Chemistry Faculty Publications

 

Please note that the content of this page does not necessarily constitute a comprehensive list of all faculty publications produced by this department.

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Submissions from 2008

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Cd2+-induced Conformational Change Of A Synthetic Metallopeptide: Slow Metal Binding Followed By A Slower Conformational Change, Madhumita Mukherjee, Xianchun Zhu, and Michael Y. Ogawa

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Rational Design Of A Minimal Size Sensor Array For Metal Ion Detection, Manuel A. Palacios, Zhuo Wang, Victor A. Montes, Grigory V. Zyryanov, and Pavel Anzenbacher Jr.

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Relationship Between The Excited State Relaxation Paths Of Rhodopsin And Isorhodopsin, Angela Strambi, Pedro B. Coto, Luis Manuel Frutos, Nicolas Ferre, and Massimo Olivucci

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2d Regional Correlation Analysis Of Single-molecule Time Trajectories, Xuefei Wang and H. Peter Lu

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Fluorescence Sensor Array For Metal Ion Detection Based On Various Coordination Chemistries: General Performance And Potential Application, Zhuo Wang, Manuel A. Palacios, and Pavel Anzenbacher Jr.

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Simple Molecule-based Fluorescent Sensors For Vapor Detection Of Tnt, Grigory V. Zyryanov, Manuel A. Palacios, and Pavel Anzenbacher Jr.

Submissions from 2007

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Watching Ultrafast Barrierless Excited-state Isomerization Of Pseudocyanine In Real Time, Benjamin Dietzek, Arkady Yartsev, and Alexander N. Tarnovsky

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Triplet Energy Studies Of Thiophene And Para-phenylene Based Oligomers, Leandro A. Estrada, Victor A. Montes, Grigory Zyryanov, and Pavel Anzenbacher Jr.

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The Role Of The Intersection Space In The Photochemistry Of Tricyclo[3.3.0.0(2,6)]octa-3,7-diene, Luis Manuel Frutos, Unai Sancho, Marco Garavelli, Massimo Olivucci, and Obis Castano

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Luminescent Charge-transfer Platinum(ii) Metallacycle, Fei Hua, Solen Kinayyigit, Aaron A. Rachford, Elena A. Shikhova, Sebastien Goeb, John R. Cable, Christopher J. Adams, Kristin Kirschbaum, A. Alan Pinkerton, and Felix N. Castellano

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Exploring the Mechanism of Flexible Biomolecular Recognition with Single Molecule Dynamics, H. Peter Lu, Qiang Lu, and Jin Wang

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Ultrafast Dynamics Of Triplet Excitons In Alq(3)-bridge-pt(ii)porphyrin Electroluminescent Materials, Victor A. Montes, Cesar Perez-Bolivar, Leandro A. Estrada, Joseph Shinar, and Pavel Anzenbacher Jr.

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Excited-state Equilibration Over 30 Angstrom In A Platinum(ii) Quinolinolate-bridge-platinum(ii) Porphyrin Complex, Victor A. Montes, Michael A. J. Rodgers, and Pavel Anzenbacher Jr.

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Supramolecular Chemistry Approach To The Design Of A High-resolution Sensor Array For Multianion Detection In Water, Manuel A. Palacios, Ryuhei Nishiyabu, Manuel Marquez, and Pavel Anzenbacher Jr.

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Fluctuating Two-state Light Harvesting In A Photosynthetic Membrane, Duohai Pan, Dehong Hu, Ruchuan Liu, Xiaohua Zeng, Samuel Kaplan, and H. Peter Lu

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Reactivity Of Iso-diiodomethane And Iso-iodoform, Isomers Of Ch2i2 And Chi3, Toward The Double Bond Of A Variety Of Cycloalkenes, Alexander N. Tarnovsky, Irmin Pascher, and Torbjorn Pascher

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Formation Of Peptide Nanospheres And Nanofibrils By Metal Coordination, Mikhail V. Tsurkan and Michael Y. Ogawa

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Metal-mediated Peptide Assembly: Use Of Metal Coordination To Change The Oligornerization State Of An Alpha-helical Coiled-coil, Mikhail V. Tsurkan and Michael Y. Ogawa

Submissions from 2006

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Generating New Specific Rna Interaction Interfaces Using C-loops, Kirill A. Afonin and Neocles B. Leontis

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Incorporating Electron-transfer Functionality Into Synthetic Metalloproteins From The Bottom-up, Jing Hong, Olesya A. Kharenko, and Michael Y. Ogawa

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Platinum(ii) Diimine Diacetylides: Metallacyclization Enhances Photophysical Properties, Fei Hua, Solen Kinayyigit, John R. Cable, and Felix N. Castellano

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Structural and Evolutionary Classification of G/U Wobble Basepairs in the Ribosome, Neocles B. Leontis, Ali Mokdad, Maryna V. Krasovska, and Jiří Sponer

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Controlling RNA Self-Assembly to Form Filaments, Neocles B. Leontis, Lorena Nasalean, Stéphanie Baudrey, and Luc Jaeger

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Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal its Essential Role in Replication, Neocles B. Leontis, Xuehua Zhong, Shuiming Qian, Asuka Itaya, Yijun Qi, Kathleen Boris-Lawrie, and Biao Ding

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Structural and Evolutionary Classification of G/U Wobble Basepairs in the Ribosome, Ali Mokdad, Maryna V. Krasovska, J Sponer, and Neocles B. Leontis

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Ribostral: An RNA 3D Alignment Analyzer and Viewer Based on Basepair Isostericities, Ali Mokdad and Neocles B. Leontis

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Molecular-wire Behavior Of Oled Materials: Exciton Dynamics In Multichromophoric Alq(3)-oligofluorene-pt(ii) Porphyrin Triads, Victor A. Montes, Cesar Perez-Bolıvar, Neeraj Agarwal, Joseph Shinar, and Pavel Anzenbacher Jr.

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Controlling RNA Self-Assembly to Form Filaments, Lorena Nasalean, Stéphanie Baudrey, Neocles B. Leontis, and Luc Jaeger

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1,3-indane-based Chromogenic Calixpyrroles With Push-pull Chromophores: Synthesis And Anion Sensing, Ryuhei Nishiyabu and Pavel Anzenbacher Jr.

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Synthesis, Structure, Anion Binding, And Sensing By Calix[4] Pyrrole Isomers, Ryuhei Nishiyabu, Manuel A. Palacios, Wim Dehaen, and Pavel Anzenbacher Jr.

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True Blue: Blue-emitting Aluminum(iii) Quinolinolate Complexes, Cesar Perez-Bolivar, Victor A. Montes, and Pavel Anzenbacher Jr.

Submissions from 2005

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Benzothiadiazoles And Dipyrrolyl Quinoxalines With Extended Conjugated Chromophores-fluorophores And Anion Sensors, Dmitry Aldakov, Manuel A. Palacios, and Pavel Anzenbacher Jr.

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Simple Electrooptical Sensors For Inorganic Anions, Pavel Anzenbacher Jr., Karolina Jursikova, and Manuel Marquez

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Green Photoluminescence From Platinum(ii) Complexes Bearing Silylacetylide Ligands, Fei Hua, Solen Kinayyigit, John R. Cable, and Felix Castellano

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Cu(i) Luminescence From The Tetranuclear Cu4s4 Cofactor Of A Synthetic 4-helix Bundle, Olesya A. Kharenko, David C. Kennedy, Borries Demeler, Michael J. Maroney, and Michael Y. Ogawa

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Interaction Of Porphyrins With A Dendrimer Template: Self-aggregation Controlled By Ph, Pavel Kubat, Kamil Lang, Pavel Janda, and Pavel Anzenbacher Jr.

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Recurrent Structural RNA Motifs, Isostericity Matrices and Sequence Alignments, Neocles B. Leontis, Aurélie Lescoute, Christian Massire, and Eric Westhof

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Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases, Neocles B. Leontis, Filip Rázga, Jaroslav Koča, and Jiří Šponer

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Sensing Of Antipyretic Carboxylates By Simple Chromogenic Calix[4]pyrroles, Ryuhei Nishiyabu and Pavel Anzenbacher Jr.

Submissions from 2004

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Sensing Of Aqueous Phosphates By Polymers With Dual Modes Of Signal Transduction, Dmitry Aldakov and Pavel Anzenbacher Jr.

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Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Jaroslav Koča, and Jiří Šponer

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Gated Electron Transfer As A Probe Of The Configurational Dynamics Of Peptide-protein Complexes, Liu Liu, Jing Hong, and Michael Y. Ogawa

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Red-green-blue Emission From Tris(5-aryl-8-quinolinolate)al(iii) Complexes, Radek Pohl, Victor A. Montes, Joseph Shinar, and Pavel Anzenbacher Jr.

Submissions from 2003

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Photoinduced Electron-transfer Along Alpha-helical And Coiled-coil Metallopeptides, Anna Fedorova, Anita Chaudhari, and Michael Y. Ogawa

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Self-aggregates Of Cationic Meso-tetratolylporphyrins In Aqueous Solutions, Pavel Kubat, Kamil Lang, Kristina Prochazkova, and Pavel Anzenbacher Jr.

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Peptide-protein Interactions: Photoinduced Electron-transfer Within The Preformed And Encounter Complexes Of A Designed Metallopeptide And Cytochrome C, Robin C. Lasey, Liu Liu, Ling Zang, and Michael Y. Ogawa

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Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, and J Sponer

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Tools for the Automatic Identification and Classification of RNA Base Pairs, Neocles B. Leontis, Huanwang Yang, Fabrice Jossinet, Li Chen, John Westbrook, Helen Berman, and Eric Westhof

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Emission Color Tuning In Alq(3) Complexes With Extended Conjugated Chromophores, Radek Pohl and Pavel Anzenbacher Jr.

Submissions from 2002

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Luminescence Lifetime-based Sensor For Cyanide And Related Anions, Pavel Anzenbacher Jr., Daniel S. Tyson, Karolina Jursı´kova, and Felix N. Castellano

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Site-specific Modification Of De Novo Designed Coiled-coil Polypeptides With Inorganic Redox Complexes, Anna Fedorova and Michael Y. Ogawa

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Preprogramming Of Porphyrin-nucleic Acid Assemblies Via Variation Of The Alkyl/aryl Substituents Of Phosphonium Tetratolylporphyrins, Pavel Kubat, Kamil Lang, Vladimir Kral, and Pavel Anzenbacher Jr.

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Computational Simulation of the Docking of Prochlorothrix Hollandica Plastocyanin to Photosystem I: Modeling the Electron Transfer Complex, Neocles B. Leontis, Eugene Myshkin, and George S. Bullerjahn

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The Non-Watson-Crick Base Pairs and their Associated Isostericity Matrices, Neocles B. Leontis, Jesse Stombaugh, and Eric Westhof

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RNAML: A Standard Syntax for Exchanging RNA Information, Neocles B. Leontis, Allison Waugh, Patrick Gendron, Russ Altman, James W. Brown, David Case, Daniel Gautheret, Stephen C. Harvey, John Westbrook, Eric Westhof, Michael Zuker, and François Major

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The Annotation of RNA Motifs, Neocles B. Leontis and Eric Westhof

Submissions from 2001

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Infrared Spectroscopy Of H-bonded Bridges Stretched Across The Cis-amide Group: I. Water Bridges, Joel R. Carney, A. V. Fedorov, John R. Cable, and Timothy S. Zwier

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Infrared Spectroscopy of H-Bonded Bridges Stretched across the cis-Amide Group: II. Ammonia and Mixed Ammonia/Water Bridges, A. V. Fedorov, John R. Cable, Joel R. Carney, and Timothy S. Zwier

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Effect Of Surface Charges On The Rates Of Intermolecular Electron-transfer Between De Novo Designed Metalloproteins, Anna Y. Kornilova, James F. Wishart, and Michael Y. Ogawa

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TectoRNA: Modular Assembly Units for the Construction of RNA Nano-Objects, Neocles B. Leontis, Luc Jaeger, and Eric Westhof

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Geometric Nomenclature and Classification of RNA Base Pairs, Neocles B. Leontis and Eric Westhof

Submissions from 2000

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Spectroscopy Of Hydrogen-bonded Formanilide Clusters In A Supersonic Jet: Solvation Of A Model Trans Amide, A. V. Fedorov and John R. Cable

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Design And Characterization Of A Synthetic Electron-transfer Protein, Anna Y. Kornilova, James F. Wishart, Wenzhong Xiao, Robin C. Lasey, Anna Fedorova, Yeon-Kyun Shin, and Michael Y. Ogawa

Submissions from 1999

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Cationic 5,10,15,20-tetrakis(n-methylpyridinium-4-yl)porphyrin Fully Intercalates At 5 '-cg-3 ' Steps Of Duplex Dna In Solution, Anton B. Guliaev and Neocles B. Leontis

Submissions from 1998

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Sequence-specific Photomodification Of Dna By An Oligonucleotide-phenanthrodihydrodioxin Conjugate, Kestutis G. Bendinskas, Andreas Harsch, R. Marshall Wilson, and W. Robert Midden

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Distance Dependence Of Electron Transfer Along Artificial Beta-strands At 298 And 77 K, S. R. L. Fernando, Gennady V. Kozlov, and Michael Y. Ogawa

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Conserved Geometrical Base-Pairing Patterns in RNA, Neocles B. Leontis and Eric Westhof

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The 5S rRNA Loop E: Chemical Probing and Phylogenetic Data Versus Crystal Structure, Neocles B. Leontis and Eric Westhof

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The 5S rRNA Loop E: Chemical Probing and Phylogenetic Data Versus Crystal Structure, Neocles B. Leontis and Eric Westhof

Submissions from 1997

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Electron Transfer Across A Peptide-peptide Interface Within A Designed Metalloprotein, Gennady V. Kozlov and Michael Y. Ogawa

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Conformations And Relative Stabilities Of The Cis And Trans Isomers In A Series Of Isolated N-phenylamides, V. P. Manea, K. J. Wilson, and John R. Cable

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Rounding Numbers: Why The ''new System'' Doesn't Work, W. Robert Midden

Submissions from 1996

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Electronic Spectroscopy of Jet-Cooled Benzylidenecyclobutane, a Sterically Hindered Styrene, John R. Cable and V. P. Manea

A Negative Activation Energy For Luminescence Decay: Specific Solvation Effects On The Emission Properties Of Bis(2,2'-bipyridine)(3,5-dicarboxy-2,2'-bipyridine)ruthenium(ii) Chloride, S. R. L. Fernando, U. S. M. Maharoof, Kurt D. Deshayes, Thomas H. Kinstle, and Michael Y. Ogawa

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Photoinduced Electron Transfer Along A Beta-sheet Mimic, Alexei B. Gretchikhine and Michael Y. Ogawa

Submissions from 1995

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Helical Stacking in DNA 3-Way Junctions Containing 2 Unpaired Pyrimidines - Proton NMR-Studies, Neocles B. Leontis, Michael T. Hills, Martial Piotto, Igor V. Ouporov, Arun Malhotra, and David G. Gorenstein

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Helical Stacking in DNA Three-Way Junctions Containing Two Unpaired Pyrimidines: Proton NMR Studies, Neocles B. Leontis, Michael T. Hills, Martial Piotto, Igor V. Ouporov, Arun Malhotra, and David G. Gorenstein

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Relative Stabilities of DNA 3-Way, 4-Way and 5-Way Junctions (Multi-Helix Junction Loops) - Unpaired Nucleotides Can Be Stabilizing or Destabilizing, Neocles B. Leontis, Julie L. Kardmas, and Amy J. Ravin

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Refinement of the Solution Structure of a Branched DNA Three-Way Junction, Neocles B. Leontis and Igor V. Ouporov

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Refinement of the Solution Structure of a Branched DNA Three-Way Junction, Neocles B. Leontis and Igor V. Ouporov

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Synthesis And Characterization Of A Water-soluble Metallopeptide That Resembles A Parallel Beta-pleated Sheet, Michael Y. Ogawa, Alexei B. Gretchikhine, Sunil-Datta Soni, and Steven M. Davis

Submissions from 1994

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The Thermodynamics Of Formation Of A 3-strand, Dna 3-way Junction Complex, John E. Ladbury, Julian M. Sturtevant, and Neocles B. Leontis

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Effects Of Unpaired Bases On The Conformation And Stability Of 3-arm Dna Junctions, Min Zhong, Michael S. Rashes, Neocles B. Leontis, and Neville R. Kallenbach

Submissions from 1991

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Stability and Structure of Three-Way DNA Junctions Containing Unpaired Nucleotides, Neocles B. Leontis, Wendy Kwok, and Jennifer S. Newman

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Stability and Structure of Three-Way DNA Junctions Containing Unpaired Nucleotides, Neocles B. Leontis, Wendy Kwok, and Jennifer S. Newman

Submissions from 1990

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Substituent Effects on the Electronic Spectroscopy of Tryptophan Derivatives in Jet Expansions, John R. Cable, Michael J. Tubergen, and Donald H. Levy

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Photoinduced Electron-transfer In Self-associated Complexes Of Several Uroporphyrins And Cytochrome-c, J. S. Zhou, E. S. V. Granada, Neocles B. Leontis, and M. A. J. Rodgers

Submissions from 1989

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Photocycloaddition Of 4,5',8-trimethylpsoralen And Oleic-acid Methyl-ester - Product Structures And Reaction-mechanism, Kathleen G. Specht, W. Robert Midden, and Miles R. Chedekel