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Articles 1 - 18 of 18
Full-Text Articles in Chemistry
Quantum Chemical Studies Of Nucleic Acids Can We Construct A Bridge To The Rna Structural Biology And Bioinformatics Communities?, Jiri Sponer,, Judit Sponer, Anton I. Petrov, Neocles B. Leontis
Quantum Chemical Studies Of Nucleic Acids Can We Construct A Bridge To The Rna Structural Biology And Bioinformatics Communities?, Jiri Sponer,, Judit Sponer, Anton I. Petrov, Neocles B. Leontis
Chemistry Faculty Publications
In this feature article we provide a side-by-side introduction for two research fields quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics Our main aim is to demonstrate that these research areas while largely separated in contemporary literature have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches The ultimate aim is to attain valuable physicochemical insights …
Electronic Properties Of N(5)-Ethyl Flavinium Ion, Vincent Sichula, Pavel Kucheryavy, Renat Khatmullin, Ying Hu, Ekaterina Mirzakulova, Shubham Vyas, Samuel F. Manzer, Christopher M. Hadad, Ksenija D. Glusac
Electronic Properties Of N(5)-Ethyl Flavinium Ion, Vincent Sichula, Pavel Kucheryavy, Renat Khatmullin, Ying Hu, Ekaterina Mirzakulova, Shubham Vyas, Samuel F. Manzer, Christopher M. Hadad, Ksenija D. Glusac
Chemistry Faculty Publications
We investigated the electronic properties of N(5)-ethyl flavinium perchlorate (Et-Fl(+)) and compared them to those of its parent compound, 3-methyllumiflavin (Fl). Absorption and fluorescence spectra of Fl and Et-Fl(+) exhibit similar spectral features, but the absorption energy of Et-Fl(+) is substantially lower than that of Fl. We calculated the absorption signatures of Fl and Et-Fl(+) using time-dependent density functional theory (TD-DFT) methods and found that the main absorption bands of Fl and Et-Fl(+) are (pi,pi*) transitions for the S(1) and S(3) excited states. Furthermore, calculations predict that the S(2) state has (n,pi*) character. Using cyclic voltammetry and a simplistic consideration …
Photoinduced Charge Separation In Platinum Acetylide Oligomers, Chen Liao, James E. Yarnell, Ksenija D. Glusac, Kirk S. Schanze
Photoinduced Charge Separation In Platinum Acetylide Oligomers, Chen Liao, James E. Yarnell, Ksenija D. Glusac, Kirk S. Schanze
Chemistry Faculty Publications
The series of three donor-spacer-acceptor complexes, DPAF-Ptn-NDI, has been synthesized and characterized using time-resolved absorption spectroscopy In these complexes, the donor is a (diphenylamino)-2,7-fluorenylene (DPAF) unit, the acceptor is a naphthalene diimide (NDI), and the spacers are a series of platinum acetylides of varying lengths, [-Pt(PBu(3))(2)C C-Ph-C C-](n) (where Bu = n-butyl Ph = 1,4-phenylene and n = 1 2, and 3) Electrochemistry indicates that the DPAF-Ptn-NDI system has a charge transfer state at ca 1 5 eV above the ground state that is based on one electron transfer from the DPAF donor to the NDI acceptor Transient absorption spectroscopy …
Nanometer To Millimeter Scale Peptide-Porphyrin Materials, Daniil V. Zaytsev, Fei Xie, Madhumita Mukherjee, Alexey Bludin, Borries Demeler, Robert M. Breece, David L. Tierney, Michael Y. Ogawa
Nanometer To Millimeter Scale Peptide-Porphyrin Materials, Daniil V. Zaytsev, Fei Xie, Madhumita Mukherjee, Alexey Bludin, Borries Demeler, Robert M. Breece, David L. Tierney, Michael Y. Ogawa
Chemistry Faculty Publications
AQ-Pal14 is a 30-residue polypeptide that was designed to form an alpha-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal 14)(2) species that creates two coiled-coil oligomerization domains Coordinated to opposite laces of the porphyrin ring. It is found that this species undergoes a buffer-dependent Self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like …
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Chemistry Faculty Publications
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90-92 (H90-H92) of 23S rRNA; the 3WJ formed by H42-H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3'-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess …
Spectroscopic And Computational Studies Of The Laser Photolysis Of Matrix Isolated 1,2-Dibromoethanes: Formation And Fate Of The Bromoethyl Radicals, A. Kalume, L. George, P. Z. El-Khoury, Alexander N. Tarnovsky, S. A. Reid
Spectroscopic And Computational Studies Of The Laser Photolysis Of Matrix Isolated 1,2-Dibromoethanes: Formation And Fate Of The Bromoethyl Radicals, A. Kalume, L. George, P. Z. El-Khoury, Alexander N. Tarnovsky, S. A. Reid
Chemistry Faculty Publications
We report experimental and computational studies of the photolysis of atmospherically important 1,2-dibromoethanes (1,2-C(2)X(4)Br(2); X = H, F) in Ar matrixes at 5 K. Using the pulsed deposition method, we find that significant conformational relaxation occurs for 1,2-C(2)H(4)Br(2) (EDB; observed anti/gauche ratio =30:1) but not for 1,2-C(2)F(4)Br(2) (TFEDB; anti/gauche = 3:1), which is traced to a larger barrier to rotation about the C-C bond in the latter. Laser photolysis of matrix-isolated EDB at 220 nm reveals the growth of infrared bands assigned to the gauche conformer and C(2)H(4)-Br(2) charge transfer complex (both as major products), and the C(2)H(4)Br radical and …
Mechanism Of N(5)-Ethyl-Flavinium Cation Formation Upon Electrochemical Oxidation Of N(5)-Ethyl-4a-Hydroxyflavin Pseudobase, Vincent Sichula, Ying Hu, Ekaterina Mirzakulova, Samuel F. Manzer, Shubham Vyas, Christopher M. Hadad, Ksenija D. Glusac
Mechanism Of N(5)-Ethyl-Flavinium Cation Formation Upon Electrochemical Oxidation Of N(5)-Ethyl-4a-Hydroxyflavin Pseudobase, Vincent Sichula, Ying Hu, Ekaterina Mirzakulova, Samuel F. Manzer, Shubham Vyas, Christopher M. Hadad, Ksenija D. Glusac
Chemistry Faculty Publications
We investigated the oxidation behavior of 5-ethyl-4a-hydroxy-3-methy1-4a,5-dihydrolumitlavin (pseudobase Et-FlH) in acetonitrile with the aim of determining if the two-electron oxidized Et-FlOH(2+) undergoes a release of hydroxyl cation and the production of 5-ethyl-3methyllumiflavinium cation (Et-Fl(+)). The focus of this work is to investigate the possibility of using Et-FlOH as a catalyst for water oxidation. The cyclic voltammetry demonstrates that Et-FlOH exhibits two one-electron oxidation potentials at +0.95 and +1.4 V versus normal hydrogen electrode (NHE), with the second oxidation potential being irreversible. The production of Et-FY' is observed in the cyclic voltammetry of Et-FlOH and has been previously assigned to the …
Modeling, Preparation, And Characterization Of A Dipole Moment Switch Driven By Z/E Photoisomerization, Alfonso Melloni, Riccardo Rossi Paccani, Donato Donati, Vinicio Zanirato, Adalgisa Sinicropi, Maria Laura Parisi, Elena Martin, Mikhail Ryazantsev, Wan Jian Ding, Luis Manuel Frutos, Riccardo Basosi, Stefania Fusi, Loredana Latterini, Nicolas Ferre, Massimo Olivucci
Modeling, Preparation, And Characterization Of A Dipole Moment Switch Driven By Z/E Photoisomerization, Alfonso Melloni, Riccardo Rossi Paccani, Donato Donati, Vinicio Zanirato, Adalgisa Sinicropi, Maria Laura Parisi, Elena Martin, Mikhail Ryazantsev, Wan Jian Ding, Luis Manuel Frutos, Riccardo Basosi, Stefania Fusi, Loredana Latterini, Nicolas Ferre, Massimo Olivucci
Chemistry Faculty Publications
We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can …
Synthesis Of Pbs/Tio2 Colloidal Heterostructures For Photovoltaic Applications, Krishna P. Acharya, Nishshanka N. Hewa-Kasakarage, Taiwo R. Alabi, Ian Nemitz, Elena Khon, Bruno Ullrich, Pavel Anzenbacher Jr., Mikhail Zamkov
Synthesis Of Pbs/Tio2 Colloidal Heterostructures For Photovoltaic Applications, Krishna P. Acharya, Nishshanka N. Hewa-Kasakarage, Taiwo R. Alabi, Ian Nemitz, Elena Khon, Bruno Ullrich, Pavel Anzenbacher Jr., Mikhail Zamkov
Chemistry Faculty Publications
We report on heteroepitaxial growth of nearly monodisperse PbS nanocrystals onto the surface of TiO2 nanoparticles via colloidal hot-injection routes. Fabricated PbS/TiO2 nanocomposites can be dispersed in nonpolar solvents, which enables an easy solution processing of these materials into mesoporous films for use as light-absorbing layers in nanocrystal-sensitized solar cells. High-temperature deposition of the sensitizer material allows controlling both the size and the number of PbS domains grown onto TiO2 nanoparticles, whereby providing synthetic means for tuning the absorbance spectrum of PbS/TiO2 nanocomposites and simultaneously enhancing their photocatalytic response in the visible and near-infrared. Compared with conventional ionic bath deposition …
Bunching Effect In Single-Molecule T4 Lysozyme Nonequilibrium Conformational Dynamics Under Enzymatic Reactions, Yuanmin Wang, H. Peter Lu
Bunching Effect In Single-Molecule T4 Lysozyme Nonequilibrium Conformational Dynamics Under Enzymatic Reactions, Yuanmin Wang, H. Peter Lu
Chemistry Faculty Publications
The bunching effect, implying that conformational motion times tend to bunch in a finite and narrow time window, is observed and identified to be associated with substrate enzyme complex formation in T4 lysozyme conformational dynamics under enzymatic reactions. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of polysaccharide of E. coli 13 cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor acceptor probe pair tethered to T4 lysozyme domains involving open close hinge-bending motions. On the basis of the single-molecule spectroscopic results, molecular dynamics simulation, and a random walk …
Ultrafast Carrier Dynamics In Type Ii Znse/Cds/Znse Nanobarbells, Nishshanka N. Hewa-Kasakarage, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Maria Kirsanova, Ian Nemitz, Alexander Nemchinov, Mikhail Zamkov
Ultrafast Carrier Dynamics In Type Ii Znse/Cds/Znse Nanobarbells, Nishshanka N. Hewa-Kasakarage, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Maria Kirsanova, Ian Nemitz, Alexander Nemchinov, Mikhail Zamkov
Chemistry Faculty Publications
We employ femtosecond transient absorption spectroscopy to get an insight into ultrafast processes occurring at the interface of type II ZnSe/CdS heterostructured nimocrystals fabricated via colloidal routes and comprising a barbell-like arrangement of ZnSe tips and CdS nanorods. Our study shows that resonant excitation of ZnSe tips results in an unprecedently fast transfer of excited Electrons into CdS domains of nanobarbells (<0.35 ps), whereas selective pumping of CdS components loads to a relatively slow injection of photoinduced holes into ZnSe tips (tau(h) = 95 ps). A qualitative thermodynamic description of observed electron processes within the classical limit of Marcus theory was used to identify a specific charge transfer regime associated with the ultrafast electron injection into CdS. Potential photocatalytic applications of the observed fast separation of carriers along the main axis of ZnSe/CdS barbells are discussed.
Combined Single-Molecule Photon-Stamping Spectroscopy And Femtosecond Transient Absorption Spectroscopy Studies Of Interfacial Electron Transfer Dynamics, Lijun Guo, Yuanmin Wang, H. Peter Lu
Combined Single-Molecule Photon-Stamping Spectroscopy And Femtosecond Transient Absorption Spectroscopy Studies Of Interfacial Electron Transfer Dynamics, Lijun Guo, Yuanmin Wang, H. Peter Lu
Chemistry Faculty Publications
The inhomogeneous interfacial electron transfer (IET) dynamics of 9-phenyl-2,3,7-trihydroxy-6-fluorone (PF)-sensitized TiO2 nanoparticles (NPs) has been probed by a single-molecule photon-stamping technique as well as ensemble-averaged femtosecond transient absorption spectroscopy. The forward electron transfer (FET) time shows a broad distribution at the single-molecule level, indicating the inhomogeneous interactions and ET reactivity of the PF/TiO2 NP system. The broad distribution of the FET time is measured to be 0.4 ± 0.1 ps in the transient absorption and picoseconds to nanoseconds in the photon-stamping measurements. The charge recombination time, having a broad distribution at the single-molecule level, clearly shows a biexponential dynamic behavior …
Energy Barrier, Charge Carrier Balance, And Performance Improvement In Organic Light-Emitting Diodes, Pavel Anzenbacher Jr., Amare Benor, Shin-Ya Takizawa, C. Pérez-Bolivar
Energy Barrier, Charge Carrier Balance, And Performance Improvement In Organic Light-Emitting Diodes, Pavel Anzenbacher Jr., Amare Benor, Shin-Ya Takizawa, C. Pérez-Bolivar
Chemistry Faculty Publications
The charge injection properties of poly(3,4-ethylenedioxythiophene): polystyrene sulfonate anodes are crucial for performance of organic photovoltaics and organic light-emitting diodes (OLEDs). A simple method for tuning hole injection efficiency using UV-ozone is shown to change anode work-function and optimized carriers balance in the devices and improved efficiency in OLEDs. The optimum time of treatment and work-function differs with device architecture. © 2010 American Institute of Physics.
8-Methoxy-4-(4-Methoxyphenyl)Quinoline, Pavel Anzenbacher Jr., Ligia Llovera, Teresa González, Simón E. López
8-Methoxy-4-(4-Methoxyphenyl)Quinoline, Pavel Anzenbacher Jr., Ligia Llovera, Teresa González, Simón E. López
Chemistry Faculty Publications
In the title compound, C 17H 15NO 2, the dihedral angle between the quinoline and benzene ring systems is 62.17 (1)°. In the crystal, zigzag chains propagating in c are linked by C-H⋯O hydrogen bonds, and weak C-H⋯π inter-actions link the chains.
Characterization Of Iso -Cf2 I2 In Frequency And Ultrafast Time Domains, Alexander N. Tarnovsky, Patrick Z. El-Khoury, Lisa George, Aimable Kalume, Scott A. Reid, Bruce S. Ault
Characterization Of Iso -Cf2 I2 In Frequency And Ultrafast Time Domains, Alexander N. Tarnovsky, Patrick Z. El-Khoury, Lisa George, Aimable Kalume, Scott A. Reid, Bruce S. Ault
Chemistry Faculty Publications
The photolysis of diiododifluoromethane (CF2 I2) in condensed phases was studied by a combination of matrix isolation and ultrafast time-resolved spectroscopy, in concert with ab initio calculations. Photolysis at wavelengths of 355 or 266 nm of CF2 I2:Ar samples (1:5000) held at ∼8 K yielded iso -CF2 I2 (F2 C-I-I), a metastable isomer of CF2 I2, characterized here for the first time. The infrared (IR) spectra of this isomer were recorded in matrix experiments, and the derived positions of the C-F stretching modes are in very good agreement with the predictions of high level ab initio calculations, which show that …
Pulsed Laser Deposition Of Graphite Counter Electrodes For Dye-Sensitized Solar Cells, Pavel Anzenbacher Jr., Krishna P. Acharya, Himal Khatri, Sylvain Marsillac, Bruno Ullrich, Mikhail Zamkov
Pulsed Laser Deposition Of Graphite Counter Electrodes For Dye-Sensitized Solar Cells, Pavel Anzenbacher Jr., Krishna P. Acharya, Himal Khatri, Sylvain Marsillac, Bruno Ullrich, Mikhail Zamkov
Chemistry Faculty Publications
We report on pulsed laser deposition of graphite onto flexible plastic and conductive glass substrates for use as a counter electrode in dye-sensitized solar cells. The efficiency of as-prepared graphite electrodes was tested using CdS-sensitized solar cell architecture resulting in external quantum efficiency comparable to that of conventional platinum counter electrodes. This work highlights the possibility of using pulsed laser deposited graphite as a low-cost alternative to platinum, which could be fabricated both on flexible and rigid substrates. © 2010 American Institute of Physics.
Matrix Isolation And Computational Study Of Isodifluorodibromomethane (F2 Cbr-Br): A Route To Br2 Formation In Cf2 Br2 Photolysis, Alexander N. Tarnovsky, Lisa George, Aimable Kalume, Patrick Z. El-Khoury, Scott A. Reid
Matrix Isolation And Computational Study Of Isodifluorodibromomethane (F2 Cbr-Br): A Route To Br2 Formation In Cf2 Br2 Photolysis, Alexander N. Tarnovsky, Lisa George, Aimable Kalume, Patrick Z. El-Khoury, Scott A. Reid
Chemistry Faculty Publications
The photolysis products of dibromodifluoromethane (CF2 Br 2) were characterized by matrix isolation infrared and UV/Visible spectroscopy, supported by ab initio calculations. Photolysis at wavelengths of 240 and 266 nm of CF2 Br2:Ar samples (∼1:5000) held at ∼5 K yielded iso- CF2 Br2 (F2 CBrBr), a weakly bound isomer of CF2 Br2, which is characterized here for the first time. The observed infrared and UV/Visible absorptions of iso- CF2 Br2 are in excellent agreement with computational predictions at the B3LYP/aug-cc-pVTZ level. Single point energy calculations at the CCSD(T)/aug-cc-pVDZ level on the B3LYP optimized geometries suggest that the isoform is a …
Revealing Linear Aggregates Of Light Harvesting Antenna Proteins In Photosynthetic Membranes, Yufan He, Xiaohua Zeng, Saptarshi Mukherjee, Suneth Rajapaksha, Samuel Kaplan, H. Peter Lu
Revealing Linear Aggregates Of Light Harvesting Antenna Proteins In Photosynthetic Membranes, Yufan He, Xiaohua Zeng, Saptarshi Mukherjee, Suneth Rajapaksha, Samuel Kaplan, H. Peter Lu
Chemistry Faculty Publications
How light energy is harvested in a natural photosynthetic membrane through energy transfer is closely related to the stoichiometry and arrangement of light harvesting antenna proteins in the membrane. The specific photosynthetic architecture facilitates a rapid and efficient energy transfer among the light harvesting proteins (LH2 and LH1) and to the reaction center. Here we report the identification of linear aggregates of light harvesting proteins, LH2, in the photosynthetic membranes under ambient conditions by using atomic force microscopy (AFM) imaging and spectroscopic analysis. Our results suggest that the light harvesting protein, LH2, can exist as linear aggregates of 4 2 …