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Amorphous ZrF4-a molecular dynamics study

Rino, JoséPedro; Antonio, Giomal A.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 644-649
ENG
Relevância na Pesquisa
45.88%
Using an effective two-body interaction potential, a molecular dynamics study of the structural properties of amorphous ZrF4 phase is presented. The effective pair potential includes steric repulsion, Coulomb interaction due to charge transfer, and charge-dipole interaction due to the large electronic polarizability of anions. The results for structural correlations, such as pair distribution functions, coordination numbers, and bond angle distributions are presented. Excellent agreement is obtained by comparing experimental X-ray diffraction and the simulated static X-ray structure factor. © 1993.

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids

Cao, Z. W.; Xue, Y.; Han, L. Y.; Xie, B.; Zhou, H.; Zheng, C. J.; Lin, H. H.; Chen, Y. Z.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/07/2004 EN
Relevância na Pesquisa
46.04%
Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.

Density Functional Theory (DFT) Study of Triphenylamine-Based Dyes for Their Use as Sensitizers in Molecular Photovoltaics

Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguín, Norma; Almaral-Sánchez, Jorge; Glossman-Mitnik, Daniel
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 10/04/2012 EN
Relevância na Pesquisa
45.88%
In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pKa values were calculated with the semi-empirical PM6 method.

Computational Molecular Nanoscience Study of the Properties of Copper Complexes for Dye-Sensitized Solar Cells

Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguín, Norma; Almaral-Sánchez, Jorge; Glossman-Mitnik, Daniel
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 28/11/2012 EN
Relevância na Pesquisa
45.88%
In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT.

Molecular shape and the energetics of chemisorption: From simple to complex energy landscapes

Huang, D.; Harrowell, P.
Fonte: American Physical Soc Publicador: American Physical Soc
Tipo: Artigo de Revista Científica
Publicado em //2012 EN
Relevância na Pesquisa
45.9%
We enumerate all local minima of the energy landscape for model rigid adsorbates characterized by three or four equivalent binding sites (e.g., thiol groups) on a close-packed (111) surface of a face-centered-cubic crystal. We show that the number of energy minima increases linearly with molecular size with a rate of increase that depends on the degree of registry between the molecule shape and the surface structure. The sparseness of energy minima and the large variations in the center-of-mass positions of these minima vs molecular size for molecules that are incommensurate with the surface suggests a strong coupling in these molecules between surface mobility and shape or size fluctuations resulting from molecular vibrations. We also find that the variation in the binding energy with respect to molecular size decreases more rapidly with molecular size for molecules with a higher degree of registry with the surface. This indicates that surface adsorption should be better able to distinguish molecules by size if the molecules are incommensurate with the surface.; David M. Huang and Peter Harrowell

Electrical and Optical Characterization of Molecular Nanojunctions

Ward, Daniel R.
Fonte: Universidade Rice Publicador: Universidade Rice
ENG
Relevância na Pesquisa
46.11%
Electrical conduction at the single molecule scale has been studied extensively with molecular nanojunctions. Measurements have revealed a wealth of interesting physics. I3owever; our understanding is hindered by a lack of methods for simultaneous local imaging or spectroscopy to determine the conformation and local environment of the molecule of interest. Optical molecular spectroscopies have made significant progress in recent years, with single molecule sensitivity achieved through the use of surface-enhanced spectroscopies. In particular surface-enhanced Raman spectroscopy (SERS) has been demonstrated to have single molecule sensitivity for specific plasmonic structures. Many unanswered quest ions remain about the SERS process, particularly the role of chemical enhancements of the Raman signal. The primary goal of the research presented here is to combine both electrical and optical characterization techniques to obtain a more complete picture of electrical conduction at the single or few molecule level. We have successfully demonstrated that nanojunctions are excellent SERS substrates with the ability to achieve single molecule sensitivity. This is a major accomplishment with practical applications in optical sensor design. We present a method for mass producing nanojunctions with SERS sensitivity optimized through computer modeling. We have demonstrated simultaneous optical and electrical measurements of molecular junctions with single molecule electrical and SERS sensitivity. Measurements show strong correlations between electrical conductance and changes to the SERS response of nanojunctions. These results allow for one of the most conclusive demonstrations of single molecule SERS to date. This measurement technique provides the framework for three additional studies discussed here as well as opening up the possibilities for numerous other experiments. One measurement examines heating in nanowires rather than nanojunctions. We observe that...

Excitation of Molecular Vibrations by Positron Impact

Sullivan, James; Gilbert, Stephen J; Surko, Clifford M
Fonte: American Physical Society Publicador: American Physical Society
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.04%
The positron molecule collisions were investigated by measuring the vibrational excitation of Carbon monoxide, carbon dioxide, and hydrogen by positron impact. The adiabatic motion of a positron beam in a strong magnetic field was used for measuring the p

Compressed Sensing for the Fast Computation of Matrices: Application to Molecular Vibrations

Sanders, Jacob Nathan; Andrade, Xavier; Aspuru-Guzik, Alan
Fonte: American Chemical Society (ACS) Publicador: American Chemical Society (ACS)
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
46%
This article presents a new method to compute matrices from numerical simulations based on the ideas of sparse sampling and compressed sensing. The method is useful for problems where the determination of the entries of a matrix constitutes the computational bottleneck. We apply this new method to an important problem in computational chemistry: the determination of molecular vibrations from electronic structure calculations, where our results show that the overall scaling of the procedure can be improved in some cases. Moreover, our method provides a general framework for bootstrapping cheap low-accuracy calculations in order to reduce the required number of expensive high-accuracy calculations, resulting in a significant 3⇥ speed-up in actual calculations.; Chemistry and Chemical Biology

Molecular vibrations-induced quantum beats in two-dimensional electronic spectroscopy

Butkus, Vytautas; Valkunas, Leonas; Abramavicius, Darius
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.19%
Quantum beats in nonlinear spectroscopy of molecular aggregates are often attributed to electronic phenomena of excitonic systems, while nuclear degrees of freedom are commonly included into models as overdamped oscillations of bath constituents responsible for dephasing. However, molecular systems are coupled to various high-frequency molecular vibrations, which can cause the spectral beats hardly distinguishable from those created by purely electronic coherences. Models containing damped, undamped and overdamped vibrational modes coupled to an electronic molecular transition are discussed in this paper in context of linear absorption and two-dimensional electronic spectroscopy. Analysis of different types of bath models demonstrates how do vibrations map onto two-dimensional spectra and how the damping strength of the coherent vibrational modes can be resolved from spectroscopic signals.

A sparse-sampling approach for the fast computation of matrices: application to molecular vibrations

Sanders, Jacob N.; Andrade, Xavier; Aspuru-Guzik, Alán
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 17/10/2014
Relevância na Pesquisa
46%
This article presents a new method to compute matrices from numerical simulations based on the ideas of sparse sampling and compressed sensing. The method is useful for problems where the determination of the entries of a matrix constitutes the computational bottleneck. We apply this new method to an important problem in computational chemistry: the determination of molecular vibrations from electronic structure calculations, where our results show that the overall scaling of the procedure can be improved in some cases. Moreover, our method provides a general framework for bootstrapping cheap low-accuracy calculations in order to reduce the required number of expensive high-accuracy calculations, resulting in a significant 3x speed-up in actual calculations.; Comment: 9 pages, 7 figures

Giant absorption of light by molecular vibrations on a chip

Karabchvesky, A.; Tull, E. J.; Kavokin, A. V.; Zervas, M. N.; Wilkinson, J. S.; Lagoudakis, P. G.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 13/06/2015
Relevância na Pesquisa
46.07%
Vibrational overtone spectroscopy of molecules is a powerful tool for drawing information on molecular structure and dynamics. It relies on absorption of near infrared radiation (NIR) by molecular vibrations. Here we show the experimental evidence of giant enhancement of the absorption of light in solutions of organic molecules due to the switch from ballistic to diffusive propagation of light through a channel silicate glass waveguide. We also experimentally address a dynamics of absorption as a function of time of adsorption of the organic molecules on a waveguide. The observed enhancement in diffusion regime is by a factor of 300 in N-Methylaniline and by factor of 80 in Aniline compared to the expected values in the ballistic propagation of light in a waveguide. Our results underscore the importance of a guide surface modification and the disordered6 molecular nano-layer in enhancement of absorption by amines on engineered integrated system.

Electronic Transport in Fullerene C20 Bridge Assisted by Molecular Vibrations

Yamamoto, Takahiro; Watanabe, Kazuyuki; Watanabe, Satoshi
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 23/07/2005
Relevância na Pesquisa
46.07%
The effect of molecular vibrations on electronic transport is investigated with the smallest fullerene C20 bridge, utilizing the Keldysh nonequilibrium Green's function techniques combined with the tight-binding molecular-dynamics method. Large discontinuous steps appear in the differential conductance when the applied bias-voltage matches particular vibrational energies. The magnitude of the step is found to vary considerably with the vibrational mode and to depend on the local electronic states besides the strength of electron-vibration coupling. On the basis of this finding, a novel way to control the molecular motion by adjusting the gate voltage is proposed.; Comment: 9 pages, 4 figures, accepted for publication in Phys. Rev. Lett

Resonant interaction of molecular vibrations and surface plasmon polaritons: The weak coupling regime

Kalusniak, S.; Sadofev, S.; Henneberger, F.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 04/09/2014
Relevância na Pesquisa
46.15%
Adjusting the free-electron concentration, the surface plasmon frequency of the semiconductor ZnOGa is tuned into resonance with the molecular vibrations of the n-alkane tetracontane. Closed molecular films deposited on the semiconductor's surface in the monolayer regime generate distinct signatures in total-attenuated-reflection spectra at the frequencies of the symmetric and asymmetric stretching vibrations of the CH2 group. Their line shape undergoes profound changes from absorptive to dispersive and even anti-resonance behavior when moving along the surface- plasmon dispersion by the angel of incidence. We demonstrate that this line shape diversity results from a phase-sensitive perturbation of the surface-plasmon-polariton generation at the molecule/metal interface.

Heat, molecular vibrations, and adiabatic driving in non-equilibrium transport through interacting quantum dots

Haupt, F.; Leijnse, M.; Calvo, H. L.; Classen, L.; Splettstoesser, J.; Wegewijs, M. R.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 18/06/2013
Relevância na Pesquisa
46.08%
In this article we review aspects of charge and heat transport in interacting quantum dots and molecular junctions under stationary and time-dependent non-equilibrium conditions due to finite electrical and thermal bias. In particular, we discuss how a discrete level spectrum can be beneficial for thermoelectric applications, and investigate the detrimental effects of molecular vibrations on the efficiency of a molecular quantum dot as an energy converter. In addition, we consider the effects of a slow time-dependent modulation of applied voltages on the transport properties of a quantum dot and show how this can be used as a spectroscopic tool complementary to standard dc-measurements. Finally, we combine time-dependent driving with thermoelectrics in a double-quantum dot system - a nanoscale analogue of a cyclic heat engine - and discuss its operation and the main limitations to its performance.; Comment: Review article submitted to PSS (b) for the special issue "Quantum transport at the molecular scale"

Influence of molecular vibrations on dissociative adsorption

Gross, Axel; Scheffler, Matthias
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 10/07/1996
Relevância na Pesquisa
46%
The influence of molecular vibrations on dissociative adsorption is studied by six-dimensional quantum dynamical calculations. For the system H_2 at Pd(100), which possesses non-activated pathways, it is shown that large vibrational effects exist and that they are not due to a strongly curved reaction path and a late dissociation-hindering minimum barrier, as was previously assumed. Instead, they are caused by the lowering of the H-H vibrational frequency during the dissociation and the multi-dimensionality of the potential energy surface. Still there are quantitative discrepancies between theory and experiment identified.; Comment: RevTex, 14 pages, 5 figures, in uufiles form, to appear in Chem. Phys. Lett

Quantum theory of collective strong coupling of molecular vibrations with a microcavity mode

del Pino, Javier; Feist, Johannes; Garcia-Vidal, Francisco J.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 27/02/2015
Relevância na Pesquisa
46%
We develop a quantum mechanical formalism to treat the strong coupling between an electromagnetic mode and a vibrational excitation of an ensemble of organic molecules. By employing a Bloch-Redfield-Wangsness approach, we show that the influence of dephasing-type interactions, i.e., elastic collisions with a background bath of phonons, critically depends on the nature of the bath modes. In particular, for long-range phonons corresponding to a common bath, the dynamics of the "bright state" (the collective superposition of molecular vibrations coupling to the cavity mode) is effectively decoupled from other system eigenstates. For the case of independent baths (or short-range phonons), incoherent energy transfer occurs between the bright state and the uncoupled dark states. However, these processes are suppressed when the Rabi splitting is larger than the frequency range of the bath modes, as achieved in a recent experiment [Shalabney et al., Nat. Commun. 6, 5981 (2015)]. In both cases, the dynamics can thus be described through a single collective oscillator coupled to a photonic mode, making this system an ideal candidate to explore cavity optomechanics at room temperature.; Comment: 13 pages, 4 figures

On the relation between algebraic and configuration space calculations of molecular vibrations

Perez-Bernal, F.; Bijker, R.; Frank, A.; Lemus, R.; Arias, J. M.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 13/03/1996
Relevância na Pesquisa
46%
The relation between algebraic and traditional calculations of molecular vibrations is investigated. An explicit connection between interactions in configuration space and the corresponding algebraic interactions is established.; Comment: 9 pages, March 1996, submitted

Hole interactions with molecular vibrations on DNA

Omerzu, A.; Licer, M.; Mertelj, T.; Kabanov, V. V.; Mihailovic, D.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 13/05/2004
Relevância na Pesquisa
46%
We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms, clearly indicating the presence of localization. However, from a quantitative model analysis of the frequency shifts of vibrational modes caused by the PE holes, we find the holevibrational coupling constant to be relatively small, 0.2. This interaction leads to a change in the conformational energy of 0.015 eV, which is too small to cause selftrapping at room temperature. We conclude that, at least in the dry (A) form, DNA is best understood in terms of a double chain of coupled quantum dots arising from the pseudo-random chain sequence of base pairs, in which Anderson localization prevents the formation of a metallic state.

Electron transport through molecules in the Kondo regime: the role of molecular vibrations

Mravlje, J.; Ramsak, A.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 17/12/2009
Relevância na Pesquisa
46.19%
We discuss the electronic transport through molecules in the Kondo regime. We concentrate here on the influence of molecular vibrations. Two types of vibrations are investigated: (i) the breathing internal molecular modes, where the coupling occurs between the molecular deformation and the charge density, and (ii) the oscillations of molecule between the contacts, where the displacement affects the tunneling. The system is described by models which are solved numerically using Schoenhammer-Gunnarsson's projection operators and Wilson's numerical renormalization group methods. Case (i) is considered within the Anderson-Holstein model. Here the influence of the phonons is mainly to suppress the repulsion between the electrons at the molecular orbital. Case (ii) is described by a two-channel Anderson model with phonon-assisted hybridization. In both cases, the coupling to electrons softens the vibrational mode and in the strong coupling regime makes the displacement unstable to perturbations that break the symmetry of the confining potential. For instance, in case (ii) when the frequency of oscillations decreases below the magnitude of perturbation breaking the left-right symmetry, the molecule will be abruptly attracted to one of the electrodes. In this regime...

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e-H 2 vibrational cross section controversy

Robson, Robert; White, Ronald Douglas; Morrison, Michael A
Fonte: Institute of Physics Publishing Publicador: Institute of Physics Publishing
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
45.91%
We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann-Snider quantum kinetic equation, and insist that an electron-molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional 'echo' produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency...