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Articles 1 - 16 of 16
Full-Text Articles in Physical Sciences and Mathematics
Modeling The Fluorescence Of Protein-Embedded Tryptophans With Ab Initio Multiconfigurational Quantum Chemistry: The Limiting Cases Of Parvalbumin And Monellin, Sara Pistolesi, Adalgisa Sinicropi, Rebecca Pogni, Riccardo Basosi, Nicolas Ferre, Massimo Olivucci
Modeling The Fluorescence Of Protein-Embedded Tryptophans With Ab Initio Multiconfigurational Quantum Chemistry: The Limiting Cases Of Parvalbumin And Monellin, Sara Pistolesi, Adalgisa Sinicropi, Rebecca Pogni, Riccardo Basosi, Nicolas Ferre, Massimo Olivucci
Chemistry Faculty Publications
We show that a quantum-mechanics/molecular-mechanics strategy based on ab initio (i.e., first principle) multiconfigurational perturbation theory can reproduce the spectral properties of a tryptophan residue embedded in the contrasting hydrophobic and hydrophilic environments of parvalbumin and monellin, respectively. We show that the observed absorption and emission energies can be reproduced with a less than 3 kcal mol(-1) error. The analysis of the computed emission energies based on a protein disassembly scheme and protein electrostatic potential mapping allows for a detailed understanding of the factors modulating the tryptophan emission. It is shown that for rnonellin, where the tryptophan is exposed to …
Thermochromic Absorption And Photoluminescence In [Pt(Ppy)(Mu-Ph(2)Pz)](2), Aaron A. Rachford, Felix N. Castellano
Thermochromic Absorption And Photoluminescence In [Pt(Ppy)(Mu-Ph(2)Pz)](2), Aaron A. Rachford, Felix N. Castellano
Chemistry Faculty Publications
The temperature effects on the spectral properties and photophysics of a new d(8)-d(8) dinuclear Pt-II chromophore, [Pt(ppy)(mu-Ph(2)pz)](2) (ppy is 2-phenylpyridine and Ph(2)pz is 3,5-diphenylpyrazolate), have been investigated. The thermochromic shifts are tentatively ascribed to intramolecular sigma interactions between the two pseudocofacial d(Z2) orbitals. Substantial emission profile changes occur in the solid state, solution, and doped polymer films.
How Does The Relocation Of Internal Water Affect Resonance Raman Spectra Of Rhodopsin? An Insight From Casscf/Amber Calculations, Tadeusz Andruniow, Massimo Olivucci
How Does The Relocation Of Internal Water Affect Resonance Raman Spectra Of Rhodopsin? An Insight From Casscf/Amber Calculations, Tadeusz Andruniow, Massimo Olivucci
Chemistry Faculty Publications
The effect of relocation of the W2 crystallographic water in bovine rhodopsin has been investigated by comparing and analyzing simulated resonance Raman spectra of I HZX-and 1U19-based quantum mechanics/molecular mechanics (CASSCF/MM) models. The main target is to explore the sensitivity of the simulated resonance Raman spectra to protein cavity change. In particular, we focus on a quantitative investigation of the changes in the vibrational activity of rhodopsin induced by modifications in the protein cavity structure and in the water position. Comparison of the simulated FIR spectra of the Rh-1U19 and Rh-1HZX models with the measured spectrum of rhodopsin reveals that …
Structure Of The Photochemical Reaction Path Populated Via Promotion Of Cf2i2 Into Its First Excited State, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Igor Schapiro, Mikhail N. Ryazantsev, Massimo Olivucci
Structure Of The Photochemical Reaction Path Populated Via Promotion Of Cf2i2 Into Its First Excited State, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Igor Schapiro, Mikhail N. Ryazantsev, Massimo Olivucci
Chemistry Faculty Publications
The photochemical reaction path following the promotion of CF2I2 into its lowest-lying excited electronic singlet state has been modeled using ab initio multiconfigurational quantum chemical calculations. It is found that a conical intersection drives the electronically excited CF2I2* species either to the CF2I + I radical pair or back to the starting CF2I2 structure. The structures of the computed relaxation pathways explain the photoproduct selectivity previously observed in the gas phase. Furthermore, the results provide the basis for explaining the condensed-phase photochemistry of CF2I2.
Classification And Energetics Of The Base-Phosphate Interactions In Rna, Craig L. Zirbel, Judit E. Šponer, Jiri Šponer, Jesse Stombaugh, Neocles B. Leontis
Classification And Energetics Of The Base-Phosphate Interactions In Rna, Craig L. Zirbel, Judit E. Šponer, Jiri Šponer, Jesse Stombaugh, Neocles B. Leontis
Chemistry Faculty Publications
Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the …
Pinpointing The Extent Of Electronic Delocalization In The Re(I)-To-Tetrazine Charge-Separated Excited State Using Time-Resolved Infrared Spectroscopy, Guifeng Li, Kumar Parimal, Shubham Vyas, Christopher M. Hadad, Amar H. Flood, Ksenija D. Glusac
Pinpointing The Extent Of Electronic Delocalization In The Re(I)-To-Tetrazine Charge-Separated Excited State Using Time-Resolved Infrared Spectroscopy, Guifeng Li, Kumar Parimal, Shubham Vyas, Christopher M. Hadad, Amar H. Flood, Ksenija D. Glusac
Chemistry Faculty Publications
Femtosecond mid-IR transient absorption spectroscopy (TRIR) and time-dependent density functional theory (TD-DFT) calculations on Re(CO)(3)Cl(Me(2)BPTZ) [Me(2)BPTZ = 3,6-bis(5-methyl-2-pyridine)-1,2,4,5-tetrazine] are used to demonstrate that the lowest excited state of the complex is a triplet metal-to-ligand charge-transfer ((3)MLCT) state with a lifetime of 225 ps. The short excited-state lifetime is explained by the energy-gap taw. Vibrational cooling of the (3)MLCT state shows up as early-time dynamics (3.6 ps). The structural changes in the excited state are deduced from the frequency shifts in the TRIR vibrational bands. The vibrational frequencies of the CO groups increase upon excitation as a result of decreased back-bonding …
Fluorenylidene-Pyrroline Biomimetic Light-Driven Molecular Switches, Laura Rivado-Casas, Diego Sampedro, Pedro J. Campos, Stefania Fusi, Vinicio Zanirato, Massimo Olivucci
Fluorenylidene-Pyrroline Biomimetic Light-Driven Molecular Switches, Laura Rivado-Casas, Diego Sampedro, Pedro J. Campos, Stefania Fusi, Vinicio Zanirato, Massimo Olivucci
Chemistry Faculty Publications
A new family of biomimetic photoactivated molecular switches based in the retinal chromophore is described. Expedient synthesis allows a library of compounds with a different substitution pattern, including chiral substituents, to be obtained. The effect of substitution, solvent, and light source on the photoisomerization step has been assessed. The absorption maximum has been red-shifted ca. 50 nm with respect to related systems and rotation is now easily achieved by using visible light.
Probing Single-Molecule Interfacial Geminate Electron-Cation Recombination Dynamics, Yuanmin Wang, Xuefei Wang, H. Peter Lu
Probing Single-Molecule Interfacial Geminate Electron-Cation Recombination Dynamics, Yuanmin Wang, Xuefei Wang, H. Peter Lu
Chemistry Faculty Publications
Interfacial electron-cation recombination in zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO(2) nanoparticle system has been probed at the single-molecule level by recording and analyzing photon-to-photon pair times of the ZnTCPP fluorescence. We have. developed a novel approach to reveal the hidden single-molecule interfacial electron-cation recombination dynamics by analyzing the autocorrelation function and a proposed convoluted single-molecule interfacial electron-cation recombination model. Our results suggest that the fluctuations of the interfacial electron transfer (ET) reactivity modulate the ET cycles as well as the interfacial electron-cation recombination dynamics. On the basis of this model, the single-molecule electron-cation recombination time of ZnTCPP/-TiO(2) system is deduced to be …
The Role Of Adenine In Fast Excited-State Deactivation Of Fad: A Femtosecond Mid-Ir Transient Absorption Study, Guifeng Li, Ksenija D. Glusac
The Role Of Adenine In Fast Excited-State Deactivation Of Fad: A Femtosecond Mid-Ir Transient Absorption Study, Guifeng Li, Ksenija D. Glusac
Chemistry Faculty Publications
We present a study of excited-state dynamics of two flavin cofactors: flavin-adenine dinucleotide (FAD) and flavin-mononucleotide (FMN). We used femtosecond mid-R transient absorption spectroscopy to study the effect of FAD conformation oil its excited-state behavior. The conformation of FAD was modulated by changing the solvent polarity: in D(2)O, FAD is present predominantly in the "stacked" conformation, in which flavin and adenine moieties are in close proximity to each other, whereas the increased amount of DMSO led to an increased amount of the "open" conformer. FMN served as a model system which lacks adenine. We found that the "stacked" conformer undergoes …
Electronic Properties Of 4-Substituted Naphthalimides, Pavel Kucheryavy, Guifeng Li, Shubham Vyas, Christopher Hadad, Ksenija D. Glusac
Electronic Properties Of 4-Substituted Naphthalimides, Pavel Kucheryavy, Guifeng Li, Shubham Vyas, Christopher Hadad, Ksenija D. Glusac
Chemistry Faculty Publications
This paper describes a study of excited-state properties of naphthalmide (NI) and four 4-substituted derivatives: 4-chloronaphthalimide (Cl-NI), 4-methylthionaphthalmide (MeS-NI), 4-nitronaphthalimide (O(2)N-NI), and 4-(N,N-dimethylaminonaphthalimide (Me(2)N-NI). Steady-state absorption and fluorescence spectra were collected in solvents of varying polarity to determine the excited-state character of NI derivatives. Furthermore. the excited-state dynamics were studied Using femtosecond transient absorption spectroscopy. The experimental findings were compared to calculated data obtained using time-dependent density functional (TD-DFT) methods. We found that light absorption by all NI derivatives leads to the production of the second excited state (S(2)), which was found to have a n,pi* character. Within similar to …
Phenylbenzimidazole-Based New Bipolar Host Materials For Efficient Phosphorescent Organic Light-Emitting Diodes, Shin-Ya Takizawa, Victor A. Montes, Pavel Anzenbacher Jr.
Phenylbenzimidazole-Based New Bipolar Host Materials For Efficient Phosphorescent Organic Light-Emitting Diodes, Shin-Ya Takizawa, Victor A. Montes, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Two new bipolar host materials based on a 1,3,5-tris(N-phenylbenzimidazol-2-yl)benzene (TPBI) core with the carbazole and diphenylamine groups were designed, synthesized, and applied in phosphorescent organic light-emitting diodes (PhOLEDs). The DFT calculations indicated desirable distribution of HOMO and LUMO densities, suggesting potential for bipolar charge transport. In addition, the electrochemical and phosphorescence studies revealed that neither the LUMO level nor the triplet energies differ significantly from the parent TPBI suggesting that the new materials would be suitable as hosts capable of both electron and hole transport and suitable for harvesting green electrophosphorescence. As a result of broader charge recombination zone resulting …
Frequency And Isostericity Of Rna Base Pairs, Craig L. Zirbel, Jesse Stombaugh, Eric Westhof
Frequency And Isostericity Of Rna Base Pairs, Craig L. Zirbel, Jesse Stombaugh, Eric Westhof
Chemistry Faculty Publications
Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-WatsonCrick base pairs play a central role. Non-WatsonCrick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can …
Probing Single-Molecule Interfacial Electron Transfer Dynamics Of Porphyrin On Tio2 Nanoparticles, Yuanmin Wang, Xuefei Wang, Sujit Kumar Ghosh, H. Peter Lu
Probing Single-Molecule Interfacial Electron Transfer Dynamics Of Porphyrin On Tio2 Nanoparticles, Yuanmin Wang, Xuefei Wang, Sujit Kumar Ghosh, H. Peter Lu
Chemistry Faculty Publications
Single-molecule interfacial electron transfer (ET) dynamics has been studied by using single-molecule fluorescence spectroscopy and microscopic imaging. For a single-molecule zinc-tetra (4-carboxyphenyl) porphyrin (ZnTCPP)/TiO2 nanoparticle system, the single-molecule fluorescence trajectories show strong fluctuation and blinking between bright and dark states. The intermittency and fluctuation of the single-molecule fluorescence are attributed to the variation of the reactivity of interfacial electron transfer. The nonexponential autocorrelation function and the power-law distribution of the probability density of dark times imply the dynamic and static inhomogeneities of the interfacial ET dynamics. On the basis of the power-law analysis, the variation of single-molecule interfacial ET reactivity …
Ultrafast Energy Transfer In Oligofluorene-Aluminum Bis(8-Hydroxyquinoline)Acetylacetone Coordination Polymers, Victor A. Montes, Grigory V. Zyryanov, Evgeny Danilov, Neeraj Agarwal, Manuel A. Palacios, Pavel Anzenbacher Jr.
Ultrafast Energy Transfer In Oligofluorene-Aluminum Bis(8-Hydroxyquinoline)Acetylacetone Coordination Polymers, Victor A. Montes, Grigory V. Zyryanov, Evgeny Danilov, Neeraj Agarwal, Manuel A. Palacios, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Understanding the excited-state dynamics in conjugated systems can lead to their better utilization in optical sensors, organic photovoltaics (OPVs), and organic light-emitting diodes (OLEDs). We present the synthesis of self-assembled coordination polymers comprising two types of fluorescent moieties: discrete fluorene oligomers of a well-defined length (n = 1-9) connected via aluminum(III) bis(8-quinolinolate)acetylacetone joints. Due to their well-defined structure, these materials allowed for a detailed study of energy migration processes within the materials. Thus, femtosecond transient spectroscopy was used to study the ultrafast energy transfer from the oligofluorene to the quinolinolate moieties, which was found to proceed at a rate of …
The Effect Of Dielectric Friction On The Rate Of Charge Separation In Type Ii Znse/Cds Semiconductor Nanorods, Alexander N. Tarnovsky, Nishshanka N. Hewa-Kasakarage, Patrick Z. El-Khoury, Nickolas Schmall, Maria Kirsanova, Alexander Nemchinov, Alexey Bezryadin, Mikhail Zamkov
The Effect Of Dielectric Friction On The Rate Of Charge Separation In Type Ii Znse/Cds Semiconductor Nanorods, Alexander N. Tarnovsky, Nishshanka N. Hewa-Kasakarage, Patrick Z. El-Khoury, Nickolas Schmall, Maria Kirsanova, Alexander Nemchinov, Alexey Bezryadin, Mikhail Zamkov
Chemistry Faculty Publications
The effect of dielectric friction on the rate of charge separation in type II ZnSe/CdS semiconductor nanorods has been investigated using picosecond transient absorption spectroscopy. The spatial separation of an excited electron-hole pair was estimated from the redshift in band edge absorption corresponding to the decrease in the exciton binding energy. The present study identifies a considerable effect of the solvent polarity on the rate of charge separation in semiconductor heterostructures, which should be taken into account when selecting nanorod caging media, such as solvents or polymer matrices. © 2009 American Institute of Physics.
Radiative Recombination Of Spatially Extended Excitons In (Znse/Cds)/Cds Heterostructured Nanorods, Nishshanka N. Hewa-Kasakarage, Maria Kirsanova, Alexander Nemchinov, Nickolas Schmall, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Mikhail Zamkov
Radiative Recombination Of Spatially Extended Excitons In (Znse/Cds)/Cds Heterostructured Nanorods, Nishshanka N. Hewa-Kasakarage, Maria Kirsanova, Alexander Nemchinov, Nickolas Schmall, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Mikhail Zamkov
Chemistry Faculty Publications
We report on organometallic synthesis of luminescent (ZnSe/CdS)/CdS semiconductor heterostructured nanorods (hetero-NRs) that produce an efficient spatial separation of carriers along the main axis of the structure (type II carrier localization). Nanorods were fabricated using a seeded-type approach by nucleating the growth of 20-100 nm CdS extensions at [000 +/- 1] facets of wurtzite ZnSe/CdS core/shell nanocrystals. The difference in growth rates of CdS in each of the two directions ensures that the position of ZnSe/CdS seeds in the final structure is offset from the center of hetero-NRs, resulting in a spatially asymmetric distribution of carrier wave functions along the …