The Experts below are selected from a list of 309 Experts worldwide ranked by ideXlab platform
Ludwik Adamowicz - One of the best experts on this subject based on the ideXlab platform.
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Stabilization of an Excess Electron on uracil by a pair of HF molecules: Ab initio study
Chemical Physics Letters, 2004Co-Authors: Claudio A. Morgado, Kostyantyn Pichugin, Ludwik AdamowiczAbstract:Abstract Two HF molecules can stabilize an Excess Electron in an uracil anion in a covalent π state or in a diffuse σ state by directly interacting with the Electron. The ab initio calculations performed in this work reveal several different configurational isomers of the complex of the uracil anion with the two HF molecules. The systems differ in terms of the structure of the solvation shell around the Excess Electron.
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An Excess Electron trapped in molecular tweezers: ab initio study
Chemical Physics Letters, 2004Co-Authors: Abraham F. Jalbout, Claudio A. Morgado, Ludwik AdamowiczAbstract:Abstract In this work, we have used theoretical ab initio calculations to design a molecular trap for an Excess Electron consisting of two chains of hydrogen-bonded HF molecules and a water molecule. A system with a ‘tweezers’-type shape has been found, where the Excess Electron is localized between two HF molecules in a ⋯FH · e · HF⋯ bridge.
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Stabilization of an Excess Electron on uracil by water. Ab initio study
Physical Chemistry Chemical Physics, 2004Co-Authors: Claudio A. Morgado, Kostyantyn Pichugin, Ludwik AdamowiczAbstract:Experiments performed on the uracil anion in the gaseous phase indicated that in this system the Excess Electron is dipole-bound. The experiments, however, also indicated that water solvation changes the character of the anion from dipole-bound to covalent. In this work we have used ab initio theoretical calculations to investigate the stabilization effect that the attachment of one or two water molecules has on the Electron attached to uracil. The calculations concern both dipole-bound and covalently-bound Electrons and reveal rich configurational isomerism of the complex of the uracil anion with H2O molecules. The systems differ in terms of the structure of the solvation cluster formed around the Excess Electron.
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An Excess Electron connects uracil to glycine: Ab-initio study
The European Physical Journal D - Atomic Molecular and Optical Physics, 2003Co-Authors: Abraham F. Jalbout, Kostyantyn Pichugin, Ludwik AdamowiczAbstract:In recent work Gutowski et al. [Eur. Phys. J. D 20, 431 (2002)] reported photoElectron-spectroscopy and theoretical study of covalent anion of the uracil-glycine complex. In present work we use ab initio calculations to describe an anionic complex of uracil and glycine where the Excess Electron is localized in a diffuse state between the two monomers. In this system the uracil and glycine molecules are separated by about 4.5 A and the dipoles of the two monomers point at the Excess Electron located in the middle of the complex. The calculated fragmentation energy of the anion into a dipole-bound uracil anion and a neutral glycine molecule is 1.7 kcal/mol.
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Uracil−Adenine Dimer Connected by an Excess Electron
The Journal of Physical Chemistry A, 2003Co-Authors: Stepan G. Stepanian, Caitlin S. Hall, Abraham F. Jalbout, Ludwik AdamowiczAbstract:In this work we consider a new form of the uracil−adenine dimer anion (AU-) where the two monomers are connected by an Excess Electron suspended between them. An equilibrium structures of the anion was predicted using uncorrelated and correlated ab initio quantum-mechanical calculations. An AU- anion of this kind can be formed in the gas phase by an attachment of an adenine molecule to a dipole-bound Electron of uracil. Removal of the Excess Electron from the anion and optimization of the geometry of the neutral cluster starting from the geometry of the anion initially leads to a significant increase of the separation between the bases, but eventually the optimization converges to an H-bonded structure very dissimilar from the anion structure.
Tetsuro Majima - One of the best experts on this subject based on the ideXlab platform.
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sequence dependent photocurrent generation through long distance Excess Electron transfer in dna
Angewandte Chemie, 2016Co-Authors: Shih-hsun Lin, Mamoru Fujitsuka, Tetsuro MajimaAbstract:Given its well-ordered continuous π stacking of nucleobases, DNA has been considered as a biomaterial for charge transfer in biosensors. For cathodic photocurrent generation resulting from hole transfer in DNA, sensitivity to DNA structure and base-pair stacking has been confirmed. However, such information has not been provided for anodic photocurrent generation resulting from Excess-Electron transfer in DNA. In the present study, we measured the anodic photocurrent of a DNA-modified Au electrode. Our results demonstrate long-distance Excess-Electron transfer in DNA, which is dominated by a hopping mechanism, and the photocurrent generation is sequence dependent.
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Excess-Electron Transfer in DNA by a Fluctuation-Assisted Hopping Mechanism.
The journal of physical chemistry. B, 2016Co-Authors: Shih-hsun Lin, Mamoru Fujitsuka, Tetsuro MajimaAbstract:The dynamics of Excess-Electron transfer in DNA has attracted the attention of scientists from all kinds of research fields because of its importance in biological processes. To date, several studies on Excess-Electron transfer in consecutive adenine (A):thymine (T) sequences in donor-DNA-acceptor systems have been published. However, the reported Excess-Electron transfer rate constants for consecutive T's are in the range of 10(10)-10(11) s(-1) depending on the photosensitizing Electron donor, which provides various driving forces for Excess-Electron injection into DNA. In this study, we employed a strongly Electron-donating photosensitizer, a dimer of 3,4-ethylenedioxythiophene (2E), and an Electron acceptor, diphenylacetylene (DPA), to synthesize a series of modified DNA oligomers (2-Tn, n = 3-6) in order to investigate the Excess-Electron transfer dynamics in these donor-DNA-acceptor systems using femtosecond laser flash photolysis. The relation between the free energy change for charge injection and the Excess-Electron transfer rate among consecutive T's provided an intrinsic Excess-Electron hopping rate constant of (3.8 ± 1.5) × 10(10) s(-1) in the DNA, which is consistent with the fluctuation frequency of the DNA sugar backbone and bases (3.3 × 10(10) s(-1)). Thus, we discuss the effect of structural fluctuations on the Excess-Electron hopping in DNA.
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how does guanine cytosine base pair affect Excess Electron transfer in dna
Journal of Physical Chemistry B, 2015Co-Authors: Shih-hsun Lin, Mamoru Fujitsuka, Tetsuro MajimaAbstract:Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, Excess-Electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly Electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an Electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the Excess-Electron quenching by proton transfer with the complementary G after formation of C•– and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T’s). In the present paper, we provided useful information based on the direct kinetic measurements, whi...
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Hole and Excess Electron transfer dynamics in DNA
Physical chemistry chemical physics : PCCP, 2012Co-Authors: Mamoru Fujitsuka, Tetsuro MajimaAbstract:Charge transfer in DNA attracts substantial attention from researchers in a wide group of fields such as bioscience, nanotechnology and physical chemistry. It is well known that both positive and negative charges, which are holes and Excess Electrons, respectively, contribute to the charge transfer in DNA. In the case of hole transfer in DNA, detailed mechanisms and dynamical parameters have been estimated by means of time-resolved spectroscopic methods and product analysis. On the other hand, detailed dynamics of Excess Electron transfer have not been established yet, although several aspects have been revealed by the continuous efforts of various research groups. In the present Perspective, studies on the charge transfer dynamics in DNA are summarized.
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Excess Electron injection and transfer in terthiophene modified dna terthiophene as a photosensitizing Electron donor for thymine cytosine and adenine
Chemistry: A European Journal, 2012Co-Authors: Man Jae Park, Mamoru Fujitsuka, Kiyohiko Kawai, Tetsuro MajimaAbstract:Excess-Electron transfer (EET) in DNA has attracted wide attention owing to its close relation to DNA repair and nanowires. To clarify the dynamics of EET in DNA, a photosensitizing Electron donor that can donate an Excess Electron to a variety of DNA sequences has to be developed. Herein, a terthiophene (3T) derivative was used as the photosensitizing Electron donor. From the dyad systems in which 3T was connected to a single nucleobase, it was revealed that (1) 3T* donates an Excess Electron efficiently to thymine, cytosine, and adenine, despite adenine being a well-known hole conductor. The free-energy dependence of the Electron-transfer rate was explained on the basis of the Marcus theory. From the DNA hairpins, it became clear that (1) 3T* can donate an Excess Electron not only to the adjacent nucleobase but also to the neighbor one nucleobase further along and so on. From the charge-injection rate, the possibilities of smaller β value and/or charge delocalization were discussed. In addition, EET through consecutive cytosine nucleobases was suggested.
László Turi - One of the best experts on this subject based on the ideXlab platform.
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Excess Electron solvation in ammonia clusters.
The Journal of chemical physics, 2019Co-Authors: Bence Baranyi, László TuriAbstract:We performed a combination of quantum chemical calculations and molecular dynamics simulations to assess the stability of various size NH3n− ammonia cluster anions up to n = 32 monomers. In the n = 3–8 size range, cluster anions are optimized and the vertical detachment energy of the Excess Electron (VDE) from increasing size clusters is computed using various level methods including density functional theory, MP2, and coupled-cluster singles doubles with perturbative triples. These clusters bind the Electrons in nonbranched hydrogen bonding chains in dipole bound states. The VDE increases with size from a few milliElectron volt up to ∼200 meV. The Electron binding energy is weaker than that in water clusters but comparable to small methanol cluster VDEs. We located the first branched hydrogen bonding cluster that binds the Excess Electron at n = 7. For larger (n = 8–32) clusters, we generated cold, neutral clusters by semiempirical and ab initio molecular dynamics simulations and added an extra Electron to selected neutral configurations. VDE calculations on the adiabatic and the relaxed anionic structures suggest that the n = 12–32 neutral clusters weakly bind the Excess Electron. Electron binding energies for these clusters (∼100 meV) appear to be significantly weaker than those extrapolated from experimental data. The observed Excess Electron states are diffuse and localized outside the molecular frame (surface states) with minor (∼1%) penetration to the nitrogen frontier orbitals. Stable minima with Excess Electron states surrounded by solvent molecules (cavity states) were not found in this size regime.We performed a combination of quantum chemical calculations and molecular dynamics simulations to assess the stability of various size NH3n− ammonia cluster anions up to n = 32 monomers. In the n = 3–8 size range, cluster anions are optimized and the vertical detachment energy of the Excess Electron (VDE) from increasing size clusters is computed using various level methods including density functional theory, MP2, and coupled-cluster singles doubles with perturbative triples. These clusters bind the Electrons in nonbranched hydrogen bonding chains in dipole bound states. The VDE increases with size from a few milliElectron volt up to ∼200 meV. The Electron binding energy is weaker than that in water clusters but comparable to small methanol cluster VDEs. We located the first branched hydrogen bonding cluster that binds the Excess Electron at n = 7. For larger (n = 8–32) clusters, we generated cold, neutral clusters by semiempirical and ab initio molecular dynamics simulations and added an extra Electron ...
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interior and surface bound Excess Electron states in large water cluster anions
Journal of Chemical Physics, 2009Co-Authors: Ádám Madarász, Peter J. Rossky, László TuriAbstract:We present the results of mixed quantum/classical simulations on relaxed thermal nanoscale water cluster anions, (H(2)O)(n)(-), with n=200, 500, 1000, and 8000. By using initial equilibration with constraints, we investigate stable/metastable negatively charged water clusters with both surface-bound and interior-bound Excess Electron states. Characterization of these states is performed in terms of geometrical parameters, energetics, and optical absorption spectroscopy of the clusters. The calculations provide data characterizing these states in the gap between previously published calculations and experiments on smaller clusters and the limiting cases of either an Excess Electron in bulk water or an Excess Electron at an infinite water/air interface. The present results are in general agreement with previous simulations and provide a consistent picture of the evolution of the physical properties of water cluster anions with size over the entire size range, including results for vertical detachment energies and absorption spectra that would signify their presence. In particular, the difference in size dependence between surface-bound and interior-bound state absorption spectra is dramatic, while for detachment energies the dependence is qualitatively the same.
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Excess Electron relaxation dynamics at water air interfaces
Journal of Chemical Physics, 2007Co-Authors: Ádám Madarász, Peter J. Rossky, László TuriAbstract:We have performed mixed quantum-classical molecular dynamics simulations of the relaxation of a ground state Excess Electron at interfaces of different phases of water with air. The investigated systems included ambient water/air, supercooled water/air, Ih ice/air, and amorphous solid water/air interfaces. The present work explores the possible connections of the examined interfacial systems to finite size cluster anions and the three-dimensional infinite, fully hydrated Electron. Localization site analyses indicate that in the absence of nuclear relaxation the Electron localizes in a shallow potential trap on the interface in all examined systems in a diffuse, surface-bound (SB) state. With relaxation, the weakly bound Electron undergoes an ultrafast localization and stabilization on the surface with the concomitant collapse of its radius. In the case of the ambient liquid interface the Electron slowly (on the 10ps time scale) diffuses into the bulk to form an interior-bound state. In each other case, th...
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Excess Electron localization sites in neutral water clusters
The Journal of chemical physics, 2006Co-Authors: László Turi, Ádám Madarász, Peter J. RosskyAbstract:We present approximate pseudopotential quantum-mechanical calculations of the Excess Electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300K. Correlated Electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound Excess Electron ground states in about 50% of the configurations for the smallest cluster size studied (n=20), and in almost all configurations for larger clusters (n>66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the Electron distribution are explored. We show that the stabilization of the Electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and...
Peter J. Rossky - One of the best experts on this subject based on the ideXlab platform.
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interior and surface bound Excess Electron states in large water cluster anions
Journal of Chemical Physics, 2009Co-Authors: Ádám Madarász, Peter J. Rossky, László TuriAbstract:We present the results of mixed quantum/classical simulations on relaxed thermal nanoscale water cluster anions, (H(2)O)(n)(-), with n=200, 500, 1000, and 8000. By using initial equilibration with constraints, we investigate stable/metastable negatively charged water clusters with both surface-bound and interior-bound Excess Electron states. Characterization of these states is performed in terms of geometrical parameters, energetics, and optical absorption spectroscopy of the clusters. The calculations provide data characterizing these states in the gap between previously published calculations and experiments on smaller clusters and the limiting cases of either an Excess Electron in bulk water or an Excess Electron at an infinite water/air interface. The present results are in general agreement with previous simulations and provide a consistent picture of the evolution of the physical properties of water cluster anions with size over the entire size range, including results for vertical detachment energies and absorption spectra that would signify their presence. In particular, the difference in size dependence between surface-bound and interior-bound state absorption spectra is dramatic, while for detachment energies the dependence is qualitatively the same.
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Excess Electron relaxation dynamics at water air interfaces
Journal of Chemical Physics, 2007Co-Authors: Ádám Madarász, Peter J. Rossky, László TuriAbstract:We have performed mixed quantum-classical molecular dynamics simulations of the relaxation of a ground state Excess Electron at interfaces of different phases of water with air. The investigated systems included ambient water/air, supercooled water/air, Ih ice/air, and amorphous solid water/air interfaces. The present work explores the possible connections of the examined interfacial systems to finite size cluster anions and the three-dimensional infinite, fully hydrated Electron. Localization site analyses indicate that in the absence of nuclear relaxation the Electron localizes in a shallow potential trap on the interface in all examined systems in a diffuse, surface-bound (SB) state. With relaxation, the weakly bound Electron undergoes an ultrafast localization and stabilization on the surface with the concomitant collapse of its radius. In the case of the ambient liquid interface the Electron slowly (on the 10ps time scale) diffuses into the bulk to form an interior-bound state. In each other case, th...
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Excess Electron localization sites in neutral water clusters
The Journal of chemical physics, 2006Co-Authors: László Turi, Ádám Madarász, Peter J. RosskyAbstract:We present approximate pseudopotential quantum-mechanical calculations of the Excess Electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300K. Correlated Electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound Excess Electron ground states in about 50% of the configurations for the smallest cluster size studied (n=20), and in almost all configurations for larger clusters (n>66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the Electron distribution are explored. We show that the stabilization of the Electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and...
Christian J Leumann - One of the best experts on this subject based on the ideXlab platform.
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Enhancement of Excess Electron transfer efficiency in DNA containing a phenothiazine donor and multiple stable phenanthrenyl base pairs
Chemistry - A European Journal, 2013Co-Authors: Pascal Roethlisberger, Filip Wojciechowski, Christian J LeumannAbstract:EET grown ohm: Excess Electron transfer (EET) was observed within a DNA duplex containing π-stacked phenothiazine as an Electron donor, phenanthrenes as Electron carriers and 5-bromouracil as an Electron trap. Increasing the number of phenanthrenyl base pairs increased EET efficiency.
