Effect of molecular desorption on the electronic properties of self-assembled polarizable molecular monolayers.

PubMed

Wang, Gunuk; Jeong, Hyunhak; Ku, Jamin; Na, Seok-In; Kang, Hungu; Ito, Eisuke; Jang, Yun Hee; Noh, Jaegeun; Lee, Takhee

2014-04-01

We investigated the interfacial electronic properties of self-assembled monolayers (SAM)-modified Au metal surface at elevated temperatures. We observed that the work functions of the Au metal surfaces modified with SAMs changed differently under elevated-temperature conditions based on the type of SAMs categorized by three different features based on chemical anchoring group, molecular backbone structure, and the direction of the dipole moment. The temperature-dependent work function of the SAM-modified Au metal could be explained in terms of the molecular binding energy and the thermal stability of the SAMs, which were investigated with thermal desorption spectroscopic measurements and were explained with molecular modeling. Our study will aid in understanding the electronic properties at the interface between SAMs and metals in organic electronic devices if an annealing treatment is applied. Copyright © 2013 Elsevier Inc. All rights reserved.

Controlling charge current through a DNA based molecular transistor

NASA Astrophysics Data System (ADS)

Behnia, S.; Fathizadeh, S.; Ziaei, J.

2017-01-01

Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I-V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive.

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

Nonequilibrium, steady-state electron transport with N-representable density matrices from the anti-Hermitian contracted Schrödinger equation

NASA Astrophysics Data System (ADS)

Rothman, Adam E.; Mazziotti, David A.

2010-03-01

We study molecular conductivity for a one-electron, bath-molecule-bath model Hamiltonian. The primary quantum-mechanical variable is the one-electron reduced density matrix (1-RDM). By identifying similarities between the steady-state Liouville equation and the anti-Hermitian contracted Schrödinger equation (ACSE) [D. A. Mazziotti, Phys. Rev. A 75, 022505 (2007)], we develop a way of enforcing nonequilibrium, steady-state behavior in a time-independent theory. Our results illustrate the relationship between current and voltage in molecular junctions assuming that the total number of electrons under consideration can be fixed across all driving potentials. The impetus for this work is a recent study by Subotnik et al. that also uses the 1-RDM to study molecular conductivity under different assumptions regarding the total number of electrons [J. E. Subotnik et al., J. Chem. Phys. 130, 144105 (2009)]. Unlike calculations in the previous study, our calculations result in 1-RDMs that are fully N-representable. The present work maintains N-representability through a bath-bath mixing that is related to a time-independent relaxation of the baths in the absence of the molecule, as governed by the ACSE. A lack of N-representability can be important since it corresponds to occupying energy states in the molecule or baths with more than one electron or hole (the absence of an electron) in violation of the Pauli principle. For this reason the present work may serve as an important, albeit preliminary, step in designing a 2-RDM/ACSE method for studying steady-state molecular conductivity with an explicit treatment of electron correlation.

Future Technology-Driven Revolutions in Military Operations. Results of a Workshop

DTIC Science & Technology

1994-01-01

sensor missions. "• Biomolecular Electronics - The use of techniques from molecular biology and biotechnology to develop new molecular electronic materials...34* Biomolecular electronics - The use of techniques from molecular biology and biotechnology to develop new molecular electronic materials, components, and...occurring in molecular biology . 42 Biotechnology Molecular Biologists Arm Develoni "Magical" Caoabilitles "• To mynthsieh genm (frm satch) with conboi

Electronic state and optical response in a hydrogen-bonded molecular conductor

NASA Astrophysics Data System (ADS)

Naka, Makoto; Ishihara, Sumio

2018-06-01

Motivated by recent experimental studies of hydrogen-bonded molecular conductors κ -X 3(Cat-EDT-TTF) 2[X =H , D], interplays of protons and correlated electrons, and their effects on magnetic, dielectric, and optical properties, are studied theoretically. We introduce a model Hamiltonian for κ -X 3(Cat-EDT-TTF) 2, in which molecular dimers are connected by hydrogen bonds. Ground-state phase diagram and optical conductivity spectra are examined by using the mean-field approximation and the exact diagonalization method in finite-size cluster. Three types of the competing electronic and protonic phases, charge density wave phase, polar charge-ordered phase, and antiferromagnetic dimer-Mott insulating phase are found. Observed softening of the interdimer excitation due to the electron-proton coupling implies reduction of the effective electron-electron repulsion, i.e., "Hubbard U ," due to the quantum proton motion. Contrastingly, the intradimer charge excitation is hardened due to the proton-electron coupling. Implications of the theoretical calculations to the recent experimental results in κ -X 3(Cat-EDT-TTF) 2 are discussed.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen

2015-02-09

In this study, the response of titanate pyrochlores (A 2Ti 2O 7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O 2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization inmore » titanate pyrochlores under laser, electron and ion irradiations.« less

Transfer coefficients in ultracold strongly coupled plasma

NASA Astrophysics Data System (ADS)

Bobrov, A. A.; Vorob'ev, V. S.; Zelener, B. V.

2018-03-01

We use both analytical and molecular dynamic methods for electron transfer coefficients in an ultracold plasma when its temperature is small and the coupling parameter characterizing the interaction of electrons and ions exceeds unity. For these conditions, we use the approach of nearest neighbor to determine the average electron (ion) diffusion coefficient and to calculate other electron transfer coefficients (viscosity and electrical and thermal conductivities). Molecular dynamics simulations produce electronic and ionic diffusion coefficients, confirming the reliability of these results. The results compare favorably with experimental and numerical data from earlier studies.

A molecular Debye-Hückel approach to the reorganization energy of electron transfer reactions in an electric cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Tiejun; Department of Chemistry, Iowa State University, Ames, Iowa 50011; Song, Xueyu

2014-10-07

Electron transfer near an electrode immersed in ionic fluids is studied using the linear response approximation, namely, mean value of the vertical energy gap can be used to evaluate the reorganization energy, and hence any linear response model that can treat Coulomb interactions successfully can be used for the reorganization energy calculation. Specifically, a molecular Debye-Hückel theory is used to calculate the reorganization energy of electron transfer reactions in an electric cell. Applications to electron transfer near an electrode in molten salts show that the reorganization energies from our molecular Debye-Hückel theory agree well with the results from MD simulations.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

PubMed Central

Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.

2015-01-01

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

PubMed

Xiao, H Y; Weber, W J; Zhang, Y; Zu, X T; Li, S

2015-02-09

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

Oxidation of Carbon Nanotubes in an Ionizing Environment.

PubMed

Koh, Ai Leen; Gidcumb, Emily; Zhou, Otto; Sinclair, Robert

2016-02-10

In this work, we present systematic studies on how an illuminating electron beam which ionizes molecular gas species can influence the mechanism of carbon nanotube oxidation in an environmental transmission electron microscope (ETEM). We found that preferential attack of the nanotube tips is much more prevalent than for oxidation in a molecular gas environment. We establish the cumulative electron doses required to damage carbon nanotubes from 80 keV electron beam irradiation in gas versus in high vacuum. Our results provide guidelines for the electron doses required to study carbon nanotubes within or without a gas environment, to determine or ameliorate the influence of the imaging electron beam. This work has important implications for in situ studies as well as for the oxidation of carbon nanotubes in an ionizing environment such as that occurring during field emission.

The merger of electrochemistry and molecular electronics.

PubMed

McCreery, Richard L

2012-02-01

Molecular Electronics has the potential to greatly enhance existing silicon-based microelectronics to realize new functions, higher device density, lower power consumption, and lower cost. Although the investigation of electron transport through single molecules and molecular monolayers in "molecular junctions" is a recent development, many of the relevant concepts and phenomena are derived from electrochemistry, as practiced for the past several decades. The past 10+ years have seen an explosion of research activity directed toward how the structure of molecules affects electron transport in molecular junctions, with the ultimate objective of "rational design" of molecular components with new electronic functions, such as chemical sensing, interactions with light, and low-cost, low-power consumer electronics. In order to achieve these scientifically and commercially important objectives, the factors controlling charge transport in molecules "connected" to conducting contacts must be understood, and methods for massively parallel manufacturing of molecular circuits must be developed. This Personal Account describes the development of reproducible and robust molecular electronic devices, starting with modified electrodes used in electrochemistry and progressing to manufacturable molecular junctions. Although the field faced some early difficulties in reliability and characterization, the pieces are now in place for rapid advances in understanding charge transport at the molecular level. Inherent in the field of Molecular Electronics are many electrochemical concepts, including tunneling, redox exchange, activated electron transfer, and electron coupling between molecules and conducting contacts. Copyright © 2012 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Molecular Electronic Terms and Molecular Orbital Configurations.

ERIC Educational Resources Information Center

Mazo, R. M.

1990-01-01

Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

Analysis of multiple scattering contributions in electron-impact ionization of molecular hydrogen

NASA Astrophysics Data System (ADS)

Ren, Xueguang; Hossen, Khokon; Wang, Enliang; Pindzola, M. S.; Dorn, Alexander; Colgan, James

2017-10-01

We report a combined experimental and theoretical study on the low-energy (E 0 = 31.5 eV) electron-impact ionization of molecular hydrogen (H2). Triple differential cross sections are measured for a range of fixed emission angles of one outgoing electron between {θ }1=-70^\\circ and -130° covering the full 4π solid angle of the second electron. The energy sharing of the outgoing electrons varies from symmetric ({E}1={E}2=8 eV) to highly asymmetric (E 1 = 1 eV and E 2 = 15 eV). In addition to the binary and recoil lobes, a structure is observed perpendicular to the incoming beam direction which is due to multiple scattering of the projectile inside the molecular potential. The absolutely normalized experimental cross sections are compared with results from the time-dependent close-coupling (TDCC) calculations. Molecular alignment dependent TDCC results demonstrate that these structures are only present if the molecule axis is lying in the scattering plane.

Mode-selective vibrational modulation of charge transport in organic electronic devices

NASA Astrophysics Data System (ADS)

Bakulin, Artem A.; Lovrincic, Robert; Yu, Xi; Selig, Oleg; Bakker, Huib J.; Rezus, Yves L. A.; Nayak, Pabitra K.; Fonari, Alexandr; Coropceanu, Veaceslav; Brédas, Jean-Luc; Cahen, David

2015-08-01

The soft character of organic materials leads to strong coupling between molecular, nuclear and electronic dynamics. This coupling opens the way to influence charge transport in organic electronic devices by exciting molecular vibrational motions. However, despite encouraging theoretical predictions, experimental realization of such approach has remained elusive. Here we demonstrate experimentally that photoconductivity in a model organic optoelectronic device can be modulated by the selective excitation of molecular vibrations. Using an ultrafast infrared laser source to create a coherent superposition of vibrational motions in a pentacene/C60 photoresistor, we observe that excitation of certain modes in the 1,500-1,700 cm-1 region leads to photocurrent enhancement. Excited vibrations affect predominantly trapped carriers. The effect depends on the nature of the vibration and its mode-specific character can be well described by the vibrational modulation of intermolecular electronic couplings. This presents a new tool for studying electron-phonon coupling and charge dynamics in (bio)molecular materials.

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations

NASA Astrophysics Data System (ADS)

Romero, Jonathan; Posada, Edwin; Flores-Moreno, Roberto; Reyes, Andrés

2012-08-01

In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.

Effect of Molecular Rotation on Charge Transport Phenomena

NASA Astrophysics Data System (ADS)

Garg, O. P.; Lamba, Vijay Kr; Kaushik, D. K.

2015-12-01

The study of electron transport properties of molecular systems could be explained on the basis of the Landauer formalism. Unfortunately, due to the complexity of the experimental setup, most of these measurements have no control over the details of the electrode geometry, rotation of molecules, variation in angle of contacts, effect of fano resonances associated with side groups attached to rigid backbones, which results in a spectrum of IV-characteristics. Theoretical models can therefore help to understand and helps to develop new applications such as molecular sensors, etc. Thus we used simulation methods that generate the required structural ensemble, which is then analyzed with Green’s function methods to characterize the electronic transport properties. In present work we had discussed applications of this approach to understand the conductance in molecular system in the direction of controlling electron transport through molecules and studied the effect of rotation of sandwiched molecule.

Application of electron beam plasma for biopolymers modification

NASA Astrophysics Data System (ADS)

Vasilieva, T. M.

2012-06-01

The effects of the Electron Beam Plasma treatment on natural polysaccharide chitosan were studied experimentally. Low molecular water-soluble products of chitosan and chitooligosaccharides were obtained by treating the original polymers in the Electron Beam Plasma of oxygen and water vapor. The molecular mass of the products varied from 18 kDa to monomeric fragments. The degradation of the original polymers was due to the action of active oxygen particles (atomic and singlet oxygen) and the particles of the water plasmolysis (hydroxyl radicals, hydrogen peroxides). The 95% yield of low molecular weight chitosans was attained by optimizing the treatment conditions. The studies of the antimicrobial activity of low molecular products showed that they strongly inhibit the multiplication of colon bacillus, aurococcus and yeast-like fungi. The EBP-stimulated degradation of polysaccharides and proteins were found to result from breaking β-1,4 glycosidic bounds and peptide bonds, respectively.

Organic molecules on metal and oxide semiconductor substrates: Adsorption behavior and electronic energy level alignment

NASA Astrophysics Data System (ADS)

Ruggieri, Charles M.

Modern devices such as organic light emitting diodes use organic/oxide and organic/metal interfaces for crucial processes such as charge injection and charge transfer. Understanding fundamental physical processes occurring at these interfaces is essential to improving device performance. The ultimate goal of studying such interfaces is to form a predictive model of interfacial interactions, which has not yet been established. To this end, this thesis focuses on obtaining a better understanding of fundamental physical interactions governing molecular self-assembly and electronic energy level alignment at organic/metal and organic/oxide interfaces. This is accomplished by investigating both the molecular adsorption geometry using scanning tunneling microscopy, as well as the electronic structure at the interface using direct and inverse photoemission spectroscopy, and analyzing the results in the context of first principles electronic structure calculations. First, we study the adsorption geometry of zinc tetraphenylporphyrin (ZnTPP) molecules on three noble metal surfaces: Au(111), Ag(111), and Ag(100). These surfaces were chosen to systematically compare the molecular self-assembly and adsorption behavior on two metals of the same surface symmetry and two surface symmetries of one metal. From this investigation, we improve the understanding of self-assembly at organic/metal interfaces and the relative strengths of competing intermolecular and molecule-substrate interactions that influence molecular adsorption geometry. We then investigate the electronic structure of the ZnTPP/Au(111), Ag(111), and Ag(100) interfaces as examples of weakly-interacting systems. We compare these cases to ZnTPP on TiO2(110), a wide-bandgap oxide semiconductor, and explain the intermolecular and molecule-substrate interactions that determine the electronic energy level alignment at the interface. Finally we study tetracyanoquinodimethane (TCNQ), a strong electron acceptor, on TiO2(110), which exhibits chemical hybridization accompanied by molecular distortion, as well as extreme charge transfer resulting in the development of a space charge layer in the oxide. Thus, we present a broad experimental and theoretical perspective on the study of organic/metal and organic/oxide interfaces, elucidating fundamental physical interactions that govern molecular organization and energy level alignment.

Molecular Kondo effect in flat-band lattices

NASA Astrophysics Data System (ADS)

Tran, Minh-Tien; Nguyen, Thuy Thi

2018-04-01

The Kondo effect of a single magnetic impurity embedded in the Lieb lattice is studied by the numerical renormalization group. When the band flatness is present in the local density of states at the impurity site, it quenches the participation of all dispersive electrons in the Kondo singlet formation and reduces the many-body Kondo problem to a two-electron molecular Kondo problem. A quantum entanglement of two spins, which is the two-electron molecular analog of the many-body Kondo singlet, is stable at low temperature, and the impurity contributions to thermodynamical and dynamical quantities are qualitatively different from that obtained in the many-body Kondo effect. The conditions for existence of the molecular Kondo effect in narrow band systems are also presented.

Low-energy electron scattering from CO. 2: Ab-initio study using the frame-transformation theory

NASA Technical Reports Server (NTRS)

Chandra, N.

1976-01-01

The Wigner-Eisenbud R matrix method has been combined with the frame transformation theory to study electron scattering from molecular systems. The R matrix, calculated at the boundary point of the molecular core radius, has been transformed to the space frame in order to continue the solution of the scattering equations in the outer region where rotational motion of the nuclei is taken into account. This procedure has been applied to a model calculation of thermal energy electron scattering from CO.

Interference effects on vibration-mediated tunneling through interacting degenerate molecular states.

PubMed

Zhong, X; Cao, J C

2009-07-22

We study the combined effects of quantum electronic interference and Coulomb interaction on electron transport through near-degenerate molecular states with strong electron-vibration interaction. It is found that quantum electronic interference strongly affects the current and its noise properties. In particular, destructive interference induces pronounced negative differential conductances (NDCs) accompanying the vibrational excited states, and such NDC characters are not related to asymmetric tunnel coupling and are robust to the damping of a thermal bath. In a certain transport regime, the non-equilibrium vibration distribution even shows a peculiar sub-Poissonian behavior, which is enhanced by quantum electronic interference.

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

NASA Astrophysics Data System (ADS)

Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

2014-05-01

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.

ERIC Educational Resources Information Center

Willis, Christopher J.

1988-01-01

Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)

``Making the Molecular Movie'': First Frames

NASA Astrophysics Data System (ADS)

Miller, R. J. Dwayne

2011-03-01

Femtosecond Electron Diffraction has enabled atomic resolution to structural changes as they occur, essentially watching atoms move in real time--directly observe transition states. This experiment has been referred to as ``making the molecular movie'' and has been previously discussed in the context of a gedanken experiment. With the recent development of femtosecond electron pulses with sufficient number density to execute single shot structure determinations, this experiment has been finally realized. A new concept in electron pulse generation was developed based on a solution to the N-body electron propagation problem involving up to 10,000 interacting electrons that has led to a new generation of extremely bright electron pulsed sources that minimizes space charge broadening effects. Previously thought intractable problems of determining t=0 and fully characterizing electron pulses on the femtosecond time scale have now been solved through the use of the laser pondermotive potential to provide a time dependent scattering source. Synchronization of electron probe and laser excitation pulses is now possible with an accuracy of 10 femtoseconds to follow even the fastest nuclear motions. The camera for the ``molecular movie'' is well in hand based on high bunch charge electron sources. Several movies depicting atomic motions during passage through structural transitions will be shown. Atomic level views of the simplest possible structural transition, melting, will be presented for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated to the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron systems will be presented in which an exceptionally cooperative phase transitions has been observed. The primitive origin of molecular cooperativity has also been discovered in recent studies of molecular crystals. These new developments will be discussed in the context of developing the necessary technology to directly observe the structure-function correlation in biomolecules--the fundamental molecular basis of biological systems.

Molecular-Scale Electronics: From Concept to Function.

PubMed

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction

NASA Astrophysics Data System (ADS)

Kosov, Daniel S.

2017-09-01

Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ1 and τ2 means that the density matrix of the molecule is not fully renewed after time τ1 and the probability of observing waiting time τ2 for the second electron transfer depends on the previous electron waiting time τ1. The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.

Electron and fluorescence spectra of a water molecule irradiated by an x-ray free-electron laser pulse

NASA Astrophysics Data System (ADS)

Schäfer, Julia M.; Inhester, Ludger; Son, Sang-Kil; Fink, Reinhold F.; Santra, Robin

2018-05-01

With the highly intense x-ray light generated by x-ray free-electron lasers (XFELs), molecular samples can be ionized many times in a single pulse. Here we report on a computational study of molecular spectroscopy at the high x-ray intensity provided by XFELs. Calculated photoelectron, Auger electron, and x-ray fluorescence spectra are presented for a single water molecule that reaches many electronic hole configurations through repeated ionization steps. The rich details shown in the spectra depend on the x-ray pulse parameters in a nonintuitive way. We discuss how the observed trends can be explained by the competition of microscopic electronic transition processes. A detailed comparison between spectra calculated within the independent-atom model and within the molecular-orbital framework highlights the chemical sensitivity of the spectral lines of multiple-hole configurations. Our results demonstrate how x-ray multiphoton ionization-related effects such as charge-rearrangement-enhanced x-ray ionization of molecules and frustrated absorption manifest themselves in the electron and fluorescence spectra.

On the physical interpretation of the nuclear molecular orbital energy.

PubMed

Charry, Jorge; Pedraza-González, Laura; Reyes, Andrés

2017-06-07

Recently, several groups have extended and implemented molecular orbital (MO) schemes to simultaneously obtain wave functions for electrons and selected nuclei. Many of these schemes employ an extended Hartree-Fock approach as a first step to find approximate electron-nuclear wave functions and energies. Numerous studies conducted with these extended MO methodologies have explored various effects of quantum nuclei on physical and chemical properties. However, to the best of our knowledge no physical interpretation has been assigned to the nuclear molecular orbital energy (NMOE) resulting after solving extended Hartree-Fock equations. This study confirms that the NMOE is directly related to the molecular electrostatic potential at the position of the nucleus.

Molecular tips for scanning tunneling microscopy: intermolecular electron tunneling for single-molecule recognition and electronics.

PubMed

Nishino, Tomoaki

2014-01-01

This paper reviews the development of molecular tips for scanning tunneling microscopy (STM). Molecular tips offer many advantages: first is their ability to perform chemically selective imaging because of chemical interactions between the sample and the molecular tip, thus improving a major drawback of conventional STM. Rational design of the molecular tip allows sophisticated chemical recognition; e.g., chiral recognition and selective visualization of atomic defects in carbon nanotubes. Another advantage is that they provide a unique method to quantify electron transfer between single molecules. Understanding such electron transfer is mandatory for the realization of molecular electronics.

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires. Using quantum-based calculations, we modeled 'p-type' polaron transport through oligophenylenethiophene (OPTI) wires and assigned transport activation energies to specific modes of nuclear motion. We also show control over 'n-type', LUMO-mediated transport in short ( 2 nm) redox-active perylenediimide (PDI) SAMs bound to contacts through isocyano linkers. By changing the contact work function (φ) and temperature, we were able to verify thermally-assisted LUMO transport. Transition voltage spectroscopy and the single level model was employed to fit the experimental I-V curves and extract the electronic coupling (epsilon) and the EF-LUMO offset (epsilonl). It was found that epsilonl does not change with φ (LUMO pinning), while Gamma changes with both φ and temperature. Further, the PDI SAMs could be reversibly chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

Carbon Nanotubes: Molecular Electronic Components

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1997-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

NASA Astrophysics Data System (ADS)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

Nanogap structures for molecular nanoelectronics.

PubMed

Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

2012-02-09

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

Molecular electronics: some views on transport junctions and beyond.

PubMed

Joachim, Christian; Ratner, Mark A

2005-06-21

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

Molecular electronics: Some views on transport junctions and beyond

PubMed Central

Joachim, Christian; Ratner, Mark A.

2005-01-01

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of “conduction as scattering” generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions. PMID:15956192

Electronic properties of electron-doped [6,6]-phenyl-C61-butyric acid methyl ester and silylmethylfullerene

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2017-06-01

Electronic properties of electron-doped chemically decorated C60 fullerenes, [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and silylmethylfullerene (SIMEF), by a planar electrode were studied using density functional theory combined with the effective screening medium method to simulate the heterointerface between the chemically decorated C60 and cationic counter materials. We find that the distribution of accumulated electrons and induced electric field depend on the molecular arrangement with respect to the external electric field of the electrode. We also show that the quantum capacitance of the molecule is sensitive to molecular arrangement owing to the asymmetric distribution of the accumulated electrons.

Electronic properties of a molecular system with Platinum

NASA Astrophysics Data System (ADS)

Ojeda, J. H.; Medina, F. G.; Becerra-Alonso, David

2017-10-01

The electronic properties are studied using a finite homogeneous molecule called Trans-platinum-linked oligo(tetraethenylethenes). This system is composed of individual molecules such as benzene rings, platinum, Phosphore and Sulfur. The mechanism for the study of the electron transport through this system is based on placing the molecule between metal contacts to control the current through the molecular system. We study this molecule based on the tight-binding approach for the calculation of the transport properties using the Landauer-Büttiker formalism and the Fischer-Lee relationship, based on a semi-analytic Green's function method within a real-space renormalization approach. Our results show a significant agreement with experimental measurements.

Complementary study of molecular dynamics and domain sizes in heterogenous nanocomposites PBT/DA-C{sub 60} and PBT/TCNEO-C{sub 60}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woźniak-Braszak, A., E-mail: abraszak@amu.edu.pl; Baranowski, M.; Jurga, K.

2014-05-28

A comprehensive study of molecular dynamics and structure in new heterogenous nanocomposites based on poly(butylene terephthalate) and nanoparticles C{sub 60} modified by n-decylamine or tetracyanoethylene oxide has been performed. The domain structure of new nanocomposites has been investigated by Fourier transform infrared spectroscopy, wide-angle X-ray scattering, and differential scanning calorimetry techniques. Solid-state {sup 1}H NMR techniques were used to study molecular dynamics and domain sizes in new nanocomposites. Information about the electronic properties of these nanocomposites was obtained by means of electron paramagnetic resonance method. It was shown that the structure and molecular dynamics of new nanocomposites were strongly dependentmore » on the properties and concentration of fullerene derivates.« less

Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

PubMed

Georgieva, I; Mihaylov, Tz; Trendafilova, N

2014-06-01

The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Nanomorphology of P3HT:PCBM-based absorber layers of organic solar cells after different processing conditions analyzed by low-energy scanning transmission electron microscopy.

PubMed

Pfaff, Marina; Klein, Michael F G; Müller, Erich; Müller, Philipp; Colsmann, Alexander; Lemmer, Uli; Gerthsen, Dagmar

2012-12-01

In this study the nanomorphology of P3HT:PC61BM absorber layers of organic solar cells was studied as a function of the processing parameters and for P3HT with different molecular weight. For this purpose we apply scanning transmission electron microscopy (STEM) at low electron energies in a scanning electron microscope. This method exhibits sensitive material contrast in the high-angle annular dark-field (HAADF) mode, which is well suited to distinguish materials with similar densities and mean atomic numbers. The images taken with low-energy HAADF STEM are compared with conventional transmission electron microscopy and atomic force microscopy images to illustrate the capabilities of the different techniques. For the interpretation of the low-energy HAADF STEM images, a semiempirical equation is used to calculate the image intensities. The experiments show that the nanomorphology of the P3HT:PC61BM blends depends strongly on the molecular weight of the P3HT. Low-molecular-weight P3HT forms rod-like domains during annealing. In contrast, only small globular features are visible in samples containing high-molecular-weight P3HT, which do not change significantly after annealing at 150°C up to 30 min.

Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N.; Harrabi, K.

2015-07-14

Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect onmore » the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.« less

Super-reduced polyoxometalates: excellent molecular cluster battery components and semipermeable molecular capacitors.

PubMed

Nishimoto, Yoshio; Yokogawa, Daisuke; Yoshikawa, Hirofumi; Awaga, Kunio; Irle, Stephan

2014-06-25

Theoretical investigations are presented on the molecular and electronic structure changes that occur as α-Keggin-type polyoxometalate (POM(3-)) clusters [PM12O40](3-) (M = Mo, W) are converted toward their super-reduced POM(27-) state during the discharging process in lithium-based molecular cluster batteries. Density functional theory was employed in geometry optimization, and first-principles molecular dynamics simulations were used to explore local minima on the potential energy surface of neutral POM clusters adorned with randomly placed Li atoms as electron donors around the cluster surface. On the basis of structural, electron density, and molecular orbital studies, we present evidence that the super-reduction is accompanied by metal-metal bond formation, beginning from the 12th to 14th excess electron transferred to the cluster. Afterward, the number of metal-metal bonds increases nearly linearly with the number of additionally transferred excess electrons. In α-Keggin-type POMs, metal triangles are a prominently emerging structural feature. The origin of the metal triangle formation during super-reduction stems from the formation of characteristic three-center two-electron bonds in triangular metal atom sites, created under preservation of the POM skeleton via "squeezing out" of oxygen atoms bridging two metal atoms when the underlying metal atoms form covalent bonds. The driving force for this unusual geometrical and electronic structure change is a local Jahn-Teller distortion at individual transition-metal octahedral sites, where the triply degenerate t2 d orbitals become partially filled during reduction and gain energy by distortion of the octahedron in such a way that metal-metal bonds are formed. The bonding orbitals show strong contributions from mixing with metal-oxygen antibonding orbitals, thereby "shuffling away" excess electrons from the cluster center to the outside of the cage. The high density of negatively charged yet largely separated oxygen atoms on the surface of the super-reduced POM(27-) polyanion allows the huge Coulombic repulsion due to the presence of the excess electrons to be counterbalanced by the presence of Li countercations, which partially penetrate into the outer oxygen shell. This "semiporous molecular capacitor" structure is likely the reason for the effective electron uptake in POMs.

Nanoscale rotary motors driven by electron tunneling.

PubMed

Wang, Boyang; Vuković, Lela; Král, Petr

2008-10-31

We examine by semiclassical molecular dynamics simulations the possibility of driving nanoscale rotary motors by electron tunneling. The model systems studied have a carbon nanotube shaft with covalently attached "isolating" molecular stalks ending with "conducting" blades. Periodic charging and discharging of the blades at two metallic electrodes maintains an electric dipole on the blades that is rotated by an external electric field. Our simulations demonstrate that these molecular motors can be efficient under load and in the presence of noise and defects.

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

PubMed

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

Dicopper(II) metallacyclophanes as multifunctional magnetic devices: a joint experimental and computational study.

PubMed

Castellano, María; Ruiz-García, Rafael; Cano, Joan; Ferrando-Soria, Jesús; Pardo, Emilio; Fortea-Pérez, Francisco R; Stiriba, Salah-Eddine; Julve, Miguel; Lloret, Francesc

2015-03-17

Metallosupramolecular complexes constitute an important advance in the emerging fields of molecular spintronics and quantum computation and a useful platform in the development of active components of spintronic circuits and quantum computers for applications in information processing and storage. The external control of chemical reactivity (electro- and photochemical) and physical properties (electronic and magnetic) in metallosupramolecular complexes is a current challenge in supramolecular coordination chemistry, which lies at the interface of several other supramolecular disciplines, including electro-, photo-, and magnetochemistry. The specific control of current flow or spin delocalization through a molecular assembly in response to one or many input signals leads to the concept of developing a molecule-based spintronics that can be viewed as a potential alternative to the classical molecule-based electronics. A great variety of factors can influence over these electronically or magnetically coupled, metallosupramolecular complexes in a reversible manner, electronic or photonic external stimuli being the most promising ones. The response ability of the metal centers and/or the organic bridging ligands to the application of an electric field or light irradiation, together with the geometrical features that allow the precise positioning in space of substituent groups, make these metal-organic systems particularly suitable to build highly integrated molecular spintronic circuits. In this Account, we describe the chemistry and physics of dinuclear copper(II) metallacyclophanes with oxamato-containing dinucleating ligands featuring redox- and photoactive aromatic spacers. Our recent works on dicopper(II) metallacyclophanes and earlier ones on related organic cyclophanes are now compared in a critical manner. Special focus is placed on the ligand design as well as in the combination of experimental and computational methods to demonstrate the multifunctionality nature of these metallosupramolecular complexes. This new class of oxamato-based dicopper(II) metallacyclophanes affords an excellent synthetic and theoretical set of models for both chemical and physical fundamental studies on redox- and photo-triggered, long-distance electron exchange phenomena, which are two major topics in molecular magnetism and molecular electronics. Apart from their use as ground tests for the fundamental research on the relative importance of the spin delocalization and spin polarization mechanisms of the electron exchange interaction through extended π-conjugated aromatic ligands in polymetallic complexes, oxamato-based dicopper(II) metallacyclophanes possessing spin-containing electro- and chromophores at the metal and/or the ligand counterparts emerge as potentially active (magnetic and electronic) molecular components to build a metal-based spintronic circuit. They are thus unique examples of multifunctional magnetic complexes to get single-molecule spintronic devices by controlling and allowing the spin communication, when serving as molecular magnetic couplers and wires, or by exhibiting bistable spin behavior, when acting as molecular magnetic rectifiers and switches. Oxamato-based dicopper(II) metallacyclophanes also emerge as potential candidates for the study of coherent electron transport through single molecules, both experimentally and theoretically. The results presented herein, which are a first step in the metallosupramolecular approach to molecular spintronics, intend to attract the attention of physicists and materials scientists with a large expertice in the manipulation and measurement of single-molecule electron transport properties, as well as in the processing and addressing of molecules on different supports.

Molecular electrostatics for probing lone pair-π interactions.

PubMed

Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

2013-11-14

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Role of topographical defects in organic film growth of 4,4' -biphenyldicarboxylic acid on graphene: A low-energy electron microscopy study

NASA Astrophysics Data System (ADS)

Khokhar, Fawad S.; van Gastel, Raoul; Poelsema, Bene

2010-11-01

We have used low-energy electron microscopy (LEEM) to study the formation of self-assembled molecular networks on graphene sheets. 4,4' -biphenyldicarboxylic acid (BDA) molecular networks were grown using organic molecular beam epitaxy. LEEM images provide direct insight in the growth dynamics and show that defects in the graphene play a crucial role in the final morphology of the molecular film that forms. BDA is demonstrated to form hydrogen bond-stabilized chains on graphene. Dark-field LEEM images reveal that the same defects that determine the morphology of the film, also direct the orientation of the domains, highlighting the importance of understanding the role of defects in epitaxial processes on graphene.

Molecular implementation of molecular shift register memories

NASA Technical Reports Server (NTRS)

Beratan, David N. (Inventor); Onuchic, Jose N. (Inventor)

1991-01-01

An electronic shift register memory (20) at the molecular level is described. The memory elements are based on a chain of electron transfer molecules (22) and the information is shifted by photoinduced (26) electron transfer reactions. Thus, multi-step sequences of charge transfer reactions are used to move charge with high efficiency down a molecular chain. The device integrates compositions of the invention onto a VLSI substrate (36), providing an example of a molecular electronic device which may be fabricated. Three energy level schemes, molecular implementation of these schemes, optical excitation strategies, charge amplification strategies, and error correction strategies are described.

Mechanically controllable break junctions for molecular electronics.

PubMed

Xiang, Dong; Jeong, Hyunhak; Lee, Takhee; Mayer, Dirk

2013-09-20

A mechanically controllable break junction (MCBJ) represents a fundamental technique for the investigation of molecular electronic junctions, especially for the study of the electronic properties of single molecules. With unique advantages, the MCBJ technique has provided substantial insight into charge transport processes in molecules. In this review, the techniques for sample fabrication, operation and the various applications of MCBJs are introduced and the history, challenges and future of MCBJs are discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The study of molecular spectroscopy by ab initio methods

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1991-01-01

This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

2018-03-01

The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

NASA Astrophysics Data System (ADS)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

Mode-selective vibrational modulation of charge transport in organic electronic devices

PubMed Central

Bakulin, Artem A.; Lovrincic, Robert; Yu, Xi; Selig, Oleg; Bakker, Huib J.; Rezus, Yves L. A.; Nayak, Pabitra K.; Fonari, Alexandr; Coropceanu, Veaceslav; Brédas, Jean-Luc; Cahen, David

2015-01-01

The soft character of organic materials leads to strong coupling between molecular, nuclear and electronic dynamics. This coupling opens the way to influence charge transport in organic electronic devices by exciting molecular vibrational motions. However, despite encouraging theoretical predictions, experimental realization of such approach has remained elusive. Here we demonstrate experimentally that photoconductivity in a model organic optoelectronic device can be modulated by the selective excitation of molecular vibrations. Using an ultrafast infrared laser source to create a coherent superposition of vibrational motions in a pentacene/C60 photoresistor, we observe that excitation of certain modes in the 1,500–1,700 cm−1 region leads to photocurrent enhancement. Excited vibrations affect predominantly trapped carriers. The effect depends on the nature of the vibration and its mode-specific character can be well described by the vibrational modulation of intermolecular electronic couplings. This presents a new tool for studying electron–phonon coupling and charge dynamics in (bio)molecular materials. PMID:26246039

Possibility designing XNOR and NAND molecular logic gates by using single benzene ring

NASA Astrophysics Data System (ADS)

Abbas, Mohammed A.; Hanoon, Falah H.; Al-Badry, Lafy F.

2017-09-01

This study focused on examining electronic transport through single benzene ring and suggested how such ring can be employed to design XNOR and NAND molecular logic gates. The single benzene ring was threaded by a magnetic flux. The magnetic flux and applied gate voltages were considered as the key tuning parameter in the XNOR and NAND gates operation. All the calculations are achieved by using steady-state theoretical model, which is based on the time-dependent Hamiltonian model. The transmission probability and the electric current are calculated as functions of electron energy and bias voltage, respectively. The application of the anticipated results can be a base for the progress of molecular electronics.

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

PubMed

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Carbon nanorings with inserted acenes: Breaking symmetry in excited state dynamics

DOE PAGES

Franklin-Mergarejo, R.; Alvarez, D. Ondarse; Tretiak, S.; ...

2016-08-10

Conjugated cycloparaphenylene rings have unique electronic properties being the smallest segments of carbon nanotubes. Their conjugated backbones support delocalized electronic excitations, which dynamics is strongly influenced by cyclic geometry. Here we present a comparative theoretical study of the electronic and vibrational energy relaxation and redistribution in photoexcited cycloparaphenylene carbon nanorings with inserted naphthalene, anthracene, and tetracene units using non-adiabatic excited-state molecular dynamics simulations. Calculated excited state structures reflect modifications of optical selection rules and appearance of low-energy electronic states localized on the acenes due to gradual departure from a perfect circular symmetry. After photoexcitation, an ultrafast electronic energy relaxation tomore » the lowest excited state is observed on the time scale of hundreds of femtoseconds in all molecules studied. Concomitantly, the efficiency of the exciton trapping in the acene raises when moving from naphthalene to anthracene and to tetracene, being negligible in naphthalene, and ~60% and 70% in anthracene and tetracene within the first 500 fs after photoexcitation. Observed photoinduced dynamics is further analyzed in details using induced molecular distortions, delocatization properties of participating electronic states and non-adiabatic coupling strengths. Lastly, our results provide a number of insights into design of cyclic molecular systems for electronic and light-harvesting applications.« less

Single-Molecule Interfacial Electron Transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, H. Peter

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static andmore » dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO 2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO 2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO 2 nanoparticle surfaces by using ultrafast single-molecule spectroscopy and electrochemical AFM metal tip scanning microscopy, focusing on understanding the interfacial electron transfer dynamics at specific nanoscale electron transfer sites with high-spatially and temporally resolved topographic-and-spectroscopic characterization at individual molecule basis, characterizing single-molecule rate processes, reaction driving force, and molecule-substrate electronic coupling. One of the most significant characteristics of our new approach is that we are able to interrogate the complex interfacial electron transfer dynamics by actively pin-point energetic manipulation of the surface interaction and electronic couplings, beyond the conventional excitation and observation.« less

Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study.

PubMed

Gu, Bin; Smyth, Maeve; Kohanoff, Jorge

2014-11-28

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study.

PubMed

Fuchs, Andreas; Steinbrecher, Thomas; Mommer, Mario S; Nagata, Yuki; Elstner, Marcus; Lennartz, Christian

2012-03-28

In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.

Spin resolved electronic transport through N@C20 fullerene molecule between Au electrodes: A first principles study

NASA Astrophysics Data System (ADS)

Caliskan, Serkan

2018-05-01

Using first principles study, through Density Functional Theory combined with Non Equilibrium Green's Function Formalism, electronic properties of endohedral N@C20 fullerene molecule joining Au electrodes (Au-N@C20) was addressed in the presence of spin property. The electronic transport behavior across the Au-N@C20 molecular junction was investigated by spin resolved transmission, density of states, molecular orbitals, differential conductance and current-voltage (I-V) characteristics. Spin asymmetric variation was clearly observed in the results due to single N atom encapsulated in the C20 fullerene cage, where the N atom played an essential role in the electronic behavior of Au-N@C20. This N@C20 based molecular bridge, exhibiting a spin dependent I-V variation, revealed a metallic behavior within the bias range from -1 V to 1 V. The induced magnetic moment, spin polarization and other relevant quantities associated with the spin resolved transport were elucidated.

Molecular polarizability of water from local dielectric response theory

DOE PAGES

Ge, Xiaochuan; Lu, Deyu

2017-08-08

Here, we propose a fully ab initio theory to compute the electron density response under the perturbation in the local field. This method is based on our recently developed local dielectric response theory [Phys. Rev. B 92, 241107(R), 2015], which provides a rigorous theoretical framework to treat local electronic excitations in both nite and extended systems beyond the commonly employed dipole approximation. We have applied this method to study the electronic part of the molecular polarizability of water in ice Ih and liquid water. Our results reveal that the crystal field of the hydrogen-bond network has strong anisotropic effects, whichmore » significantly enhance the out-of-plane component and suppress the in-plane component perpendicular to the bisector direction. The contribution from the charge transfer is equally important, which increases the isotropic molecular polarizability by 5-6%. Our study provides new insights into the dielectric properties of water, which form the basis to understand electronic excitations in water and to develop accurate polarizable force fields of water.« less

Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

ERIC Educational Resources Information Center

Hipps, K. W.; Scudiero, L.

2005-01-01

A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

Potential energy curves of the Na2+ molecular ion from all-electron ab initio relativistic calculations

NASA Astrophysics Data System (ADS)

Bewicz, Anna; Musiał, Monika; Kucharski, Stanisław A.

2017-11-01

The equation-of-motion coupled-cluster method for electron affinity calculations has been used to study potential energy curves (PECs) for the Na+2 molecular ion. Although the studied molecule represents the open shell system the applied approach employs the closed shell Na+ 22 ion as the reference. In addition the Na+ 22 system dissociates into the closed shell fragments; hence, the restricted Hartree-Fock scheme can be used within the whole range of interatomic distances, from 2 to 45 Å. We used large basis set engaging 268 basis functions with all 21 electrons correlated. The relativistic effects are included via second-order Douglas-Kroll method. The computed PECs, spectroscopic molecular constants and vibrational energy levels agree well with experimental values if the latter are available or with other theoretical data.

Electronic Rearrangement in Molecular Plasmons: An Electron Density and Electrostatic Potential-Based Study.

PubMed

Paul, Mishu; Balanarayan, P

2018-06-05

Plasmonic modes in single-molecule systems have been previously identified by scaling two-electron interactions in calculating excitation energies. Analysis of transition dipole moments for states of polyacenes based on configuration interaction is another method for characterising molecular plasmons. The principal features in the electronic absorption spectra of polyacenes are a low-intensity, lower-in-energy peak and a high-intensity, higher-in-energy peak. From calculations using time-dependent density functional theory with the B3LYP/cc-pVTZ basis set, both these peaks are found to result from the same set of electronic transitions, that is, HOMO-n to LUMO and HOMO to LUMO+n, where n varies as the number of fused rings increases. In this work, the excited states of polyacenes, naphthalene through pentacene, are analysed using electron densities and molecular electrostatic potential (MESP) topography. Compared to other excited states the bright and dark plasmonic states involve the least electron rearrangement. Quantitatively, the MESP topography indicates that the variance in MESP values and the displacement in MESP minima positions, calculated with respect to the ground state, are lowest for plasmonic states. The excited-state electronic density profiles and electrostatic potential topographies suggest the least electron rearrangement for the plasmonic states. Conversely, high electron rearrangement characterises a single-particle excitation. The molecular plasmon can be called an excited state most similar to the ground state in terms of one-electron properties. This is found to be true for silver (Ag 6 ) and sodium (Na 8 ) linear chains as well. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bias effects on the electronic spectrum of a molecular bridge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, Heidi; Prociuk, Alexander; Dunietz, Barry D

2011-01-01

In this paper the effect of bias and geometric symmetry breaking on the electronic spectrum of a model molecular system is studied. Geometric symmetry breaking can either enhance the dissipative effect of the bias, where spectral peaks are disabled, or enable new excitations that are absent under zero bias conditions. The spectralanalysis is performed on a simple model system by solving for the electronic response to an instantaneously impulsive perturbation in the dipole approximation. The dynamical response is extracted from the electronic equations of motion as expressed by the Keldysh formalism. This expression provides for the accurate treatment of themore » electronic structure of a bulk-coupled system at the chosen model Hamiltonian electronic structure level.« less

Current Progress of Nanomaterials in Molecularly Imprinted Electrochemical Sensing.

PubMed

Zhong, Chunju; Yang, Bin; Jiang, Xinxin; Li, Jianping

2018-01-02

Nanomaterials have received much attention during the past decade because of their excellent optical, electronic, and catalytic properties. Nanomaterials possess high chemical reactivity, also high surface energy. Thus, provide a stable immobilization platform for biomolecules, while preserving their reactivity. Due to the conductive and catalytic properties, nanomaterials can also enhance the sensitivity of molecularly imprinted electrochemical sensors by amplifying the electrode surface, increasing the electron transfer, and catalyzing the electrochemical reactions. Molecularly imprinted polymers that contain specific molecular recognition sites can be designed for a particular target analyte. Incorporating nanomaterials into molecularly imprinted polymers is important because nanomaterials can improve the response signal, increase the sensitivity, and decrease the detection limit of the sensors. This study describes the classification of nanomaterials in molecularly imprinted polymers, their analytical properties, and their applications in the electrochemical sensors. The progress of the research on nanomaterials in molecularly imprinted polymers and the application of nanomaterials in molecularly imprinted polymers is also reviewed.

Quantum Mechanical Studies of Molecular Hyperpolarizabilities.

DTIC Science & Technology

1980-04-30

exponent , reflects the screening of an electron in a given orbital by the interior electrons in the atom or molecule. In practice, when studying...Basis sets have evolved over the years in molecular quantum mechanics until sets of orbital exponents for the different atoms composing the molecule have...and R. P. Hurst , J. Chem. Phys. 46, 2356 (1967); S. P. LickmannI and J. W. Moskowitz, J. Chem. Phys. 54, 3622 7T971). 26. T. H. Dunning, J. Chem. Phys

Nanogap structures for molecular nanoelectronics

PubMed Central

2012-01-01

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

Electronic Transitions of Palladium Monoboride and Platinum Monoboride

NASA Astrophysics Data System (ADS)

Ng, Y. W.; Pang, H. F.; Wong, Y. S.; Qian, Yue; Cheung, A. S.-C.

2012-06-01

Electronic transition spectrum of palladium monoboride (PdB) and platinum (PtB) monoboride have been studied using the technique of laser-ablation/reaction free jet expansion and laser induced fluorescence spectroscopy. The metal monoborides were produced by reacting laser ablated metal atoms and diborane ((B_2H_6) seeded in argon. Five and six vibrational bands were observed respectively for the PdB and PtB molecules. Preliminary analysis of the rotationally resolved structure showed that both molecules have X2 Σ+ ground state. Least-squares fit of the measured line positions yielded molecular constants for the electronic states involved. Molecular and electronic structures of PdB and PtB are discussed using a molecular orbital energy level diagram. Financial support from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. HKU 701008P) is gratefully acknowledged.

Interfacial Molecular Packing Determines Exciton Dynamics in Molecular Heterostructures: The Case of Pentacene-Perfluoropentacene.

PubMed

Rinn, Andre; Breuer, Tobias; Wiegand, Julia; Beck, Michael; Hübner, Jens; Döring, Robin C; Oestreich, Michael; Heimbrodt, Wolfram; Witte, Gregor; Chatterjee, Sangam

2017-12-06

The great majority of electronic and optoelectronic devices depend on interfaces between p-type and n-type semiconductors. Finding matching donor-acceptor systems in molecular semiconductors remains a challenging endeavor because structurally compatible molecules may not necessarily be suitable with respect to their optical and electronic properties, and the large exciton binding energy in these materials may favor bound electron-hole pairs rather than free carriers or charge transfer at an interface. Regardless, interfacial charge-transfer exciton states are commonly considered as an intermediate step to achieve exciton dissociation. The formation efficiency and decay dynamics of such states will strongly depend on the molecular makeup of the interface, especially the relative alignment of donor and acceptor molecules. Structurally well-defined pentacene-perfluoropentacene heterostructures of different molecular orientations are virtually ideal model systems to study the interrelation between molecular packing motifs at the interface and their electronic properties. Comparing the emission dynamics of the heterosystems and the corresponding unitary films enables accurate assignment of every observable emission signal in the heterosystems. These heterosystems feature two characteristic interface-specific luminescence channels at around 1.4 and 1.5 eV that are not observed in the unitary samples. Their emission strength strongly depends on the molecular alignment of the respective donor and acceptor molecules, emphasizing the importance of structural control for device construction.

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Widawsky, Jonathan R.

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

DNA-Based Single-Molecule Electronics: From Concept to Function.

PubMed

Wang, Kun

2018-01-17

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

DNA-Based Single-Molecule Electronics: From Concept to Function

PubMed Central

2018-01-01

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

Vibronic coupling effect on the electron transport through molecules

NASA Astrophysics Data System (ADS)

Tsukada, Masaru; Mitsutake, Kunihiro

2007-03-01

Electron transport through molecular bridges or molecular layers connected to nano-electrodes is determined by the combination of coherent and dissipative processes, controlled by the electron-vibron coupling, transfer integrals between the molecular orbitals, applied electric field and temperature. We propose a novel theoretical approach, which combines ab initio molecular orbital method with analytical many-boson model. As a case study, the long chain model of the thiophene oligomer is solved by a variation approach. Mixed states of moderately extended molecular orbital states mediated and localised by dress of vibron cloud are found as eigen-states. All the excited states accompanied by multiple quanta of vibration can be solved, and the overall carrier transport properties including the conductance, mobility, dissipation spectra are analyzed by solving the master equation with the transition rates estimated by the golden rule. We clarify obtained in a uniform systematic way, how the transport mode changes from a dominantly coherent transport to the dissipative hopping transport.

Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

NASA Astrophysics Data System (ADS)

Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

2016-12-01

Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

Dynamics of photoionization from molecular electronic wavepacket states in intense pulse laser fields: A nonadiabatic electron wavepacket study.

PubMed

Matsuoka, Takahide; Takatsuka, Kazuo

2017-04-07

A theory for dynamics of molecular photoionization from nonadiabatic electron wavepackets driven by intense pulse lasers is proposed. Time evolution of photoelectron distribution is evaluated in terms of out-going electron flux (current of the probability density of electrons) that has kinetic energy high enough to recede from the molecular system. The relevant electron flux is in turn evaluated with the complex-valued electronic wavefunctions that are time evolved in nonadiabatic electron wavepacket dynamics in laser fields. To uniquely rebuild such wavefunctions with its electronic population being lost by ionization, we adopt the complex-valued natural orbitals emerging from the electron density as building blocks of the total wavefunction. The method has been implemented into a quantum chemistry code, which is based on configuration state mixing for polyatomic molecules. Some of the practical aspects needed for its application will be presented. As a first illustrative example, we show the results of hydrogen molecule and its isotope substitutes (HD and DD), which are photoionized by a two-cycle pulse laser. Photon emission spectrum associated with above threshold ionization is also shown. Another example is taken from photoionization dynamics from an excited state of a water molecule. Qualitatively significant effects of nonadiabatic interaction on the photoelectron spectrum are demonstrated.

Molecular electron recollision dynamics in intense circularly polarized laser pulses

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Yuan, Kai-Jun

2018-04-01

Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

UV-vis, IR and 1H NMR spectroscopic studies of some mono- and bis-azo-compounds based on 2,7-dihydroxynaphthalene and aniline derivatives

NASA Astrophysics Data System (ADS)

Issa, Raafat M.; Fayed, Tarek A.; Awad, Mohammed K.; El-Kony, Sanaa M.

2005-12-01

The absorption spectra of mono- and bis-azo-derivatives obtained by coupling the diazonium salts of aromatic amines and 2,7-dihydroxynaphthalene have been studied in six organic solvents. The different absorption bands have been assigned and the effect of solvents on the charge transfer band is also discussed. The diagnostic IR spectral bands and 1H NMR signals are assigned and discussed in relation to molecular structure. Also, semi-empirical molecular orbital calculations using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory have been performed to investigate the molecular and electronic structures of these compounds. According to these calculations, an intramolecular hydrogen bonding is essential for stabilization of such molecules.

Size-dependent single electron transfer and semi-metal-to-insulator transitions in molecular metal oxide electronics

NASA Astrophysics Data System (ADS)

Balliou, Angelika; Bouroushian, Mirtat; Douvas, Antonios M.; Skoulatakis, George; Kennou, Stella; Glezos, Nikos

2018-07-01

All-inorganic self-arranged molecular transition metal oxide hyperstructures based on polyoxometalate molecules (POMs) are fabricated and tested as electronically tunable components in emerging electronic devices. POM hyperstructures reveal great potential as charging nodes of tunable charging level for molecular memories and as enhancers of interfacial electron/hole injection for photovoltaic stacks. STM, UPS, UV–vis spectroscopy and AFM measurements show that this functionality stems from the films’ ability to structurally tune their HOMO–LUMO levels and electron localization length at room temperature. By adapting POM nanocluster size in solution, self-doping and current modulation of four orders of magnitude is monitored on a single nanocluster on SiO2 at voltages as low as 3 Volt. Structurally driven insulator-to-semi-metal transitions and size-dependent current regulation through single electron tunneling are demonstrated and examined with respect to the stereochemical and electronic structure of the molecular entities. This extends the value of self-assembly as a tool for correlation length and electronic properties tuning and demonstrate POM hyperstructures’ plausibility for on-chip molecular electronics operative at room temperature.

Size-dependent single electron transfer and semi-metal-to-insulator transitions in molecular metal oxide electronics.

PubMed

Balliou, Angelika; Bouroushian, Mirtat; Douvas, Antonios M; Skoulatakis, George; Kennou, Stella; Glezos, Nikos

2018-07-06

All-inorganic self-arranged molecular transition metal oxide hyperstructures based on polyoxometalate molecules (POMs) are fabricated and tested as electronically tunable components in emerging electronic devices. POM hyperstructures reveal great potential as charging nodes of tunable charging level for molecular memories and as enhancers of interfacial electron/hole injection for photovoltaic stacks. STM, UPS, UV-vis spectroscopy and AFM measurements show that this functionality stems from the films' ability to structurally tune their HOMO-LUMO levels and electron localization length at room temperature. By adapting POM nanocluster size in solution, self-doping and current modulation of four orders of magnitude is monitored on a single nanocluster on SiO 2 at voltages as low as 3 Volt. Structurally driven insulator-to-semi-metal transitions and size-dependent current regulation through single electron tunneling are demonstrated and examined with respect to the stereochemical and electronic structure of the molecular entities. This extends the value of self-assembly as a tool for correlation length and electronic properties tuning and demonstrate POM hyperstructures' plausibility for on-chip molecular electronics operative at room temperature.

Fundamental Studies of Hydroporphyrin Architectures for Solar-Energy Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindsey, Jonathan S.; Bocian, David F.; Holten, Dewey

2013-10-30

The long-term objective of the Bocian/Holten&Kirmaier/Lindsey research program is to design, synthesize, and characterize tetrapyrrole-based molecular architectures that absorb sunlight, funnel energy, and separate charge with high efficiency and in a manner compatible with current and future solar-energy conversion schemes. The synthetic tetrapyrroles include porphyrins and hydroporphyrins; the latter classes of molecules encompass analogues of the naturally occurring chlorophylls and bacteriochlorophylls (e.g., chlorins, bacteriochlorins, and their derivatives). The attainment of the goals of the research program requires the close interplay of molecular design and synthesis (Lindsey group), static and time-resolved optical spectroscopic measurements (Holten&Kirmaier group), and electrochemical, electron paramagnetic resonance,more » resonance Raman, and infrared studies, as well as density functional theory calculations (Bocian Group). The proposed research encompasses four interrelated themes: (i) Gain a deeper understanding of the spectral and electronic properties of bacteriochlorins, with a subsidiary aim of learning how to shift the long-wavelength absorption band deeper into the NIR region. Bacteriochlorins bearing diverse substituents, including annulated rings, will be prepared and examined. A set of bacteriochlorins with site-specific isotopic (13C, 2H) substitution patterns about the macrocycle perimeter will be prepared for studies of vibrational and electronic properties. (ii) Examine the underlying electronic origin of panchromatic absorption and excited-state behavior of strongly coupled rylene–tetrapyrrole arrays. The rylene constituents include a perylene-monoimide and a terrylene-monoimide. The tetrapyrroles include porphyrins (meso- or β-linked) and bacteriochlorins (β-linked). The objective is to achieve panchromatic absorption while preserving a viable, long-lived excited singlet state. (iii) Determine the rates of ground-state hole/electron transfer between (hydro)porphyrins as a function of array size, distance between components, linker type, site of linker connection, and frontier molecular orbital composition. (iv) Build upon the results of the aforementioned studies to design, synthesize, and characterize integrated architectures that incorporate a panchromatic absorber and other molecular components that that afford efficient hole/electron migration and long-lived charge separation. Such architectures will be examined on solid substrates to explore the viability of the component parts and processes under application-oriented conditions. Such architectures or successors may prove directly useful for solar-energy conversion systems. An equally important attribute is to serve as a test-bed for successful integration of the requisite properties and processes, some of which require rather weak coupling between constituents, some of which require very strong electronic interactions to elicit the desired behavior, and all of which should be tunable under molecular design control to the extent possible. Collectively, the proposed studies will provide fundamental insights into molecular properties, interactions, and processes relevant to the design of molecular architectures for solar-energy conversion. The accomplishment of these goals is only possible through a highly synergistic program that encompasses molecular design, synthesis, and in-depth characterization.« less

Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

NASA Astrophysics Data System (ADS)

Yip, Hin-Lap

Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Photoinduced electron transfer in a molecular dyad by nanosecond pump-pump-probe spectroscopy.

PubMed

Ha-Thi, M-H; Pham, V-T; Pino, T; Maslova, V; Quaranta, A; Lefumeux, C; Leibl, W; Aukauloo, A

2018-06-01

The design of robust and inexpensive molecular photocatalysts for the conversion of abundant stable molecules like H2O and CO2 into an energetic carrier is one of the major fundamental questions for scientists nowadays. The outstanding challenge is to couple single photoinduced charge separation events with the sequential accumulation of redox equivalents at the catalytic unit for performing multielectronic catalytic reactions. Herein, double excitation by nanosecond pump-pump-probe experiments was used to interrogate the photoinduced charge transfer and charge accumulation on a molecular dyad composed of a porphyrin chromophore and a ruthenium-based catalyst in the presence of a reversible electron acceptor. An accumulative charge transfer state is unattainable because of rapid reverse electron transfer to the photosensitizer upon the second excitation and the low driving force of the forward photodriven electron transfer reaction. Such a method allows the fundamental understanding of the relaxation mechanism after two sequential photon absorptions, deciphering the undesired electron transfer reactions that limit the charge accumulation efficiency. This study is a step toward the improvement of synthetic strategies of molecular photocatalysts for light-induced charge accumulation and more generally, for solar energy conversion.

Molecular anions.

PubMed

Simons, Jack

2008-07-24

The experimental and theoretical study of molecular anions has undergone explosive growth over the past 40 years. Advances in techniques used to generate anions in appreciable numbers as well as new ion-storage, ion-optics, and laser spectroscopic tools have been key on the experimental front. Theoretical developments on the electronic structure and molecular dynamics fronts now allow one to achieve higher accuracy and to study electronically metastable states, thus bringing theory in close collaboration with experiment in this field. In this article, many of the experimental and theoretical challenges specific to studying molecular anions are discussed. Results from many research groups on several classes of molecular anions are overviewed, and both literature citations and active (in online html and pdf versions) links to numerous contributing scientists' Web sites are provided. Specific focus is made on the following families of anions: dipole-bound, zwitterion-bound, double-Rydberg, multiply charged, metastable, cluster-based, and biological anions. In discussing each kind of anion, emphasis is placed on the structural, energetic, spectroscopic, and chemical-reactivity characteristics that make these anions novel, interesting, and important.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butkus, Vytautas; Dong, Hui; Fleming, Graham R.

2016-01-21

Here, a study is presented showing the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer. We show that depending on the amount of inhomogeneous broadening, the excitonically coupled molecular system can establish long-lived electronic coherences, caused by a disordered subensemble, for which the dephasing due to static energy disorder becomes significantly reduced. On the basis of these considerations, we present explanations for why the electronic or vibrational coherences were or were not observed in a range of recent experiments.

ELECTRON TRANSFER MECHANISM AT THE SOLID-LIQUID INTERFACE OF PHYLLOSILICATES

EPA Science Inventory

Interfacial electron transfer processes on clay minerals have significant impact in natural environments and geochemical systems. Nitrobenzene was used as molecular probes to study the electron transfer mechanism at the solid-water interfaces of Fe-containing phyllosicates. For...

Telegraph noise in Markovian master equation for electron transport through molecular junctions

NASA Astrophysics Data System (ADS)

Kosov, Daniel S.

2018-05-01

We present a theoretical approach to solve the Markovian master equation for quantum transport with stochastic telegraph noise. Considering probabilities as functionals of a random telegraph process, we use Novikov's functional method to convert the stochastic master equation to a set of deterministic differential equations. The equations are then solved in the Laplace space, and the expression for the probability vector averaged over the ensemble of realisations of the stochastic process is obtained. We apply the theory to study the manifestations of telegraph noise in the transport properties of molecular junctions. We consider the quantum electron transport in a resonant-level molecule as well as polaronic regime transport in a molecular junction with electron-vibration interaction.

A molecular shift register based on electron transfer

NASA Technical Reports Server (NTRS)

Hopfield, J. J.; Onuchic, Josenelson; Beratan, David N.

1988-01-01

An electronic shift-register memory at the molecular level is described. The memory elements are based on a chain of electron-transfer molecules and the information is shifted by photoinduced electron-transfer reactions. This device integrates designed electronic molecules onto a very large scale integrated (silicon microelectronic) substrate, providing an example of a 'molecular electronic device' that could actually be made. The design requirements for such a device and possible synthetic strategies are discussed. Devices along these lines should have lower energy usage and enhanced storage density.

Distribution of tunnelling times for quantum electron transport.

PubMed

Rudge, Samuel L; Kosov, Daniel S

2016-03-28

In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

NASA Astrophysics Data System (ADS)

Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

2017-11-01

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below those of B3LYP and M06 DFT functionals. This suggests that the NEGF-RDM method could be a viable alternative to NEGF-DFT for molecular junction calculations.

Inter-Fullerene Electronic Coupling Controls the Efficiency of Photoinduced Charge Generation in Organic Bulk Heterojunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Bryon W.; Reid, Obadiah G.; Coffey, David C.

2016-09-26

Photoinduced charge generation (PCG) dynamics are notoriously difficult to correlate with specific molecular properties in device relevant polymer:fullerene organic photovoltaic blend films due to the highly complex nature of the solid state blend morphology. Here, this study uses six judiciously selected trifluoromethylfullerenes blended with the prototypical polymer poly(3-hexylthiophene) and measure the PCG dynamics in 50 fs-500 ns time scales with time-resolved microwave conductivity and femtosecond transient absorption spectroscopy. The isomeric purity and thorough chemical characterization of the fullerenes used in this study allow for a detailed correlation between molecular properties, driving force, local intermolecular electronic coupling and, ultimately, the efficiencymore » of PCG yield. The findings show that the molecular design of the fullerene not only determines inter-fullerene electronic coupling, but also influences the decay dynamics of free holes in the donor phase even when the polymer microstructure remains unchanged.« less

Study of organic-inorganic hetero-interfaces and electrical transport in semiconducting nanostructures

NASA Astrophysics Data System (ADS)

Wagner, Sean Robert

As the electronics industry continues to evolve and move towards functional electronic devices with increasing complexity and functionality, it becomes important to explore materials outside the regime of conventional semiconductors. Organic semiconducting small molecules have received a large amount of attention due to their high degree of flexibility, the option to perform molecular synthesis to modify their electronic and magnetic properties, and their ability to organize into highly-ordered functionalized nanostructures and thin films. Being able to form complex nanostructures and thin films with molecular precision, while maintaining the ability to tune properties through modifications in the molecular chemistry could result in vast improvements in conventional device architectures. However, before this is realized, there still remains a significant lack of understanding regarding how these molecules interact with various substrate surfaces as well as their intermolecular interactions. The interplay between these interactions can produce drastic changes in the molecular orientation and ordering at the hetero-interface, which can affect the transport properties of the molecular thin film and ultimately modify the performance of the organic electronic device. This study first focuses on the growth dynamics, molecular ordering, and molecular orientation of metal phthalocyanine (MPc) molecules, particularly on Si, a substrate which is notoriously difficult to form an organized organic thin film on due to the surface dangling bonds. By deactivating these bonds, the formation of a highly ordered organic molecular thin film becomes possible. Combining scanning tunneling microscopy, scanning tunneling spectroscopy, low-energy electron diffraction, and density functional theory calculations, the growth evolution of MPc molecules ( M = Zn, Cu, Co) from the single molecule level to multilayered films on the deactivated Si(111)-B surface is investigated. Initial tests are centered around thermally evaporated ZnPc. These molecules display a highly-ordered, close-packed, tilted configuration which differs from any known bulk packing motif. The ZnPc molecules are able to diffuse rapidly on the Si surface and preferentially nucleate at Si step-edges. This is followed by the formation of highly-ordered anisotropic stripe structures which grow across the Si terraces, i.e. anisotropic step-flow growth. The step-flow growth mode further impacts the growth by reducing the allowed symmetry of the molecular domains such that thin films with an exclusive in-plane molecular ordering are formed. Additionally, the ZnPc tilted packing motif stabilizes the molecular film, allowing it to maintain this packing for multilayered films, despite the decreasing substrate influence. The strength of the MPc-substrate interaction can be modified by changing the central transition-metal ion within the molecule. Through selective p-d orbital coupling between MPc molecules and the substrate, the degree of orbital coupling can induce modifications in the molecular ordering and orientation of MPc molecules at the interface. The secondary focus of this study is to initiate preliminary experimentation towards understanding how ordered organic molecular thin films can be applied to silicon-based devices that could have a significant impact on the electronics market. Si nanomembrane is a flexible, low-dimensional nanomaterial with electronic properties that are highly sensitive to the interface condition. By merging the knowledge of MPc thin film growth on Si with Si nanomembrane technology, possibilities towards modifying the transport properties of nanomaterials through engineering the organic-inorganic hetero-interface can be explored.

Direct mapping of electrical noise sources in molecular wire-based devices

PubMed Central

Cho, Duckhyung; Lee, Hyungwoo; Shekhar, Shashank; Yang, Myungjae; Park, Jae Yeol; Hong, Seunghun

2017-01-01

We report a noise mapping strategy for the reliable identification and analysis of noise sources in molecular wire junctions. Here, different molecular wires were patterned on a gold substrate, and the current-noise map on the pattern was measured and analyzed, enabling the quantitative study of noise sources in the patterned molecular wires. The frequency spectra of the noise from the molecular wire junctions exhibited characteristic 1/f2 behavior, which was used to identify the electrical signals from molecular wires. This method was applied to analyze the molecular junctions comprising various thiol molecules on a gold substrate, revealing that the noise in the junctions mainly came from the fluctuation of the thiol bonds. Furthermore, we quantitatively compared the frequencies of such bond fluctuations in different molecular wire junctions and identified molecular wires with lower electrical noise, which can provide critical information for designing low-noise molecular electronic devices. Our method provides valuable insights regarding noise phenomena in molecular wires and can be a powerful tool for the development of molecular electronic devices. PMID:28233821

Direct mapping of electrical noise sources in molecular wire-based devices

NASA Astrophysics Data System (ADS)

Cho, Duckhyung; Lee, Hyungwoo; Shekhar, Shashank; Yang, Myungjae; Park, Jae Yeol; Hong, Seunghun

2017-02-01

We report a noise mapping strategy for the reliable identification and analysis of noise sources in molecular wire junctions. Here, different molecular wires were patterned on a gold substrate, and the current-noise map on the pattern was measured and analyzed, enabling the quantitative study of noise sources in the patterned molecular wires. The frequency spectra of the noise from the molecular wire junctions exhibited characteristic 1/f2 behavior, which was used to identify the electrical signals from molecular wires. This method was applied to analyze the molecular junctions comprising various thiol molecules on a gold substrate, revealing that the noise in the junctions mainly came from the fluctuation of the thiol bonds. Furthermore, we quantitatively compared the frequencies of such bond fluctuations in different molecular wire junctions and identified molecular wires with lower electrical noise, which can provide critical information for designing low-noise molecular electronic devices. Our method provides valuable insights regarding noise phenomena in molecular wires and can be a powerful tool for the development of molecular electronic devices.

Spatial mapping of electronic states in κ-(BEDT-TTF)2X using infrared reflectivity

PubMed Central

Sasaki, Takahiko; Yoneyama, Naoki

2009-01-01

We review our recent work on spatial inhomogeneity of the electronic states in the strongly correlated molecular conductors κ-(BEDT-TTF)2X. Spatial mapping of infrared spectra (SMIS) is used for imaging the distribution of the local electronic states. In molecular materials, the infrared response of the specific molecular vibration mode with a strong electron–molecular vibration coupling can reflect the electronic states via the change in the vibration frequency. By spatially mapping the frequency shift of the molecular vibration mode, an electronic phase separation has been visualized near the first-order Mott transition in the bandwidth-controlled organic conductor κ-(BEDT-TTF)2Cu[N(CN)2]Br. In addition to reviewing SMIS of the phase separation, we briefly mention the electronic and optical properties of κ-(BEDT-TTF)2X. PMID:27877279

Electronic states of Ca/PC61BM: Mechanism of low work function metal as interfacial material

NASA Astrophysics Data System (ADS)

Du, Ying-Ying; Chen, Guang-Hua; Li, Wen-Jie; Bai, Xin-Yuan; Lin, De-Qu; Ju, Huanxin; Hu, Shanwei; Xu, Qian; Wang, Yan; Li, Xiong; Zhu, Junfa; Li, Hong-Nian

2018-03-01

We have studied the electronic states at Ca/PC61BM interface using photoemission spectroscopy. It is found that the state of unoccupied molecular orbitals of the top molecular layer (TML) becomes occupied by the electrons transferred from the Ca atoms. The work function of the heavily doped TML of PC61BM film is smaller than that of metal Ca, and thus the contact between the TML and metal Ca is Ohmic. A transition layer (TL) of several molecular layers forms beneath the TML due to the diffusion of the Ca atoms. The TL is conductive and aligns its Fermi level with the negative integer charge transfer level of the interior PC61BM. The built-in electric field in the TL facilitates the electron transport from the interior of the PC61BM film to the TML.

Effect of protonation on the electronic properties of DNA base pairs: applications for molecular electronics.

PubMed

Mallajosyula, Sairam S; Pati, Swapan K

2007-10-11

Protonation of DNA basepairs is a reversible phenomenon that can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen-bonding pattern of the DNA basepairs undergoes a change. We study the effect of protonation on the electronic properties of the DNA basepairs to probe for possible molecular electronics applications. We find that, under mild acidic pH conditions, the A:T basepair shows excellent rectification behavior that is, however, absent in the G:C basepair. The mechanism of rectification has been discussed using a simple chemical potential model. We also consider the noncanonical A:A basepair and find that it can be used as efficient pH dependent molecular switch. The switching action in the A:A basepair is explained in the light of pi-pi interactions, which lead to efficient delocalization over the entire basepair.

Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5-18 eV) electron interactions with DNA.

PubMed

Rezaee, Mohammad; Hunting, Darel J; Sanche, Léon

2014-07-01

The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Absorbed dose and stopping cross section for the Auger electrons of 5-18 eV emitted by(125)I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure-response curves for induction of DNA strand breaks. For a single decay of(125)I within DNA, the Auger electrons of 5-18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm(3) volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.

Electronic structure and normal vibrations of the 1-ethyl-3-methylimidazolium ethyl sulfate ion pair.

PubMed

Dhumal, Nilesh R; Kim, Hyung J; Kiefer, Johannes

2011-04-21

Electronic and structural properties of the ion pair 1-ethyl-3-methylimidazolium ethyl sulfate are studied using density functional methods. Three locally stable conformers of the ion pair complex are considered to analyze molecular interactions between its cation and anion. Manifestations of these interactions in the vibrational spectra are discussed and compared with experimental IR and Raman spectroscopy data. NBO analysis and difference electron density coupled with molecular electron density topography are used to interpret the frequency shifts of the normal vibrations of the ion pair, compared to the free anion and cation. Excitation energies of low-lying singlet excited states of the conformers are also studied. The density functional theory results are found to be in a reasonable agreement with experimental UV/vis absorption spectra.

Transport mirages in single-molecule devices

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

2017-03-01

Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

Effect of chemical substitutions on photo-switching properties of 3-hydroxy-picolinic acid studied by ab initio methods

NASA Astrophysics Data System (ADS)

Rode, Michał F.; Sobolewski, Andrzej L.

2014-02-01

Effect of chemical substitutions to the molecular structure of 3-hydroxy-picolinic acid on photo-switching properties of the system operating on excited-state intramolecular double proton transfer (d-ESIPT) process [M. F. Rode and A. L. Sobolewski, Chem. Phys. 409, 41 (2012)] was studied with the aid of electronic structure theory methods. It was shown that simultaneous application of electron-donating and electron-withdrawing substitutions at certain positions of the molecular frame increases the height of the S0-state tautomerization barrier (ensuring thermal stability of isomers) and facilitates a barrierless access to the S1/S0 conical intersection from the Franck-Condon region of the S1 potential-energy surface. Results of study point to the conclusion that the most challenging issue for practical design of a fast molecular photoswitch based on d-ESIPT phenomenon are to ensure a selectivity of optical excitation of a given tautomeric form of the system.

USING MOLECULAR PROBES TO STUDY INTERFACIAL REDOX REACTION AT FE-BEARING SMECTITES

EPA Science Inventory

The interfacial electron transfer of clay-water systems has a wide range of significance in geochemical and biogeochernical environments. However the mechanism of interfacial electron transport is poorly understood. The electron transfer mechanism at the solid-water interfaces of...

Resonant electron capture by aspartame and aspartic acid molecules.

PubMed

Muftakhov, M V; Shchukin, P V

2016-12-30

The processes for dissociative electron capture are the key mechanisms for decomposition of biomolecules, proteins in particular, under interaction with low-energy electrons. Molecules of aspartic acid and aspartame, i.e. modified dipeptides, were studied herein to define the impact of the side functional groups on peptide chain decomposition in resonant electron-molecular reactions. The processes of formation and decomposition of negative ions of both aspartame and aspartic acid were studied by mass spectrometry of negative ions under resonant electron capture. The obtained mass spectra were interpreted under thermochemical analysis by quantum chemical calculations. Main channels of negative molecular ions fragmentation were found and characteristic fragment ions were identified. The СООН fragment of the side chain in aspartic acid is shown to play a key role like the carboxyl group in amino acids and aliphatic oligopeptides. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S1 states

NASA Astrophysics Data System (ADS)

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Cabellos, José Luis; Yi, John T.; Pratt, David W.; Schmitt, Michael; Merino, Gabriel; Álvarez-Valtierra, Leonardo

2015-09-01

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent -OH and -OCH3 groups plays a major role in these dynamics.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S1 states.

PubMed

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Cabellos, José Luis; Yi, John T; Pratt, David W; Schmitt, Michael; Merino, Gabriel; Álvarez-Valtierra, Leonardo

2015-09-07

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   -OH and   -OCH3 groups plays a major role in these dynamics.

Microhydration Prevents Fragmentation of Uracil and Thymine by Low-Energy Electrons.

PubMed

Kočišek, J; Pysanenko, A; Fárník, M; Fedor, J

2016-09-01

When ionizing radiation passes biological matter, a large number of secondary electrons with very low energies (<3 eV) is produced. It is known that such electrons cause an efficient fragmentation of isolated nucleobases via dissociative electron attachment. We present an experimental study of the electron attachment to microhydrated nucleobases. Our novel approach allows significant control over the hydration of molecules studied in the molecular beam. We directly show for the first time that the presence of a few water molecules suppresses the dissociative channel and leads exclusively to formation of intact molecular and hydrated anions. The suppression of fragmentation is ascribed to caging-like effects and fast energy transfer to the solvent. This is in contrast with theoretical prediction that microhydration strongly enhances the fragmentation of nucleobases. The current observation impacts mechanisms of reductive DNA strand breaks proposed to date on the basis of gas-phase experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Junay, A.; Guézo, S., E-mail: sophie.guezo@univ-rennes1.fr; Turban, P.

We study structural and electronic inhomogeneities in Metal—Organic Molecular monoLayer (OML)—semiconductor interfaces at the sub-nanometer scale by means of in situ Ballistic Electron Emission Microscopy (BEEM). BEEM imaging of Au/1-hexadecanethiols/GaAs(001) heterostructures reveals the evolution of pinholes density as a function of the thickness of the metallic top-contact. Using BEEM in spectroscopic mode in non-short-circuited areas, local electronic fingerprints (barrier height values and corresponding spectral weights) reveal a low-energy tunneling regime through the insulating organic monolayer. At higher energies, BEEM evidences new conduction channels, associated with hot-electron injection in the empty molecular orbitals of the OML. Corresponding band diagrams at buriedmore » interfaces can be thus locally described. The energy position of GaAs conduction band minimum in the heterostructure is observed to evolve as a function of the thickness of the deposited metal, and coherently with size-dependent electrostatic effects under the molecular patches. Such BEEM analysis provides a quantitative diagnosis on metallic top-contact formation on organic molecular monolayer and appears as a relevant characterization for its optimization.« less

Structures and spectroscopic properties of nonperipherally and peripherally substituted metal-free phthalocyanines: a substitution effect study based on density functional theory calculations.

PubMed

Zhong, Aimin; Zhang, Yuexing; Bian, Yongzhong

2010-11-01

The molecular structures, molecular orbitals, atomic charges, electronic absorption spectra, and infrared (IR) and Raman spectra of a series of substituted metal-free phthalocyanine compounds with four (1, 3, 5, 7) or eight (2, 4, 6, 8) methoxyl (1, 2, 5, 6) or methylthio groups (3, 4, 7, 8) on the nonperipheral (1-4) or peripheral positions (5-8) of the phthalocyanine ring are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The calculated structural parameters and simulated electronic absorption and IR spectra are compared with the X-ray crystallography structures and the experimentally observed electronic absorption and IR spectra of the similar molecules, and good agreement between the calculated and experimental results is found. The substitution of the methoxyl or methylthio groups at the nonperipheral positions of the phthalocyanine ring has obvious effects on the molecular structure and spectroscopic properties of the metal-free phthalocyanine. Nonperipheral substitution has a more significant influence than peripheral substitution. The substitution effect increases with an increase in the number of substituents. The methylthio group shows more significant influence than the methoxyl group, despite the stronger electron-donating property of the methoxyl group than the methylthio group. The octa-methylthio-substituted metal-free phthalocyanine compounds have nonplanar structures whose low-lying occupied molecular orbitals and electronic absorption spectra are significantly changed by the substituents. The present systematical study will be helpful for understanding the relationship between structures and properties in phthalocyanine compounds and designing phthalocyanines with typical properties. Copyright © 2010 Elsevier Inc. All rights reserved.

Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites

DTIC Science & Technology

2016-06-08

AFRL-AFOSR-VA-TR-2016-0231 Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites Darren Lipomi...04-2013 to 31-03-2016 4. TITLE AND SUBTITLE Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites 5a... Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites PI: Prof. Darren J. Lipomi 9500 Gilman Dr., Mail Code #0448

Electron Transport and Nonlinear Optical Properties of Substituted Aryldimesityl Boranes: A DFT Study

PubMed Central

Pandith, Altaf Hussain; Islam, Nasarul

2014-01-01

A comprehensive theoretical study was carried out on a series of aryldimesityl borane (DMB) derivatives using Density Functional theory. Optimized geometries and electronic parameters like electron affinity, reorganization energy, frontiers molecular contours, polarizability and hyperpolarizability have been calculated by employing B3PW91/6-311++G (d, p) level of theory. Our results show that the Hammett function and geometrical parameters correlates well with the reorganization energies and hyperpolarizability for the series of DMB derivatives studied in this work. The orbital energy study reveals that the electron releasing substituents increase the LUMO energies and electron withdrawing substituents decrease the LUMO energies, reflecting the electron transport character of aryldimesityl borane derivatives. From frontier molecular orbitals diagram it is evident that mesityl rings act as the donor, while the phenylene and Boron atom appear as acceptors in these systems. The calculated hyperpolarizability of secondary amine derivative of DMB is 40 times higher than DMB (1). The electronic excitation contributions to the hyperpolarizability studied by using TDDFT calculation shows that hyperpolarizability correlates well with dipole moment in ground and excited state and excitation energy in terms of the two-level model. Thus the results of these calculations can be helpful in designing the DMB derivatives for efficient electron transport and nonlinear optical material by appropriate substitution with electron releasing or withdrawing substituents on phenyl ring of DMB system. PMID:25479382

Process for attaching molecular wires and devices to carbon nanotubes and compositions thereof

NASA Technical Reports Server (NTRS)

Yang, Jiping (Inventor); Tour, James M. (Inventor); Bahr, Jeffrey L. (Inventor)

2008-01-01

The present invention is directed towards processes for covalently attaching molecular wires and molecular electronic devices to carbon nanotubes and compositions thereof. Such processes utilize diazonium chemistry to bring about this marriage of wire-like nanotubes with molecular wires and molecular electronic devices.

Same-period emission and recombination in nonsequential double-recombination high-order-harmonic generation

NASA Astrophysics Data System (ADS)

Hansen, Kenneth K.; Madsen, Lars Bojer

2016-05-01

Nonsequential double-recombination (NSDR) high-order-harmonic generation (HHG) is studied in a molecular model system. We observe a unique molecular two-electron effect with a characteristic cutoff in the HHG spectrum at higher energies than what was previously seen for NSDR HHG in atoms. The effect is corroborated with a classical model where it is found that the effect is sensitive to the molecular potential and originates from same-period emission and recombination (SPEAR) of two electrons. The effect persists for intermediate nuclear distances of R ≳8.0 a.u.

The Effects of Molecular Properties on Ready Biodegradation of Aromatic Compounds in the OECD 301B CO2 Evolution Test.

PubMed

He, Mei; Mei, Cheng-Fang; Sun, Guo-Ping; Li, Hai-Bei; Liu, Lei; Xu, Mei-Ying

2016-07-01

Ready biodegradation is the primary biodegradability of a compound, which is used for discriminating whether a compound could be rapidly and readily biodegraded in the natural ecosystems in a short period and has been applied extensively in the environmental risk assessment of many chemicals. In this study, the effects of 24 molecular properties (including 2 physicochemical parameters, 10 geometrical parameters, 6 topological parameters, and 6 electronic parameters) on the ready biodegradation of 24 kinds of synthetic aromatic compounds were investigated using the OECD 301B CO2 Evolution test. The relationship between molecular properties and ready biodegradation of these aromatic compounds varied with molecular properties. A significant inverse correlation was found for the topological parameter TD, five geometrical parameters (Rad, CAA, CMA, CSEV, and N c), and the physicochemical parameter K ow, and a positive correlation for two topological parameters TC and TVC, whereas no significant correlation was observed for any of the electronic parameters. Based on the correlations between molecular properties and ready biodegradation of these aromatic compounds, the importance of molecular properties was demonstrated as follows: geometrical properties > topological properties > physicochemical properties > electronic properties. Our study first demonstrated the effects of molecular properties on ready biodegradation by a number of experiment data under the same experimental conditions, which should be taken into account to better guide the ready biodegradation tests and understand the mechanisms of the ready biodegradation of aromatic compounds.

Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory.

PubMed

Wu, Tao; Sun, Lei; Shi, Qi; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

2016-12-21

Charge mobilities of six DNAs and RNAs have been computed using quantum chemistry calculation combined with the Marcus-Hush theory. Based on this simulation model, we obtained quite reasonable results when compared with the experiment, and the obtained charge mobility strongly depends on the molecular reorganization and electronic coupling. Besides, we find that hole mobilities are larger than electron mobilities no matter in DNAs or in RNAs, and the hole mobility of 2L8I can reach 1.09 × 10 -1 cm 2 V -1 s -1 which can be applied in the molecular wire. The findings also show that our theoretical model can be regarded as a promising candidate for screening DNA- and RNA-based molecular electronic devices.

Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory

NASA Astrophysics Data System (ADS)

Wu, Tao; Sun, Lei; Shi, Qi; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

2016-12-01

Charge mobilities of six DNAs and RNAs have been computed using quantum chemistry calculation combined with the Marcus-Hush theory. Based on this simulation model, we obtained quite reasonable results when compared with the experiment, and the obtained charge mobility strongly depends on the molecular reorganization and electronic coupling. Besides, we find that hole mobilities are larger than electron mobilities no matter in DNAs or in RNAs, and the hole mobility of 2L8I can reach 1.09 × 10-1 cm2 V-1 s-1 which can be applied in the molecular wire. The findings also show that our theoretical model can be regarded as a promising candidate for screening DNA- and RNA-based molecular electronic devices.

Charge transport with single molecules--an electrochemical approach.

PubMed

Li, Chen; Mishchenko, Artem; Pobelov, Ilya; Wandlowski, Thomas

2010-01-01

After an introduction and brief review of charge transport in nanoscale molecular systems we report on experimental studies in gold / (single) molecule / gold junctions at solid / liquid interfaces employing a scanning tunneling microscopy (STM)-based 'break junction' technique. We demonstrate attempts in developing basic relationships between molecular structure, conductance properties and nanoscale electrochemical concepts based on four case studies from our own work. In experiments with alpha, omega-alkanedithiol and biphenyldithiol molecular junctions we address the role of sulfur-gold couplings and molecular conformation, such as gauche defects in the alkyl chains and the torsion angle between two phenyl rings. Combination with quantum chemistry calculations enabled a detailed molecular-level understanding of the electronic structure and transport characteristics of both systems. Employing the concept of 'electrolyte gating' with redox-active molecules, such as thiol-terminated derivatives of viologens (HS-6V6-SH or (HS-6V6)) we demonstrate the construction of symmetric and asymmetric active molecular junctions with transistor- or diode-like behavior upon polarization in an electrochemical environment. The experimental data could be represented quantitatively by the Kutznetsov/Ulstrup model assuming a two-step electron transfer with partial vibration relaxation. Finally, we show that surface-immobilized gold nanoparticles with a diameter of (2.4 +/- 0.5) nm exhibit features of locally addressable multi-state electronic switching upon electrolyte gating, which appears to be reminiscent of a sequential charging through several 'oxidation/reduction states'.

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1981-08-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1980-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

1979-09-01

electronically excited species are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Electronic Excitation in Molecular Collisions: Structural, Dynamic and Kinetic Considerations.

DTIC Science & Technology

electronically excited specied are examined. The problem is studied both in general terms (i.e., the development of the required theoretical framework ) and in application to specific systems. (Author)

Coulomb blockade and charge ordering in a few layers of TTF-TCNQ investigated by low-temperature STM/STS

NASA Astrophysics Data System (ADS)

Jeon, Seokmin; Maksymovych, Petro

In contrast to the vast effort on bulk crystal phases of the prototypical organic charge-transfer complex, TTF-TCNQ, study of low-dimensional phases has been limited to monolayer phases on substrates. In this state, however, none of the physics of the bulk phase is observed owing to the overwhelming effect of the substrate. We investigate the molecular structure and electronic properties of a few layers of TTF-TCNQ grown on Au(111) and Ag(111) using STM/STS at 4.3 K. By decoupling the molecular electronic state from the metal surface, we have made the first observation of the effect of confinement on the electronic properties of TTF-TCNQ. STS reveals a plethora of sharp features due to molecular orbitals, each influenced by charge-transfer between the molecules. We hypothesize the existence of a Mott-insulator state in 3-layer islands, with a Coulomb gap of ~1 eV. In contrast, the corresponding bulk phase is a Peierls insulator with a gap of ~20 meV. The root cause of the nanoscale phase is traced to simultaneous electron confinement and structural frustration, which dramatically modify the energy balance of self-ionization allowing for integer charge transfer. These studies open broad opportunities to explore correlated electron physics in molecular systems. This research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

Solution processed molecular floating gate for flexible flash memories

NASA Astrophysics Data System (ADS)

Zhou, Ye; Han, Su-Ting; Yan, Yan; Huang, Long-Biao; Zhou, Li; Huang, Jing; Roy, V. A. L.

2013-10-01

Solution processed fullerene (C60) molecular floating gate layer has been employed in low voltage nonvolatile memory device on flexible substrates. We systematically studied the charge trapping mechanism of the fullerene floating gate for both p-type pentacene and n-type copper hexadecafluorophthalocyanine (F16CuPc) semiconductor in a transistor based flash memory architecture. The devices based on pentacene as semiconductor exhibited both hole and electron trapping ability, whereas devices with F16CuPc trapped electrons alone due to abundant electron density. All the devices exhibited large memory window, long charge retention time, good endurance property and excellent flexibility. The obtained results have great potential for application in large area flexible electronic devices.

Solution processed molecular floating gate for flexible flash memories

PubMed Central

Zhou, Ye; Han, Su-Ting; Yan, Yan; Huang, Long-Biao; Zhou, Li; Huang, Jing; Roy, V. A. L.

2013-01-01

Solution processed fullerene (C60) molecular floating gate layer has been employed in low voltage nonvolatile memory device on flexible substrates. We systematically studied the charge trapping mechanism of the fullerene floating gate for both p-type pentacene and n-type copper hexadecafluorophthalocyanine (F16CuPc) semiconductor in a transistor based flash memory architecture. The devices based on pentacene as semiconductor exhibited both hole and electron trapping ability, whereas devices with F16CuPc trapped electrons alone due to abundant electron density. All the devices exhibited large memory window, long charge retention time, good endurance property and excellent flexibility. The obtained results have great potential for application in large area flexible electronic devices. PMID:24172758

Structure and electronic properties of Alq3 derivatives with electron acceptor/donor groups at the C4 positions of the quinolate ligands: a theoretical study.

PubMed

Rao, Joshi Laxmikanth; Bhanuprakash, Kotamarthi

2011-12-01

The molecular structures of the ground (S(0)) and first singlet excited (S(1)) states of Alq3 derivatives in which pyrazolyl and 3-methylpyrazolyl groups are substituted at the C4 positions of the 8-hydroxyquinolate ligands as electron acceptors, and piperidinyl and N-methylpiperazinyl groups are substituted at the same positions as electron donors, have been optimized using the B3LYP/6-31G and CIS/6-31G methods, respectively. In order to analyze the electronic transitions in these derivatives, the frontier molecular orbital characteristics were analyzed systematically, and it was found that the highest occupied molecular orbital is localized on the A ligand while the lowest unoccupied molecular orbital is localized on the B ligand in their ground states, similar to what is seen for mer-Alq3. The absorption and emission spectra were evaluated at the TD-PBE0/6-31G level, and it was observed that electron acceptor substitution causes a red-shift in the emission spectra, which is also seen experimentally. The reorganization energies were calculated at the B3LYP/6-31G level and the results show that acceptor/donor substitution has a significant effect on the intrinsic charge mobilities of these derivatives as compared to mer-Alq3.

Electronic Structure of a Self-Assembled Monolayer with Two Surface Anchors: 6-Mercaptopurine on Au(111).

PubMed

Fernández, Cynthia C; Pensa, Evangelina; Carro, Pilar; Salvarezza, Roberto; Williams, Federico J

2018-05-22

The electronic structure of aromatic and aliphatic thiols on Au(111) has been extensively studied in relation to possible applications in molecular electronics. In this work, the effect on the electronic structure of an additional anchor to the S-Au bond using 6-mercaptopurine as a model system has been investigated. Results from X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and density functional theory (DFT) confirm that this molecule adsorbs on Au(111) with S-Au and iminic N-Au bonds. Combined ultraviolet photoelectron spectroscopy and DFT data reveal that formation of the 6MP self-assembled monolayer generates a molecular dipole perpendicular to the surface, with negative charges residing at the metal/monolayer interface and positive charges at the monolayer/vacuum interface, which lowers the substrate work function. Scanning tunneling microscopy shows two surface molecular domains: a well-ordered rectangular lattice where molecules are tilted on average 30° with respect to the substrate and aligned 6MP islands where molecules are standing upright. Finally, we found a new electronic state located at -1.7 eV with respect to the Fermi level that corresponds to a localized π molecular state, while the state corresponding to the N-Au bond is hybridized with Au d electrons and stabilized at much lower energies (-3 eV).

Solvation of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

Jalbout, Abraham F.

This work considers the ability of hydrogen fluoride (HF) to solvate excess electrons located on cyclic hydrocarbon surfaces. The principle applied involves the formation of systems in which excess electrons can be stabilized not only on concentrated molecular surface charge pockets but also by HF. Recent studies have shown that OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), at the same time, the hydrogen atoms on the opposite side of this surface form a pocket of positive charge can attract the excess electron. This density can be further stabilized by the addition of an HF molecule that can form an 'anion with an internally solvated electron' (AISE) state. These systems are shown to be stable with respect to vertical electron detachment (VDE).

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

Molecular processes in a high temperature shock layer

NASA Technical Reports Server (NTRS)

Guberman, S. L.

1984-01-01

Models of the shock layer encountered by an Aeroassisted Orbital Transfer Vehicle require as input accurate cross sections and rate constants for the atomic and molecular processes that characterize the shock radiation. From the estimated atomic and molecular densities in the shock layer and the expected residence time of 1 m/s, it can be expected that electron-ion collision processes will be important in the shock model. Electron capture by molecular ions followed by dissociation, e.g., O2(+) + e(-) yields 0 + 0, can be expected to be of major importance since these processes are known to have high rates (e.g., 10 to the -7th power cu/cm/sec) at room temperature. However, there have been no experimental measurements of dissociative recombination (DR) at temperatures ( 12000K) that are expected to characterize the shock layer. Indeed, even at room temperature, it is often difficult to perform experiments that determine the dependence of the translational energy and quantum yields of the product atoms on the electronic and vibrational state of the reactant molecular ions. Presented are ab initio quantum chemical studies of DR for molecular ions that are likely to be important in the atmospheric shock layer.

Visualizing electron dynamics in organic materials: Charge transport through molecules and angular resolved photoemission

NASA Astrophysics Data System (ADS)

Kümmel, Stephan

Being able to visualize the dynamics of electrons in organic materials is a fascinating perspective. Simulations based on time-dependent density functional theory allow to realize this hope, as they visualize the flow of charge through molecular structures in real-space and real-time. We here present results on two fundamental processes: Photoemission from organic semiconductor molecules and charge transport through molecular structures. In the first part we demonstrate that angular resolved photoemission intensities - from both theory and experiment - can often be interpreted as a visualization of molecular orbitals. However, counter-intuitive quantum-mechanical electron dynamics such as emission perpendicular to the direction of the electrical field can substantially alter the picture, adding surprising features to the molecular orbital interpretation. In a second study we calculate the flow of charge through conjugated molecules. The calculations show in real time how breaks in the conjugation can lead to a local buildup of charge and the formation of local electrical dipoles. These can interact with neighboring molecular chains. As a consequence, collections of ''molecular electrical wires'' can show distinctly different characteristics than ''classical electrical wires''. German Science Foundation GRK 1640.

Towards molecular electronics with large-area molecular junctions.

PubMed

Akkerman, Hylke B; Blom, Paul W M; de Leeuw, Dago M; de Boer, Bert

2006-05-04

Electronic transport through single molecules has been studied extensively by academic and industrial research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes, break junctions, metallic crossbars and nanopores. For technological applications, molecular tunnel junctions must be reliable, stable and reproducible. The conductance per molecule, however, typically varies by many orders of magnitude. Self-assembled monolayers (SAMs) may offer a promising route to the fabrication of reliable devices, and charge transport through SAMs of alkanethiols within nanopores is well understood, with non-resonant tunnelling dominating the transport mechanism. Unfortunately, electrical shorts in SAMs are often formed upon vapour deposition of the top electrode, which limits the diameter of the nanopore diodes to about 45 nm. Here we demonstrate a method to manufacture molecular junctions with diameters up to 100 microm with high yields (> 95 per cent). The junctions show excellent stability and reproducibility, and the conductance per unit area is similar to that obtained for benchmark nanopore diodes. Our technique involves processing the molecular junctions in the holes of a lithographically patterned photoresist, and then inserting a conducting polymer interlayer between the SAM and the metal top electrode. This simple approach is potentially low-cost and could pave the way for practical molecular electronics.

Tracing the Fingerprint of Chemical Bonds within the Electron Densities of Hydrocarbons: A Comparative Analysis of the Optimized and the Promolecule Densities.

PubMed

Keyvani, Zahra Alimohammadi; Shahbazian, Shant; Zahedi, Mansour

2016-10-18

The equivalence of the molecular graphs emerging from the comparative analysis of the optimized and the promolecule electron densities in two hundred and twenty five unsubstituted hydrocarbons was recently demonstrated [Keyvani et al. Chem. Eur. J. 2016, 22, 5003]. Thus, the molecular graph of an optimized molecular electron density is not shaped by the formation of the C-H and C-C bonds. In the present study, to trace the fingerprint of the C-H and C-C bonds in the electron densities of the same set of hydrocarbons, the amount of electron density and its Laplacian at the (3, -1) critical points associated with these bonds are derived from both optimized and promolecule densities, and compared in a newly proposed comparative analysis. The analysis not only conforms to the qualitative picture of the electron density build up between two atoms upon formation of a bond in between, but also quantifies the resulting accumulation of the electron density at the (3, -1) critical points. The comparative analysis also reveals a unified mode of density accumulation in the case of 2318 studied C-H bonds, but various modes of density accumulation are observed in the case of 1509 studied C-C bonds and they are classified into four groups. The four emerging groups do not always conform to the traditional classification based on the bond orders. Furthermore, four C-C bonds described as exotic bonds in previous studies, for example the inverted C-C bond in 1,1,1-propellane, are naturally distinguished from the analysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron Transport through Porphyrin Molecular Junctions

NASA Astrophysics Data System (ADS)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis over a large set of measurements. In this thesis, I focus on two factors that would affect the electron transport through the porphyrin molecules, namely, the metal ion center, and the deprotection of the end groups. The effect of metal ion center is studied by comparing the conductance of an iron (III) porphyrin (protected) to that of a free base porphyrin (protected). The in-situ deprotection of the molecules before forming the junctions is completed to study the effect of the molecular-electrode interaction. The first factor studied, that is, the metal ion center in the porphyrin molecule, show that the conductance for iron (III) porphyrin (protected) is 3.74 x10-5 G0, and the conductance for the free base porphyrin (protected) is 4.73x10-5 G0 , where G0 = e2 / pih = (25.8kO)-1 is the quantized unit of electrical conductance. Through our collaborative efforts, first principles calculations carried out by our collaborators for the molecular levels of an isolated molecule (without electrodes) show that the energy levels of an iron (III) porphyrin molecule are slightly shifted compared to that of the free base porphyrin. For the free base porphyrin, the highest occupied molecular orbital (HOMO) level (-4.952 eV) lies between the chemical potentials of the substrate (-4.7 eV) and the STM tip (-5.1 eV). This level serves as a channel for electron transport. For the iron (III) porphyrin, the HOMO is at -5.306 eV, which is not in between the chemical potentials of the substrate. Therefore, a significantly smaller conductance is expected for the iron (III) porphyrin compared to the conductance of a free base porphyrin, because of the lack of the electron transport channel. However, the conductance measured from G-S experiments is comparable, i.e. 3.74 x10-5 G0 for iron (III) porphyrin and 4.73x10-5 G0 for free base porphyrin. This suggests that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting may significantly affect the electron transport through molecular junctions. The second factor studied, that is, the deprotection of the porphyrin end groups (acetylthio, -SCOCH3), was completed in-situ for the free base porphyrin through the reaction of the acetylthio with sulfuric acid at 35° Celsius for 3 hours. MALDI spectroscopy confirms that two additional deprotected porphyrin species are formed by deprotection, with protonated (MH+) molecular masses of 721 and 679, corresponding to a partially deprotected porphyrin (i.e. only one of the two end groups deprotected), and a fully deprotected porphyrin molecule. Along with the un-reacted acetyl protected porphyrin, a total of 3 porphyrin species are in the solution. This solution is used for self-assembly on a gold/mica surface. The thickness of the in-situ deprotected SAM is determined to be ˜1.7 nm, confirming a relatively upright molecular orientation (54.0°-63.5° between the substrate surface and the molecule), compared to a thickness of ˜1.5 nm for the protected SAM that has a more flat-lying molecular orientation (˜45.6° between the substrate surface and the molecule). From G-S measurements on SAMs prepared by in-situ deprotection, junctions with lower conductance steps at mid 10-5 G0 and junctions with higher conductance steps around 10-4 G 0 are observed. Supported by computational modeling from our collaborating research group, we associate the lower conductance steps to junctions based on the protected form of thiols at the tip-molecule interface, and the higher conductance steps to the deprotected form of the thiol contacts. We suggest that the reduced conductance in the protected porphyrin originates from the presence of the acetyl end groups (-COCH3), rather than from the elongation of the sulfur-gold (S-Au) bonds at the tip-molecule interface. By studying these two factors, I expect this work to provide insights into electron transport through molecules or metal-molecule-metal junctions, and in applications related to integrating molecules as functional units in electronic devices. Future work related to this thesis may include the molecular conductance based on reduction-oxidation (redox) properties of iron ligated porphyrins for the application of molecular switches and molecular memory elements.

Computational Studies on Optoelectronic and Nonlinear Properties of Octaphyrin Derivatives

PubMed Central

Islam, Nasarul; Lone, Irfan H.

2017-01-01

The electronic and nonlinear optical (NLO) properties of octaphyrin derivatives were studied by employing the DFT/TDFT at CAM-B3LYP/6-311++G (2d, 2p) level of the theory. Thiophene, phenyl, methyl and cyano moieties were substituted on the molecular framework of octaphyrin core, in order to observe the change in optoelectronic and nonlinear response of these systems. The frontier molecular orbital studies and values of electron affinity reveals that the studied compounds are stable against the oxygen and moisture present in air. The calculated ionization energies, adiabatic electron affinity and reorganization energy values indicate that octaphyrin derivatives can be employed as effective n-type material for Organic Light Emitting Diodes (OLEDs). This character shows an enhancement with the introduction of an electron withdrawing group in the octaphyrin framework. The polarizability and hyperpolarizability values of octaphyrin derivatives demonstrate that they are good candidates for NLO devices. The nonlinear response of these systems shows enhancement on the introduction of electron donating groups on octaphyrin moiety. However, these claims needs further experimental verification. PMID:28321394

Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

NASA Astrophysics Data System (ADS)

Langhoff, P. W.; Winstead, C. L.

Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

Studies of Copper, Silver, and Gold Cluster Anions: Evidence of Electronic Shell Structure.

NASA Astrophysics Data System (ADS)

Pettiette, Claire Lynn

A new Ultraviolet Magnetic Time-of-Flight Photoelectron Spectrometer (MTOFPES) has been developed for the study of the electronic structure of clusters produced in a pulsed supersonic molecular beam. This is the first technique which has been successful in probing the valence electronic states of metal clusters. The ultraviolet photoelectron spectra of negative cluster ions of the noble metals have been taken at several different photon energies. These are presented along with the electron affinity and HOMO-LUMO gap measurements for Cu_6^- to Cu_ {41}^-, using 4.66 eV and 6.42 eV detachment energies; Ag_3^- to Ag_{21}^-, using 6.42 eV detachment energy; and Au_3^ - to Au_{21}^-, using 6.42 eV and 7.89 eV detachment energies. The spectra provide the first detailed probes of the s valence electrons of the noble metal clusters. In addition, the 6.42 eV and 7.89 eV spectra probe the first one to two electron volts of the molecular orbitals of the d valence electrons of copper and gold clusters. The electron affinity and HOMO-LUMO gap measurements of the noble metal clusters agree with the predictions of the ellipsoidal shell model for mono-valent metal clusters. In particular, cluster numbers 8, 20, and 40--which correspond to the spherical shell closings of this model--have low electron affinities and large HOMO-LUMO gaps. The spectra of the gold cluster ions indicate that the molecular orbital energies of the cluster valence electrons are more widely spaced for gold than for copper or silver. This is to be expected for the heavy atom clusters when relativistic effects are taken into account.

Epitaxial Growth of an Organic p-n Heterojunction: C60 on Single-Crystal Pentacene.

PubMed

Nakayama, Yasuo; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Tsuruta, Ryohei; Hinderhofer, Alexander; Gerlach, Alexander; Broch, Katharina; Belova, Valentina; Frank, Heiko; Yamamoto, Masayuki; Niederhausen, Jens; Glowatzki, Hendrik; Rabe, Jürgen P; Koch, Norbert; Ishii, Hisao; Schreiber, Frank; Ueno, Nobuo

2016-06-01

Designing molecular p-n heterojunction structures, i.e., electron donor-acceptor contacts, is one of the central challenges for further development of organic electronic devices. In the present study, a well-defined p-n heterojunction of two representative molecular semiconductors, pentacene and C60, formed on the single-crystal surface of pentacene is precisely investigated in terms of its growth behavior and crystallographic structure. C60 assembles into a (111)-oriented face-centered-cubic crystal structure with a specific epitaxial orientation on the (001) surface of the pentacene single crystal. The present experimental findings provide molecular scale insights into the formation mechanisms of the organic p-n heterojunction through an accurate structural analysis of the single-crystalline molecular contact.

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

PubMed

Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang

2015-08-03

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing vibrational activities, electronic properties, molecular docking and Hirshfeld surfaces analysis of 4-chlorophenyl ({[(1E)-3-(1H-imidazol-1-yl)-1-phenylpropylidene]amino}oxy)methanone: A promising anti-Candida agent

NASA Astrophysics Data System (ADS)

Jayasheela, K.; Al-Wahaibi, Lamya H.; Periandy, S.; Hassan, Hanan M.; Sebastian, S.; Xavier, S.; Daniel, Joseph C.; El-Emam, Ali A.; Attia, Mohamed I.

2018-05-01

The promising anti-Candida agent, 4-chlorophenyl ({[1E-3(1H-imidazole-1-yl)-1-phenylpropylidene}oxy)methanone (4-CPIPM) was comprehensively characterized by FT-IR, FT-Raman, UV, as well as 1H and 13C spectroscopic techniques. The theoretical calculations in the current study utilized Gaussian 09 W software with DFT approach of the B3LYP/6-311++G(d,p) method. The experimental X-ray diffraction data of the 4-CPIPM molecule were compared with the optimized structure and showed well agreement. Intermolecular electronic interactions and their stabilization energies have been analyzed by natural bond orbital method. Potential energy distribution confirmed the normal fundamental mode of vibration with the aid of MOLVIB software. The chemical shift values of the 1H and 13C spectra of the title compound were computed using gauge independent atomic orbital and the results were compared with the experimental values. The time-dependent density function theory method was used to predict the electronic, absorption wavelength and frontier molecular orbital energies. The HOMO-LUMO plots proved the charge transfer in the molecular system of the title compound through conjugated paths. The molecular electrostatic potential analysis provided the electrophilic and nucleophilic reactive sites in the title molecule which have been analyzed using Hirshfeld surface and two dimensions fingerprint plots. Non covalent interactions were also studied using reduced density gradient analysis and color filled electron density diagram. Molecular docking studies of the ligand-protein interactions along with their binding energies were carried out aiming to explain the potent anti-Candida activity of the title molecule.

Nanoplasma Formation by High Intensity Hard X-rays

PubMed Central

Tachibana, T.; Jurek, Z.; Fukuzawa, H.; Motomura, K.; Nagaya, K.; Wada, S.; Johnsson, P.; Siano, M.; Mondal, S.; Ito, Y.; Kimura, M.; Sakai, T.; Matsunami, K.; Hayashita, H.; Kajikawa, J.; Liu, X.-J.; Robert, E.; Miron, C.; Feifel, R.; Marangos, J. P.; Tono, K.; Inubushi, Y.; Yabashi, M.; Son, S.-K.; Ziaja, B.; Yao, M.; Santra, R.; Ueda, K.

2015-01-01

Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo- and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays. PMID:26077863

A new look into the quantum chemical and spectroscopic investigations of 5-chloro-1-methyl-4-nitroimidazole.

PubMed

Arjunan, V; Raj, Arushma; Anitha, R; Mohan, S

2014-05-05

Optimised geometrical structural parameters, harmonic vibrational frequencies, natural bonding orbital analysis and frontier molecular orbitals are determined by B3LYP and B3PW91 methods. The exact geometry of 5-chloro-1-methyl-4-nitroimidazole is determined through conformational analysis. The experimentally observed infrared and Raman bands have been assigned and analysed. The (13)C and (1)H NMR chemical shifts of the compound are investigated. The total electron density and molecular electrostatic potentials are determined. The electrostatic potential (electron+nuclei) distribution, molecular shape, size and dipole moments of the molecule have been displayed. The energies of the frontier molecular orbitals and LUMO-HOMO energy gap are measured. The possible electronic transitions of the molecule are studied by TD-DFT method along with the UV-Visible spectrum. The structure-activity relationship of the compound is also investigated by conceptual DFT methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Kondo blockade due to quantum interference in single-molecule junctions

PubMed Central

Mitchell, Andrew K.; Pedersen, Kim G. L.; Hedegård, Per; Paaske, Jens

2017-01-01

Molecular electronics offers unique scientific and technological possibilities, resulting from both the nanometre scale of the devices and their reproducible chemical complexity. Two fundamental yet different effects, with no classical analogue, have been demonstrated experimentally in single-molecule junctions: quantum interference due to competing electron transport pathways, and the Kondo effect due to entanglement from strong electronic interactions. Here we unify these phenomena, showing that transport through a spin-degenerate molecule can be either enhanced or blocked by Kondo correlations, depending on molecular structure, contacting geometry and applied gate voltages. An exact framework is developed, in terms of which the quantum interference properties of interacting molecular junctions can be systematically studied and understood. We prove that an exact Kondo-mediated conductance node results from destructive interference in exchange-cotunneling. Nonstandard temperature dependences and gate-tunable conductance peaks/nodes are demonstrated for prototypical molecular junctions, illustrating the intricate interplay of quantum effects beyond the single-orbital paradigm. PMID:28492236

EDITORIAL: Focus on Molecular Electronics FOCUS ON MOLECULAR ELECTRONICS

NASA Astrophysics Data System (ADS)

Scheer, Elke; Reineker, Peter

2008-06-01

The notion 'molecular electronics' has been used more frequently since the 1970s and summarizes a series of physical phenomena and ideas for their application in connection with organic molecules, oligomers, polymers, organic aggregates and solids. The properties studied in this field were connected to optical and electrical phenomena, such as optical absorption, fluorescence, nonlinear optics, energy transport, charge transfer, electrical conductance, and electron and nuclear spin-resonance. The final goal was and is to build devices which can compete or surpass some aspects of inorganic semiconductor devices. For example, on the basis of organic molecules there exist rectifiers, transistors, molecular wires, organic light emitting diodes, elements for photovoltaics, and displays. With respect to applications, one aspect of the organic materials is their broad variability and the lower effort and costs for their processability. The step from microstructures to the investigation of nanostructures is a big challenge also in this field and has lead to what nowadays is called molecular electronics in its narrow sense. In this field the subjects of the studies are often single molecules, e.g. single molecule optical spectroscopy, electrical conductance, i.e. charge transport through a single molecule, the influence of vibrational degrees of freedom, etc. A challenge here is to provide the techniques for addressing in a reproducible way the molecular scale. In another approach small molecular ensembles are studied in order to avoid artefacts from particular contact situations. The recent development of the field is presented in [1-8]. In this Focus Issue we present new results in the field of 'molecular electronics', both in its broad and specialized sense. One of the basic questions is the distribution of the energy levels responsible for optical absorption on the one hand and for the transport of charge on the other. A still unanswered question is whether the Wannier exciton model applies in which the excitation is distributed over several molecules or whether a good description is given by the Frenkel exciton model with the electron and the whole being localized at the same molecular unit. In organic semiconductors the charge transport usually occurs on the basis of holes because of the presence of many defects giving rise to a localization of the electrons. It is therefore a challenge to produce materials with both positive and negative mobile charge carriers. In the 1990s V M Agranovich introduced the idea of hybrid excitons, i.e. of nanostructured materials consisting of both organic and inorganic semiconductors. At the interface between the organic and inorganic parts new excitons can appear, being a superposition of both Frenkel and Wannier excitons and having both the high oscillator strength of the Frenkel and the large optical nonlinearity of the Wannier exciton. The problem is to find optimum combinations of the organic and inorganic parts to enable the hybrid structure concept to work. Micro-cavities also play an important role in the investigation of organic materials resulting in a new state (polariton) as the superposition of a photon and an exciton because of the large exciton-photon interaction. A similar excitation arises because of the interaction between plasmons and photons. A special geometrical shape of a nano-cavity increases the interaction between the electromagnetic radiation and a dipole sitting in the cavity. The interaction between vibronic degrees of freedom and electronic excitations plays an important role for various phenomena such as nonlinear processes, the question of coherence, information on the shape of a potential hypersurface, etc. With the help of femtosecond laser pulses, detailed information on such vibrations can be obtained. Also of great importance is the investigation of the energy transfer in artificial light-harvesting systems, e.g. in dendrimers. Finally the combination of experimental and theoretical investigations allows for a comparison of the spectra of two molecules with the same backbone (tetracene and rubrene). The transport of charge through a molecule occurs possibly in a stationary, but at any rate in a non-equilibrium situation. The study of dissipation in such situations requires special approaches, both in theory and in experiments. One key issue is the understanding of the role of the microscopic phenomena such as the excitation of vibrational modes and their macroscopic outcome, i.e. the dissipation. This topic is addressed in several contributions both theoretically and experimentally. From the theoretical side, for the investigation of the heat production during the electron transfer, non-equilibrium Green's functions have been utilized. In another contribution a combination of the non-equilibrium Green's function technique together with the density functional method has been developed for the calculation of the elastic and inelastic electronic transport. To calculate the transport of indistinguishable particles a path integral Monte Carlo approach has been put forward. In single-molecule transistors the gate-voltage dependence on the Kondo temperature and an accompanying strong Coulomb blockade can be explained by taking into account a strong electron-vibron interaction including anharmonicities of the molecular potential surface. The transport of charges is heavily influenced by disorder. The case of static disorder is investigated for linear chains, carbon nanotubes and graphene ribbons. Finally it is shown that the charge transport through a single energy level coupled to a localized vibrational mode and two leads shows hysteretic effects which could possibly be used in a memory device. For applications the control of the current through a molecular junction is considered theoretically. Two possible mechanisms are discussed: the control via coherent destruction using predefined ultrafast laser pulses and the formation of laser pulses using optimal control theory. A group of contributions is dedicated to the study of electronic transport through molecules using various techniques ranging from scanning-tunnelling methods via controllable break-junctions to printing techniques and molecular networks. The molecules under study can be classified into two main groups. On the one hand the functionalization of aromatic or alkane molecules with thiols is used for establishing chemical binding to metal electrodes; in the other set of experiments fullerenes are used as model systems for studying the influence of orientation and heat dissipation. Molecular conducting networks are important under various aspects. Such networks are formed by an array of gold nanoparticles connected by conjugated molecular chains with one or two thiol ends and conduction investigations are performed under various conditions. A careful investigation of the experimental conditions is necessary when comparing conductance measurements using the break junction method. For example there are results demonstrating that several molecular junctions are formed in parallel between the electrodes. Other experiments use different materials for the junctions and measurements are performed at various temperatures. The transport of charge through an alkane-monolayer is investigated using micro-transfer printing to establish contacts without shorts. It is shown that both tunnelling between the electrodes and transport through the states of the molecules contribute to the conductance. C60 plays a role in various fields of molecular electronics. One aspect is the conductance through the molecule as a function of the orientation of the molecule on the surface. It is found that there is a strong orientation dependence of the transport on Au(111) surfaces and that it is almost independent on a Cu(100) surface. A further important phenomenon is the heating and cooling of C60 during charge transport depending on the surface of C60 adsorption. The differences are ascribed to the amount of charge transfer into C60 upon adsorption on different surfaces. In summary, in the field of molecular electronics new materials and structures are developed and investigated, both with respect to a basic understanding of the materials and their compositions and with respect to possible applications in electronics. While in the field of molecular electronics on the microscale the techniques are well established, they still need to be refined in the field of nano-molecular electronics. Nevertheless, both subfields share some of the most challenging questions: e.g. the problems of charge and energy transport, of excitations and the formation of new quasi-particles. Another question is the role of vibrational degrees of freedom, where on the one hand one has to cope with the unavoidable effect of heat dissipation. On the other hand, vibrational excitations are intimately connected to the individual molecule under study and thus offer the possibility to be used in functional devices based on intrinsic molecular properties. This Focus Issue represents a snapshot of the state of the art of this emerging field in the first half of 2008. We expect that the fast development which the research has undergone in recent years will even speed up in the near future. References [1] Pope M and Sweenberg Ch E 1999 Electronic Processes in Organic Crystals and Polymers 2nd edn (Oxford: Oxford University Press) [2] Silinsh E A and Capek V 1994 Organic Molecular Crystals (New York: AIP Press) [3] Agranovich V M and La Rocca G C 2002 Organic Nanostructures: Science and Applications, Proc. Int. School of Physics 'Enrico Fermi', Course CXLIX (Amsterdam: IOS Press) [4] Schwoerer M and Wolf H C 2007 Organic Molecular Solids (Weinheim: Wiley-VCH) [5] Cuniberti G, Fagas G and Richter K (ed) 2005 Introducing Molecular Electronics, Lecture Notes in Physics (Berlin: Springer) [6] Reed M and Lee T 2003 Molecular Nanoelectronics (Stevenson Ranch, CA: American Scientific Publishers) [7] Petty M C 2007 Molecular Electronics, (Weinheim: Wiley-VCH) [8] 2006 Molecular Wires and Nanoscale Conductors Faraday Discuss. 131 1-420 Focus on Molecular Electronics Contents Model of mixed Frenkel and charge-transfer excitons in donor-acceptor molecular crystals: investigation of vibronic spectra I J Lalov, C Warns and P Reineker Suppressing the current through molecular wires: comparison of two mechanisms GuangQi Li, Michael Schreiber and Ulrich Kleinekathöfer Charge-memory effect in a polaron model: equation-of-motion method for Green functions Pino D'Amico, Dmitry A Ryndyk, Gianaurelio Cuniberti and Klaus Richter Determination of transport levels of organic semiconductors by UPS and IPS S Krause, M B Casu, A Schöll and E Umbach Electrical characterization of alkane monolayers using micro-transfer printing: tunneling and molecular transport C Kreuter, S Bächle, E Scheer and A Erbe Correlated charge transfer along molecular chains L Mühlbacher and J Ankerhold Non-equilibrium Green's functions in density functional tight binding: method and applications A Pecchia, G Penazzi, L Salvucci and A Di Carlo Asymmetric Coulomb blockade and Kondo temperature of single-molecule transistors Florian Elste and Felix von Oppen Electron-phonon scattering in molecular electronics: from inelastic electron tunnelling spectroscopy to heating effects Alessio Gagliardi, Giuseppe Romano, Alessandro Pecchia, Aldo Di Carlo, Thomas Frauenheim and Thomas A Niehaus Interlinking Au nanoparticles in 2D arrays via conjugated dithiolated molecules Jianhui Liao, Markus A Mangold, Sergio Grunder, Marcel Mayor, Christian Schönenberger and Michel Calame Conductance values of alkanedithiol molecular junctions M Teresa González, Jan Brunner, Roman Huber, Songmei Wu, Christian Schönenberger and Michel Calame Particularities of surface plasmon-exciton strong coupling with large Rabi splitting C Symonds, C Bonnand, J C Plenet, A Bréhier, R Parashkov, J S Lauret, E Deleporte and J Bellessa Excitonic and vibrational nonlinear processes in a polydiacetylene studied by a few-cycle pulse laser T Kobayashi, I Iwakura and A Yabushita Correlations of instantaneous transition energy and intensity of absorption peaks during molecular vibration: toward potential hyper-surface Takayoshi Kobayashi and Zhuan Wang Diffusion and localization in carbon nanotubes and graphene nanoribbons Norbert Nemec, Klaus Richter and Gianaurelio Cuniberti Molecular electronics in junctions with energy disorder Franz J Kaiser, Peter Hänggi and Sigmund Kohler Spatially resolved conductance of oriented C60 G Schull, N Néel, M Becker, J Kröger and R Berndt A design for an optical-nanocavity optimized for use with surface-bound light-emitting materials A M Adawi and D G Lidzey Electronic coupling of optical excitations in organic/inorganic semiconductor hybrid structures S Blumstengel, S Sadofev and F Henneberger The relation between the symmetry of vibrational modes and the potential curve displacement associated with electronic transition studied by using real-time vibrational spectroscopy Takayoshi Kobayashi, Zhuan Wang and Izumi Iwakura Lithographic mechanical break junctions for single-molecule measurements in vacuum: possibilities and limitations Christian A Martin, Dapeng Ding, Herre S J van der Zant and Jan M van Ruitenbeek Strong exciton-photon coupling at room temperature in microcavities containing two-dimensional layered perovskite compounds G Lanty, A Bréhier, R Parashkov, J S Lauret and E Deleporte Bipolar transport in organic field-effect transistors: organic semiconductor blends versus contact modification Andreas Opitz, Michael Kraus, Markus Bronner, Julia Wagner and Wolfgang Brütting Resonant heating and substrate-mediated cooling of a single C60 molecule in a tunnel junction Gunnar Schulze, Katharina J Franke and Jose Ignacio Pascual

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2017-02-09

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.

Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5–18 eV) electron interactions with DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezaee, Mohammad, E-mail: Mohammad.Rezaee@USherbrooke.ca; Hunting, Darel J.; Sanche, Léon

2014-07-15

Purpose: The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Methods: Absorbed dose and stopping cross section for the Auger electrons of 5–18 eV emitted by{sup 125}I withinmore » DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure–response curves for induction of DNA strand breaks. Results: For a single decay of{sup 125}I within DNA, the Auger electrons of 5–18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm{sup 3} volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Conclusions: Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.« less

Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5–18 eV) electron interactions with DNA

PubMed Central

Rezaee, Mohammad; Hunting, Darel J.; Sanche, Léon

2015-01-01

Purpose The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Methods Absorbed dose and stopping cross section for the Auger electrons of 5–18 eV emitted by 125I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure–response curves for induction of DNA strand breaks. Results For a single decay of 125I within DNA, the Auger electrons of 5–18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm3 volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Conclusions Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide. PMID:24989405

Synthesis of one-dimensional metal-containing insulated molecular wire with versatile properties directed toward molecular electronics materials.

PubMed

Masai, Hiroshi; Terao, Jun; Seki, Shu; Nakashima, Shigeto; Kiguchi, Manabu; Okoshi, Kento; Fujihara, Tetsuaki; Tsuji, Yasushi

2014-02-05

We report, herein, the design, synthesis, and properties of new materials directed toward molecular electronics. A transition metal-containing insulated molecular wire was synthesized through the coordination polymerization of a Ru(II) porphyrin with an insulated bridging ligand of well-defined structure. The wire displayed not only high linearity and rigidity, but also high intramolecular charge mobility. Owing to the unique properties of the coordination bond, the interconversion between the monomer and polymer states was realized under a carbon monoxide atmosphere or UV irradiation. The results demonstrated a high potential of the metal-containing insulated molecular wire for applications in molecular electronics.

Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

PubMed

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

Gate-controlled current and inelastic electron tunneling spectrum of benzene: a self-consistent study.

PubMed

Liang, Y Y; Chen, H; Mizuseki, H; Kawazoe, Y

2011-04-14

We use density functional theory based nonequilibrium Green's function to self-consistently study the current through the 1,4-benzenedithiol (BDT). The elastic and inelastic tunneling properties through this Au-BDT-Au molecular junction are simulated, respectively. For the elastic tunneling case, it is found that the current through the tilted molecule can be modulated effectively by the external gate field, which is perpendicular to the phenyl ring. The gate voltage amplification comes from the modulation of the interaction between the electrodes and the molecules in the junctions. For the inelastic case, the electron tunneling scattered by the molecular vibrational modes is considered within the self-consistent Born approximation scheme, and the inelastic electron tunneling spectrum is calculated.

Rotationally resolved electronic spectroscopy study of the conformational space of 3-methoxyphenol

NASA Astrophysics Data System (ADS)

Wilke, Martin; Schneider, Michael; Wilke, Josefin; Ruiz-Santoyo, José Arturo; Campos-Amador, Jorge J.; González-Medina, M. Elena; Álvarez-Valtierra, Leonardo; Schmitt, Michael

2017-07-01

Conformational preferences are determined by (de-)stabilization effects like intramolecular hydrogen bonds or steric hindrance of adjacent substituents and thus, influence the stability and reactivity of the conformers. In the present contribution, we investigate the conformational landscape of 3-methoxyphenol using a combination of high resolution electronic spectroscopy and ab initio calculations. Three of the four possible conformational isomers were characterized in their electronic ground and lowest excited singlet states on the basis of their rotational constants and other molecular parameters. The absence of one conformer in molecular beam studies can be explained by its non-planar structure in the excited state, which leads to a vanishingly small Franck-Condon factor of the respective origin excitation.

Silicon oxide: a non-innocent surface for molecular electronics and nanoelectronics studies.

PubMed

Yao, Jun; Zhong, Lin; Natelson, Douglas; Tour, James M

2011-02-02

Silicon oxide (SiO(x)) has been widely used in many electronic systems as a supportive and insulating medium. Here, we demonstrate various electrical phenomena such as resistive switching and related nonlinear conduction, current hysteresis, and negative differential resistance intrinsic to a thin layer of SiO(x). These behaviors can largely mimic numerous electrical phenomena observed in molecules and other nanomaterials, suggesting that substantial caution should be paid when studying conduction in electronic systems with SiO(x) as a component. The actual electrical phenomena can be the result of conduction from SiO(x) at a post soft-breakdown state and not the presumed molecular or nanomaterial component. These electrical properties and the underlying mechanisms are discussed in detail.

Electronic Spectra from Molecular Dynamics: A Simple Approach.

DTIC Science & Technology

1983-10-01

82.30.Cr. 33.20K. S2.40.1s The authors provided phototypeset copy for this paper using REFER TlL EON, TOFF On UNIX I ELECTRONIC SPECTRA FROM MOLECULAR...Alamos National Laboratory Los Alamos, NM 87545 I. INTRODUCTION In this paper we show how molecular dynamics can be used in a simple manner to com...could equally use Monte Carlo or explicit integration over coordinates to compute equilibrium electronic absorption bands. How- ever, molecular

Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

DOE PAGES

Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...

2014-10-20

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less

InP and GaAs characterization with variable stoichiometry obtained by molecular spray

NASA Technical Reports Server (NTRS)

Massies, J.; Linh, N. T.; Olivier, J.; Faulconnier, P.; Poirier, R.

1979-01-01

Both InP and GaAs surfaces were studied in parallel. A molecular spray technique was used to obtain two semiconductor surfaces with different superficial compositions. The structures of these surfaces were examined by electron diffraction. Electron energy loss was measured spectroscopically in order to determine surface electrical characteristics. The results are used to support conclusions relative to the role of surface composition in establishing a Schottky barrier effect in semiconductor devices.

Preface: Special Topic on Frontiers in Molecular Scale Electronics

NASA Astrophysics Data System (ADS)

Evers, Ferdinand; Venkataraman, Latha

2017-03-01

The electronic, mechanical, and thermoelectric properties of molecular scale devices have fascinated scientists across several disciplines in natural sciences and engineering. The interest is partially technological, driven by the fast miniaturization of integrated circuits that now have reached characteristic features at the nanometer scale. Equally important, a very strong incentive also exists to elucidate the fundamental aspects of structure-function relations for nanoscale devices, which utilize molecular building blocks as functional units. Thus motivated, a rich research field has established itself, broadly termed "Molecular Electronics," that hosts a plethora of activities devoted to this goal in chemistry, physics, and electrical engineering. This Special Topic on Frontiers of Molecular Scale Electronics captures recent theoretical and experimental advances in the field.

Electronic shift register memory based on molecular electron-transfer reactions

NASA Technical Reports Server (NTRS)

Hopfield, J. J.; Onuchic, Jose Nelson; Beratan, David N.

1989-01-01

The design of a shift register memory at the molecular level is described in detail. The memory elements are based on a chain of electron-transfer molecules incorporated on a very large scale integrated (VLSI) substrate, and the information is shifted by photoinduced electron-transfer reactions. The design requirements for such a system are discussed, and several realistic strategies for synthesizing these systems are presented. The immediate advantage of such a hybrid molecular/VLSI device would arise from the possible information storage density. The prospect of considerable savings of energy per bit processed also exists. This molecular shift register memory element design solves the conceptual problems associated with integrating molecular size components with larger (micron) size features on a chip.

The electronic properties of potassium doped copper-phthalocyanine studied by electron energy-loss spectroscopy.

PubMed

Flatz, K; Grobosch, M; Knupfer, M

2007-06-07

The authors have studied the electronic structure of potassium doped copper-phthalocyanine using electron energy-loss spectroscopy. The evolution of the loss function indicates the formation of distinct KxCuPc phases. Taking into account the C1s and K2p core level excitations and recent results by Giovanelli et al. [J. Chem. Phys. 126, 044709 (2007)], they conclude that these are K2CuPc and K4CuPc. They discuss the changes in the electronic excitations upon doping on the basis of the molecular electronic levels and the presence of electronic correlations.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

2017-11-01

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Zethrene biradicals: How pro-aromaticity is expressed in the ground electronic state and in the lowest energy singlet, triplet, and ionic states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zafra, José Luis; González Cano, Rafael C.; Ruiz Delgado, M. Carmen

A analysis of the electronic and molecular structures of new molecular materials based on zethrene is presented with particular attention to those systems having a central benzo-quinoidal core able to generate Kekulé biradicals whose stability is provided by the aromaticity recovery in this central unit. These Kekulé biradicals display singlet ground electronic states thanks to double spin polarization and have low-energy lying triplet excited states also featured by the aromaticity gain. Pro-aromatization is also the driving force for the stabilization of the ionized species. Moreover, the low energy lying singlet excited states also display a profound biradical fingerprint allowing tomore » singlet exciton fission. These properties are discussed in the context of the size of the zethrene core and of its substitution. The work encompasses all known long zethrenes and makes use of a variety of experimental techniques, such as Raman, UV-Vis-NIR absorption, transient absorption, in situ spectroelectrochemistry and quantum chemical calculations. This study reveals how the insertion of suitable molecular modules (i.e., quinoidal) opens the door to new intriguing molecular properties exploitable in organic electronics.« less

Low energy electron induced fragmentation and reactions of DNA and its molecular components

NASA Astrophysics Data System (ADS)

Bass, Andrew

2005-05-01

Much research has been stimulated by the recognition that ionizing radiation can, in condensed matter, generate large numbers of secondary electrons with energies less than 20 eV [1] and by the experimental demonstration that such electrons may induce both single and double strand breaks in plasmid DNA [2]. Identifying the underlying mechanisms involves several research methodologies, from further experiments with DNA to studies of the electron interaction with the component `sub-units' of DNA in both the gas and condensed phases [3]. In particular, understanding electron-induced strand break damage, the type of damage most difficult for organisms to repair, necessitates study of the sub-units of DNA back-bone, and here Tetrahyrofuran (THF) and its derivatives, provide a useful model for the furyl ring at the centre of the deoxyribose sugar. In this contribution, we review with particular reference to DNA and related molecules, the use of electron spectroscopy and mass spectrometry to study electron-induced fragmentation and reactions in thin molecular solids. We describe a newly completed instrument that combines laser post-ionization with a time-of-flight mass analyzer for highly sensitive ion and neutral detection. Use of the instrument is illustrated with results for THF and derivatives. Anion desorption measurements reveal the role of transient negative ions (TNI) and Dissociative Electron Attachment in significant molecular fragmentation and permit effective cross sections for this electron-induced damage to be obtained. The neutral yield functions also illustrate the importance of TNI, mirroring features seen in recently measured cross sections for electron induced aldehyde production in THF [4]. 1. J. A. Laverne and S. M. Pimblott, Radiat. Res. 141, 208 (1995) 2. B. Boudaiffa, et al, Science 287, 1658 (2000) 3. L. Sanche. Physica Scripta. 68, C108, (2003) 4. S.-P. Breton, et al.,J. Chem. Phys. 121, 11240 (2004)

An overview of the first half-century of molecular electronics.

PubMed

Hush, Noel S

2003-12-01

The seminal ideas from which molecular electronics has developed were the theories of molecular conduction advanced in the late 1940s by Robert S. Mulliken and Albert Szent-Gyorgi. These were, respectively, the concept of donor-acceptor charge transfer complexes and the possibility that proteins might in fact not be insulators The next two decades saw a burgeoning of experimental and theoretical work on electron transfer systems, together with a lone effort by D.D. Eley on conduction in proteins. The call by Feynman in his famous 1959 lecture There's Plenty of Room at the Bottom for chemists, engineers and physicists to combine to build up structures from the molecular level was influential in turning attention to the possibility of engineering single molecules to function as elements in information-processing systems. This was made tangible by the proposal of Aviram and Ratner in 1974 to use a Mulliken-like electron donor-acceptor molecule as a molecular diode, generalizing molecular conduction into molecular electronics. In the early 1970s the remarkably visionary work of Forrest L. Carter of the U.S. Naval Research Laboratories began to appear: designs for molecular wires, switches, complex molecular logic elements, and a host of related ideas were advanced. Shortly after that, conferences on molecular electronics began to be held, and the interdisciplinary programs that Feynman envisaged. There was a surge in both experimental and theoretical work in molecular electronics, and the establishment of many research centres. The past five years or so have seen extraordinarily rapid progress in fabrication and theoretical understanding. The history of how separate lines of research emanating from fundamental insights of about 50 years ago have coalesced into a thriving international research program in what might be called the ultimate nanotechnology is the subject of this review; it concentrates on the lesser-appreciated early developments in the field.

Molecular transistors based on BDT-type molecular bridges.

PubMed

Wheeler, W D; Dahnovsky, Yu

2008-10-21

In this work we study the effect of electron correlations in molecular transistors with molecular bridges based on 1,4-benzene-dithiol (BDT) and 2-nitro-1,4-benzene-dithiol (nitro-BDT) by using ab initio electron propagator calculations. We find that there is no gate field effect for the BDT based transistor in accordance with the experimental data. After verifying the computational method on the BDT molecule, we consider a transistor with a nitro-BDT molecular bridge. From the electron propagator calculations, we predict strong negative differential resistance at small positive and negative values of source-drain voltages. The explanation of the peak and the minimum in the current is given in terms of the molecular orbital picture and switch-on (-off) properties due to the voltage dependencies of the Dyson poles (ionization potentials). When the current is off, the electronic states on both electrodes are populated resulting in the vanishing tunneling probability due to the Pauli principle. Besides the minimum and the maximum in the I-V characteristics, we find a strong gate field effect in the conductance where the peak at V(sd) = 0.15 eV and E(g) = 4x10(-3) a.u. switches to the minimum at E(g) = -4x10(-3) a.u. A similar behavior is discovered at the negative V(sd). Such a feature can be used for fast current modulation by changing the polarity of a gate field.

Structures, mechanical properties, equations of state, and electronic properties of β-HMX under hydrostatic pressures: a DFT-D2 study.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; De, Suvranu

2014-10-07

We report the hydrostatic compression studies of the β-polymorph of a cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using DFT-D2, a first-principles calculation based on density functional theory (DFT) with van der Waals (vdW) corrections. The molecular structure, mechanical properties, electronic properties, and equations of state of β-HMX are investigated. For the first time, we predict the elastic constants of β-HMX using DFT-D2 studies. The equations of state under hydrostatic compression are studied for pressures up to 100 GPa. We found that the N-N bonds along the minor axis are responsible for the sensitivity of β-HMX. The analysis of the charge distribution shows that the electronic charge is transferred from hydrogen atoms to nitro groups with the amount of 0.131 and 0.064e for the nitro groups along the minor axis and major axis, respectively, when pressure changes from 0 GPa to 100 GPa. The electronic energy band gap changes from direct at a pressure of 0 GPa to indirect at a pressure of 50 GPa and higher. The band gap decreases with respect to an increase in pressure, implying that the impact sensitivity increases with compression. Our study suggests that the van der Waals interactions are critically important in modeling the mechanical properties of this molecular crystal.

Molecular gap and energy level diagram for pentacene adsorbed on filled d-band metal surfaces

NASA Astrophysics Data System (ADS)

Baldacchini, Chiara; Mariani, Carlo; Betti, Maria Grazia; Gavioli, L.; Fanetti, M.; Sancrotti, M.

2006-10-01

The authors present a combined photoemission and scanning-tunneling spectroscopy study of the filled electronic states, the molecular energy gap, and the energy level diagram of highly ordered arrays of pentacene deposited on the Cu(119) vicinal surface. The states localized at the interface are clearly singled out, comparing the results at different pentacene thicknesses and with gas-phase photoemission data. The molecular gap of 2.35eV, the hole injection barrier of 1.05eV, and the electron injection barrier of 1.30eV determine the energy level diagram of the states localized at the pentacene molecules.

Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S{sub 1} states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Álvarez-Valtierra, Leonardo, E-mail: leoav@fisica.ugto.mx, E-mail: gmerino@mda.cinvestav.mx

2015-09-07

The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, butmore » it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   –OH and   –OCH{sub 3} groups plays a major role in these dynamics.« less

Modeling Biophysical and Biological Properties From the Characteristics of the Molecular Electron Density, Electron Localization and Delocalization Matrices, and the Electrostatic Potential

PubMed Central

Matta*, Chérif F

2014-01-01

The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pKa's, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme–substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as “interacting quantum atoms (IQA)” energies which are expressible into an interaction matrix of two body terms (and diagonal one body “self” terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established. © 2014 The Author and the Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:24777743

Adiabatic quantum computing with spin qubits hosted by molecules.

PubMed

Yamamoto, Satoru; Nakazawa, Shigeaki; Sugisaki, Kenji; Sato, Kazunobu; Toyota, Kazuo; Shiomi, Daisuke; Takui, Takeji

2015-01-28

A molecular spin quantum computer (MSQC) requires electron spin qubits, which pulse-based electron spin/magnetic resonance (ESR/MR) techniques can afford to manipulate for implementing quantum gate operations in open shell molecular entities. Importantly, nuclear spins, which are topologically connected, particularly in organic molecular spin systems, are client qubits, while electron spins play a role of bus qubits. Here, we introduce the implementation for an adiabatic quantum algorithm, suggesting the possible utilization of molecular spins with optimized spin structures for MSQCs. We exemplify the utilization of an adiabatic factorization problem of 21, compared with the corresponding nuclear magnetic resonance (NMR) case. Two molecular spins are selected: one is a molecular spin composed of three exchange-coupled electrons as electron-only qubits and the other an electron-bus qubit with two client nuclear spin qubits. Their electronic spin structures are well characterized in terms of the quantum mechanical behaviour in the spin Hamiltonian. The implementation of adiabatic quantum computing/computation (AQC) has, for the first time, been achieved by establishing ESR/MR pulse sequences for effective spin Hamiltonians in a fully controlled manner of spin manipulation. The conquered pulse sequences have been compared with the NMR experiments and shown much faster CPU times corresponding to the interaction strength between the spins. Significant differences are shown in rotational operations and pulse intervals for ESR/MR operations. As a result, we suggest the advantages and possible utilization of the time-evolution based AQC approach for molecular spin quantum computers and molecular spin quantum simulators underlain by sophisticated ESR/MR pulsed spin technology.

First-principles investigation on structural and electronic properties of antimonene nanoribbons and nanotubes

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Chandiramouli, R.

2018-03-01

The electronic properties of antimonene nanotubes and nanoribbons hydrogenated along the zigzag and armchair borders are investigated with the help of density functional theory (DFT) method. The structural stability of antimonene nanostructures is confirmed with the formation energy. The electronic properties of hydrogenated zigzag and armchair antimonene nanostructures are studied in terms of highest occupied molecular orbital (HOMO) & lowest unoccupied molecular orbital (LUMO) gap and density of states (DOS) spectrum. Moreover, due to the influence of buckled orientation, hydrogen passivation and width of antimonene nanostructures, the HOMO-LUMO gap widens in the range of 0.15-0.41 eV. The findings of the present study confirm that the electronic properties of antimonene nanostructures can be tailored with the influence of width, orientation of the edges, passivation with hydrogen and morphology of antimonene nanostructures (nanoribbons, nanotubes), which can be used as chemical sensor and for spintronic devices.

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

ERIC Educational Resources Information Center

Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

2012-01-01

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

Control of π-Electron Rotations in Chiral Aromatic Molecules Using Intense Laser Pulses

NASA Astrophysics Data System (ADS)

Kanno, Manabu; Kono, Hirohiko; Fujimura, Yuichi

Our recent theoretical studies on laser-induced π-electron rotations in chiral aromatic molecules are reviewed. π electrons of a chiral aromatic molecule can be rotated along its aromatic ring by a nonhelical, linearly polarized laser pulse. An ansa aromatic molecule with a six-membered ring, 2,5-dichloro[n](3,6) pyrazinophane, which belongs to a planar-chiral molecule group, and its simplified molecule 2,5-dichloropyrazine are taken as model molecules. Electron wavepacket simulations in the frozen-molecular-vibration approximation show that the initial direction of π-electron rotation depends on the polarization direction of a linearly polarized laser pulse applied. Consecutive unidirectional rotation can be achieved by applying a sequence of linearly polarized pump and dump pulses to prevent reverse rotation. Optimal control simulations of π-electron rotation show that another controlling factor for unidirectional rotation is the relative optical phase between the different frequency components of an incident pulse in addition to photon polarization direction. Effects of nonadiabatic coupling between π-electron rotation and molecular vibrations are also presented, where the constraints of the frozen approximation are removed. The angular momentum gradually decays mainly owing to nonadiabatic coupling, while the vibrational amplitudes greatly depend on their rotation direction. This suggests that the direction of π-electron rotation on an attosecond timescale can be identified by detecting femtosecond molecular vibrations.

Theoretical and experimental study of electron-deficient core substitution effect of diketopyrrolopyrrole derivatives on optoelectrical and charge transport properties

NASA Astrophysics Data System (ADS)

Ding, Guodong; Mahmood, Asif; Tang, Ailing; Chen, Fan; Zhou, Erjun

2018-01-01

Three new diketopyrrolopyrrole based compounds with Acceptor-Donor-Acceptor-Donor-Acceptor (A-D-A-D-A) skeletons were designed and synthesized through varying the electron-deficient core from diphenylquinoxaline (DP-Qx), thieno[3,4-c]pyrrole-4,6-dione (DP-TPD) to 2-dodecyl-6,7-diphenyl-2H-[1,2,3]triazole[4,5-g]quinoxaline (DP-TQx). We have calculated and studied the effect of central acceptor units on electronic, optical and non-optical properties. As well as, we have predicted the charge transport properties. Results indicate that change of central acceptor unit remarkably affects the molecular electronic, optical and non-optical properties. And the molecular band gap and UV/vis adsorption spectra are significantly changed. It should be noted that Compound 3 with 2-dodecyl-6,7-diphenyl-2H-[1,2,3]triazole[4,5-g]quinoxaline as core show superior non-optical properties as compare to other compounds. Our study here indicate that inserting the strong electron-deficient moieties improves intramolecular charge transfer (ICT) and charge transport properties dramatically.

An Imide-Based Pentacyclic Building Block for n-Type Organic Semiconductors

DOE PAGES

Wu, Fu-Peng; Un, Hio-Ieng; Li, Yongxi; ...

2017-10-09

For this study a new electron-deficient unit with fused 5-heterocyclic ring was developed by replacing a cyclopenta-1,3-diene from electron-rich donor indacenodithiophene (IDT) with cyclohepta-4,6-diene-1,3-diimde unit. The imide bridging endows BBI with fixed planar configuration and both low the highest occupied molecular orbital (HOMO) (-6.24 eV) and the lowest unoccupied molecular orbit (LUMO) (-2.57 eV) energy levels. Organic field-effect transistors (OFETs) based on BBI polymers exhibit electron mobility up to 0.34 cm 2 V -1 s -1, which indicates that the BBI is a promising n-type building block for optoelectronics.

An Imide-Based Pentacyclic Building Block for n-Type Organic Semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Fu-Peng; Un, Hio-Ieng; Li, Yongxi

For this study a new electron-deficient unit with fused 5-heterocyclic ring was developed by replacing a cyclopenta-1,3-diene from electron-rich donor indacenodithiophene (IDT) with cyclohepta-4,6-diene-1,3-diimde unit. The imide bridging endows BBI with fixed planar configuration and both low the highest occupied molecular orbital (HOMO) (-6.24 eV) and the lowest unoccupied molecular orbit (LUMO) (-2.57 eV) energy levels. Organic field-effect transistors (OFETs) based on BBI polymers exhibit electron mobility up to 0.34 cm 2 V -1 s -1, which indicates that the BBI is a promising n-type building block for optoelectronics.

Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

PubMed

Beckman, Robert; Beverly, Kris; Boukai, Akram; Bunimovich, Yuri; Choi, Jang Wook; DeIonno, Erica; Green, Johnny; Johnston-Halperin, Ezekiel; Luo, Yi; Sheriff, Bonnie; Stoddart, Fraser; Heath, James R

2006-01-01

We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.

Ultrafast direct electron transfer at organic semiconductor and metal interfaces.

PubMed

Xiang, Bo; Li, Yingmin; Pham, C Huy; Paesani, Francesco; Xiong, Wei

2017-11-01

The ability to control direct electron transfer can facilitate the development of new molecular electronics, light-harvesting materials, and photocatalysis. However, control of direct electron transfer has been rarely reported, and the molecular conformation-electron dynamics relationships remain unclear. We describe direct electron transfer at buried interfaces between an organic polymer semiconductor film and a gold substrate by observing the first dynamical electric field-induced vibrational sum frequency generation (VSFG). In transient electric field-induced VSFG measurements on this system, we observe dynamical responses (<150 fs) that depend on photon energy and polarization, demonstrating that electrons are directly transferred from the Fermi level of gold to the lowest unoccupied molecular orbital of organic semiconductor. Transient spectra further reveal that, although the interfaces are prepared without deliberate alignment control, a subensemble of surface molecules can adopt conformations for direct electron transfer. Density functional theory calculations support the experimental results and ascribe the observed electron transfer to a flat-lying polymer configuration in which electronic orbitals are found to be delocalized across the interface. The present observation of direct electron transfer at complex interfaces and the insights gained into the relationship between molecular conformations and electron dynamics will have implications for implementing novel direct electron transfer in energy materials.

Assessment of strontium oxide functionalized graphene nanoflakes for enhanced photocatalytic activity: A density functional theory approach

NASA Astrophysics Data System (ADS)

Divya, A.; Mathavan, T.; Asath, R. Mohamed; Archana, J.; Hayakawa, Y.; Benial, A. Milton Franklin

2016-05-01

A series of strontium oxide functionalized graphene nanoflakes were designed and their optoelectronic properties were studied for enhanced photocatalytic activity. The efficiency of designed molecules was studied using various parameters such as HOMO-LUMO energy gap, light harvesting efficiency and exciton binding energy. The computed results show that by increasing the degree of functionalization of strontium oxide leads to lowering the band gap of hydrogen terminated graphene nanoflakes. Furthermore, the study explores the role of strontium oxide functionalization in Frontier Molecular Orbitals, ionization potential, electron affinity, exciton binding energy and light harvesting efficiency of designed molecules. The infrared and Raman spectra were simulated for pure and SrO functionalized graphene nanoflakes. The electron rich and electron deficient regions which are favorable for electrophilic and nucleophilic attacks respectively were analyzed using molecular electrostatic potential surface analysis.

Computational modeling of Metal-Organic Frameworks

NASA Astrophysics Data System (ADS)

Sung, Jeffrey Chuen-Fai

In this work, the metal-organic frameworks MIL-53(Cr), DMOF-2,3-NH 2Cl, DMOF-2,5-NH2Cl, and HKUST-1 were modeled using molecular mechanics and electronic structure. The effect of electronic polarization on the adsorption of water in MIL-53(Cr) was studied using molecular dynamics simulations of water-loaded MIL-53 systems with both polarizable and non-polarizable force fields. Molecular dynamics simulations of the full systems and DFT calculations on representative framework clusters were utilized to study the difference in nitrogen adsorption between DMOF-2,3-NH2Cl and DMOF-2,5-NH 2Cl. Finally, the control of proton conduction in HKUST-1 by complexation of molecules to the Cu open metal site was investigated using the MS-EVB methodology.

Thienoacene-based organic semiconductors.

PubMed

Takimiya, Kazuo; Shinamura, Shoji; Osaka, Itaru; Miyazaki, Eigo

2011-10-11

Thienoacenes consist of fused thiophene rings in a ladder-type molecular structure and have been intensively studied as potential organic semiconductors for organic field-effect transistors (OFETs) in the last decade. They are reviewed here. Despite their simple and similar molecular structures, the hitherto reported properties of thienoacene-based OFETs are rather diverse. This Review focuses on four classes of thienoacenes, which are classified in terms of their chemical structures, and elucidates the molecular electronic structure of each class. The packing structures of thienoacenes and the thus-estimated solid-state electronic structures are correlated to their carrier transport properties in OFET devices. With this perspective of the molecular structures of thienoacenes and their carrier transport properties in OFET devices, the structure-property relationships in thienoacene-based organic semiconductors are discussed. The discussion provides insight into new molecular design strategies for the development of superior organic semiconductors. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Glauber-theory approach for molecular vibrational excitations

NASA Technical Reports Server (NTRS)

Chang, T. N.; Poe, R. T.; Ray, P.

1973-01-01

Molecular vibrational excitations by charged-particle impact are investigated within the Glauber-theory approach. Theoretical results for electron-H2 scattering give good agreement with experimental data. We study the physical effects responsible for the structures in the differential cross section.

Theoretical study of (e, 2e) process of atomic and molecular targets*

NASA Astrophysics Data System (ADS)

Houamer, Salim; Chinoune, Mehdi; Cappello, Claude Dal

2017-01-01

Triple differential ionization cross sections (TDCSs) by electron impact are calculated for some atomic and molecular targets by using several models where Post Collisional Interaction (PCI) is taken in account. We also investigate the effect of the short range potential and describe the ejected electron either by a Coulomb wave or by a distorted wave. Significant differences are observed between these models. A better agreement with experimental data is achieved when the short range potential and distortion effects are included.

Covalent Linking Greatly Enhances Photoinduced Electron Transfer in Fullerene-Quantum Dot Nanocomposites: Time-Domain Ab Initio Study.

PubMed

Chaban, Vitaly V; Prezhdo, Victor V; Prezhdo, Oleg V

2013-01-03

Nonadiabatic molecular dynamics combined with time-domain density functional theory are used to study electron transfer (ET) from a CdSe quantum dot (QD) to the C60 fullerene, occurring in several types of hybrid organic/inorganic nanocomposites. By unveiling the time dependence of the ET process, we show that covalent bonding between the QD and C60 is particularly important to ensure ultrafast transmission of the excited electron from the QD photon-harvester to the C60 electron acceptor. Despite the close proximity of the donor and acceptor species provided by direct van der Waals contact, it leads to a notably weaker QD-C60 interaction than a lengthy molecular bridge. We show that the ET rate in a nonbonded mixture of QDs and C60 can be enhanced by doping. The photoinduced ET is promoted primarily by mid- and low-frequency vibrations. The study establishes the basic design principles for enhancing photoinduced charge separation in nanoscale light harvesting materials.

Fundamental studies of energy-and hole/electron- transfer in hydroporphyrin architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bocian, David F.

2014-08-20

The long-term objective of the Bocian/Holten/Lindsey research program is to design, synthesize, and characterize tetrapyrrole-based molecular architectures that absorb sunlight, funnel energy, and separate charge with high efficiency and in a manner compatible with current and future solar-energy conversion schemes. The synthetic tetrapyrroles include porphyrins and hydroporphyrins; the latter classes of molecules encompass analogues of the naturally occurring chlorophylls and bacteriochlorophylls (e.g., chlorins, bacteriochlorins, and their derivatives). The attainment of the goals of the research program requires the close interplay of molecular design and synthesis (Lindsey group), static and time-resolved optical spectroscopic measurements (Holten group), and electrochemical, electron paramagnetic resonance,more » and resonance Raman studies, as well as density functional theory calculations (Bocian Group). The proposed research encompasses four interrelated themes: (1) Determination of the rates of ground-state hole/electron transfer between (hydro)porphyrins in multipigment arrays as a function of array size, distance between components, linker type, site of linker connection, and frontier molecular orbital composition. (2) Examination of excited-state energy transfer among hydroporphyrins in multipigment arrrays, including both pairwise and non-adjacent transfer, with a chief aim to identify the relative contributions of through-space (Förster) and through-bond (Dexter) mechanisms of energy transfer, including the roles of site of linker connection and frontier molecular orbital composition. (3) Elucidation of the role of substituents in tuning the spectral and electronic properties of bacteriochlorins, with a primary aim of learning how to shift the long-wavelength absorption band deeper into the near-infrared region. (4) Continued development of the software package PhotochemCAD for spectral manipulations and calculations through the compilation of a database of spectra for naturally occurring and synthetic hydroporphyrins. The availability of such data should augment efforts in the design of light-harvesting systems where spectral coverage in the red and near-infrared regions is desired. Collectively, the proposed studies will provide fundamental insights into molecular properties, interactions, and processes relevant to the design of molecular architectures for solar-energy conversion. The accomplishment of these goals is only possible through a highly synergistic program that encompasses molecular design, synthesis, and characterization.« less

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

DOE PAGES

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.; ...

2017-01-30

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

The effect of electrodes on 11 acene molecular spin valve: Semi-empirical study

NASA Astrophysics Data System (ADS)

Aadhityan, A.; Preferencial Kala, C.; John Thiruvadigal, D.

2017-10-01

A new revolution in electronics is molecular spintronics, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. The key point is the creation of molecular spin valve which consists of a diamagnetic molecule in between two magnetic leads. In this paper, non-equilibrium Green's function (NEGF) combined with Extended Huckel Theory (EHT); a semi-empirical approach is used to analyse the electron transport characteristics of 11 acene molecular spin valve. We examine the spin-dependence transport on 11 acene molecular junction with various semi-infinite electrodes as Iron, Cobalt and Nickel. To analyse the spin-dependence transport properties the left and right electrodes are joined to the central region in parallel and anti-parallel configurations. We computed spin polarised device density of states, projected device density of states of carbon and the electrode element, and transmission of these devices. The results demonstrate that the effect of electrodes modifying the spin-dependence behaviours of these systems in a controlled way. In Parallel and anti-parallel configuration the separation of spin up and spin down is lager in the case of iron electrode than nickel and cobalt electrodes. It shows that iron is the best electrode for 11 acene spin valve device. Our theoretical results are reasonably impressive and trigger our motivation for comprehending the transport properties of these molecular-sized contacts.

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prezhdo, Oleg V.

2012-03-22

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results weremore » reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical excitations. Conduction and valence band transitions that are not available in neutral NCs dominate low energy electronic excitations and show weak optical activity. At higher energies these transitions mix with both single excitons (SEs) and multiple excitons (MEs) associated with transitions across the band-gap. As a result, both SEs and MEs are significantly blue-shifted, and ME generation is drastically hampered. The overall contribution of MEs to the electronic excitations of the charged NCs is small even at very high energies. The calculations supported the recent view that the observed strong dependence of the ME yields on the experimental conditions is likely due to the effects of NC charging. The electron-hole excitonic nature of high energy states was investigated in neutral and charged Si clusters, motivated by the ME generation (MEG) process that is highly debated in photovoltaic literature.« less

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Exploring the formation and electronic structure properties of the g-C3N4 nanoribbon with density functional theory

NASA Astrophysics Data System (ADS)

Wu, Hong-Zhang; Zhong, Qing-Hua; Bandaru, Sateesh; Liu, Jin; Lau, Woon Ming; Li, Li-Li; Wang, Zhenling

2018-04-01

The optical properties and condensation degree (structure) of polymeric g-C3N4 depend strongly on the process temperature. For polymeric g-C3N4, its structure and condensation degree depend on the structure of molecular strand(s). Here, the formation and electronic structure properties of the g-C3N4 nanoribbon are investigated by studying the polymerization and crystallinity of molecular strand(s) employing first-principle density functional theory. The calculations show that the width of the molecular strand has a significant effect on the electronic structure of polymerized and crystallized g-C3N4 nanoribbons, a conclusion which would be indirect evidence that the electronic structure depends on the structure of g-C3N4. The edge shape also has a distinct effect on the electronic structure of the crystallized g-C3N4 nanoribbon. Furthermore, the conductive band minimum and valence band maximum of the polymeric g-C3N4 nanoribbon show a strong localization, which is in good agreement with the quasi-monomer characters. In addition, molecular strands prefer to grow along the planar direction on graphene. These results provide new insight on the properties of the g-C3N4 nanoribbon and the relationship between the structure and properties of g-C3N4.

Exploring the formation and electronic structure properties of the g-C3N4 nanoribbon with density functional theory.

PubMed

Wu, Hong-Zhang; Zhong, Qing-Hua; Bandaru, Sateesh; Liu, Jin; Lau, Woon Ming; Li, Li-Li; Wang, Zhenling

2018-04-18

The optical properties and condensation degree (structure) of polymeric g-C 3 N 4 depend strongly on the process temperature. For polymeric g-C 3 N 4 , its structure and condensation degree depend on the structure of molecular strand(s). Here, the formation and electronic structure properties of the g-C 3 N 4 nanoribbon are investigated by studying the polymerization and crystallinity of molecular strand(s) employing first-principle density functional theory. The calculations show that the width of the molecular strand has a significant effect on the electronic structure of polymerized and crystallized g-C 3 N 4 nanoribbons, a conclusion which would be indirect evidence that the electronic structure depends on the structure of g-C 3 N 4 . The edge shape also has a distinct effect on the electronic structure of the crystallized g-C 3 N 4 nanoribbon. Furthermore, the conductive band minimum and valence band maximum of the polymeric g-C 3 N 4 nanoribbon show a strong localization, which is in good agreement with the quasi-monomer characters. In addition, molecular strands prefer to grow along the planar direction on graphene. These results provide new insight on the properties of the g-C 3 N 4 nanoribbon and the relationship between the structure and properties of g-C 3 N 4 .

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

NASA Astrophysics Data System (ADS)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Delocalization error and "functional tuning" in Kohn-Sham calculations of molecular properties.

PubMed

Autschbach, Jochen; Srebro, Monika

2014-08-19

Kohn-Sham theory (KST) is the "workhorse" of numerical quantum chemistry. This is particularly true for first-principles calculations of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and "tuning" of functionals in KST calculations of molecular ground-state and response properties. Tuning refers to a nonempirical molecule-specific determination of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the highest occupied molecular orbital (HOMO) should be equal to the negative vertical ionization potential (IP) or that the energy as a function of fractional electron numbers should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of molecular optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for molecular properties. We discuss a number of different molecular properties, with examples from recent studies from our laboratory and related literature. The selected properties probe different aspects of molecular electronic structure. Electric field gradients and hyperfine coupling constants can be exquisitely sensitive to the DE because it affects the ground-state electron density and spin density distributions. For π-conjugated molecules, it is shown how the DE manifests itself either in too strong or too weak delocalization of localized molecular orbitals (LMOs). Optical rotation is an electric-magnetic linear response property that is calculated in a similar fashion as the electric polarizability, but it is more sensitive to approximations and can benefit greatly from tuning and small DE. Hyperpolarizabilities of π-conjugated "push-pull" systems are examples of NLO properties that can be greatly improved by tuning of range-separated exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different molecular properties exhibit varying sensitivity to approximations in the electronic structure model. The utility of analyzing molecular properties and the impact of the DE in terms of LMOs, representing "chemist's orbitals" such as individual lone pairs and bonds, is highlighted.

The Holographic Electron Density Theorem, de-quantization, re-quantization, and nuclear charge space extrapolations of the Universal Molecule Model

NASA Astrophysics Data System (ADS)

Mezey, Paul G.

2017-11-01

Two strongly related theorems on non-degenerate ground state electron densities serve as the basis of "Molecular Informatics". The Hohenberg-Kohn theorem is a statement on global molecular information, ensuring that the complete electron density contains the complete molecular information. However, the Holographic Electron Density Theorem states more: the local information present in each and every positive volume density fragment is already complete: the information in the fragment is equivalent to the complete molecular information. In other words, the complete molecular information provided by the Hohenberg-Kohn Theorem is already provided, in full, by any positive volume, otherwise arbitrarily small electron density fragment. In this contribution some of the consequences of the Holographic Electron Density Theorem are discussed within the framework of the "Nuclear Charge Space" and the Universal Molecule Model. In the Nuclear Charge Space" the nuclear charges are regarded as continuous variables, and in the more general Universal Molecule Model some other quantized parameteres are also allowed to become "de-quantized and then re-quantized, leading to interrelations among real molecules through abstract molecules. Here the specific role of the Holographic Electron Density Theorem is discussed within the above context.

Exploring the relative reactivities of the hydroxyl groups of monosaccharides by molecular modeling and molecular mechanics

NASA Astrophysics Data System (ADS)

Box, V. G. S.; Evans-Lora, T.

2000-01-01

The molecular modeling program STR3DI.EXE, and its molecular mechanics module, QVBMM, were used to simulate, and evaluate, the stereo-electronic effects in the mono-alkoxides of the 4,6- O-ethylideneglycopyranosides of allose, mannose, galactose and glucose. This study has confirmed the ability of these molecular modeling tools to predict the regiochemistry and reactivity of these sugar derivatives, and holds considerable implications for unraveling the chemistry of the rare monosaccharides.

On the electron affinity of cytosine in bulk water and at hydrophobic aqueous interfaces.

PubMed

Vöhringer-Martinez, Esteban; Dörner, Ciro; Abel, Bernd

2014-10-01

In the past one possible mechanism of DNA damage in bulk water has been attributed to the presence of hydrated electrons in water. Recently, one important property of hydrated electrons, namely their binding energy, was reported to be smaller at hydrophobic interfaces than in bulk aqueous solution. This possibly opens up new reaction possibilities with different solutes such as the DNA at hydrophobic, aqueous interfaces. Here, we use QM/MM molecular dynamics simulation to study how the molecular environment at the vacuum-water interface and in the bulk alters the electron affinity of cytosine being a characteristic part of the DNA. The electron affinity at the interface is closer to the corresponding binding energy of the partially hydrated electron. The increased energy resonance makes the electron capture process more probable and suggests that hydrated electrons at hydrophobic interfaces may be more reactive than the fully hydrated ones. Additionally, we found that the relaxation of the anionic form after electron attachment also induces a proton transfer from the surrounding solvent that was confirmed by comparison with the experimental reduction potential.

Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

NASA Astrophysics Data System (ADS)

Ding, Feizhi

Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear motion. All these developments and applications will open up new computational and theoretical tools to be applied to the development and understanding of chemical reactions, nonlinear optics, electromagnetism, and spintronics. Lastly, we present a new algorithm for large-scale MCSCF calculations that can utilize massively parallel machines while still maintaining optimal performance for each single processor. This will great improve the efficiency in the MCSCF calculations for studying chemical dissociation and high-accuracy quantum-mechanical simulations.

Selective scanning tunnelling microscope electron-induced reactions of single biphenyl molecules on a Si(100) surface.

PubMed

Riedel, Damien; Bocquet, Marie-Laure; Lesnard, Hervé; Lastapis, Mathieu; Lorente, Nicolas; Sonnet, Philippe; Dujardin, Gérald

2009-06-03

Selective electron-induced reactions of individual biphenyl molecules adsorbed in their weakly chemisorbed configuration on a Si(100) surface are investigated by using the tip of a low-temperature (5 K) scanning tunnelling microscope (STM) as an atomic size source of electrons. Selected types of molecular reactions are produced, depending on the polarity of the surface voltage during STM excitation. At negative surface voltages, the biphenyl molecule diffuses across the surface in its weakly chemisorbed configuration. At positive surface voltages, different types of molecular reactions are activated, which involve the change of adsorption configuration from the weakly chemisorbed to the strongly chemisorbed bistable and quadristable configurations. Calculated reaction pathways of the molecular reactions on the silicon surface, using the nudge elastic band method, provide evidence that the observed selectivity as a function of the surface voltage polarity cannot be ascribed to different activation energies. These results, together with the measured threshold surface voltages and the calculated molecular electronic structures via density functional theory, suggest that the electron-induced molecular reactions are driven by selective electron detachment (oxidation) or attachment (reduction) processes.

Molecular electronics: insight from first-principles transport simulations.

PubMed

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2010-01-01

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

Pulsed, high-current, in-line reversal electron attachment detector

NASA Technical Reports Server (NTRS)

Bernius, Mark T.; Chutjian, Ara

1989-01-01

A new, pulsed, high-current, in-line reversal electron attachment ionizer/detector is described. The ionizer is capable of delivering a beam of electrons into an electrostatic mirror field to form a planar wall of electrons having zero kinetic energy. Electron attachment to a molecular target at the reversal point produces either parent or fragment negative ions through a zero-energy (s-wave) state. The atomic or molecular ion is pulsed out of the attachment region approximately 2 microsec after the electrons are pulsed off, and focused onto the entrance plane of a quadrupole mass analyzer. The sensitivity of the apparatus is preliminarily assessed, and its higher-energy behavior with regard to molecular attachment and ionization is described.

a Moessbauer Effect and Fenske-Hall Molecular Orbital Study of the Electronic Properties of Organoiron Clusters.

NASA Astrophysics Data System (ADS)

Buhl, Margaret Linn

The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.

Evaluation of a novel electronic eigenvalue (EEVA) molecular descriptor for QSAR/QSPR studies: validation using a benchmark steroid data set.

PubMed

Tuppurainen, Kari; Viisas, Marja; Laatikainen, Reino; Peräkylä, Mikael

2002-01-01

A novel electronic eigenvalue (EEVA) descriptor of molecular structure for use in the derivation of predictive QSAR/QSPR models is described. Like other spectroscopic QSAR/QSPR descriptors, EEVA is also invariant as to the alignment of the structures concerned. Its performance was tested with respect to the CBG (corticosteroid binding globulin) affinity of 31 benchmark steroids. It appeared that the electronic structure of the steroids, i.e., the "spectra" derived from molecular orbital energies, is directly related to the CBG binding affinities. The predictive ability of EEVA is compared to other QSAR approaches, and its performance is discussed in the context of the Hammett equation. The good performance of EEVA is an indication of the essential quantum mechanical nature of QSAR. The EEVA method is a supplement to conventional 3D QSAR methods, which employ fields or surface properties derived from Coulombic and van der Waals interactions.

Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deumens, E.; Diz, A.; Longo, R.

1994-07-01

An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems.more » The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the [ital ab] [ital initio] Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed.« less

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

NASA Astrophysics Data System (ADS)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

Molecular and nanoscale materials and devices in electronics.

PubMed

Fu, Lei; Cao, Lingchao; Liu, Yunqi; Zhu, Daoben

2004-12-13

Over the past several years, there have been many significant advances toward the realization of electronic computers integrated on the molecular scale and a much greater understanding of the types of materials that will be useful in molecular devices and their properties. It was demonstrated that individual molecules could serve as incomprehensibly tiny switch and wire one million times smaller than those on conventional silicon microchip. This has resulted very recently in the assembly and demonstration of tiny computer logic circuits built from such molecular scale devices. The purpose of this review is to provide a general introduction to molecular and nanoscale materials and devices in electronics.

Origin of Vibrational Instabilities in Molecular Wires with Separated Electronic States.

PubMed

Foti, Giuseppe; Vázquez, Héctor

2018-06-07

Current-induced heating in molecular junctions stems from the interaction between tunneling electrons and localized molecular vibrations. If the electronic excitation of a given vibrational mode exceeds heat dissipation, a situation known as vibrational instability is established, which can seriously compromise the integrity of the junction. Using out of equilibrium first-principles calculations, we demonstrate that vibrational instabilities can take place in the general case of molecular wires with separated unoccupied electronic states. From the ab initio results, we derive a model to characterize unstable vibrational modes and construct a diagram that maps mode stability. These results generalize previous theoretical work and predict vibrational instabilities in a new regime.

Bottom-up, Robust Graphene Ribbon Electronics in All-Carbon Molecular Junctions.

PubMed

Supur, Mustafa; Van Dyck, Colin; Bergren, Adam J; McCreery, Richard L

2018-02-21

Large-area molecular electronic junctions consisting of 5-carbon wide graphene ribbons (GR) with lengths of 2-12 nm between carbon electrodes were fabricated by electrochemical reduction of diazotized 1,8-diaminonaphthalene. Their conductance greatly exceeds that observed for other molecular junctions of similar thicknesses, by a factor of >1 × 10 4 compared to polyphenylenes and >1 × 10 7 compared to alkane chains. The remarkable increase of conductance of the GR nanolayer results from (i) uninterrupted planarity of fused-arene structure affording extensive π-electron delocalization and (ii) enhanced electronic coupling of molecular layer with the carbon bottom contact by two-point covalent bonding, in agreement with DFT-based simulations.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Directing the path of light-induced electron transfer at a molecular fork using vibrational excitation

NASA Astrophysics Data System (ADS)

Delor, Milan; Archer, Stuart A.; Keane, Theo; Meijer, Anthony J. H. M.; Sazanovich, Igor V.; Greetham, Gregory M.; Towrie, Michael; Weinstein, Julia A.

2017-11-01

Ultrafast electron transfer in condensed-phase molecular systems is often strongly coupled to intramolecular vibrations that can promote, suppress and direct electronic processes. Recent experiments exploring this phenomenon proved that light-induced electron transfer can be strongly modulated by vibrational excitation, suggesting a new avenue for active control over molecular function. Here, we achieve the first example of such explicit vibrational control through judicious design of a Pt(II)-acetylide charge-transfer donor-bridge-acceptor-bridge-donor 'fork' system: asymmetric 13C isotopic labelling of one of the two -C≡C- bridges makes the two parallel and otherwise identical donor→acceptor electron-transfer pathways structurally distinct, enabling independent vibrational perturbation of either. Applying an ultrafast UVpump(excitation)-IRpump(perturbation)-IRprobe(monitoring) pulse sequence, we show that the pathway that is vibrationally perturbed during UV-induced electron transfer is dramatically slowed down compared to its unperturbed counterpart. One can thus choose the dominant electron transfer pathway. The findings deliver a new opportunity for precise perturbative control of electronic energy propagation in molecular devices.

Vibrational relaxation of hot carriers in C60 molecule

NASA Astrophysics Data System (ADS)

Madjet, Mohamed; Chakraborty, Himadri

2017-04-01

Electron-phonon coupling in molecular systems is at the heart of several important physical phenomena, including the mobility of carriers in organic electronic devices. Following the optical absorption, the vibrational relaxation of excited (hot) electrons and holes to the fullerene band-edges driven by electron-phonon coupling, known as the hot carrier thermalization process, is of particular fundamental interest. Using the non-adiabatic molecular dynamical methodology (PYXAID + Quantum Espresso) based on density functional approach, we have performed a simulation of vibrionic relaxations of hot carriers in C60. Time-dependent population decays and transfers in the femtosecond scale from various excited states to the states at the band-edge are calculated to study the details of this relaxation process. This work was supported by the U.S. National Science Foundation.

Understanding charge transport in molecular electronics.

PubMed

Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

2003-12-01

For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

Effect of Molecular Coupling on Ultrafast Electron-Transfer and Charge-Recombination Dynamics in a Wide-Gap ZnS Nanoaggregate Sensitized by Triphenyl Methane Dyes.

PubMed

Debnath, Tushar; Maity, Partha; Dana, Jayanta; Ghosh, Hirendra N

2016-03-03

Wide-band-gap ZnS nanocrystals (NCs) were synthesized, and after sensitizing the NCs with series of triphenyl methane (TPM) dyes, ultrafast charge-transfer dynamics was demonstrated. HRTEM images of ZnS NCs show the formation of aggregate crystals with a flower-like structure. Exciton absorption and lumimescence, due to quantum confinement of the ZnS NCs, appear at approximately 310 and 340 nm, respectively. Interestingly, all the TPM dyes (pyrogallol red, bromopyrogallol red, and aurin tricarboxylic acid) form charge-transfer complexes with the ZnS NCs, with the appearance of a red-shifted band. Electron injection from the photoexcited TPM dyes into the conduction band of the ZnS NCs is shown to be a thermodynamically viable process, as confirmed by steady-state and time-resolved emission studies. To unravel charge-transfer (both electron injection and charge recombination) dynamics and the effect of molecular coupling, femtosecond transient absorption studies were carried out in TPM-sensitized ZnS NCs. The electron-injection dynamics is pulse-width-limited in all the ZnS/TPM dye systems, however, the back electron transfer differs, depending on the molecular coupling of the sensitizers (TPM dyes). The detailed mechanisms for the above-mentioned processes are discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unconventional molecule-resolved current rectification in diamondoid–fullerene hybrids

PubMed Central

Randel, Jason C.; Niestemski, Francis C.; Botello-Mendez, Andrés R.; Mar, Warren; Ndabashimiye, Georges; Melinte, Sorin; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Butova, Ekaterina D.; Fokin, Andrey A.; Schreiner, Peter R.; Charlier, Jean-Christophe; Manoharan, Hari C.

2014-01-01

The unimolecular rectifier is a fundamental building block of molecular electronics. Rectification in single molecules can arise from electron transfer between molecular orbitals displaying asymmetric spatial charge distributions, akin to p–n junction diodes in semiconductors. Here we report a novel all-hydrocarbon molecular rectifier consisting of a diamantane–C60 conjugate. By linking both sp3 (diamondoid) and sp2 (fullerene) carbon allotropes, this hybrid molecule opposingly pairs negative and positive electron affinities. The single-molecule conductances of self-assembled domains on Au(111), probed by low-temperature scanning tunnelling microscopy and spectroscopy, reveal a large rectifying response of the molecular constructs. This specific electronic behaviour is postulated to originate from the electrostatic repulsion of diamantane–C60 molecules due to positively charged terminal hydrogen atoms on the diamondoid interacting with the top electrode (scanning tip) at various bias voltages. Density functional theory computations scrutinize the electronic and vibrational spectroscopic fingerprints of this unique molecular structure and corroborate the unconventional rectification mechanism. PMID:25202942

Advance of Mechanically Controllable Break Junction for Molecular Electronics.

PubMed

Wang, Lu; Wang, Ling; Zhang, Lei; Xiang, Dong

2017-06-01

Molecular electronics stands for the ultimate size of functional elements, keeping up with an unstoppable trend over the past few decades. As a vital component of molecular electronics, single molecular junctions have attracted significant attention from research groups all over the world. Due to its pronounced superiority, the mechanically controllable break junctions (MCBJ) technique has been widely applied to characterize the dynamic performance of single molecular junctions. This review presents a system analysis for single-molecule junctions and offers an overview of four test-beds for single-molecule junctions, thus offering more insight into the mechanisms of electron transport. We mainly focus on the development of state-of-the-art mechanically controlled break junctions. The three-terminal gated MCBJ approaches are introduced to manipulate the electron transport of molecules, and MCBJs are combined with characterization techniques. Additionally, applications of MCBJs and remarkable properties of single molecules are addressed. Finally, the challenges and perspective for the mechanically controllable break junctions technique are provided.

First-principles study of the variation of electron transport in a single molecular junction with the length of the molecular wire

NASA Astrophysics Data System (ADS)

Pal, Partha Pratim; Pati, Ranjit

2010-07-01

We report a first-principles study of quantum transport in a prototype two-terminal device consisting of a molecular nanowire acting as an inter-connect between two gold electrodes. The wire is composed of a series of bicyclo[1.1.1]pentane (BCP) cage-units. The length of the wire (L) is increased by sequentially increasing the number of BCP cage units in the wire from 1 to 3. A two terminal model device is made out of each of the three wires. A parameter free, nonequilibrium Green’s function approach, in which the bias effect is explicitly included within a many body framework, is used to calculate the current-voltage characteristics of each of the devices. In the low bias regime that is considered in our study, the molecular devices are found to exhibit Ohmic behavior with resistances of 0.12, 1.4, and 6.5μΩ for the wires containing one, two, and three cages respectively. Thus the conductance value, Gc , which is the reciprocal of resistance, decreases as e-βL with a decay constant (β) of 0.59Å-1 . This observed variation of conductance with the length of the wire is in excellent agreement with the earlier reported exponential decay feature of the electron transfer rate predicted from the electron transfer coupling matrix values obtained using the two-state Marcus-Hush model and the Koopman’s theorem approximation. The downright suppression of the computed electrical current for a bias up to 0.4 V in the longest wire can be exploited in designing a three terminal molecular transistor; this molecular wire could potentially be used as a throttle to avoid leakage gate current.

Cells from icons to symbols: molecularizing cell biology in the 1980s.

PubMed

Serpente, Norberto

2011-12-01

Over centuries cells have been the target of optical and electronic microscopes as well as others technologies, with distinctive types of visual output. Whilst optical technologies produce images 'evident to the eye', the electronic and especially the molecular create images that are more elusive to conceptualization and assessment. My study applies the semiotic approach to the production of images in cell biology to capture the shift from microscopic images to non-traditional visual technologies around 1980. Here I argue that the visual shift that coincides with the growing dominance of molecular biology involves a change from iconic to symbolic forms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unexpectedly high pressure for molecular dissociation in liquid hydrogen by electronic simulation.

PubMed

Mazzola, Guglielmo; Yunoki, Seiji; Sorella, Sandro

2014-03-19

The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the electronic correlation and treat a large number of hydrogen atoms, allowing a realistic and reliable prediction of thermodynamic properties. We find that the molecular liquid phase is unexpectedly stable, and the transition towards a fully atomic liquid phase occurs at much higher pressure than previously believed. The old standing problem of low-temperature atomization is, therefore, still far from experimental reach.

Molecular orbital imaging via above-threshold ionization with circularly polarized pulses.

PubMed

Zhu, Xiaosong; Zhang, Qingbin; Hong, Weiyi; Lu, Peixiang; Xu, Zhizhan

2011-07-18

Above-threshold ionization (ATI) for aligned or orientated linear molecules by circularly polarized laser pulsed is investigated. It is found that the all-round structural information of the molecular orbital is extracted with only one shot by the circularly polarized probe pulse rather than with multi-shot detections in a linearly polarized case. The obtained photoelectron momentum spectrum directly depicts the symmetry and electron distribution of the occupied molecular orbital, which results from the strong sensitivity of the ionization probability to these structural features. Our investigation indicates that the circularly polarized probe scheme would present a simple method to study the angle-dependent ionization and image the occupied electronic orbital.

Electronic structure of the benzene dimer cation

NASA Astrophysics Data System (ADS)

Pieniazek, Piotr A.; Krylov, Anna I.; Bradforth, Stephen E.

2007-07-01

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20kcal/mol, while the t-shaped isomer is 6kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between σ and πu states, which correlate to the B˜ and C˜ bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.

Computational design of intrinsic molecular rectifiers based on asymmetric functionalization of N-phenylbenzamide

DOE PAGES

Ding, Wendu; Koepf, Matthieu; Koenigsmann, Christopher; ...

2015-11-03

Here, we report a systematic computational search of molecular frameworks for intrinsic rectification of electron transport. The screening of molecular rectifiers includes 52 molecules and conformers spanning over 9 series of structural motifs. N-Phenylbenzamide is found to be a promising framework with both suitable conductance and rectification properties. A targeted screening performed on 30 additional derivatives and conformers of N-phenylbenzamide yielded enhanced rectification based on asymmetric functionalization. We demonstrate that electron-donating substituent groups that maintain an asymmetric distribution of charge in the dominant transport channel (e.g., HOMO) enhance rectification by raising the channel closer to the Fermi level. These findingsmore » are particularly valuable for the design of molecular assemblies that could ensure directionality of electron transport in a wide range of applications, from molecular electronics to catalytic reactions.« less

Tuning the Direction of Intramolecular Charge Transfer and the Nature of the Fluorescent State in a T-Shaped Molecular Dyad.

PubMed

Felouat, Abdellah; D'Aléo, Anthony; Charaf-Eddin, Azzam; Jacquemin, Denis; Le Guennic, Boris; Kim, Eunsun; Lee, Kwang Jin; Woo, Jae Heun; Ribierre, Jean-Charles; Wu, Jeong Weon; Fages, Frédéric

2015-06-18

Controlling photoinduced intramolecular charge transfer at the molecular scale is key to the development of molecular devices for nanooptoelectronics. Here, we describe the design, synthesis, electronic characterization, and photophysical properties of two electron donor-acceptor molecular systems that consist of tolane and BF2-containing curcuminoid chromophoric subunits connected in a T-shaped arrangement. The two π-conjugated segments intersect at the electron acceptor dioxaborine core. From steady-state electronic absorption and fluorescence emission, we find that the photophysics of the dialkylamino-substituted analogue is governed by the occurrence of two closely lying excited states. From DFT calculations, we show that excitation in either of these two states results in a distinct shift of the electron density, whether it occurs along the curcuminoid or tolane moiety. Femtosecond transient absorption spectroscopy confirmed these findings. As a consequence, the nature of the emitting state and the photophysical properties are strongly dependent on solvent polarity. Moreover, these characteristics can also be switched by protonation or complexation at the nitrogen atom of the amino group. These features set new approaches toward the construction of a three-terminal molecular system in which the lateral branch would transduce a change of electronic state and ultimately control charge transport in a molecular-scale device.

Geometry dependence of electron donating or accepting abilities of amine groups in 4,4‧-disulfanediylbis(methylene)dithiazol-2-amine: Pyramidal versus planar

NASA Astrophysics Data System (ADS)

Karabıyık, Hasan; Kırılmış, Cumhur; Karabıyık, Hande

2017-08-01

The molecular and crystal structure of the title compound in which two thiazole-2-amine rings are linked to each other by disulfide bridge (sbnd Csbnd Ssbnd Ssbnd Csbnd) were studied by single-crystal X-ray diffraction, FT-IR, NMR spectroscopy, quantum chemical calculations and topological analyses on the electron density. A novel synthesis route for the compounds having symmetrical disulfide bridge is reported. The most important result regarding the compound is about electron donating or accepting properties of the terminal amine groups. Planar amine group acts as an electron-donating group, while pyramidal amine behaves as electron-accepting group. This inference was confirmed by scrutiny of crystallographic geometry and quantum chemical studies. To ascertain underlying reasons for this fact, intermolecular interactions (Nsbnd H⋯N type H-bonds and Csbnd H···π interactions) were studied. These interactions involving aromatic thiazole rings are verified by topological electron density and Hirshfeld surface analyses. Intermolecular interactions do not have an effect on the differentiation in electron donating or accepting ability of amine groups, because both amine groups are involved in Nsbnd H⋯N type H-bonds. In methodological sense, it has been understood that Ehrenfest forces acting on electron density are useful theoretical probe to analyze intra-molecular charge transfer processes.

Remote control of the dissociative ionization of H2 based on electron-H2 + entanglement

NASA Astrophysics Data System (ADS)

Wang, Jun-Ping; He, Feng

2018-04-01

The single ionization of H2 in strong laser fields creates the correlated electron-H2 + pair. Based on such a correlation, we conceive a strategy to control the energy spectra of the freed electron or dissociative fragments by simulating the time-dependent Schrödinger equation. Two attosecond pulses in a train produce the replica of electron-H2 + pairs, which are to be steered by a time-delayed phase-stabilized (mid)infrared laser pulse. By controlling the behavior of the freed electron, the dissociation of H2 + can be controlled even though there is no direct laser-H2 + coupling. On the other hand, the photoelectron energy spectra can be manipulated via laser-H2 + coupling. This study demonstrates the entanglement of molecular quantum wave packets, and affords a route to remotely control molecular dissociative ionization.

Excitation and decay of aluminum bulk plasmons at the aluminum/copper phthalocyanine interface

NASA Astrophysics Data System (ADS)

Di Filippo, Gianluca; Sbroscia, Marco; Stefani, Giovanni; Bartynski, Robert A.; Ruocco, Alessandro

2018-06-01

We present the results of an experiment aimed at studying the archetypal properties of the aluminum bulk plasmon at an organic/metal interface. Electron-electron coincidence spectroscopy is used to determine the contribution of aluminum bulk plasmon decay to the ionization of a thin copper phthalocyanine film. The latter directly depends on the amplitude of the bulk plasmon electric field (generated in the metal substrate) protruding inside the molecular overlayer. The emission of low-energy electrons from the clean substrate is dominated by plasmon-assisted ionization events. These events are not observed when the molecules are adsorbed onto the surface. Our findings suggest that, for the considered system, the bulk plasmon wave is confined within the medium in which it is generated and the interaction of the plasmon field with electrons located in the molecular overlayer does not lead to the emission of low-energy electrons.

Design of a Molecular Memory Device: The Electron Transfer Shift Register Memory

NASA Technical Reports Server (NTRS)

Beratan, D.

1993-01-01

A molecular shift register memory at the molecular level is described. The memory elements consist of molecules can exit in either an oxidized or reduced state and the bits are shifted between the cells with photoinduced electron transfer reactions.

Electronuclear paths in the nuclear conversion of molecular hydrogen in silicon

NASA Astrophysics Data System (ADS)

Ilisca, Ernest; Ghiglieno, Filippo

2017-01-01

The ortho-para conversion of hydrogen molecules oscillating inside tetrahedral cages of silicon compounds relies on the interaction of the nuclear protons with the silicon electrons. At each collision against the cage hard walls, the electron repulsion changes the molecular rotation while projecting a valence electron in the antibonding molecular state dressed by a group of conduction ones. That «bridge» facilitates the hyperfine contact of the electrons with the protons. At room temperature, the angular momentum transfer is enhanced by electron fluctuations that overcome the silicon gap and accelerate the nuclear rates by more than one order of magnitude.

Zigzag-Elongated Fused π-Electronic Core: A Molecular Design Strategy to Maximize Charge-Carrier Mobility.

PubMed

Yamamoto, Akito; Murata, Yoshinori; Mitsui, Chikahiko; Ishii, Hiroyuki; Yamagishi, Masakazu; Yano, Masafumi; Sato, Hiroyasu; Yamano, Akihito; Takeya, Jun; Okamoto, Toshihiro

2018-01-01

Printed and flexible electronics requires solution-processable organic semiconductors with a carrier mobility (μ) of ≈10 cm 2 V -1 s -1 as well as high chemical and thermal durability. In this study, chryseno[2,1- b :8,7- b ']dithiophene (ChDT) and its derivatives, which have a zigzag-elongated fused π-electronic core (π-core) and a peculiar highest occupied molecular orbital (HOMO) configuration, are reported as materials with conceptually new semiconducting π-cores. ChDT and its derivatives are prepared by a versatile synthetic procedure. A comprehensive investigation reveals that the ChDT π-core exhibits increasing structural stability in the bulk crystal phase, and that it is unaffected by a variation of the transfer integral, induced by the perpetual molecular motion of organic materials owing to the combination of its molecular shape and its particular HOMO configuration. Notably, ChDT derivatives exhibit excellent chemical and thermal stability, high charge-carrier mobility under ambient conditions (μ ≤ 10 cm 2 V -1 s -1 ), and a crystal phase that is highly stable, even at temperatures above 250 °C.

Evaluating molecular cobalt complexes for the conversion of N2 to NH3.

PubMed

Del Castillo, Trevor J; Thompson, Niklas B; Suess, Daniel L M; Ung, Gaël; Peters, Jonas C

2015-10-05

Well-defined molecular catalysts for the reduction of N2 to NH3 with protons and electrons remain very rare despite decades of interest and are currently limited to systems featuring molybdenum or iron. This report details the synthesis of a molecular cobalt complex that generates superstoichiometric yields of NH3 (>200% NH3 per Co-N2 precursor) via the direct reduction of N2 with protons and electrons. While the NH3 yields reported herein are modest by comparison to those of previously described iron and molybdenum systems, they intimate that other metals are likely to be viable as molecular N2 reduction catalysts. Additionally, a comparison of the featured tris(phosphine)borane Co-N2 complex with structurally related Co-N2 and Fe-N2 species shows how remarkably sensitive the N2 reduction performance of potential precatalysts is. These studies enable consideration of the structural and electronic effects that are likely relevant to N2 conversion activity, including the π basicity, charge state, and geometric flexibility.

Theory of diatomic molecules in an external electromagnetic field from first quantum mechanical principles.

PubMed

Sindelka, Milan; Moiseyev, Nimrod

2006-04-27

We study a general problem of the translational/rotational/vibrational/electronic dynamics of a diatomic molecule exposed to an interaction with an arbitrary external electromagnetic field. The theory developed in this paper is relevant to a variety of specific applications, such as alignment or orientation of molecules by lasers, trapping of ultracold molecules in optical traps, molecular optics and interferometry, rovibrational spectroscopy of molecules in the presence of intense laser light, or generation of high order harmonics from molecules. Starting from the first quantum mechanical principles, we derive an appropriate molecular Hamiltonian suitable for description of the center of mass, rotational, vibrational, and electronic molecular motions driven by the field within the electric dipole approximation. Consequently, the concept of the Born-Oppenheimer separation between the electronic and the nuclear degrees of freedom in the presence of an electromagnetic field is introduced. Special cases of the dc/ac-field limits are then discussed separately. Finally, we consider a perturbative regime of a weak dc/ac field, and obtain simple analytic formulas for the associated Born-Oppenheimer translational/rotational/vibrational molecular Hamiltonian.

1H NMR study of the effect of variable ligand on heme oxygenase electronic and molecular structure

PubMed Central

Ma, Li-Hua; Liu, Yangzhong; Zhang, Xuhong; Yoshida, Tadashi; La Mar, Gerd N.

2009-01-01

Heme oxygenase carries out stereospecific catabolism of protohemin to yield iron, CO and biliverdin. Instability of the physiological oxy complex has necessitated the use of model ligands, of which cyanide and azide are amenable to solution NMR characterization. Since cyanide and azide are contrasting models for bound oxygen, it is of interest to characterize differences in their molecular and/or electronic structures. We report on detailed 2D NMR comparison of the azide and cyanide substrate complexes of heme oxygenase from Neisseria meningitidis, which reveals significant and widespread differences in chemical shifts between the two complexes. To differentiate molecular from electronic structural changes between the two complexes, the anisotropy and orientation of the paramagnetic susceptibility tensor were determined for the azide complex for comparison with those for the cyanide complex. Comparison of the predicted and observed dipolar shifts reveals that shift differences are strongly dominated by differences in electronic structure and do not provide any evidence for detectable differences in molecular structure or hydrogen bonding except in the immediate vicinity of the distal ligand. The readily cleaved C-terminus interacts with the active site and saturation-transfer allows difficult heme assignments in the high-spin aquo complex. PMID:18976815

Vibrational studies on (E)-1-((pyridine-2-yl)methylene)semicarbazide using experimental and theoretical method

NASA Astrophysics Data System (ADS)

Subashchandrabose, S.; Ramesh Babu, N.; Saleem, H.; Syed Ali Padusha, M.

2015-08-01

The (E)-1-((pyridine-2-yl)methylene)semicarbazide (PMSC) was synthesized. The experimental and theoretical study on molecular structure and vibrational spectra were carried out. The FT-IR (400-4000 cm-1), FT-Raman (50-3500 cm-1) and UV-Vis (200-500 nm) spectra of PMSC were recorded. The geometric structure, conformational analysis, vibrational wavenumbers of PMSC in the ground state have been calculated using B3LYP method of 6-311++G(d,p) basis set. The complete vibrational assignments were made on the basis of TED, calculated by SQM method. The Non-linear optical activity was measured by means of first order hyperpolarizability calculation and π-electrons of conjugative bond in the molecule. The intra-molecular charge transfer, mode hyperconjugative interaction and molecular stabilization energies were calculated. The band gap energies between occupied and unoccupied molecular orbitals were analyzed; it proposes lesser band gap with more reactivity. To understand the electronic properties of this molecule the Mulliken charges were also calculated.

NGC 3503 and its molecular environment

NASA Astrophysics Data System (ADS)

Duronea, N. U.; Vasquez, J.; Cappa, C. E.; Corti, M.; Arnal, E. M.

2012-01-01

Aims: We present a study of the molecular gas and interstellar dust distribution in the environs of the Hii region NGC 3503 associated with the open cluster Pis 17 with the aim of investigating the spatial distribution of the molecular gas linked to the nebula and achieving a better understanding of the interaction of the nebula and Pis 17 with their molecular environment. Methods: We based our study on 12CO(1-0) observations of a region of ~0.6° in size obtained with the 4-m NANTEN telescope, unpublished radio continuum data at 4800 and 8640 MHz obtained with the ATCA telescope, radio continuum data at 843 MHz obtained from SUMSS, and available IRAS, MSX, IRAC-GLIMPSE, and MIPSGAL images. Results: We found a molecular cloud (Component 1) having a mean velocity of -24.7 km s-1 ,compatible with the velocity of the ionized gas, which is associated with the nebula and its surroundings. Adopting a distance of 2.9 ± 0.4 kpc, the total molecular mass yields (7.6 ± 2.1) × 103M⊙ and density yields 400 ± 240 cm-3. The radio continuum data confirm the existence of an electron density gradient in NGC 3503. The IR emission shows a PDR bordering the higher density regions of the nebula. The spatial distribution of the CO emission shows that the nebula coincides with a molecular clump, and the strongest CO emission peak is located close to the higher electron density region. The more negative velocities of the molecular gas (about -27 km s-1), are coincident with NGC 3503. Candidate young stellar objects (YSOs) were detected toward the Hii region, suggesting that embedded star formation may be occurring in the neighborhood of the nebula. The clear electron density gradient, along with the spatial distribution of the molecular gas and PAHs in the region indicates that NGC 3503 is a blister-type Hii region that has probably undergone a champagne phase.

A computational study on the electronic and nonlinear optical properties of graphyne subunit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bahat, Mehmet, E-mail: bahat@gazi.edu.tr; Güney, Merve Nurhan, E-mail: merveng87@gmail.com; Özbay, Akif, E-mail: aozbay@gazi.edu.tr

2016-03-25

After discovery of graphene, it has been considered as basic material for the future nanoelectronic devices. Graphyne is a two- dimensional carbon allotropes as graphene which expected that its electronic properties is potentialy superior to graphene. The compound C{sub 24}H{sub 12} (tribenzocyclyne; TBC) is a substructure of graphyne. The electronic, and nonlinear optical properties of the C{sub 24}H{sub 12} and its some fluoro derivatives were calculated. The calculated properties are electric dipole moment, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies, polarizability and first hyperpolarizability. All calculations were performed at the B3LYP/6-31+G(d,p) level.

Multichannel modeling and two-photon coherent transfer paths in NaK

NASA Astrophysics Data System (ADS)

Schulze, T. A.; Temelkov, I. I.; Gempel, M. W.; Hartmann, T.; Knöckel, H.; Ospelkaus, S.; Tiemann, E.

2013-08-01

We explore possible pathways for the creation of ultracold polar NaK molecules in their absolute electronic and rovibrational ground state starting from ultracold Feshbach molecules. In particular, we present a multichannel analysis of the electronic ground and K(4p)+Na(3s) excited-state manifold of NaK, analyze the spin character of both the Feshbach molecular state and the electronically excited intermediate states and discuss possible coherent two-photon transfer paths from Feshbach molecules to rovibronic ground-state molecules. The theoretical study is complemented by the demonstration of stimulated Raman adiabatic passage from the X1Σ+(v=0) state to the a3Σ+ manifold on a molecular beam experiment.

SOMO–HOMO Level Inversion in Biologically Important Radicals

PubMed Central

2017-01-01

Conventionally, the singly occupied molecular orbital (SOMO) of a radical species is considered to be the highest occupied molecular orbital (HOMO), but this is not the case always. In this study, we considered a number of radicals from smallest diatomic anion radicals such as superoxide anion radical to one-electron oxidized DNA related base radicals that show the SOMO is energetically lower than one or more doubly occupied molecular orbitals (MOs) (SOMO–HOMO level inversion). The electronic configurations are calculated employing the B3LYP/6-31++G** method, with the inclusion of aqueous phase via the integral equation formalism of the polarized continuum model solvation model. From the extensive study of the electronic configurations of radicals produced by one-electron oxidation or reduction of natural-DNA bases, bromine-, sulfur-, selenium-, and aza-substituted DNA bases, as well as 20 diatomic molecules, we highlight the following important findings: (i) SOMO–HOMO level inversion is a common phenomenon in radical species. (ii) The more localized spin density in σ-orbital on a single atom (carbon, nitrogen, oxygen, sulfur, or selenium), the greater the gap between HOMO and SOMO. (iii) In species with SOMO–HOMO level inversion, one-electron oxidation takes place from HOMO not from the SOMO, which produces a molecule in its triplet ground state. Oxidation of aqueous superoxide anion producing triplet molecular oxygen is one example of many. (iv) These results are for conventional radicals and in contrast with those reported for distonic radical anions in which SOMO–HOMO gaps are smaller for more localized radicals and the orbital inversions vanish in water. Our findings yield new insights into the properties of free radical systems. PMID:29240424

TCNQ molecular semiconductor of the Cu(II)TAAB macrocycle: Optical and electrical properties.

PubMed

Sánchez Vergara, M E; Salcedo, R; Molina, Bertha; Carrera-Téllez, R; Álvarez-Bada, J R; Hernández-García, A; Gómez-Vidales, V

2018-07-05

The present study reports the doping of a semiconducting molecular material through the formation of hydrogen bonds between the macrocycle Cu(II)(TAAB) and the electronic acceptor TCNQ. According to density functional theory (DFT) calculations and electron paramagnetic resonance (EPR) analysis, the doped compound has the shape of a distorted square pyramid, with four nitrogen atoms in the equatorial position and the apical oxygen atom from the water ligands. These water molecules can generate strong hydrogen bonds with TCNQ and the TAAB metallic complex. Thin films of copper molecular material were obtained through high vacuum evaporation and were structurally characterized by IR spectroscopy, EPR and scanning electron microscopy (SEM). Additionally, the absorption coefficient (α) and photon energy (hν) were calculated from UV-vis spectroscopy and used to determine the optical activation energy in each film, from which its semiconducting behavior was established. An important aspect to consider is that the presence of hydrogen bonds is essential to establish the semiconducting nature of these species; this chemical behavior, as well as the resulting electronic mobility, have been studied by DFT theoretical calculations, which reinforce the experimental conclusion of a relationship between Cu(II)TAAB and TCNQ moieties generated by a weak bond. Finally, I-V characteristics have been obtained from a glass/ITO/doped molecular semiconductor/Ag device using Ag and ITO electrodes. Results for the copper-based device show that, at low voltages, the conduction process is of an ohmic nature while, at higher voltages, space-charge-limited current (SCLC) is found. It is highly probable that the doping effect in TCNQ favors electronic transport due to the formation of conduction channels caused by dopant-favored anisotropy. Copyright © 2018 Elsevier B.V. All rights reserved.

GRC-2011-C-03754

NASA Image and Video Library

2007-09-26

Molecular Electronics; Polymeric Films; Two-Terminal and Three-Terminal Devices Intended for the Development and/or Demonstration of Molecular Electronics Devices such as Field Effect Transistors, FETs

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

PubMed

Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

2014-02-25

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Nuclear conversion theory: molecular hydrogen in non-magnetic insulators

NASA Astrophysics Data System (ADS)

Ilisca, Ernest; Ghiglieno, Filippo

2016-09-01

The hydrogen conversion patterns on non-magnetic solids sensitively depend upon the degree of singlet/triplet mixing in the intermediates of the catalytic reaction. Three main `symmetry-breaking' interactions are brought together. In a typical channel, the electron spin-orbit (SO) couplings introduce some magnetic excitations in the non-magnetic solid ground state. The electron spin is exchanged with a molecular one by the electric molecule-solid electron repulsion, mixing the bonding and antibonding states and affecting the molecule rotation. Finally, the magnetic hyperfine contact transfers the electron spin angular momentum to the nuclei. Two families of channels are considered and a simple criterion based on the SO coupling strength is proposed to select the most efficient one. The denoted `electronic' conversion path involves an emission of excitons that propagate and disintegrate in the bulk. In the other denoted `nuclear', the excited electron states are transients of a loop, and the electron system returns to its fundamental ground state. The described model enlarges previous studies by extending the electron basis to charge-transfer states and `continui' of band states, and focuses on the broadening of the antibonding molecular excited state by the solid conduction band that provides efficient tunnelling paths for the hydrogen conversion. After working out the general conversion algebra, the conversion rates of hydrogen on insulating and semiconductor solids are related to a few molecule-solid parameters (gap width, ionization and affinity potentials) and compared with experimental measures.

Molecular alignment effect on the photoassociation process via a pump-dump scheme.

PubMed

Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

2015-09-07

The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X(1)Σ(+)) is associated into the molecule in the bound states of the excited state (A(1)Σ(+)) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

Molecular alignment effect on the photoassociation process via a pump-dump scheme

NASA Astrophysics Data System (ADS)

Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

2015-09-01

The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1Σ+) is associated into the molecule in the bound states of the excited state (A1Σ+) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j> on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

Binding energies of benzene on coinage metal surfaces: Equal stability on different metals

NASA Astrophysics Data System (ADS)

Maaß, Friedrich; Jiang, Yingda; Liu, Wei; Tkatchenko, Alexandre; Tegeder, Petra

2018-06-01

Interfaces between organic molecules and inorganic solids adapt a prominent role in fundamental science, catalysis, molecular sensors, and molecular electronics. The molecular adsorption geometry, which is dictated by the strength of lateral and vertical interactions, determines the electronic structure of the molecule/substrate system. In this study, we investigate the binding properties of benzene on the noble metal surfaces Au(111), Ag(111), and Cu(111), respectively, using temperature-programmed desorption and first-principles calculations that account for non-locality of both electronic exchange and correlation effects. In the monolayer regime, we observed for all three systems a decrease of the binding energy with increasing coverage due to repulsive adsorbate/adsorbate interactions. Although the electronic properties of the noble metal surfaces are rather different, the binding strength of benzene on these surfaces is equal within the experimental error (accuracy of 0.05 eV), in excellent agreement with our calculations. This points toward the existence of a universal trend for the binding energy of aromatic molecules resulting from a subtle balance between Pauli repulsion and many-body van der Waals attraction.

Intermolecular Coulombic Decay (ICD) Occuring in Triatomic Molecular Dimer

NASA Astrophysics Data System (ADS)

Iskandar, Wael; Gatton, Averell; Gaire, Bishwanath; Champenois, Elio; Larsen, Kirk; Shivaram, Niranjan; Moradmand, Ali; Severt, Travis; Williams, Joshua; Slaughter, Daniel; Weber, Thorsten

2017-04-01

For over two decades, the production of ICD process has been extensively investigated theoretically and experimentally in different systems bounded by a week force (ex. van-der-Waals or Hydrogen force). Furthermore, the ICD process has been demonstrated a strong implication in biological system (DNA damage and DNA repair mechanism) because of the production of genotoxic low energy electrons during the decay cascade. Studying large complex system such as triatomic molecular dimer may be helpful for further exploration of ``Auger electron driven cancer therapy''. The present experiment investigates the dissociation dynamics happened in collision between a photons and CO2 dimer. We will focus more specifically on the CO2++CO2+ fragmentation channel and the detection in coincidence of the two ionic fragments and the two electrons will be done using a COld Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The measurements of the Kinetic Energy Release of the two fragments and the relative angular distribution of the electrons in the molecular frame reveal that the ICD is the only mechanism responsible for the production of this fragmentation channel.

Calculations of Electron Transport through Radicals

NASA Astrophysics Data System (ADS)

Smeu, Manuel; Dilabio, Gino

2010-03-01

Organic radicals are of interest in molecular electronics because a singly occupied molecular orbital (SOMO) would have a higher energy than its doubly occupied analog, suggesting they might make better conductors. The unpaired electron present in a radical leads to degeneracy splitting in other energy levels and such molecules may act as spin filters. Our study employs first principles transport calculations that are performed using a combination of density functional theory and a non-equilibrium Green's function technique. The conductance of 1,4-benzenediamine (BDA) molecules bridging two Au electrodes was modeled. These molecules were substituted in the 2-position with: -CH3, -NH2, and -OH; as well as with their radical analogs: -CH2, -NH, and -O, all of which have π-type SOMOs. The conductance of a radical with a σ-type SOMO was also calculated from a BDA molecule with the H atom in the 2-position removed. Comparing the transmission spectra for these species will yield insight into the nature of electron transport through radicals vs. transport through their reduced form as well as the nature of transport through π- and σ-type molecular orbitals.

Reactions of hydrated electrons (H2O)n- with carbon dioxide and molecular oxygen: hydration of the CO2- and O2- ions.

PubMed

Balaj, O Petru; Siu, Chi-Kit; Balteanu, Iulia; Beyer, Martin K; Bondybey, Vladimir E

2004-10-04

The gas-phase reactions of hydrated electrons with carbon dioxide and molecular oxygen were studied by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Both CO2 and O2 react efficiently with (H2O)n- because they possess low-lying empty pi* orbitals. The molecular CO2- and O2- anions are concurrently solvated and stabilized by the water ligands to form CO2(-)(H2O)n and O2(-)(H2O)n. Core exchange reactions are also observed, in which CO2(-)(H2O)n is transformed into O2(-)(H2O)n upon collision with O2. This is in agreement with the prediction based on density functional theory calculations that O2(-)(H2O)n clusters are thermodynamically favored with respect to CO2(-)(H2O)n. Electron detachment from the product species is only observed for CO2(-)(H2O)2, in agreement with the calculated electron affinities and solvation energies.

Probing molecular dynamics in solution with x-ray valence-to-core spectroscopy

NASA Astrophysics Data System (ADS)

Doumy, Gilles; March, Anne Marie; Tu, Ming-Feng; Al Haddad, Andre; Southworth, Stephen; Young, Linda; Walko, Donald; Bostedt, Christoph

2017-04-01

Hard X-ray spectroscopies are powerful tools for probing the electronic and geometric structure of molecules in complex or disordered systems and have been particularly useful for studying molecules in the solution phase. They are element specific, sensitive to the electronic structure and the local arrangements of surrounding atoms of the element being selectively probed. When combined in a pump-probe scheme with ultrafast lasers, X-ray spectroscopies can be used to track the evolution of structural changes that occur after photoexcitation. Efficient use of hard x-ray radiation coming from high brilliance synchrotrons and upcoming high repetition rate X-ray Free Electron Lasers requires MHz repetition rate lasers and data acquisition systems. High information content Valence-to-Core x-ray emission is directly sensitive to the molecular orbitals involved in photochemistry. We report on recent progress towards fully enabling this photon-hungry technique for the study of time-resolved molecular dynamics, including efficient detection and use of polychromatic x-ray micro-probe at the Advanced Photon Source. Work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation.

PubMed

Heck, Alexander; Woiczikowski, P Benjamin; Kubař, Tomáš; Giese, Bernd; Elstner, Marcus; Steinbrecher, Thomas B

2012-02-23

Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist. © 2012 American Chemical Society

Multi-channel dynamics in high harmonic generation of aligned CO2: ab initio analysis with time-dependent B-spline algebraic diagrammatic construction.

PubMed

Ruberti, M; Decleva, P; Averbukh, V

2018-03-28

Here we present a fully ab initio study of the high-order harmonic generation (HHG) spectrum of aligned CO 2 molecules. The calculations have been performed by using the molecular time-dependent (TD) B-spline algebraic diagrammatic construction (ADC) method. We quantitatively study how the sub-cycle laser-driven multi-channel dynamics, as reflected in the position of the dynamical minimum in the HHG spectrum, is affected by the full inclusion of both correlation-driven and laser-driven dipole interchannel couplings. We calculate channel-resolved spectral intensities as well as the phase differences between contributions of the different ionization-recombination channels to the total HHG spectrum. Our results show that electron correlation effectively controls the relative contributions of the different channels to the total HHG spectrum, leading to the opening of the new ones (1 2 Π u , 1 2 Σ), previously disregarded for the aligned molecular setup. We conclude that inclusion of many-electron effects into the theoretical interpretation of molecular HHG spectra is essential in order to correctly extract ultrafast electron dynamics using HHG spectroscopy.

Observation of molecular level behavior in molecular electronic junction device

NASA Astrophysics Data System (ADS)

Maitani, Masato

In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs utilized with strong surface dipole-dipole intermolecular interaction based on hydrogen bonding and ionic bonding potentially preventing the metal penetration. The observed results are discussed with kinetic paths of metal atoms on each SAM including temporal vacancies controlled by the intermolecular interactions in SAM upon the comparison with the spectroscopic results previously reported. The results in chapter 2 and 3 strongly suggests that AFM based characterization technique is powerful tool especially for detecting molecular-size local phenomena in vapor phase metal deposition process, especially, the electric short-circuit filaments growing through SAMs, which may induce critical misinterpretation of M3 junction device properties. In Chapter 4, an altered metal deposition process on inert SAM with using a buffer layer is performed to diminish the kinetic energy of impinging metal atoms. SPM characterization reveals an abrupt metal-SAM interface without any metal penetration. Examined electric characteristics also revealed typical non-resonant tunneling characteristics of long chain alkane thiolate SAMs. In chapter 5, the buffer layer assisted growth process is used to prepare a nano particles-SAM pristine interface on SAMs to control the metal-SAM interaction in order to study the fundamental issue of chemical enhancement mechanism of SERS. Identical Au nanoparticles-SAM-Au M3 structures with different Au-SAM interactions reveal a large discrepancy of enhancement factors of ˜100 attributed to the chemical interaction. In chapter 6, Raman spectroscopy of M3 junction is applied to the characterization of molecular electronics devices. A crossed nanowire junction (X-nWJ) device is employed for in-situ electronic-spectroscopic simultaneous characterization using Raman spectroscopy. A detailed study reveals the multi-probe capability of X-nWJ for in-situ Raman and in-elastic electron tunneling spectroscopy (IETS) as vibrational spectroscopies to diagnose molecular electronic devices. In chapter 7, aniline oligomer (OAn) based redox SAMs are characterized by spectroscopic and microscopic methods under different chemical redox states by reflection absorption infrared spectroscopy (RAIRS), Raman, x-ray photoelectron spectroscopy (XPS), and AFM in order to elucidate the mechanism of electric switching molecular junctions previously reported. Obtained results are discussed in terms of the chemical and geometrical conformations of molecules in closely packed SAM domains. In chapter 8, in-situ Raman spectroscopy and cp-AFM microscopic techniques are applied to study the electric switching characteristics of X-nWJ incorporating OAn based SAM. The results of tunneling current and in-situ Raman spectroscopy are discussed with the conformational change of OAn component. The conductance switching mechanism associated with domain conformation change of OAn SAM is proposed and evaluated based on the results.

Electronic excitations in molecular solids: bridging theory and experiment.

PubMed

Skelton, Jonathan M; da Silva, E Lora; Crespo-Otero, Rachel; Hatcher, Lauren E; Raithby, Paul R; Parker, Stephen C; Walsh, Aron

2015-01-01

As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.

Toward tunable doping in graphene FETs by molecular self-assembled monolayers

NASA Astrophysics Data System (ADS)

Li, Bing; Klekachev, Alexander V.; Cantoro, Mirco; Huyghebaert, Cedric; Stesmans, André; Asselberghs, Inge; de Gendt, Stefan; de Feyter, Steven

2013-09-01

In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant.In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant. Electronic supplementary information (ESI) available: AFM images of self-assembled monolayers of OA on HOPG; AFM height image of the graphene surface on a SiC substrate; high resolution STM image of a self-assembled monolayer of OA on HOPG; transfer curves of a graphene FET with and without baking steps; transfer curves of a graphene FET under high vacuum conditions; transfer curves of a graphene FET and its Raman response before and after OA treatment; transfer curves of a graphene FET before and after rinsing with n-hexane. See DOI: 10.1039/c3nr01255g

Electronic and transport properties of a molecular junction with asymmetric contacts.

PubMed

Tsai, M-H; Lu, T-H

2010-02-10

Asymmetric molecular junctions have been shown experimentally to exhibit a dual-conductance transport property with a pulse-like current-voltage characteristic, by Reed and co-workers. Using a recently developed first-principles integrated piecewise thermal equilibrium current calculation method and a gold-benzene-1-olate-4-thiolate-gold model molecular junction, this unusual transport property has been reproduced. Analysis of the electrostatics and the electronic structure reveals that the high-current state results from subtle bias induced charge transfer at the electrode-molecule contacts that raises molecular orbital energies and enhances the current-contributing molecular density of states and the probabilities of resonance tunneling of conduction electrons from one electrode to another.

Chapter 5 Multiple, Localized, and Delocalized/Conjugated Bonds in the Orbital Communication Theory of Molecular Systems

NASA Astrophysics Data System (ADS)

Nalewajski, Roman F.

Information theory (IT) probe of the molecular electronic structure, within the communication theory of chemical bonds (CTCB), uses the standard entropy/information descriptors of the Shannon theory of communication to characterize a scattering of the electronic probabilities and their information content throughout the system chemical bonds generated by the occupied molecular orbitals (MO). These "communications" between the basis-set orbitals are determined by the two-orbital conditional probabilities: one- and two-electron in character. They define the molecular information system, in which the electron-allocation "signals" are transmitted between various orbital "inputs" and "outputs". It is argued, using the quantum mechanical superposition principle, that the one-electron conditional probabilities are proportional to the squares of corresponding elements of the charge and bond-order (CBO) matrix of the standard LCAO MO theory. Therefore, the probability of the interorbital connections in the molecular communication system is directly related to Wiberg's quadratic covalency indices of chemical bonds. The conditional-entropy (communication "noise") and mutual-information (information capacity) descriptors of these molecular channels generate the IT-covalent and IT-ionic bond components, respectively. The former reflects the electron delocalization (indeterminacy) due to the orbital mixing, throughout all chemical bonds in the system under consideration. The latter characterizes the localization (determinacy) in the probability scattering in the molecule. These two IT indices, respectively, indicate a fraction of the input information lost in the channel output, due to the communication noise, and its surviving part, due to deterministic elements in probability scattering in the molecular network. Together, these two components generate the system overall bond index. By a straightforward output reduction (condensation) of the molecular channel, the IT indices of molecular fragments, for example, localized bonds, functional groups, and forward and back donations accompanying the bond formation, and so on, can be extracted. The flow of information in such molecular communication networks is investigated in several prototype molecules. These illustrative (model) applications of the orbital communication theory of chemical bonds (CTCB) deal with several classical issues in the electronic structure theory: atom hybridization/promotion, single and multiple chemical bonds, bond conjugation, and so on. The localized bonds in hydrides and delocalized [pi]-bonds in simple hydrocarbons, as well as the multiple bonds in CO and CO2, are diagnosed using the entropy/information descriptors of CTCB. The atom promotion in hydrides and bond conjugation in [pi]-electron systems are investigated in more detail. A major drawback of the previous two-electron approach to molecular channels, namely, two weak bond differentiation in aromatic systems, has been shown to be remedied in the one-electron approach.

Electronic and mechanical characteristics of stacked dimer molecular junctions.

PubMed

Magyarkuti, András; Adak, Olgun; Halbritter, Andras; Venkataraman, Latha

2018-02-15

Break-junction measurements are typically aimed at characterizing electronic properties of single molecules bound between two metal electrodes. Although these measurements have provided structure-function relationships for such devices, there is little work that studies the impact of molecule-molecule interactions on junction characteristics. Here, we use a scanning tunneling microscope based break-junction technique to study pi-stacked dimer junctions formed with two amine-terminated conjugated molecules. We show that the conductance, force and flicker noise of such dimers differ dramatically when compared with the corresponding monomer junctions and discuss the implications of these results on intra- and inter-molecular charge transport.

Quantitative structure-retention relationship studies using immobilized artificial membrane chromatography I: amended linear solvation energy relationships with the introduction of a molecular electronic factor.

PubMed

Li, Jie; Sun, Jin; Cui, Shengmiao; He, Zhonggui

2006-11-03

Linear solvation energy relationships (LSERs) amended by the introduction of a molecular electronic factor were employed to establish quantitative structure-retention relationships using immobilized artificial membrane (IAM) chromatography, in particular ionizable solutes. The chromatographic indices, log k(IAM), were determined by HPLC on an IAM.PC.DD2 column for 53 structurally diverse compounds, including neutral, acidic and basic compounds. Unlike neutral compounds, the IAM chromatographic retention of ionizable compounds was affected by their molecular charge state. When the mean net charge per molecule (delta) was introduced into the amended LSER as the sixth variable, the LSER regression coefficient was significantly improved for the test set including ionizable solutes. The delta coefficients of acidic and basic compounds were quite different indicating that the molecular electronic factor had a markedly different impact on the retention of acidic and basic compounds on IAM column. Ionization of acidic compounds containing a carboxylic group tended to impair their retention on IAM, while the ionization of basic compounds did not have such a marked effect. In addition, the extra-interaction with the polar head of phospholipids might cause a certain change in the retention of basic compounds. A comparison of calculated and experimental retention indices suggested that the semi-empirical LSER amended by the addition of a molecular electronic factor was able to reproduce adequately the experimental retention factors of the structurally diverse solutes investigated.

Noncovalent Molecular Electronics.

PubMed

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

Molecular engineering of phosphole-based conjugated materials

NASA Astrophysics Data System (ADS)

Ren, Yi

The work in this thesis focuses on the molecular engineering of phosphorus-based conjugated materials. In the first part (Chapters Two and Three), new phosphorus-based conjugated systems were designed and synthesized to study the effect of the heteroelement on the electronic properties of the π-conjugated systems. The second part (Chapters Four and Five) deals with the self-assembly features of specifically designed phosphorus-based conjugated systems. In Chapter Two, electron-poor and electron-rich aromatic substituents were introduced to the dithienophosphole core in order to balance the electron-accepting and electron-donating character of the systems. Furthermore, an intriguing intramolecular charge transfer process could be observed between two dithienophosphole cores in a bridged bisphosphole-system. In Chapter Three, a secondary heteroelement (Si, P, S) was incorporated in the phosphorus-based conjugated systems. Extensive structure-property studies revealed that the secondary heteroelement can effectively manipulate the communication in phosphinine-based systems. The study of a heterotetracene system allowed for selectively applying distinct heteroatom (S/P) chemistries, which offers a powerful tool for the modification of the electronic structure of the system. More importantly, the heteroatom-specific electronic nature (S/P) can be utilized to selectively control different photophysical aspects (energy gap and fluorescence quantum yield). Furthermore, additional molecular engineering of the heterotetracene provided access to well-defined 1D microstructures, which opened the door for designing multi-functional self-assembled phosphorus-based materials. In Chapter Four, the self-organizing phosphole-lipid system is introduced, which combines the features of phospholipids with the electronics of phospholes. Its amphiphilic nature induces intriguing self-assembly features - liquid crystal and soft crystal architectures, both exhibiting well-organized lamellar structure at a wide range of temperatures. Importantly, its dynamic structure endows the phosphole-lipid system with intriguing external stimuli-responsive features allowing for the modification of the emission of the system without further chemical modification. Chapter Five describes how further molecular engineering allowed for access to a series of new highly fluorescent phosphole-lipid organogels. Remarkably, the external-stimuli responsive features of the system can be amplified in a donor-acceptor system accessible through changes in long distance fluorescence resonance energy transfer processes. In addition, the first fluorescent liquid phospholes could also be accessed in the context of the work on the new phosphole-lipid system.

The molecular shape and the field similarities as criteria to interpret SAR studies for fragment-based design of platinum(IV) anticancer agents. Correlation of physicochemical properties with cytotoxicity.

PubMed

Lorenzo, Julia; Montaña, Ángel M

2016-09-01

Molecular shape similarity and field similarity have been used to interpret, in a qualitative way, the structure-activity relationships in a selected series of platinum(IV) complexes with anticancer activity. MM and QM calculations have been used to estimate the electron density, electrostatic potential maps, partial charges, dipolar moments and other parameters to correlate the stereo-electronic properties with the differential biological activity of complexes. Extended Electron Distribution (XED) field similarity has been also evaluated for the free 1,4-diamino carrier ligands, in a fragment-based drug design approach, comparing Connolly solvent excluded surface, hydrophobicity field surface, Van der Waals field surface, nucleophilicity field surface, electrophilicity field surface and the extended electron-distribution maxima field points. A consistency has been found when comparing the stereo-electronic properties of the studied series of platinum(IV) complexes and/or the free ligands evaluated and their in vitro anticancer activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular spintronics using single-molecule magnets

NASA Astrophysics Data System (ADS)

Bogani, Lapo; Wernsdorfer, Wolfgang

2008-03-01

A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

Development of an apparatus for obtaining molecular beams in the energy range from 2 to 200 eV

NASA Technical Reports Server (NTRS)

Clapier, R.; Devienne, F. M.; Roustan, A.; Roustan, J. C.

1985-01-01

The formation and detection of molecular beams obtained by charge exchange from a low-energy ion source is discussed. Dispersion in energy of the ion source was measured and problems concerning detection of neutral beams were studied. Various methods were used, specifically secondary electron emissivity of a metallic surface and ionization of a gas target with a low ionization voltage. The intensities of neutral beams as low as 10 eV are measured by a tubular electron multiplier and a lock-in amplifier.

Comparison of molecular structure of alkali metal o-, m- and p-nitrobenzoates

NASA Astrophysics Data System (ADS)

Regulska, E.; Świsłocka, R.; Samsonowicz, M.; Lewandowski, W.

2008-09-01

The influence of nitro-substituent in ortho, meta and para positions as well as lithium, sodium, potassium, rubidium and cesium on the electronic system of aromatic ring and the distribution of electronic charge in carboxylic group of the nitrobenzoates were estimated. Optimized geometrical structures were calculated (B3LYP/6-311++G ∗∗). To make quantitative evaluation of aromaticity of studied molecules the geometric (A J, BAC, I 6 and HOMA) as well as magnetic (NICS) aromaticity indices were calculated. Electronic charge distribution was also examined by molecular spectroscopic study, which may be the source of quality criterion for aromaticity. Experimental and theoretical FT-IR, FT-Raman and NMR ( 1H and 13C) spectra of the title compounds were analyzed. The calculated parameters were compared to experimental characteristics of these molecules.

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

NASA Astrophysics Data System (ADS)

Balliou, A.; Douvas, A. M.; Normand, P.; Tsikritzis, D.; Kennou, S.; Argitis, P.; Glezos, N.

2014-10-01

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW12O403-, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

Atomic selectivity in dissociative electron attachment to dihalobenzenes.

PubMed

Kim, Namdoo; Sohn, Taeil; Lee, Sang Hak; Nandi, Dhananjay; Kim, Seong Keun

2013-10-21

We investigated electron attachment to three dihalobenzene molecules, bromochlorobenzene (BCB), bromoiodobenzene (BIB) and chloroiodobenzene (CIB), by molecular beam photoelectron spectroscopy. The most prominent product of electron attachment in the anion mass spectra was the atomic fragment of the less electronegative halogen of the two, i.e., Br(-) for BCB and I(-) for BIB and CIB. Photoelectron spectroscopy and ab initio calculations suggested that the approaching electron prefers to attack the less electronegative atom, a seemingly counterintuitive finding but consistent with the mass spectrometric result. For the iodine-containing species BIB and CIB, the photoelectron spectrum consists of bands from both the molecular anion and atomic I(-), the latter of which is produced by photodissociation of the former. Molecular orbital analysis revealed that a large degree of orbital energy reordering takes place upon electron attachment. These phenomena were shown to be readily explained by simple molecular orbital theory and the electronegativity of the halogen atoms.

Method for Trace Oxygen Detection

NASA Technical Reports Server (NTRS)

Man, Kim Fung (Inventor); Boumsellek, Said (Inventor); Chutjian, Ara (Inventor)

1997-01-01

Trace levels of molecular oxygen are measured by introducing a gas containing the molecular oxygen into a target zone, and impacting the molecular oxygen in the target zone with electrons at the O(-) resonant energy level for dissociative electron attachment to produce O(-) ions. Preferably, the electrons have an energy of about 4 to about 10 eV. The amount of O(-) ions produced is measured, and is correlated with the molecular oxygen content in the target zone. The technique is effective for measuring levels of oxygen below 50 ppb. and even less than 1 ppb. The amount of O(-) can be measured in a quadrupole mass analyzer. Best results are obtained when the electrons have an energy of about 6 to about 8 eV. and preferably about 6.8 eV. The method can be used for other species by selecting the appropriate electron energy level.

Electron- and positron-molecule scattering: development of the molecular convergent close-coupling method

NASA Astrophysics Data System (ADS)

Zammit, Mark C.; Fursa, Dmitry V.; Savage, Jeremy S.; Bray, Igor

2017-06-01

Starting from first principles, this tutorial describes the development of the adiabatic-nuclei convergent close-coupling (CCC) method and its application to electron and (single-centre) positron scattering from diatomic molecules. We give full details of the single-centre expansion CCC method, namely the formulation of the molecular target structure; solving the momentum-space coupled-channel Lippmann-Schwinger equation; deriving adiabatic-nuclei cross sections and calculating V-matrix elements. Selected results are presented for electron and positron scattering from molecular hydrogen H2 and electron scattering from the vibrationally excited molecular hydrogen ion {{{H}}}2+ and its isotopologues (D2 +, {{{T}}}2+, HD+, HT+ and TD+). Convergence in both the close-coupling (target state) and projectile partial-wave expansions of fixed-nuclei electron- and positron-molecule scattering calculations is demonstrated over a broad energy-range and discussed in detail. In general, the CCC results are in good agreement with experiments.

Mechanical properties and the electronic structure of transition of metal alloys

NASA Technical Reports Server (NTRS)

Arsenault, R. J.; Drew, H. D.

1977-01-01

This interdiscipline research program was undertaken in an effort to investigate the relationship between the mechanical strength of Mo based alloys with their electronic structure. Electronic properties of these alloys were examined through optical studies, and the classical solid solution strengthening mechanisms were considered, based on size and molecular differences to determine if these mechanisms could explain the hardness data.

The molecular electronic device and the biochip computer: present status.

PubMed

Haddon, R C; Lamola, A A

1985-04-01

The idea that a single molecule might function as a self-contained electronic device has been of interest for some time. However, a fully integrated version--the biochip or the biocomputer, in which both production and assembly of molecular electronic components is achieved through biotechnology-is a relatively new concept that is currently attracting attention both within the scientific community and among the general public. In the present article we draw together some of the approaches being considered for the construction of such devices and delineate the revolutionary nature of the current proposals for molecular electronic devices (MEDs) and biochip computers (BCCs). With the silicon semiconductor conductor industry already in place and in view of the continuing successes of the lithographic process it seems appropriate to ask why the highly speculative MED or BCC has engendered such interest. In some respects the answer is paradigmatic as much as it is real. It is perhaps best stated as the promise of the realm of the molecular. Thus it is envisioned that devices will be constructed by assembly of individual molecular electronic components into arrays, thereby engineering from small upward rather than large downward as do current lithographic techniques. An important corollary of the construction technique is that the functional elements of such an array would be individual molecules rather than macroscopic ensembles. These two aspects of the MED/BCC--assembly of molecular arrays and individually accessible functional molecular units--are truly revolutionary. Both require scientific breakthroughs and the necessary principles, quite apart from the technology, remain essentially unknown. It is concluded that the advent of the MED/BCC still lies well before us. The twin criteria of utilization of individual molecules as functional elements and the assembly of such elements remains as elusive as ever. Biology engineers structures on the molecular scale but biomolecules do not seem to be imbued with useful electronic properties. Molecular beam epitaxy and thin-film techniques produce electronic devices but they "engineer down" and are currently unable to generate individual molecular units. The potential of the MED/BCC field is matched only by the obstacles that must be surmounted for its realization.

The molecular electronic device and the biochip computer: present status.

PubMed Central

Haddon, R C; Lamola, A A

1985-01-01

The idea that a single molecule might function as a self-contained electronic device has been of interest for some time. However, a fully integrated version--the biochip or the biocomputer, in which both production and assembly of molecular electronic components is achieved through biotechnology-is a relatively new concept that is currently attracting attention both within the scientific community and among the general public. In the present article we draw together some of the approaches being considered for the construction of such devices and delineate the revolutionary nature of the current proposals for molecular electronic devices (MEDs) and biochip computers (BCCs). With the silicon semiconductor conductor industry already in place and in view of the continuing successes of the lithographic process it seems appropriate to ask why the highly speculative MED or BCC has engendered such interest. In some respects the answer is paradigmatic as much as it is real. It is perhaps best stated as the promise of the realm of the molecular. Thus it is envisioned that devices will be constructed by assembly of individual molecular electronic components into arrays, thereby engineering from small upward rather than large downward as do current lithographic techniques. An important corollary of the construction technique is that the functional elements of such an array would be individual molecules rather than macroscopic ensembles. These two aspects of the MED/BCC--assembly of molecular arrays and individually accessible functional molecular units--are truly revolutionary. Both require scientific breakthroughs and the necessary principles, quite apart from the technology, remain essentially unknown. It is concluded that the advent of the MED/BCC still lies well before us. The twin criteria of utilization of individual molecules as functional elements and the assembly of such elements remains as elusive as ever. Biology engineers structures on the molecular scale but biomolecules do not seem to be imbued with useful electronic properties. Molecular beam epitaxy and thin-film techniques produce electronic devices but they "engineer down" and are currently unable to generate individual molecular units. The potential of the MED/BCC field is matched only by the obstacles that must be surmounted for its realization. PMID:3856865

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Study of the subpicosecond rotational molecular dynamics in liquids

NASA Astrophysics Data System (ADS)

Nikiforov, V. G.; Lobkov, Vladimir S.

2006-10-01

The parameters of the femtosecond vibration—rotation molecular dynamics of liquid acetonitrile CH3CN, trimethylacetonitrile (CH3)3CCN, propionitrile CH3CH2CN, fluoroform CHF3, and chloroform CHCl3 are found by analysing the ultrafast optical Kerr effect. The influence of the molecular structure on the features of rotational (diffusion and libration) motions is studied. It is shown that the distribution of libration frequencies is described by the Maxwell distribution.

Electronic structure studies of La2CuO4

NASA Astrophysics Data System (ADS)

Wachs, A. L.; Turchi, P. E. A.; Jean, Y. C.; Wetzler, K. H.; Howell, R. H.; Fluss, M. J.; Harshman, D. R.; Remeika, J. P.; Cooper, A. S.; Fleming, R. M.

1988-07-01

We report results of positron-electron momentum-distribution measurements of single-crystal La2CuO4 using two-dimensional angular correlation of positron-annihilation-radiation techniques. The data contain two components: a large (~85%), isotropic corelike electron contribution and a remaining, anisotropic valence-electron contribution modeled using a linear combination of atomic orbitals-molecular orbital method and a localized ion scheme, within the independent-particle model approximation. This work suggests a ligand-field Hamiltonian to be justified for describing the electronic properties of perovskite materials.

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e H2 vibrational cross section controversy

NASA Astrophysics Data System (ADS)

Robson, R. E.; White, R. D.; Morrison, Michael A.

2003-10-01

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, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent 'source' term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established.

Absolute cross section for low-energy-electron damage to condensed macromolecules: A case study of DNA

PubMed Central

Rezaee, Mohammad; Cloutier, Pierre; Bass, Andrew D.; Michaud, Marc; Hunting, Darel J.; Sanche, Léon

2013-01-01

Cross sections (CSs) for the interaction of low-energy electrons (LEE) with condensed macromolecules are essential parameters for accurate modeling of radiation-induced molecular decomposition and chemical synthesis. Electron irradiation of dry nanometer-scale macromolecular solid films has often been employed to measure CSs and other quantitative parameters for LEE interactions. Since such films have thicknesses comparable with electron thermalization distances, energy deposition varies throughout the film. Moreover, charge accumulation occurring inside the films shields a proportion of the macromolecules from electron irradiation. Such effects complicate the quantitative comparison of the CSs obtained in films of different thicknesses and limit the applicability of such measurements. Here, we develop a simple mathematical model, termed the molecular survival model, that employs a CS for a particular damage process together with an attenuation length related to the total CS, to investigate how a measured CS might be expected to vary with experimental conditions. As a case study, we measure the absolute CS for the formation of DNA strand breaks (SBs) by electron irradiation at 10 and 100 eV of lyophilized plasmid DNA films with thicknesses between 10 and 30 nm. The measurements are shown to depend strongly on the thickness and charging condition of the nanometer-scale films. Such behaviors are in accord with the model and support its validity. Via this analysis, the CS obtained for SB damage is nearly independent of film thickness and charging effects. In principle, this model can be adapted to provide absolute CSs for electron-induced damage or reactions occurring in other molecular solids across a wider range of experimental conditions. PMID:23030950

Probe-based measurement of lateral single-electron transfer between individual molecules

PubMed Central

Steurer, Wolfram; Fatayer, Shadi; Gross, Leo; Meyer, Gerhard

2015-01-01

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques. PMID:26387533

Computational Nanotechnology of Molecular Materials, Electronics, and Actuators with Carbon Nanotubes and Fullerenes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

The role of computational nanotechnology in developing next generation of multifunctional materials, molecular scale electronic and computing devices, sensors, actuators, and machines is described through a brief review of enabling computational techniques and few recent examples derived from computer simulations of carbon nanotube based molecular nanotechnology.

Intra-molecular Charge Transfer and Electron Delocalization in Non-fullerene Organic Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Qinghe; Zhao, Donglin; Goldey, Matthew B.

Two types of electron acceptors were synthesized by coupling two kinds of electron-rich cores with four equivalent perylene diimides (PDIs) at the a position. With fully aromatic cores, TPB and TPSe have pi-orbitals spread continuously over the whole aromatic conjugated backbone, unlike TPC and TPSi, which contain isolated PDI units due to the use of a tetrahedron carbon or silicon linker. Density functional theory calculations of the projected density of states showed that the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) for TPB are localized in separate regions of space. Further, the LUMO of TPB showsmore » a greater contribution from the orbitals belonging to the connective core of the molecules than that of TPC. Overall, the properties of the HOMO and LUMO point at increased intra-molecular delocalization of negative charge carriers for TPB and TPSe than for TPC and TPSi and hence at a more facile intra-molecular charge transfer for the former. The film absorption and emission spectra showed evidences for the inter -molecular electron delocalization in TPB and TPSe, which is consistent with the network structure revealed by X-ray diffraction studies on single crystals of TPB. These features benefit the formation of charge transfer states and/or facilitate charge transport. Thus, higher electron mobility and higher charge dissociation probabilities under J(sc) condition were observed in blend films of TPB:PTB7-Th and TPSe:PTB7-Th than those in TPC:PTB7Th and TPSi:PTB7-Th blend films. As a result, the J(sc) and fill factor values of 15.02 mA/cm(2), 0.58 and 14.36 mA/cm(2), 0.55 for TPB- and TPSe-based solar cell are observed, whereas those for TPC and TPSi are 11.55 mA/cm2, 0.47 and 10.35 mA/cm(2), 0.42, respectively.« less

Charge transfer complex between 2,3-diaminopyridine with chloranilic acid. Synthesis, characterization and DFT, TD-DFT computational studies

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2018-05-01

New charge transfer complex (CTC) between the electron donor 2,3-diaminopyridine (DAP) with the electron acceptor chloranilic (CLA) acid has been synthesized and characterized experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of elemental analysis, UV-vis, IR and 1H NMR studies to characterize the complex. Electronic spectra have been carried out in different hydrogen bonded solvents, methanol (MeOH), acetonitrile (AN) and 1:1 mixture from AN-MeOH. The molecular composition of the complex was identified to be 1:1 from Jobs and molar ratio methods. The stability constant was determined using minimum-maximum absorbances method where it recorded high values confirming the high stability of the formed complex. The solid complex was prepared and characterized by elemental analysis that confirmed its formation in 1:1 stoichiometric ratio. Both IR and NMR studies asserted the existence of proton and charge transfers in the formed complex. For supporting the experimental results, DFT computations were carried out using B3LYP/6-31G(d,p) method to compute the optimized structures of the reactants and complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential map and frontier molecular orbitals. The analysis of DFT results strongly confirmed the high stability of the formed complex based on existing charge transfer beside proton transfer hydrogen bonding concordant with experimental results. The origin of electronic spectra was analyzed using TD-DFT method where the observed λmax are strongly consisted with the computed ones. TD-DFT showed the contributed states for various electronic transitions.

Molecular devices: Caroviologens as an approach to molecular wires—synthesis and incorporation into vesicle membranes

PubMed Central

Arrhenius, Thomas S.; Blanchard-Desce, Mireille; Dvolaitzky, Maya; Lehn, Jean-Marie; Malthete, Jacques

1986-01-01

Molecular wires, which would allow electron flow to take place between different components, are important elements in the design of molecular devices. An approach to such species would be molecules possessing an electron-conducting conjugated chain, terminal electroactive polar groups, and a length sufficient to span a lipid membrane. To this end, bispyridinium polyenes of different lengths have been synthesized and their incorporation into the bilayer membrane of sodium dihexadecyl phosphate vesicles has been studied. Since they combine the features of carotenoids and of viologens, they may be termed caroviologens. Vesicles containing the caroviologen whose length approximately corresponds to the thickness of the sodium dihexadecyl phosphate bilayer display temperature-dependent changes of its absorption spectrum reflecting the gel → liquid-crystal phase transition of the membrane. The data agree with a structural model in which the caroviologens of sufficient length span the bilayer membrane, the pyridinium sites being close to the negatively charged outer and inner surfaces of the sodium dihexadecyl phosphate vesicles and the polyene chain crossing the lipidic interior of the membrane. These membranes may now be tested in processes in which the caroviologen would function as a continuous, transmembrane electron channel—i.e., as a molecular wire. Various further developments may be envisaged along these lines. PMID:16593731

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

PubMed

Xu, ZongRong; Matsika, Spiridoula

2006-11-02

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Karna, Shashi P.

2002-01-01

The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

Electron Solvation in Two Dimensions

NASA Astrophysics Data System (ADS)

Miller, A. D.; Bezel, I.; Gaffney, K. J.; Garrett-Roe, S.; Liu, S. H.; Szymanski, P.; Harris, C. B.

2002-08-01

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.

The impact of long-range electron-hole interaction on the charge separation yield of molecular photocells

NASA Astrophysics Data System (ADS)

Nemati Aram, Tahereh; Ernzerhof, Matthias; Asgari, Asghar; Mayou, Didier

2017-01-01

We discuss the effects of charge carrier interaction and recombination on the operation of molecular photocells. Molecular photocells are devices where the energy conversion process takes place in a single molecular donor-acceptor complex attached to electrodes. Our investigation is based on the quantum scattering theory, in particular on the Lippmann-Schwinger equation; this minimizes the complexity of the problem while providing useful and non-trivial insight into the mechanism governing photocell operation. In this study, both exciton pair creation and dissociation are treated in the energy domain, and therefore there is access to detailed spectral information, which can be used as a framework to interpret the charge separation yield. We demonstrate that the charge carrier separation is a complex process that is affected by different parameters, such as the strength of the electron-hole interaction and the non-radiative recombination rate. Our analysis helps to optimize the charge separation process and the energy transfer in organic solar cells and in molecular photocells.

Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

PubMed

Schwaben, Jonas; Münster, Niels; Klues, Michael; Breuer, Tobias; Hofmann, Philipp; Harms, Klaus; Witte, Gregor; Koert, Ulrich

2015-09-21

Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-activity relationships for novel drug precursor N-substituted-6-acylbenzothiazolon derivatives: A theoretical approach

NASA Astrophysics Data System (ADS)

Sıdır, Yadigar Gülseven; Sıdır, İsa

2013-08-01

In this study, the twelve new modeled N-substituted-6-acylbenzothiazolon derivatives having analgesic analog structure have been investigated by quantum chemical methods using a lot of electronic parameters and structure-activity properties; such as molecular polarizability (α), dipole moment (μ), EHOMO, ELUMO, q-, qH+, molecular volume (Vm), ionization potential (IP), electron affinity (EA), electronegativity (χ), molecular hardness (η), molecular softness (S), electrophilic index (ω), heat of formation (HOF), molar refractivity (MR), octanol-water partition coefficient (log P), thermochemical properties (entropy (S), capacity of heat (Cv)); as to investigate activity relationships with molecular structure. The correlations of log P with Vm, MR, ω, EA, EHOMO - ELUMO (ΔE), HOF in aqueous phase, χ, μ, S, η parameters, respectively are obtained, while the linear relation of log P with IP, Cv, HOF in gas phase are not observed. The log P parameter is obtained to be depending on different properties of compounds due to their complexity.

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Metastable Oxygen Production by Electron-Impact of Oxygen

NASA Astrophysics Data System (ADS)

Hein, Jeffrey; Johnson, Paul; Kanik, Isik; Malone, Charles

2014-05-01

Electron-impact excitation processes involving atomic and molecular oxygen are important in atmospheric interactions. The production of long-lived metastable O(1S) and O(1D) through electron impact of atomic O and molecular O2 play a significant role in the dynamics of oxygen-containing atmospheres (Earth, Europa, Io). Emissions from metastable O (1S --> 1D) produce the well-recognized green light from terrestrial aurora. Electron-impact excitation to 1S and 1D are sensitive channels for determining energy partitioning and dynamics from space weather. Electron-impact excitation cross sections determined through fundamental experimental studies are necessary for modeling of natural phenomena and observation data. The detection of metastable states in laboratory experiments requires a novel approach, since typical detection techniques (e.g., fluorescence by radiative de-excitation) cannot be performed due to the long-lived nature of the excited species. In this work, metastable O is produced through electron impact, and is incident on a cryogenically cooled rare gas matrix. The excimer production and subsequent rapid radiative de-excitation provides measurable signal that is directly related to the originating electron-impact excitation process.

Trapped in imidazole: how to accumulate multiple photoelectrons on a black-absorbing ruthenium complex.

PubMed

Zedler, Linda; Kupfer, Stephan; de Moraes, Inês Rabelo; Wächtler, Maria; Beckert, Rainer; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-03-24

Ruthenium dyes incorporating a 4H-imidazole chromophore as a ligand exhibit a spectrally broad absorption in the UV/Vis region. Furthermore, they show the ability to store two electrons within the 4H-imidazole ligand. These features render them promising molecular systems, for example, as inter- or intramolecular electron relays. To optimize the structures with respect to their electron-storage capability, it is crucial to understand the impact of structural changes accompanying photoinduced charge transfer in the electronic intermediates of multistep electron-transfer processes. The photophysical properties of these (reactive) intermediates might impact the function of the molecular systems quite substantially. However, the spectroscopic study of short-lived intermediates in stepwise multielectron-transfer processes is experimentally challenging. To this end, this contribution reports on the electrochemical generation of anions identical to intermediate structures and their spectroscopic characterization by in situ resonance Raman and UV/Vis spectroelectrochemistry and computational methods. Thereby, an efficient two-electron pathway to the 4H-imidazole electron-accepting ligand is identified. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Astrochemistry at the Cryogenic Storage Ring

NASA Astrophysics Data System (ADS)

Kreckel, Holger; Becker, Arno; Blaum, Klaus; Breitenfeldt, Christian; George, Sebastian; Göck, Jürgen; Grieser, Manfred; Grussie, Florian; Guerin, Elisabeth; Heber, Oded; Karthein, Jonas; Krantz, Claude; Meyer, Christian; Mishra, Preeti; Novotny, Oldrich; O'Connor, Aodh; Saurabh, Sunny; Schippers, Stefan; Spruck, Kaija; Kumar, S. Sunil; Urbain, Xavier; Vogel, Stephen; von Hahn, Robert; Wilhelm, Patrick; Wolf, Andreas; Zajfman, Daniel

2017-01-01

Almost 200 different molecular species have been identified in space, and this number continues to grow steadily. This surprising molecular diversity bears witness to an active reaction network, in which molecular ions are the main drivers of chemistry in the gas phase. To study these reactions under controlled conditions in the laboratory is a major experimental challenge. The new Cryogenic Storage Ring (CSR) that has recently been commissioned at the Max Planck Institute for Nuclear Physics in Heidelberg will serve as an ideal testbed to study cold molecular ions in the gas phase. With residual gas densities of <140 cm-3 and temperatures below 10K, the CSR will allow for merged beams collision studies involving molecular ions, neutral atoms, free electrons and photons under true interstellar conditions.

A Computational Study of Structure and Reactivity of N-Substitued-4-Piperidones Curcumin Analogues and Their Radical Anions.

PubMed

Martínez-Cifuentes, Maximiliano; Weiss-López, Boris; Araya-Maturana, Ramiro

2016-12-02

In this work, a computational study of a series of N -substitued-4-piperidones curcumin analogues is presented. The molecular structure of the neutral molecules and their radical anions, as well as their reactivity, are investigated. N -substituents include methyl and benzyl groups, while substituents on the aromatic rings cover electron-donor and electron-acceptor groups. Substitutions at the nitrogen atom do not significantly affect the geometry and frontier molecular orbitals (FMO) energies of these molecules. On the other hand, substituents on the aromatic rings modify the distribution of FMO. In addition, they influence the capability of these molecules to attach an additional electron, which was studied through adiabatic (AEA) and vertical electron affinities (VEA), as well as vertical detachment energy (VDE). To study electrophilic properties of these structures, local reactivity indices, such as Fukui ( f ⁺) and Parr ( P ⁺) functions, were calculated, and show the influence of the aromatic rings substituents on the reactivity of α,β-unsaturated ketones towards nucleophilic attack. This study has potential implications for the design of curcumin analogues based on a 4-piperidone core with desired reactivity.

Molecular charge distribution and dispersion of electronic states in the contact layer between pentacene and Cu(119) and beyond

NASA Astrophysics Data System (ADS)

Annese, E.; Fujii, J.; Baldacchini, C.; Zhou, B.; Viol, C. E.; Vobornik, I.; Betti, M. G.; Rossi, G.

2008-05-01

The interaction of pentacene molecules in contact with the Cu(119) stepped surface has been directly imaged by scanning tunneling microscopy and analyzed by angle resolved photoemission spectroscopy. Interacting molecules, which are in contact with copper, generate dispersive electronic states associated with a perturbed electron charge density distribution of the molecular orbitals. In contrast, the electron charge density of molecules of the pentacene on top of the first layer, which is not in direct contact with the Cu surface, shows an intramolecular structure very similar to that of the free molecule. Our results indicate that the delocalization of the molecular states in the pentacene/Cu system is confined to the very first molecular layer at the interface.

Electronic Properties of Carbon Nanotubes and Junctions

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Han, Jie; Yang, Liu; Govindan, T. R.; Jaffe, R.; Saini, Subhash (Technical Monitor)

1998-01-01

Metallic and semiconducting Single Wall Carbon Nanotubes (CNT) have recently been characterized using scanning tunneling microscopy (STM) and the manipulation of individual CNT has been demonstrated. These developments make the prospect of using CNT as molecular wires and possibly as electronic devices an even more interesting one. We have been modeling various electronic properties such as the density of states and the transmission coefficient of CNT wires and junctions. These studies involve first calculating the stability of junctions using molecular dynamics simulations and then calculating the electronic properties using a pi-electron tight binding Hamiltonian. We have developed the expertise to calculate the electronic properties of both finite-sized CNT and CNT systems with semi-infinite boundary conditions. In this poster, we will present an overview of some of our results. The electronic application of CNT that is most promising at this time is their use as molecular wires. The conductance can however be greatly reduced because of reflection due to defects and contacts. We have modeled the transmission through CNT in the presence of two types of defects: weak uniform disorder and strong isolated scatterers. We find that the conductance is affected in significantly different manners due to these defects Junctions of CNT have also been imaged using STM. This makes it essential to derive rules for the formation of junctions between tubes of different chirality, study their relative energies and electronic properties. We have generalized the rules for connecting two different CNT and have calculated the transmission and density of states through CNT junctions. Metallic and semiconducting CNT can be joined to form a stable junction and their current versus voltage characteristics are asymmetric. CNT are deformed by the application of external forces including interactions with a substrate or other CNT. In many experiments, these deformation are expected to occur naturally. We will present some preliminary results of our calculations of the modification of CNT electronic properties as a result of deformations.

Exploring the molecular mechanisms of electron shuttling across the microbe/metal space

PubMed Central

Paquete, Catarina M.; Fonseca, Bruno M.; Cruz, Davide R.; Pereira, Tiago M.; Pacheco, Isabel; Soares, Cláudio M.; Louro, Ricardo O.

2014-01-01

Dissimilatory metal reducing organisms play key roles in the biogeochemical cycle of metals as well as in the durability of submerged and buried metallic structures. The molecular mechanisms that support electron transfer across the microbe-metal interface in these organisms remain poorly explored. It is known that outer membrane proteins, in particular multiheme cytochromes, are essential for this type of metabolism, being responsible for direct and indirect, via electron shuttles, interaction with the insoluble electron acceptors. Soluble electron shuttles such as flavins, phenazines, and humic acids are known to enhance extracellular electron transfer. In this work, this phenomenon was explored. All known outer membrane decaheme cytochromes from Shewanella oneidensis MR-1 with known metal terminal reductase activity and a undecaheme cytochrome from Shewanella sp. HRCR-6 were expressed and purified. Their interactions with soluble electron shuttles were studied using stopped-flow kinetics, NMR spectroscopy, and molecular simulations. The results show that despite the structural similarities, expected from the available structural data and sequence homology, the detailed characteristics of their interactions with soluble electron shuttles are different. MtrC and OmcA appear to interact with a variety of different electron shuttles in the close vicinity of some of their hemes, and with affinities that are biologically relevant for the concentrations typical found in the medium for this type of compounds. All data support a view of a distant interaction between the hemes of MtrF and the electron shuttles. For UndA a clear structural characterization was achieved for the interaction with AQDS a humic acid analog. These results provide guidance for future work of the manipulation of these proteins toward modulation of their role in metal attachment and reduction. PMID:25018753

Coherent coupling of molecular resonators with a microcavity mode

NASA Astrophysics Data System (ADS)

Shalabney, A.; George, J.; Hutchison, J.; Pupillo, G.; Genet, C.; Ebbesen, T. W.

2015-01-01

The optical hybridization of the electronic states in strongly coupled molecule-cavity systems have revealed unique properties, such as lasing, room temperature polariton condensation and the modification of excited electronic landscapes involved in molecular isomerization. Here we show that molecular vibrational modes of the electronic ground state can also be coherently coupled with a microcavity mode at room temperature, given the low vibrational thermal occupation factors associated with molecular vibrations, and the collective coupling of a large ensemble of molecules immersed within the cavity-mode volume. This enables the enhancement of the collective Rabi-exchange rate with respect to the single-oscillator coupling strength. The possibility of inducing large shifts in the vibrational frequency of selected molecular bonds should have immediate consequences for chemistry.

Theoretical study on electronic structure of bathocuproine: Renormalization of the band gap in the crystalline state and the large exciton binding energy

NASA Astrophysics Data System (ADS)

Yanagisawa, Susumu; Hatada, Shin-No-Suke; Morikawa, Yoshitada

Bathocuproine (BCP) is a promising organic material of a hole blocking layer in organic light-emitting diodes or an electron buffer layer in organic photovoltaic cells. The nature of the unoccupied electronic states is a key characteristic of the material, which play vital roles in the electron transport. To elucidate the electronic properties of the molecular or crystalline BCP, we use the GW approximation for calculation of the fundamental gap, and the long-range corrected density functional theory for the molecular optical absorption. It is found that the band gap of the BCP single crystal is 4.39 eV, and it is in agreement with the recent low-energy inverse photoemission spectroscopy measurement. The polarization energy is estimated to be larger than 1 eV, demonstrating the large polarization effects induced by the electronic clouds surrounding the injected charge. The theoretical optical absorption energy is 3.68 eV, and the exciton binding energy is estimated to be 0.71 eV, implying the large binding in the eletron-hole pair distributed around the small part of the molecular region. This work was supported by the Grants-in-Aid for Young Scientists (B) (No. 26810009), and for Scientific Research on Innovative Areas ``3D Active-Site Science'' (No. 26105011) from Japan Society for the Promotion of Science.

Developing sensor activity relationships for the JPL electronic nose sensors using molecular modeling and QSAR techniques

NASA Technical Reports Server (NTRS)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Jewell, A. D.; Zhou, H.; Manatt, K.; Kisor, A. K.

2005-01-01

We report a Quantitative Structure-Activity Relationships (QSAR) study using Genetic Function Approximations (GFA) to describe the polymer-carbon composite sensor activities in the JPL Electronic Nose, when exposed to chemical vapors at parts-per-million concentration levels.

Density functional theory and phytochemical study of Pistagremic acid

NASA Astrophysics Data System (ADS)

Ullah, Habib; Rauf, Abdur; Ullah, Zakir; Fazl-i-Sattar; Anwar, Muhammad; Shah, Anwar-ul-Haq Ali; Uddin, Ghias; Ayub, Khurshid

2014-01-01

We report here for the first time a comparative theoretical and experimental study of Pistagremic acid (P.A). We have developed a theoretical model for obtaining the electronic and spectroscopic properties of P.A. The simulated data showed nice correlation with the experimental data. The geometric and electronic properties were simulated at B3LYP/6-31 G (d, p) level of density functional theory (DFT). The optimized geometric parameters of P.A were found consistent with those from X-ray crystal structure. Differences of about 0.01 and 0.15 Å in bond length and 0.19-1.30° degree in the angles, respectively; were observed between the experimental and theoretical data. The theoretical vibrational bands of P.A were found to correlate with the experimental IR spectrum after a common scaling factor of 0.963. The experimental and predicted UV-Vis spectra (at B3LYP/6-31+G (d, p)) have 36 nm differences. This difference from experimental results is because of the condensed phase nature of P.A. Electronic properties such as Ionization Potential (I.P), Electron Affinities (E.A), co-efficient of highest occupied molecular orbital (HOMO), co-efficient of lowest unoccupied molecular orbital (LUMO) of P.A were estimated for the first time however, no correlation can be made with experiment. Inter-molecular interaction and its effect on vibrational (IR), electronic and geometric parameters were simulated by using Formic acid as model for hydrogen bonding in P.A.

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study.

PubMed

Panek, Jarosław J; Filarowski, Aleksander; Jezierska-Mazzarello, Aneta

2013-10-21

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Electronic Transport through Self Assembled Thiol Molecules: Effect of Monolayer Order, Dynamics and Temperature

NASA Technical Reports Server (NTRS)

Dholakia, Geetha; Fan, Wendy; Meyyappan, M.

2005-01-01

We present the charge transport and tunneling conductance of self assembled organic thiol molecules and discuss the influence of order and dynamics in the monolayer on the transport behavior and the effect of temperature. Conjugated thiol molecular wires and organometals such as terpyridine metal complexes provide a new platform for molecular electronic devices and we study their self assembly on Au(111) substrates by the scanning tunneling microscope. Determining the organization of the molecule and the ability to control the nature of its interface with the substrate is important for reliable performance of the molecular electronic devices. By concurrent scanning tunneling microscopy and spectroscopy studies on SAMs formed from oligo (phenelyne ethynelyne) monolayers with and without molecular order, we show that packing and order determine the response of a self assembled monolayer (SAM) to competing interactions. Molecular resolution STM imaging in vacuum shows that the OPES adopt an imcommensurate SAM structure on Au(111) with a rectangular unit cell. Tunneling spectroscopic measurements were performed on the SAM as a function of junction resistance. STS results show that the I-Vs are non linear and asymmetric due to the inherent asymmetry in the molecular structure, with larger currents at negative sample biases. The asymmetry increases with increasing junction resistance due to the asymmetry in the coupling to the leads. This is brought out clearly in the differential conductance, which also shows a gap at the Fermi level. We also studied the effect of order and dynamics in the monolayer on the charge transport and found that competing forces between the electric field, intermolecular interactions, tip-molecule physisorption and substrate-molecule chemisorption impact the transport measurements and its reliability and that the presence of molecular order is very important for reproducible transport measurements. Thus while developing new electronic platforms based on molecules, it is important to have a good control of the molecule-substrate interface, for the devices to perform reliably. While such a control would minimize fluctuations and dynamics in the ensemble, the real challenge is to develop device architectures that are tolerant to fluctuations, since they cannot be totally eliminated in these low dimensional soft systems. Results of temperature dependent STS measurements will also be discussed.

Electronic Structure and Band Gap of Fullerenes on Tungsten Surfaces: Transition from a Semiconductor to a Metal Triggered by Annealing.

PubMed

Monazami, Ehsan; McClimon, John B; Rondinelli, James; Reinke, Petra

2016-12-21

The understanding and control of molecule-metal interfaces is critical to the performance of molecular electronics and photovoltaics devices. We present a study of the interface between C 60 and W, which is a carbide-forming transition metal. The complex solid-state reaction at the interface can be exploited to adjust the electronic properties of the molecule layer. Scanning tunneling microscopy/spectroscopy measurements demonstrate the progression of this reaction from wide band gap (>2.5 eV) to metallic molecular surface during annealing from 300 to 800 K. Differential conduction maps with 10 4 scanning tunneling spectra are used to quantify the transition in the density of states and the reduction of the band gap during annealing with nanometer spatial resolution. The electronic transition is spatially homogeneous, and the surface band gap can therefore be adjusted by a targeted annealing step. The modified molecules, which we call nanospheres, are quite resistant to ripening and coalescence, unlike any other metallic nanoparticle of the same size. Densely packed C 60 and isolated C 60 molecules show the same transition in electronic structure, which confirms that the transformation is controlled by the reaction at the C 60 -W interface. Density functional theory calculations are used to develop possible reaction pathways in agreement with experimentally observed electronic structure modulation. Control of the band gap by the choice of annealing temperature is a unique route to tailoring molecular-layer electronic properties.

Nuclear conversion theory: molecular hydrogen in non-magnetic insulators

PubMed Central

Ghiglieno, Filippo

2016-01-01

The hydrogen conversion patterns on non-magnetic solids sensitively depend upon the degree of singlet/triplet mixing in the intermediates of the catalytic reaction. Three main ‘symmetry-breaking’ interactions are brought together. In a typical channel, the electron spin–orbit (SO) couplings introduce some magnetic excitations in the non-magnetic solid ground state. The electron spin is exchanged with a molecular one by the electric molecule–solid electron repulsion, mixing the bonding and antibonding states and affecting the molecule rotation. Finally, the magnetic hyperfine contact transfers the electron spin angular momentum to the nuclei. Two families of channels are considered and a simple criterion based on the SO coupling strength is proposed to select the most efficient one. The denoted ‘electronic’ conversion path involves an emission of excitons that propagate and disintegrate in the bulk. In the other denoted ‘nuclear’, the excited electron states are transients of a loop, and the electron system returns to its fundamental ground state. The described model enlarges previous studies by extending the electron basis to charge-transfer states and ‘continui’ of band states, and focuses on the broadening of the antibonding molecular excited state by the solid conduction band that provides efficient tunnelling paths for the hydrogen conversion. After working out the general conversion algebra, the conversion rates of hydrogen on insulating and semiconductor solids are related to a few molecule–solid parameters (gap width, ionization and affinity potentials) and compared with experimental measures. PMID:27703681

3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

PubMed

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

Theoretical study of ArH+ dissociative recombination and electron-impact vibrational excitation

NASA Astrophysics Data System (ADS)

Abdoulanziz, A.; Colboc, F.; Little, D. A.; Moulane, Y.; Mezei, J. Zs; Roueff, E.; Tennyson, J.; Schneider, I. F.; Laporta, V.

2018-06-01

Cross sections are presented for dissociative recombination and electron-impact vibrational excitation of the ArH+ molecular ion at electron energies appropriate for the interstellar environment. The R-matrix method is employed to determine the molecular structure data, i.e. the position and width of the resonance states. The cross sections and the corresponding Maxwellian rate coefficients are computed using a method based on the Multichannel Quantum Defect Theory. The main result of the paper is the very low dissociative recombination rate found at temperatures below 1000K. This is in agreement with the previous upper limit measurement in merged beams and offers a realistic explanation to the presence of ArH+ in exotic interstellar conditions.

3D structure of eukaryotic flagella/cilia by cryo-electron tomography

PubMed Central

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

Exploring coherent electron excitation and migration dynamics by electron diffraction with ultrashort X-ray pulses.

PubMed

Yuan, Kai-Jun; Bandrauk, André D

2017-10-04

Exploring ultrafast charge migration is of great importance in biological and chemical reactions. We present a scheme to monitor attosecond charge migration in molecules by electron diffraction with spatial and temporal resolutions from ab initio numerical simulations. An ultraviolet pulse creates a coherent superposition of electronic states, after which a time-delayed attosecond X-ray pulse is used to ionize the molecule. It is found that diffraction patterns in the X-ray photoelectron spectra show an asymmetric structure, which is dependent on the time delay between the pump-probe pulses, encoding the information of molecular orbital symmetry and chemical bonding. We describe these phenomena by developing an electronic time-dependent ultrafast molecular photoionization model of a coherent superposition state. The periodical distortion of electron diffraction patterns illustrates the evolution of the electronic coherence, providing a tool for attosecond imaging of ultrafast molecular reaction processes.

Humic Acid Reduction by Propionibacterium freudenreichii and Other Fermenting Bacteria

PubMed Central

Benz, Marcus; Schink, Bernhard; Brune, Andreas

1998-01-01

Iron-reducing bacteria have been reported to reduce humic acids and low-molecular-weight quinones with electrons from acetate or hydrogen oxidation. Due to the rapid chemical reaction of amorphous ferric iron with the reduced reaction products, humic acids and low-molecular-weight redox mediators may play an important role in biological iron reduction. Since many anaerobic bacteria that are not able to reduce amorphous ferric iron directly are known to transfer electrons to other external acceptors, such as ferricyanide, 2,6-anthraquinone disulfonate (AQDS), or molecular oxygen, we tested several physiologically different species of fermenting bacteria to determine their abilities to reduce humic acids. Propionibacterium freudenreichii, Lactococcus lactis, and Enterococcus cecorum all shifted their fermentation patterns towards more oxidized products when humic acids were present; P. freudenreichii even oxidized propionate to acetate under these conditions. When amorphous ferric iron was added to reoxidize the electron acceptor, humic acids were found to be equally effective when they were added in substoichiometric amounts. These findings indicate that in addition to iron-reducing bacteria, fermenting bacteria are also capable of channeling electrons from anaerobic oxidations via humic acids towards iron reduction. This information needs to be considered in future studies of electron flow in soils and sediments. PMID:9797315

[Comparison study on adsorption of middle molecular substances with multiwalled carbon nanotubes and activated carbon].

PubMed

Li, Guifeng; Wan, Jianxin; Huang, Xiangqian; Zeng, Qiao; Tang, Jing

2011-08-01

In recent years, multi-walled carbon nanotubes (MWCTs) are very favorable to the adsorption of middle molecular substances in the hemoperfusion because of their multiporous structure, large surface area and high reactivity, which are beneficial to the excellent absorption properties. The purpose of this study was to study the MWCTs on the adsorption capacity of the middle molecular substances. Vitamin B12 (VB12) was selected as a model of the middle molecular substances. The morphologies of MWCTs and activated carbon from commercial "carbon kidney" were observed with scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The adsorption behavior of VB12 was compared to each other with UV-visible absorption spectra. The MWCTs formed a sophistaicate gap structure, and compared to the activated carbon, MWCTs had a larger surface area. By Langmuir equation and Freundlich equation fitting analysis, VB12 adsorption on MWCTs is fit for multi-molecular layer adsorption, and the adsorption type of activated carbon is more inclined to the model corresponding to Langmuir monolayer adsorption. The adsorption rate of MWCTs is faster than that of the activated carbon and the adsorption capacity is greater, which could be expected to become the new adsorbent in the hemoperfusion.

Inorganic and Organometallic Molecular Wires for Single-Molecule Devices.

PubMed

Tanaka, Yuya; Kiguchi, Manabu; Akita, Munetaka

2017-04-06

Recent developments of single-molecule conductance measurements allow us to understand fundamental conducting properties of molecular wires. While a wide variety of organic molecular wires have been studied so far, inorganic and organometallic molecular wires have received much less attention. However, molecular wires with transition-metal atoms show interesting features and functions distinct from those of organic wires. These properties originate mainly from metal-ligand dπ-pπ interactions and metal-metal d-d interactions. Thanks to the rich combination of metal atoms and supporting ligands, frontier orbital energies of the molecular wires can be finely tuned to lead to highly conducting molecular wires. Moreover, the unique electronic structures of metal complexes are susceptible to subtle environmental changes, leading to potential functional molecular devices. This article reviews recent advances in the single-molecule conductance study of inorganic and organometallic molecular wires. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light and redox switchable molecular components for molecular electronics.

PubMed

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

Synthesis of a Neutral Mixed-Valence Diferrocenyl Carborane for Molecular Quantum-Dot Cellular Automata Applications.

PubMed

Christie, John A; Forrest, Ryan P; Corcelli, Steven A; Wasio, Natalie A; Quardokus, Rebecca C; Brown, Ryan; Kandel, S Alex; Lu, Yuhui; Lent, Craig S; Henderson, Kenneth W

2015-12-14

The preparation of 7-Fc(+) -8-Fc-7,8-nido-[C2 B9 H10 ](-) (Fc(+) FcC2 B9 (-) ) demonstrates the successful incorporation of a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed-valence Fe(II) /Fe(III) complex overcomes the proximal electronic bias imposed by external counterions, a practical limitation in the use of molecular switches. A combination of UV/Vis-NIR spectroscopic and TD-DFT computational studies indicate that electron transfer within Fc(+) FcC2 B9 (-) is achieved through a bridge-mediated mechanism. This electronic framework therefore provides the possibility of an all-neutral null state, a key requirement for the implementation of quantum-dot cellular automata (QCA) molecular computing. The adhesion, ordering, and characterization of Fc(+) FcC2 B9 (-) on Au(111) has been observed by scanning tunneling microscopy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

DOE PAGES

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas; ...

2018-06-13

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Quasi-chemical theory of F-(aq): The "no split occupancies rule" revisited

NASA Astrophysics Data System (ADS)

Chaudhari, Mangesh I.; Rempe, Susan B.; Pratt, Lawrence R.

2017-10-01

We use ab initio molecular dynamics (AIMD) calculations and quasi-chemical theory (QCT) to study the inner-shell structure of F-(aq) and to evaluate that single-ion free energy under standard conditions. Following the "no split occupancies" rule, QCT calculations yield a free energy value of -101 kcal/mol under these conditions, in encouraging agreement with tabulated values (-111 kcal/mol). The AIMD calculations served only to guide the definition of an effective inner-shell constraint. QCT naturally includes quantum mechanical effects that can be concerning in more primitive calculations, including electronic polarizability and induction, electron density transfer, electron correlation, molecular/atomic cooperative interactions generally, molecular flexibility, and zero-point motion. No direct assessment of the contribution of dispersion contributions to the internal energies has been attempted here, however. We anticipate that other aqueous halide ions might be treated successfully with QCT, provided that the structure of the underlying statistical mechanical theory is absorbed, i.e., that the "no split occupancies" rule is recognized.

Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

NASA Astrophysics Data System (ADS)

Wang, Minglang; Wang, Hao; Zhang, Guangping; Wang, Yongfeng; Sanvito, Stefano; Hou, Shimin

2018-05-01

The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, EF, thus hardly affect the transmission around EF; the Au-S interface hybrid states couple with σ-bonds in the molecular backbone forming the conduction channel at EF, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some π-type oxygen orbitals coupling with the Au-S interface hybrid states contribute to the transmission around EF. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols.

Contribution of Methyl Substituent on the Conductivity Properties and Behaviour of CMC-Alkoxy Thiourea Polymer Electrolyte

DTIC Science & Technology

2014-12-15

article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan...This study reported the synthetic, characterization and theoretical evaluation of molecular wire candidate bearing alkoxy thiourea derivative... studies . Therefore, this type of A-ArC(O)NHC(S)NHAr-D molecular framework has opened wide possibilities to be applied in many micro-electronic

Comparative study of inelastic squared form factors of the vibronic states of B 1Σu+ , C 1Πu , and E F 1Σg+ for molecular hydrogen: Inelastic x-ray and electron scattering

NASA Astrophysics Data System (ADS)

Xu, Long-Quan; Kang, Xu; Peng, Yi-Geng; Xu, Xin; Liu, Ya-Wei; Wu, Yong; Yang, Ke; Hiraoka, Nozomu; Tsuei, Ku-Ding; Wang, Jian-Guo; Zhu, Lin-Fan

2018-03-01

A joint experimental and theoretical investigation of the valence-shell excitations of hydrogen has been performed by the high-resolution inelastic x-ray scattering and electron scattering as well as the multireference single- and double-excitation configuration-interaction method. Momentum-transfer-dependent inelastic squared form factors for the vibronic series belonging to the B 1Σu+ ,C 1Πu , and E F 1Σg+ electronic states of molecular hydrogen have been derived from the inelastic x-ray scattering method at an impact photon energy around 10 keV, and the electron energy-loss spectra measured at an incident electron energy of 1500 eV. It is found that both the present and the previous calculations cannot satisfactorily reproduce the inelastic squared form-factor profiles for the higher vibronic transitions of the B 1Σu+ state of molecular hydrogen, which may be due to the electronic-vibrational coupling for the higher vibronic states. For the C 1Πu state and some vibronic excitations of E F 1Σg+ state, the present experimental results are in good agreement with the present and previous calculations, while the slight differences between the inelastic x-ray scattering and electron energy-loss spectroscopy results in the larger squared momentum-transfer region may be attributed to the increasing role of the higher-order Born terms in the electron-scattering process.

Molecular characterization of organic electronic films.

PubMed

DeLongchamp, Dean M; Kline, R Joseph; Fischer, Daniel A; Richter, Lee J; Toney, Michael F

2011-01-18

Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

Conductance of carbon based macro-molecular structures

NASA Astrophysics Data System (ADS)

Stafström, S.; Hansson, A.; Paulsson, M.

2000-11-01

Electron transport through metallic nanotubes and stacks of wide bandgap polyaromatic hydrocarbons (PAH) are studied theoretically using the Landauer formalism. These two systems constitute examples of different types of carbon based nanostructured materials of potential use in molecular electronics. The studies are carried out for structures with finite length that bridge two contact pads. In the case of perfect metallic nanotubes, the current is observed to increase stepwise with the applied voltage and the resistance is independent on the length of the tube. In the PAH stacks, the off resonance tunneling conductance decreases exponentially with the number of molecules in the stack and shows a near linear increase with the number of carbon atoms in each molecule.

Automatic Thesaurus Generation for an Electronic Community System.

ERIC Educational Resources Information Center

Chen, Hsinchun; And Others

1995-01-01

This research reports an algorithmic approach to the automatic generation of thesauri for electronic community systems. The techniques used include term filtering, automatic indexing, and cluster analysis. The Worm Community System, used by molecular biologists studying the nematode worm C. elegans, was used as the testbed for this research.…

Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase

PubMed Central

Sündermann, Axel; Oostenbrink, Chris

2013-01-01

Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies. PMID:23832577

Zigzag‐Elongated Fused π‐Electronic Core: A Molecular Design Strategy to Maximize Charge‐Carrier Mobility

PubMed Central

Yamamoto, Akito; Murata, Yoshinori; Mitsui, Chikahiko; Yamagishi, Masakazu; Yano, Masafumi; Sato, Hiroyasu; Yamano, Akihito; Takeya, Jun

2017-01-01

Abstract Printed and flexible electronics requires solution‐processable organic semiconductors with a carrier mobility (μ) of ≈10 cm2 V−1 s−1 as well as high chemical and thermal durability. In this study, chryseno[2,1‐b:8,7‐b′]dithiophene (ChDT) and its derivatives, which have a zigzag‐elongated fused π‐electronic core (π‐core) and a peculiar highest occupied molecular orbital (HOMO) configuration, are reported as materials with conceptually new semiconducting π‐cores. ChDT and its derivatives are prepared by a versatile synthetic procedure. A comprehensive investigation reveals that the ChDT π‐core exhibits increasing structural stability in the bulk crystal phase, and that it is unaffected by a variation of the transfer integral, induced by the perpetual molecular motion of organic materials owing to the combination of its molecular shape and its particular HOMO configuration. Notably, ChDT derivatives exhibit excellent chemical and thermal stability, high charge‐carrier mobility under ambient conditions (μ ≤ 10 cm2 V−1 s−1), and a crystal phase that is highly stable, even at temperatures above 250 °C. PMID:29375963

Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

NASA Astrophysics Data System (ADS)

El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

2016-12-01

Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

Molecular electronics: The technology of sixth generation computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jarvis, M.T.; Miller, R.K.

1987-01-01

In February 1986, Japan began the 6th Generation project. At the 1987 Economic Summit in Venice, Prime Minister Yashuhiro Makasone opened the project to world collaboration. A project director suggests that the 6th Generation ''may just be a turning point for human society.'' The major rationale for building molecular electronic devices is to achieve advances in computational densities and speeds. Proposed chromophore chains for molecular-scale chips, for example, could be spaced closer than today's silicone elements by a factor of almost 100. This book describes the research and proposed designs for molecular electronic devices and computers. It examines specific potentialmore » applications and the relationship to molecular electronics to silicon technology and presents the first published survey of experts on research issues, applications, and forecast of future developments and also includes market forecast. An interesting suggestion of the survey is that the chemical industry may become a significant factor in the computer industry as the sixth generation unfolds.« less

Photochromic molecules as building blocks for molecular electronics.

PubMed

Peter, Belser

2010-01-01

Energy and electron transfer processes can be easily induced by a photonic excitation of a donor metal complex ([Ru(bpy)3]2), which is connected via a wire-type molecular fragment to an acceptor metal complex ([Os(bpy)3]2+). The rate constant for the transfer process can be determined by emission measurements of the two connected metal complexes. The system can be modified by incorporation of a switching unit or an interrupter into the wire, influencing the transfer process. Such a molecular device corresponds to an interrupter, mimic the same function applied in molecular electronics. We have used organic switches, which show photochromic properties. By irradiation with light of different wavelengths, the switch changes its functionality by a photochemical reaction from an OFF- to an ON-state and vice versa. The ON- respectively OFF-state is manifested by a color change but also in different conductivity properties for energy and electron transfer processes. Therefore, the mentioned molecular device can work as a simple interrupter, controlling the rate of the transfer processes.

Challenges for single molecule electronic devices with nanographene and organic molecules. Do single molecules offer potential as elements of electronic devices in the next generation?

NASA Astrophysics Data System (ADS)

Enoki, Toshiaki; Kiguchi, Manabu

2018-03-01

Interest in utilizing organic molecules to fabricate electronic materials has existed ever since organic (molecular) semiconductors were first discovered in the 1950s. Since then, scientists have devoted serious effort to the creation of various molecule-based electronic systems, such as molecular metals and molecular superconductors. Single-molecule electronics and the associated basic science have emerged over the past two decades and provided hope for the development of highly integrated molecule-based electronic devices in the future (after the Si-based technology era has ended). Here, nanographenes (nano-sized graphene) with atomically precise structures are among the most promising molecules that can be utilized for electronic/spintronic devices. To manipulate single small molecules for an electronic device, a single molecular junction has been developed. It is a powerful tool that allows even small molecules to be utilized. External electric, magnetic, chemical, and mechanical perturbations can change the physical and chemical properties of molecules in a way that is different from bulk materials. Therefore, the various functionalities of molecules, along with changes induced by external perturbations, allows us to create electronic devices that we cannot create using current top-down Si-based technology. Future challenges that involve the incorporation of condensed matter physics, quantum chemistry calculations, organic synthetic chemistry, and electronic device engineering are expected to open a new era in single-molecule device electronic technology.

Donor-acceptor-donor thienyl/bithienyl-benzothiadiazole/quinoxaline model oligomers: experimental and theoretical studies.

PubMed

Pina, João; de Melo, J Seixas; Breusov, D; Scherf, Ullrich

2013-09-28

A comprehensive spectral and photophysical investigation of four donor-acceptor-donor (DAD) oligomers consisting of electron-deficient 2,1,3-benzothiadiazole or quinoxaline moieties linked to electron-rich thienyl or bithienyl units has been undertaken. Additionally, a bis(dithienyl) substituted naphthalene was also investigated. The D-A-D nature of these oligomers resulted in the presence of an intramolecular charge transfer (ICT) state, which was further substantiated by solvatochromism studies (analysis with the Lippert-Mataga formalism). Hereby, significant differences have been obtained for the fluorescence quantum yields of the oligomers in the non-polar solvent methylcyclohexane vs. the polar ethanol. The study was further complemented with the determination of the optimized ground-state molecular geometries for the oligomers together with the prediction of the lowest vertical one-electron excitation energy and the relevant molecular orbital contours using DFT calculations. The electronic transitions show a clear HOMO to LUMO charge-transfer character. In contrast to the thiophene oligomers (the oligothiophenes with n = 1-7), where the intersystem crossing (ISC) yield decreases with n, the studied DAD oligomers were found to show an increase in the ISC efficiency with the number of (donor) thienyl units.

Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.

PubMed

Uma Maheswari, J; Muthu, S; Sundius, Tom

2014-04-05

A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Two-temperature model in molecular dynamics simulations of cascades in Ni-based alloys

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-01-03

In high-energy irradiation events, energy from the fast moving ion is transferred to the system via nuclear and electronic energy loss mechanisms. The nuclear energy loss results in the creation of point defects and clusters, while the energy transferred to the electrons results in the creation of high electronic temperatures, which can affect the damage evolution. In this paper, we perform molecular dynamics simulations of 30 keV and 50 keV Ni ion cascades in nickel-based alloys without and with the electronic effects taken into account. We compare the results of classical molecular dynamics (MD) simulations, where the electronic effects aremore » ignored, with results from simulations that include the electronic stopping only, as well as simulations where both the electronic stopping and the electron-phonon coupling are incorporated, as described by the two temperature model (2T-MD). Finally, our results indicate that the 2T-MD leads to a smaller amount of damage, more isolated defects and smaller defect clusters.« less

Molecular Engineering of UV/Vis Light-Emitting Diode (LED)-Sensitive Donor-π-Acceptor-Type Sulfonium Salt Photoacid Generators: Design, Synthesis, and Study of Photochemical and Photophysical Properties.

PubMed

Wu, Xingyu; Jin, Ming; Xie, Jianchao; Malval, Jean-Pierre; Wan, Decheng

2017-11-07

A series of donor-π-acceptor-type sulfonium salt photoacid generators (PAGs) were designed and synthesized by systematically changing electron-donating groups, π-conjugated systems, electron-withdrawing groups, and the number of branches through molecular engineering. These PAGs can effectively decompose under UV/Vis irradiation from a light-emitting diode (LED) light source because of the matching absorption and emitting spectra of the LEDs. The absorption and acid-generation properties of these sulfonium salts were elucidated by UV/Vis spectroscopy and so forth. Results indicated that the PAG performance benefited from the introduction of strong electron-donating groups, specific π-conjugated structures, certain electron-withdrawing groups, or two-branched structures. Most sulfonium salts showed potential as photoinitiators under irradiation by a wide variety of UV and visible LEDs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimized unconventional superconductivity in a molecular Jahn-Teller metal

PubMed Central

Zadik, Ruth H.; Takabayashi, Yasuhiro; Klupp, Gyöngyi; Colman, Ross H.; Ganin, Alexey Y.; Potočnik, Anton; Jeglič, Peter; Arčon, Denis; Matus, Péter; Kamarás, Katalin; Kasahara, Yuichi; Iwasa, Yoshihiro; Fitch, Andrew N.; Ohishi, Yasuo; Garbarino, Gaston; Kato, Kenichi; Rosseinsky, Matthew J.; Prassides, Kosmas

2015-01-01

Understanding the relationship between the superconducting, the neighboring insulating, and the normal metallic state above Tc is a major challenge for all unconventional superconductors. The molecular A3C60 fulleride superconductors have a parent antiferromagnetic insulator in common with the atom-based cuprates, but here, the C603– electronic structure controls the geometry and spin state of the structural building unit via the on-molecule Jahn-Teller effect. We identify the Jahn-Teller metal as a fluctuating microscopically heterogeneous coexistence of both localized Jahn-Teller–active and itinerant electrons that connects the insulating and superconducting states of fullerides. The balance between these molecular and extended lattice features of the electrons at the Fermi level gives a dome-shaped variation of Tc with interfulleride separation, demonstrating molecular electronic structure control of superconductivity. PMID:26601168

Electron-intramolecular-vibration interactions in positively charged phenanthrene-edge-type hydrocarbons

NASA Astrophysics Data System (ADS)

Kato, Takashi; Yamabe, Tokio

2004-02-01

Electron-phonon interactions in positively charged phenanthrene-edge-type hydrocarbons such as phenanthrene, chrysene, and picene are studied. The C-C stretching modes around 1500 cm-1 and the low-frequency modes around 500 cm-1 strongly couple to the highest occupied molecular orbitals (HOMO) in phenanthrene-edge-type hydrocarbons. The total electron-phonon coupling constants for the monocations (lHOMO) of 0.251, 0.135, and 0.149 eV for phenanthrene, chrysene, and picene, respectively, are estimated to be larger than those of 0.130, 0.107, and 0.094 eV for anthracene, tetracene, and pentacene, respectively. The phase patterns difference between the HOMO localized on carbon atoms which are located at the molecular edge in acene-edge-type hydrocarbons and the delocalized HOMO in phenanthrene-edge-type hydrocarbons is the main reason for the result. Strengths of orbital interactions between two neighboring carbon atoms in the HOMO become weaker with an increase in molecular size because the electron density on each carbon atom in the HOMO becomes smaller with an increase in molecular size in phenanthrene-edge-type hydrocarbons. On the other hand, the frontier orbitals of acene-edge-type hydrocarbons have somewhat nonbonding characters and thus cannot strongly couple to the totally symmetric vibrational modes compared with the frontier orbitals of phenanthrene-edge-type hydrocarbons. This is the reason why the lHOMO value for phenanthrene-edge-type hydrocarbons decreases with an increase in molecular size more significantly than that for acene-edge-type hydrocarbons, and the reason why the lHOMO value for polyphenanthrene with C2v geometry (0.033 eV) is estimated to be similar to that for polyacene (0.036 eV). The reorganization energies between the neutral molecules and the corresponding monocations for phenanthrene-edge-type hydrocarbons with large molecular size are estimated to be larger than those for acene-edge-type hydrocarbons with large molecular size.

Ultrafast studies of excess electrons in liquid acetonitrile: revisiting the solvated electron/solvent dimer anion equilibrium.

PubMed

Doan, Stephanie C; Schwartz, Benjamin J

2013-04-25

We examine the ultrafast relaxation dynamics of excess electrons injected into liquid acetonitrile using air- and water-free techniques and compare our results to previous work on this system [Xia, C. et al. J. Chem. Phys. 2002, 117, 8855]. Excess electrons in liquid acetonitrile take on two forms: a "traditional" solvated electron that absorbs in the near-IR, and a solvated molecular dimer anion that absorbs weakly in the visible. We find that excess electrons initially produced via charge-transfer-to-solvent excitation of iodide prefer to localize as solvated electrons, but that there is a subsequent equilibration to form the dimer anion on an ~80 ps time scale. The spectral signature of this interconversion between the two forms of the excess electron is a clear isosbestic point. The presence of the isosbestic point makes it possible to fully deconvolute the spectra of the two species. We find that solvated molecular anion absorbs quite weakly, with a maximum extinction coefficient of ~2000 M(-1)cm(-1). With the extinction coefficient of the dimer anion in hand, we are also able to determine the equilibrium constant for the two forms of excess electron, and find that the molecular anion is favored by a factor of ~4. We also find that relatively little geminate recombination takes place, and that the geminate recombination that does take place is essentially complete within the first 20 ps. Finally, we show that the presence of small amounts of water in the acetonitrile can have a fairly large effect on the observed spectral dynamics, explaining the differences between our results and those in previously published work.

Electron Driven Processes in Atmospheric Behaviour

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.; Teubner, P. J. O.

2006-11-01

Electron impact plays an important role in many atmospheric processes. Calculation of these is important for basic understanding, atmospheric modeling and remote sensing. Accurate atomic and molecular data, including electron impact cross sections, are required for such calculations. Five electron-driven processes are considered: auroral and dayglow emissions, the reduction of atmospheric electron density by vibrationally excited N2, NO production and infrared emission from NO. In most cases the predictions are compared with measurements. The dependence on experimental atomic and molecular data is also investigated.

Fullerenes, carbon nanotubes, and graphene for molecular electronics.

PubMed

Pinzón, Julio R; Villalta-Cerdas, Adrián; Echegoyen, Luis

2012-01-01

With the constant growing complexity of electronic devices, the top-down approach used with silicon based technology is facing both technological and physical challenges. Carbon based nanomaterials are good candidates to be used in the construction of electronic circuitry using a bottom-up approach, because they have semiconductor properties and dimensions within the required physical limit to establish electrical connections. The unique electronic properties of fullerenes for example, have allowed the construction of molecular rectifiers and transistors that can operate with more than two logical states. Carbon nanotubes have shown their potential to be used in the construction of molecular wires and FET transistors that can operate in the THz frequency range. On the other hand, graphene is not only the most promising material for replacing ITO in the construction of transparent electrodes but it has also shown quantum Hall effect and conductance properties that depend on the edges or chemical doping. The purpose of this review is to present recent developments on the utilization carbon nanomaterials in molecular electronics.

Complex basis functions for molecular resonances: Methodology and applications

NASA Astrophysics Data System (ADS)

White, Alec; McCurdy, C. William; Head-Gordon, Martin

The computation of positions and widths of metastable electronic states is a challenge for molecular electronic structure theory because, in addition to the difficulty of the many-body problem, such states obey scattering boundary conditions. These resonances cannot be addressed with naïve application of traditional bound state electronic structure theory. Non-Hermitian electronic structure methods employing complex basis functions is one way that we may rigorously treat resonances within the framework of traditional electronic structure theory. In this talk, I will discuss our recent work in this area including the methodological extension from single determinant SCF-based approaches to highly correlated levels of wavefunction-based theory such as equation of motion coupled cluster and many-body perturbation theory. These approaches provide a hierarchy of theoretical methods for the computation of positions and widths of molecular resonances. Within this framework, we may also examine properties of resonances including the dependence of these parameters on molecular geometry. Some applications of these methods to temporary anions and dianions will also be discussed.

Resonant- and avalanche-ionization amplification of laser-induced plasma in air

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yue; Zhang, Zhili, E-mail: zzhang24@utk.edu; Jiang, Naibo

2014-10-14

Amplification of laser-induced plasma in air is demonstrated utilizing resonant laser ionization and avalanche ionization. Molecular oxygen in air is ionized by a low-energy laser pulse employing (2 + 1) resonance-enhanced multi-photon ionization (REMPI) to generate seed electrons. Subsequent avalanche ionization of molecular oxygen and nitrogen significantly amplifies the laser-induced plasma. In this plasma-amplification effect, three-body attachments to molecular oxygen dominate the electron-generation and -loss processes, while either nitrogen or argon acts as the third body with low electron affinity. Contour maps of the electron density within the plasma obtained in O₂/N₂ and O₂/Ar gas mixtures are provided to showmore » relative degrees of plasma amplification with respect to gas pressure and to verify that the seed electrons generated by O₂ 2 + 1 REMPI are selectively amplified by avalanche ionization of molecular nitrogen in a relatively low-pressure condition (≤100 Torr). Such plasma amplification occurring in air could be useful in aerospace applications at high altitude.« less

Molecular modeling of polymer composite interactions with analytes in electronic nose sensors for environmental monitoring in International Space Station

NASA Technical Reports Server (NTRS)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K.

2002-01-01

We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL Electronic Nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings (with no hydrogens). The Dreiding 2.21 force field is used for the polymer and solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4- vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic (ammonia) and organic (methanol, toluene, hydrazine) compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites.

Molecular modeling of polymer composite-analyte interactions in electronic nose sensors

NASA Technical Reports Server (NTRS)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K. S.

2003-01-01

We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL electronic nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereoisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings with no hydrogens. The Dreiding 2.21 force field is used for the polymer, solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4-vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic and organic compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites. c2003 Elsevier Science B.V. All rights reserved.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile

NASA Astrophysics Data System (ADS)

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K.; Kant, Rajni; Khajuria, Yugal

2015-04-01

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800 nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity.

Molecular adsorption on graphene

NASA Astrophysics Data System (ADS)

Kong, Lingmei; Enders, Axel; Rahman, Talat S.; Dowben, Peter A.

2014-11-01

Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H2O, H2, O2, CO, NO2, NO, and NH3), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH2, An-CH3, An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene’s electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

Molecular Electronic Angular Motion Transducer Broad Band Self-Noise.

PubMed

Zaitsev, Dmitry; Agafonov, Vadim; Egorov, Egor; Antonov, Alexander; Shabalina, Anna

2015-11-20

Modern molecular electronic transfer (MET) angular motion sensors combine high technical characteristics with low cost. Self-noise is one of the key characteristics which determine applications for MET sensors. However, until the present there has not been a model describing the sensor noise in the complete operating frequency range. The present work reports the results of an experimental study of the self-noise level of such sensors in the frequency range of 0.01-200 Hz. Based on the experimental data, a theoretical model is developed. According to the model, self-noise is conditioned by thermal hydrodynamic fluctuations of the operating fluid flow in the frequency range of 0.01-2 Hz. At the frequency range of 2-100 Hz, the noise power spectral density has a specific inversely proportional dependence of the power spectral density on the frequency that could be attributed to convective processes. In the high frequency range of 100-200 Hz, the noise is conditioned by the voltage noise of the electronics module input stage operational amplifiers and is heavily reliant to the sensor electrical impedance. The presented results allow a deeper understanding of the molecular electronic sensor noise nature to suggest the ways to reduce it.

Molecular alignment effect on the photoassociation process via a pump-dump scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Bin-Bin; Han, Yong-Chang, E-mail: ychan@dlut.edu.cn; Cong, Shu-Lin

The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na{sub 2}) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X{sup 1}Σ{sup +}) is associated into the molecule in the bound states of the excited state (A{sup 1}Σ{sup +}) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found thatmore » the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.« less

Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes.

PubMed

Liu, Kexi; Lei, Yinkai; Wang, Guofeng

2013-11-28

Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O2 adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N4 chelation, as well as the molecular and electronic structures for the O2 adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O2 on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d(z(2)), d(xy), d(xz), and d(yz)) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O2 adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

PubMed

Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

2015-05-08

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

n-type dopants in (001) β-Ga2O3 grown on (001) β-Ga2O3 substrates by plasma-assisted molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Han, Sang-Heon; Mauze, Akhil; Ahmadi, Elaheh; Mates, Tom; Oshima, Yuichi; Speck, James S.

2018-04-01

Ge and Sn as n-type dopants in (001) β-Ga2O3 films were investigated using plasma-assisted molecular beam epitaxy. The Ge concentration showed a strong dependence on the growth temperature, whereas the Sn concentration remains independent of the growth temperature. The maximum growth temperature at which a wide range of Ge concentrations (from 1017 to 1020 cm-3) could be achieved was 675 °C while the same range of Sn concentration could be achieved at growth temperature of 750 °C. Atomic force microscopy results revealed that higher growth temperature shows better surface morphology. Therefore, our study reveals a tradeoff between higher Ge doping concentration and high quality surface morphology on (001) β-Ga2O3 films grown by plasma-assisted molecular beam epitaxy. The Ge doped films had an electron mobility of 26.3 cm2 V-1 s-1 at the electron concentration of 6.7 × 1017 cm-3 whereas the Sn doped films had an electron mobility of 25.3 cm2 V-1 s-1 at the electron concentration of 1.1 × 1018 cm-3.

First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

PubMed

Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

2015-02-01

Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.

Dynamic molecular structure retrieval from low-energy laser-induced electron diffraction spectra

NASA Astrophysics Data System (ADS)

Vu, Dinh-Duy T.; Phan, Ngoc-Loan T.; Hoang, Van-Hung; Le, Van-Hoang

2017-12-01

A recently developed quantitative rescattering theory showed that a laser-free elastic cross section can be separated from laser-induced electron diffraction (LIED) spectra. Based upon this idea, Blaga et al investigated the possibility of reconstructing molecular structure from LIED spectra (2012 Nature 483 7388). In the above study, an independent atoms model (IAM) was used to interpret high-energy electron-molecule collisions induced by a mid-infrared laser. Our research aims to extend the application range of this structural retrieval method to low-energy spectra induced by more common near-infrared laser sources. The IAM is insufficient in this case, so we switch to a more comprehensive model—the multiple scattering (MS) theory. From the original version concerning only neutral targets, we upgrade the model so that it is compatible with electron-ion collisions at low energy. With available LIED experiment data of CO2 and O2, the upgraded MS is shown to be greatly effective as a tool for molecular imaging from spectra induced by a near-infrared laser. The captured image is at about 2 fs after the ionization, shorter than the period 4-6 fs by using the mid-infrared laser in Blaga’s experiment.

Adsorption of alcohols on a two-dimensional SiO2 single crystal - Alcohol adsorption on silicatene

NASA Astrophysics Data System (ADS)

Nayakasinghe, M. T.; Sivapragasam, N.; Burghaus, U.

2017-12-01

The adsorption kinetics of alcohols (methanol, ethanol, 1-propanol, 1-butanol, 1-pentanol) was studied on monoatomic, two-dimensional SiO2 single crystals (silicatene) using thermal desorption spectroscopy (TDS). Silicatene was grown on Mo(1 1 2) at ultra-high vacuum. In contrast to Mo, the alcohols physisorb molecularly on the hydrophobic SiO2/Mo surface. Zero coverage binding energies vary from 46.5 to 65.5 kJ/mol and increase with molecular size. Silicatene was characterized by Auger electron spectroscopy (AES), low energy electron diffraction (LEED), and water TDS.

Reactive collisions of electrons with H2+ , HD+, BeH+, BeD+ and SH+

NASA Astrophysics Data System (ADS)

Pop, Nicolina; Iacob, Felix; Mezei, János Zsolt; Motapon, Ousmanou; Niyonzima, Sebastien; Kashinski, David O.; Talbi, Dahbia; Hickman, Albert Peet; Schneider, Ioan F.

2017-12-01

In numerous cold ionized gases the dissociative recombination (DR), the elastic collisions (EC), the vibrational excitation (VE) (inelastic collisions) and the vibrational de-excitation (VdE) (super-elastic collisions) of molecular cations with electrons are major elementary processes. Using a stepwise method based on the Multichannel Quantum Defect Theory (MQDT), cross sections and rate coefficients have been obtained for reactions induced on HD+, H2+, BeH+, BeD+ and SH+. Moreover, the relative importance of the different reaction mechanisms, direct vs. indirect and rotational vs. non-rotational, have been studied for these molecular systems.

Regioregular narrow-bandgap-conjugated polymers for plastic electronics

NASA Astrophysics Data System (ADS)

Ying, Lei; Huang, Fei; Bazan, Guillermo C.

2017-03-01

Progress in the molecular design and processing protocols of semiconducting polymers has opened significant opportunities for the fabrication of low-cost plastic electronic devices. Recent studies indicate that field-effect transistors and organic solar cells fabricated using narrow-bandgap regioregular polymers with translational symmetries in the direction of the backbone vector often outperform those containing analogous regiorandom polymers. This review addresses the cutting edge of regioregularity chemistry, in particular how to control the spatial distribution in the molecular structures and how this order translates to more ordered bulk morphologies. The effect of regioregularity on charge transport and photovoltaic properties is also outlined.

Molecular Electronic Shift Registers

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose N.

1990-01-01

Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

Epitaxial growth of pentacene on alkali halide surfaces studied by Kelvin probe force microscopy.

PubMed

Neff, Julia L; Milde, Peter; León, Carmen Pérez; Kundrat, Matthew D; Eng, Lukas M; Jacob, Christoph R; Hoffmann-Vogel, Regina

2014-04-22

In the field of molecular electronics, thin films of molecules adsorbed on insulating surfaces are used as the functional building blocks of electronic devices. Control of the structural and electronic properties of the thin films is required for reliably operating devices. Here, noncontact atomic force and Kelvin probe force microscopies have been used to investigate the growth and electrostatic landscape of pentacene on KBr(001) and KCl(001) surfaces. We have found that, together with molecular islands of upright standing pentacene, a new phase of tilted molecules appears near step edges on KBr. Local contact potential differences (LCPD) have been studied with both Kelvin experiments and density functional theory calculations. Our images reveal that differently oriented molecules display different LCPD and that their value is independent of the number of molecular layers. These results point to the formation of an interface dipole, which may be explained by a partial charge transfer from the pentacene to the surface. Moreover, the monitoring of the evolution of the pentacene islands shows that they are strongly affected by dewetting: Multilayers build up at the expense of monolayers, and in the Kelvin images, previously unknown line defects appear, which reveal the epitaxial growth of pentacene crystals.

Excitation of Mercuric Bromide by Electrons.

DTIC Science & Technology

1982-08-30

molecular beam of IHgBr 2 . The apparatus permits simultaneous meas- urements of negative ion, positive ion, and wavelength resolved photon production...system has proven to be trouble-free and allows very close control of the IHgBr 2, vapor pressure and conseqt’ent molecular beam intensity. The...experiment is represented schematicallv in Figure 1. The gas under study is introduced into the collision region in the form of a molecular beam, directed

Dual-comb spectroscopy of molecular electronic transitions in condensed phases

NASA Astrophysics Data System (ADS)

Cho, Byungmoon; Yoon, Tai Hyun; Cho, Minhaeng

2018-03-01

Dual-comb spectroscopy (DCS) utilizes two phase-locked optical frequency combs to allow scanless acquisition of spectra using only a single point detector. Although recent DCS measurements demonstrate rapid acquisition of absolutely calibrated spectral lines with unprecedented precision and accuracy, complex phase-locking schemes and multiple coherent averaging present significant challenges for widespread adoption of DCS. Here, we demonstrate Global Positioning System (GPS) disciplined DCS of a molecular electronic transition in solution at around 800 nm, where the absorption spectrum is recovered by using a single time-domain interferogram. We anticipate that this simplified dual-comb technique with absolute time interval measurement and ultrabroad bandwidth will allow adoption of DCS to tackle molecular dynamics investigation through its implementation in time-resolved nonlinear spectroscopic studies and coherent multidimensional spectroscopy of coupled chromophore systems.

Metastable Oxygen Production by Electron-Impact of Oxygen

NASA Astrophysics Data System (ADS)

Hein, J. D.; Malone, C. P.; Kanik, I.; Johnson, P. V.

2013-12-01

Electron-impact excitation processes involving atomic and molecular oxygen are important in atmospheric interactions. The production of long-lived metastable O(1S) and O(1D) through electron impact of atomic O and molecular O2 play a significant role in the dynamics of oxygen-containing atmospheres (Earth, Europa, Io). Emissions from metastable O (1S → 1D) produce the well-recognized green light from terrestrial aurora. Electron-impact excitation to 1S and 1D are sensitive channels for determining energy partitioning and dynamics from space weather. Electron-impact excitation cross sections determined through fundamental experimental studies are necessary for modeling of natural phenomena and observation data. The detection of metastable states in laboratory experiments requires a novel approach, since typical detection techniques (e.g., fluorescence by radiative de-excitation) cannot be performed due to the long-lived nature of the excited species. In this work, metastable O is incident on a cryogenically cooled rare gas matrix, where excimer production and subsequent rapid radiative de-excitation provides measurable signal that is directly related to the originating electron-impact excitation process.

Holomorphic Hartree-Fock Theory: The Nature of Two-Electron Problems.

PubMed

Burton, Hugh G A; Gross, Mark; Thom, Alex J W

2018-02-13

We explore the existence and behavior of holomorphic restricted Hartree-Fock (h-RHF) solutions for two-electron problems. Through algebraic geometry, the exact number of solutions with n basis functions is rigorously identified as 1 / 2 (3 n - 1), proving that states must exist for all molecular geometries. A detailed study on the h-RHF states of HZ (STO-3G) then demonstrates both the conservation of holomorphic solutions as geometry or atomic charges are varied and the emergence of complex h-RHF solutions at coalescence points. Using catastrophe theory, the nature of these coalescence points is described, highlighting the influence of molecular symmetry. The h-RHF states of HHeH 2+ and HHeH (STO-3G) are then compared, illustrating the isomorphism between systems with two electrons and two electron holes. Finally, we explore the h-RHF states of ethene (STO-3G) by considering the π electrons as a two-electron problem and employ NOCI to identify a crossing of the lowest energy singlet and triplet states at the perpendicular geometry.

A comparative study on vibrational, conformational and electronic structure of 2-chloro-4-methyl-3-nitropyridine and 2-chloro-6-methylpyridine

NASA Astrophysics Data System (ADS)

Arjunan, V.; Saravanan, I.; Marchewka, Mariusz K.; Mohan, S.

Experimental FTIR and FT-Raman spectroscopic analysis of 2-chloro-4-methyl-3-nitropyridine (2C4M3NP) and 2-chloro-6-methylpyridine (2C6MP) have been performed. A detailed quantum chemical calculations have been carried out using B3LYP and B3PW91 methods with 6-311++G** and cc-pVTZ basis sets. Conformation analysis was carried for 2C4M3NP and 2C6MP. The temperature dependence of thermodynamic properties has been analysed. The atomic charges, electronic exchange interaction and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach.

Light, Molecules, Action: Broadband UV-visible transient absorption studies of excited state dynamics in photoactive molecules

NASA Astrophysics Data System (ADS)

Sension, Roseanne

2015-03-01

Broadband UV-visible transient absorption spectroscopy provides a powerful tool for the investigation of the dynamics of electronically excited molecules in the condensed phase. It is now possible to obtain transient spectra on a routine basis spanning the range from <300 nm to >800 nm with femtosecond time resolution. We have used this method to study the excited state dynamics and internal conversion of a range of molecular systems with potential application as optically powered molecular devices. The cyclohexadiene ring-opening reaction is the basis of a class of important optical switches and of the biological synthesis of previtamin D3. The ring-opening reaction is ultrafast, occurring on a picosecond to subpicosecond times scale depending on the substituents around the ring. These have a significant influence on the dynamics and electronic structure of the electronically excited molecule. The results of a series of transient absorption studies as a function of chromophore substitution and environment will be presented. The cis-trans isomerization of polyene molecules, especially substituted stilbenes, provides another important class of functional molecular transformations. Again the excited state dynamics can be ultrafast with photochemistry controlled by details of the curve crossings and conical intersections. Finally the photochemistry of the even more complex set of cobalamin chromophores with a photoalabile C-Co bond has been proposed as a tool for spatio-temporal control of molecule delivery including drug delivery. Broadband transient absorption spectroscopy has been used to investigate the ultrafast electronic dynamics of a range of cobalamin compounds with comparison to detailed theoretical calculations. The results of these studies will be presented.

Asymmetric molecular-orbital tomography by manipulating electron trajectories

NASA Astrophysics Data System (ADS)

Wang, Bincheng; Zhang, Qingbin; Zhu, Xiaosong; Lan, Pengfei; Rezvani, Seyed Ali; Lu, Peixiang

2017-11-01

We present a scheme for tomographic imaging of asymmetric molecular orbital based on high-order harmonic generation with a two-color orthogonally polarized multicycle laser field. With the two-dimensional manipulation of the electron trajectories, the electrons can recollide with the target molecule from two noncollinear directions, and then the dipole moment generated from the single direction can be obtained to reconstructed the asymmetric molecular orbital. The recollision is independent from the molecular structure and the angular dependence of the ionization rate in the external field. For this reason, this scheme can avoid the negative effects arising from the modification of the angle-dependent ionization rate induced by Stark shift and be applied to various molecules.

Orbit-orbit relativistic correction calculated with all-electron molecular explicitly correlated Gaussians.

PubMed

Stanke, Monika; Palikot, Ewa; Kȩdziera, Dariusz; Adamowicz, Ludwik

2016-12-14

An algorithm for calculating the first-order electronic orbit-orbit magnetic interaction correction for an electronic wave function expanded in terms of all-electron explicitly correlated molecular Gaussian (ECG) functions with shifted centers is derived and implemented. The algorithm is tested in calculations concerning the H 2 molecule. It is also applied in calculations for LiH and H 3 + molecular systems. The implementation completes our work on the leading relativistic correction for ECGs and paves the way for very accurate ECG calculations of ground and excited potential energy surfaces (PESs) of small molecules with two and more nuclei and two and more electrons, such as HeH - , H 3 + , HeH 2 + , and LiH 2 + . The PESs will be used to determine rovibrational spectra of the systems.

Probing the Properties of the Molecular Adlayers on Metal Substrates: Scanning Tunneling Microscopy Study of Amine Adsorption on Gold(111) and Graphene Nanoislands on Cobalt(0001)

NASA Astrophysics Data System (ADS)

Zhou, Hui

In this thesis, we present our findings on two major topics, both of which are studies of molecules on metal surfaces by scanning tunneling microscopy (STM). The first topic is on adsorption of a model amine compound, 1,4-benzenediamine (BDA), on the reconstructed Au(111) surface, chosen for its potential application as a molecular electronic device. The molecules were deposited in the gas phase onto the substrate in the vacuum chamber. Five different patterns of BDA molecules on the surface at different coverages, and the preferred adsorption sites of BDA molecules on reconstructed Au(111) surface, were observed. In addition, BDA molecules were susceptible to tip-induced movement, suggesting that BDA molecules on metal surfaces can be a potential candidate in STM molecular manipulations. We also studied graphene nanoislands on Co(0001) in the hope of understanding interaction of expitaxially grown graphene and metal substrates. This topic can shed a light on the potential application of graphene as an electronic device, especially in spintronics. The graphene nanoislands were formed by annealing contorted hexabenzocoronene (HBC) on the Co(0001) surface. In our experiments, we have determined atop registry of graphene atoms with respect to the underlying Co surface. We also investigated the low-energy electronic structures of graphene nanoislands by scanning tunneling spectroscopy. The result was compared with a first-principle calculation using density functional theory (DFT) which suggested strong coupling between graphene pi-bands and cobalt d-electrons. We also observed that the islands exhibit zigzag edges, which exhibits unique electronic structures compared with the center areas of the islands.

Desulfurization of benzonaphthothiophenes and dibenzothiophene with a Raney nickel catalyst and its relationship to the. pi. -electron density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagai, M.; Urimoto, H.; Uetake, K.

The hydrodesulfurization of heavy petroleum feedstocks and coal-derived liquids requires the conversion of high molecular weight compounds like dibenzothiophene and benzonaphthothiophenes. There are several studies in the literature which deal with the mechanism of the hydrodesulfurization of multi-ring thiophenic compounds on cobalt or nickel molybdenum catalysts at high pressure. However, there are only a few studies which relate the chemical reactivity of these compounds to their electronic structure. The reactivity of a multi-ring sulfur-containing compound is not determined solely by the size of the molecule. In addition, others studied the relationship between the first step in the hydrotreating reaction ofmore » benzonaphthothiophene and the Coulombic interaction term of the compounds using the CNDO/S method. Because there is competition between the different processes (hydrogenation and desulfurization) during reaction, it is difficult to understand the relationship between desulfurization and the electronic properties of the compounds under reaction conditions. The calculation of electronic structures necessarily involves many sigma bonds of hydrogenated aromatic rings as well as many electrons of high molecular weight compounds. For this reason, it is best to select a catalyst and reaction conditions under which desulfurization takes place without hydrogenation.« less

Excess electron localization in solvated DNA bases.

PubMed

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Excess Electron Localization in Solvated DNA Bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

An electron momentum spectroscopy and density functional theory study of the outer valence electronic structure of stella-2,6-dione

NASA Astrophysics Data System (ADS)

Nixon, K. L.; Wang, F.; Campbell, L.; Maddern, T.; Winkler, D.; Gleiter, R.; Loeb, P.; Weigold, E.; Brunger, M. J.

2003-07-01

We report on the first electron momentum spectroscopy (EMS) study into the outer valence electronic structure of the ground electronic state for the organic molecule stella-2,6-dione (C8H8O2). Experimentally measured binding-energy spectra are compared against a He(Ialpha) photoelectron spectroscopy result, while our derived momentum distributions (MDs) are compared against corresponding results from the plane wave impulse approximation (PWIA) level calculations. These computations employed density functional theory (DFT) basis states at the triple zeta valence polarization (TZVP) level, with a range of exchange-correlation (XC) functionals. A detailed comparison between the experimental and PWIA DFT-XC/TZVP calculated MDs enabled us to evaluate the accuracy of the various functionals, the Becke-Perdew (BP) XC functional being found to provide the most accurate description here. The importance of the through-bond interaction to the molecular orbitals (MOs) of stella-2,6-dione is demonstrated using the orbital imaging capability of EMS. Finally we show that the molecular geometry of this molecule, as derived from BP/TZVP, is in quite good agreement with corresponding independent experimental data.

Electronic Structure in Pi Systems: Part I. Huckel Theory with Electron Repulsion.

ERIC Educational Resources Information Center

Fox, Marye Anne; Matsen, F. A.

1985-01-01

Pi-CI theory is a simple, semi-empirical procedure which (like Huckel theory) treats pi and pseudo-pi orbitals; in addition, electron repulsion is explicitly included and molecular configurations are mixed. Results obtained from application of pi-CI to ethylene are superior to either the Huckel molecular orbital or valence bond theories. (JN)

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

NASA Astrophysics Data System (ADS)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on metal surfaces, focusing on electronic and vibrational spectroscopy in one case and scanning tunneling microscopy studies in the other. Original research articles describe results in many aspects of the field, including: Self-assembly, self-organization, and controlled growth of molecular layers on various substrates. Highly-ordered arrays provide model systems with extraordinary structural properties, allowing one to adjust interactions between molecules and between molecule and substrate, and can be robustly prepared from solution, an essential prerequisite for applications. Conformational or electronic switching of molecules adsorbed at metal and semiconductor surfaces. These studies highlight the elementary processes governing molecular switching at surfaces as well as the wide range of possible stimuli. Carbon-based substrates such as graphene or carbon nanotubes. These substrates are attractive due to their effective two-dimensionality which implies that switching of adsorbed molecules can effect a significant back-action on the substrate. Mechanisms of conformational switching. Several contributions study the role of electron-vibron coupling and heating in current-induced conformational switching. We hope that the collection of articles presented here will stimulate and encourage researchers in surface physics and interfacial chemistry to contribute to the still emerging field of molecular switches at surfaces. We wish to acknowledge the support and input from many colleagues in preparing this special section. A significant part of this work has been conducted in the framework of the Sonderforschungsbereich 658 Elementary Processes in Molecular Switches at Surfaces of the Deutsche Forschungsgemeinschaft, to which we are grateful for financial support. Molecular surfaces at switches contents Molecular switches at surfacesMartin Weinelt and Felix von Oppen Optically and thermally induced molecular switching processes at metal surfacesPetra Tegeder Effects of electron-vibration coupling in transport through single moleculesKatharina J Franke and Jose Ignacio Pascual Vibrational heating in single-molecule switches: an energy-dependent density-of-states approachT Brumme, R Gutierrez and G Cuniberti Reversible switching of single tin phthalocyanine molecules on the InAs(111)A surfaceC Nacci, K Kanisawa and S Fölsch Tuning the interaction between carbon nanotubes and dipole switches: the influence of the change of the nanotube-spiropyran distanceP Bluemmel, A Setaro, C Maity, S Hecht and S Reich Carbon nanotubes as substrates for molecular spiropyran-based switchesE Malic, A Setaro, P Bluemmel, Carlos F Sanz-Navarro, Pablo Ordejón, S Reich and A Knorr Ultrafast dynamics of dithienylethenes differently linked to the surface of TiO2 nanoparticlesLars Dworak, Marc Zastrow, Gehad Zeyat, Karola Rück-Braun and Josef Wachtveitl Switching the electronic properties of Co-octaethylporphyrin molecules on oxygen-covered Ni films by NO adsorptionC F Hermanns, M Bernien, A Krüger, J Miguel and W Kuch STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100)K Zenichowski, Ch Nacci, S Fölsch, J Dokić, T Klamroth and P Saalfrank A switch based on self-assembled thymineFatih Kalkan, Michael Mehlhorn and Karina Morgenstern The growth and electronic structure of azobenzene-based functional molecules on layered crystalsJ Iwicki, E Ludwig, J Buck, M Kalläne, F Köhler, R Herges, L Kipp and K Rossnagel Voltage-dependent conductance states of a single-molecule junctionY F Wang, N Néel, J Kröger, H Vázquez, M Brandbyge, B Wang and R Berndt Molecules with multiple switching units on a Au(111) surface: self-organization and single-molecule manipulationJohannes Mielke, Sofia Selvanathan, Maike Peters, Jutta Schwarz, Stefan Hecht and Leonhard Grill Preparing and regulating a bi-stable molecular switch by atomic manipulationS Sakulsermsuk, R E Palmer and P A Sloan Mixed self-assembled monolayers of azobenzene photoswitches with trifluoromethyl and cyano end groupsDaniel Brete, Daniel Przyrembel, Christian Eickhoff, Robert Carley, Wolfgang Freyer, Karsten Reuter, Cornelius Gahl and Martin Weinelt Reversible electron-induced cis-trans isomerization mediated by intermolecular interactionsCh Lotze, Y Luo, M Corso, K J Franke, R Haag and J I Pascual Transport properties of graphene functionalized with molecular switchesNiels Bode, Eros Mariani and Felix von Oppen

Contorted Organic Semiconductors for Molecular Electronics

NASA Astrophysics Data System (ADS)

Zhong, Yu

This thesis focuses on the synthesis, properties and applications of two types of contorted organic molecules: contorted molecular ribbons and conjugated corrals. We utilized the power of reaction chemistry to writing information into conjugated molecules with contorted structures and studied "structure-property" relationships. The unique properties of the molecules were expressed in electronic and optoelectronic devices such as field-effect transistors, solar cells, photodetectors, etc. In Chapter 2, I describe the design and synthesis of a new graphene ribbon architecture that consists of perylenediimide (PDI) subunits fused together by ethylene bridges. We created a prototype series of oligomers consisting of the dimer, trimer, and tetramer. The steric congestion at the fusion point between the PDI units creates helical junctions, and longer oligomers form helical ribbons. Thin films of these oligomers form the active layer in n-type field effect transistors. UV-vis spectroscopy reveals the emergence of an intense long-wavelength transition in the tetramer. From DFT calculations, we find that the HOMO-2 to LUMO transition is isoenergetic with the HOMO to LUMO transition in the tetramer. We probe these transitions directly using femtosecond transient absorption spectroscopy. The HOMO-2 to LUMO transition electronically connects the PDI subunits with the ethylene bridges, and its energy depends on the length of the oligomer. In Chapter 3, I describe an efficiency of 6.1% for a solution processed non-fullerene solar cell using a helical PDI dimer as the electron acceptor. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces, indicating that charge carriers are created from photogenerated excitons in both the electron donor and acceptor phases. Light-intensity-dependent current?voltage measurements suggested different recombination rates under short-circuit and open-circuit conditions. In Chapter 4, I discuss helical molecular semiconductors as electron acceptors that are on par with fullerene derivatives in efficient solar cells. We achieved an 8.3% power conversion efficiency in a solar cell, which is a record high for non-fullerene bulk heterojunctions. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces. Atomic force microscopy reveals a mesh-like network of acceptors with pores that are tens of nanometers in diameter for efficient exciton separation and charge transport. This study describes a new motif for designing highly efficient acceptors for organic solar cells. In Chapter 5, I compare analogous cyclic and acyclic pi-conjugated molecules as n-type electronic materials and find that the cyclic molecules have numerous benefits in organic photovoltaics. We designed two conjugated cycles for this study. Each comprises four subunits; one combines four electron-accepting, redox-active, diphenyl-perylenediimide subunits, and the other alternates two electron-donating bithiophene units with two diphenyl-perylenediimide units. We compare the macrocycles to acyclic versions of these molecules and find that, relative to the acyclic analogs, the conjugated macrocycles have bathochromically shifted UV-vis absorbances and are more easily reduced. In blended films, macrocycle-based devices show higher electron mobility and good morphology. All of these factors contribute to the more than doubling of the power conversion efficiency observed in organic photovoltaic devices with these macrocycles as the n-type, electron transporting material. This study highlights the importance of geometric design in creating new molecular semiconductors. In Chapter 6, I describe a new molecular design that enables high performance organic photodetectors. We use a rigid, conjugated macrocycle as the electron acceptor in devices to obtain high photocurrent and low dark current. We directly compare the macrocyclic acceptor devices to an acyclic control device; we find that the superior performance of the macrocycle originates from its rigid, conjugated, and cyclic structure. The macrocycle's rigid structure reduces the number of charged defects originating from deformed sp 2 carbons and covalent defects from photo/thermo-activation. With this molecular design we are able to suppress dark current density while retaining high responsivity in an ultra-sensitive non-fullerene organic photodetector. Importantly, we achieve a detectivity of 1014 Jones at near zero bias voltage. This is without the need for extra carrier blocking layers commonly employed in fullerene-based devices. Our devices are comparable to the best fullerene-based photodetectors, and the sensitivity at low working voltages (< 0.1 V) is a record for non-fullerene OPDs.

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

PubMed Central

Yuan, Kai-Jun; Bandrauk, André D.

2015-01-01

We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented. PMID:26798785

DFT and TD-DFT computation of charge transfer complex between o-phenylenediamine and 3,5-dinitrosalicylic acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afroz, Ziya; Zulkarnain,; Ahmad, Afaq, E-mail: afaqahmad3@gmail.com

2016-05-23

DFT and TD-DFT studies of o-phenylenediamine (PDA), 3,5-dinitrosalicylic acid (DNSA) and their charge transfer complex have been carried out at B3LYP/6-311G(d,p) level of theory. Molecular geometry and various other molecular properties like natural atomic charges, ionization potential, electron affinity, band gap, natural bond orbital (NBO) and frontier molecular analysis have been presented at same level of theory. Frontier molecular orbital and natural bond orbital analysis show the charge delocalization from PDA to DNSA.

Electron transport in single molecules: from benzene to graphene.

PubMed

Chen, F; Tao, N J

2009-03-17

Electron movement within and between molecules--that is, electron transfer--is important in many chemical, electrochemical, and biological processes. Recent advances, particularly in scanning electrochemical microscopy (SECM), scanning-tunneling microscopy (STM), and atomic force microscopy (AFM), permit the study of electron movement within single molecules. In this Account, we describe electron transport at the single-molecule level. We begin by examining the distinction between electron transport (from semiconductor physics) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows us to apply our understanding of single-molecule electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a molecule reaches 100%; the corresponding conductance is then 2e(2)/h (e is the charge of the electron and h is the Planck constant). This ideal conduction has been observed in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a molecule connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the molecule and its local environment. Molecular length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the molecular wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chemical and biological phenomena and is potentially useful for device applications. Polycyclic aromatic hydrocarbons (PAHs) afford unique insight into electron transport in single molecules. The simplest one, benzene, has a conductance much less than 2e(2)/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene sheets and carbon nanotubes--consisting of infinite numbers of aromatic rings--have small or even zero energy gaps between the conduction and valence bands. Between these two limits are intermediate molecules with rich properties, such as perylene derivatives made of seven aromatic rings; the properties of these types of molecules have yet to be fully explored. Studying PAHs is important not only in answering fundamental questions about electron transport but also in the ongoing quest for molecular-scale electronic devices. This line of research also helps bridge the gap between electron transfer phenomena in small redox molecules and electron transport properties in nanostructures.

Molecular and electronic structures of mononuclear iron complexes using strongly electron-donating ligands and their oxidized forms.

PubMed

Strautmann, Julia B H; George, Serena DeBeer; Bothe, Eberhard; Bill, Eckhard; Weyhermüller, Thomas; Stammler, Anja; Bögge, Hartmut; Glaser, Thorsten

2008-08-04

The ligand L (2-) (H 2L = N, N'-dimethyl- N, N'-bis(3,5-di- t-butyl-2-hydroxybenzyl)-1,2-diaminoethane) has been employed for the synthesis of two mononuclear Fe (III) complexes, namely, [LFe(eta (2)-NO 3)] and [LFeCl]. L (2-) is comprised of four strongly electron-donating groups (two tert-amines and two phenolates) that increase the electron density at the coordinated ferric ions. This property should facilitate oxidation of the complexes, that is, stabilization of the oxidized species. The molecular structures in the solid state have been established by X-ray diffraction studies. [LFeCl] is five-coordinate in a square-pyramidal coordination environment with the ligand adopting a trans-conformation, while [LFe(eta (2)-NO 3)] is six-coordinate in a distorted octahedral environment with the ligand in a beta-cis conformation. The electronic structures have been studied using magnetization, EPR, Mossbauer (with and without applied field), UV-vis-NIR, and X-ray absorption spectroscopies, which demonstrate highly anisotropic covalency from the strong sigma- and pi-donating phenolates. This analysis is supported by DFT calculations on [LFeCl]. The variations of the well-understood spectroscopic data in the solid state to the spectroscopic data in solution have been used to obtain insight in the molecular structure of the two complexes in solution. While the molecular structures of the solid states are retained in solutions of nonpolar aprotic solvents, there is, however, one common molecular structure in all protic polar solvents. The analysis of the LMCT transitions and the rhombicity E/ D clearly establish that both compounds exhibit a beta-cis conformation in these protic polar solvents. These two open coordination sites, cis to each other, allow access for two potential ligands in close proximity. Electrochemical analysis establishes two reversible oxidation waves for [LFeCl] at +0.55 V and +0.93 V vs Fc (+)/Fc and one reversible oxidation wave at +0.59 V with an irreversible oxidation at +1.07 V vs Fc (+)/Fc for [LFe(eta (2)-NO 3)]. The one- and the two-electron oxidations of [LFeCl] by chronoamperometry have been followed spectroscopically. The increase of a strong band centered at 420 nm indicates the formulation of [LFeCl] (+) as a Fe (III) monophenoxyl radical complex and of [LFeCl] (2+) as a Fe (III) bisphenoxyl radical complex. These studies imply that the ligand L (2-) is capable of providing a flexible coordination geometry with two binding sites for substrates and the allocation of two oxidation equivalents on the ligand.

Measuring the density of a molecular cluster injector via visible emission from an electron beam.

PubMed

Lundberg, D P; Kaita, R; Majeski, R; Stotler, D P

2010-10-01

A method to measure the density distribution of a dense hydrogen gas jet is presented. A Mach 5.5 nozzle is cooled to 80 K to form a flow capable of molecular cluster formation. A 250 V, 10 mA electron beam collides with the jet and produces H(α) emission that is viewed by a fast camera. The high density of the jet, several 10(16) cm(-3), results in substantial electron depletion, which attenuates the H(α) emission. The attenuated emission measurement, combined with a simplified electron-molecule collision model, allows us to determine the molecular density profile via a simple iterative calculation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Builth-Williams, J. D.; Chiari, L.; Jones, D. B., E-mail: darryl.jones@flinders.edu.au, E-mail: michael.brunger@flinders.edu.au

We present experimental and theoretical results for the electron-impact ionization of the highest occupied molecular orbitals of tetrahydropyran and 1,4-dioxane. Using an (e,2e) technique in asymmetric coplanar kinematics, angular distributions of the slow ejected electron, with an energy of 20 eV, are measured when incident electrons at 250 eV ionize the target and scatter through an angle of either −10° or −15°. The data are compared with calculations performed at the molecular 3-body distorted wave level. Fair agreement between the theoretical model and the experimental measurements was observed. The similar structures for these targets provide key insights for assessing themore » limitations of the theoretical calculations. This study in turn facilitates an improved understanding of the dynamics in the ionization process.« less

High quality atomically thin PtSe2 films grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Yan, Mingzhe; Wang, Eryin; Zhou, Xue; Zhang, Guangqi; Zhang, Hongyun; Zhang, Kenan; Yao, Wei; Lu, Nianpeng; Yang, Shuzhen; Wu, Shilong; Yoshikawa, Tomoki; Miyamoto, Koji; Okuda, Taichi; Wu, Yang; Yu, Pu; Duan, Wenhui; Zhou, Shuyun

2017-12-01

Atomically thin PtSe2 films have attracted extensive research interests for potential applications in high-speed electronics, spintronics and photodetectors. Obtaining high quality thin films with large size and controlled thickness is critical. Here we report the first successful epitaxial growth of high quality PtSe2 films by molecular beam epitaxy. Atomically thin films from 1 ML to 22 ML have been grown and characterized by low-energy electron diffraction, Raman spectroscopy and x-ray photoemission spectroscopy. Moreover, a systematic thickness dependent study of the electronic structure is revealed by angle-resolved photoemission spectroscopy (ARPES), and helical spin texture is revealed by spin-ARPES. Our work provides new opportunities for growing large size single crystalline films to investigate the physical properties and potential applications of PtSe2.

Spintronics: The molecular way

NASA Astrophysics Data System (ADS)

Cornia, Andrea; Seneor, Pierre

2017-05-01

Molecular spintronics is an interdisciplinary field at the interface between organic spintronics, molecular magnetism, molecular electronics and quantum computing, which is advancing fast and promises large technological payoffs.

Beating the thermodynamic limit with photo-activation of n-doping in organic semiconductors

NASA Astrophysics Data System (ADS)

Lin, Xin; Wegner, Berthold; Lee, Kyung Min; Fusella, Michael A.; Zhang, Fengyu; Moudgil, Karttikay; Rand, Barry P.; Barlow, Stephen; Marder, Seth R.; Koch, Norbert; Kahn, Antoine

2017-12-01

Chemical doping of organic semiconductors using molecular dopants plays a key role in the fabrication of efficient organic electronic devices. Although a variety of stable molecular p-dopants have been developed and successfully deployed in devices in the past decade, air-stable molecular n-dopants suitable for materials with low electron affinity are still elusive. Here we demonstrate that photo-activation of a cleavable air-stable dimeric dopant can result in kinetically stable and efficient n-doping of host semiconductors, whose reduction potentials are beyond the thermodynamic reach of the dimer’s effective reducing strength. Electron-transport layers doped in this manner are used to fabricate high-efficiency organic light-emitting diodes. Our strategy thus enables a new paradigm for using air-stable molecular dopants to improve conductivity in, and provide ohmic contacts to, organic semiconductors with very low electron affinity.

Conformational gating of DNA conductance

PubMed Central

Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M. P.; Hihath, Joshua

2015-01-01

DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

Conformational gating of DNA conductance.

PubMed

Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M P; Hihath, Joshua

2015-12-09

DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature.

Monolayer atomic crystal molecular superlattices.

PubMed

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A; Huang, Yu; Duan, Xiangfeng

2018-03-07

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 10 7 , along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Monolayer atomic crystal molecular superlattices

NASA Astrophysics Data System (ADS)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Magnetic properties and core electron binding energies of liquid water

NASA Astrophysics Data System (ADS)

Galamba, N.; Cabral, Benedito J. C.

2018-01-01

The magnetic properties and the core and inner valence electron binding energies of liquid water are investigated. The adopted methodology relies on the combination of molecular dynamics and electronic structure calculations. Born-Oppenheimer molecular dynamics with the Becke and Lee-Yang-Parr functionals for exchange and correlation, respectively, and includes an empirical correction (BLYP-D3) functional and classical molecular dynamics with the TIP4P/2005-F model were carried out. The Keal-Tozer functional was applied for predicting magnetic shielding and spin-spin coupling constants. Core and inner valence electron binding energies in liquid water were calculated with symmetry adapted cluster-configuration interaction. The relationship between the magnetic shielding constant σ(17O), the role played by the oxygen atom as a proton acceptor and donor, and the tetrahedral organisation of liquid water are investigated. The results indicate that the deshielding of the oxygen atom in water is very dependent on the order parameter (q) describing the tetrahedral organisation of the hydrogen bond network. The strong sensitivity of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between σ(17O) and the energy gap between the 1a1[O1s] (core) and the 2a1 (inner valence) orbitals of water. Although several studies discussed the eventual connection between magnetic properties and core electron binding energies, such a correlation could not be clearly established. Here, we demonstrate that for liquid water this correlation exists although involving the gap between electron binding energies of core and inner valence orbitals.

Optogalvanic photodetachment spectroscopy

NASA Technical Reports Server (NTRS)

Mcdermid, I. S.; Webster, C. R.

1983-01-01

A new extension to optogalvanic spectroscopy, in which electrons detached from negative ions formed in the discharge are observed as a function of incident laser wavelength, has been developed. The determination of the electron affinities of I(-) and Cl(-) atomic ions is described. The potential of the technique for studying the spectroscopy of molecular negative ions is also discussed.

Conductance of three-terminal molecular bridge based on tight-binding theory

NASA Astrophysics Data System (ADS)

Wang, Li-Guang; Li, Yong; Yu, Ding-Wen; Katsunori, Tagami; Masaru, Tsukada

2005-05-01

The quantum transmission characteristic of three-benzene ring nano-molecular bridge is investigated theoretically by using Green's function approach based on tight-binding theory with only a π orbital per carbon atom at the site. The transmission probabilities that electrons transport through the molecular bridge from one terminal to the other two terminals are obtained. The electronic current distributions inside the molecular bridge are calculated and shown in graphical analogy by the current density method based on Fisher-Lee formula at the energy points E = ±0.42, ±1.06 and ±1.5, respectively, where the transmission spectra appear peaks. We find that the transmission spectra are related to the incident electronic energy and the molecular levels strongly and the current distributions agree well with Kirchhoff quantum current momentum conservation law.

Tuning Charge and Correlation Effects for a Single Molecule on a Graphene Device

NASA Astrophysics Data System (ADS)

Tsai, Hsin-Zon; Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; Omrani, Arash A.; Riss, Alexander; Karrasch, Christoph; Jung, Han Sae; Khajeh, Ramin; Wong, Dillon; Watanabe, Kenji; Taniguchi, Takashi; Zettl, Alex; Louie, Steven G.; Crommie, Michael F.

Controlling electronic devices down to the single molecule level is a grand challenge of nanotechnology. Single-molecules have been integrated into devices capable of tuning electronic response, but a drawback for these systems is that their microscopic structure remains unknown due to inability to image molecules in the junction region. Here we present a combined STM and nc-AFM study demonstrating gate-tunable control of the charge state of individual F4TCNQ molecules at the surface of a graphene field effect transistor. This is different from previous studies in that the Fermi level of the substrate was continuously tuned across the molecular orbital energy level. Using STS we have determined the resulting energy level evolution of the LUMO, its associated vibronic modes, and the graphene Dirac point (ED). We show that the energy difference between ED and the LUMO increases as EF is moved away from ED due to electron-electron interactions that renormalize the molecular quasiparticle energy. This is attributed to gate-tunable image-charge screening in graphene and corroborated by ab initio calculations.

Electron and Ion Reactions in Molecular Solids: from water ice to DNA

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2002-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving non-thermal ions, radicals, and ballistic secondary electrons, which in turn may lead to substantial physical and chemical modifications of a medium. The detailed study of the fundamental reaction mechanisms which occur on a molecular level aids our general understanding of radiation induced processes in a variety of contexts, ranging from radiobiology to astrochemistry. Here I present measurements of electron (1 - 80 eV) and some ion (1 - 8 eV) mediated reactions in molecular films that resemble biological model systems. These consist of cryogenic films (pure or mixed) of rare gases, oxygen, water, methane, or aromatic hydrocarbons of increasing complexity, including bases, sugars, single and double stranded DNA. Although the basic nature of the electron or ion reaction mechanisms are found to be similar to those in the gas phase, they are often modulated by the physico-chemical characteristics of the medium. Depending on the latter, some reaction channels may be strongly enhanced, some may be quenched, and new reaction pathways, unavailable in the gas phase, may open. Thus, a given reaction cascade may lead to different end-points even in the same target. Although the goal of these studies is to unravel some of the nascent secondary-electron and reactive-ion induced events that contribute to radiation damage in living tissue, the basic observed reactions relate to other areas of application which will be briefly discussed. This research is supported by the Canadian Institutes of Health Research (CIHR), the National Cancer Institutes of Canada, the Natural Science and Engineering Research Council, and NATO.

Quantum chemical calculations, molecular dynamic (MD) simulations and experimental studies of using some azo dyes as corrosion inhibitors for iron. Part 2: Bis-azo dye derivatives

NASA Astrophysics Data System (ADS)

Madkour, Loutfy H.; Kaya, Savaş; Guo, Lei; Kaya, Cemal

2018-07-01

The adsorption behavior and inhibition mechanism of five synthesized bis-azo dye (BAD) derivatives on the corrosion of iron in aerated HNO3 and NaOH were investigated by performing potentiostatic polarization, weight loss (WL), thermometric and UV-visible spectra measurements. DFT calculations is applied to study the correlation between corrosion inhibition and global reactivity descriptors such as: EHOMO, ELUMO, molecular gap (ΔE), the dipole moment (μ), the global hardness (η), softness(S), electronegativity (χ), proton affinity (PA), electrophilicity (ω), nucleophilicity (ɛ), electrons transferred from inhibitors to metal surface (ΔN), initial molecule-metal interaction energy (Δψ), total electronic energy (E) and the energy change during electronic back-donation process (ΔEb-d). To mimic the real environment of corrosion inhibition, molecular dynamic (MD) simulations in aqueous phase have also been modelled consisting of all concerned species (inhibitor molecule, H2O, H3O+ ion, NO3- ion, OH- and Fe surface). The results confirmed that BAD molecules inhibit iron by adsorption behavior through donating and accepting electrons together with the formation of [Fe (II) and Fe (III)-BAD] chelate complex compounds. BAD's behavior is mainly chemisorption with some physisorption obeyed Frumkin and that of El-Awady adsorption isotherm. Kinetic parameters such as: (Kb, 1/y, Kads, f, ΔG°ads) have been determined and discussed. Binding energies of BAD molecules on Fe (110) surface followed the order: BAD_ 2 > BAD_ 1 > BAD_ 3 > BAD_ 4 > BAD_ 5. Theoretical results were found to be consistent with the experimental data reported. Our results provide important atomic/molecular insights into the anticorrosive mechanism of inhibitor molecules, which could help in understanding the organic-metal interface and designing more appropriate organic corrosion inhibitors.

Gene expression profiling of breast cancer cell lines treated with proton and electron radiations.

PubMed

Bravatà, Valentina; Minafra, Luigi; Cammarata, Francesco Paolo; Pisciotta, Pietro; Lamia, Debora; Marchese, Valentina; Manti, Lorenzo; Cirrone, Giuseppe Ap; Gilardi, Maria Carla; Cuttone, Giacomo; Forte, Giusi Irma; Russo, Giorgio

2018-06-11

Technological advances in radiation therapy are evolving with the use of hadrons, such as protons, indicated for tumors where conventional radiotherapy does not give significant advantages or for tumors located in sensitive regions, which need the maximum of dose-saving of the surrounding healthy tissues. The genomic response to conventional and non conventional Linear Energy Transfer exposure is a poor investigated topic and became an issue of radiobiological interest. The aim of this work was to analyze and compare molecular responses in term of gene expression profiles, induced by electron and proton irradiation in breast cancer cell lines. We studied the gene expression profiling differences by cDNA microarray activated in response to electron and proton irradiation with different Linear Energy Transfer values, among three breast cell lines (the tumorigenic MCF7 and MDA-MB-231 and the non tumorigenic MCF10A), exposed to the same sub-lethal dose of 9 Gy. Gene expression profiling pathway analyses showed the activation of different signaling and molecular networks in a cell line and radiation type-dependent manner. MCF10A and MDA-MB-231 cell lines were found to induce factors and pathways involved in the immunological process control. Here we describe in a detailed way the gene expression profiling and pathways activated after electron and proton irradiation in breast cancer cells. Summarizing, although specific pathways are activated in a radiation type-dependent manner, each cell line activates overall similar molecular networks in response to both these two types of ionizing radiation. Advances in knowledge: In the era of personalized medicine and breast cancer target-directed intervention, we trust that this study could drive radiation therapy towards personalized treatments, evaluating possible combined treatments, based on the molecular characterization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Mingsen; Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Institute of Applied Physics, Guizhou Normal College, Guiyang, 550018; Ye, Gui

The probe of flexible molecular conformation is crucial for the electric application of molecular systems. We have developed a theoretical procedure to analyze the couplings of molecular local vibrations with the electron transportation process, which enables us to evaluate the structural fingerprints of some vibrational modes in the inelastic electron tunneling spectroscopy (IETS). Based on a model molecule of Bis-(4-mercaptophenyl)-ether with a flexible center angle, we have revealed and validated a simple mathematical relationship between IETS signals and molecular angles. Our results might open a route to quantitatively measure key geometrical parameters of molecular junctions, which helps to achieve precisemore » control of molecular devices.« less

The Spectroscopy and Photophysics of Aniline, 2-AMINOPYRIDINE, and 3-AMINOPYRIDINE

NASA Astrophysics Data System (ADS)

Kim, Byungjoo

1995-01-01

Two-photon ionization photoelectron spectroscopic techniques have been employed in concert with a picosecond laser system and molecular beam machine to study the vibrational structure of molecular ions and the intramolecular dynamics of optically prepared intermediate states. From photoelectron spectra of 2-aminopyridine via various S_1 vibronic resonances, the frequencies of several vibrations in the ionic state are assigned. The ionization potential of the molecule is found to be 8.099 +/- 0.003 eV. Using two-color ionization techniques, the electronic overlap effects in the photoionization of excited molecules have been studied, on the example of 2-aminopyridine, 3-aminopyridine, and aniline. The molecules are excited to their S_1 states, and ionized by a 200 nm laser pulse within 50 ps. The spectra of the aminopyridines show a striking absence of transitions to excited electronic states of the ions, indicating small electronic overlap factors in the ionization transitions and very little configuration interaction in the S _1 states. The spectra of aniline show the vibrationally resolved first excited electronic state band of the ion, which is very weak compared to the ground electronic state band, indicating a small amount of orbital mixing in the S_1 state. The vibrational peaks in the band were assigned by comparison of the spectra via two different vibronic resonances. The observations demonstrate that electronic overlap effects play a very general role in the ionization of polyatomic molecules in electronically excited states, and that orbital mixing patterns of the excited electronic states may become observable by projecting molecular electronic wavefunctions onto the ion states. In the time-delayed experiments for these molecules, all spectra reveal only one product of the nonradiative relaxation process. Careful considerations of electronic and vibrational overlap propensity rules for the ionization step lead to the conclusion that the dominant nonradiative decay mechanism in these molecules is the intersystem crossing to excited vibrational states of the T_1 state. This technique has been applied to study the predissociation process of CS_2 in the S_3 vibronic levels near 200 nm. The spectra show extensive vibrational structure, with unusual activity in the antisymmetric vibrations, indicating the possibility of level mixing in the intermediate state by the IVR couplings.

Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

NASA Astrophysics Data System (ADS)

Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

2018-03-01

Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial properties.

Monitoring the Reaction Process During the S2 → S3 Transition in Photosynthetic Water Oxidation Using Time-Resolved Infrared Spectroscopy.

PubMed

Sakamoto, Hiroki; Shimizu, Tatsuki; Nagao, Ryo; Noguchi, Takumi

2017-02-08

Photosynthetic water oxidation performed at the Mn 4 CaO 5 cluster in photosystem II plays a crucial role in energy production as electron and proton sources necessary for CO 2 fixation. Molecular oxygen, a byproduct, is a source of the oxygenic atmosphere that sustains life on earth. However, the molecular mechanism of water oxidation is not yet well-understood. In the reaction cycle of intermediates called S states, the S 2 → S 3 transition is particularly important; it consists of multiple processes of electron transfer, proton release, and water insertion, and generates an intermediate leading to O-O bond formation. In this study, we monitored the reaction process during the S 2 → S 3 transition using time-resolved infrared spectroscopy to clarify its molecular mechanism. A change in the hydrogen-bond interaction of the oxidized Y Z • radical, an immediate electron acceptor of the Mn 4 CaO 5 cluster, was clearly observed as a ∼100 μs phase before the electron-transfer phase with a time constant of ∼350 μs. This observation provides strong experimental evidence that rearrangement of the hydrogen-bond network around Y Z • , possibly due to the movement of a water molecule located near Y Z • to the Mn site, takes place before the electron transfer. The electron transfer was coupled with proton release, as revealed by a relatively high deuterium kinetic isotope effect of 1.9. This proton release, which decreases the redox potential of the Mn 4 CaO 5 cluster to facilitate electron transfer to Y Z • , was proposed to determine, as a rate-limiting step, the relatively slow electron-transfer rate of the S 2 → S 3 transition.

Nanogap Electrodes towards Solid State Single-Molecule Transistors.

PubMed

Cui, Ajuan; Dong, Huanli; Hu, Wenping

2015-12-01

With the establishment of complementary metal-oxide-semiconductor (CMOS)-based integrated circuit technology, it has become more difficult to follow Moore's law to further downscale the size of electronic components. Devices based on various nanostructures were constructed to continue the trend in the minimization of electronics, and molecular devices are among the most promising candidates. Compared with other candidates, molecular devices show unique superiorities, and intensive studies on molecular devices have been carried out both experimentally and theoretically at the present time. Compared to two-terminal molecular devices, three-terminal devices, namely single-molecule transistors, show unique advantages both in fundamental research and application and are considered to be an essential part of integrated circuits based on molecular devices. However, it is very difficult to construct them using the traditional microfabrication techniques directly, thus new fabrication strategies are developed. This review aims to provide an exclusive way of manufacturing solid state gated nanogap electrodes, the foundation of constructing transistors of single or a few molecules. Such single-molecule transistors have the potential to be used to build integrated circuits. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases

NASA Astrophysics Data System (ADS)

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-01

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.

Shock compression and flash-heating of molecular adsorbates on the picosecond time scale

NASA Astrophysics Data System (ADS)

Berg, Christopher Michael

An ultrafast nonlinear coherent laser spectroscopy termed broadband multiplex vibrational sum-frequency generation (SFG) with nonresonant suppression was employed to monitor vibrational transitions of molecular adsorbates on metallic substrates during laser-driven shock compression and flash-heating. Adsorbates were in the form of well-ordered self-assembled monolayers (SAMs) and included molecular explosive simulants, such as nitroaromatics, and long chain-length alkanethiols. Based on reflectance measurements of the metallic substrates, femtosecond flash-heating pulses were capable of producing large-amplitude temperature jumps with DeltaT = 500 K. Laser-driven shock compression of SAMs produced pressures up to 2 GPa, where 1 GPa ≈ 1 x 104 atm. Shock pressures were estimated via comparison with frequency shifts observed in the monolayer vibrational transitions during hydrostatic pressure measurements in a SiC anvil cell. Molecular dynamics during flash-heating and shock loading were probed with vibrational SFG spectroscopy with picosecond temporal resolution and sub-nanometer spatial resolution. Flash-heating studies of 4-nitrobenzenethiolate (NBT) on Au provided insight into effects from hot-electron excitation of the molecular adsorbates at early pump-probe delay times. At longer delay times, effects from the excitation of SAM lattice modes and lower-energy NBT vibrations were shown. In addition, flash-heating studies of alkanethiolates demonstrated chain disordering behaviors as well as interface thermal conductances across the Au-SAM junction, which was of specific interest within the context of molecular electronics. Shock compression studies of molecular explosive simulants, such as 4-nitrobenzoate (NBA), demonstrated the proficiency of this technique to observe shock-induced molecular dynamics, in this case orientational dynamics, on the picosecond time scale. Results validated the utilization of these refined shock loading techniques to probe the shock initiation or first bond-breaking reactions in molecular explosives such as delta-HMX: a necessary study for the development of safer and more effective energetic materials.

Molecular dewetting on insulators.

PubMed

Burke, S A; Topple, J M; Grütter, P

2009-10-21

Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C(60) on alkali halides, and the technologically important system of pentacene on SiO(2). These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure.

Two-center interference effects in (e, 2e) ionization of H2 and CO2 at large momentum transfer

NASA Astrophysics Data System (ADS)

Yamazaki, Masakazu; Nakajima, Isao; Satoh, Hironori; Watanabe, Noboru; Jones, Darryl; Takahashi, Masahiko

2015-09-01

In recent years, there has been considerable interest in understanding quantum mechanical interference effects in molecular ionization. Since this interference appears as a consequence of coherent electron emission from the different molecular centers, it should depend strongly on the nature of the ionized molecular orbital. Such molecular orbital patterns can be investigated by means of binary (e, 2e) spectroscopy, which is a kinematically-complete electron-impact ionization experiment performed under the high-energy Bethe ridge conditions. In this study, two-center interference effects in the (e, 2e) cross sections of H2 and CO2 at large momentum transfer are demonstrated with a high-statistics experiment, in order to elucidate the relationship between molecular orbital patterns and the interference structure. It is shown that the two-center interference is highly sensitive to the phase, spatial pattern, symmetry of constituent atomic orbital, and chemical bonding nature of the molecular orbital. This work was partially supported by Grant-in-Aids for Scientific Research (S) (No. 20225001) and for Young Scientists (B) (No. 21750005) from the Ministry of Education, Culture, Sports, Science and Technology.

Epitaxially grown strained pentacene thin film on graphene membrane.

PubMed

Kim, Kwanpyo; Santos, Elton J G; Lee, Tae Hoon; Nishi, Yoshio; Bao, Zhenan

2015-05-06

Organic-graphene system has emerged as a new platform for various applications such as flexible organic photovoltaics and organic light emitting diodes. Due to its important implication in charge transport, the study and reliable control of molecular packing structures at the graphene-molecule interface are of great importance for successful incorporation of graphene in related organic devices. Here, an ideal membrane of suspended graphene as a molecular assembly template is utilized to investigate thin-film epitaxial behaviors. Using transmission electron microscopy, two distinct molecular packing structures of pentacene on graphene are found. One observed packing structure is similar to the well-known bulk-phase, which adapts a face-on molecular orientation on graphene substrate. On the other hand, a rare polymorph of pentacene crystal, which shows significant strain along the c-axis, is identified. In particular, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene. Through ab initio electronic structure calculations, including van der Waals interactions, the unusual polymorph is attributed to the strong graphene-pentacene interaction. The observed strained organic film growth on graphene demonstrates the possibility to tune molecular packing via graphene-molecule interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular electronics with single molecules in solid-state devices.

PubMed

Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-09-01

The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong.

Molecular diodes based on conjugated diblock co-oligomers.

PubMed

Ng, Man-Kit; Lee, Dong-Chan; Yu, Luping

2002-10-09

This report describes synthesis and characterization of a molecular diode based upon a diblock conjugated oligomer system. This system consists of two conjugated blocks with opposite electronic demand. The molecular structure exhibits a built-in electronic asymmetry, much like a semiconductor p-n junction. Electrical measurements by scanning tunneling spectroscopy (STS) clearly revealed a pronounced rectifying effect. Definitive proof for the molecular nature of the rectifying effect in this conjugated diblock molecule is provided by control experiments with a structurally similar reference compound.

Information storage at the molecular level - The design of a molecular shift register memory

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose Nelson; Hopfield, J. J.

1989-01-01

The control of electron transfer rates is discussed and a molecular shift register memory at the molecular level is described. The memory elements are made up of molecules which can exist in either an oxidized or reduced state and the bits can be shifted between the cells with photoinduced electron transfer reactions. The device integrates designed molecules onto a VLSI substrate. A control structure to modify the flow of information along a shift register is indicated schematically.

Carbon Nanotube Based Molecular Electronics

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1998-01-01

Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

Atomic and molecular physics in the gas phase

NASA Astrophysics Data System (ADS)

Toburen, L. H.

1990-09-01

The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

Computational analysis of molecular properties and spectral characteristics of cyano-containing liquid crystals: role of alkyl chains.

PubMed

Praveen, P Lakshmi; Ojha, Durga P

2011-05-01

The electronic transitions in the uv-visible range of 4'-n-alkyl-4-cyanobiphenyl (nCB) with propyl, pentyl, and heptyl groups, which are of commercial and application interests, have been studied. The uv-visible and circular dichroism spectra of nCB (n = 3,5,7) molecules have been simulated using the time dependent density functional theory Becke3-Lee-Yang-Parr hybrid functional-6-31 + G (d) method. Mulliken atomic charges for each molecule have been compared with Loewdin atomic charges to analyze the molecular charge distribution and phase stability. The highest occupied molecular orbital and lowest unoccupied molecular orbital energies corresponding to the electronic transitions in the uv-visible range have been reported. Excited states have been calculated via the configuration interaction single level with a semiempirical Hamiltonian (intermediate neglect of differential overlap method, as parametrized by Zerner and co-workers). Further, two types of calculations have been performed for model systems containing single and double molecules of nCB. Furthermore, the dimer complexes during the different modes of molecular interactions have also been studied. The interaction energies of dimer complexes have been taken into consideration in order to investigate the most energetically stable configuration. These studies are helpful for understanding the role and flexibility of end chains, in particular, phase behavior and stability.

Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.

PubMed

Parandekar, Priya V; Hratchian, Hrant P; Raghavachari, Krishnan

2008-10-14

Hybrid QM:QM (quantum mechanics:quantum mechanics) and QM:MM (quantum mechanics:molecular mechanics) methods are widely used to calculate the electronic structure of large systems where a full quantum mechanical treatment at a desired high level of theory is computationally prohibitive. The ONIOM (our own N-layer integrated molecular orbital molecular mechanics) approximation is one of the more popular hybrid methods, where the total molecular system is divided into multiple layers, each treated at a different level of theory. In a previous publication, we developed a novel QM:QM electronic embedding scheme within the ONIOM framework, where the model system is embedded in the external Mulliken point charges of the surrounding low-level region to account for the polarization of the model system wave function. Therein, we derived and implemented a rigorous expression for the embedding energy as well as analytic gradients that depend on the derivatives of the external Mulliken point charges. In this work, we demonstrate the applicability of our QM:QM method with point charge embedding and assess its accuracy. We study two challenging systems--zinc metalloenzymes and silicon oxide cages--and demonstrate that electronic embedding shows significant improvement over mechanical embedding. We also develop a modified technique for the energy and analytic gradients using a generalized asymmetric Mulliken embedding method involving an unequal splitting of the Mulliken overlap populations to offer improvement in situations where the Mulliken charges may be deficient.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Effect of Molecular Guest Binding on the d-d Transitions of Ni2+ of CPO-27-Ni: A Combined UV-Vis, Resonant-Valence-to-Core X-ray Emission Spectroscopy, and Theoretical Study.

PubMed

Gallo, Erik; Gorelov, Evgeny; Guda, Alexander A; Bugaev, Aram L; Bonino, Francesca; Borfecchia, Elisa; Ricchiardi, Gabriele; Gianolio, Diego; Chavan, Sachin; Lamberti, Carlo

2017-12-04

We used Ni K-edge resonant-valence-to-core X-ray emission spectroscopy (RVtC-XES, also referred to as direct RIXS), an element-selective bulk-sensitive synchrotron-based technique, to investigate the electronic structure of the CPO-27-Ni metal-organic framework (MOF) upon molecular adsorption of significant molecular probes: H 2 O, CO, H 2 S, and NO. We compare RVtC-XES with UV-vis spectroscopy, and we show that the element selectivity of RVtC-XES is of strategic significance to observe the full set of d-d excitations in Ni 2+ , which are partially overshadowed by the low-energy π-π* transitions of the Ni ligands in standard diffuse-reflectance UV-vis experiments. Our combined RVtC-XES/UV-vis approach provides access to the whole set of d-d excitations, allowing us a complete discussion of the changes undergone by the electronic configuration of the Ni 2+ sites hosted within the MOF upon molecular adsorption. The experimental data have been interpreted by multiplet ligand-field theory calculations based on Wannier orbitals. This study represents a step further in understanding the ability of the CPO-27-Ni MOFs in molecular sorption and separation applications.

Molecular Modeling of Ammonium, Calcium, Sulfur, and Sodium Lignosulphonates in Acid and Basic Aqueous Environments

NASA Astrophysics Data System (ADS)

Salazar Valencia, P. J.; Bolívar Marinez, L. E.; Pérez Merchancano, S. T.

2015-12-01

Lignosulphonates (LS), also known as lignin sulfonates or sulfite lignin, are lignins in sulfonated forms, obtained from the "sulfite liquors," a residue of the wood pulp extraction process. Their main utility lies in its wide range of properties, they can be used as additives, dispersants, binders, fluxing, binder agents, etc. in fields ranging from food to fertilizer manufacture and even as agents in the preparation of ion exchange membranes. Since they can be manufactured relatively easy and quickly, and that its molecular size can be manipulated to obtain fragments of very low molecular weight, they are used as transport agents in the food industry, cosmetics, pharmaceutical and drug development, and as molecular elements for the treatment of health problems. In this paper, we study the electronic structural and optical characteristics of LS incorporating ammonium, sulfur, calcium, and sodium ions in acidic and basic aqueous media in order to gain a better understanding of their behavior and the very interesting properties exhibit. The studies were performed using the molecular modeling program HyperChem 5 using the semiempirical method PM3 of the NDO Family (neglect of differential overlap), to calculate the structural properties. We calculated the electronic and optical properties using the semiempirical method ZINDO / CI.

Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation.

PubMed

Rahimi, Ehsan; Reimers, Jeffrey R

2018-06-20

The use of molecules to enact quantum cellular automata (QCA) cells has been proposed as a new way for performing electronic logic operations at sub-nm dimensions. A key question that arises concerns whether chemical or physical processes are to be exploited. The use of chemical reactions allows the state of a switch element to be latched in molecular form, making the output of a cell independent of its inputs, but costs energy to do the reaction. Alternatively, if purely electronic polarization is manipulated then no internal latching occurs, but no power is dissipated provided the fields from the inputs change slowly compared to the molecular response times. How these scenarios pan out is discussed by considering calculated properties of the 1,4-diallylbutane cation, a species often used as a paradigm for molecular electronic switching. Utilized are results from different calculation approaches that depict the ion either as a charge-localized mixed-valence compound functioning as a bistable switch, or else as an extremely polarizable molecule with a delocalized electronic structure. Practical schemes for using molecular cells in QCA and other devices emerge.

Development of an electrically driven molecular motor.

PubMed

Murphy, Colin J; Sykes, E Charles H

2014-10-01

For molecules to be used as components in molecular machinery, methods are required that couple individual molecules to external energy sources in order to selectively excite motion in a given direction. While significant progress has been made in the construction of synthetic molecular motors powered by light and by chemical reactions, there are few experimental examples of electrically driven molecular motors. To this end, we pioneered the use of a new, stable and tunable molecular rotor system based on surface-bound thioethers to comprehensively study many aspects of molecular rotation. As biological molecular motors often operate at interfaces, our synthetic system is especially amenable to microscopic interrogation as compared to solution-based systems. Using scanning tunneling microscopy (STM) and density functional theory, we studied the rotation of surface-bound thioethers, which can be induced either thermally or by electrons from the STM tip in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. This work culminated in the first experimental demonstration of a single-molecule electric motor, where the electrically driven rotation of a butyl methyl sulfide molecule adsorbed on a copper surface could be directionally biased. The direction and rate of the rotation are related to the chirality of both the molecule and the STM tip (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interrogating selectivity in catalysis using molecular vibrations

NASA Astrophysics Data System (ADS)

Milo, Anat; Bess, Elizabeth N.; Sigman, Matthew S.

2014-03-01

The delineation of molecular properties that underlie reactivity and selectivity is at the core of physical organic chemistry, and this knowledge can be used to inform the design of improved synthetic methods or identify new chemical transformations. For this reason, the mathematical representation of properties affecting reactivity and selectivity trends, that is, molecular parameters, is paramount. Correlations produced by equating these molecular parameters with experimental outcomes are often defined as free-energy relationships and can be used to evaluate the origin of selectivity and to generate new, experimentally testable hypotheses. The premise behind successful correlations of this type is that a systematically perturbed molecular property affects a transition-state interaction between the catalyst, substrate and any reaction components involved in the determination of selectivity. Classic physical organic molecular descriptors, such as Hammett, Taft or Charton parameters, seek to independently probe isolated electronic or steric effects. However, these parameters cannot address simultaneous, non-additive variations to more than one molecular property, which limits their utility. Here we report a parameter system based on the vibrational response of a molecule to infrared radiation that can be used to mathematically model and predict selectivity trends for reactions with interlinked steric and electronic effects at positions of interest. The disclosed parameter system is mechanistically derived and should find broad use in the study of chemical and biological systems.

Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

PubMed

Lin, Hai; Zhao, Yan; Tishchenko, Oksana; Truhlar, Donald G

2006-09-01

The multiconfiguration molecular mechanics (MCMM) method is a general algorithm for generating potential energy surfaces for chemical reactions by fitting high-level electronic structure data with the help of molecular mechanical (MM) potentials. It was previously developed as an extension of standard MM to reactive systems by inclusion of multidimensional resonance interactions between MM configurations corresponding to specific valence bonding patterns, with the resonance matrix element obtained from quantum mechanical (QM) electronic structure calculations. In particular, the resonance matrix element is obtained by multidimensional interpolation employing a finite number of geometries at which electronic-structure calculations of the energy, gradient, and Hessian are carried out. In this paper, we present a strategy for combining MCMM with hybrid quantum mechanical molecular mechanical (QM/MM) methods. In the new scheme, electronic-structure information for obtaining the resonance integral is obtained by means of hybrid QM/MM calculations instead of fully QM calculations. As such, the new strategy can be applied to the studies of very large reactive systems. The new MCMM scheme is tested for two hydrogen-transfer reactions. Very encouraging convergence is obtained for rate constants including tunneling, suggesting that the new MCMM method, called QM/MM-MCMM, is a very general, stable, and efficient procedure for generating potential energy surfaces for large reactive systems. The results are found to converge well with respect to the number of Hessians. The results are also compared to calculations in which the resonance integral data are obtained by pure QM, and this illustrates the sensitivity of reaction rate calculations to the treatment of the QM-MM border. For the smaller of the two systems, comparison is also made to direct dynamics calculations in which the potential energies are computed quantum mechanically on the fly.

Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

NASA Astrophysics Data System (ADS)

Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

Outer membrane cytochromes/flavin interactions in Shewanella spp.—A molecular perspective

DOE PAGES

Babanova, Sofia; Matanovic, Ivana; Cornejo, Jose; ...

2017-05-31

Extracellular electron transfer (EET) is intrinsically associated with the core phenomena of energy harvesting/energy conversion in natural ecosystems and biotechnology applications. But, the mechanisms associated with EET are complex and involve molecular interactions that take place at the “bionano interface” where biotic/abiotic interactions are usually explored. Our work provides molecular perspective on the electron transfer mechanism(s) employed by Shewanella oneidensis MR-1. Molecular docking simulations were used to explain the interfacial relationships between two outer-membrane cytochromes (OMC) OmcA and MtrC and riboflavin (RF) and flavin mononucleotide (FMN), respectively. OMC-flavin interactions were analyzed by studying the electrostatic potential, the hydrophilic/hydrophobic surface properties,more » and the van der Waals surface of the OMC proteins. As a result, it was proposed that the interactions between flavins and OMCs are based on geometrical recognition event. The possible docking positions of RF and FMN to OmcA and MtrC were also shown.« less

Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

NASA Astrophysics Data System (ADS)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

PubMed

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently.

Structure and dynamics in self-organized C60 fullerenes.

PubMed

Patnaik, Archita

2007-01-01

This manuscript on 'structure and dynamics in self-organized C60 fullerenes' has three sections dealing with: (A) pristine C60 aggregate structure and geometry in solvents of varying dielectric constant. Here, using positronium (Ps) as a fundamental probe which maps changes in the local electron density of the microenvironment, the onset concentration for stable C60 aggregate formation and its phase behavior is deduced from the specific interactions of the Ps atom with the surrounding. (B) A novel methanofullerene dyad, based on a hydrophobic (acceptor C60 moiety)-hydrophilic (bridge with benzene and ester functionalities)-hydrophobic (donor didodecyloxybenzene) network is chosen for investigation of characteristic self-assembly it undergoes leading to supramolecular aggregates. The pi-electronic amphiphile, necessitating a critical dielectric constant epsilon > or = 30 in binary THF-water mixtures, dictated the formation of bilayer vesicles as precursors for spherical fractal aggregates upon complete dyad extraction into a more polar water phase. (C) While the molecular orientation is dependent on the packing density, the ordering of the molecular arrangement, indispensable for self-assembly depends on the balance between the structures demanded by inter-molecular and molecule-substrate interactions. The molecular orientation in a monolayer affects the orientation in a multilayer, formed on the monolayer, suggesting the possibility of the latter to act as a template for controlling the structure of the three dimensionally grown self-assembled molecular aggregation. A systematic study on the electronic structure and orientation associated with C60 functionalized aminothiol self-assembled monolayers on Au(111) surface is presented using surface sensitive Ultra-Violet Photoelectron Spectroscopy (UPS) and C-K edge Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. The results revealed drastic modifications to d-band structure of Au(111) and the electronic structure was found sensitive towards the S-Au interface and the C60 end functional moiety with formation of localized sigma-(S-Au) and sigma(N-C) bonds, respectively. Upon binding C60 to the amine-terminated alkanethiol SAM, a drastically reduced HOMO-LUMO gap of 2.7 eV as compared to a large electronic gap of approximately 8 eV in alkanethiols enables the SAM to be a potential electron transport medium.

Membrane Fusion Involved in Neurotransmission: Glimpse from Electron Microscope and Molecular Simulation

PubMed Central

Yang, Zhiwei; Gou, Lu; Chen, Shuyu; Li, Na; Zhang, Shengli; Zhang, Lei

2017-01-01

Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters. Subsequently, this work summarizes the research on the fusion process in synaptic transmission, using electron microscopy (EM) and molecular simulation approaches. Finally, we propose the future outlook for more exciting applications of membrane fusion involved in synaptic transmission, with the aid of stochastic optical reconstruction microscopy (STORM), cryo-EM (cryo-EM), and molecular simulations. PMID:28638320

Molecular and electronic structure of thin films of protoporphyrin(IX)Fe(III)Cl

NASA Astrophysics Data System (ADS)

Snyder, Shelly R.; White, Henry S.

1991-11-01

Electrochemical, scanning tunneling microscopy (STM), and tunneling spectroscopy studies of the molecular and electronic properties of thin films of protoporphyrin(IX)Fe(III)Cl (abbreviated as PP(IX)Fe(III)Cl) on highly oriented pyrolytic graphite (HOPG) electrodes are reported. PP(IX)Fe(III)Cl films are prepared by two different methods: (1) adsorption, yielding an electrochemically-active film, and (2) irreversible electrooxidative polymerization, yielding an electrochemically-inactive film. STM images, in conjunction with electro-chemical results, indicate that adsorption of PP(IX)Fe(III)Cl from aqueous solutions onto freshly cleaved HOPG results in a film comprised of molecular aggregates. In contrast, films prepared by irreversible electrooxidative polymerization of PP(IX)Fe(III)Cl have a denser, highly structured morphology, including what appear to be small pinholes (approx. 50A diameter) in an otherwise continuous film.

Fabrication and characterization of graphene/molecule/graphene vertical junctions with aryl alkane monolayers

NASA Astrophysics Data System (ADS)

Jeong, Inho; Song, Hyunwook

2017-11-01

In this study, we fabricated and characterized graphene/molecule/graphene (GMG) vertical junctions with aryl alkane monolayers. The constituent molecules were chemically self-assembled via electrophilic diazonium reactions into a monolayer on the graphene bottom electrode, while the other end physically contacted the graphene top electrode. A full understanding of the transport properties of molecular junctions is a key step in the realization of molecular-scale electronic devices and requires detailed microscopic characterization of the junction's active region. Using a multiprobe approach combining a variety of transport techniques, we elucidated the transport mechanisms and electronic structure of the GMG junctions, including temperature- and length-variable transport measurements, and transition voltage spectroscopy. These results provide criteria to establish a valid molecular junction and to determine the most probable transport characteristics of the GMG junctions.

Resonant tunneling via a Ru-dye complex using a nanoparticle bridge junction.

PubMed

Nishijima, Satoshi; Otsuka, Yoichi; Ohoyama, Hiroshi; Kajimoto, Kentaro; Araki, Kento; Matsumoto, Takuya

2018-06-15

Nonlinear current-voltage (I-V) characteristics is an important property for the realization of information processing in molecular electronics. We studied the electrical conduction through a Ru-dye complex (N-719) on a 2-aminoethanethiol (2-AET) monolayer in a nanoparticle bridge junction system. The nonlinear I-V characteristics exhibited a threshold voltage at around 1.2 V and little temperature dependence. From the calculation of the molecular states using density functional theory and the energy alignment between the electrodes and molecules, the conduction mechanism in this system was considered to be resonant tunneling via the HOMO level of N-719. Our results indicate that the weak electronic coupling of electrodes and molecules is essential for obtaining nonlinear I-V characteristics with a clear threshold voltage that reflect the intrinsic molecular state.

Resonant tunneling via a Ru–dye complex using a nanoparticle bridge junction

NASA Astrophysics Data System (ADS)

Nishijima, Satoshi; Otsuka, Yoichi; Ohoyama, Hiroshi; Kajimoto, Kentaro; Araki, Kento; Matsumoto, Takuya

2018-06-01

Nonlinear current–voltage (I–V) characteristics is an important property for the realization of information processing in molecular electronics. We studied the electrical conduction through a Ru–dye complex (N-719) on a 2-aminoethanethiol (2-AET) monolayer in a nanoparticle bridge junction system. The nonlinear I–V characteristics exhibited a threshold voltage at around 1.2 V and little temperature dependence. From the calculation of the molecular states using density functional theory and the energy alignment between the electrodes and molecules, the conduction mechanism in this system was considered to be resonant tunneling via the HOMO level of N-719. Our results indicate that the weak electronic coupling of electrodes and molecules is essential for obtaining nonlinear I–V characteristics with a clear threshold voltage that reflect the intrinsic molecular state.

Low-voltage electron microscopy of polymer and organic molecular thin films.

PubMed

Drummy, Lawrence F; Yang, Junyan; Martin, David C

2004-06-01

We have demonstrated the capabilities of a novel low-voltage electron microscope (LVEM) for imaging polymer and organic molecular thin films. The LVEM can operate in transmission electron microscopy, scanning transmission electron microscopy, scanning electron microscopy, and electron diffraction modes. The microscope operates at a nominal accelerating voltage of 5 kV and fits on a tabletop. A detailed discussion of the electron-sample interaction processes is presented, and the mean free path for total electron scattering was calculated to be 15 nm for organic samples at 5 kV. The total end point dose for the destruction of crystallinity at 5 kV was estimated at 5 x 10(-4) and 3.5 x 10(-2) C/cm2 for polyethylene and pentacene, respectively. These values are significantly lower than those measured at voltages greater than 100 kV. A defocus series of colloidal gold particles allowed us to estimate the experimental contrast transfer function of the microscope. Images taken of several organic materials have shown high contrast for low atomic number elements and a resolution of 2.5 nm. The materials studied here include thin films of the organic semiconductor pentacene, triblock copolymer films, single-molecule dendrimers, electrospun polymer fibers and gold nanoparticles. Copyright 2004 Elsevier B.V.

Solitons in a nonlinear model of spin transport in helical molecules

NASA Astrophysics Data System (ADS)

Albares, P.; Díaz, E.; Cerveró, Jose M.; Domínguez-Adame, F.; Diez, E.; Estévez, P. G.

2018-02-01

We study an effective integrable nonlinear model describing an electron moving along the axis of a deformable helical molecule. The helical conformation of dipoles in the molecular backbone induces an unconventional Rashba-like interaction that couples the electron spin with its linear momentum. In addition, a focusing nonlinearity arises from the electron-lattice interaction, enabling the formation of a variety of stable solitons such as bright solitons, breathers, and rogue waves. A thorough study of the soliton solutions for both focusing and defocusing nonlinear interaction is presented and discussed.

The any particle molecular orbital grid-based Hartree-Fock (APMO-GBHF) approach

NASA Astrophysics Data System (ADS)

Posada, Edwin; Moncada, Félix; Reyes, Andrés

2018-02-01

The any particle molecular orbital grid-based Hartree-Fock approach (APMO-GBHF) is proposed as an initial step to perform multi-component post-Hartree-Fock, explicitly correlated, and density functional theory methods without basis set errors. The method has been applied to a number of electronic and multi-species molecular systems. Results of these calculations show that the APMO-GBHF total energies are comparable with those obtained at the APMO-HF complete basis set limit. In addition, results reveal a considerable improvement in the description of the nuclear cusps of electronic and non-electronic densities.

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

NASA Astrophysics Data System (ADS)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Ab initio quantum chemical study of electron transfer in carboranes

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.

2005-05-01

The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.

Controlling electron localization in H2 + by intense plasmon-enhanced laser fields

NASA Astrophysics Data System (ADS)

Yavuz, I.; Ciappina, M. F.; Chacón, A.; Altun, Z.; Kling, M. F.; Lewenstein, M.

2016-03-01

We present a theoretical study of the H2 + molecular ion wave-packet dynamics in plasmon-enhanced laser fields. These fields may be produced, for instance, when metallic nanostructures are illuminated by a laser pulse of moderated intensity. Their main property is that they vary in space on a nanometric scale. We demonstrate that the spatial inhomogeneous character of the plasmonic fields leads to an enhancement of electron localization (EL), an instrumental phenomenon to control molecular fragmentation. We suggest that the charge imbalance induced by the surface-plasmon resonance near the metallic nanostructure is the origin of the increase in the EL.

A multidisciplinary approach to describe protists: a morphological, ultrastructural, and molecular study on Peritromus kahli Villeneuve-Brachon, 1940 (Ciliophora, Heterotrichea).

PubMed

Rosati, Giovanna; Modeo, Letizia; Melai, Michele; Petroni, Giulio; Verni, Franco

2004-01-01

This study represents the first extended report on a species of the ciliate genus Peritromus, widespread in marine biotopes, characterized by a dorso-ventral differentiation peculiar among Heterotrichea. Morphological observations (live, stained, scanning, and transmission electron microscope) were combined with behavioral and molecular data. On the basis of the whole body of observations, the species was recognized as Peritromus kahli. Scanning and transmission electron microscopy have revealed a number of features such as peculiar chalice-like structures external to the dorsal surface, two types of extrusomes, and differences between dorsal and ventral somatic ciliature. The almost complete SSrDNA gene sequence was also determined. A molecular phylogenetic analysis indicated that Peritromus diverged early from other members of the Class Heterotrichea. The dorso-ventral differentiation that certainly influences the behavior of P. kahli (e.g. preference for crawling and thigmotaxis) may have been selected as an adaptation to the constraints of the interstitial habitat.

Negative differential resistance and switch behavior of T-BxNy (x, y = 5, 6, 11) molecular junctions

NASA Astrophysics Data System (ADS)

Wang, Shi-Liang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Xin, Jian-Guo

2017-05-01

The electronic transport properties of T-BxNy (x, y = 5, 6, 11) molecular junction are investigated based on first-principle density functional theory and non-equilibrium Green's function method. Strong negative differential resistance (NDR) behavior is observed for T-B5N6 molecule under negative and positive bias voltages, with an obvious switch effect for T-B6N5. However, only small NDR is shown for the complex of the two molecules. The projected device density of states, the spatial distribution of molecular orbitals, and the effect of transmission spectra under various bias voltages on the electronic transport properties are analyzed. The obvious effect of bias voltage on the changes in the electronic distribution of frontier molecular orbitals is responsible for the NDR or switch behavior. Therefore, different functional molecular devices can be obtained with different structures of T-BxNy.

Stable Organic Monolayers on Oxide-Free Silicon/Germanium in a Supercritical Medium: A New Route to Molecular Electronics.

PubMed

Puniredd, Sreenivasa Reddy; Jayaraman, Sundaramurthy; Yeong, Sai Hooi; Troadec, Cedric; Srinivasan, M P

2013-05-02

Oxide-free Si and Ge surfaces have been passivated and modified with organic molecules by forming covalent bonds between the surfaces and reactive end groups of linear alkanes and aromatic species using single-step deposition in supercritical carbon dioxide (SCCO2). The process is suitable for large-scale manufacturing due to short processing times, simplicity, and high resistance to oxidation. It also allows the formation of monolayers with varying reactive terminal groups, thus enabling formation of nanostructures engineered at the molecular level. Ballistic electron emission microscopy (BEEM) spectra performed on the organic monolayer on oxide-free silicon capped by a thin gold layer reveals for the first time an increase in transmission of the ballistic current through the interface of up to three times compared to a control device, in contrast to similar studies reported in the literature suggestive of oxide-free passivation in SCCO2. The SCCO2 process combined with the preliminary BEEM results opens up new avenues for interface engineering, leading to molecular electronic devices.

Proton cooling in ultracold low-density electron gas

NASA Astrophysics Data System (ADS)

Bobrov, A. A.; Bronin, S. Y.; Manykin, E. A.; Zelener, B. B.; Zelener, B. V.; Khikhlukha, D. R.

2015-11-01

A sole proton energy loss processes in an electron gas and the dependence of these processes on temperature and magnetic field are studied using molecular dynamics techniques in present work. It appears that for electron temperatures less than 100 K many body collisions affect the proton energy loss and these collisions must be taken into account. The influence of a strong magnetic field on the relaxation processes is also considered in this work. Calculations were performed for electron densities 10 cm-3, magnetic field 1-3 Tesla, electron temperatures 10-50 K, initial proton energies 100-10000 K.

Ionospheric E-region electron density and neutral atmosphere variations

NASA Technical Reports Server (NTRS)

Stick, T. L.

1976-01-01

Electron density deviations from a basic variation with the solar zenith angle were investigated. A model study was conducted in which the effects of changes in neutral and relative densities of atomic and molecular oxygen on calculated electron densities were compared with incoherent scatter measurements in the height range 100-117 km at Arecibo, Puerto Rico. The feasibility of determining tides in the neutral atmosphere from electron density profiles was studied. It was determined that variations in phase between the density and temperature variation and the comparable magnitudes of their components make it appear improbable that the useful information on tidal modes can be obtained in this way.

Hot-electron-mediated surface chemistry: toward electronic control of catalytic activity.

PubMed

Park, Jeong Young; Kim, Sun Mi; Lee, Hyosun; Nedrygailov, Ievgen I

2015-08-18

Energy dissipation at surfaces and interfaces is mediated by excitation of elementary processes, including phonons and electronic excitation, once external energy is deposited to the surface during exothermic chemical processes. Nonadiabatic electronic excitation in exothermic catalytic reactions results in the flow of energetic electrons with an energy of 1-3 eV when chemical energy is converted to electron flow on a short (femtosecond) time scale before atomic vibration adiabatically dissipates the energy (in picoseconds). These energetic electrons that are not in thermal equilibrium with the metal atoms are called "hot electrons". The detection of hot electron flow under atomic or molecular processes and understanding its role in chemical reactions have been major topics in surface chemistry. Recent studies have demonstrated electronic excitation produced during atomic or molecular processes on surfaces, and the influence of hot electrons on atomic and molecular processes. We outline research efforts aimed at identification of the intrinsic relation between the flow of hot electrons and catalytic reactions. We show various strategies for detection and use of hot electrons generated by the energy dissipation processes in surface chemical reactions and photon absorption. A Schottky barrier localized at the metal-oxide interface of either catalytic nanodiodes or hybrid nanocatalysts allows hot electrons to irreversibly transport through the interface. We show that the chemicurrent, composed of hot electrons excited by the surface reaction of CO oxidation or hydrogen oxidation, correlates well with the turnover rate measured separately by gas chromatography. Furthermore, we show that hot electron flows generated on a gold thin film by photon absorption (or internal photoemission) can be amplified by localized surface plasmon resonance. The influence of hot charge carriers on the chemistry at the metal-oxide interface are discussed for the cases of Au, Ag, and Pt nanoparticles on oxide supports and Pt-CdSe-Pt nanodumbbells. We show that the accumulation or depletion of hot electrons on metal nanoparticles, in turn, can also influence catalytic reactions. Mechanisms suggested for hot-electron-induced chemical reactions on a photoexcited plasmonic metal are discussed. We propose that the manipulation of the flow of hot electrons by changing the electrical characteristics of metal-oxide and metal-semiconductor interfaces can give rise to the intriguing capability of tuning the catalytic activity of hybrid nanocatalysts.

Hydration of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

Jalbout, Abraham F.; Del Castillo, R.; Adamowicz, Ludwik

2007-01-01

In this work we strive to design a novel electron trap located on a molecular surface. The process of electron trapping involves hydration of the trapped electron. Previous calculations on surface electron trapping revealed that clusters of OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), while the hydrogen atoms on the opposite side of the surface form pockets of positive charge that can attract extra negative charge. The excess electron density on such surfaces can be further stabilized by interactions with water molecules. Our calculations show that these anionic systems are stable with respect to vertical electron detachment (VDE).

Charge transport in organic multi-layer devices under electric and optical fields

NASA Astrophysics Data System (ADS)

Park, June Hyoung

2007-12-01

Charge transport in small organic molecules and conjugated conducting polymers under electric or optical fields is studied by using field effect transistors and photo-voltaic cells with multiple thin layers. With these devices, current under electric field, photo-current under optical field, and luminescence of optical materials are measured to characterize organic and polymeric materials. For electric transport studies, poly(3,4-ethylenedioxythiophene) doped by polystyrenesulfonic acid is used, which is conductive with conductivity of approximately 25 S/cm. Despite their high conductance, field effect transistors based on the films are successfully built and characterized by monitoring modulations of drain current by gate voltage and IV characteristic curves. Due to very thin insulating layers of poly(vinylphenol), the transistors are relative fast under small gate voltage variation although heavy ions are involved in charge transport. In IV characteristic curves, saturation effects can be observed. Analysis using conventional field effect transistor model indicates high mobility of charge carriers, 10 cm2/V·sec, which is not consistent with the mobility of the conducting polymer. It is proposed that the effect of a small density of ions injected via polymer dielectric upon application of gate voltage and the ion compensation of key hopping sites accounts for the operation of the field effect transistors. For the studies of transport under optical field, photovoltaic cells with 3 different dendrons, which are efficient to harvest photo-excited electrons, are used. These dendrons consist of two electron-donors (tetraphenylporphyrin) and one electron-accepter (naphthalenediimide). Steady-state fluorescence measurements show that inter-molecular interaction is dominant in solid dendron film, although intra-molecular interaction is still present. Intra-molecular interaction is suggested by different fluorescence lifetimes between solutions of donor and dendrons. This intra-molecular interaction has two processes, transport via pi-stackings and transport via linking functional groups in the dendrons. IV characteristic spectra of the photovoltaic cells suggest that the transport route of photo-excited charges depends on wavelength of incident light on the cells. For excitation by the Soret band and the lowest Q band, a photo-excited electron can transport directly to a neighbor dendron. For excitation by high-energy Q bands, a photo-excited electron transports via the electron-accepters.

Electron-impact ionization and electron attachment cross sections of radicals important in transient gaseous discharges

NASA Technical Reports Server (NTRS)

Lee, Long C.; Srivastava, Santosh K.

1990-01-01

Electron-impact ionization and electron attachment cross sections of radicals and excited molecules were measured using an apparatus that consists of an electron beam, a molecular beam and a laser beam. The information obtained is needed for the pulse power applications in the areas of high power gaseous discharge switches, high energy lasers, particle beam experiments, and electromagnetic pulse systems. The basic data needed for the development of optically-controlled discharge switches were also investigated. Transient current pulses induced by laser irradiation of discharge media were observed and applied for the study of electron-molecule reaction kinetics in gaseous discharges.

Electron localization of anions probed by nitrile vibrations

DOE PAGES

Mani, Tomoyasu; Grills, David C.; Newton, Marshall D.; ...

2015-08-02

Localization and delocalization of electrons is a key concept in chemistry, and is one of the important factors determining the efficiency of electron transport through organic conjugated molecules, which have potential to act as “molecular wires”. This, in turn, substantially influences the efficiencies of organic solar cells and other molecular electronic devices. It is also necessary to understand the electronic energy landscape and the dynamics of electrons through molecular chain that govern their transport capabilities in one-dimensional conjugated chains so that we can better define the design principles of conjugated molecules for their applications. We show that nitrile ν(C≡N) vibrationsmore » respond to the degree of electron localization in nitrile-substituted organic anions by utilizing time-resolved infrared (TRIR) detection combined with pulse radiolysis. Measurements of a series of aryl nitrile anions allow us to construct a semi-empirical calibration curve between the changes in the ν(C≡N) IR shifts and the changes in the electronic charges from the neutral to the anion states in the nitriles; more electron localization in the nitrile anion results in larger IR shifts. Furthermore, the IR linewidth in anions can report a structural change accompanying changes in the electronic density distribution. Probing the shift of the nitrile ν(C≡N) IR vibrational bands enables us to determine how the electron is localized in anions of nitrile-functionalized oligofluorenes, considered as organic mixed-valence compounds. We estimate the diabatic electron transfer distance, electronic coupling strengths, and energy barriers in these organic mixed-valence compounds. The analysis reveals a dynamic picture, showing that the electron is moving back and forth within the oligomers with a small activation energy of ≤ k BT, likely controlled by the movement of dihedral angles between monomer units. Thus, implications for the electron transport capability in "molecular wires" are discussed.« less

Molecular geometry of vanadium dichloride and vanadium trichloride: a gas-phase electron diffraction and computational study.

PubMed

Varga, Zoltán; Vest, Brian; Schwerdtfeger, Peter; Hargittai, Magdolna

2010-03-15

The molecular geometries of VCl2 and VCl3 have been determined by computations and gas-phase electron diffraction (ED). The ED study is a reinvestigation of the previously published analysis for VCl2. The structure of the vanadium dichloride dimer has also been calculated. According to our joint ED and computational study, the evaporation of a solid sample of VCl2 resulted in about 66% vanadium trichloride and 34% vanadium dichloride in the vapor. Vanadium dichloride is unambiguously linear in its 4Sigma(g)+ ground electronic state. For VCl3, all computations yielded a Jahn-Teller-distorted ground-state structure of C(2v) symmetry. However, it lies merely less than 3 kJ/mol lower than the 3E'' state (D(3h) symmetry). Due to the dynamic nature of the Jahn-Teller effect in this case, rigorous distinction cannot be made between the planar models of either D(3h) symmetry or C(2v) symmetry for the equilibrium structure of VCl3. Furthermore, the presence of several low-lying excited electronic states of VCl3 is expected in the high-temperature vapor. To our knowledge, this is the first experimental and computational study of the VCl3 molecule.

Molecular gearing systems

DOE PAGES

Gakh, Andrei A.; Sachleben, Richard A.; Bryan, Jeff C.

1997-11-01

The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion. Complex synergistic biochemical complexes driven by sophisticated biomechanical processes are quite common. Their biochemical functions are based on the interplay of mechanical and chemical processes, including allosteric effects. In addition, the complexity of this interplay far exceeds thatmore » of typical chemical reactions. Understanding the behavior of artificial molecular devices as well as complex natural molecular biomechanical systems is difficult. Fortunately, the problem can be successfully resolved by direct molecular engineering of simple molecular systems that can mimic desired mechanical or electronic devices. These molecular systems are called technomimetics (the name is derived, by analogy, from biomimetics). Several classes of molecular systems that can mimic mechanical, electronic, or other features of macroscopic devices have been successfully synthesized by conventional chemical methods during the past two decades. In this article we discuss only one class of such model devices: molecular gearing systems.« less

Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

PubMed

Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

2012-11-28

Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

The Three Forms of Molecular Oxygen.

ERIC Educational Resources Information Center

Laing, Michael

1989-01-01

Finds that a logical application of the simple rules of the molecular orbital bonding theory for diatomic molecules predicted the existence of three spin isomers of the oxygen molecule: one triplet form with two unpaired electrons and two singlet forms with all electrons paired. (MVL)

Electron tomography and 3D molecular simulations of platinum nanocrystals

NASA Astrophysics Data System (ADS)

Florea, Ileana; Demortière, Arnaud; Petit, Christophe; Bulou, Hervé; Hirlimann, Charles; Ersen, Ovidiu

2012-07-01

This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface.This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30990d

Electronic structure of uracil-like nucleobases adsorbed on Si(001): uracil, thymine and 5-fluorouracil

NASA Astrophysics Data System (ADS)

Molteni, Elena; Onida, Giovanni; Cappellini, Giancarlo

2016-04-01

We study the electronic properties of the Si(001):Uracil, Si(001):Thymine, and Si(001):5-Fluorouracil systems, focusing on the Si dimer-bridging configuration with adsorption governed by carbonyl groups. While the overall structural and electronic properties are similar, with small differences due to chemical substitutions, much larger effects on the surface band dispersion and bandgap show up as a function of the molecular orientation with respect to the surface. An off-normal orientation of the molecular planes is favored, showing larger bandgap and lower total energy than the upright position. We also analyze the localization of gap-edge occupied and unoccupied surface states. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjb/e2016-70011-1

Electronic tunneling through a fullerene-like molecular bridge

NASA Astrophysics Data System (ADS)

Vanaie, H.; Yaghobi, M.

2018-04-01

This study was conducted to consider the electronic transport properties of the N_{36} B_{36} molecule, using the Green's function method based on the GW model. The number, width, height and position of density of state peaks are dramatically dependent on the correlation effect, the contact type and symmetric properties of the molecule. Also, negative differential resistance behavior was observed for all modes in voltages 4.4 V (- 4.5 V) to 4.7 V (- 4.7 V). The N_{36} B_{36} molecule behaves as an insulator where the total current becomes zero for the same values of the gate voltages but acts as a metal at other values. Therefore, the physical picture of electron conduction may change in N_{36} B_{36}—based molecular devices and it could behave as a semiconductor.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Communication: Charge transfer dominates over proton transfer in the reaction of nitric acid with gas-phase hydrated electrons

NASA Astrophysics Data System (ADS)

Lengyel, Jozef; Med, Jakub; Slavíček, Petr; Beyer, Martin K.

2017-09-01

The reaction of HNO3 with hydrated electrons (H2O)n- (n = 35-65) in the gas phase was studied using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and ab initio molecular dynamics simulations. Kinetic analysis of the experimental data shows that OH-(H2O)m is formed primarily via a reaction of the hydrated electron with HNO3 inside the cluster, while proton transfer is not observed and NO3-(H2O)m is just a secondary product. The reaction enthalpy was determined using nanocalorimetry, revealing a quite exothermic charge transfer with -241 ± 69 kJ mol-1. Ab initio molecular dynamics simulations indicate that proton transfer is an allowed reaction pathway, but the overall thermochemistry favors charge transfer.

Molecular Electronic Angular Motion Transducer Broad Band Self-Noise

PubMed Central

Zaitsev, Dmitry; Agafonov, Vadim; Egorov, Egor; Antonov, Alexander; Shabalina, Anna

2015-01-01

Modern molecular electronic transfer (MET) angular motion sensors combine high technical characteristics with low cost. Self-noise is one of the key characteristics which determine applications for MET sensors. However, until the present there has not been a model describing the sensor noise in the complete operating frequency range. The present work reports the results of an experimental study of the self-noise level of such sensors in the frequency range of 0.01–200 Hz. Based on the experimental data, a theoretical model is developed. According to the model, self-noise is conditioned by thermal hydrodynamic fluctuations of the operating fluid flow in the frequency range of 0.01–2 Hz. At the frequency range of 2–100 Hz, the noise power spectral density has a specific inversely proportional dependence of the power spectral density on the frequency that could be attributed to convective processes. In the high frequency range of 100–200 Hz, the noise is conditioned by the voltage noise of the electronics module input stage operational amplifiers and is heavily reliant to the sensor electrical impedance. The presented results allow a deeper understanding of the molecular electronic sensor noise nature to suggest the ways to reduce it. PMID:26610502

Synthesis of novel anthraquinones: Molecular structure, molecular chemical reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs

NASA Astrophysics Data System (ADS)

Al-Otaibi, Jamelah S.; EL Gogary, Tarek M.

2017-02-01

Anthraquinones are well-known anticancer drugs. Anthraquinones anticancer drugs carry out their cytotoxic activities through their interaction with DNA, and inhibition of topoisomerase II activity. Anthraquinones (AQ5 and AQ5H) were synthesized and studied with 1,5-DAAQ by computational and experimental tools. The purpose of this study is to shade more light on mechanism of interaction between anthraquinone DNA affinic agents and different types of DNA. This study will lead to gain of information useful for drug design and development. Molecular structures were optimized using DFT B3LYP/6-31 + G(d). Depending on intramolecular hydrogen bonding interactions four conformers of AQ5 were detected within the range of about 42 kcal/mol. Molecular reactivity of the anthraquinone compounds was explored using global and condensed descriptors (electrophilicity and Fukui functions). NMR and UV-VIS electronic absorption spectra of anthraquinones/DNA were investigated at the physiological pH. The interaction of the anthraquinones (AQ5 and AQ5H) were studied with different DNA namely, calf thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]). UV-VIS electronic absorption spectral data were employed to measure the affinity constants of drug/DNA binding using Scatchard analysis. NMR study confirms qualitatively the drug/DNA interaction in terms of peak shift and broadening.

Photodissociation spectroscopy of the dysprosium monochloride molecular ion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunning, Alexander, E-mail: alexander.dunning@gmail.com; Schowalter, Steven J.; Puri, Prateek

2015-09-28

We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl{sup +}. The photodissociation cross section for the photon energy range 35 500 cm{sup −1} to 47 500 cm{sup −1} is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm{sup −1}. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl{sup +} is extremely complex due to the presence of multiple open electronic shells,more » including the 4f{sup 10} configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy{sup +} ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.« less

In-situ spectro-microscopy on organic films: Mn-Phthalocyanine on Ag(100)

NASA Astrophysics Data System (ADS)

Al-Mahboob, Abdullah; Sadowski, Jerzy T.; Vescovo, Elio

2013-03-01

Metal phthalocyanines are attracting significant attention, owing to their potential for applications in chemical sensors, solar cells and organic magnets. As the electronic properties of molecular films are determined by their crystallinity and molecular packing, the optimization of film quality is important for improving the performance of organic devices. Here, we present the results of in situ low-energy electron microscopy / photoemission electron microscopy (LEEM/PEEM) studies of incorporation-limited growth of manganese-phthalocyanine (MnPc) on Ag(100) surfaces. MnPc thin films were grown on both, bulk Ag(100) surface and thin Ag(100)/Fe(100) films, where substrate spin-polarized electronic states can be modified through tuning the thickness of the Ag film. We also discuss the electronic structure and magnetic ordering in MnPc thin films, investigated by angle- and spin-resolved photoemission spectroscopy. Research carried out at the Center for Functional Nanomaterials and National Synchrotron Light Source, Brookhaven National Laboratory, which are supported by the U.S. Dept. of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

Elucidating nitric oxide synthase domain interactions by molecular dynamics.

PubMed

Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

2016-02-01

Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

Bound and resonance states of the dipolar anion of hydrogen cyanide: Competition between threshold effects and rotation in an open quantum system

DOE PAGES

Fossez, K.; Michel, N.; Nazarewicz, W.; ...

2015-01-12

In this paper, bound and resonance states of the dipole-bound anion of hydrogen cyanide HCN – are studied using a nonadiabatic pseudopotential method and the Berggren expansion technique involving bound states, decaying resonant states, and nonresonant scattering continuum. We devise an algorithm to identify the resonant states in the complex energy plane. To characterize spatial distributions of electronic wave functions, we introduce the body-fixed density and use it to assign families of resonant states into collective rotational bands. We find that the nonadiabatic coupling of electronic motion to molecular rotation results in a transition from the strong-coupling to weak-coupling regime.more » In the strong-coupling limit, the electron moving in a subthreshold, spatially extended halo state follows the rotational motion of the molecule. Above the ionization threshold, the electron's motion in a resonance state becomes largely decoupled from molecular rotation. Finally, the widths of resonance-band members depend primarily on the electron orbital angular momentum.« less

Surface molecular imprinting onto fluorescein-coated magnetic nanoparticlesvia reversible addition fragmentation chain transfer polymerization: A facile three-in-one system for recognition and separation of endocrine disrupting chemicals

NASA Astrophysics Data System (ADS)

Li, Ying; Dong, Cunku; Chu, Jia; Qi, Jingyao; Li, Xin

2011-01-01

In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals.In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals. Electronic supplementary information (ESI) available: Supplementary figure S1. The hysteresis loop of Fe3O4 (a), Fe3O4@SiO2 (b), and Fe3O4@SiO2-Dye-SiO2 (c). See DOI: 10.1039/c0nr00614a

Solution-processed ultrathin chemically derived graphene films as soft top contacts for solid-state molecular electronic junctions.

PubMed

Li, Tao; Hauptmann, Jonas Rahlf; Wei, Zhongming; Petersen, Søren; Bovet, Nicolas; Vosch, Tom; Nygård, Jesper; Hu, Wenping; Liu, Yunqi; Bjørnholm, Thomas; Nørgaard, Kasper; Laursen, Bo W

2012-03-08

A novel method using solution-processed ultrathin chemically derived graphene films as soft top contacts for the non-destructive fabrication of molecular junctions is demonstrated. We believe this protocol will greatly enrich the solid-state test beds for molecular electronics due to its low-cost, easy-processing and flexible nature. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations of the orientation properties of cytochrome c on the surface of single-walled carbon nanotubes.

PubMed

Zhang, Bing; Xu, Jia; Mo, Shu-Fan; Yao, Jian-Xi; Dai, Song-Yuan

2016-12-01

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.

Discrete Optimization of Electronic Hyperpolarizabilities in a Chemical Subspace

DTIC Science & Technology

2009-05-01

molecular design. Methods for optimization in discrete spaces have been studied extensively and recently reviewed ( 5). Optimization methods include...integer programming, as in branch-and-bound techniques (including dead-end elimination [ 6]), simulated annealing ( 7), and genetic algorithms ( 8...These algorithms have found renewed interest and application in molecular and materials design (9- 12) . Recently, new approaches have been

Electron-flux infrared response to varying π-bond topology in charged aromatic monomers

PubMed Central

Álvaro Galué, Héctor; Oomens, Jos; Buma, Wybren Jan; Redlich, Britta

2016-01-01

The interaction of delocalized π-electrons with molecular vibrations is key to charge transport processes in π-conjugated organic materials based on aromatic monomers. Yet the role that specific aromatic motifs play on charge transfer is poorly understood. Here we show that the molecular edge topology in charged catacondensed aromatic hydrocarbons influences the Herzberg-Teller coupling of π-electrons with molecular vibrations. To this end, we probe the radical cations of picene and pentacene with benchmark armchair- and zigzag-edges using infrared multiple-photon dissociation action spectroscopy and interpret the recorded spectra via quantum-chemical calculations. We demonstrate that infrared bands preserve information on the dipolar π-electron-flux mode enhancement, which is governed by the dynamical evolution of vibronically mixed and correlated one-electron configuration states. Our results reveal that in picene a stronger charge π-flux is generated than in pentacene, which could justify the differences of electronic properties of armchair- versus zigzag-type families of technologically relevant organic molecules. PMID:27577323

Single Molecule Electronics and Devices

PubMed Central

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Interface Engineering for Nanoelectronics.

PubMed

Hacker, C A; Bruce, R C; Pookpanratana, S J

2017-01-01

Innovation in the electronics industry is tied to interface engineering as devices increasingly incorporate new materials and shrink. Molecular layers offer a versatile means of tuning interfacial electronic, chemical, physical, and magnetic properties enabled by a wide variety of molecules available. This paper will describe three instances where we manipulate molecular interfaces with a specific focus on the nanometer scale characterization and the impact on the resulting performance. The three primary themes include, 1-designer interfaces, 2-electronic junction formation, and 3-advancing metrology for nanoelectronics. We show the ability to engineer interfaces through a variety of techniques and demonstrate the impact on technologies such as molecular memory and spin injection for organic electronics. Underpinning the successful modification of interfaces is the ability to accurately characterize the chemical and electronic properties and we will highlight some measurement advances key to our understanding of the interface engineering for nanoelectronics.

Interface Engineering for Nanoelectronics

PubMed Central

Hacker, C. A.; Bruce, R. C.; Pookpanratana, S. J.

2017-01-01

Innovation in the electronics industry is tied to interface engineering as devices increasingly incorporate new materials and shrink. Molecular layers offer a versatile means of tuning interfacial electronic, chemical, physical, and magnetic properties enabled by a wide variety of molecules available. This paper will describe three instances where we manipulate molecular interfaces with a specific focus on the nanometer scale characterization and the impact on the resulting performance. The three primary themes include, 1-designer interfaces, 2-electronic junction formation, and 3-advancing metrology for nanoelectronics. We show the ability to engineer interfaces through a variety of techniques and demonstrate the impact on technologies such as molecular memory and spin injection for organic electronics. Underpinning the successful modification of interfaces is the ability to accurately characterize the chemical and electronic properties and we will highlight some measurement advances key to our understanding of the interface engineering for nanoelectronics. PMID:29276553

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile.

PubMed

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K; Kant, Rajni; Khajuria, Yugal

2015-04-05

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity. Copyright © 2014 Elsevier B.V. All rights reserved.

Vibrational, NMR and UV-visible spectroscopic investigation and NLO studies on benzaldehyde thiosemicarbazone using computational calculations

NASA Astrophysics Data System (ADS)

Moorthy, N.; Prabakar, P. C. Jobe; Ramalingam, S.; Pandian, G. V.; Anbusrinivasan, P.

2016-04-01

In order to investigate the vibrational, electronic and NLO characteristics of the compound; benzaldehyde thiosemicarbazone (BTSC), the XRD, FT-IR, FT-Raman, NMR and UV-visible spectra were recorded and were analysed with the calculated spectra by using HF and B3LYP methods with 6-311++G(d,p) basis set. The XRD results revealed that the stabilized molecular systems were confined in orthorhombic unit cell system. The cause for the change of chemical and physical properties behind the compound has been discussed makes use of Mulliken charge levels and NBO in detail. The shift of molecular vibrational pattern by the fusing of ligand; thiosemicarbazone group with benzaldehyde has been keenly observed. The occurrence of in phase and out of phase molecular interaction over the frontier molecular orbitals was determined to evaluate the degeneracy of the electronic energy levels. The thermodynamical studies of the temperature region 100-1000 K to detect the thermal stabilization of the crystal phase of the compound were investigated. The NLO properties were evaluated by the determination of the polarizability and hyperpolarizability of the compound in crystal phase. The physical stabilization of the geometry of the compound has been explained by geometry deformation analysis.

Heteroatom-bridged benzothiazolyls for organic solar cells: a theoretical study.

PubMed

Chen, Runfeng; Wang, Yang; Chen, Ting; Li, Huanhuan; Zheng, Chunhua; Yuan, Kai; Wang, Zhixiang; Tao, Ye; Zheng, Chao; Huang, Wei

2015-01-15

On the basis of a typical organic photovoltaic (OPV) building block of 4,7-di(thiophen-2-yl)benzo[c][1,2,5]thiadiazole (DTBT), a series of novel DTBT derivatives were designed following a heteroatom-bridging strategy to take advantage of the diversified interactions between heteroatoms and π-conjugated systems. These heteroatom-bridged DTBTs, whose outer electron-rich thiophene moieties are covalently fastened to the central electron-deficient benzothiadiazole with additional heteroatom bridges, exhibit promising features for OPV applications with rigid molecular structures, properly lain frontier molecular orbitals (FMOs), broad and intense absorption spectra, and adequate charge transport properties, as revealed by systematic theoretical calculations on molecular geometries, FMOs, absorption spectra, and relaxation and reorganization energies. The structure-property relationship investigations show that the mono-/di-heteroatom bridging is effective not only in tuning the rigidity of the molecular geometries but also in adjusting the optoelectronic properties of the resulting materials. Among the studied heteroatoms, the C and Si were found to be the most efficient in designing novel molecules for OPV applications. These theoretical insights may provide a solid basis for experimental synthesis and device investigations of the proposed heteroatom-bridged DTBTs as potential high-performance building blocks for bulk heterojunction OPV molecules.

Configuration-specific electronic structure of strongly interacting interfaces: TiOPc on Cu(110)

NASA Astrophysics Data System (ADS)

Maughan, Bret; Zahl, Percy; Sutter, Peter; Monti, Oliver L. A.

2017-12-01

We use low-temperature scanning tunneling microscopy in combination with angle-resolved ultraviolet and two-photon photoemission spectroscopy to investigate the interfacial electronic structure of titanyl phthalocyanine (TiOPc) on Cu(110). We show that the presence of two unique molecular adsorption configurations is crucial for a molecular-level analysis of the hybridized interfacial electronic structure. Specifically, thermally induced self-assembly exposes marked adsorbate-configuration-specific contributions to the interfacial electronic structure. The results of this work demonstrate an avenue towards understanding and controlling interfacial electronic structure in chemisorbed films even for the case of complex film structure.

Fragment molecular orbital study on electron tunneling mechanisms in bacterial photosynthetic reaction center.

PubMed

Kitoh-Nishioka, Hirotaka; Ando, Koji

2012-11-01

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling T(DA) and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (H(L)) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe(2+) and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe(2+) ion, its replacement by Zn(2+), or its removal are found to affect the T(DA) value by factors within 2.2. The calculated T(DA) values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments.

Energy transfer and photochemistry on a metal surface: Mo(CO)/sub 6/ on Rh(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Germer, T.A.; Ho, W.

1989-05-01

The occurrence of photoinduced reactions on solid surfaces depends on the relative rates between the excited-state decomposition and the energy transfer to the surface. In this study, the photodecomposition of Mo(CO)/sub 6/ on Rh(100) at 90 K by 325-nm UV irradiation has been studied as a function of coverage and surface preparation using thermal desorption spectroscopy, electron energy-loss spectroscopy, and photoinduced desorption spectroscopy. It is found that Mo(CO)/sub 6/ adsorbs dissociatively on Rh(100) into carbonyl fragments and CO in the first monolayer and molecularly in multilayers. Photoinduced desorption of CO is observed for the multilayers adsorbed onto the dissociated firstmore » layer via a nonthermal electronic excitation of adsorbed metal carbonyls. The presence of the metal surface prevents complete decarbonylation as in the gas phase; deexcitation of electronically excited carbonyls is not sufficiently fast to quench all the observed photochemistry. It is also found that Mo(CO)/sub 6/ adsorbs molecularly on a presaturated CO ordered overlayer on Rh(100) and undergoes photodissociation to a greater degree than on the dissociated and disordered surface of carbonyl fragments. The ordered CO layer effectively screens the interaction between the molecular carbonyls and the Rh(100) layer surface.« less

DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells.

PubMed

Rezvani, M; Darvish Ganji, M; Jameh-Bozorghi, S; Niazi, A

2018-04-05

In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω + ) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C 60 -Porphyrine-Metalloporphyrine (C 60 -P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C 60 -P-Mptriad system due to C 60 -Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes. In addition, the performance of solar cells favors better with doubly and increasing the π conjugated of the bridge. Copyright © 2018 Elsevier B.V. All rights reserved.

DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Rezvani, M.; Darvish Ganji, M.; Jameh-Bozorghi, S.; Niazi, A.

2018-04-01

In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω+) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C60-Porphyrine-Metalloporphyrine (C60-P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C60-P-Mptriad system due to C60-Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes. In addition, the performance of solar cells favors better with doubly and increasing the π conjugated of the bridge.

The road not taken: Applications of fluorescence spectroscopy and electronic structure theory to systems of materials and biological relevance

NASA Astrophysics Data System (ADS)

Carlson, Philip Joseph

Applications of Fluorescence Spectroscopy and Electronic Structure Theory to Systems of Materials and Biological Relevance. The photophysics of curcumin was studied in micelles and the solvation dynamics were probed. The high-energy ionic liquid HEATN was also studied using the fragment molecular orbital method. The solvation dynamics of the HEATN system were determined. This marks the first study of the solvation dynamics in a triazolium ionic liquid system.

Molecular structures and intramolecular dynamics of pentahalides

NASA Astrophysics Data System (ADS)

Ischenko, A. A.

2017-03-01

This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

Multilevel Molecular Modeling Approach for a Rational Design of Ionic Current Sensors for Nanofluidics.

PubMed

Kirch, Alexsandro; de Almeida, James M; Miranda, Caetano R

2018-05-10

The complexity displayed by nanofluidic-based systems involves electronic and dynamic aspects occurring across different size and time scales. To properly model such kind of system, we introduced a top-down multilevel approach, combining molecular dynamics simulations (MD) with first-principles electronic transport calculations. The potential of this technique was demonstrated by investigating how the water and ionic flow through a (6,6) carbon nanotube (CNT) influences its electronic transport properties. We showed that the confinement on the CNT favors the partially hydrated Na, Cl, and Li ions to exchange charge with the nanotube. This leads to a change in the electronic transmittance, allowing for the distinguishing of cations from anions. Such an ionic trace may handle an indirect measurement of the ionic current that is recorded as a sensing output. With this case study, we are able to show the potential of this top-down multilevel approach, to be applied on the design of novel nanofluidic devices.

Molecular helices as electron acceptors in high-performance bulk heterojunction solar cells

DOE PAGES

Yu M. Zhong; Nam, Chang -Yong; Trinh, M. Tuan; ...

2015-09-18

Despite numerous organic semiconducting materials synthesized for organic photovoltaics in the past decade, fullerenes are widely used as electron acceptors in highly efficient bulk-heterojunction solar cells. None of the non-fullerene bulk heterojunction solar cells have achieved efficiencies as high as fullerene-based solar cells. Design principles for fullerene-free acceptors remain unclear in the field. Here we report examples of helical molecular semiconductors as electron acceptors that are on par with fullerene derivatives in efficient solar cells. We achieved an 8.3% power conversion efficiency in a solar cell, which is a record high for non-fullerene bulk heterojunctions. Femtosecond transient absorption spectroscopy revealedmore » both electron and hole transfer processes at the donor–acceptor interfaces. Atomic force microscopy reveals a mesh-like network of acceptors with pores that are tens of nanometres in diameter for efficient exciton separation and charge transport. As a result, this study describes a new motif for designing highly efficient acceptors for organic solar cells.« less

Molecular helices as electron acceptors in high-performance bulk heterojunction solar cells.

PubMed

Zhong, Yu; Trinh, M Tuan; Chen, Rongsheng; Purdum, Geoffrey E; Khlyabich, Petr P; Sezen, Melda; Oh, Seokjoon; Zhu, Haiming; Fowler, Brandon; Zhang, Boyuan; Wang, Wei; Nam, Chang-Yong; Sfeir, Matthew Y; Black, Charles T; Steigerwald, Michael L; Loo, Yueh-Lin; Ng, Fay; Zhu, X-Y; Nuckolls, Colin

2015-09-18

Despite numerous organic semiconducting materials synthesized for organic photovoltaics in the past decade, fullerenes are widely used as electron acceptors in highly efficient bulk-heterojunction solar cells. None of the non-fullerene bulk heterojunction solar cells have achieved efficiencies as high as fullerene-based solar cells. Design principles for fullerene-free acceptors remain unclear in the field. Here we report examples of helical molecular semiconductors as electron acceptors that are on par with fullerene derivatives in efficient solar cells. We achieved an 8.3% power conversion efficiency in a solar cell, which is a record high for non-fullerene bulk heterojunctions. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces. Atomic force microscopy reveals a mesh-like network of acceptors with pores that are tens of nanometres in diameter for efficient exciton separation and charge transport. This study describes a new motif for designing highly efficient acceptors for organic solar cells.