susan Anderson Dixon, Optimization and quality control
of the lectin microarray. (M)
Ku-Lung Hsu, A systems approach to analyzing bacterial
glycans and glycan-binding proteins. (D)
Lakshmi Krishnamoorthy, Glycomic approaches to understanding HIV-1 budding in T cells. (D)
KIRSHENBAUM, KENT Associate Professor. B.A,
1994, Reed College; Ph.D, 1999, University of California, San Francisco. Research Fellow, 1999-2002, California Institute of Technology. Bioorganic Chemistry.
My primary topics of research interest are in the fields of
bioorganic chemistry, biomimetic chemistry, protein
conformation and dynamics, and macromolecular design.
We are pursuing two complementary strategies: The
chemical synthesis of biomimetic sequence-specific
heteropolymers, and the biosynthesis of proteins incorporating abiotic amino acids. TEL: (212) 998-8486 FAX:
(212) 260-7905
Web: www.nyu.edu/pages/chemistry/Faculty/
kirshenbaum.html
Email: kent@nyu.edu
Aaron T. Fafarman, Peter P. Borbat, Jack H. Freed and
Kent Kirshenbaum, Characterizing the structure and dynamics of folded oligomers: Pulsed ESR studies of peptoid helices, Chem. Commun. (Cambridge, U. K.), 377-379 (2007).
Sung Bin Y. Shin, Barney Yoo, Louis J. Todaro and Kent
Kirshenbaum, Cyclic peptoids, J. Am. Chem. Soc, 129, 32183225 (2007).
Justin M. Holub, Hangjun Jang and Kent Kirshenbaum, Fit
To Be Tied: Conformation-Directed Macrocyclization of
Peptoid Foldamers, Org. Lett, 9, 3275-3278 (2007).
Sung Bin Y. Shin and Kent Kirshenbaum, Conformational
Rearrangements by Water-Soluble Peptoid Foldamers, Org.
Lett, 9, 5003-5006 (2007).
Justin M. Holub, Michael J. Garabedian and Kent Kirshenbaum, Peptoids on steroids: precise multivalent estradiol—peptidomimetic conjugates generated via azide—alkyne [3 + 2] cycloaddition reactions, QSAR Comb. Sci, 26,
1175-1180 (2007).
Barney Yoo and Kent Kirshenbaum, Peptoid architectures:
Elaboration, actuation, and application, Current Opinion in
Chemical Biology, 12, 714-721 (2008).
Neel H. Shah, Glenn L. Butterfoss, Khanh Nguyen, Barney
Yoo, Richard Bonneau, Dallas L. Rabenstein and Kent Kirshenbaum, Oligo(N-aryl glycines): A new twist on structured
peptoids, J Am Chem Soc, 130, 16622-16632 (2008).
Neel H. Shah and Kent Kirshenbaum, Direct generation of
polymer films on copper surfaces through azide-alkyne cycloaddition reactions between peptidomimetic oligomers,
Macromol. Rapid Commun, 29, 1134-1139 (2008).
Kent Kirshenbaum and Paramjit S. Arora, Cross-dressing
proteins by olefin metathesis, Nat. Chem. Biol, 4, 527-528
(2008).
Neel H. Shah and Kent Kirshenbaum, Photoresponsive
peptoid oligomers bearing azobenzene side chains, Org.
Biomol. Chem, 6, 2516-2521 (2008).
Galia Maayan, Barney Yoo and Kent Kirshenbaum, Heterocyclic amines for the construction of peptoid oligomers
bearing multi-dentate ligands, Tetrahedron Lett, 49, 335-338
(2008).
MAHAL, LARA K. Associate Professor. B.A, 1995,
University of California, Santa Cruz; Ph.D, 2000, University of California, Berkeley. Research Associate,
2000-2003, Sloan-Kettering Insitute. Chemical Biology;
Organic Chemistry. Glycosylation is crucial to a myriad
of biological processes including bacterial pathogenesis,
cell signaling, tumor cell metastasis and neuronal development. Research in my laboratory is focused on the creation and application of chemical, biological and systems-based methods to the study of glycosylation. TEL:
(212) 998-8400 FAX: (212) 260-7905
Email: lkmahal@nyu.edu
Kanoelani T. Pilobello and Lara K. Mahal, Deciphering the
glycocode: the complexity and analytical challenge of glycomics, Curr. Opin. Chem. Biol, 11, 300-305 (2007).
Kanoelani T. Pilobello and Lara K. Mahal, Lectin microarrays for glycoprotein analysis, Methods Mol. Biol. (Totowa,
NJ, U. S.), 385, 193-203 (2007).
Kanoelani T. Pilobello, Deepika E. Slawek and Lara K.
Mahal, A ratiometric lectin microarray approach to analysis
of the dynamic mammalian glycome, Proc. Natl. Acad. Sci.
U. S. A, 104, 11534-11539 (2007).
Lara K. Mahal, Glycomics: towards bioinformatic approaches to understanding glycosylation, Anti-Cancer Agents
Med. Chem, 8, 37-51 (2008).
Ku-Lung Hsu, Jeffrey C. Gildersleeve and Lara K. Mahal,
SCHLICK, TAMAR Professor. B.S, 1982, Wayne
State University; M.S, 1985, New York University;
Ph.D, 1987, New York University. NSF Posdoctoral Fellowship, Mathematical Society, 1987-1989, New York
University; Weizmann Postdoctoral Fellowship, 1988,
Weizmann Institute of Science. Biophysics/Biophysical
Chemistry; Computational Chemistry. Computational
biology and biophysics and macromolecular structure
and function. Molecular modeling and dynamics of regulatory nucleic acid and protein/nucleic-acid systems on
various levels of spatial resulation, special forces on
chromatin structure and folding, DNA polymerase mechanisms, and RNA structure and design using a graphtheory approach. TEL: (212) 998-3116 FAX: (212) 9954152
Web: www.monod.biomath.nyu.edu
Email: schlick@nyu.edu
Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark
Gan and Tamar Schlick, RagPools: RNA-As-Graph-Pools-a
web server for assisting the design of structured RNA pools
for in vitro selection, Bioinformatics, 23, 2959-2960 (2007).
Yanli Wang, Sujatha Reddy, William A. Beard, Samuel H.
Wilson and Tamar Schlick, Differing conformational pathways before and after chemistry for insertion of dATP versus
dCTP opposite 8-OxoG in DNA polymerase ␤, Biophys. J,
92, 3063-3070 (2007).
Yanli Wang and Tamar Schlick, Distinct energetics and
closing pathways for DNA polymerase ␤ with 8-oxoG template and different incoming nucleotides, BMC Struct. Biol, 7,
No pp. given (2007).
Ian L. Alberts, Yanli Wang and Tamar Schlick, DNA
Polymerase ␤ Catalysis: Are Different Mechanisms Possible?, J. Am. Chem. Soc, 129, 11100-11110 (2007).
Gaurav Arya and Tamar Schlick, Efficient global biopolymer sampling with end-transfer configurational bias Monte
Carlo, J. Chem. Phys, 126, 044107/1-044107/12 (2007).
Mihaela D. Bojin and Tamar Schlick, A Quantum Mechanical Investigation of Possible Mechanisms for the Nucleotidyl Transfer Reaction Catalyzed by DNA Polymerase ␤, J.
Phys. Chem. B, 111, 11244-11252 (2007).
Namhee Kim, Hin Hark Gan and Tamar Schlick, A computational proposal for designing structured RNA pools for
in vitro selection of RNAs, RNA, 13, 478-492 (2007).
Yurong Xin, Giulio Quarta, Hin Hark Gan and Tamar
Schlick, Estimating the fraction of noncoding RNAs in Mammalian Transcriptomes, Bioinformatics and Biology Insights,
2, 77-95 (2008).
Katarzyna Bebenek, Miguel Garcia-Diaz, Meredith C. Foley, Lars C. Pedersen, Tamar Schlick and Thomas A. Kunkel, Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase ␭, EMBO Rep, 9, 459-464
(2008).
Yanli Wang and Tamar Schlick, Quantum Mechanics/Molecular Mechanics Investigation of the Chemical Reaction in
Dpo4 Reveals Water-Dependent Pathways and Requirements
for Active Site Reorganization, J. Am. Chem. Soc, 130,
13240-13250 (2008).
Meredith C. Foley and Tamar Schlick, Simulations of
DNA Pol ␭ R517 Mutants Indicate 517’s Crucial Role in
Ternary Complex Stability and Suggest DNA Slippage Origin, J. Am. Chem. Soc, 130, 3967-3977 (2008).
Padmavati Sridhar, Hin Hark Gan and Tamar Schlick, A
computational screen for C/D box snoRNAs in the human
genomic region associated with Prader-Willi and Angelman
syndromes, J. Biomed. Sci, 15, 697-705 (2008).
Benedetta A. Sampoli Benitez, Karunesh Arora, L. Balistreri and Tamar Schlick, Mismatched base pair simulations for
ASFV Pol X/DNA complexes help interpret frequent G:G
misincorporation, J. Mol. Bio, 384, 1086-1097 (2008).
Yurong Xin, Christian Laing, N. B. Leontis and Tamar
Schlick, Annotation of tertiary interactions in RNA structures
reveals variations and correlations, RNA, 14, 2465-2477
(2008).
SCHUSTER, DAVID I. (b.1935) Professor Emeritus.
B.A, 1956, Columbia University; Ph.D, 1961, California
Institute of Technology. Research Associate, 1960-1961,
University of Wisconsin. Organic Chemistry;
Photochemistry. Mechanistic organic photochemistry;
study of transient intermediates by femtosecond, picose-
3
cond and nanosecond laser flash photolysis; synthesis of
biologically active fullerene derivatives; synthesis and
photophysics of porphyrin-fullerene dyads; photoinduced
electron transfer processes in donor-acceptor systems incorporating fullerenes; supramolecular interactions with
fullerenes and fullerene derivatives; synthesis of catenanes and rotaxanes including electron donor and acceptor
moieties. TEL: (212) 998-8447 FAX: (212) 260-7905
Web: chemistry.fas.nyu.edu/object/davidischuster.html
Email: david.schuster@nyu.edu
David I. Schuster, Ke Li, Dirk M. Guldi, Amit Palkar, Luis
Echegoyen, Christopher Stanisky, R. James Cross, Marja
Niemi, Nikolai V. Tkachenko and Helge Lemmetyinen,
Azobenzene-Linked Porphyrin-Fullerene Dyads, J. Am.
Chem. Soc, 129, 15973-15982 (2007).
Jackson D. Megiatto, Jr. and David I. Schuster, General
Method for Synthesis of Functionalized Macrocycles and Catenanes Utilizing “Click” Chemistry, J. Am. Chem. Soc, 130,
12872-12873 (2008).
Michael A. Fazio, Olivia P. Lee and David I. Schuster,
First Triazole-Linked Porphyrin-Fullerene Dyads, Org. Lett,
10, 4979-4982 (2008).
SEEMAN, NADRIAN C. (b.1945) Professor. B.S,
1966, University of Chicago; Ph.D, 1970, University of
Pittsburgh. Research Associate, 1970-1972, Columbia
University; Damon Runyon Fellowship, 1972-1973,
Massachusetts Institute of Technology (MIT); NIH Fellowship, 1973-1976, Massachusetts Institute of Technology (MIT). Biophysics/Biophysical Chemistry; Nanochemistry. Structural DNA nanotechnology; DNA-based
computation; molecular biophysics of recombinational
intermediates; crystal design; crystallography; singlestranded DNA topology. TEL: (212) 998-8395 FAX:
(212) 260-7905
Web: seemanlab4.chem.nyu.edu
Email: ned.seeman@nyu.edu
Chenxiang Lin, Xing Wang, Yan Liu, Nadrian C. Seeman
and Hao Yan, Rolling Circle Enzymatic Replication of a
Complex Multi-Crossover DNA Nanostructure, J. Am.
Chem. Soc, 129, 14475-14481 (2007).
Xing Wang and Nadrian C. Seeman, Assembly and Characterization of 8-Arm and 12-Arm DNA Branched Junctions,
J. Am. Chem. Soc, 129, 8169-8176 (2007).
Nadrian C. Seeman, An overview of structural DNA nanotechnology, Mol. Biotechnol, 37, 246-257 (2007).
Akinori Kuzuya, Risheng Wang, Ruojie Sha and Nadrian
C. Seeman, Six-Helix and Eight-Helix DNA Nanotubes Assembled from Half-Tubes, Nano Lett, 7, 1757-1763 (2007).
Alejandra V. Garibotti, Shiping Liao and Nadrian C. Seeman, A Simple DNA-Based Translation System, Nano Lett,
7, 480-483 (2007).
N. C. Seeman, Nanotechnology and the double helix, Scientific American Reports, Sept, 30-39 (2007).
Jianping Lin, Nadrian C. Seeman and Nagarajan Vaidehi,
Molecular-dynamics simulations of insertion of chemically
modified DNA nanostructures into a water-chloroform interface, Biophys. J, 95, 1099-1107 (2008).
Jiwen Zheng, Philip S. Lukeman, William B. Sherman,
Christine Micheel, A. Paul Alivisatos, Pamela E. Constantinou and Nadrian C. Seeman, Metallic nanoparticles used to
estimate the structural integrity of DNA motifs, Biophys. J,
95, 3340-3348 (2008).
Y. Liu, R. Wang, L. Ding, R. Sha, P. S. Lukeman, J. W.
Canary and N. C. Seeman, Thermodynamic analysis of nylon
nucleic acids, ChemBioChem, 9, 1641-1648 (2008).
Philip S. Lukeman, Mary L. Stevenson and Nadrian C.
Seeman, Morphology Change of Calcium Carbonate in the
Presence of Polynucleotides, Cryst. Growth Des, 8, 12001202 (2008).
Yu Liu, Akinori Kuzuya, Ruojie Sha, Johan Guillaume,
Risheng Wang, James W. Canary and Nadrian C. Seeman,
Coupling Across a DNA Helical Turn Yields a Hybrid DNA/
Organic Catenane Doubly Tailed with Functional Termini, J.
Am. Chem. Soc, 130, 10882-10883 (2008).
Wenyan Liu, Xing Wang, Tong Wang, Ruojie Sha and
Nadrian C. Seeman, PX DNA Triangle Oligomerized Using
a Novel Three-Domain Motif, Nano Lett, 8, 317-322 (2008).
B. Chakraborty, R. Sha and N. C. Seeman, A DNA-based
nanomechanical device with three robust states, Proc. Nat.
Acad. Sci. (USA), 105, 17245-17249 (2008).
C. Lin, S. Rinker, X. Wang, Y. Liu, N. C. Seeman and H.
Yan, In vivo cloning of artificial DNA nanostructures, Proc.
Nat. Acad. Sci. (USA), 105, 17626-17631 (2008).
Yu Liu, Ruojie Sha, Risheng Wang, Liang Ding, James W.
Canary and Nadrian C. Seeman, 2’,2’-Ligation demonstrates
the thermal dependence of DNA-directed positional control,
Tetrahedron, 64, 8417-8422 (2008).
Banani Chakraborty, Putting DNA to work as nanomechanical computing and diagnostic devices. (D)
Gang Wu, Using DNA to solve mathematical problems:
Multiplication and 3-colorability computation. (D)
Hong Zhong, Structural DNA nanotechnology-RNA used
to control a DNA rotary nanomachine & DNA origami arrays. (D)
Tong Wang, Structural DNA nanotechnology design and
self-assembly of 2D and 3D crystalline lattices. (D)
4
NEW YORK
Xing Wang, Motif, 2D lattice, and connection with biology
in DNA nanotechnology. (D)
SHAPIRO, ROBERT (b.1935) Professor Emeritus
and Senior Research Scientist. B.S, 1956, City College
of New York; A.M, 1957, Harvard University; Ph.D,
1959, Harvard University. NATO Fellow, 1959-1960,
Cambridge University; Postdoctoral Fellowship, 19601961, New York University Medical School. Biochemistry; Structural Biology. Chemistry of DNA and RNA,
chemical mechanisms of mutation and genetic damage,
origin of life, astrobiology. TEL: (212) 998-8484 FAX:
(212) 260-7905
Web: chemistry.fas.nyu.edu/object/robertshapiro.html
Email: rs2@nyu.edu
Shuang Ding, Robert Shapiro, Nicholas E. Geacintov and
Suse Broyde, 4-Hydroxyequilenin-Adenine Lesions in DNA
Duplexes: Stereochemistry, Damage Site, and Structure, Biochemistry, 46, 182-191 (2007).
Robert Shapiro, A Simpler Origin for Life, Sci. Am, 296,
46-53 (2007).
Shuang Ding, Robert Shapiro, Yuqin Cai, Nicholas E.
Geacintov and Suse Broyde, Conformational Properties of
Equilenin-DNA Adducts: Stereoisomer and Base Effects,
Chem. Res. Toxicol, 21, 1064-1073 (2008).
TUCKERMAN, MARK E. (b.1964) Professor. B.S,
1986, University of California, Bekeley; M.S, 1988, Columbia University; Ph.D, 1993, Columbia University.
IBM Postdoctoral Fellowship, 1993-1994, IBM, Forschungslaboratorium, Switzerland; NSF/ASC Postdoctoral Fellow, 1995-1996, University of Pennsylvania.
Chemical Physics; Theoretical Chemistry. Advances in
modern theoretical methods allow the microscopic details of chemical processes to be investigated in novel
ways. My research aims to further develop and exploit
these emerging capabilities. Current projects include:
New conformational sampling and free-energy techniques; methods for linear-scaling and massively parallel
electronic structure and ab initio molecular dynamics
calculations; applications to protein folding, surface
chemistry, proton transport in hydrogen-bonded media.
TEL: (212) 998-8471 FAX: (212) 995-4203
Web: www.homepages.nyu.edu/~mt33
Email: mark.tuckerman@nyu.edu
Robin L. Hayes and Mark E. Tuckerman, Role of Surface
Dimer Dynamics in Creating Ordered Organic-Semiconductor Interfaces, J. Am. Chem. Soc, 129, 12172-12180 (2007).
Hee-Seung Lee and Mark E. Tuckerman, Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit, J. Chem. Phys, 126,
164501/1-164501/16 (2007).
Otto Anatole von Lilienfeld and Mark E. Tuckerman, Alchemical variations of intermolecular energies according to
molecular grand-canonical ensemble density functional theory, Journal of Chemical Theory and Computation, 3, 10831090 (2007).
Amalendu Chandra, Mark E. Tuckerman and Dominik
Marx, Connecting Solvation Shell Structure to Proton Transport Kinetics in Hydrogen-Bonded Networks via Population
Correlation Functions, Phys. Rev. Lett, 99, 145901/1-145901/
4 (2007).
Eric Bohm, Abhinav Bhatele, Laxmikant V. Kale, Mark E.
Tuckerman, Sameer Kumar, John A. Gunnels and Glenn J.
Martyna, Fine-grained parallelization of the Car-Parrinello ab
initio molecular dynamics method on the IBM Blue Gene/L
supercomputer, IBM Journal of Research and Development,
52, 159-175 (2008).
Robin L. Hayes and Mark E. Tuckerman, Kinetic Effects
on the Cycloaddition of 1,3-Cyclohexadiene to the 3C-SiC
(001)-3 ␮e 2 Surface Studied via Ab Initio Molecular Dynamics, J. Phys. Chem. C, 112, 5880-5887 (2008).
Hee-Seung Lee and Mark E. Tuckerman, The Structure
and Proton Transport Mechanisms in the Superprotonic
Phase of CsH2PO4: An Ab Initio Molecular Dynamics Study,
J. Phys. Chem. C, 112, 9917-9930 (2008).
Hee-Seung Lee and Mark E. Tuckerman, Efficient solution
of Poisson’s equation using discrete variable representation
basis sets for Car-Parrinello ab initio molecular dynamics
simulations with cluster boundary conditions, Journal of
Chemical Physics, 129, 224108 (2008).
Jerry B. Abrams and Mark E. Tuckerman, Efficient and direct generation of multidimensional free energy surfaces via
adiabatic dynamics without coordinate transformations, Journal of Physical Chemistry B, 112, 15742-15757 (2008).
Peter Minary, Mark E. Tuckerman and Glenn J. Martyna,
Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure, SIAM Journal on
Scientific Computing, 30, 2055-2083 (2008).
Jerry B. Abrams, Novel approaches to free energy calculations via adiabatic molecular dynamics. (D)
VOLOGODSKII, ALEXANDER (b.1948) Research
Professor. M.S, 1972, Moscow Physical-Technical Institute, Russia; Ph.D, 1975, Moscow Physical-Technical Institute, Russia; D.Sc, 1985, Moscow University, Russia.
Biophysics/Biophysical Chemistry. Conformational prop-
erties of DNA, mechanisms of enzymes capable to
change DNA topology. TEL: (212) 998-3599 FAX:
(212) 260-7905
Web: www.crab.chem.nyu.edu/lab_site.html/
Email: alex.vologodskii@gmail.com
alex.vologodskii@nyu.edu
Yury S. Polikanov, Vladimir A. Bondarenko, Vladimir
Tchernaenko, Yong I. Jiang, Leonard C. Lutter, Alexander
Vologodskii and Vasily M. Studitsky, Probability of the site
juxtaposition determines the rate of protein-mediated DNA
looping, Biophys. J, 93, 2726-2731 (2007).
Quan Du, Alexei Livshits, Agnieszka Kwiatek, Makkuni
Jayaram and Alexander Vologodskii, Protein-induced Local
DNA Bends Regulate Global Topology of Recombination
Products, J. Mol. Biol, 368, 170-182 (2007).
Quan Du, Alexander Kotlyar and Alexander Vologodskii,
Kinking the double helix by bending deformation, Nucleic
Acids Res, 36, 1120-1128 (2008).
WALTERS, MARC A. (b.1952) Associate Professor.
B.S, 1976, City College of New York; Ph.D, 1981,
Princeton University. Eppley Foundation, 1981-1982,
Massachusetts Institute of Technology (MIT); NIH Fellowship, 1982-1985, Massachusetts Institute of Technology (MIT). Bioinorganic Chemistry; Nanochemistry.
Transition metal-sulfur chemistry; metalloprotein model
compound synthesis; hydrogen bonding; sulfur and thiol
compound chemistry; vibrational spectroscopy; chemistry of metal complexes in nanostructures; design of MRI
contrast agents. TEL: (212) 998-8477 FAX: (212) 2607905
Web: www.nyu.edu/pages/chemistry/faculty/walters.
html
Email: marc.walters@nyu.edu
No publication information submitted for this edition.
WARD, MICHAEL D. (b.1955) Professor. B.A,
1977, William Paterson College of New Jersey; Ph.D,
1981, Princeton University. Welch Postdoctoral Fellow,
1981-1982, University of Texas, Austin. Materials Science. Organic and inorganic solid state chemistry, scanning probe and force microscopy, nucleation and crystal
growth, electrochemistry, biomineralization. TEL: (212)
998-8439 FAX: (212) 995-4895
Web: www.nyu.edu/fas/dept/chemistry/wardgroup/
Email: mdw3@nyu.edu
Sandra E. Fritz, Siddharth Mohapatra, Brian T. Holmes,
Amelia M. Anderson, Cathal F. Prendergast, C. Daniel Frisbie, Michael D. Ward and Michael F. Toney, Thin Film
Transistors Based on Alkylphenyl Quaterthiophenes: Structure and Electrical Transport Properties, Chem. Mater, 19,
1355-1361 (2007).
Jeffrey A. Wesson and Michael D. Ward, Pathological
biomineralization of kidney stones, Elements (Chantilly, VA,
U. S.), 3, 415-421 (2007).
John C. Jeffery, Thomas Riis-Johannessen, Callum J. Anderson, Christopher J. Adams, Adam Robinson, Stephen P.
Argent, Michael D. Ward and Craig R. Rice, Localization
and Delocalization in a Mixed-Valence Dicopper Helicate,
Inorg. Chem. (Washington, DC, U. S.), 46, 2417-2426
(2007).
Matthew J. Horner, K. Travis Holman and Michael D.
Ward, Architectural Diversity and Elastic Networks in Hydrogen-Bonded Host Frameworks: From Molecular Jaws to
Cylinders, J. Am. Chem. Soc, 129, 14640-14660 (2007).
Benjamin D. Hamilton, Marc A. Hillmyer and Michael D.
Ward, Glycine Polymorphism in Nanoscale Crystallization
Chambers, Cryst. Growth Des, 8, 3368-3375 (2008).
WECK, MARCUS (b.1968) Associate Professor.
M.Sc, 1994, University of Mainz (Germany); Ph.D,
1998, California Institute of Technology. Postdoctoral
Fellow, 1998-2000, Harvard University. Organic Chemistry; Polymer Science. Self-assembled copolymers; materials science; nanoscience; self-assembly; supramolecular chemistry; polymers; catalysis. TEL: (212) 9927968 FAX: (212) 995-4895
Publication list has not been verified by the department.
Clinton R. South, Caroline Burd and Marcus Weck, Modular and Dynamic Functionalization of Polymeric Scaffolds,
Acc. Chem. Res, 40, 63-74 (2007).
Christopher W. Jones, Michael Holbach, John Richardson,
William Sommer, Marcus Weck, Kunquan Yu and Xiaolai
Zheng, On the use of immobilized metal complex catalysts in
organic synthesis, Chem. Ind. (Boca Raton, FL, U. S.), 115,
3-12 (2007).
Alpay Kimyonok, Benoit Domercq, Andreas Haldi, JianYang Cho, Joseph R. Carlise, Xian-Yong Wang, Lauren E.
Hayden, Simon C. Jones, Stephen Barlow, Seth R. Marder,
Bernard Kippelen and Marcus Weck, Norbornene-Based
Copolymers with Iridium Complexes and Bis(carbazolyl)fluorene Groups in Their Side-Chains and Their Use in LightEmitting Diodes, Chem. Mater, 19, 5602-5608 (2007).
Warren W. Gerhardt, Anthony J. Zucchero, Clinton R.
South, Uwe H. F. Bunz and Marcus Weck, Controlling polymer properties through dynamic metal-ligand interactions:
supramolecular cruciforms made easy, Chem.—Eur. J, 13,
4467-4474 (2007).
Poorva Goyal, Kunsang Yoon and Marcus Weck, Multifunctionalization of dendrimers through orthogonal transformations, Chem.—Eur. J, 13, 8801-8810 (2007).
William J. Sommer and Marcus Weck, Supported N-heterocyclic carbene complexes in catalysis, Coord. Chem. Rev,
251, 860-873 (2007).
Joseph R. Carlisle and Marcus Weck, Functional materials
via multiple noncovalent interactions, Funct. Org. Mater,
261-292 (2007).
Marcus Weck and Christopher W. Jones, Mizoroki-Heck
Coupling Using Immobilized Molecular Precatalysts: Leaching Active Species from Pd Pincers, Entrapped Pd Salts, and
Pd NHC Complexes, Inorg. Chem. (Washington, DC, U. S.),
46, 1865-1875 (2007).
Surbhi Jain, Xiaolai Zheng, Christopher W. Jones, Marcus
Weck and Robert J. Davis, Importance of Counterion Reactivity on the Deactivation of Co-Salen Catalysts in the Hydrolytic Kinetic Resolution of Epichlorohydrin, Inorg. Chem.
(Washington, DC, U. S.), 46, 8887-8896 (2007).
Xiaolai Zheng, Christopher W. Jones and Marcus Weck,
Ring-Expanding Olefin Metathesis: A Route to Highly Active Unsymmetrical Macrocyclic Oligomeric Co-Salen Catalysts for the Hydrolytic Kinetic Resolution of Epoxides, J.
Am. Chem. Soc, 129, 1105-1112 (2007).
William J. Sommer and Marcus Weck, Facile Functionalization of Gold Nanoparticles via Microwave-Assisted 1,3 Dipolar Cycloaddition, Langmuir, 23, 11991-11995 (2007).
Alpay Kimyonok and Marcus Weck, Poly(cyclooctene)s
with pendant fluorescent and phosphorescent metal complexes, Macromol. Rapid Commun, 28, 152-157 (2007).
Clinton R. South and Marcus Weck, Template-Enhanced
Ring-Opening Metathesis Polymerization, Macromolecules,
40, 1386-1394 (2007).
Kamlesh P. Nair and Marcus Weck, Noncovalently Functionalized Poly(norbornene)s Possessing both Hydrogen
Bonding and Coulombic Interactions, Macromolecules, 40,
211-219 (2007).
Kunsang Yoon, Poorva Goyal and Marcus Weck, Monofunctionalization of Dendrimers with Use of Microwave-Assisted 1,3-Dipolar Cycloadditions, Org. Lett, 9, 2051-2054
(2007).
Jian-Yang Cho, Benoit Domercq, Stephen Barlow, Kyrill
Yu. Suponitsky, Jennifer Li, Tatiana V. Timofeeva, Simon C.
Jones, Lauren E. Hayden, Alpay Kimyonok, Clinton R.
South, Marcus Weck, Bernard Kippelen and Seth R. Marder,
Synthesis and Characterization of Polymerizable Phosphorescent Platinum(II) Complexes for Solution-Processible Organic Light-Emitting Diodes, Organometallics, 26, 4816-4829
(2007).
David E. Noga, Anjli Kumar, David M. Collard, Marcus
Weck and Andres Garcia, Synthesis of functional lactide
copolymers, PMSE Prepr, 96, 777 (2007).
Marcus Weck, Side-chain functionalized supramolecular
polymers, Polym. Int, 56, 453-460 (2007).
Kamlesh P. Nair, Victor Breedveld and Marcus Weck,
Tunable thermo-reversible polymer networks by multifunctional hydrogen bonding self-assembly, Polym. Prepr. (Am.
Chem. Soc., Div. Polym. Chem.), 48, 346-347 (2007).
Alpay Kimyonok and Marcus Weck, Side-chain functionalized polymers for organic light emitting diode applications,
Polym. Prepr. (Am. Chem. Soc., Div. Polym. Chem.), 48, 612
(2007).
Nandita Madhavan, Christopher W. Jones and Marcus
Weck, Rational Approach to Polymer-Supported Catalysts:
Synergy between Catalytic Reaction Mechanism and Polymer Design, Acc. Chem. Res, 41, 1153-1165 (2008).
Clinton R. South, Victor Pinon, III and Marcus Weck, Erasable coordination polymer multilayers on gold, Angew.
Chem., Int. Ed, 47, 1425-1428 (2008).
David E. Noga, Timothy A. Petrie, Anjli Kumar, Marcus
Weck, Andres J. Garcia and David M. Collard, Synthesis and
Modification of Functional Poly(lactide) Copolymers:
Toward Biofunctional Materials, Biomacromolecules, 9,
2056-2062 (2008).
Christopher S. Gill, Krishnan Venkatasubbaiah, Nam T. S.
Phan, Marcus Weck and Christopher W. Jones, Enhanced
cooperativity through design: pendant CoIII-salen polymer
brush catalysts for the hydrolytic kinetic resolution of
epichlorohydrin
(salen=N,N’-bis(salicylidene)ethylenediamine dianion), Chem.—Eur. J, 14, 7306-7313 (2008).
Caroline Burd and Marcus Weck, Solvent influence on the
orthogonality of noncovalently functionalized terpolymers, J.
Polym. Sci., Part A: Polym. Chem, 46, 1936-1944 (2008).
Clinton R. South and Marcus Weck, Bridged Coordination
Polymer Multilayers with Tunable Properties, Langmuir, 24,
7506-7511 (2008).
Kamlesh P. Nair, Victor Breedveld and Marcus Weck,
Complementary Hydrogen-Bonded Thermoreversible Polymer Networks with Tunable Properties, Macromolecules
(Washington, DC, U. S.), 41, 3429-3438 (2008).
Si Kyung Yang and Marcus Weck, Modular Covalent Multifunctionalization of Copolymers, Macromolecules (Washington, DC, U. S.), 41, 346-351 (2008).
David E. Noga, Timothy A. Petrie, Marcus Weck, Andres
Garcia and David M. Collard, Functional poly(lactide) synthesis for use in biomedical applications, Polym. Prepr. (Am.
Chem. Soc., Div. Polym. Chem.), 49, 844 (2008).
NEW YORK
ZHANG, JOHN Z. H. (b.1961) Professor. B.S, 1982,
East China Normal University; Ph.D, 1987, University of
Houston. Postdoctoral Fellowship, 1987-1990, University of California, Berkeley. Chemical Physics; Theoretical Chemistry. Development of quantum mechanical
methods for biological molecules: protein-ligand binding; protein solvation and dynamics; theoretical study of
chemical reaction dynamics. TEL: (212) 998-8412 FAX:
(212) 260-7905
Web: p150.chem.nyu.edu
Email: john.zhang@nyu.edu
jz2@nyu.edu
Publication list has not been verified by the department.
Emilia L. Wu, Ye Mei, KeLi Han and John Z. H. Zhang,
Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human ␣-thrombin, Biophys. J, 92,
4244-4253 (2007).
Li L. Duan, Yan Tong, Ye Mei, Qing G. Zhang and John
Z. H. Zhang, Quantum study of HIV-1 protease-bridge water
interaction, J. Chem. Phys, 127, 145101/1-145101/6 (2007).
Xu Qiang Zhang, Qian Cui, John Z. H. Zhang and Ke Li
Han, Quantum dynamics study of H+NH3=H2+NH2 reaction,
J. Chem. Phys, 126, 234304/1-234304/6 (2007).
Yun Ding, Ye Mei, John Z. H. Zhang and Fu-Ming Tao,
Efficient bond function basis set for ␲-␲ interaction energies,
J. Comput. Chem, 29, 275-279 (2007).
Changge Ji, Ye Mei and John Z. H. Zhang, Developing polarized protein-specific charges for protein dynamics: MD
free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin, Biophys. J, 95, 1080-1088 (2008).
Yun Ding, Ye Mei and John Z. H. Zhang, Quantum Mechanical Studies of Residue-Specific Hydrophobic Interactions in p53-MDM2 Binding, J. Phys. Chem. B, 112, 1139611401 (2008).
ZHANG, YINGKAI (b.1972) Associate Professor.
B.Sc, 1993, Nanjing University; Ph.D, 2000, Duke University. Research Associate, 2000-2003, Howard Hughes
Medical Institute, University of California at San Diego.
Computational Chemistry; Theoretical Chemistry. We
are interested in developing and applying novel computational and theoretical methods to understand the inner
workings of important biological processes. The specific
research interests are: development of ab initio QM/MM
methods, theoretical investigation of metalloenzymes,
computational studies of histone post-modification and
recognition, development of multiscale simulation methods, rational redesign of biocatalysts. TEL: (212) 9987882 FAX: (212) 260-7905
Web: www.nyu.edu/projects/yzhang
Email: yingkai.zhang@nyu.edu
Zhigang Liu, Anne W. Young, Po Hu, Amanda J. Rice,
Chunhui Zhou, Yingkai Zhang and Neville R. Kallenbach,
Tuning the membrane selectivity of antimicrobial peptides by
using multivalent design, ChemBioChem, 8, 2063-2065
(2007).
Lihua Wang, Xinyun Yu, Po Hu, Suse Broyde and Yingkai
Zhang, A Water-Mediated and Substrate-Assisted Catalytic
Mechanism for Sulfolobus solfataricus DNA Polymerase IV,
J. Am. Chem. Soc, 129, 4731-4737 (2007).
Chuanyun Xiao and Yingkai Zhang, Design-atom approach for the quantum mechanical/molecular mechanical
covalent boundary: A design—carbon atom with five valence
electrons, J. Chem. Phys, 127, 124102/1-124102/9 (2007).
Shenglong Wang, Po Hu and Yingkai Zhang, Ab Initio
Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Enzyme Catalysis: The Case of Histone Lysine Methyltransferase SET7/9, J. Phys. Chem. B,
111, 3758-3764 (2007).
Chuanyun Xiao and Yingkai Zhang, Catalytic Mechanism
and Metal Specificity of Bacterial Peptide Deformylase: A
Density Functional Theory QM/MM Study, J. Phys. Chem.
B, 111, 6229-6235 (2007).
Po Hu, Shenglong Wang and Yingkai Zhang, Highly Dissociative and Concerted Mechanism for the Nicotinamide
Cleavage Reaction in Sir2Tm Enzyme Suggested by Ab Initio QM/MM Molecular Dynamics Simulations, J. Am. Chem.
Soc, 130, 16721-16728 (2008).
Po Hu, Shenglong Wang and Yingkai Zhang, How Do
SET-Domain Protein Lysine Methyltransferases Achieve the
Methylation State Specificity? Revisited by Ab Initio QM/
MM Molecular Dynamics Simulations, J. Am. Chem. Soc,
130, 3806-3813 (2008).
Han Zheng and Yingkai Zhang, Determination of free energy profiles by repository based adaptive umbrella sampling: Bridging nonequilibrium and quasiequilibrium simulations, J. Chem. Phys, 128, 204106/1-204106/8 (2008).
Zhenyu Lu and Yingkai Zhang, Interfacing ab Initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of
Chemical Reactions, J. Chem. Theory Comput, 4, 1237-1248
(2008).
Po Hu, Computer simulation of histone modifying enzymes. (D)
5