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.

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.

The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

PubMed

Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

2017-07-19

Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

Field-induced structural control of COx molecules adsorbed on graphene

NASA Astrophysics Data System (ADS)

Matsubara, Manaho; Okada, Susumu

2018-05-01

Using the density functional theory combined with both the van der Waals correction and the effective screening medium method, we investigate the energetics and electronic structures of CO and CO2 molecules adsorbed on graphene surfaces in the field-effect-transistor structure with respect to the external electric field by the excess electrons/holes. The binding energies of CO and CO2 molecules to graphene monotonically increase with increasing hole and electron concentrations. The increase occurs regardless of the molecular conformations to graphene and the counter electrode, indicating that the carrier injection substantially enhances the molecular adsorption on graphene. Injected carriers also modulate the stable molecular conformation, which is metastable in the absence of an electric field.

Protonated o-semiquinone radical as a mimetic of the humic acids native radicals: A DFT approach to the molecular structure and EPR properties

NASA Astrophysics Data System (ADS)

Witwicki, Maciej; Jezierska, Julia

2012-06-01

Organic radicals are known to be an indispensable component of the humic acids (HA) structure. In HA two forms of radicals, stable (native) and short-lived (transient), are identified. Importantly, these radical forms can be easily differentiated by electron paramagnetic resonance (EPR) spectroscopy. This article provides a DFT-based insight into the electronic and molecular structure of the native radicals. The molecular models including an increase of the radical aromaticity and the hydrogen bonding between the radical and other functional groups of HA are taken under investigation. In consequence the interesting pieces of information on the structure of the native radical centers in HA are revealed and discussed, especially in terms of differences between the electronic structure of the native and transient forms.

Molecular Spintronics: Theory of Spin-Dependent Electron Transport in Fe/BDT/Fe Molecular Wire Systems

NASA Astrophysics Data System (ADS)

Dalgleish, Hugh; Kirczenow, George

2004-03-01

Metal/Molecule/Metal junction systems forming molecular wires are currently the focus of intense study. Recently, spin-dependent electron transport in molecular wires with magnetic Ni electrodes has been studied theoretically, and spin-valve effects have been predicted.* Here we explore theoretically another magnetic molecular wire system, namely, ferromagnetic Fe nano-contacts bridged with 1,4-benzene-dithiolate (BDT). We estimate the essential structural and electronic parameters for this system based on ab initio density functional calculations (DFT) for some simple model systems involving thiol groups and Fe clusters as well as semi-empirical considerations and the known electronic structure of bulk Fe. We then use Lippmann-Schwinger and Green's function techniques together with the Landauer formalism to study spin-dependent transport. *E. G. Emberly and G. Kirczenow, Chem. Phys. 281, 311 (2002); R. Pati, L. Senapati, P.M. Ajayan and S.K. Nayak, Phys. Rev. B68, 100407 (2003).

Localized variations in electronic structure of AlGaN/GaN heterostructures grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Smith, K. V.; Yu, E. T.; Elsass, C. R.; Heying, B.; Speck, J. S.

2001-10-01

Local electronic properties in a molecular-beam-epitaxy-grown AlxGa1-xN/GaN heterostructure field-effect transistor epitaxial layer structure are probed using depth-resolved scanning capacitance microscopy. Theoretical analysis of contrast observed in scanning capacitance images acquired over a range of bias voltages is used to assess the possible structural origins of local inhomogeneities in electronic structure, which are shown to be concentrated in areas where Ga droplets had formed on the surface during growth. Within these regions, there are significant variations in the local electronic structure that are attributed to variations in both AlxGa1-xN layer thickness and Al composition. Increased charge trapping is also observed in these regions.

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.

Density functional theory studies on the structures and electronic communication of meso-ferrocenylporphyrins: long range orbital coupling via porphyrin core.

PubMed

Zhang, Lijuan; Qi, Dongdong; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

2011-02-01

The molecular and electronic structures together with the electronic absorption spectra of a series of metal free meso-ferrocenylporphyrins, namely 5-ferrocenylporphyrin (1), 5,10-diferrocenylporphyrin (2), 5,15-diferrocenylporphyrin (3), 5,10,15-triferrocenylporphyrin (4), and 5,10,15,20-tetraferrocenylporphyrin (5) have been studied with the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. For the purpose of comparative studies, metal free porphyrin without any ferrocenyl group (0) and isolated ferrocene (6) were also calculated. The effects of the number and position of meso-attached ferrocenyl substituents on their molecular and electronic structures, atomic charges, molecular orbitals, and electronic absorption spectra of 1-5 were systematically investigated. The orbital coupling is investigated in detail, explaining well the long range coupling of ferrocenyl substituents connected via porphyrin core and the systematic change in the electronic absorption spectra of porphyrin compounds. Copyright © 2010 Elsevier Inc. All rights reserved.

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.

Organic-based molecular switches for molecular electronics.

PubMed

Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

2011-10-05

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

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.

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.

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.

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.

Theoretical investigations of molecular wires: Electronic spectra and electron transport

NASA Astrophysics Data System (ADS)

Palma, Julio Leopoldo

The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with respect to the azo group. The results showed that the molecular structure is crucial in optimizing the electron transport properties of chemical structures, and that the transport properties in electronic devices at the molecular level can be manipulated, enhanced or suppressed by a careful consideration of the effects of chemical modification.

Understanding molecular structure from molecular mechanics.

PubMed

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

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).

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

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.

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

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

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.

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.

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.

Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

USGS Publications Warehouse

Sherman, David M.

1986-01-01

A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

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.

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.

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.

Theoretical modeling of the electronic structure and exchange interactions in Cu(II)Pc

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.; Wang, Hai; Wu, Zhenlin; Gardener, Jules; Heutz, Sandrine; Jones, Tim; Aeppli, Gabriel

2012-12-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine (Cu(II)Pc) crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green's function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α- and β-phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Ultrafast Structural Dynamics in Combustion Relevant Model Systems

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

Weber, Peter M.

2014-03-31

The research project explored the time resolved structural dynamics of important model reaction system using an array of novel methods that were developed specifically for this purpose. They include time resolved electron diffraction, time resolved relativistic electron diffraction, and time resolved Rydberg fingerprint spectroscopy. Toward the end of the funding period, we also developed time-resolved x-ray diffraction, which uses ultrafast x-ray pulses at LCLS. Those experiments are just now blossoming, as the funding period expired. In the following, the time resolved Rydberg Fingerprint Spectroscopy is discussed in some detail, as it has been a very productive method. The binding energymore » of an electron in a Rydberg state, that is, the energy difference between the Rydberg level and the ground state of the molecular ion, has been found to be a uniquely powerful tool to characterize the molecular structure. To rationalize the structure sensitivity we invoke a picture from electron diffraction: when it passes the molecular ion core, the Rydberg electron experiences a phase shift compared to an electron in a hydrogen atom. This phase shift requires an adjustment of the binding energy of the electron, which is measurable. As in electron diffraction, the phase shift depends on the molecular, geometrical structure, so that a measurement of the electron binding energy can be interpreted as a measurement of the molecule’s structure. Building on this insight, we have developed a structurally sensitive spectroscopy: the molecule is first elevated to the Rydberg state, and the binding energy is then measured using photoelectron spectroscopy. The molecule’s structure is read out as the binding energy spectrum. Since the photoionization can be done with ultrafast laser pulses, the technique is inherently capable of a time resolution in the femtosecond regime. For the purpose of identifying the structures of molecules during chemical reactions, and for the analysis of molecular species in the hot environments of combustion processes, there are several features that make the Rydberg ionization spectroscopy uniquely useful. First, the Rydberg electron’s orbit is quite large and covers the entire molecule for most molecular structures of combustion interest. Secondly, the ionization does not change vibrational quantum numbers, so that even complicated and large molecules can be observed with fairly well resolved spectra. In fact, the spectroscopy is blind to vibrational excitation of the molecule. This has the interesting consequence for the study of chemical dynamics, where the molecules are invariably very energetic, that the molecular structures are observed unobstructed by the vibrational congestion that dominates other spectroscopies. This implies also that, as a tool to probe the time-dependent structural dynamics of chemically interesting molecules, Rydberg spectroscopy may well be better suited than electron or x-ray diffraction. With recent progress in calculating Rydberg binding energy spectra, we are approaching the point where the method can be evolved into a structure determination method. To implement the Rydberg ionization spectroscopy we use a molecular beam based, time-resolved pump-probe multi-photon ionization/photoelectron scheme in which a first laser pulse excites the molecule to a Rydberg state, and a probe pulse ionizes the molecule. A time-of-flight detector measures the kinetic energy spectrum of the photoelectrons. The photoelectron spectrum directly provides the binding energy of the electron, and thereby reveals the molecule’s time-dependent structural fingerprint. Only the duration of the laser pulses limits the time resolution. With a new laser system, we have now reached time resolutions better than 100 fs, although very deep UV wavelengths (down to 190 nm) have slightly longer instrument functions. The structural dynamics of molecules in Rydberg-excited states is obtained by delaying the probe ionization photon from the pump photon; the structural dynamics of molecules in their ground state or excited valence states is measured by inducing the dynamics using a near UV laser pulse, and employing a multi-photon ionization scheme via the Rydberg states as a probe process. Thus, the technique is capable of measuring the reaction dynamics in any electronic state of neutral molecules.« less

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

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.

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.

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

Electronic Structure of pi Systems: Part II. The Unification of Huckel and Valence Bond Theories.

ERIC Educational Resources Information Center

Fox, Marye Anne; Matsen, F. A.

1985-01-01

Presents a new view of the electronic structure of pi systems that unifies molecular orbital and valence bond theories. Describes construction of electronic structure diagrams (central to this new view) which demonstrate how configuration interaction can improve qualitative predictions made from simple Huckel theory. (JN)

Electronic structure and optical properties of metal doped tetraphenylporphyrins

NASA Astrophysics Data System (ADS)

Shah, Esha V.; Roy, Debesh R.

2018-05-01

A density functional scrutiny on the structure, electronic and optical properties of metal doped tetraphenylporphyrins MTPP (M=Fe, Co, Ni) is performed. The structural stability of the molecules is evaluated based on the electronic parameters like HOMO-LUMO gap (HLG), chemical hardness (η) and binding energy of the central metal atom to the molecular frame etc. The computed UltraViolet-Visible (UV-Vis) optical absorption spectra for all the compounds are also compared. The molecular structures reported are the lowest energy configurations. The entire calculations are carried out with a widely reliable functional, viz. B3LYP with a popular basis set which includes a scaler relativistic effect, viz. LANL2DZ.

Nanoscale inhomogeneity and photoacid generation dynamics in extreme ultraviolet resist materials

NASA Astrophysics Data System (ADS)

Wu, Ping-Jui; Wang, Yu-Fu; Chen, Wei-Chi; Wang, Chien-Wei; Cheng, Joy; Chang, Vencent; Chang, Ching-Yu; Lin, John; Cheng, Yuan-Chung

2018-03-01

The development of extreme ultraviolet (EUV) lithography towards the 22 nm node and beyond depends critically on the availability of resist materials that meet stringent control requirements in resolution, line edge roughness, and sensitivity. However, the molecular mechanisms that govern the structure-function relationships in current EUV resist systems are not well understood. In particular, the nanoscale structures of the polymer base and the distributions of photoacid generators (PAGs) should play a critical roles in the performance of a resist system, yet currently available models for photochemical reactions in EUV resist systems are exclusively based on homogeneous bulk models that ignore molecular-level details of solid resist films. In this work, we investigate how microscopic molecular organizations in EUV resist affect photoacid generations in a bottom-up approach that describes structure-dependent electron-transfer dynamics in a solid film model. To this end, molecular dynamics simulations and stimulated annealing are used to obtain structures of a large simulation box containing poly(4-hydroxystyrene) (PHS) base polymers and triphenylsulfonium based PAGs. Our calculations reveal that ion-pair interactions govern the microscopic distributions of the polymer base and PAG molecules, resulting in a highly inhomogeneous system with nonuniform nanoscale chemical domains. Furthermore, the theoretical structures were used in combination of quantum chemical calculations and the Marcus theory to evaluate electron transfer rates between molecular sites, and then kinetic Monte Carlo simulations were carried out to model electron transfer dynamics with molecular structure details taken into consideration. As a result, the portion of thermalized electrons that are absorbed by the PAGs and the nanoscale spatial distribution of generated acids can be estimated. Our data reveal that the nanoscale inhomogeneous distributions of base polymers and PAGs strongly affect the electron transfer and the performance of the resist system. The implications to the performances of EUV resists and key engineering requirements for improved resist systems will also be discussed in this work. Our results shed light on the fundamental structure dependence of photoacid generation and the control of the nanoscale structures as well as base polymer-PAG interactions in EVU resist systems, and we expect these knowledge will be useful for the future development of improved EUV resist systems.

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.

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

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

Kim, Jeongho; Kim, Kyung Hwan; Oang, Key Young

Characterization of transient molecular structures formed during chemical and biological processes is essential for understanding their mechanisms and functions. Over the last decade, time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TRXAS) have emerged as powerful techniques for molecular and electronic structural analysis of photoinduced reactions in the solution phase. Both techniques make use of a pump–probe scheme that consists of (1) an optical pump pulse to initiate a photoinduced process and (2) an X-ray probe pulse to monitor changes in the molecular structure as a function of time delay between pump and probe pulses. TRXL is sensitive tomore » changes in the global molecular structure and therefore can be used to elucidate structural changes of reacting solute molecules as well as the collective response of solvent molecules. On the other hand, TRXAS can be used to probe changes in both local geometrical and electronic structures of specific X-ray-absorbing atoms due to the element-specific nature of core-level transitions. These techniques are complementary to each other and a combination of the two methods will enhance the capability of accurately obtaining structural changes induced by photoexcitation. Here we review the principles of TRXL and TRXAS and present recent application examples of the two methods for studying chemical and biological processes in solution. Furthermore, we briefly discuss the prospect of using X-ray free electron lasers for the two techniques, which will allow us to keep track of structural dynamics on femtosecond time scales in various solution-phase molecular reactions.« less

Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

NASA Astrophysics Data System (ADS)

Li, Hao; Wu, Chao; Malinin, Sergey V.; Tretiak, Sergei; Chernyak, Vladimir Y.

2016-12-01

The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized "particle in a box" problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

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.

Real-space visualization of conformation-independent oligothiophene electronic structure

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

Taber, Benjamen N.; Kislitsyn, Dmitry A.; Gervasi, Christian F.

2016-05-21

We present scanning tunneling microscopy and spectroscopy (STM/STS) investigations of the electronic structures of different alkyl-substituted oligothiophenes on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes adopted distinct straight and bent conformations. By combining STS maps with STM images, we visualize, in real space, particle-in-a-box-like oligothiophene molecular orbitals. We demonstrate that different planar conformers with significant geometrical distortions of oligothiophene backbones surprisingly exhibit very similar electronic structures, indicating a low degree of conformation-induced electronic disorder. The agreement of these results with gas-phase density functional theory calculations implies that the oligothiophene interaction with the Au(111) surface is generally insensitivemore » to molecular conformation.« less

A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations.

PubMed

Becucci, M; Pietraperzia, G; Pasquini, M; Piani, G; Zoppi, A; Chelli, R; Castellucci, E; Demtroeder, W

2004-03-22

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy. (c) 2004 American Institute of Physics

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.

The Eighteen-Electron Rule

ERIC Educational Resources Information Center

Mitchell, P. R.; Parish, R. V.

1969-01-01

Discusses the stability of the structures of transition metal complexes (primarily carbonyls and organometallic compounds) having 18 electrons or less in their valence shell. Presents molecular orbital diagrams for various structures involving alpha and pi bonding and describes the conditions under which the 18 electron rule applies. (RR)

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)

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

Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

NASA Astrophysics Data System (ADS)

Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

2012-10-01

This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

Instructional Approach to Molecular Electronic Structure Theory

ERIC Educational Resources Information Center

Dykstra, Clifford E.; Schaefer, Henry F.

1977-01-01

Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

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.

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

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

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

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

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.

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.

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.

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.

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.

Even the Odd Numbers Help: Failure Modes of SAM-Based Tunnel Junctions Probed via Odd-Even Effects Revealed in Synchrotrons and Supercomputers.

PubMed

Thompson, Damien; Nijhuis, Christian A

2016-10-18

This Account describes a body of research in atomic level design, synthesis, physicochemical characterization, and macroscopic electrical testing of molecular devices made from ferrocene-functionalized alkanethiol molecules, which are molecular diodes, with the aim to identify, and resolve, the failure modes that cause leakage currents. The mismatch in size between the ferrocene headgroup and alkane rod makes waxlike highly dynamic self-assembled monolayers (SAMs) on coinage metals that show remarkable atomic-scale sensitivity in their electrical properties. Our results make clear that molecular tunnel junction devices provide an excellent testbed to probe the electronic and supramolecular structures of SAMs on inorganic substrates. Contacting these SAMs to a eutectic "EGaIn" alloy top-electrode, we designed highly stable long-lived molecular switches of the form electrode-SAM-electrode with robust rectification ratios of up to 3 orders of magnitude. The graphic that accompanies this conspectus displays a computed SAM packing structure, illustrating the lollipop shape of the molecules that gives dynamic SAM supramolecular structures and also the molecule-electrode van der Waals (vdW) contacts that must be controlled to form good SAM-based devices. In this Account, we first trace the evolution of SAM-based electronic devices and rationalize their operation using energy level diagrams. We describe the measurement of device properties using near edge X-ray absorption fine structure spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy complemented by molecular dynamics and electronic structure calculations together with large numbers of electrical measurements. We discuss how data obtained from these combined experimental/simulation codesign studies demonstrate control over the supramolecular and electronic structure of the devices, tuning odd-even effects to optimize inherent packing tendencies of the molecules in order to minimize leakage currents in the junctions. It is now possible, but still very costly to create atomically smooth electrodes and we discuss progress toward masking electrode imperfections using cooperative molecule-electrode contacts that are only accessible by dynamic SAM structures. Finally, the unique ability of SAM devices to achieve simultaneously high and atom-sensitive electrical switching is summarized and discussed. While putting these structures to work as real world electronic devices remains very challenging, we speculate on the scientific and technological advances that are required to further improve electronic and supramolecular structure, toward the creation of high yields of long-lived molecular devices with (very) large, reproducible rectification ratios.

Signature properties of water: Their molecular electronic origins

PubMed Central

Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

2015-01-01

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

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.

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.

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.

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.

Tracking reaction dynamics in solution by pump-probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering).

PubMed

Kim, Jeongho; Kim, Kyung Hwan; Oang, Key Young; Lee, Jae Hyuk; Hong, Kiryong; Cho, Hana; Huse, Nils; Schoenlein, Robert W; Kim, Tae Kyu; Ihee, Hyotcherl

2016-03-07

Characterization of transient molecular structures formed during chemical and biological processes is essential for understanding their mechanisms and functions. Over the last decade, time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TRXAS) have emerged as powerful techniques for molecular and electronic structural analysis of photoinduced reactions in the solution phase. Both techniques make use of a pump-probe scheme that consists of (1) an optical pump pulse to initiate a photoinduced process and (2) an X-ray probe pulse to monitor changes in the molecular structure as a function of time delay between pump and probe pulses. TRXL is sensitive to changes in the global molecular structure and therefore can be used to elucidate structural changes of reacting solute molecules as well as the collective response of solvent molecules. On the other hand, TRXAS can be used to probe changes in both local geometrical and electronic structures of specific X-ray-absorbing atoms due to the element-specific nature of core-level transitions. These techniques are complementary to each other and a combination of the two methods will enhance the capability of accurately obtaining structural changes induced by photoexcitation. Here we review the principles of TRXL and TRXAS and present recent application examples of the two methods for studying chemical and biological processes in solution. Furthermore, we briefly discuss the prospect of using X-ray free electron lasers for the two techniques, which will allow us to keep track of structural dynamics on femtosecond time scales in various solution-phase molecular reactions.

First-principle simulations of electronic structure in semicrystalline polyethylene

NASA Astrophysics Data System (ADS)

Moyassari, A.; Unge, M.; Hedenqvist, M. S.; Gedde, U. W.; Nilsson, F.

2017-05-01

In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (˜0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.

Artificial photosynthetic systems: assemblies of slipped cofacial porphyrins and phthalocyanines showing strong electronic coupling.

PubMed

Satake, Akiharu; Kobuke, Yoshiaki

2007-06-07

This paper reviews selected types of structurally well defined assemblies of porphyrins and phthalocyanines with strong electronic coupling. Face-to-face, head-to-tail, slipped cofacial, and non-parallel dimeric motifs constructed by covalent and non-covalent bonds are compared in the earlier sections. Their molecular orientation, electronic overlap, and absorption and fluorescence properties are discussed with a view towards the development of artificial photosynthetic systems and molecular electronics. Complementary coordination dimers are fully satisfactory in terms of structural stability, orientation factor, pi-electronic overlap, and zero fluorescence quenching. In later sections, several polymeric and macrocyclic porphyrin assemblies constructed by a combination of covalent bonds and complementary coordination bonds are discussed from the viewpoint of light-harvesting antenna functions.

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces

DOE PAGES

Jeon, Seokmin; Doak, Peter W.; Sumpter, Bobby G.; ...

2016-07-26

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions and superconducting ground states. In contrast, few of these phenomena have so far been observed in low-dimensional molecular structures, including thin films, nanoparticles and molecular blends, not in the least because most of such structures have so far been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional molecular structures of ionic molecules toward fundamental studies and potential applications. Here we present detailed analysis of monolayer-thick structures of the canonical TTF-TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctivemore » property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of 1:1 ratio in the bulk. We propose the existence of the surface phase-diagram that controls the structures of TTF-TCNQ on the surfaces, and demonstrate phase-transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram and the corresponding phase-transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases.« less

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.

Trans-pent-2-ene. Electron diffraction, vibrational analysis and molecular mechanics

NASA Astrophysics Data System (ADS)

Ter Brake, J. H. M.; Mijlhoff, F. C.

1981-12-01

The molecular structure of trans-pent-2-ene has been investigated, using electron diffraction, vibrational analysis and molecular mechanics. It is possible to Fit a model, describing trans-pent-2-ene as a semi-rigid molecule with one conformer only, to the electron diffraction data. However, molecular mechanics shows that trans-pent-2-ene is not a semi-rigid molecule. The large-amplitude motion is described, using all pseudo-conformers at 10° intervals around the circle of rotation. The resulting rα structure is: r[-C-C] = 148.4(1), r[-CC-] = 133.4(2), r[-C-C-] = 157.6(5), r[C-H] = 108.2(1)pm; ∠[-C-CC-] = 125.4(3), ∠[C-C-C-] = 115.6(6), ∠[-C-C-H] = 12.7(6), ∠[-CC-H] = 129(2)°. Standard deviations given in parentheses refer to the last significant digit.

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.

Localized and Spectroscopic Orbitals: Squirrel Ears on Water.

ERIC Educational Resources Information Center

Martin, R. Bruce

1988-01-01

Reexamines the electronic structure of water considering divergent views. Discusses several aspects of molecular orbital theory using spectroscopic molecular orbitals and localized molecular orbitals. Gives examples for determining lowest energy spectroscopic orbitals. (ML)

Simulation study on the effects of chemical structure and molecular size on the acceptor strength in poly(3-hexylthiophene)-based copolymer with alternating donor and acceptor for photovoltaic applications

NASA Astrophysics Data System (ADS)

Rassamesard, Areefen; Pengpan, Teparksorn

2017-02-01

This research assessed the effects of various chemical structures and molecular sizes on the simulated geometric parameters, electron structures, and spectroscopic properties of single-chain complex alternating donor-acceptor (D-A) monomers and copolymers that are intended for use as photoactive layer in a polymer solar cell by using Kohn-Sham density functional theory with B3LYP exchange-correlation functional. The 3-hexylthiophene (3HT) was selected for electron donor, while eight chemicals, namely thiazole (Z), thiadiazole (D), thienopyrazine (TP), thienothiadiazole (TD), benzothiadiazole (BT), thiadiazolothieno-pyrazine (TPD), oxadiazole (OXD) and 5-diphenyl-1,2,4-triazole (TAZ), were employed as electron acceptor functional groups. The torsional angle, bridge bond length, intramolecular charge transfer, energy levels, and molecular orbitals were analyzed. The simulation results reveal that the geometry and electron structure of donor-acceptor monomer and copolymer are significantly impacted by heterocyclic rings, heteroatoms, fused rings, degree of steric hindrance and coplanarity of the acceptor molecular structure. Planar conformation was obtained from the D copolymer, and a pseudo-planar structure with the TD copolymer. The TAZ acceptor exhibited strong steric hindrance due to its bulky structure and non-planarity of its structure. An analysis of the electron structures indicated that the degree of intramolecular electron-withdrawing capability had the rank order TAZ  <  Z  <  D  <  TPD  <  OXD  <  TP  <  BT  <  TD. The TD is indicated as the most effective acceptor among those that were simulated. However, the small energy gaps of TD as well as TPD copolymer indicate that these two copolymers can be used in transparent conducting materials. The copolymer based on BT acceptor exhibited good intramolecular charge transfer and absorbed at 656 nm wavelength which is close to the maximum flux of solar spectrum. Hence, the BT acceptor functional group provides a compromise in the characteristics of a donor-acceptor copolymer, useful in a polymeric candidate material for the photoactive layer in a polymer solar cell.

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.

Bottom-up synthesis of multifunctional nanoporous graphene

NASA Astrophysics Data System (ADS)

Moreno, César; Vilas-Varela, Manuel; Kretz, Bernhard; Garcia-Lekue, Aran; Costache, Marius V.; Paradinas, Markos; Panighel, Mirko; Ceballos, Gustavo; Valenzuela, Sergio O.; Peña, Diego; Mugarza, Aitor

2018-04-01

Nanosize pores can turn semimetallic graphene into a semiconductor and, from being impermeable, into the most efficient molecular-sieve membrane. However, scaling the pores down to the nanometer, while fulfilling the tight structural constraints imposed by applications, represents an enormous challenge for present top-down strategies. Here we report a bottom-up method to synthesize nanoporous graphene comprising an ordered array of pores separated by ribbons, which can be tuned down to the 1-nanometer range. The size, density, morphology, and chemical composition of the pores are defined with atomic precision by the design of the molecular precursors. Our electronic characterization further reveals a highly anisotropic electronic structure, where orthogonal one-dimensional electronic bands with an energy gap of ∼1 electron volt coexist with confined pore states, making the nanoporous graphene a highly versatile semiconductor for simultaneous sieving and electrical sensing of molecular species.

Tailoring Dirac Fermions in Molecular Graphene

NASA Astrophysics Data System (ADS)

Gomes, Kenjiro K.; Mar, Warren; Ko, Wonhee; Camp, Charlie D.; Rastawicki, Dominik K.; Guinea, Francisco; Manoharan, Hari C.

2012-02-01

The dynamics of electrons in solids is tied to the band structure created by a periodic atomic potential. The design of artificial lattices, assembled through atomic manipulation, opens the door to engineer electronic band structure and to create novel quantum states. We present scanning tunneling spectroscopic measurements of a nanoassembled honeycomb lattice displaying a Dirac fermion band structure. The artificial lattice is created by atomic manipulation of single CO molecules with the scanning tunneling microscope on the surface of Cu(111). The periodic potential generated by the assembled CO molecules reshapes the band structure of the two-dimensional electron gas, present as a surface state of Cu(111), into a ``molecular graphene'' system. We create local defects in the lattice to observe the quasiparticle interference patterns that unveil the underlying band structure. We present direct comparison between the tunneling data, first-principles calculations of the band structure, and tight-binding models.

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.

Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum. [atomic spectra and electronic structure of alkali metals

NASA Technical Reports Server (NTRS)

Hartmann, S. R.; Happer, W.

1974-01-01

The report discusses completed and proposed research in atomic and molecular physics conducted at the Columbia Radiation Laboratory from July 1972 to June 1973. Central topics described include the atomic spectra and electronic structure of alkali metals and helium, molecular microwave spectroscopy, the resonance physics of photon echoes in some solid state systems (including Raman echoes, superradiance, and two photon absorption), and liquid helium superfluidity.

Interface electronic structures of reversible double-docking self-assembled monolayers on an Au(111) surface

PubMed Central

Zhang, Tian; Ma, Zhongyun; Wang, Linjun; Xi, Jinyang; Shuai, Zhigang

2014-01-01

Double-docking self-assembled monolayers (DDSAMs), namely self-assembled monolayers (SAMs) formed by molecules possessing two docking groups, provide great flexibility to tune the work function of metal electrodes and the tunnelling barrier between metal electrodes and the SAMs, and thus offer promising applications in both organic and molecular electronics. Based on the dispersion-corrected density functional theory (DFT) in comparison with conventional DFT, we carry out a systematic investigation on the dual configurations of a series of DDSAMs on an Au(111) surface. Through analysing the interface electronic structures, we obtain the relationship between single molecular properties and the SAM-induced work-function modification as well as the level alignment between the metal Fermi level and molecular frontier states. The two possible conformations of one type of DDSAM on a metal surface reveal a strong difference in the work-function modification and the electron/hole tunnelling barriers. Fermi-level pinning is found to be a key factor to understand the interface electronic properties. PMID:24615153

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.

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

Synthesis and CV Studies of Dithiol-terminated Metal Terpyridine Complexes

NASA Technical Reports Server (NTRS)

Asano, Sylvia; Fan, Wendy; Ng, Hou-Tee; Han, Jie; Meyyappan, M.

2003-01-01

Transition metal coordination complexes possess unique electronic structures that should be a good model for studying electronic transport behavior at a molecular level. The discrete, multiple redox states, low redox potential and the superb ability to establish contact with other molecular and electronic components by coordination chemistry have made this a subject of investigation for their possible application as active electronic components in molecular devices. We present the synthesis and electrochemical characterization of 4'-thioacetylphenyl-2'2:6',2"-terpyridine iron(II) complex and compare it with a model bis-terpyridine iron(II) complex by cyclic voltammetry. With the use of different working electrodes, the behavior of these complexes show different electron transfer rates.

Stacking the Deck: Leveraging Surface Interactions to Tune Interfacial Electronic Structure

NASA Astrophysics Data System (ADS)

Maughan, Bret; Eads, Calley; Zahl, Percy; Sutter, Peter; Monti, Oliver

We present results from a series of experiments aimed at understanding and controlling molecular interactions in phthalocyanine (Pc) thin-films on Cu(110) to tailor the interfacial electronic structure. Using low-temperature scanning tunneling microscopy (LT-STM), we identify interactions that drive surface-molecule coupling, molecular self-assembly and thin-film order. We provide evidence that interactions with native Cu adatoms play a pivotal role in self-assembly of Pc systems, along with anisotropic nanoribbon growth dynamics, supported by an agent-based kinetic Monte Carlo (AB-KMC) simulation. We show further that self-assembled nanoribbon length can be controlled using surface diffusion barriers and that ordered 2D thin-film growth is promoted by diminishing surface-molecule interactions that otherwise dominate native Cu(110) interfaces. Altogether, this detailed structural understanding allows us to interpret interfacial electronic structure and dynamics, uncovered through ultraviolet (UPS) and two-photon photoemission (2PPE) spectroscopy experiments, in molecular configuration-specific detail. In all, our understanding of interfacial processes guides strategic modifications to both surface and molecule to harness interfacial interactions and thereby modify the collective electronic structure of the interface. NSF No. CHE-1213243 and No. CHE-1565497, Arizona TRIF, DOE/BNL Cntrct No. DE-SC0012704, and DOE No. DE-SC0016343.

Electron Microscopy.

ERIC Educational Resources Information Center

Beer, Michael

1980-01-01

Reviews technical aspects of structure determination in biological electron microscopy (EM). Discusses low dose EM, low temperature microscopy, electron energy loss spectra, determination of mass or molecular weight, and EM of labeled systems. Cites 34 references. (CS)

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

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.

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

Scattering of an electronic wave packet by a one-dimensional electron-phonon-coupled structure

NASA Astrophysics Data System (ADS)

Brockt, C.; Jeckelmann, E.

2017-02-01

We investigate the scattering of an electron by phonons in a small structure between two one-dimensional tight-binding leads. This model mimics the quantum electron transport through atomic wires or molecular junctions coupled to metallic leads. The electron-phonon-coupled structure is represented by the Holstein model. We observe permanent energy transfer from the electron to the phonon system (dissipation), transient self-trapping of the electron in the electron-phonon-coupled structure (due to polaron formation and multiple reflections at the structure edges), and transmission resonances that depend strongly on the strength of the electron-phonon coupling and the adiabaticity ratio. A recently developed TEBD algorithm, optimized for bosonic degrees of freedom, is used to simulate the quantum dynamics of a wave packet launched against the electron-phonon-coupled structure. Exact results are calculated for a single electron-phonon site using scattering theory and analytical approximations are obtained for limiting cases.

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.

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

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.

Hybrid organic-inorganic rotaxanes and molecular shuttles.

PubMed

Lee, Chin-Fa; Leigh, David A; Pritchard, Robin G; Schultz, David; Teat, Simon J; Timco, Grigore A; Winpenny, Richard E P

2009-03-19

The tetravalency of carbon and its ability to form covalent bonds with itself and other elements enables large organic molecules with complex structures, functions and dynamics to be constructed. The varied electronic configurations and bonding patterns of inorganic elements, on the other hand, can impart diverse electronic, magnetic, catalytic and other useful properties to molecular-level structures. Some hybrid organic-inorganic materials that combine features of both chemistries have been developed, most notably metal-organic frameworks, dense and extended organic-inorganic frameworks and coordination polymers. Metal ions have also been incorporated into molecules that contain interlocked subunits, such as rotaxanes and catenanes, and structures in which many inorganic clusters encircle polymer chains have been described. Here we report the synthesis of a series of discrete rotaxane molecules in which inorganic and organic structural units are linked together mechanically at the molecular level. Structural units (dialkyammonium groups) in dumb-bell-shaped organic molecules template the assembly of essentially inorganic 'rings' about 'axles' to form rotaxanes consisting of various numbers of rings and axles. One of the rotaxanes behaves as a 'molecular shuttle': the ring moves between two binding sites on the axle in a large-amplitude motion typical of some synthetic molecular machine systems. The architecture of the rotaxanes ensures that the electronic, magnetic and paramagnetic characteristics of the inorganic rings-properties that could make them suitable as qubits for quantum computers-can influence, and potentially be influenced by, the organic portion of the molecule.

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

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.

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.

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

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.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

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.

Cis-pent-2-ene. Electron diffraction, vibrational analysis and molecular mechanics

NASA Astrophysics Data System (ADS)

Ter Brake, J. H. M.

1984-08-01

The molecular structure of cis-pent-2-ene has been investigated by using electron diffraction, vibrational analysis and molecular mechanics. It is possible to fit a model, describing cis-pent-2-ene as a semi-rigid molecule with one conformer only, to the electron diffraction data. However, molecular mechanics, ab initio self-consistent field molecular orbital calculations and microwave spectroscopy show that cis-pent-2-ene is not a semi-rigid molecule. The large-amplitude motion is described, using all pseudo-conformers at 10° intervals around the circle of rotation. The resulting rα structure is: r[CC] = 149.0(1), r[CC] = 133.8(2), r[CC] = 156.1(2), r[CH] = 109.2(2), r[CH] = 105.8(5) pm, ∠[CCC] = 127.4(2), ∠[CCC] = 112.4(4), ∠[CCH] = 124(2), ∠[CCH] = 114.2(3)° (standard deviations given in parentheses refer to the last significant digit).

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.

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.

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

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

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

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.

Influence of orbital symmetry on diffraction imaging with rescattering electron wave packets

DOE PAGES

Pullen, M. G.; Wolter, B.; Le, A. -T.; ...

2016-06-22

The ability to directly follow and time-resolve the rearrangement of the nuclei within molecules is a frontier of science that requires atomic spatial and few-femtosecond temporal resolutions. While laser-induced electron diffraction can meet these requirements, it was recently concluded that molecules with particular orbital symmetries (such as pg) cannot be imaged using purely backscattering electron wave packets without molecular alignment. Here, we demonstrate, in direct contradiction to these findings, that the orientation and shape of molecular orbitals presents no impediment for retrieving molecular structure with adequate sampling of the momentum transfer space. We overcome previous issues by showcasing retrieval ofmore » the structure of randomly oriented O 2 and C 2H 2 molecules, with π g and π u symmetries, respectively, and where their ionization probabilities do not maximize along their molecular axes. As a result, while this removes a serious bottleneck for laser-induced diffraction imaging, we find unexpectedly strong backscattering contributions from low-Z atoms.« less

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.

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.

Exciton Scattering approach for conjugated macromolecules: from electronic spectra to electron-phonon coupling

NASA Astrophysics Data System (ADS)

Tretiak, Sergei

2014-03-01

The exciton scattering (ES) technique is a multiscale approach developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, the electronic excitations in the molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph. The exciton propagation on the linear segments is characterized by the exciton dispersion, whereas the exciton scattering on the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized ``particle in a box'' problems on the graph that represents the molecule. All parameters can be extracted from quantum-chemical computations of small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within considered molecular family could be performed with negligible numerical effort. The exciton scattering properties of molecular vertices can be further described by tight-binding or equivalently lattice models. The on-site energies and hopping constants are obtained from the exciton dispersion and scattering matrices. Such tight-binding model approach is particularly useful to describe the exciton-phonon coupling, energetic disorder and incoherent energy transfer in large branched conjugated molecules. Overall the ES applications accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

Structural, stability, and vibrational properties of BinPm clusters

NASA Astrophysics Data System (ADS)

Shen, Wanting; Han, Lihong; Liang, Dan; Zhang, Chunfang; Ruge, Quhe; Wang, Shumin; Lu, Pengfei

2018-04-01

An in-depth investigation is performed on stability mechanisms, electronic and optical properties of III-V semiconductor vapor phases clusters. First principles electronic structure calculations of CAM-B3LYP are performed on neutral BinPm (n + m ≤ 14) clusters. The geometrical evolution of all stable structures remains amorphous as the clusters size increases. Binding energies (BEs), energy gains and highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gaps confirm that all four-atom structures of BinPm clusters have more stable optical properties. Orbitals composition and vibrational spectra of stable clusters are analyzed. Our calculations will contribute to the study of diluted bismuth alloys and compounds.

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.

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.

Synthesis, electronic structure, molecular packing/morphology evolution, and carrier mobilities of pure oligo-/poly(alkylthiophenes).

PubMed

Zhang, Lei; Colella, Nicholas S; Liu, Feng; Trahan, Stephan; Baral, Jayanta K; Winter, H Henning; Mannsfeld, Stefan C B; Briseno, Alejandro L

2013-01-16

Monodispersed conjugated oligothiophenes are receiving attention in fundamental and applied science due to their interesting optical, optoelectronic, and charge transport properties. These "low molecular weight" polymers serve as model structures for the corresponding polymer analogues, which are inherently polydispersed. Here we report the synthesis, electronic structure, molecular packing/morphology, and charge transport properties of monodispersed oligothiophenes with up to six didodecylquaterthiophene (DDQT) building block repeat units (i.e., 24 thiophene units). At the point where the effective conjugation length is reached, the electronic structure showed convergence behavior to the corresponding polymer, poly(3,3"-didodecyl-quaterthiophene) (PQT-12). X-ray crystal structure analysis of the dimer (DDQT-2) showed that terminal thiophenes exhibit syn-conformations, similar to the terminal syn-conformations observed in the trimer (DDQT-3). The dimer also exhibits a rare bending of the terminal alkyl side chains in order to prevent steric hindrance with neighboring hydrogens attached to core thiophenes. Grazing incidence X-ray scattering measurements revealed a morphology evolution from small molecule-like packing to polymer-like packing in thin films, with a morphology transition occurring near the effective conjugation length. Charge transport measurements showed a mobility increase with decreasing chain length. We correlated the molecular packing and morphology to charge transport and determined that carrier mobilities are most sensitive to crystallinity and crystal grain misorientation. This indicates that molecular weight is not a decisive factor for improved carrier mobility in the low molecular weight region, but rather the degree in crystallinity and in-plane crystal orientation. These results represent a fundamental advancement in understanding the relationship between conjugation length and carrier mobilities in oligothiophene semiconductors.

Theoretical and experimental investigations of superconductivity. Amorphous semiconductors, superconductivity and magnetism

NASA Technical Reports Server (NTRS)

Cohen, M. H.

1973-01-01

The research activities from 1 March 1963 to 28 February 1973 are summarized. Major lectures are listed along with publications on superconductivity, superfluidity, electronic structures and Fermi surfaces of metals, optical spectra of solids, electronic structure of insulators and semiconductors, theory of magnetic metals, physics of surfaces, structures of metals, and molecular physics.

Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

NASA Astrophysics Data System (ADS)

Endah Saraswati, Teguh; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

2017-01-01

Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH3). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory.

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.

Electronic structure of multi-walled carbon fullerenes

NASA Astrophysics Data System (ADS)

Doore, Keith; Cook, Matthew; Clausen, Eric; Lukashev, Pavel V.; Kidd, Tim E.; Stollenwerk, Andrew J.

2017-02-01

Despite an enormous amount of research on carbon based nanostructures, relatively little is known about the electronic structure of multi-walled carbon fullerenes, also known as carbon onions. In part, this is due to the very high computational expense involved in estimating electronic structure of large molecules. At the same time, experimentally, the exact crystal structure of the carbon onion is usually unknown, and therefore one relies on qualitative arguments only. In this work we present the results of a computational study on a series of multi-walled fullerenes and compare their electronic structures to experimental data. Experimentally, the carbon onions were fabricated using ultrasonic agitation of isopropanol alcohol and deposited onto the surface of highly ordered pyrolytic graphite using a drop cast method. Scanning tunneling microscopy images indicate that the carbon onions produced using this technique are ellipsoidal with dimensions on the order of 10 nm. The majority of differential tunneling spectra acquired on individual carbon onions are similar to that of graphite with the addition of molecular-like peaks, indicating that these particles span the transition between molecules and bulk crystals. A smaller, yet sizable number exhibited a semiconducting gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels. These results are compared with the electronic structure of different carbon onion configurations calculated using first-principles. Similar to the experimental results, the majority of these configurations are metallic with a minority behaving as semiconductors. Analysis of the configurations investigated here reveals that each carbon onion exhibiting an energy band gap consisted only of non-metallic fullerene layers, indicating that the interlayer interaction is not significant enough to affect the total density of states in these structures.

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.

XUV ionization of aligned molecules

NASA Astrophysics Data System (ADS)

Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

2011-11-01

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra.

PubMed

Zheng, Lianjun; Polizzi, Nicholas F; Dave, Adarsh R; Migliore, Agostino; Beratan, David N

2016-03-24

The effectiveness of solar energy capture and conversion materials derives from their ability to absorb light and to transform the excitation energy into energy stored in free carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum rule mandates that the integrated (electronic) oscillator strength of an absorber equals the total number of electrons in the structure. Typical molecular chromophores place only about 1% of their oscillator strength in the UV-vis window, so individual chromophores operate at about 1% of their theoretical limit. We explore the distribution of oscillator strength as a function of excitation energy to understand this circumstance. To this aim, we use familiar independent-electron model Hamiltonians as well as first-principles electronic structure methods. While model Hamiltonians capture the qualitative electronic spectra associated with π electron chromophores, these Hamiltonians mistakenly focus the oscillator strength in the fewest low-energy transitions. Advanced electronic structure methods, in contrast, spread the oscillator strength over a very wide excitation energy range, including transitions to Rydberg and continuum states, consistent with experiment. Our analysis rationalizes the low oscillator strength in the UV-vis spectral region in molecules, a step toward the goal of oscillator strength manipulation and focusing.

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.

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.

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.

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.

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.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

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.

Fullerene Derived Molecular Electronic Devices

NASA Technical Reports Server (NTRS)

Menon, Madhu; Srivastava, Deepak; Saini, Subbash

1998-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale electronic devices. 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 grapheme sheet, more complex joints require other mechanisms. In this work we explore structural and electronic properties of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme.

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 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.

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.

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.

Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF

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

Breuer, Marian; Zarzycki, Piotr P.; Shi, Liang

2012-12-01

The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable force fieldmore » dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.« less

Electronic structure investigation of neutral titanium oxide molecules TixOy

NASA Astrophysics Data System (ADS)

Jeong, K. S.; Chang, Ch; Sedlmayr, E.; Sülzle, D.

2000-09-01

Electronic and structural properties of energetically low-lying isomers of isolated TixOy (x = 1-6, y = 1-12) molecular systems have been investigated by density functional theoretical methods. A variety of stationary points are thoroughly characterized. We report total cluster energies, equilibrium geometries and harmonic vibrational wavenumbers.

Synthesis of core-shell structured FAU/SBA-15 composite molecular sieves and their performance in catalytic cracking of polystyrene

NASA Astrophysics Data System (ADS)

Du, Jinlong; Shi, Chunwei; Wu, Wenyuan; Bian, Xue; Chen, Ping; Cui, Qingzhu; Cui, Zhixuan

2017-12-01

Composite molecular sieves, FAU/SBA-15, having core-shell structure were synthesized. The synthesized composite sieves were characterized by X-ray diffractometry (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), pyrolysis fourier transform infrared (Py-FTIR) spectroscopy, temperature programmed desorption spectra (NH3-TPD), UV Raman spectroscopy, nuclear magnetic resonance (NMR) and other techniques. XRD, SEM, TEM, N2 adsorption-desorption, mass spectrometry, NMR and EDS results showed that the composite molecular sieve contained two pore channels. Py-FTIR results showed that the addition of HY molecular sieves improved the acidity of the composite zeolite. The crystallization mechanism during the growth of FAU/SBA-15 shell was deduced from the influence of crystallization time on the synthesis of FAU/SBA-15 core-shell structured composite molecular sieve. HY dissociated partially in H2SO4 solution, and consisted of secondary structural units. This framework structure was more stable than its presence in the isolated form on the same ring or in the absence of Al. Thus it played a guiding role and connected with SBA-15 closely through the Si-O bond. This resulted in the gradual covering of the exterior surface of FAU phase by SBA-15 molecular sieves. The presence of SBA-15 restricted the formation of the other high mass components and increased the selectivity towards ethylbenzene.

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

XUV ionization of aligned molecules

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

Kelkensberg, F.; Siu, W.; Gademann, G.

2011-11-15

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

Two-photon absorption in conjugated energetic molecule

DOE PAGES

Bjorgaard, Josiah August; Sifain, Andrew; Nelson, Tammie Renee; ...

2016-06-03

Time-dependent density functional theory (TD-DFT) is used to investigate the relationship between molecular structure and one- and two-photon absorption (OPA and TPA, respectively) properties in novel and recently synthesized conjugated energetic molecules (CEMs). The molecular structure of CEMs can be strategically altered to influence the heat of formation and oxygen balance, two factors that can contribute to the sensitivity and strength of an explosive material. OPA and TPA are sensitive to changes in molecular structure as well, influencing optical range of excitation. We find calculated vertical excitation energies in good agreement with experiment for most molecules. Peak TPA intensities aremore » significant and on the order of 102 GM. Natural transition orbitals for essential electronic states defining TPA peaks of relatively large intensity to examine the character of relevant transitions. Minor modification of molecular substituents, such as additional oxygen and other functional groups, produces significant changes in electronic structure, OPA, TPA, and improves the oxygen balance. Results show that select molecules are apt to nonlinear absorption, opening the possibility for controlled, direct optical initiation of CEMs through photochemical pathways.« less

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.

Rationalizing the photophysical properties of BODIPY laser dyes via aromaticity and electron-donor-based structural perturbations

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

Waddell, Paul G.; Liu, Xiaogang; Zhao, Teng

2015-05-01

The absorption and fluorescence properties of six boron dipyrromethene (BODIPY) laser dyes with simple non-aromatic substituents are rationalized by relating them to observable structural perturbations within the molecules of the dyes. An empirical relationship involving the structure and the optical properties is derived using a combination of single-crystal X-ray diffraction data, quantum chemical calculations and electronic constants: i.e. the tendency of the pyrrole bond lengths towards aromaticity and the UV-vis absorption and fluorescence wavelengths correlating with the electron-donor properties of the substituents. The effect of molecular conformation on the solid-state optical properties of the dyes is also discussed. The findingsmore » in this study also demonstrate the usefulness and limitations of using crystal structure data to develop structure-property relationships in this class of optical materials, contributing to the growing effort to design optoelectronic materials with tunable properties via molecular engineering.« less

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.

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.

Conductance and thermopower in molecular nanojunctions

NASA Astrophysics Data System (ADS)

Sen, Arijit

2013-02-01

Electronic transport through short channels in a molecular junction is an intricate quantum scattering problem [1]. To garner insight on how the structure and the electrical properties of a nanoscale junction are correlated is thus of both fundamental and technological interest [1-3]. As observed experimentally in the last couple of years by several independent research groups [4-5], a two-terminal molecular junction comprising of a simple alkane chain with varying length can exhibit high as well as low conductance. However, what causes the simultaneous unveiling of multiple conductances remained largely obscure. We have recently demonstrated [6] that the binary conductance in these heterostructures is due mainly to two distinct electrode orientations that control the electrode-molecule coupling as well as the tunneling strength through quantum interference following diversity in the electrode band structures. Our detailed analysis on the transmission spectra indicates that even a single-molecule nanojunction can potentially serve as a realistic double-quantum-dot kind of system to yield tunable Fano resonance, as often desired for nanoscale switching. In this talk, I intend to give a brief account of molecular electronics and its future applications along with the challenges and possibilities in the current perspective. A few deliberations may as well include how the inter-dot tunneling strength may affect the non-equilibrium charge transport and thermoelectricity in a myriad of molecular junctions based on different molecular conformations and electrode structures. Finally, I shall try to touch upon the effect of electron-phonon interaction on the nanoscale charge transport, and also, the phonon-mediated thermal transport in molecular nanodevices.

Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory.

PubMed

Huang, Ying; Rong, Chunying; Zhang, Ruiqin; Liu, Shubin

2017-01-01

Wave function theory (WFT) and density functional theory (DFT)-the two most popular solutions to electronic structure problems of atoms and molecules-share the same origin, dealing with the same subject yet using distinct methodologies. For example, molecular orbitals are artifacts in WFT, whereas in DFT, electron density plays the dominant role. One question that needs to be addressed when using these approaches to appreciate properties related to molecular structure and reactivity is if there is any link between the two. In this work, we present a piece of strong evidence addressing that very question. Using five polymeric systems as illustrative examples, we reveal that using quantities from DFT such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, Onicescu information energy, Rényi entropy, etc., one is able to accurately evaluate orbital-related properties in WFT like frontier orbital energies and the HOMO (highest occupied molecular orbital)/LUMO (lowest unoccupied molecular orbital) gap. We verified these results at both the whole molecule level and the atoms-in-molecules level. These results provide compelling evidence suggesting that WFT and DFT are complementary to each other, both trying to comprehend the same properties of the electronic structure and molecular reactivity from different perspectives using their own characteristic vocabulary. Hence, there should be a bridge or bridges between the two approaches.

Topography and transport properties of oligo(phenylene ethynylene) molecular wires studied by scanning tunneling microscopy

NASA Technical Reports Server (NTRS)

Dholakia, Geetha R.; Fan, Wendy; Koehne, Jessica; Han, Jie; Meyyappan, M.

2003-01-01

Conjugated phenylene(ethynylene) molecular wires are of interest as potential candidates for molecular electronic devices. Scanning tunneling microscopic study of the topography and current-voltage (I-V) characteristics of self-assembled monolayers of two types of molecular wires are presented here. The study shows that the topography and I-Vs, for small scan voltages, of the two wires are quite similar and that the electronic and structural changes introduced by the substitution of an electronegative N atom in the central phenyl ring of these wires does not significantly alter the self-assembly or the transport properties.

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)

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

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.

Coupled electron-ion Monte Carlo simulation of hydrogen molecular crystals

NASA Astrophysics Data System (ADS)

Rillo, Giovanni; Morales, Miguel A.; Ceperley, David M.; Pierleoni, Carlo

2018-03-01

We performed simulations for solid molecular hydrogen at high pressures (250 GPa ≤ P ≤ 500 GPa) along two isotherms at T = 200 K (phase III) and at T = 414 K (phase IV). At T = 200 K, we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T = 414 K in phase IV, we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD). The latter is based on Density Functional Theory (DFT) with the van der Waals approximation (vdW-DF). The comparison between the two methods allows us to address the question of the accuracy of the exchange-correlation approximation of DFT for thermal and quantum protons without recurring to perturbation theories. In general, we find that atomic and molecular fluctuations in PIMD are larger than in CEIMC which suggests that the potential energy surface from vdW-DF is less structured than the one from quantum Monte Carlo. We find qualitatively different behaviors for systems prepared in the C2c structure for increasing pressure. Within PIMD, the C2c structure is dynamically partially stable for P ≤ 250 GPa only: it retains the symmetry of the molecular centers but not the molecular orientation; at intermediate pressures, it develops layered structures like Pbcn or Ibam and transforms to the metallic Cmca-4 structure at P ≥ 450 GPa. Instead, within CEIMC, the C2c structure is found to be dynamically stable at least up to 450 GPa; at increasing pressure, the molecular bond length increases and the nuclear correlation decreases. For the other two structures, the two methods are in qualitative agreement although quantitative differences remain. We discuss various structural properties and the electrical conductivity. We find that these structures become conducting around 350 GPa but the metallic Drude-like behavior is reached only at around 500 GPa, consistent with recent experimental claims.

Transmission electron microscopy in molecular structural biology: A historical survey.

PubMed

Harris, J Robin

2015-09-01

In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

Group-III nitride VCSEL structures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Ng, HockMin; Moustakas, Theodore D.

2000-07-01

III-nitride VCSEL structures designed for electron-beam pumping have been grown by molecular beam epitaxy (MBE). The structures consist of a sapphire substrate on which an AlN/GaN distributed Bragg reflector (DBR) with peak reflectance >99% at 402 nm is deposited. The active region consists of a 2-(lambda) cavity with 25 In0.1Ga0.9N/GaN multiquantum wells (MQWs) whose emission coincides with the high reflectance region of the DBR. The thicknesses of the InGaN wells and the GaN barriers are 35 angstrom and 75 angstrom respectively. The top reflector consists of a silver metallic mirror which prevents charging effects during electron-beam pumping. The structure was pumped from the top- side with a cw electron-beam using a modified cathodoluminescence (CL) system mounted on a scanning electron microscope chamber. Light output was collected from the polished sapphire substrate side. Measurements performed at 100 K showed intense emission at 407 nm with narrowing of the linewidth with increasing beam current. A narrow emission linewidth of 0.7 nm was observed indicating the onset of stimulated emission.

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

Scanning tunneling microscopy of the formation, transformation, and property of oligothiophene self-organizations on graphite and gold surfaces.

PubMed

Yang, Zhi-Yong; Zhang, Hui-Min; Yan, Cun-Ji; Li, Shan-Shan; Yan, Hui-Juan; Song, Wei-Guo; Wan, Li-Jun

2007-03-06

Two alkyl-substituted dual oligothiophenes, quarterthiophene (4T)-trimethylene (tm)-octithiophene (8T) and 4T-tm-4T, were used to fabricate molecular structures on highly oriented pyrolytic graphite and Au(111) surfaces. The resulted structures were investigated by scanning tunneling microscopy. The 4T-tm-8T and 4T-tm-4T molecules self-organize into long-range ordered structures with linear and/or quasi-hexagonal patterns on highly oriented pyrolytic graphite at ambient temperature. Thermal annealing induced a phase transformation from quasi-hexagonal to linear in 4T-tm-8T adlayer. The molecules adsorbed on Au(111) surface in randomly folded and linear conformation. Based on scanning tunneling microscopy results, the structural models for different self-organizations were proposed. Scanning tunneling spectroscopy measurement showed the electronic property of individual molecules in the patterns. These results are significant in understanding the chemistry of molecular structure, including its formation, transformation, and electronic properties. They also help to fabricate oligothiophene assemblies with desired structures for future molecular devices.

Investigating molecule-semiconductor interfaces with nonlinear spectroscopies

NASA Astrophysics Data System (ADS)

Giokas, Paul George

Knowledge of electronic structures and transport mechanisms at molecule-semiconductor interfaces is motivated by their ubiquity in photoelectrochemical cells. In this dissertation, optical spectroscopies are used uncover the influence of electronic coupling, coherent vibrational motion, and molecular geometry, and other factors on dynamics initiated by light absorption at such interfaces. These are explored for a family of ruthenium bipyridyl chromophores bound to titanium dioxide. Transient absorption measurements show molecular singlet state electron injection in 100 fs or less. Resonance Raman intensity analysis suggests the electronic excitations possess very little charge transfer character. The connections drawn in this work between molecular structure and photophysical behavior contribute to the general understanding of photoelectrochemical cells. Knowledge of binding geometry in nanocrystalline films is challenged by heterogeneity of semiconductor surfaces. Polarized resonance Raman spectroscopy is used to characterize the ruthenium chromophore family on single crystal titanium dioxide . Chromophores display a broad distribution of molecular geometries at the interface, with increased variation in binding angle due to the presence of a methylene bridge, as well as additional phosphonate anchors. This result implies multiple binding configurations for chromophores which incorporate multiple phosphonate ligands, and indicates the need for careful consideration when developing surface-assembled chromophore-catalyst cells. Electron transfer transitions occurring on the 100 fs time scale challenge conventional second-order approximations made when modeling these reactions. A fourth-order perturbative model which includes the relationship between coincident electron transfer and nuclear relaxation processes is presented. Insights provided by the model are illustrated for a two-level donor molecule. The presented fourth-order rate formula constitutes a rigorous and intuitive framework for understanding sub-picosecond photoinduced electron transfer dynamics. Charge transfer systems fit by this model include catechol-sensitized titanium dioxide nanoparticles and a closely-related molecular complex. These systems exhibit vibrational coherence coincident with back-electron transfer in the first picosecond after excitation, which suggests that intramolecular nuclear motion strongly influences the electronic transfer process and plays an important role in the dynamics of interfacial systems following light absorption.

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.

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

A nanometre-scale electronic switch consisting of a metal cluster and redox-addressable groups.

PubMed

Gittins, D I; Bethell, D; Schiffrin, D J; Nichols, R J

2000-11-02

So-called bottom-up fabrication methods aim to assemble and integrate molecular components exhibiting specific functions into electronic devices that are orders of magnitude smaller than can be fabricated by lithographic techniques. Fundamental to the success of the bottom-up approach is the ability to control electron transport across molecular components. Organic molecules containing redox centres-chemical species whose oxidation number, and hence electronic structure, can be changed reversibly-support resonant tunnelling and display promising functional behaviour when sandwiched as molecular layers between electrical contacts, but their integration into more complex assemblies remains challenging. For this reason, functionalized metal nanoparticles have attracted much interest: they exhibit single-electron characteristics (such as quantized capacitance charging) and can be organized through simple self-assembly methods into well ordered structures, with the nanoparticles at controlled locations. Here we report scanning tunnelling microscopy measurements showing that organic molecules containing redox centres can be used to attach metal nanoparticles to electrode surfaces and so control the electron transport between them. Our system consists of gold nanoclusters a few nanometres across and functionalized with polymethylene chains that carry a central, reversibly reducible bipyridinium moiety. We expect that the ability to electronically contact metal nanoparticles via redox-active molecules, and to alter profoundly their tunnelling properties by charge injection into these molecules, can form the basis for a range of nanoscale electronic switches.

Scattering electrons in Budapest (and elsewhere)

NASA Astrophysics Data System (ADS)

Hargittai, István

1983-07-01

Some of the recent research of the Budapest Electron Diffraction Group is described in anecdotal—historical perspective (as suggested by the Editor of the Journal of Molecular Structure). The importance of international cooperation is emphasized.

Does the thermal evolution of molecular structures critically affect the magnetic anisotropy?† †Electronic supplementary information (ESI) available. CCDC 1045631–1045633. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01245g

PubMed Central

Qian, Kang; Baldoví, José J.; Zhang, Yi-Quan; Overgaard, Jacob; Wang, Bing-Wu

2015-01-01

A dysprosium based single-ion magnet is synthesized and characterized by the angular dependence of the single-crystal magnetic susceptibility. Ab initio and effective electrostatic analyses are performed using the molecular structures determined from single crystal X-ray diffraction at 20 K, 100 K and 300 K. Contrary to the common assumption, the results reveal that the structural thermal effects that may affect the energy level scheme and magnetic anisotropy below 100 K are negligible. PMID:29568416

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.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

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.

The molecular structure and vibrational spectra of corrolazine metal complexes (CzM) by density functional theory

NASA Astrophysics Data System (ADS)

Wang, Hongming; Yang, Chuanlu; Zhang, Zhihong; Wang, Meishan; Han, Keli

2006-06-01

The ground-state geometries, electronic structures and vibrational frequencies of metal corrolazine complexes, CzM (M = Mn, Co, Ni and Fe) have been studied using B3LYP/6-311g(d) method. The molecular geometries are sensitive to the species of the metal, and the bond length of the M sbnd N is increase with the metal atom radii. The ground-state electronic structures indicate that there are strong interactions between d of the metal fragments and the corrolazine fragments. The calculations also indicate that the CzNi is the stabilest among the four metal corrolazine complexes. Vibrational frequencies of these metal corrolazine complexes were also calculated and were assigned to the local coordinates of the corrolazine ring, which reveals the some common feature of the molecular vibrations of the metal corrolazine complexes as four-coordination metallocorrolazines.

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

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

Linko, R. V., E-mail: rlinko@mail.ru; Sokol, V. I.; Polyanskaya, N. A.

2013-05-15

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} aremore » studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.« less

Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis.

PubMed

Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

2016-08-26

A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Electronic structures of 1-ML C84/Ag(111): Energy level alignment and work function variation

NASA Astrophysics Data System (ADS)

Wang, Peng; Zhao, Li-Li; Zhang, Jin-Juan; Li, Wen-Jie; Liu, Wei-Hui; Chen, Da; Sheng, Chun-Qi; Wang, Jia-Ou; Qian, Hai-Jie; Ibrahim, Kurash; Li, Hong-Nian

2017-12-01

The electronic structures of fullerene/metal interface are critical to the performance of devices based on fullerene in molecular electronics and organic electronics. Herein, we investigate the electronic structures at the interface between C84 and Ag(111) by photoelectron spectroscopy and soft X-ray absorption spectroscopy techniques. It is observed that C84 monolayer on Ag(111) surface (1-ML C84/Ag(111)) has metallic nature. A charge transfer from substrate to the unoccupied states of C84 is determined to be 1.3 electrons per molecule. However, the work function of 1-ML C84 (4.72 eV) is observed slightly larger than that of the clean Ag(111) substrate (4.50 eV). A bidirectional charge transfer model is introduced to understand the work function variation of the fullerene/metal system. In addition to the charge transfer from substrate to the adsorbate's unoccupied states, there exists non-negligible back charge transfer from fullerene occupied molecular orbital to the metal substrate through interfacial hybridization. The Fermi level will be pinned at ∼4.72 eV for C84 monolayer on coinage metal substrate.

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.

X-ray circular dichroism signals: a unique probe of local molecular chirality

DOE PAGES

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen; ...

2017-06-26

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

X-ray circular dichroism signals: a unique probe of local molecular chirality

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

Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

Synthesis of core–shell structured FAU/SBA-15 composite molecular sieves and their performance in catalytic cracking of polystyrene

PubMed Central

Du, Jinlong; Shi, Chunwei; Wu, Wenyuan; Bian, Xue; Chen, Ping; Cui, Qingzhu; Cui, Zhixuan

2017-01-01

Abstract Composite molecular sieves, FAU/SBA-15, having core-shell structure were synthesized. The synthesized composite sieves were characterized by X-ray diffractometry (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), pyrolysis fourier transform infrared (Py-FTIR) spectroscopy, temperature programmed desorption spectra (NH3-TPD), UV Raman spectroscopy, nuclear magnetic resonance (NMR) and other techniques. XRD, SEM, TEM, N2 adsorption-desorption, mass spectrometry, NMR and EDS results showed that the composite molecular sieve contained two pore channels. Py-FTIR results showed that the addition of HY molecular sieves improved the acidity of the composite zeolite. The crystallization mechanism during the growth of FAU/SBA-15 shell was deduced from the influence of crystallization time on the synthesis of FAU/SBA-15 core-shell structured composite molecular sieve. HY dissociated partially in H2SO4 solution, and consisted of secondary structural units. This framework structure was more stable than its presence in the isolated form on the same ring or in the absence of Al. Thus it played a guiding role and connected with SBA-15 closely through the Si-O bond. This resulted in the gradual covering of the exterior surface of FAU phase by SBA-15 molecular sieves. The presence of SBA-15 restricted the formation of the other high mass components and increased the selectivity towards ethylbenzene. PMID:29383044

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

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

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

PubMed

Guizard, C; Chanzy, H; Sarko, A

1985-06-05

The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

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.

Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy.

PubMed

Fischer, Audrey; Garcia-Rodriguez, Consuelo; Geren, Isin; Lou, Jianlong; Marks, James D; Nakagawa, Terunaga; Montal, Mauricio

2008-02-15

Clostridial botulinum neurotoxin (BoNT) causes a neuroparalytic condition recognized as botulism by arresting synaptic vesicle exocytosis. Although the crystal structures of full-length BoNT/A and BoNT/B holotoxins are known, the molecular architecture of the five other serotypes remains elusive. Here, we present the structures of BoNT/A and BoNT/E using single particle electron microscopy. Labeling of the particles with three different monoclonal antibodies raised against BoNT/E revealed the positions of their epitopes in the electron microscopy structure, thereby identifying the three hallmark domains of BoNT (protease, translocation, and receptor binding). Correspondingly, these antibodies selectively inhibit BoNT translocation activity as detected using a single molecule assay. The global structure of BoNT/E is strikingly different from that of BoNT/A despite strong sequence similarity. We postulate that the unique architecture of functionally conserved modules underlies the distinguishing attributes of BoNT/E and contributes to differences with BoNT/A.

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.

DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

NASA Astrophysics Data System (ADS)

Sienkiewicz-Gromiuk, Justyna

2018-01-01

The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

PubMed

Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

2012-08-02

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Leaving the structural ivory tower, assisted by interactive 3D PDF.

PubMed

Kumar, Pravin; Ziegler, Alexander; Grahn, Alexander; Hee, Chee Seng; Ziegler, Andreas

2010-08-01

The ability to embed interactive three-dimensional (3D) models into electronic publications in portable document format (PDF) greatly enhances the accessibility of molecular structures. Here, we report advances in this procedure and discuss what is needed to develop this format into a truly useful tool for the structural biology community as well as for readers who are less well trained in molecular visualization. Copyright 2010 Elsevier Ltd. All rights reserved.

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

Crystal Structure, Conformational Analysis, and Charge Density Distribution for Eng-Epifisetinidol: An Explanation for Regiospecific Aromatic Substitution of 5-Deoxyflavan

Treesearch

Fred L. Tobiason; Frank R. Fronczek; Jan P. Steynberg; Elizabeth C. Steynberg; Richard W. Hemingway; Wayne L. Mattice

1993-01-01

Molecular modeling and molecular orbital analyses of ent-epifisetinidol gave &ood predictions of the approximate "reverse half-chair" conformation found for the crystal structure. MNDO and AM1 analyses of HOMO electron densities provided an explanation for the stereospecific electrophilic aromatic substitution at C(6) in 5-deoxy-flavans...

Characteristics of Organic-Metal Interaction: A Perspective from Bonding Distance to Orbital Delocalization

NASA Astrophysics Data System (ADS)

Kera, Satoshi; Hosokai, Takuya; Duhm, Steffen

2018-06-01

Understanding the mechanisms of energy-level alignment and charge transfer at the interface is one of the key issues in realizing organic electronics. However, the relation between the interface structure and the electronic structure is still not resolved in sufficient detail. An important character of materials used in organic electronics is the electronic localization of organic molecules at interfaces. To elucidate the impact of the molecular orbital distribution on the electronic structure, detailed structural information is required, particularly the vertical bonding distance at the interface, which is a signature of the interaction strength. We describe the recent progress in experimental studies on the impact of the molecule-metal interaction on the electronic structure of organic-metal interfaces by using various photoelectron spectroscopies, and review the results, focusing on the X-ray standing wave technique, to demonstrate the evaluation of the vertical bonding distance.

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.

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.

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.

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.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

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.

Molecular Level Understanding of Interfaces and Excited State Electronic Structure in Organic Solar Cells Using Soft X-ray Techniques

NASA Astrophysics Data System (ADS)

Gliboff, Matthew

Transparent conductive oxides like indium tin oxide (ITO) are common substrates for optoelectronic devices, including organic light emitting diodes and organic solar cells. Tailoring the interface between the oxide and the active layer by adjusting the work function or wettability of the oxide can improve the performance of these devices in both emissive and photovoltaic applications. Molecular design of self-assembled monolayers (SAMs) allows for a range of surface properties using the same oxide material. The molecular ordering and conformation adopted by the SAMs determine properties such as work function and wettability at these critical interfaces. I use angle-dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy, to determine the molecular orientations of a variety of dipolar phosphonic acid surface modifiers. For a model system, phenylphosphonic acid on indium zinc oxide, the SAMs prove to be surprisingly well-oriented, with the phenyl ring adopting a well-defined tilt angle of 12-16° from the surface normal. The NEXAFS results agree with polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) results and orientations calculated from density functional theory (DFT). These results not only provide a detailed picture of the molecular structure of a technologically important class of SAMs, but they also resolve a long-standing ambiguity regarding the vibrational-mode assignments for phosphonic acids on oxide surfaces, thus improving the utility of PM-IRRAS for future studies. The effect of fluorination on the orientation of these phosponic-acid SAMs is non-trivial, due to the combined effects of the fluorination on binding mode and steric packing. The latter effects are found to be more dominant in aliphatic SAMs, leading to a more upright orientation in the fluorinated SAM. In the aromatic case, the fluorinated SAM adopted a less upright orientation which I attribute to changes in binding mode. The relationship between structure and performance in active layer polymers for organic electronics is not yet well understood. To gain insight into the effect of the excited state electronic structure on device performance, we examine two similar donor-acceptor polymers: PCPDTBT and PCDTBT, which produce devices with internal quantum efficiency (IQE) of 70% and 100% respectively. We use time-dependent density functional theory (TD-DFT) in combination with near edge x-ray absorption fine structure (NEXAFS) and resonant Auger spectroscopy to predict the electronic structure of the lowest unoccupied molecular orbital (LUMO). The resonant Auger results are found to be independent of film morphology and likely dominated by monomer structure. We show that the degree of LUMO localization onto the benzothiadiazole acceptor group in each polymer is similar, indicating that that the differences in IQE between these two polymers are driven by larger-scale morphology and not explained by the electronic structure of the excited state.

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.

Projected quasiparticle theory for molecular electronic structure

NASA Astrophysics Data System (ADS)

Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

2011-09-01

We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

Modular Homogeneous Chromophore–Catalyst Assemblies

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

Mulfort, Karen L.; Utschig, Lisa M.

2016-05-17

Photosynthetic reaction center (RC) proteins convert incident solar energy to chemical energy through a network of molecular cofactors which have been evolutionarily tuned to couple efficient light-harvesting, directional electron transfer, and long-lived charge separation with secondary reaction sequences. These molecular cofactors are embedded within a complex protein environment which precisely positions each cofactor in optimal geometries along efficient electron transfer pathways with localized protein environments facilitating sequential and accumulative charge transfer. By contrast, it is difficult to approach a similar level of structural complexity in synthetic architectures for solar energy conversion. However, by using appropriate self-assembly strategies, we anticipate thatmore » molecular modules, which are independently synthesized and optimized for either light-harvesting or redox catalysis, can be organized into spatial arrangements that functionally mimic natural photosynthesis. In this Account, we describe a modular approach to new structural designs for artificial photosynthesis which is largely inspired by photosynthetic RC proteins. We focus on recent work from our lab which uses molecular modules for light-harvesting or proton reduction catalysis in different coordination geometries and different platforms, spanning from discrete supramolecular assemblies to molecule–nanoparticle hybrids to protein-based biohybrids. Molecular modules are particularly amenable to high-resolution characterization of the ground and excited state of each module using a variety of physical techniques; such spectroscopic interrogation helps our understanding of primary artificial photosynthetic mechanisms. In particular, we discuss the use of transient optical spectroscopy, EPR, and X-ray scattering techniques to elucidate dynamic structural behavior and light-induced kinetics and the impact on photocatalytic mechanism. Two different coordination geometries of supramolecular photocatalyst based on the [Ru(bpy)3]2+ (bpy = 2,2'-bipyridine) light-harvesting module with cobaloxime-based catalyst module are compared, with progress in stabilizing photoinduced charge separation identified. These same modules embedded in the small electron transfer protein ferredoxin exhibit much longer charge-separation, enabled by stepwise electron transfer through the native [2Fe-2S] cofactor. We anticipate that the use of interchangeable, molecular modules which can interact in different coordination geometries or within entirely different structural platforms will provide important fundamental insights into the effect of environment on parameters such as electron transfer and charge separation, and ultimately drive more efficient designs for artificial photosynthesis.« 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.

FAST TRACK COMMUNICATION: Attosecond correlation dynamics during electron tunnelling from molecules

NASA Astrophysics Data System (ADS)

Walters, Zachary B.; Smirnova, Olga

2010-08-01

In this communication, we present an analytical theory of strong-field ionization of molecules, which takes into account the rearrangement of multiple interacting electrons during the ionization process. We show that such rearrangement offers an alternative pathway to the ionization of orbitals more deeply bound than the highest occupied molecular orbital. This pathway is not subject to the full exponential suppression characteristic of direct tunnel ionization from the deeper orbitals. The departing electron produces an 'attosecond correlation pulse' which controls the rearrangement during the tunnelling process. The shape and duration of this pulse are determined by the electronic structure of the relevant states, molecular orientation and laser parameters.

Self-assembly patterning of organic molecules on a surface

DOEpatents

Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

2017-04-04

The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

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.

A structural biology perspective on bioactive small molecules and their plant targets.

PubMed

Kumari, Selva; van der Hoorn, Renier A L

2011-10-01

Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design. Copyright © 2011 Elsevier Ltd. All rights reserved.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

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'.

Envelope molecular-orbital theory of extended systems. I. Electronic states of organic quasilinear nanoheterostructures

NASA Astrophysics Data System (ADS)

Arce, J. C.; Perdomo-Ortiz, A.; Zambrano, M. L.; Mujica-Martínez, C.

2011-03-01

A conceptually appealing and computationally economical course-grained molecular-orbital (MO) theory for extended quasilinear molecular heterostructures is presented. The formalism, which is based on a straightforward adaptation, by including explicitly the vacuum, of the envelope-function approximation widely employed in solid-state physics leads to a mapping of the three-dimensional single-particle eigenvalue equations into simple one-dimensional hole and electron Schrödinger-like equations with piecewise-constant effective potentials and masses. The eigenfunctions of these equations are envelope MO's in which the short-wavelength oscillations present in the full MO's, associated with the atomistic details of the molecular potential, are smoothed out automatically. The approach is illustrated by calculating the envelope MO's of high-lying occupied and low-lying virtual π states in prototypical nanometric heterostructures constituted by oligomers of polyacetylene and polydiacetylene. Comparison with atomistic electronic-structure calculations reveals that the envelope-MO energies agree very well with the energies of the π MO's and that the envelope MO's describe precisely the long-wavelength variations of the π MO's. This envelope MO theory, which is generalizable to extended systems of any dimensionality, is seen to provide a useful tool for the qualitative interpretation and quantitative prediction of the single-particle quantum states in mesoscopic molecular structures and the design of nanometric molecular devices with tailored energy levels and wavefunctions.

Versatile Molecular Functionalization for Inhibiting Concentration Quenching of Thermally Activated Delayed Fluorescence.

PubMed

Lee, Jiyoung; Aizawa, Naoya; Numata, Masaki; Adachi, Chihaya; Yasuda, Takuma

2017-01-01

Concentration quenching of thermally activated delayed fluorescence is found to be dominated by electron-exchange interactions, as described by the Dexter energy-transfer model. Owing to the short-range nature of the electron-exchange interactions, even a small modulation in the molecular geometric structure drastically affects the concentration-quenching, leading to enhanced solid-state photoluminescence and electroluminescence quantum efficiencies. © 2016 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.

Fine- and hyperfine-structure effects in molecular photoionization. I. General theory and direct photoionization.

PubMed

Germann, Matthias; Willitsch, Stefan

2016-07-28

We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra, we derive highly symmetrized forms of the squared photoionization dipole matrix elements from which we derive the salient selection and propensity rules for fine- and hyperfine resolved photoionizing transitions. Our theoretical results are validated by the analysis of the fine-structure resolved photoelectron spectrum of O2 reported by Palm and Merkt [Phys. Rev. Lett. 81, 1385 (1998)] and are used for predicting hyperfine populations of molecular ions produced by photoionization.

A molecular dynamics and ab initio analysis of the electronic structure of single-walled carbon nanotubes adhered to a substrate

NASA Astrophysics Data System (ADS)

Van Der Geest, A. G.; Lu, Z.; Lusk, M. T.; Dunn, M. L.

2011-04-01

Single-wall nanotubes can adhere to planar surfaces via van der Waals forces, and this causes the tubes to deform. We use classical molecular dynamics to estimate this deformation and density functional theory to quantify its impact on electronic band structure. For (n,0) tubes, adhesion causes the maximum bandgap to rise more rapidly with diameter, but the value of the maximum is not affected. The influence of adhesion forces on bandgap was found to correlate with that associated with lateral, uniaxial compression for moderate values of adhesion energy and compressive distortion.

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.

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.

Seamless growth of a supramolecular carpet

PubMed Central

Kim, Ju-Hyung; Ribierre, Jean-Charles; Yang, Yu Seok; Adachi, Chihaya; Kawai, Maki; Jung, Jaehoon; Fukushima, Takanori; Kim, Yousoo

2016-01-01

Organic/metal interfaces play crucial roles in the formation of intermolecular networks on metal surfaces and the performance of organic devices. Although their purity and uniformity have profound effects on the operation of organic devices, the formation of organic thin films with high interfacial uniformity on metal surfaces has suffered from the intrinsic limitation of molecular ordering imposed by irregular surface structures. Here we demonstrate a supramolecular carpet with widely uniform interfacial structure and high adaptability on a metal surface via a one-step process. The high uniformity is achieved with well-balanced interfacial interactions and site-specific molecular rearrangements, even on a pre-annealed amorphous gold surface. Co-existing electronic structures show selective availability corresponding to the energy region and the local position of the system. These findings provide not only a deeper insight into organic thin films with high structural integrity, but also a new way to tailor interfacial geometric and electronic structures. PMID:26839053

Rotational and fine structure of open-shell molecules in nearly degenerate electronic states

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2018-03-01

An effective Hamiltonian without symmetry restriction has been developed to model the rotational and fine structure of two nearly degenerate electronic states of an open-shell molecule. In addition to the rotational Hamiltonian for an asymmetric top, this spectroscopic model includes the energy separation between the two states due to difference potential and zero-point energy difference, as well as the spin-orbit (SO), Coriolis, and electron spin-molecular rotation (SR) interactions. Hamiltonian matrices are computed using orbitally and fully symmetrized case (a) and case (b) basis sets. Intensity formulae and selection rules for rotational transitions between a pair of nearly degenerate states and a nondegenerate state have also been derived using all four basis sets. It is demonstrated using real examples of free radicals that the fine structure of a single electronic state can be simulated with either a SR tensor or a combination of SO and Coriolis constants. The related molecular constants can be determined precisely only when all interacting levels are simulated simultaneously. The present study suggests that analysis of rotational and fine structure can provide quantitative insights into vibronic interactions and related effects.

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.

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.

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.

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

DOE PAGES

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

2017-05-22

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. In this paper, 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 calculatingmore » $V$-matrix elements. Selected results are presented for electron and positron scattering from molecular hydrogen H$$_2$$ and electron scattering from the vibrationally excited molecular hydrogen ion H$$_2^+$$ and its isotopologues (D$$_2^+$$, T$$_2^+$$, HD$^+$, HT$^+$ and TD$^+$). Finally, 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.« less

Coverage induced structural transformations of tetracene on Ag(110)

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

Takasugi, Kazushiro; Yokoyama, Takashi, E-mail: tyoko@yokohama-cu.ac.jp

2016-03-14

Self-assembly of tetracene on an anisotropic surface of Ag(110) has been investigated using scanning tunneling microscopy and low-energy electron diffraction. We observe multistage structural transformations of the self-assembled tetracene on Ag(110) as a function of molecular coverages, which are accompanied by the changes in molecular orientations. They are analyzed by a balance between multiple molecule-molecule and anisotropic substrate-molecule interactions.

Ionic conductors for solid oxide fuel cells

DOEpatents

Krumpelt, Michael; Bloom, Ira D.; Pullockaran, Jose D.; Myles, Kevin M.

1993-01-01

An electrolyte that operates at temperatures ranging from 600.degree. C. to 800.degree. C. is provided. The electrolyte conducts charge ionically as well as electronically. The ionic conductors include molecular framework structures having planes or channels large enough to transport oxides or hydrated protons and having net-positive or net-negative charges. Representative molecular framework structures include substituted aluminum phosphates, orthosilicates, silicoaluminates, cordierites, apatites, sodalites, and hollandites.

ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe; Paulus, Beate; Hege, Hans-Christian; Schild, Axel

2016-06-15

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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.

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…

Application of 3A molecular sieve layer in dye-sensitized solar cells

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

Yan, Yuan; Wang, Jinzhong, E-mail: jinzhong-wang@hit.edu.cn, E-mail: qingjiang.yu@hit.edu.cn; Yu, Qingjiang, E-mail: jinzhong-wang@hit.edu.cn, E-mail: qingjiang.yu@hit.edu.cn

2014-08-25

3A molecular sieve layer was used as dehydration and electronic-insulation layer on the TiO{sub 2} electrode of dye-sensitized solar cells. This layer diminished the effect of water in electrolyte efficiently and enhanced the performance of cells. The conversion efficiency increased from 9.58% to 10.2%. The good moisture resistance of cells was attributed to the three-dimensional interconnecting structure of 3A molecular sieve with strong adsorption of water molecule. While the performance enhancement benefited from the suppression of the charge recombination of electronic-insulation layer and scattering effect of large particles.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

PubMed Central

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed. PMID:21169680

Structural Characterization of Vapor-deposited Organic Glasses

NASA Astrophysics Data System (ADS)

Gujral, Ankit

Physical vapor deposition, a common route of thin film fabrication for organic electronic devices, has recently been shown to produce organic glassy films with enhanced kinetic stability and anisotropic structure. Anisotropic structures are of interest in the organic electronics community as it has been shown that certain structures lead to enhanced device performance, such as higher carrier mobility and better light outcoupling. A mechanism proposed to explain the origin of the stability and anisotropy of vapor-deposited glasses relies on two parameters: 1) enhanced molecular mobility at the free surface (vacuum interface) of a glass, and 2) anisotropic molecular packing at the free surface of the supercooled liquid of the glass-forming system. By vapor-depositing onto a substrate maintained at Tsubstrate < Tg (where Tg is the glass transition temperature), the enhanced molecular mobility at the free surface allows every molecule that lands on the surface to at least partially equilibrate to the preferred anisotropic molecular packing motifs before being buried by further deposition. The extent of equilibration depends on the mobility at the surface, controlled by Tsubstrate, and the residence time on the free surface, controlled by the rate of deposition. This body of work deals with the optimization of deposition conditions and system chemistry to prepare and characterize films with functional anisotropic structures. Here, we show that structural anisotropy can be attained for a variety of molecular systems including a rod-shaped non-mesogen, TPD, a rod-shaped smectic mesogen, itraconazole, two discotic mesogens, phenanthroperylene-ester and triphenylene-ester, and a disc-shaped non-mesogen, m-MTDATA. Experimental evidence is also provided of the anisotropic molecular packing at the free surface (vacuum interface) for the disc-shaped systems that are consistent with the expectations of the proposed mechanism and the final bulk state of the vapor-deposited glasses.

Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2016-10-01

We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

Determination of structure parameters in strong-field tunneling ionization theory of molecules

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

Zhao Songfeng; Jin Cheng; College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou, Gansu 730070

2010-03-15

In the strong field molecular tunneling ionization theory of Tong et al. [Phys. Rev. A 66, 033402 (2002)], the ionization rate depends on the asymptotic wave function of the molecular orbital from which the electron is removed. The orbital wave functions obtained from standard quantum chemistry packages in general are not good enough in the asymptotic region. Here we construct a one-electron model potential for several linear molecules using density functional theory. We show that the asymptotic wave function can be improved with an iteration method and after one iteration accurate asymptotic wave functions and structure parameters are determined. Withmore » the new parameters we examine the alignment-dependent tunneling ionization probabilities for several molecules and compare with other calculations and with recent measurements, including ionization from inner molecular orbitals.« less

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.

The journey from forensic to predictive materials science using density functional theory

DOE PAGES

Schultz, Peter A.

2017-09-12

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

The journey from forensic to predictive materials science using density functional theory

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

Schultz, Peter A.

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

Nanomechanics of Carbon and CxByNz Nanotubes: Via a Quantum Molecular Dynamics Method

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, M.; Cho, Kyeong Jae; Saini, Subhash (Technical Monitor)

1999-01-01

Nanomechanics of single-wall C, BN and BC$_3$ and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {\\it ab-initio} electronic structure methods. The dynamic strength of BN, BC$_3$ and B doped C nanotubes for small axial strain are comparable to each other. The main difference is in the critical strain at which structural collapse occurs. For example, even a shallow doping with B lowers the value of critical strain for C nanotubes. The critical strain for BN nanotube is found to be more than that for the similar C nanotube. Once the structural collapse starts to occur we find that carbon nanotubes irreversibly go into plastic deformation regime via the formation of tetrahedral (four-fold coordinated) bonds at the location of sharp pinches or kinks. This finding is considerably different from the classical MD (molecular dynamics) simulation results known so far. The energetics and electronic densities of states of the collapsed structures, investigated with {\\it ab-initio) methods, will also be discussed.

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.

The Electronic Structure Signature of the Spin Cross-Over Transition of [Co(dpzca)2

NASA Astrophysics Data System (ADS)

Zhang, Xin; Mu, Sai; Liu, Yang; Luo, Jian; Zhang, Jian; N'Diaye, Alpha T.; Enders, Axel; Dowben, Peter A.

2018-05-01

The unoccupied electronic structure of the spin crossover molecule cobalt (II) N-(2-pyrazylcarbonyl)-2-pyrazinecarboxamide, [Co(dpzca)2] was investigated, using X-ray absorption spectroscopy (XAS) and compared with magnetometry (SQUID) measurements. The temperature dependence of the XAS and molecular magnetic susceptibility χmT are in general agreement for [Co(dpzca)2], and consistent with density functional theory (DFT). This agreement of magnetic susceptibility and X-ray absorption spectroscopy provides strong evidence that the changes in magnetic moment can be ascribed to changes in electronic structure. Calculations show the choice of Coulomb correlation energy U has a profound effect on the electronic structure of the low spin state, but has little influence on the electronic structure of the high spin state. In the temperature dependence of the XAS, there is also evidence of an X-ray induced excited state trapping for [Co(dpzca)2] at 15 K.

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.

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Pentacene on Au(1 1 1), Ag(1 1 1) and Cu(1 1 1): From physisorption to chemisorption.

PubMed

Lu, Meng-Chao; Wang, Rong-Bin; Yang, Ao; Duhm, Steffen

2016-03-09

We measured the electronic and the molecular surface structure of pentacene deposited on the (1 1 1)-surfaces of coinage metals by means of ultraviolet photoelectron spectroscopy (UPS) and low-energy electron diffraction (LEED). Pentacene is almost flat-lying in monolayers on all three substrates and highly ordered on Au(1 1 1) and on Cu(1 1 1). On Ag(1 1 1), however, weak chemisorption leads to almost disordered monolayers, both, at room temperature and at 78 K. On Cu(1 1 1) pentacene is strongly chemisorbed and the lowest unoccupied molecular orbital becomes observable in UPS by a charge transfer from the substrate. On Ag(1 1 1) and Cu(1 1 1) multilayers adopt a tilted orientation and a high degree of crystallinity. On Au(1 1 1), most likely, also in multilayers the molecular short and long axes are parallel to the substrate, leading to a distinctively different electronic structure than on Ag(1 1 1) and Cu(1 1 1). Overall, it could be demonstrated that the substrate not only determines the geometric and electronic characteristics of molecular monolayer films but also plays a crucial role for multilayer film growth.

Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic Nim Cun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters.

PubMed

Singh, Raman K; Iwasa, Takeshi; Taketsugu, Tetsuya

2018-05-25

A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCu n -1 and Ni 2 Cu n -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cu n , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCu n -1 and Ni 2 Cu n -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters. The averaged binding energy, the fragmentation energies and the second-order energy differences signified that the Ni doped clusters can continue to gain an energy during the growth process. The electronic structures revealed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies of the LC-DFT are reliable and can be used to predict the vertical ionization potential and the vertical electron affinity of the systems. The reactivity descriptors such as the chemical potential, chemical hardness and electrophilic power, and the reactivity principle such as the minimum polarizability principle are operative for characterizing and rationalizing the electronic structures of these clusters. Moreover, doping of Ni atoms into the copper clusters carry most of the total spin magnetic moment. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Conjugated Organosilicon Materials for Organic Electronics and Photonics

NASA Astrophysics Data System (ADS)

Ponomarenko, Sergei A.; Kirchmeyer, Stephan

In this chapter different types of conjugated organosilicon materials possessing luminescent and/or semiconducting properties will be described. Such macromolecules have various topologies and molecular structures: linear, branched and hyperbranched oligomers, polymers, and dendrimers. Specific synthetic approaches to access these structures will be discussed. Special attention is devoted to the role of silicon in these structures and its influence on their optical and electrical properties, leading to their potential application in the emerging areas of organic and hybrid electronics.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

NASA Astrophysics Data System (ADS)

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-04-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices.We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00459g

Depopulation of Single-Phthalocyanine Molecular Orbitals upon Pyrrolic-Hydrogen Abstraction on Graphene.

PubMed

Néel, Nicolas; Lattelais, Marie; Bocquet, Marie-Laure; Kröger, Jörg

2016-02-23

Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule-metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the differential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π states of intact molecules are proposed to be emptied via intramolecular electron transfer to dangling σ states of H-free N atoms.

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.

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

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.

Structural changes caused by H 2 adsorption on the Si(111)7 × 7 surface

NASA Astrophysics Data System (ADS)

Wolff, S. H.; Wagner, S.; Gibson, J. M.; Loretto, D.; Robinson, I. K.; Bean, J. C.

1990-12-01

Structural changes caused by the adsorption of molecular hydrogen adsorption onto the Si(111)7 × 7 surface reconstruction are quantified using the first structure parameter refinement on transmission electron diffraction (TED) data. We find that initial adsorption of molecular hydrogen onto the Si(111)7 × 7 surface causes a preferential decrease in the occupancy of the center adatoms. Further adsorption of hydrogen results in the breaking of the dimer bonds and the removal of the corner adatoms.

Tunable molecular plasmons in polycyclic aromatic hydrocarbons.

PubMed

Manjavacas, Alejandro; Marchesin, Federico; Thongrattanasiri, Sukosin; Koval, Peter; Nordlander, Peter; Sánchez-Portal, Daniel; García de Abajo, F Javier

2013-04-23

We show that chemically synthesized polycyclic aromatic hydrocarbons (PAHs) exhibit molecular plasmon resonances that are remarkably sensitive to the net charge state of the molecule and the atomic structure of the edges. These molecules can be regarded as nanometer-sized forms of graphene, from which they inherit their high electrical tunability. Specifically, the addition or removal of a single electron switches on/off these molecular plasmons. Our first-principles time-dependent density-functional theory (TDDFT) calculations are in good agreement with a simpler tight-binding approach that can be easily extended to much larger systems. These fundamental insights enable the development of novel plasmonic devices based upon chemically available molecules, which, unlike colloidal or lithographic nanostructures, are free from structural imperfections. We further show a strong interaction between plasmons in neighboring molecules, quantified in significant energy shifts and field enhancement, and enabling molecular-based plasmonic designs. Our findings suggest new paradigms for electro-optical modulation and switching, single-electron detection, and sensing using individual molecules.

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.

Molecular switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

Comparative structural and electronic studies of hydrogen interaction with isolated versus ordered silicon nanoribbons grown on Ag(110)

NASA Astrophysics Data System (ADS)

Dávila, M. E.; Marele, A.; De Padova, P.; Montero, I.; Hennies, F.; Pietzsch, A.; Shariati, M. N.; Gómez-Rodríguez, J. M.; Le Lay, G.

2012-09-01

We have investigated the geometry and electronic structure of two different types of self-aligned silicon nanoribbons (SiNRs), forming either isolated SiNRs or a self-assembled 5 × 2/5 × 4 grating on an Ag(110) substrate, by scanning tunnelling microscopy and high resolution x-ray photoelectron spectroscopy. At room temperature we further adsorb on these SiNRs either atomic or molecular hydrogen. The hydrogen absorption process and hydrogenation mechanism are similar for isolated or 5 × 2/5 × 4 ordered SiNRs and are not site selective; the main difference arises from the fact that the isolated SiNRs are more easily attacked and destroyed faster. In fact, atomic hydrogen strongly interacts with any Si atoms, modifying their structural and electronic properties, while molecular hydrogen has first to dissociate. Hydrogen finally etches the Si nanoribbons and their complete removal from the Ag(110) surface could eventually be expected.

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

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

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

PubMed

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

DOE PAGES

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; ...

2017-05-24

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

NASA Astrophysics Data System (ADS)

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; van Driel, Tim B.; Chollet, Matthieu; Glownia, James M.; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Matar, Samir F.; Nielsen, Martin M.; Benfatto, Maurizio; Gaffney, Kelly J.; Collet, Eric; Cammarata, Marco

2017-05-01

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.

Theoretical study on the spectroscopic and third-order nonlinear optical properties of two-dimensional charge-transfer pyrazine derivatives

NASA Astrophysics Data System (ADS)

Li, Haipeng; Zhang, Yi; Bi, Zetong; Xu, Runfeng; Li, Mingxue; Shen, Xiaopeng; Tang, Gang; Han, Kui

2017-12-01

In this paper, density functional theory method was employed to study the electronic absorption spectrum and electronic static second hyperpolarisability of X-shaped pyrazine derivatives with two-dimensional charge-transfer structures. Computational results show that the push-pull electron abilities of the substituent groups and the length of the conjugated chains affect the electronic spectrum and static second hyperpolarisability of the pyrazine derivatives. As the push-pull electron abilities of the substituent groups or the length of the conjugated chains increases, the frontier molecular orbital energy gap decreases, resulting in increased second hyperpolarisability and redshift of the electronic absorption bands. The electronic absorption spectra of the pyrazine derivatives maintain good transparency in the blue light band. The electronic static second hyperpolarisability exhibits a linear relationship to the frontier molecular orbital energy gap. Particularly, increasing/decreasing the push-pull electron abilities of the substituent groups considerably affect the static second hyperpolarisability in long conjugated systems, which is important to the modulation of molecular organic nonlinear optical (NLO) properties. The studied pyrazine derivatives show large third-order NLO response and good transparency in the blue light band and are thus promising candidates as NLO materials for photonics applications.

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

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.

Electrical Matching at Metal/Molecule Contacts for Efficient Heterogeneous Charge Transfer.

PubMed

Sato, Shino; Iwase, Shigeru; Namba, Kotaro; Ono, Tomoya; Hara, Kenji; Fukuoka, Atsushi; Uosaki, Kohei; Ikeda, Katsuyoshi

2018-02-27

In a metal/molecule hybrid system, unavoidable electrical mismatch exists between metal continuum states and frontier molecular orbitals. This causes energy loss in the electron conduction across the metal/molecule interface. For efficient use of energy in a metal/molecule hybrid system, it is necessary to control interfacial electronic structures. Here we demonstrate that electrical matching between a gold substrate and π-conjugated molecular wires can be obtained by using monatomic foreign metal interlayers, which can change the degree of d-π* back-donation at metal/anchor contacts. This interfacial control leads to energy level alignment between the Fermi level of the metal electrode and conduction molecular orbitals, resulting in resonant electron conduction in the metal/molecule hybrid system. When this method is applied to molecule-modified electrocatalysts, the heterogeneous electrochemical reaction rate is considerably improved with significant suppression of energy loss at the internal electron conduction.

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

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

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. In this paper, 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 calculatingmore » $V$-matrix elements. Selected results are presented for electron and positron scattering from molecular hydrogen H$$_2$$ and electron scattering from the vibrationally excited molecular hydrogen ion H$$_2^+$$ and its isotopologues (D$$_2^+$$, T$$_2^+$$, HD$^+$, HT$^+$ and TD$^+$). Finally, 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.« less

Ab initio calculations of optical properties of silver clusters: cross-over from molecular to nanoscale behavior

NASA Astrophysics Data System (ADS)

Titantah, John T.; Karttunen, Mikko

2016-05-01

Electronic and optical properties of silver clusters were calculated using two different ab initio approaches: (1) based on all-electron full-potential linearized-augmented plane-wave method and (2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter ~1.7 nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag147, gives way to a dominant plasmon peak localized at wavelengths 350 nm ≤ λ ≤ 600 nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters.

Density functional theory molecular modeling, chemical synthesis, and antimicrobial behaviour of selected benzimidazole derivatives

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Tudorache, Diana Gabriela; Marton, George Iuliu; Zalaru, Christina-Marie; Popa, Marcela; Chifiriuc, Mariana-Carmen; Stavarache, Cristina-Elena; Constantinescu, Catalin

2017-02-01

Eco-friendly, one-pot, solvent-free synthesis of biologically active 2-substituted benzimidazoles is presented and discussed herein. Novel N-Mannich bases are synthesized from benzimidazoles, secondary amines and formaldehyde, and their structures are confirmed by 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and elemental analysis. All benzimidazole derivatives are evaluated by qualitative and quantitative methods against 9 bacterial strains. The largest microbicide and anti-biofilm effect is observed for the 2-(1-hydroxyethyl)-compounds. Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software. Antimicrobial activity is correlated with the electronic parameters (chemical hardness, electronic chemical potential, global electrophilicity index), Mullikan atomic charges and geometric parameters of the benzimidazole compounds. The planarity of the compound, symmetry of the molecule, and the presence of a nucleophilic group, are advantages for a high antimicrobial activity. Finally, we briefly show that further accurate processing of such compounds into thin films and hybrid structures, e.g. by laser ablation matrix-assisted pulsed laser evaporation and/or laser-induced forward transfer, may indeed provide simple and environmental friendly, state-of-the-art solutions for antimicrobial coatings.

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

DOE PAGES

Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; ...

2016-09-26

During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlinedmore » for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.« less

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier

NASA Astrophysics Data System (ADS)

Ryng, Stanisław; Zimecki, Michał; Jezierska-Mazzarello, Aneta; Panek, Jarosław J.; Mączyński, Marcin; Głowiak, Tadeusz; Sawka-Dobrowolska, Wanda; Koll, Aleksander

2011-07-01

A new potential lead structure with immunological activity, 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate, was synthesized. A detailed description of synthesis is presented together with X-ray structural analysis. In vitro assays showed that the compound had a potent immunosuppressive activity. Next, Density Functional Theory (DFT) was employed to shed a light on molecular properties of the investigated isoxazole derivative. The molecular modeling part included geometric as well as electronic structure descriptions: (i) the conformational analysis was performed to localize the most appropriate conformation; (ii) the coordination energy and Basis Set Superposition Error (BSSE) were estimated for the complex of the isoxazole derivative interacting with water molecule; (iii) the potential energy distribution was used to assign molecular vibrations, and NBO population analysis served to describe the electronic structure; (iv) the electrostatic potential map was generated to provide the graphical presentation of regions exposed for intermolecular interactions. The contacts between the water molecule and the nitrogen atom of the isoxazole ring edge were present in the solid phase. On the other hand, the theoretical DFT prediction was that the oxygen atom of the edge should form a more stable complex with the water molecule.

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.

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.

Unravelling the structural-electronic impact of arylamine electron-donating antennas on the performances of efficient ruthenium sensitizers for dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Chen, Wang-Chao; Kong, Fan-Tai; Ghadari, Rahim; Li, Zhao-Qian; Guo, Fu-Ling; Liu, Xue-Peng; Huang, Yang; Yu, Ting; Hayat, Tasawar; Dai, Song-Yuan

2017-04-01

We report a systematic research to understand the structural-electronic impact of the arylamine electron-donating antennas on the performances of the ruthenium complexes for dye-sensitized solar cells. Three ruthenium complexes functionalized with different arylamine electron-donating antennas (N,N-diethyl-aniline in RC-31, julolidine in RC-32 and N,N-dibenzyl-aniline in RC-36) are designed and synthesized. The photoelectric properties of RC dyes exhibit apparent discrepancy, which are ascribed to different structural nature and electronic delocalization ability of these arylamine electron-donating system. In conjunction with TiO2 microspheres photoanode and a typical coadsorbent DPA, the devices sensitized by RC-36 achieve the best conversion efficiency of 10.23%. The UV-Vis absorption, electrochemical measurement, incident photon-to-current conversion efficiency and transient absorption spectra confirm that the excellent performance of RC-36 is induced by synergistically structural-electronic impacts from enhanced absorption capacity and well-tuned electronic characteristics. These observations provide valuable insights into the molecular engineering methodology based on fine tuning structural-electronic impact of electron-donating antenna in efficient ruthenium sensitizers.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

PubMed

Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

2016-07-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

Development of lamellar structures in natural waxes - an electron diffraction investigation

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1999-06-01

When they are recrystallized from the melt, natural plant or insect waxes tend to form solid phases with a nematic-like structure (i.e. a parallel array of polymethylene chains with little or no aggregation of the molecules into distinct layers). An electron diffraction study of carnauba wax and two types of beeswax has shown that the degree of molecular organization into lamellar structures can be enhanced by annealing in the presence of benzoic acid, which also acts as an epitaxial substrate. Nevertheless, the resultant layer structure in the annealed solid is not the same as that found for paraffin wax fractions refined from petroleum. Probably because of a small but significant fraction of a very long chain ingredient, the lamellar separation is incomplete, incorporating a number of `bridging molecules' that span the nascent lamellar interface.The same phenomenon has been described recently for a low molecular weight polyethylene.

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

NASA Astrophysics Data System (ADS)

Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

2010-08-01

In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

Electron cryo-microscopy structure of the canonical TRPC4 ion channel

PubMed Central

Vinayagam, Deivanayagabarathy; Mager, Thomas; Apelbaum, Amir; Bothe, Arne; Merino, Felipe; Hofnagel, Oliver; Gatsogiannis, Christos

2018-01-01

Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca2+ signaling and have been proposed to act as store-operated channels (SOC). Their malfunction is related to cardiomyopathies and their modulation by small molecules has been shown to be effective against renal cancer cells. The molecular mechanism underlying the complex activation and regulation is poorly understood. Here, we report the electron cryo-microscopy structure of zebrafish TRPC4 in its unliganded (apo), closed state at an overall resolution of 3.6 Å. The structure reveals the molecular architecture of the cation conducting pore, including the selectivity filter and lower gate. The cytoplasmic domain contains two key hubs that have been shown to interact with modulating proteins. Structural comparisons with other TRP channels give novel insights into the general architecture and domain organization of this superfamily of channels and help to understand their function and pharmacology. PMID:29717981

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.

Fine- and hyperfine-structure effects in molecular photoionization. I. General theory and direct photoionization

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

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch

2016-07-28

We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra, we derive highly symmetrized forms of the squared photoionization dipole matrix elements from which we derive the salient selection and propensity rules for fine- and hyperfine resolved photoionizing transitions. Our theoretical results are validated by the analysis of the fine-structure resolved photoelectron spectrum of O{sub 2} reported by Palm and Merkt [Phys. Rev. Lett. 81, 1385 (1998)] and are used for predicting hyperfine populations of molecular ionsmore » produced by photoionization.« less

Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach.

PubMed

Prucker, V; Bockstedte, M; Thoss, M; Coto, P B

2018-03-28

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.

Highly Conducting Molecular Crystals.

NASA Astrophysics Data System (ADS)

Whitehead, Roger James

Available from UMI in association with The British Library. Requires signed TDF. As the result of a wide ranging effort towards the preparation of new electrically conducting molecular crystals, high quality samples were prepared of the organic radical-ion salt (TMTSF)_2SbCl _2F_4 {bis-tetramethyltetraselenafulvalene-dichlorotetrafluoroantimonate(V) }. A collaborative effort to investigate the electronic and structural properties of this material has yielded the necessary depth of information required to give a satisfactory understanding of its rather complicated behaviour. The combination of x-ray structural studies with d.c. transport, reflectance and magnetic measurements has served to underline the importance of crystalline perfection, electronic dimensionality and conduction electron correlation in determining the materials overall behaviour. This thesis describes the method of preparation and characterization of (TMTSF)_2SbCl _2F_4 and the experimental arrangements used to determine the temperature dependence of its ambient pressure electrical conductivity, thermopower and electron spin resonance spectra. The crystal structure and optical reflectance measurements at room temperature are also presented. The results into a study of the low temperature diffraction pattern are described along with the temperature dependence in the static magnetic susceptibility and in the conductivity behaviour under elevated hydrostatic pressures. These findings are rationalized by reference to other materials which show similar behaviour in their electronic and/or structural properties, and also to the various theoretical models currently enjoying favour.

Diffusion in liquid Germanium using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

1996-03-01

We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

Density functional theory molecular modeling and antimicrobial behaviour of selected 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Cinteza, Ludmila Otilia; Marton, George Iuliu; Marutescu, Luminita Gabriela; Chifiriuc, Mariana-Carmen; Constantinescu, Catalin

2017-09-01

A series of 9-substituted 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides is evaluated against 12 bacterial and fungal strains, for their microbicidal and anti-pathogenic features. The largest spectrum of the antibacterial activity is evidenced for the nitro- (2b) and hydroxy- (5b) N-oxides, followed by the amino-N-oxide (3b). Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied/lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software at M11/ktzvp level of theory in order to find their structural and electronic parameters. We show that the planarity of the molecules and the presence of the electron withdrawing group are advantages for its antimicrobial activity. Finally, we briefly present and discuss results on the processing of such compounds into thin films and hybrid structures by laser-assisted techniques, i.e. matrix-assisted pulsed laser evaporation (MAPLE) or laser-induced forward transfer (LIFT), to provide simple and environmental friendly, state-of-the-art solutions for antimicrobial/medical coatings and devices.

PAREMD: A parallel program for the evaluation of momentum space properties of atoms and molecules

NASA Astrophysics Data System (ADS)

Meena, Deep Raj; Gadre, Shridhar R.; Balanarayan, P.

2018-03-01

The present work describes a code for evaluating the electron momentum density (EMD), its moments and the associated Shannon information entropy for a multi-electron molecular system. The code works specifically for electronic wave functions obtained from traditional electronic structure packages such as GAMESS and GAUSSIAN. For the momentum space orbitals, the general expression for Gaussian basis sets in position space is analytically Fourier transformed to momentum space Gaussian basis functions. The molecular orbital coefficients of the wave function are taken as an input from the output file of the electronic structure calculation. The analytic expressions of EMD are evaluated over a fine grid and the accuracy of the code is verified by a normalization check and a numerical kinetic energy evaluation which is compared with the analytic kinetic energy given by the electronic structure package. Apart from electron momentum density, electron density in position space has also been integrated into this package. The program is written in C++ and is executed through a Shell script. It is also tuned for multicore machines with shared memory through OpenMP. The program has been tested for a variety of molecules and correlated methods such as CISD, Møller-Plesset second order (MP2) theory and density functional methods. For correlated methods, the PAREMD program uses natural spin orbitals as an input. The program has been benchmarked for a variety of Gaussian basis sets for different molecules showing a linear speedup on a parallel architecture.

Definition of molecular structure: by choice or by appeal to observation?

PubMed

Bader, Richard F W

2010-07-22

There are two schools of thought in chemistry: one derived from the valence bond and molecular orbital models of bonding, the other appealing directly to the measurable electron density and the quantum mechanical theorems that determine its behavior, an approach embodied in the quantum theory of atoms in molecules, QTAIM. No one questions the validity of the former approach, and indeed molecular orbital models and QTAIM play complementary roles, the models finding expression in the principles of physics. However, some orbital proponents step beyond the models to impose their personal stamp on their use in interpretive chemistry, by denying the possible existence of a physical basis for the concepts of chemistry. This places them at odds with QTAIM, whose very existence stems from the discovery in the observable topology of the electron density, the definitions of atoms, of the bonding between atoms and hence of molecular structure. Relating these concepts to the electron density provides the necessary link for their ultimate quantum definition. This paper explores in depth the possible causes of the difficulties some have in accepting the quantum basis of structure beginning with the arguments associated with the acceptance of a "bond path" as a criterion for bonding. This identification is based on the finding that all classical structures may be mapped onto molecular graphs consisting of bond paths linking neighboring atoms, a mapping that has no known exceptions and one that is further bolstered by the finding that there are no examples of "missing bond paths". Difficulties arise when the quantum concept is applied to systems that are not amenable to the classical models of bonding. Thus one is faced with the recurring dilemma of science, of having to escape the constraints of a model that requires a change in the existing paradigm, a process that has been in operation since the discovery of new and novel structures necessitated the extension of the Lewis model and the octet rule. The paper reviews all facets of bonding beginning with the work of Pauling and Slater in their accounting for crystal structures, taking note of Pauling's advocating possible bonding between large anions. Many examples of nonbonded or van der Waals interactions are considered from both points of view. The final section deals with the consequences of the realization that bonded quantum atoms that share an interatomic surface do not "overlap". The time has come for entering students of chemistry to be taught that the electron density can be seen, touched, and measured and that the chemical structures they learn are in fact the tracings of "bonds" onto lines of maximum density that link bonded nuclei. Matter, as we perceive it, is bound by the electrostatic force of attraction between the nuclei and the electron density.

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.

Machine learning of molecular electronic properties in chemical compound space

NASA Astrophysics Data System (ADS)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.

Molecular beam epitaxy growth of high electron mobility InAs/AlSb deep quantum well structure

NASA Astrophysics Data System (ADS)

Wang, Juan; Wang, Guo-Wei; Xu, Ying-Qiang; Xing, Jun-Liang; Xiang, Wei; Tang, Bao; Zhu, Yan; Ren, Zheng-Wei; He, Zhen-Hong; Niu, Zhi-Chuan

2013-07-01

InAs/AlSb deep quantum well (QW) structures with high electron mobility were grown by molecular beam epitaxy (MBE) on semi-insulating GaAs substrates. AlSb and Al0.75Ga0.25Sb buffer layers were grown to accommodate the lattice mismatch (7%) between the InAs/AlSb QW active region and GaAs substrate. Transmission electron microscopy shows abrupt interface and atomic force microscopy measurements display smooth surface morphology. Growth conditions of AlSb and Al0.75Ga0.25Sb buffer were optimized. Al0.75Ga0.25Sb is better than AlSb as a buffer layer as indicated. The sample with optimal Al0.75Ga0.25Sb buffer layer shows a smooth surface morphology with root-mean-square roughness of 6.67 Å. The electron mobility has reached as high as 27 000 cm2/Vs with a sheet density of 4.54 × 1011/cm2 at room temperature.

Enhancing the Thermoelectric Figure of Merit by Low-Dimensional Electrical Transport in Phonon-Glass Crystals.

PubMed

Mi, Xue-Ya; Yu, Xiaoxiang; Yao, Kai-Lun; Huang, Xiaoming; Yang, Nuo; Lü, Jing-Tao

2015-08-12

Low-dimensional electronic and glassy phononic transport are two important ingredients of highly efficient thermoelectric materials, from which two branches of thermoelectric research have emerged. One focuses on controlling electronic transport in the low dimension, while the other focuses on multiscale phonon engineering in the bulk. Recent work has benefited much from combining these two approaches, e.g., phonon engineering in low-dimensional materials. Here we propose to employ the low-dimensional electronic structure in bulk phonon-glass crystals as an alternative way to increase the thermoelectric efficiency. Through first-principles electronic structure calculations and classical molecular dynamics simulations, we show that the π-π-stacking bis(dithienothiophene) molecular crystal is a natural candidate for such an approach. This is determined by the nature of its chemical bonding. Without any optimization of the material parameters, we obtained a maximum room-temperature figure of merit, ZT, of 1.48 at optimal doping, thus validating our idea.

Effects of surface functionalization on the electronic and structural properties of carbon nanotubes: A computational approach

NASA Astrophysics Data System (ADS)

Ribeiro, M. S.; Pascoini, A. L.; Knupp, W. G.; Camps, I.

2017-12-01

Carbon nanotubes (CNTs) have important electronic, mechanical and optical properties. These features may be different when comparing a pristine nanotube with other presenting its surface functionalized. These changes can be explored in areas of research and application, such as construction of nanodevices that act as sensors and filters. Following this idea, in the current work, we present the results from a systematic study of CNT's surface functionalized with hydroxyl and carboxyl groups. Using the entropy as selection criterion, we filtered a library of 10k stochastically generated complexes for each functional concentration (5, 10, 15, 20 and 25%). The structurally related parameters (root-mean-square deviation, entropy, and volume/area) have a monotonic relationship with functionalization concentration. Differently, the electronic parameters (frontier molecular orbital energies, electronic gap, molecular hardness, and electrophilicity index) present and oscillatory behavior. For a set of concentrations, the nanotubes present spin polarized properties that can be used in spintronics.

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.

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

Molecularly Stretchable Electronics for Energy and Healthcare

NASA Astrophysics Data System (ADS)

Lipomi, Darren

The term ``plastic electronics'' masks the wide range of mechanical behavior possessed by films of π-conjugated (semiconducting) small molecules and polymers. Such materials are promising for biosensors, large-area displays, low-energy lighting, and low-cost photovoltaic modules. There is also an apparent trade-off between electronic performance and mechanical compliance in films of some of the best-performing semiconducting polymers, which fracture at tensile strains not significantly greater than those at which conventional inorganic semiconductors fail. The design of intrinsically deformable electronic materials-i.e., imagine a semiconducting rubber band-would facilitate roll-to-roll production, mechanical robustness for potable applications, and conformal bonding to curved surfaces. This seminar describes my group's efforts to understand and control the structural parameters that influence the mechanical properties of π-conjugated polymers. The techniques we employ include synthetic chemistry, spectroscopy and microstructural characterization, computation from the molecular to continuum level, and electrical measurements of devices. A complex picture emerges for the interplay between molecular structure, the way the process of solidification influences the morphology, and how molecular structure and morphology combine to produce a film with a given modulus, elastic range, ductility, and toughness. We are also exploring ways to introduce other properties into organic semiconductors that are inspired by biological tissue. That is, not just elasticity and toughness, but also biodegradability and the capacity for self-repair. The seminar will also touch on our use of self-assembled metallic nanoislands on graphene for ultra-sensitive mechanical sensing using piezoresistive and ``piezoplasmonic'' mechanisms. The applications for these materials are in detecting human motion and measuring the mechanics of cardiac and musculoskeletal cells. My group is broadly interested in the intersection of soft materials and human touch for virtual and augmented reality, and I will briefly mention our work in these areas. Invited speaker #45067.

Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

PubMed

Stashans, Arvids; Chamba, Gaston; Pinto, Henry

2008-02-01

The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. (c) 2007 Wiley Periodicals, Inc.

Scanning Tunneling Microscopy Analysis of a Pentacene/Graphene/SiC(0001) system

NASA Astrophysics Data System (ADS)

Yost, Andrew; Suzer, Ozgun; Smerdon, Joseph; Chien, Teyu; Guest, Jeffrey

2014-03-01

A complete understanding of the structure of molecular assemblies, as well as an understanding of donor-acceptor interactions is crucial in the development of emergent molecular electronics technologies such as organic photovoltaics. The pentacene (C22H14) is a good electron donor in Pentacene-C60 system, which is a model system of an organic photovoltaic cell.. Here we present scanning tunneling microscopy studies of the pentacene(Pn) molecule on Graphene(G) that is epitaxially grown on SiC(0001). In addition to the morphologies reported in literature, several new structures of Pn on on G/SiC(0001) were observed with different periodicity and registry both in monolayer and bilayer coverages of molecules on the surface. Preliminary scanning tunneling spectroscopy of the molecular system is also discussed; well-isolated states and a large HOMO-LUMO gap indicate the Pn is weakly coupled to the grapheme and underlying substrate.

A theoretical study of structural, opto-electronic and nonlinear properties of arylboroxine derivatives

NASA Astrophysics Data System (ADS)

Islam, Nasarul; Pandith, Altaf Hussain

2018-01-01

Density functional theory at CAM-B3LYP/6-311G++ (2d, 2p) level was employed to study the Triphenylboroxine derivatives ( TB) containing electron donating and electron substituents, for their charge transfer and nonlinear optical properties. The results reveal that electron donating groups facilitate the rapid electron injection as compared to unsubstituted TB. It was observed that upon substitution with electron donating groups, the TB derivatives show an increased double bond character in the B3-C18 bond indicating an increase in the degree of conjugation. The Frontier molecular orbital studies indicate that highest occupied molecular orbitals of the neutral molecules delocalize primarily over the three phenyl rings and bridging oxygen atoms, whereas the lowest unoccupied molecular orbitals localize largely on the two phenyl rings and the boron atoms. Further, the TD-DFT studies indicate that the maximum absorption band results from the electron transitions from the initial states that are contributed by the HOMO and HOMO-1 to the final states that are mainly contributed by the LUMOs. In addition, we have observed that the introduction of electron donating group to the TB-7 leads to more active nonlinear performance.

Low-energy electron interaction with retusin extracted from Maackia amurensis: towards a molecular mechanism of the biological activity of flavonoids.

PubMed

Pshenichnyuk, Stanislav A; Elkin, Yury N; Kulesh, Nadezda I; Lazneva, Eleonora F; Komolov, Alexei S

2015-07-14

The antioxidant isoflavone retusin efficiently attaches low-energy electrons in vacuo, generating fragment species via dissociative electron attachment (DEA), as has been shown by DEA spectroscopy. According to in silico results obtained by means of density functional theory, retusin is able to attach solvated electrons and could be decomposed under reductive conditions in vivo, for instance, near the mitochondrial electron transport chain, analogous to gas-phase DEA. The most intense decay channels of retusin temporary negative ions were found to be associated with the elimination of H atoms and H2 molecules. Doubly dehydrogenated fragment anions were predicted to possess a quinone structure. It is thought that molecular hydrogen, known for its selective antioxidant properties, can be efficiently generated via electron attachment to retusin in mitochondria and may be responsible for its antioxidant activity. The second abundant species, i.e., quinone bearing an excess negative charge, can serve as an electron carrier and can return the captured electron back to the respiration cycle. The number of OH substituents and their relative positions are crucial for the present molecular mechanism, which can explain the radical scavenging activity of polyphenolic compounds.

Electrostatically self-assembled polyoxometalates on molecular-dye-functionalized diamond.

PubMed

Zhong, Yu Lin; Ng, Wibowo; Yang, Jia-Xiang; Loh, Kian Ping

2009-12-30

We have successfully immobilized phosphotungstic acid (PTA), a polyoxometalate, on the surface of boron-doped diamond (BDD) surface through electrostatic self-assembly of PTA on pyridinium dye-functionalized-BDD. The inorganic/organic bilayer structure on BDD is found to exhibit fast surface-confined reversible electron transfer. The molecular dye-grafted BDD can undergo controllable electrical stripping and regeneration of PTA which can be useful for electronics or sensing applications. Furthermore, we have demonstrated the use of PTA as a molecular switch in which the direction of photocurrent from diamond to methyl viologen is reversed by the surface bound PTA. Robust photocurrent converter based on such molecular system-diamond platform can operate in corrosive medium which is not tolerated by indium tin oxide electrodes.

Harnessing Reversible Electronic Energy Transfer: From Molecular Dyads to Molecular Machines.

PubMed

Denisov, Sergey A; Yu, Shinlin; Pozzo, Jean-Luc; Jonusauskas, Gediminas; McClenaghan, Nathan D

2016-06-17

Reversible electronic energy transfer (REET) may be instilled in bi-/multichromophoric molecule-based systems, following photoexcitation, upon judicious structural integration of matched chromophores. This leads to a new set of photophysical properties for the ensemble, which can be fully characterized by steady-state and time-resolved spectroscopic methods. Herein, we take a comprehensive look at progress in the development of this type of supermolecule in the last five years, which has seen systems evolve from covalently tethered dyads to synthetic molecular machines, exemplified by two different pseudorotaxanes. Indeed, REET holds promise in the control of movement in molecular machines, their assembly/disassembly, as well as in charge separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 correlations of the electronic structure and film growth of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on SiO2.

PubMed

Lyu, Lu; Niu, Dongmei; Xie, Haipeng; Zhao, Yuan; Cao, Ningtong; Zhang, Hong; Zhang, Yuhe; Liu, Peng; Gao, Yongli

2017-01-04

Combining ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), atomic force microscopy (AFM) and small angle X-ray diffraction (SAXD) measurements, we perform a systematic investigation on the correlations of the electronic structure, film growth and molecular orientation of 2,7-diocty[1]benzothieno[3,2-b]benzothiophene (C8-BTBT) on silicon oxide (SiO 2 ). AFM analysis reveals a phase transition of disorderedly oriented molecules in clusters in thinner films to highly ordered standing-up molecules in islands in thicker films. SAXD peaks consistently support the standing-up configuration in islands. The increasing ordering of the molecular orientation with film thickness contributes to the changing of the shape and lowering of the leading edge of the highest occupied molecular orbital (HOMO). The end methyl of the highly ordered standing molecules forms an outward pointing dipole layer which makes the work function (WF) decrease with increasing thickness. The downward shift of the HOMO and a decrease of WF result in unconventional downward band bending and decreased ionization potential (IP). The correlations of the orientation ordering of molecules, film growth and interface electronic structures provide a useful design strategy to improve the performance of C8-BTBT thin film based field effect transistors.

Proper Resonance Depiction of Acylium Cation: A High-Level and Student Computational Investigation

ERIC Educational Resources Information Center

Esselman, Brian J.; Hill, Nicholas J.

2015-01-01

The electronic and molecular structure of the acylium cation ([CH[subscript 3]CO][superscript +], 1) receives varied treatment in undergraduate textbooks and online resources. The overall structure of 1 is typically represented as an equal combination of resonance structures containing C-O triple and double bonds, the latter structure occasionally…

Investigations of photosynthetic light harvesting by two-dimensional electronic spectroscopy

NASA Astrophysics Data System (ADS)

Read, Elizabeth Louise

Photosynthesis begins with the harvesting of sunlight by antenna pigments, organized in a network of pigment-protein complexes that rapidly funnel energy to photochemical reaction centers. The intricate design of these systems---the widely varying structural motifs of pigment organization within proteins and protein organization within a larger, cooperative network---underlies the remarkable speed and efficiency of light harvesting. Advances in femtosecond laser spectroscopy have enabled researchers to follow light energy on its course through the energetic levels of photosynthetic systems. Now, newly-developed femtosecond two-dimensional electronic spectroscopy reveals deeper insight into the fundamental molecular interactions and dynamics that emerge in these structures. The following chapters present investigations of a number of natural light-harvesting complexes using two-dimensional electronic spectroscopy. These studies demonstrate the various types of information contained in experimental two-dimensional spectra, and they show that the technique makes it possible to probe pigment-protein complexes on the length- and time-scales relevant to their functioning. New methods are described that further extend the capabilities of two-dimensional electronic spectroscopy, for example, by independently controlling the excitation laser pulse polarizations. The experiments, coupled with theoretical simulation, elucidate spatial pathways of energy flow, unravel molecular and electronic structures, and point to potential new quantum mechanical mechanisms of light harvesting.

Trends in the Electron Microscopy Data Bank (EMDB).

PubMed

Patwardhan, Ardan

2017-06-01

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.

Trends in the Electron Microscopy Data Bank (EMDB)

PubMed Central

Patwardhan, Ardan

2017-01-01

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved. PMID:28580912

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.

Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

PubMed

Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

2016-11-15

Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1 H, 13 C, and 15 N nuclei. Due to their higher sensitivity to polarization effects, 17 O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.

Electronic structure and properties of unsubstituted rhodamine in different electron states

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

Artyukhov, V.Ya.

1988-04-01

An analysis is given of the electron density distribution, dipole moment variation, and proton acceptor properties of unsubstituted rhodamine molecules in different electron states. It is shown that the electron density redistribution between the pyronine and benzoin parts of rhodamine may be large and strongly affect the molecular properties. In one of the electron transitions (S/sub 4/) producing the third absorption band the proton acceptor power markedly increases, giving rise to a protonated form under suitable conditions.

Electronic structure and properties of unsubstituted rhodamine in different electron states

NASA Astrophysics Data System (ADS)

Artyukhov, V. Ya.

1987-10-01

An analysis is given of the electron density distribution, dipole moment variation, and proton acceptor properties of unsubstituted rhodamine molecules in different electron states. It is shown that the electron density redistribution between the pyronine and benzoin parts of rhodamine may be large and strongly affect the molecular properties. In one of the electron transitions (S4) producing the third absorption band the proton acceptor power markedly increases, giving rise to a protonated form under suitable conditions.

The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap.

PubMed

Brown, Jeffrey W; Bullitt, Esther; Sriswasdi, Sira; Harper, Sandra; Speicher, David W; McKnight, C James

2015-06-01

The primary, secondary, and tertiary structures of spectrin are reasonably well defined, but the structural basis for the known dramatic molecular shape change, whereby the molecular length can increase three-fold, is not understood. In this study, we combine previously reported biochemical and high-resolution crystallographic data with structural mass spectroscopy and electron microscopic data to derive a detailed, experimentally-supported quaternary structure of the spectrin heterotetramer. In addition to explaining spectrin's physiological resting length of ~55-65 nm, our model provides a mechanism by which spectrin is able to undergo a seamless three-fold extension while remaining a linear filament, an experimentally observed property. According to the proposed model, spectrin's quaternary structure and mechanism of extension is similar to a Chinese Finger Trap: at shorter molecular lengths spectrin is a hollow cylinder that extends by increasing the pitch of each spectrin repeat, which decreases the internal diameter. We validated our model with electron microscopy, which demonstrated that, as predicted, spectrin is hollow at its biological resting length of ~55-65 nm. The model is further supported by zero-length chemical crosslink data indicative of an approximately 90 degree bend between adjacent spectrin repeats. The domain-domain interactions in our model are entirely consistent with those present in the prototypical linear antiparallel heterotetramer as well as recently reported inter-strand chemical crosslinks. The model is consistent with all known physical properties of spectrin, and upon full extension our Chinese Finger Trap Model reduces to the ~180-200 nm molecular model currently in common use.

Teaching Chemistry with Electron Density Models

NASA Astrophysics Data System (ADS)

Shusterman, Gwendolyn P.; Shusterman, Alan J.

1997-07-01

Linus Pauling once said that a topic must satisfy two criteria before it can be taught to students. First, students must be able to assimilate the topic within a reasonable amount of time. Second, the topic must be relevant to the educational needs and interests of the students. Unfortunately, the standard general chemistry textbook presentation of "electronic structure theory", set as it is in the language of molecular orbitals, has a difficult time satisfying either criterion. Many of the quantum mechanical aspects of molecular orbitals are too difficult for most beginning students to appreciate, much less master, and the few applications that are presented in the typical textbook are too limited in scope to excite much student interest. This article describes a powerful new method for teaching students about electronic structure and its relevance to chemical phenomena. This method, which we have developed and used for several years in general chemistry (G.P.S.) and organic chemistry (A.J.S.) courses, relies on computer-generated three-dimensional models of electron density distributions, and largely satisfies Pauling's two criteria. Students find electron density models easy to understand and use, and because these models are easily applied to a broad range of topics, they successfully convey to students the importance of electronic structure. In addition, when students finally learn about orbital concepts they are better prepared because they already have a well-developed three-dimensional picture of electronic structure to fall back on. We note in this regard that the types of models we use have found widespread, rigorous application in chemical research (1, 2), so students who understand and use electron density models do not need to "unlearn" anything before progressing to more advanced theories.

Using Synchrotron Radiation and Electron Microscopy to Map the Huge Structural Changes that Occur in Viruses During Their Life Cycle

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

Rossman, Michael

2011-09-07

The crystallographic techniques for structure determination of proteins and neucleic acids at near atomic resolution using synchrotron X-radiation has become almost automatic. However the limits of this procedure are determined by the availability of crystals. As the size and complexity of the molecular assemblies being studied increases, the likelihood of growing useful crystals diminishes. Cryo electron microscopy and tomography have extended the range of biological objects that can be determined at near atomic resolution. Furthermore it is now becoming apparent that the function of the molecular assemblies most often requires very large conformational changes that could never be contained withinmore » a crystal, Examples will be presented of the structural changes that occur in viruses as they assembly and prepare to infect new cells.« less

Electronic properties of semiconductor-water interfaces: Predictions from ab-initio molecular dynamics and many-body perturbation theory

NASA Astrophysics Data System (ADS)

Pham, Tuan Anh

2015-03-01

Photoelectrochemical cells offer a promising avenue for hydrogen production from water and sunlight. The efficiency of these devices depends on the electronic structure of the interface between the photoelectrode and liquid water, including the alignment between the semiconductor band edges and the water redox potential. In this talk, we will present the results of first principles calculations of semiconductor-water interfaces that are obtained with a combination of density functional theory (DFT)-based molecular dynamics simulations and many-body perturbation theory (MBPT). First, we will discuss the development of an MBPT approach that is aimed at improving the efficiency and accuracy of existing methodologies while still being applicable to complex heterogeneous interfaces consisting of hundreds of atoms. We will then present studies of the electronic structure of liquid water and aqueous solutions using MBPT, which represent an essential step in establishing a quantitative framework for computing the energy alignment at semiconductor-water interfaces. Finally, using a combination of DFT-based molecular dynamics simulations and MBPT, we will describe the relationship between interfacial structure, electronic properties of semiconductors and their reactivity in aqueous solutions through a number of examples, including functionalized Si surfaces and GaP/InP surfaces in contact with liquid water. T.A.P was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by the Lawrence Fellowship Program.

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.

Keggin-type polyoxometalate nanosheets: synthesis and characterization via scanning transmission electron microscopy.

PubMed

Hiyoshi, Norihito

2018-05-17

Polyoxometalate nanosheets were synthesized at the gas/liquid interface of an aqueous solution of Keggin-type silicotungstic acid, cesium chloride, and n-octylamine. The structure of the nanosheets was elucidated via aberration-corrected scanning transmission electron microscopy at the atomic and molecular levels.

Investigation of low-loss spectra and near-edge fine structure of polymers by PEELS

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

Heckmann, W.

Transmission electron microscopy has changed from a purely imaging method to an analytical method. This has been facilitated particularly by equipping electron microscopes with energy filters and with parallel electron energy loss spectrometers (PEELS). Because of their relatively high energy resolution (1 to 2 eV) they provide information not only on the elements present but also on the type of bonds between the molecular groups. Polymers are radiation sensitive and the molecular bonds change as the spectrum is being recorded. This can be observed with PEEL spectrometers that are able to record spectra with high sensitivity and in rapid succession.

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

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction.

PubMed

Bilić, Ante; Reimers, Jeffrey R; Hush, Noel S

2005-03-01

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

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.

Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A.

PubMed

Markovic-Mueller, Sandra; Stuttfeld, Edward; Asthana, Mayanka; Weinert, Tobias; Bliven, Spencer; Goldie, Kenneth N; Kisko, Kaisa; Capitani, Guido; Ballmer-Hofer, Kurt

2017-02-07

Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel development upon activation of three receptor tyrosine kinases: VEGFR-1, -2, and -3. Partial structures of VEGFR/VEGF complexes based on single-particle electron microscopy, small-angle X-ray scattering, and X-ray crystallography revealed the location of VEGF binding and domain arrangement of individual receptor subdomains. Here, we describe the structure of the full-length VEGFR-1 extracellular domain in complex with VEGF-A at 4 Å resolution. We combined X-ray crystallography, single-particle electron microscopy, and molecular modeling for structure determination and validation. The structure reveals the molecular details of ligand-induced receptor dimerization, in particular of homotypic receptor interactions in immunoglobulin homology domains 4, 5, and 7. Functional analyses of ligand binding and receptor activation confirm the relevance of these homotypic contacts and identify them as potential therapeutic sites to allosterically inhibit VEGFR-1 activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Chemical and quantum simulation of electron transfer through a polypeptide

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

Ungar, L.W.; Voth, G.A.; Newton, M.D.

1999-08-26

Quantum rate theory, molecular dynamics simulations, and semiempirical electronic structure calculations are used to fully investigate electron transfer mediated by a solvated polypeptide for the first time. Using a stationary-phase approximation, the nonadiabatic electron-transfer rate constant is calculated from the nuclear free energies and the electronic coupling between the initial and final states. The former are obtained from quantum path integral and classical molecular dynamics simulations; the latter are calculated using semiempirical electronic structure calculations and the generalized Mulliken-Hush method. Importantly, no parameters are fit to kinetic data. The simulated system consists of a solvated four-proline polypeptide with a tris(bipyridine)rutheniummore » donor group and an oxypentamminecobalt acceptor group. From the simulation data entropy and energy contributions to the free energies are distinguished. Quantum suppression of the barrier, including important solvent contributions, is demonstrated. Although free energy profiles along the reaction coordinate are nearly parabolic, pronounced departures from harmonic behavior are found for the separate energy and entropy functions. Harmonic models of the system are compared to simulation results in order to quantify anharmonic effects. Electronic structure calculations show that electronic coupling elements vary considerably with system conformation, even when the effective donor-acceptor separation remains roughly constant. The calculations indicate that electron transfer in a significant range of conformations linking the polypeptide to the acceptor may contribute to the overall rate constant. After correction for limitations of the solvent model, the simulations and calculations agree well with the experimental activation energy and Arrhenius prefactor.« less

Electronic structure and partial charge distribution of doxorubicin under different molecular environments

NASA Astrophysics Data System (ADS)

Poudel, Lokendra

Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio calculations on realistic models are an important step towards a more accurate description of biomolecular interaction and in the eventual understanding of long-range interactions in biomolecular systems.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

The Molecular Density of States in Bacterial Nanowires

PubMed Central

El-Naggar, Mohamed Y.; Gorby, Yuri A.; Xia, Wei; Nealson, Kenneth H.

2008-01-01

The recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. We here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells and bioremediation of heavy metals and radionuclides. The Shewanella nanowires display a surprising nonlinear electrical transport behavior, where the voltage dependence of the conductance reveals peaks indicating discrete energy levels with higher electronic density of states. Our results indicate that the molecular constituents along the Shewanella nanowires possess an intricate electronic structure that plays a role in mediating transport. PMID:18441026

Evolution from S3 to S4 States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics.

PubMed

Narzi, Daniele; Capone, Matteo; Bovi, Daniele; Guidoni, Leonardo

2018-04-16

Water oxidation in the early steps of natural photosynthesis is fulfilled by photosystem II, which is a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of photosystem II, which consists of a Mn4Ca metal cluster, at which, after the accumulation of four oxidising equivalents through five steps (S0-S4) of the Kok-Joliot cycle, two water molecules are split into electrons, protons, and molecular oxygen. In recent years, by combining experimental and theoretical approaches, new insights have been achieved into the structural and electronic properties of different steps of the catalytic cycle. Nevertheless, the exact catalytic mechanism, especially concerning the final stages of the cycle, remains elusive and greatly debated. Herein, by means of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, from the structural, electronic, and magnetic points of view, the S 3 state before and upon oxidation has been characterised. In contrast with the S 2 state, the oxidation of the S 3 state is not followed by a spontaneous proton-coupled electron-transfer event. Nevertheless, upon modelling the reduction of the tyrosine residue in photosystem II (Tyr Z ) and the protonation of Asp61, spontaneous proton transfer occurs, leading to the deprotonation of an oxygen atom bound to Mn1; thus making it available for O-O bond formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

NASA Astrophysics Data System (ADS)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

Does Compound I Vary Significantly between Isoforms of Cytochrome P450?

PubMed Central

2011-01-01

The cytochrome P450 (CYP) enzymes are important in many areas, including pharmaceutical development. Subtle changes in the electronic structure of the active species, Compound I, have been postulated previously to account partly for the experimentally observed differences in reactivity between isoforms. Current predictive models of CYP metabolism typically assume an identical Compound I in all isoforms. Here we present a method to calculate the electronic structure and to estimate the Fe–O bond enthalpy of Compound I, and apply it to several human and bacterial CYP isoforms. Conformational flexibility is accounted for by sampling large numbers of structures from molecular dynamics simulations, which are subsequently optimized with density functional theory (B3LYP) based quantum mechanics/molecular mechanics. The observed differences in Compound I between human isoforms are small: They are generally smaller than the spread of values obtained for the same isoform starting from different initial structures. Hence, it is unlikely that the variation in activity between human isoforms is due to differences in the electronic structure of Compound I. A larger difference in electronic structure is observed between the human isoforms and P450cam and may be explained by the slightly different hydrogen-bonding environment surrounding the cysteinyl sulfur. The presence of substrate in the active site of all isoforms studied appears to cause a slight decrease in the Fe–O bond enthalpy, apparently due to displacement of water out of the active site, suggesting that Compound I is less stable in the presence of substrate. PMID:21863858

Luminescence studies of HgCdTe- and InAsSb-based quantum-well structures

NASA Astrophysics Data System (ADS)

Izhnin, I. I.; Izhnin, A. I.; Fitsych, O. I.; Voitsekhovskii, A. V.; Gorn, D. I.; Semakova, A. A.; Bazhenov, N. L.; Mynbaev, K. D.; Zegrya, G. G.

2018-04-01

Results of photoluminescence studies of single-quantum-well HgCdTe-based structures and electroluminescence studies of multiple-quantum-well InAsSb-based structures are reported. HgCdTe structures were grown with molecular beam epitaxy on GaAs substrates. InAsSb-based structures were grown with metal-organic chemical vapor deposition on InAs substrates. The common feature of luminescence spectra of all the structures was the presence of peaks with the energy much larger than that of calculated optical transitions between the first quantization levels for electrons and heavy holes. Possibility of observation of optical transitions between the quantization levels of electrons and first and/or second heavy and light hole levels is discussed in the paper in relation to the specifics of the electronic structure of the materials under consideration.

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

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Investigation on Fluorescence Quenching Mechanism of Perylene Diimide Dyes by Graphene Oxide.

PubMed

Zhao, Yuzhen; Li, Kexuan; He, Zemin; Zhang, Yongming; Zhao, Yang; Zhang, Haiquan; Miao, Zongcheng

2016-11-30

Perylene diimide derivatives were used as probes to investigate the effect of the molecular structures on the fluorescence quenching mechanism in a perylene diimide/graphene oxide system. The electrons transferred from the excited state of dyes to the conductive band of graphene oxide with different concentrations were determined by fluorescence spectra. The results indicated that the quenching efficiency of perylene diimides by graphene oxide was not only dependent on the difference between the lowest unoccupied molecular orbital level of dyes and the conduction band of the graphene oxide, but also mainly on the difference in the molecular structures.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

Electron transfer from alpha-keggin anions to dioxygen

Treesearch

Yurii V. Geletii; Rajai H. Atalla; Craig L. Hill; Ira A. Weinstock

2004-01-01

Polyoxometalates (POMs), of which alpha-Keggin anions are representative, are a diverse and rapidly growing class of water-soluble cluster-anion structures with applications ranging from molecular catalysis to materials. [1] POMs are inexpensive, minimally or non-toxic, negatively charged clusters comprised of early transition-metals, usually in their do electronic...

Photophysical Properties of Aromatic and Antiaromatic Porphyrinoids

DTIC Science & Technology

2011-04-14

possible to control the number of conjugated π-electrons by changing the number of connected pyrrole rings, ii) by providing a comparable set of [4n...Hexaphyrins: Effects of Confusion of Pyrrole Rings and Molecular Shape on Electronic Structures  Jong Min Lim, Jae Seok Lee, Hyun Woo Chung, Hee Won

Spin-dependent Otto quantum heat engine based on a molecular substance

NASA Astrophysics Data System (ADS)

Hübner, W.; Lefkidis, G.; Dong, C. D.; Chaudhuri, D.; Chotorlishvili, L.; Berakdar, J.

2014-07-01

We explore the potential of single molecules for thermodynamic cycles. To this end we propose two molecular heat engines based on the Ni2 dimer in the presence of a static magnetic field: (a) a quantum Otto engine and (b) a modified quantum Otto engine for which optical excitations induced by a laser pulse substitute for one of the heat-exchange points. For reliable predictions and to inspect the role of spin and electronic correlations we perform fully correlated ab initio calculations of the molecular electronic structure including spin-orbital effects. We analyze the efficiency of the engines in dependence of the electronic level scheme and the entanglement and find a significant possible enhancement connected to the quantum nature and the heat capacity of the dimer, as well as to the zero-field triplet states splitting.

Electron correlation by polarization of interacting densities

NASA Astrophysics Data System (ADS)

Whitten, Jerry L.

2017-02-01

Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus r12-1. A method of avoiding redundancy is described. Applications to atoms, negative ions, and molecules representing different types of bonding and spin states are discussed.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

DOE PAGES

Ophus, Colin; Ciston, Jim; Pierce, Jordan; ...

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, makingmore » it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Ultimately, simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.« less

X-ray absorption investigation of the electronic structure of the CuI@SWCNT nanocomposite

NASA Astrophysics Data System (ADS)

Generalov, A. V.; Brzhezinskaya, M. M.; Vinogradov, A. S.; Püttner, R.; Chernysheva, M. V.; Lukashin, A. V.; Eliseev, A. A.

2011-03-01

The Cu 2 p, I 3 d, and C 1 sX-ray absorption spectra of the CuI@SWCNT nanocomposite prepared by filling single-walled carbon nanotubes (SWCNTs) with the CuI melt by the capillary technique have been measured with a high-energy resolution using the equipment of the Russian-German beamline at the BESSY electron storage ring. In order to characterize the electronic structure of the nanocomposite and possible changes in the atomic and electronic structures of CuI and SWCNTs in the CuI@SWCNT nanocomposite, the spectra obtained have been analyzed in the framework of the quasi-molecular approach by comparing with the spectra of the pristine (CuI and SWCNT) and reference (CuO) systems. It has been revealed that the encapsulation of the CuI compound inside SWCNTs is accompanied by changes in the electronic structure of CuI and SWCNTs due to the chemical interaction between the filler and carbon nanotubes and the change in the atomic structure of CuI.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry.

PubMed

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R; Chess, Jordan; McMorran, Benjamin J; Czarnik, Cory; Rose, Harald H; Ercius, Peter

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

PubMed Central

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R.; Chess, Jordan; McMorran, Benjamin J.; Czarnik, Cory; Rose, Harald H.; Ercius, Peter

2016-01-01

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals. PMID:26923483

Highly charged ion based time of flight emission microscope

DOEpatents

Barnes, Alan V.; Schenkel, Thomas; Hamza, Alex V.; Schneider, Dieter H.; Doyle, Barney

2001-01-01

A highly charged ion based time-of-flight emission microscope has been designed, which improves the surface sensitivity of static SIMS measurements because of the higher ionization probability of highly charged ions. Slow, highly charged ions are produced in an electron beam ion trap and are directed to the sample surface. The sputtered secondary ions and electrons pass through a specially designed objective lens to a microchannel plate detector. This new instrument permits high surface sensitivity (10.sup.10 atoms/cm.sup.2), high spatial resolution (100 nm), and chemical structural information due to the high molecular ion yields. The high secondary ion yield permits coincidence counting, which can be used to enhance determination of chemical and topological structure and to correlate specific molecular species.

Theoretical calculations of Electron Paramagnetic Resonance parameters of liquid phase Orotic acid radical

NASA Astrophysics Data System (ADS)

Sarikaya, Ebru Karakaş; Dereli, Ömer

2017-02-01

To obtain liquid phase molecular structure, conformational analysis of Orotic acid was performed and six conformers were determined. For these conformations, eight possible radicals were modelled by using Density Functional Theory computations with respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were performed using Becke's three-parameter hybrid-exchange functional combined with the Lee-Yang-Parr correlation functional of Density Functional Theory and 6-311++G(d,p) basis sets in p-dioxane solution. Because Orotic acid can be mutagenic in mammalian somatic cells and it is also mutagenic for bacteria and yeast, it has been studied.

The effect of annulation of benzene rings on the photophysics and electronic structure of tetraazachlorin molecules

NASA Astrophysics Data System (ADS)

Pershukevich, P. P.; Volkovich, D. I.; Gladkov, L. L.; Dudkin, S. V.; Kuzmitsky, V. A.; Makarova, E. A.; Solovyev, K. N.

2017-10-01

The photophysics and electronic structure of tribenzotetraazachlorins (H2, Zn, and Mg), which are novel analogues of phtalocyanines, have been studied experimentally and theoretically. At 293 K, the electronic absorption, fluorescence, and fluorescence excitation spectra are recorded and the fluorescence quantum yield and lifetime, as well as the quantum yield of singlet oxygen generation, are measured; at 77 K, the fluorescence, fluorescence excitation, and fluorescence polarization spectra are recorded and the fluorescence lifetime values are measured. The dependences of the absorption spectra and photophysical parameters on the structure variation are analyzed in detail. Quantum-chemical calculations of the electronic structure and absorption spectra of tribenzotetraazachlorins (H2, Mg) are performed using the INDO/Sm method (modified INDO/S method) based on molecular-geometry optimization by the DFT PBE/TZVP method. The results of quantum-chemical calculations of the electronic absorption spectra are in very good agreement with the experimental data for the transitions to two lower electronic states.

Anisotropy induced Kondo splitting in a mechanically stretched molecular junction: A first-principles based study

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

Wang, Xiaoli; Hou, Dong, E-mail: houdong@ustc.edu.cn; Zheng, Xiao, E-mail: xz58@ustc.edu.cn

2016-01-21

The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy–SH){sub 2} sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It ismore » confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.« less

Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

PubMed

Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

2016-08-17

Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

Mapping molecular motions leading to charge delocalization with ultrabright electrons

NASA Astrophysics Data System (ADS)

Sciaini, German

2014-05-01

Ultrafast diffraction has broken the barrier to atomic exploration by combining the atomic spatial resolution of diffraction techniques with the temporal resolution of ultrafast spectroscopy. X-ray free electron lasers, slicing techniques and femtosecond laser-driven X-ray and electron sources have been successfully applied for the study of ultrafast structural dynamics in a variety of samples. Yet, the application of fs-diffraction to the study of rather sensitive organic molecular crystals remains unexplored. Organic crystals are composed by weak scattering centres, often present low melting points, poor heat conductivity and are, typically, radiation sensitive. Low repetition rates (about tens of Hertz) are therefore required to overcome accumulative heating effects from the laser excitation that can degrade the sample and mask the structural dynamics. This imparts tremendous constraints on source brightness to acquire enough diffraction data before adverse photo-degradation effects have played a non-negligible role in the crystalline structure. We implemented ultra-bright femtosecond electron diffraction to obtain a movie of the relevant molecular motions driving the photo-induced insulator-to-metal phase transition in the organic charge-transfer salt (EDO-TTF)2PF6. On the first few picoseconds (0 - 10 ps) the structural evolution, well-described by three main reaction coordinates, reaches a transient intermediate state (TIS). Model structural refinement calculations indicate that fast sliding of flat EDO-TTF molecules with consecutive motion of PF6 counter-ions drive the formation of TS instead of the expected flattening of initially bent EDO-TTF moieties which seems to evolve through a slower thermal pathway that brings the system into a final high temperature-type state. These findings establish the potential of ultrabright femtosecond electron sources for probing the primary processes governing structural dynamics with atomic resolution in labile systems relevant to chemistry and biology. For more information vide-infra Gao et al., Funding for this project was provided by the Natural Sciences and Engineering Research Council of Canada and the Canada Foundation for Innovation and Grant Agencies in Japan, vide infra Nature reference for more details.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

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.

The Relationship Between Chemical Structure and Dielectric Properties of Plasma-Enhanced Chemical Vapor Deposited Polymer Thin Films (Postprint)

DTIC Science & Technology

2007-01-01

C6H6, Aldrich Co., liquid , high performance liquid chromatography (HPLC) grade with a purity of 99.9%) and octafluorocyclobutane (C4F8, OFCB...attributed to the lack of molecular mobility (confined by the crosslinking) and low ionic polarization of the molecular structures [6]. The frequency...in dielectric constant at low frequencies can be traced to orientational polarizations of trapped free radicals, unpaired electron sites, oligomeric

Heavy ion track-structure calculations for radial dose in arbitrary materials

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Katz, Robert; Wilson, John W.; Dubey, Rajendra R.

1995-01-01

The delta-ray theory of track structure is compared with experimental data for the radial dose from heavy ion irradiation. The effects of electron transmission and the angular dependence of secondary electron ejection are included in the calculations. Several empirical formulas for electron range and energy are compared in a wide variety of materials in order to extend the application of the track-structure theory. The model of Rudd for the secondary electron-spectrum in proton collisions, which is based on a modified classical kinematics binary encounter model at high energies and a molecular promotion model at low energies, is employed. For heavier projectiles, the secondary electron spectrum is found by scaling the effective charge. Radial dose calculations for carbon, water, silicon, and gold are discussed. The theoretical data agreed well with the experimental data.

Electric Field Tuning Molecular Packing and Electrical Properties of Solution-Shearing Coated Organic Semiconducting Thin Films

DOE PAGES

Molina-Lopez, Francisco; Yan, Hongping; Gu, Xiaodan; ...

2017-01-17

Recent improvements in solution-coated organic semiconductors (OSCs) evidence their high potential for cost-efficient organic electronics and sensors. Molecular packing structure determines the charge transport property of molecular solids. However, it remains challenging to control the molecular packing structure for a given OSC. Here, the application of alternating electric fields is reported to fine-tune the crystal packing of OSC solution-shearing coated at ambient conditions. First, a theoretical model based on dielectrophoresis is developed to guide the selection of the optimal conditions (frequency and amplitude) of the electric field applied through the solution-shearing blade during coating of OSC thin films. Next, electricmore » field-induced polymorphism is demonstrated for OSCs with both herringbone and 2D brick-wall packing motifs in 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene and 6,13-bis(triisopropylsilylethynyl) pentacene, respectively. Favorable molecular packing can be accessible in some cases, resulting in higher charge carrier mobilities. In conclusion, this work provides a new approach to tune the properties of solution-coated OSCs in functional devices for high-performance printed electronics.« less

Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid State NMR

PubMed Central

Luca, Sorin; Yau, Wai-Ming; Leapman, Richard; Tycko, Robert

2008-01-01

The 37-residue amylin peptide, also known as islet amyloid polypeptide, forms fibrils that are the main peptide or protein component of amyloid that develops in the pancreas of type 2 diabetes patients. Amylin also readily forms amyloid fibrils in vitro that are highly polymorphic under typical experimental conditions. We describe a protocol for the preparation of synthetic amylin fibrils that exhibit a single predominant morphology, which we call a striated ribbon, in electron microscope and atomic force microscope images. Solid state nuclear magnetic resonance (NMR) measurements on a series of isotopically labeled samples indicate a single molecular structure within the striated ribbons. We use scanning transmission electron microscopy and several types of one-dimensional and two-dimensional solid state NMR techniques to obtain constraints on the peptide conformation and supramolecular structure in these amylin fibrils, and derive molecular structural models that are consistent with the experimental data. The basic structural unit in amylin striated ribbons, which we call the protofilament, contains four-layers of parallel β-sheets, formed by two symmetric layers of amylin molecules. The molecular structure of amylin protofilaments in striated ribbons closely resembles the protofilament in amyloid fibrils with similar morphology formed by the 40-residue β-amyloid peptide that is associated with Alzheimer's disease. PMID:17979302

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

PubMed Central

Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

2016-01-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

Amyloid Structure and Assembly: Insights from Scanning Transmission Electron Microscopy

PubMed Central

Goldsbury, Claire; Baxa, Ulrich; Simon, Martha N.; Steven, Alasdair C.; Engel, Andreas; Wall, Joseph S.; Aebi, Ueli; Müller, Shirley A.

2010-01-01

Amyloid fibrils are filamentous protein aggregates implicated in several common diseases like Alzheimer’s disease and type II diabetes. Similar structures are also the molecular principle of the infectious spongiform encephalopathies like Creutzfeldt-Jakob disease in humans, scrapie in sheep, and of the so-called yeast prions, inherited non-chromosomal elements found in yeast and fungi. Scanning transmission electron microscopy (STEM) is often used to delineate the assembly mechanism and structural properties of amyloid aggregates. In this review we consider specifically contributions and limitations of STEM for the investigation of amyloid assembly pathways, fibril polymorphisms and structural models of amyloid fibrils. This type of microscopy provides the only method to directly measure the mass-per-length (MPL) of individual filaments. Made on both in vitro assembled and ex vivo samples, STEM mass measurements have illuminated the hierarchical relationships between amyloid fibrils and revealed that polymorphic fibrils and various globular oligomers can assemble simultaneously from a single polypeptide. The MPLs also impose strong constraints on possible packing schemes, assisting in molecular model building when combined with high-resolution methods like solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). PMID:20868754

Modulation of electronic structures of bases through DNA recognition of protein.

PubMed

Hagiwara, Yohsuke; Kino, Hiori; Tateno, Masaru

2010-04-21

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.

Infrared vibrational nanocrystallography and nanoimaging

PubMed Central

Muller, Eric A.; Pollard, Benjamin; Bechtel, Hans A.; van Blerkom, Peter; Raschke, Markus B.

2016-01-01

Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids. PMID:27730212

Isolated molecular dopants in pentacene observed by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Ha, Sieu D.; Kahn, Antoine

2009-11-01

Doping is essential to the control of electronic structure and conductivity of semiconductor materials. Whereas doping of inorganic semiconductors is well established, doping of organic molecular semiconductors is still relatively poorly understood. Using scanning tunneling microscopy, we investigate, at the molecular scale, surface and subsurface tetrafluoro-tetracyanoquinodimethane p -dopants in the prototypical molecular semiconductor pentacene. Surface dopants diffuse to pentacene vacancies and appear as negatively charged centers, consistent with the standard picture of an ionized acceptor. Subsurface dopants, however, have the effect of a positive charge, evidence that the donated hole is localized by the parent acceptor counterion, in contrast to the model of doping in inorganic semiconductors. Scanning tunneling spectroscopy shows that the electron potential energy is locally lowered near a subsurface dopant feature, in agreement with the localized hole model.

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

High-Resolution Laser Spectroscopy of Free Radicals in Nearly Degenerate Electronic States

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2017-06-01

Rovibronic structure of molecules in orbitally degenerate electronic states including Renner-Teller (RT) and Jahn-Teller (JT) active molecules has been extensively studied. Less is known about rotational structure of polyatomic molecules in nearly degenerate states, especially those with low (e.g., C_s) symmetry that are subject to the pseudo-Jahn-Teller (pJT) effect. In the case of free radicals, the unpaired electron further complicates energy levels by inducing spin-orbit (SO) and spin-rotation (SR) splittings. Asymmetric deuteration or methyl substitution of C_{3v} free radicals such as CH_3O, CaCH_3, and CaOCH_3 lowers the molecular symmetry, lifts the vibronic degeneracy, and reduces the JT effect to the pJT effect. New spectroscopic models are required to reproduce the rovibronic structure and simulate the experimentally obtained spectra of pJT-active free radicals. It has been found that rotational and fine-structure analysis of spectra involving nearly degenerate states may aid in vibronic analysis and interpretation of effective molecular constants. Especially, SO and Coriolis interactions that couple the two states can be determined accurately from fitting the experimental spectra. Coupling between the two electronic states also affects the intensities of rotational and vibronic transitions. The study on free radicals in nearly degenerate states provides a promising avenue of research which may bridge the gap between symmetry-induced degenerate states and the Born-Oppenheimer (BO) limit of unperturbed electronic states.

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.

Ultrafast electron microscopy integrated with a direct electron detection camera.

PubMed

Lee, Young Min; Kim, Young Jae; Kim, Ye-Jin; Kwon, Oh-Hoon

2017-07-01

In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM), which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates. This approach is expected to promote UEM to a more powerful platform to visualize molecular and collective motions and dissect fundamental physical, chemical, and materials phenomena in space and time.

Systematic Analysis of Polymer Molecular Weight Influence on the Organic Photovoltaic Performance.

PubMed

Katsouras, Athanasios; Gasparini, Nicola; Koulogiannis, Chrysanthos; Spanos, Michael; Ameri, Tayebeh; Brabec, Christoph J; Chochos, Christos L; Avgeropoulos, Apostolos

2015-10-01

The molecular weight of an electron donor-conjugated polymer is as essential as other well-known parameters in the chemical structure of the polymer, such as length and the nature of any side groups (alkyl chains) positioned on the polymeric backbone, as well as their placement, relative strength, the ratio of the donor and acceptor moieties in the backbone of donor-acceptor (D-A)-conjugated polymers, and the arrangement of their energy levels for organic photovoltaic performance. Finding the "optimal" molecular weight for a specific conjugated polymer is an important aspect for the development of novel photovoltaic polymers. Therefore, it is evident that the chemistry of functional conjugated polymers faces major challenges and materials have to adopt a broad range of specifications in order to be established for high photovoltaic performance. In this review, the approaches followed for enhancing the molecular weight of electron-donor polymers are presented in detail, as well as how this influences the optoelectronic properties, charge transport properties, structural conformation, morphology, and the photovoltaic performance of the active layer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

XAFS and XEOL of tetramesityldigermene - An electronic structure study of a heavy group 14 ethylene analogue

NASA Astrophysics Data System (ADS)

Ward, Matthew J.; Rupar, Paul A.; Murphy, Michael W.; Yiu, Yun-Mui; Baines, Kim M.; Sham, Tsun-Kong

2013-04-01

Digermene, the germanium analogue of ethylene, has a multiple bonding motif that differs greatly from that of alkenes and exhibits no pure σ or π type bonds. The electronic structure of digermenes is difficult to study experimentally due to their reactivity, and is computationally challenging because of their shallow potential energy surfaces. Using X-ray absorption near edge structures at both the germanium K and L edges we have been able to directly probe the unoccupied electronic states, or the lowest unoccupied molecular orbital (LUMO), and LUMO+ etc. in the Ge=Ge bond of tetramesityldigermene. We have demonstrated that the LUMO, LUMO+, etc. are composed of hybrid Ge 4s and 4p orbitals. Additionally, our data suggest that the LUMO exhibits relatively more Ge 4s character, whereas the LUMO+ and LUMO+2 exhibit relatively more Ge 4p character. An X-ray excited optical luminescence study of Ge2Mes4 revealed one broad optical emission band at 620 nm, which is significantly red shifted compared to the known energy gap of this molecular germanium compound.

Nanopatterning on calixarene thin films via low-energy field-emission scanning probe lithography.

PubMed

He, Xiaoyue; Li, Peng; Liu, Pengchong; Zhang, Xiaoxian; Zhou, Xiangqian; Liu, Wei; Qiu, Xiaohui

2018-08-10

Field-emitted, low-energy electrons from the conducting tip of an atomic force microscope were adopted for nanolithography on calixarene ultrathin films coated on silicon wafers. A structural evolution from protrusion to depression down to a 30 nm spatial resolution was reproducibly obtained by tuning the sample voltage and exposure current in the lithography process. Close analyses of the profiles showed that the nanostructures formed by a single exposure with a high current are almost identical to those created by cumulative exposure with a lower current but an equal number of injected electrons. Surface potential imaging by Kelvin probe force microscopy found a negatively charged region surrounding the groove structures once the structures were formed. We conclude that the mechanism related to the formation of a temporary negative state and molecule decomposition, rather than thermal ablation, is responsible for the low-energy field-emission electron lithography on a calixarene molecular resist. We hope that our elucidation of the underlying mechanism is helpful for molecular resist design and further improving the reproducibility and throughput of nanolithography.

Growing Cobalt Silicide Columns In Silicon

NASA Technical Reports Server (NTRS)

Fathauer, Obert W.

1991-01-01

Codeposition by molecular-beam epitaxy yields variety of structures. Proposed fabrication process produces three-dimensional nanometer-sized structures on silicon wafers. Enables control of dimensions of metal and semiconductor epitaxial layers in three dimensions instead of usual single dimension (perpendicular to the plane of the substrate). Process used to make arrays of highly efficient infrared sensors, high-speed transistors, and quantum wires. For fabrication of electronic devices, both shapes and locations of columns controlled. One possible technique for doing this electron-beam lithography, see "Making Submicron CoSi2 Structures on Silicon Substrates" (NPO-17736).

Synthesis of Norbornene Derived Helical Copolymer by Simple Molecular Marriage Approach to Produce Smart Nanocarrier

NASA Astrophysics Data System (ADS)

Mane, Shivshankar R.; Sathyan, Ashlin; Shunmugam, Raja

2017-03-01

A novel library of norbornene derived helical copolymer has been synthesized through the coupling of two homopolymers via Molecular Marriage Approach. The helicity is governed by the non-covalent interactions like hydrogen bonding, π-π stacking and the influence of hydrophobic and hydrophilic motifs. The detailed characterization of the copolymer (Copoly 1) has been provided and the super structures are confirmed through dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The observed size of the aggregates was about 200 nm. The density functional theory (DFT) is favorably supported for the formation of proposed structure of Copoly 1. Circular dichroism (CD) measurement has confirmed the one handed helical structure of the copolymer. Reservoir capability of this pH responsive polymer (Copoly 1) to encapsulate anti-cancer drug doxorubicin (DOX) warrants its potential applications in the field of bio-medical sciences.

Synthesis of Norbornene Derived Helical Copolymer by Simple Molecular Marriage Approach to Produce Smart Nanocarrier.

PubMed

Mane, Shivshankar R; Sathyan, Ashlin; Shunmugam, Raja

2017-03-22

A novel library of norbornene derived helical copolymer has been synthesized through the coupling of two homopolymers via Molecular Marriage Approach. The helicity is governed by the non-covalent interactions like hydrogen bonding, π-π stacking and the influence of hydrophobic and hydrophilic motifs. The detailed characterization of the copolymer (Copoly 1) has been provided and the super structures are confirmed through dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The observed size of the aggregates was about 200 nm. The density functional theory (DFT) is favorably supported for the formation of proposed structure of Copoly 1. Circular dichroism (CD) measurement has confirmed the one handed helical structure of the copolymer. Reservoir capability of this pH responsive polymer (Copoly 1) to encapsulate anti-cancer drug doxorubicin (DOX) warrants its potential applications in the field of bio-medical sciences.

Contributions of Phenoxazone-Based Pigments to the Structure and Function of Nanostructured Granules in Squid Chromatophores.

PubMed

Williams, Thomas L; DiBona, Christopher W; Dinneen, Sean R; Labadie, Stephanie F Jones; Chu, Feixia; Deravi, Leila F

2016-04-19

Understanding the structure-function relationships of pigment-based nanostructures can provide insight into the molecular mechanisms behind biological signaling, camouflage, or communication experienced in many species. In squid Doryteuthis pealeii, combinations of phenoxazone-based pigments are identified as the source of visible color within the nanostructured granules that populate dermal chromatophore organs. In the absence of the pigments, granules experience a reduction in diameter with the loss of visible color, suggesting important structural and functional features. Energy gaps are estimated from electronic absorption spectra, revealing highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energies that are dependent upon the varying carboxylated states of the pigment. These results implicate a hierarchical mechanism for the bulk coloration in cephalopods originating from the molecular components confined within in the nanostructured granules of chromatophore organs.

Future directions of electron crystallography.

PubMed

Fujiyoshi, Yoshinori

2013-01-01

In biological science, there are still many interesting and fundamental yet difficult questions, such as those in neuroscience, remaining to be answered. Structural and functional studies of membrane proteins, which are key molecules of signal transduction in neural and other cells, are essential for understanding the molecular mechanisms of many fundamental biological processes. Technological and instrumental advancements of electron microscopy have facilitated comprehension of structural studies of biological components, such as membrane proteins. While X-ray crystallography has been the main method of structure analysis of proteins including membrane proteins, electron crystallography is now an established technique to analyze structures of membrane proteins in the lipid bilayer, which is close to their natural biological environment. By utilizing cryo-electron microscopes with helium-cooled specimen stages, structures of membrane proteins were analyzed at a resolution better than 3 Å. Such high-resolution structural analysis of membrane proteins by electron crystallography opens up the new research field of structural physiology. Considering the fact that the structures of integral membrane proteins in their native membrane environment without artifacts from crystal contacts are critical in understanding their physiological functions, electron crystallography will continue to be an important technology for structural analysis. In this chapter, I will present several examples to highlight important advantages and to suggest future directions of this technique.

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.

Carbon Nanomembranes

NASA Astrophysics Data System (ADS)

Angelova, Polina; Gölzhäuser, Armin

2017-03-01

This chapter describes the formation and properties of one nanometer thick carbon nanomembranes (CNMs), made by electron induced cross-linking of aromatic self-assembled monolayers (SAMs). The cross-linked SAMs are robust enough to be released from the surface and placed on solid support or over holes as free-standing membranes. Annealing at 1000K transforms CNMs into graphene accompanied by a change of mechanical stiffness and electrical resistance. The developed fabrication approach is scalable and provides molecular level control over thickness and homogeneity of the produced CNMs. The mechanisms of electron-induced cross-linking process are discussed in details. A variety of polyaromatic thiols: oligophenyls as well as small and extended condensed polycyclic hydrocarbons have been successfully employed, demonstrating that the structural and functional properties of the resulting nanomembranes are strongly determined by the structure of molecular monolayers. The mechanical properties of CNMs (Young's modulus, tensile strength and prestress) are characterized by bulge testing. The interpretation of the bulge test data relates the Young's modulus to the properties of single molecules and to the structure of the pristine SAMs. The gas transport through the CNM is measured onto polydimethylsiloxane (PDMS) - thin film composite membrane. The established relationship of permeance and molecular size determines the molecular sieving mechanism of permeation through this ultrathin sheet.

Charge transport in molecular junctions: From tunneling to hopping with the probe technique

NASA Astrophysics Data System (ADS)

Kilgour, Michael; Segal, Dvira

2015-07-01

We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-Büttiker's probe technique" can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, kBT/ɛB > 1/25, with ɛB as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker's probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

Application of semiempirical electronic structure theory to compute the force generated by a single surface-mounted switchable rotaxane.

PubMed

Sohlberg, Karl; Bazargan, Gloria; Angelo, Joseph P; Lee, Choongkeun

2017-01-01

Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391-5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100-200 pN range, consistent with published experimental estimates. Graphical Abstract A single surface-mounted switchable rotaxane.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

PubMed

Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

2014-11-18

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Organic heterojunctions: Contact-induced molecular reorientation, interface states, and charge re-distribution

PubMed Central

Opitz, Andreas; Wilke, Andreas; Amsalem, Patrick; Oehzelt, Martin; Blum, Ralf-Peter; Rabe, Jürgen P.; Mizokuro, Toshiko; Hörmann, Ulrich; Hansson, Rickard; Moons, Ellen; Koch, Norbert

2016-01-01

We reveal the rather complex interplay of contact-induced re-orientation and interfacial electronic structure – in the presence of Fermi-level pinning – at prototypical molecular heterojunctions comprising copper phthalocyanine (H16CuPc) and its perfluorinated analogue (F16CuPc), by employing ultraviolet photoelectron and X-ray absorption spectroscopy. For both layer sequences, we find that Fermi-level (EF) pinning of the first layer on the conductive polymer substrate modifies the work function encountered by the second layer such that it also becomes EF-pinned, however, at the interface towards the first molecular layer. This results in a charge transfer accompanied by a sheet charge density at the organic/organic interface. While molecules in the bulk of the films exhibit upright orientation, contact formation at the heterojunction results in an interfacial bilayer with lying and co-facial orientation. This interfacial layer is not EF-pinned, but provides for an additional density of states at the interface that is not present in the bulk. With reliable knowledge of the organic heterojunction’s electronic structure we can explain the poor performance of these in photovoltaic cells as well as their valuable function as charge generation layer in electronic devices. PMID:26887445

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.

Computational Evaluation of Amorphous Carbon Coating for Durable Silicon Anodes for Lithium-Ion Batteries

PubMed Central

Hwang, Jeongwoon; Ihm, Jisoon; Lee, Kwang-Ryeol; Kim, Seungchul

2015-01-01

We investigate the structural, mechanical, and electronic properties of graphite-like amorphous carbon coating on bulky silicon to examine whether it can improve the durability of the silicon anodes of lithium-ion batteries using molecular dynamics simulations and ab-initio electronic structure calculations. Structural models of carbon coating are constructed using molecular dynamics simulations of atomic carbon deposition with low incident energies (1–16 eV). As the incident energy decreases, the ratio of sp2 carbons increases, that of sp3 decreases, and the carbon films become more porous. The films prepared with very low incident energy contain lithium-ion conducting channels. Also, those films are electrically conductive to supplement the poor conductivity of silicon and can restore their structure after large deformation to accommodate the volume change during the operations. As a result of this study, we suggest that graphite-like porous carbon coating on silicon will extend the lifetime of the silicon anodes of lithium-ion batteries. PMID:28347087

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Computational Evaluation of Amorphous Carbon Coating for Durable Silicon Anodes for Lithium-Ion Batteries.

PubMed

Hwang, Jeongwoon; Ihm, Jisoon; Lee, Kwang-Ryeol; Kim, Seungchul

2015-10-13

We investigate the structural, mechanical, and electronic properties of graphite-like amorphous carbon coating on bulky silicon to examine whether it can improve the durability of the silicon anodes of lithium-ion batteries using molecular dynamics simulations and ab-initio electronic structure calculations. Structural models of carbon coating are constructed using molecular dynamics simulations of atomic carbon deposition with low incident energies (1-16 eV). As the incident energy decreases, the ratio of sp ² carbons increases, that of sp ³ decreases, and the carbon films become more porous. The films prepared with very low incident energy contain lithium-ion conducting channels. Also, those films are electrically conductive to supplement the poor conductivity of silicon and can restore their structure after large deformation to accommodate the volume change during the operations. As a result of this study, we suggest that graphite-like porous carbon coating on silicon will extend the lifetime of the silicon anodes of lithium-ion batteries.

Electronic structure and molecular dynamics of Na2Li

NASA Astrophysics Data System (ADS)

Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

NASA Astrophysics Data System (ADS)

Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

2015-02-01

Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

Oligomer Molecules for Efficient Organic Photovoltaics.

PubMed

Lin, Yuze; Zhan, Xiaowei

2016-02-16

Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability, and film-forming properties. Therefore, OMs are a good choice for solution-processed reproducible OSCs toward scalable commercialized applications. Considerable efforts have been dedicated to developing new OM electron donors and electron acceptors for OSCs. So far, the highest PCEs of solution-processed OSCs based on OM donors and acceptors are 9-10% and 6-7%, respectively. OM materials have become promising alternatives to polymer and/or fullerene materials for efficient and stable OSCs. In this Account, we present a brief survey of the recent developments in solution-processable OM electron donors and acceptors and their application in OSCs. Rational design of OMs with star- and linear-shaped structures based on triphenylamine, benzodithiophene, and indacenodithiophene units and their impacts on device performance are discussed. Structure-property relationships are also proposed. Furthermore, the remaining challenges and the key research directions in the near future are also addressed. In the next years, an interdisciplinary approach involving novel OM materials, especially electron acceptor materials, accurate morphology optimization, and advanced device technologies will probably bring high-efficiency and stable OSCs to final commercialization.

π-Extended Isoindigo-Based Derivative: A Promising Electron-Deficient Building Block for Polymer Semiconductors.

PubMed

Xu, Long; Zhao, Zhiyuan; Xiao, Mingchao; Yang, Jie; Xiao, Jian; Yi, Zhengran; Wang, Shuai; Liu, Yunqi

2017-11-22

The exploration of novel electron-deficient building blocks is a key task for developing high-performance polymer semiconductors in organic thin-film transistors. In view of the situation of the lack of strong electron-deficient building blocks, we designed two novel π-extended isoindigo-based electron-deficient building blocks, IVI and F 4 IVI. Owing to the strong electron-deficient nature and the extended π-conjugated system of the two acceptor units, their copolymers, PIVI2T and PF 4 IVI2T, containing 2,2'-bithiophene donor units, are endowed with deep-lying highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels and strong intermolecular interactions. In comparison to PIVI2T, the fluorinated PF 4 IVI2T exhibits stronger intra- and intermolecular interactions, lower HOMO/LUMO energy levels up to -5.74/-4.17 eV, and more ordered molecular packing with a smaller π-π stacking distance of up to 3.53 Å, resulting in an excellent ambipolar transporting behavior and a promising application in logic circuits for PF 4 IVI2T in ambient with hole and electron mobilities of up to 1.03 and 1.82 cm 2 V -1 s -1 , respectively. The results reveal that F 4 IVI is a promising and strong electron-deficient building unit to construct high-performance semiconducting polymers, which provides an insight into the structure-property relationships for the exploration and molecular engineering of excellent electron-deficient building blocks in the field of organic electronics.

The high-pressure electronic structure of magnesiowustite (Mg, Fe)O: applications to the physics and chemistry of the lower mantle

USGS Publications Warehouse

Sherman, David M.

1991-01-01

The electronic structure of magnesiowustite is investigated using self-consistent field X?? scattered wave (SCF-X??-SW) molecular orbital calculations on (FeO6)10- and (FeMg12O14)2- clusters. Calculated one-electron transition energies are used to interpret the optical spectrum of (Mg, Fe)O. The results are applied to the electrical and thermal conductivity of the lower mantle. This is especially true if Fe2+ adopts the low-spin configuration. The geophysically significant properties of (Fe, Mg)O probably result from defect Fe3+. -from Author

The World as Viewed by and with Unpaired Electrons

PubMed Central

Eaton, Sandra S.; Eaton, Gareth R.

2012-01-01

Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models. PMID:22975244

Characterization of pi-Conjugated Polymers for Transistor and Photovoltaic Applications

NASA Astrophysics Data System (ADS)

Paulsen, Bryan D.

pi-Conjugated polymers represent a unique class of optoelectronic materials. Being polymers, they are solution processable and inherently "soft" materials. This makes them attractive candidates for the production of roll-to-roll printed electronic devices on flexible substrates. The optical and electronic properties of pi-conjugated polymers are synthetically tunable allowing material sets to be tailored to specific applications. Two of the most heavily researched applications are the thin film transistor, the building block of electronic circuits, and the bulk heterojunction solar cell, which holds great potential as a renewable energy source. Key to developing commercially feasible pi-conjugated polymer devices is a thorough understanding of the electronic structure and charge transport behavior of these materials in relationship with polymer structure. Here this structure property relationship has been investigated through electrical and electrochemical means in concert with a variety of other characterization techniques and device test beds. The tunability of polymer optical band gap and frontier molecular orbital energy level was investigated in systems of vinyl incorporating statistical copolymers. Energy levels and band gaps are crucial parameters in developing efficient photovoltaic devices, with control of these parameters being highly desirable. Additionally, charge transport and density of electronic states were investigated in pi-conjugated polymers at extremely high electrochemically induced charge density. Finally, the effects of molecular weight on pi-conjugated polymer optical properties, energy levels, charge transport, morphology, and photovoltaic device performance was examined.

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.

Bohm's Quantum Potential and the Visualization of Molecular Structure

NASA Technical Reports Server (NTRS)

Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

Defect formation in fluoropolymer films at their condensation from a gas phase

NASA Astrophysics Data System (ADS)

Luchnikov, P. A.

2018-01-01

The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

c -Axis Dimer and Its Electronic Breakup: The Insulator-to-Metal Transition in Ti2 O3

NASA Astrophysics Data System (ADS)

Chang, C. F.; Koethe, T. C.; Hu, Z.; Weinen, J.; Agrestini, S.; Zhao, L.; Gegner, J.; Ott, H.; Panaccione, G.; Wu, Hua; Haverkort, M. W.; Roth, H.; Komarek, A. C.; Offi, F.; Monaco, G.; Liao, Y.-F.; Tsuei, K.-D.; Lin, H.-J.; Chen, C. T.; Tanaka, A.; Tjeng, L. H.

2018-04-01

We report on our investigation of the electronic structure of Ti2 O3 using (hard) x-ray photoelectron and soft x-ray absorption spectroscopy. From the distinct satellite structures in the spectra, we have been able to establish unambiguously that the Ti-Ti c -axis dimer in the corundum crystal structure is electronically present and forms an a1 ga1 g molecular singlet in the low-temperature insulating phase. Upon heating, we observe a considerable spectral weight transfer to lower energies with orbital reconstruction. The insulator-metal transition may be viewed as a transition from a solid of isolated Ti-Ti molecules into a solid of electronically partially broken dimers, where the Ti ions acquire additional hopping in the a -b plane via the egπ channel, the opening of which requires consideration of the multiplet structure of the on-site Coulomb interaction.

Nanoscale probing of electron-regulated structural transitions in silk proteins by near-field IR imaging and nano-spectroscopy

PubMed Central

Qin, Nan; Zhang, Shaoqing; Jiang, Jianjuan; Corder, Stephanie Gilbert; Qian, Zhigang; Zhou, Zhitao; Lee, Woonsoo; Liu, Keyin; Wang, Xiaohan; Li, Xinxin; Shi, Zhifeng; Mao, Ying; Bechtel, Hans A.; Martin, Michael C.; Xia, Xiaoxia; Marelli, Benedetto; Kaplan, David L.; Omenetto, Fiorenzo G.; Liu, Mengkun; Tao, Tiger H.

2016-01-01

Silk protein fibres produced by silkworms and spiders are renowned for their unparalleled mechanical strength and extensibility arising from their high-β-sheet crystal contents as natural materials. Investigation of β-sheet-oriented conformational transitions in silk proteins at the nanoscale remains a challenge using conventional imaging techniques given their limitations in chemical sensitivity or limited spatial resolution. Here, we report on electron-regulated nanoscale polymorphic transitions in silk proteins revealed by near-field infrared imaging and nano-spectroscopy at resolutions approaching the molecular level. The ability to locally probe nanoscale protein structural transitions combined with nanometre-precision electron-beam lithography offers us the capability to finely control the structure of silk proteins in two and three dimensions. Our work paves the way for unlocking essential nanoscopic protein structures and critical conditions for electron-induced conformational transitions, offering new rules to design protein-based nanoarchitectures. PMID:27713412

FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem

NASA Astrophysics Data System (ADS)

Levin, Alan R.; Zhang, Deyin; Polizzi, Eric

2012-11-01

In a recent article Polizzi (2009) [15], the FEAST algorithm has been presented as a general purpose eigenvalue solver which is ideally suited for addressing the numerical challenges in electronic structure calculations. Here, FEAST is presented beyond the “black-box” solver as a fundamental modeling framework which can naturally address the original numerical complexity of the electronic structure problem as formulated by Slater in 1937 [3]. The non-linear eigenvalue problem arising from the muffin-tin decomposition of the real-space domain is first derived and then reformulated to be solved exactly within the FEAST framework. This new framework is presented as a fundamental and practical solution for performing both accurate and scalable electronic structure calculations, bypassing the various issues of using traditional approaches such as linearization and pseudopotential techniques. A finite element implementation of this FEAST framework along with simulation results for various molecular systems is also presented and discussed.

Conduction mechanism of nitronyl-nitroxide molecular magnetic compounds

NASA Astrophysics Data System (ADS)

Dotti, N.; Heintze, E.; Slota, M.; Hübner, R.; Wang, F.; Nuss, J.; Dressel, M.; Bogani, L.

2016-04-01

We investigate the conduction mechanisms of nitronyl-nitroxide (NIT) molecular radicals, as useful for the creation of nanoscopic molecular spintronic devices, finding that it does not correspond to standard Mott behavior, as previously postulated. We provide a complete investigation using transport measurements, low-energy, sub-THz spectroscopy and introducing differently substituted phenyl appendages. We show that a nontrivial surface-charge-limited regime is present in addition to the standard low-voltage Ohmic conductance. Scaling analysis allows one to determine all the main transport parameters for the compounds and highlights the presence of charge-trapping effects. Comparison among the different compounds shows the relevance of intermolecular stacking between the aromatic ring of the phenyl appendix and the NIT motif in the creation of useful electron transport channels. The importance of intermolecular pathways is further highlighted by electronic structure calculations, which clarify the nature of the electronic channels and their effect on the Mott character of the compounds.

Rotary ATPases

PubMed Central

Stewart, Alastair G.; Sobti, Meghna; Harvey, Richard P.; Stock, Daniela

2013-01-01

Rotary ATPases are molecular rotary motors involved in biological energy conversion. They either synthesize or hydrolyze the universal biological energy carrier adenosine triphosphate. Recent work has elucidated the general architecture and subunit compositions of all three sub-types of rotary ATPases. Composite models of the intact F-, V- and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual subunits or sub-complexes into low-resolution electron densities of the intact enzymes derived from electron cryo-microscopy. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria and mass-spectrometry has started to identify specifically bound lipids presumed to be essential for function. Taken together these molecular snapshots show that nano-scale rotary engines have much in common with basic design principles of man made machines from the function of individual “machine elements” to the requirement of the right “fuel” and “oil” for different types of motors. PMID:23369889

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

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

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Structural Ordering of Semiconducting Polymers and Small-Molecules for Organic Electronics

NASA Astrophysics Data System (ADS)

O'Hara, Kathryn Allison

Semiconducting polymers and small-molecules can be readily incorporated into electronic devices such as organic photovoltaics (OPVs), thermoelectrics (OTEs), organic light emitting diodes (OLEDs), and organic thin film transistors (OTFTs). Organic materials offer the advantage of being processable from solution to form flexible and lightweight thin films. The molecular design, processing, and resulting thin film morphology of semiconducting polymers drastically affect the optical and electronic properties. Charge transport within films of semiconducting polymers relies on the nanoscale organization to ensure electronic coupling through overlap of molecular orbitals and to provide continuous transport pathways. While the angstrom-scale packing details can be studied using X-ray scattering methods, an understanding of the mesoscale, or the length scale over which smaller ordered regions connect, is much harder to achieve. Grain boundaries play an important role in semiconducting polymer thin films where the average grain size is much smaller than the total distance which charges must traverse in order to reach the electrodes in a device. The majority of semiconducting polymers adopt a lamellar packing structure in which the conjugated backbones align in parallel pi-stacks separated by the alkyl side-chains. Only two directions of transport are possible--along the conjugated backbone and in the pi-stacking direction. Currently, the discussion of transport between crystallites is centered around the idea of tie-chains, or "bridging" polymer chains connecting two ordered regions. However, as molecular structures become increasingly complex with the development of new donor-acceptor copolymers, additional forms of connectivity between ordered domains should be considered. High resolution transmission electron microscopy (HRTEM) is a powerful tool for directly imaging the crystalline grain boundaries in polymer and small-molecule thin films. Recently, structures comparable to quadrites were discovered in the semiconducting polymer, PSBTBT, where the angle of chain overlap could be predicted by the geometry of the backbone and alkyl side-chains. Such structures are hypothesized to improve the electronic connectivity and enable 3D transport. Now, it has been determined that another semiconducting polymer, PBDTTPD, forms cross-chain structures in thin films. PBDTTPD is a low band-gap donor-acceptor copolymer used in high efficiency OPVs. The effect of the alkyl side-chains on intercrystallite order is determined by examining three different derivatives of the PBDTTPD polymer with HRTEM. Additionally, the expansion and contraction of films during thermal annealing and slow cooling is monitored through in-situ grazing incidence wide-angle X-ray scattering (GIWAXS) measurements. Results show that minor variations in side-chain structure drive both crystallite orientation and the formation of crossed structures. Overall, these studies suggest design principles to continue to advance the field of organic electronics.

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

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

DOE PAGES

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

2014-10-29

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Galloylglucoses of low molecular weight as mordant in electron microscopy. I. Procedure, and evidence for mordanting effect

PubMed Central

1976-01-01

Gallotannin, consisting mainly of low molecular weight esters such as penta- and hexagalloylglucoses (commercially available as tannic acid produced from Turkish nutgall), can be used for increasing and diversifying tissue contrast in electron microscopy. When applied on tissue specimens previously fixed by conventional methods (aldehydes and OsO4), the low molecular weight galloylglucoses (LMGG) penetrate satisfactorily the cells and induce general high contrast with fine delineation of extra- and intracellular structures, especially membranes. In some features, additional details of their intimate configuration are revealed. Various experimental conditions tested indicate that the LMGG display a complex effect on fixed tissues: they act primarily as a mordant between osmium-treated structures and lead, and concomitantly stabilize some tissue components against extraction incurred during dehydration and subsequent processing. Experiments with aldehyde blocking reagents (sodium borohydride and glycine) suggested that the LMGG mordanting effect is not dependent on residual aldehydes groups in tissues. PMID:783172

Structure-Property Relationship of Phenylene-Based Self-Assembled-Monolayers for Record Low Work Function of Indium Tin Oxide.

PubMed

Benneckendorf, Frank S; Hillebrandt, Sabina; Ullrich, Florian; Rohnacher, Valentina; Hietzschold, Sebastian; Jänsch, Daniel; Freudenberg, Jan; Beck, Sebastian; Mankel, Eric; Jaegermann, Wolfram; Pucci, Annemarie; Bunz, Uwe H F; Müllen, Klaus

2018-06-20

Studying the structure-property relations of tailored dipolar phenyl and biphenylphosphonic acids we report self-assembled monolayers with a significant decrease of the work function (WF) of indium-tin oxide (ITO) electrodes. While the strengths of the dipoles are varied through the different molecular lengths and the introduction of electron-withdrawing fluorine atoms, the surface energy is kept constant through the electron-donating N,N dimethylamine head groups. The self-assembled monolayer formation and its modification of the electrodes are investigated via infrared reflection absorption spectroscopy, contact angle measurements, and photoelectron spectroscopy. The WF decrease of ITO correlates with increasing molecular dipoles. The lowest ever recorded WF of 3.7 eV is achieved with the fluorinated biphenylphosphonic acid.

Integral equation model for warm and hot dense mixtures.

PubMed

Starrett, C E; Saumon, D; Daligault, J; Hamel, S

2014-09-01

In a previous work [C. E. Starrett and D. Saumon, Phys. Rev. E 87, 013104 (2013)] a model for the calculation of electronic and ionic structures of warm and hot dense matter was described and validated. In that model the electronic structure of one atom in a plasma is determined using a density-functional-theory-based average-atom (AA) model and the ionic structure is determined by coupling the AA model to integral equations governing the fluid structure. That model was for plasmas with one nuclear species only. Here we extend it to treat plasmas with many nuclear species, i.e., mixtures, and apply it to a carbon-hydrogen mixture relevant to inertial confinement fusion experiments. Comparison of the predicted electronic and ionic structures with orbital-free and Kohn-Sham molecular dynamics simulations reveals excellent agreement wherever chemical bonding is not significant.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

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.

Synthesis, Structure, and Molecular Recognition of S6 - and (SO2 )6 -Corona[6](het)arenes: Control of Macrocyclic Conformation and Properties by the Oxidation State of the Bridging Heteroatoms.

PubMed

Guo, Qing-Hui; Zhao, Liang; Wang, Mei-Xiang

2016-05-10

We report herein the synthesis, structure, and molecular recognition of S6 - and (SO2 )6 -corona[6](het)arenes, and demonstrate a unique and efficient strategy of regulating macrocyclic conformation and properties by adjusting the oxidation state of the heteroatom linkages. The one-pot nucleophilic aromatic substitution reaction of 1,4-benzenedithiol derivatives, biphenyl-4,4'-dithiol and 9,9-dipropyl-9H-fluorene-2,7-dithiol with 3,6-dichlorotetrazine afforded S6 -corona[3]arene[3]tetrazines. These compounds underwent inverse-electron-demand Diels-Alder reaction with enamines and norbornadiene to produce S6 -corona[3]arene[3]pyridazines. Facile oxidation of sulfide linkages yielded (SO2 )6 -corona[3]arene[3]pyridazines. All corona[6](het)arenes adopted generally hexagonal macrocyclic ring structures; however, their electronic properties and conformation could be fine-tuned by altering the oxidation state of the sulfur linkages. Whereas (SO2 )6 -corona[3]arene[3]pyridazines were electron-deficient, S6 -corona[3]arene[3]pyridazines acted as electron-rich macrocyclic hosts that recognized various organic cations in both aqueous and organic solutions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-Assembly Strategies for Integrating Light Harvesting and Charge Separation in Artificial Photosynthetic Systems

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

Wasielewski, Michael R.

In natural photosynthesis, organisms optimize solar energy conversion through organized assemblies of photofunctional chromophores and catalysts within proteins that provide specifically tailored environments for chemical reactions. As with their natural counterparts, artificial photosynthetic systems for practical solar fuels production must collect light energy, separate charge, and transport charge to catalytic sites where multielectron redox processes will occur. While encouraging progress has been made on each aspect of this complex problem, researchers have not yet developed self-ordering and self-assembling components and the tailored environments necessary to realize a fully-functional artificial system. Previously researchers have used complex, covalent molecular systems comprised ofmore » chromophores, electron donors, and electron acceptors to mimic both the light-harvesting and the charge separation functions of photosynthetic proteins. These systems allow for study of the dependencies of electron transfer rate constants on donor?acceptor distance and orientation, electronic interaction, and the free energy of the reaction. The most useful and informative systems are those in which structural constraints control both the distance and the orientation between the electron donors and acceptors. Self-assembly provides a facile means for organizing large numbers of molecules into supramolecular structures that can bridge length scales from nanometers to macroscopic dimensions. The resulting structures must provide pathways for migration of light excitation energy among antenna chromophores, and from antennas to reaction centers. They also must incorporate charge conduits, that is, molecular 'wires' that can efficiently move electrons and holes between reaction centers and catalytic sites. The central scientific challenge is to develop small, functional building blocks with a minimum number of covalent linkages, which also have the appropriate molecular recognition properties to facilitate self-assembly of complete, functional artificial photosynthetic systems. In this Account, we explore how self-assembly strategies involving ?-stacking can be used to integrate light harvesting with charge separation and transport.« less

DFT investigation on the electronic structure of Faujasite

NASA Astrophysics Data System (ADS)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

2013-11-01

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

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.

Structural changes induced by lattice-electron interactions: SiO2 stishovite and FeTiO3 ilmenite.

PubMed

Yamanaka, Takamitsu

2005-09-01

The bright source and highly collimated beam of synchrotron radiation offers many advantages for single-crystal structure analysis under non-ambient conditions. The structure changes induced by the lattice-electron interaction under high pressure have been investigated using a diamond anvil pressure cell. The pressure dependence of electron density distributions around atoms is elucidated by a single-crystal diffraction study using deformation electron density analysis and the maximum entropy method. In order to understand the bonding electrons under pressure, diffraction intensity measurements of FeTiO3 ilmenite and gamma-SiO2 stishovite single crystals at high pressures were made using synchrotron radiation. Both diffraction studies describe the electron density distribution including bonding electrons and provide the effective charge of the cations. In both cases the valence electrons are more localized around the cations with increasing pressure. This is consistent with molecular orbital calculations, proving that the bonding electron density becomes smaller with pressure. The thermal displacement parameters of both samples are reduced with increasing pressure.

Electronic structure calculations on multiply charged anions containing M bond S bonds (M = Cr, Mo, W) and their heterobimetallic cluster complexes

NASA Astrophysics Data System (ADS)

Gili, Pedro; Tsipis, Athanassios C.

Molecular and electronic structures of multiply charged mononuclear [CrS4]2-/3-, [MoOxS4-x]2-/3- (x = 0-4) and [WS4]2-/3- anionic species, and their heterobimetallic dinuclear and trinuclear clusters formulated as [MoOS3(CuCl)]2-, [WOS3(CuCl)]2-, [MoS4{Cu(CN)}]2-, [(CN)Cu(?-CrS4)Cu(CN)]2-, [(CN)Cu(?-MoS4)Cu(CN)]2-, [ClCu(?-MoS4)CuCl]2-, [Cl2Fe(?-MoS4)CuCl2]2-, and [(CN)Cu(?-WS4)Cu(CN)]2- have been investigated using electronic structure calculation (HF, MP4SDQ and DFT) methods. For the discrete mononuclear anions HF/lanl2dz(M)?6-31+G*(S,O) method provided the best description of their molecular structures, while for the heterobimetallic dinuclear and trinuclear clusters the B3LYP/lanl2dz(M)?6-31+G* method gave equilibrium geometries closely resembling the experimental ones. Electronic and spectroscopic (IR, UV-Vis) properties of the thiometalates are discussed in relation to their structures, while the bonding mechanism was analyzed in the framework of the natural bond orbital (NBO) approach. The nature of the highest occupied molecular orbitals (HOMOs) of all thiometalates indicated their ability to act as ligands coordinated with metal centers and forming clusters of higher nuclearity. The lowest-lying vertical one-electron detachment processes from the ground state of the [CrS4]2/3-, [MoOxS4-x]2/3- (x = 0-4) and [WS4]2/3- anions have been calculated using the outer valence Green's function (OVGF) method. Interestingly, in the heterobimetallic dinuclear and trinuclear clusters intemetallic M?M? interactions exist corresponding to d10 ? d0 dative bonding. Finally, the complete energetic and geometric profile of the successive acid-catalyzed formation reactions:and the reverse hydrolysis reactions have been delineated and details of the mechanism have been furnished.

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.

p-π Conjugated Polymers Based on Stable Triarylborane with n-Type Behavior in Optoelectronic Devices.

PubMed

Meng, Bin; Ren, Yi; Liu, Jun; Jäkle, Frieder; Wang, Lixiang

2018-02-19

p-π conjugation with embedded heteroatoms offers unique opportunities to tune the electronic structure of conjugated polymers. An approach is presented to form highly electron-deficient p-π conjugated polymers based on triarylboranes, demonstrate their n-type behavior, and explore device applications. By combining alternating [2,4,6-tris(trifluoromethyl)phenyl]di(thien-2-yl)borane (FBDT) and electron-deficient isoindigo (IID)/pyridine-flanked diketopyrrolopyrrole (DPPPy) units, we achieve low-lying lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels, high electron mobilities, and broad absorptions in the visible region. All-polymer solar cells with these polymers as electron acceptors exhibit encouraging photovoltaic performance with power conversion efficiencies of up to 2.83 %. These results unambiguously prove the n-type behavior and demonstrate the photovoltaic applications of p-π conjugated polymers based on triarylborane. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decoupled electron and phonon transports in hexagonal boron nitride-silicene bilayer heterostructure

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

Cai, Yongqing; Pei, Qing-Xiang, E-mail: peiqx@ihpc.a-star.edu.sg, E-mail: zhangg@ihpc.a-star.edu.sg; Zhang, Gang, E-mail: peiqx@ihpc.a-star.edu.sg, E-mail: zhangg@ihpc.a-star.edu.sg

2016-02-14

Calculations based on the density functional theory and empirical molecular dynamics are performed to investigate interlayer interaction, electronic structure and thermal transport of a bilayer heterostructure consisting of silicene and hexagonal boron nitride (h-BN). In this heterostructure, the two layers are found to interact weakly via a non-covalent binding. As a result, the Dirac cone of silicene is preserved with the Dirac cone point being located exactly at the Fermi level, and only a small amount of electrons are transferred from h-BN to silicene, suggesting that silicene dominates the electronic transport. Molecular dynamics calculation results demonstrate that the heat currentmore » along h-BN is six times of that along silicene, suggesting that h-BN dominates the thermal transport. This decoupled role of h-BN and silicene in thermal and electronic transport suggests that the BN-silicene bilayer heterostructure is promising for thermoelectric applications.« less

Interface Structure of MoO3 on Organic Semiconductors

PubMed Central

White, Robin T.; Thibau, Emmanuel S.; Lu, Zheng-Hong

2016-01-01

We have systematically studied interface structure formed by vapor-phase deposition of typical transition metal oxide MoO3 on organic semiconductors. Eight organic hole transport materials have been used in this study. Ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy are used to measure the evolution of the physical, chemical and electronic structure of the interfaces at various stages of MoO3 deposition on these organic semiconductor surfaces. For the interface physical structure, it is found that MoO3 diffuses into the underlying organic layer, exhibiting a trend of increasing diffusion with decreasing molecular molar mass. For the interface chemical structure, new carbon and molybdenum core-level states are observed, as a result of interfacial electron transfer from organic semiconductor to MoO3. For the interface electronic structure, energy level alignment is observed in agreement with the universal energy level alignment rule of molecules on metal oxides, despite deposition order inversion. PMID:26880185

C-Ni-Pd and CNT-Ni-Pd film's molecular and crystalline structure investigations by FTIR spectroscopy and XRD diffraction

NASA Astrophysics Data System (ADS)

Stepińska, Izabela; Czerwosz, ElŻbieta; Diduszko, Ryszard; Kozłowski, Mirosław; Wronka, Halina

2017-08-01

In this work molecular and crystalline structure of new type of nanocomposite films were investigated. These films compose of CNT decorated with palladium nanograins. They were prepared on a base of C-Ni films modified in CVD process. C-Ni nanocomposite films were obtained by PVD process and their modification by CVD leads to a growth of CNT film. CNTs-Ni or C-Ni films were treated with additional PVD process with palladium. Nickel and palladium acetate and fulleren C60 are precursors of films in PVD process. FTIR spectroscopy was used to studied the molecular structure of film in every stage of preparation . The crystalline structure of these films was studied by X-ray diffraction. SEM (scanning electron microscopy) was applied to investigate film's surface topography.

Properties of the Only Thorium Fullerene, Th@C84, Uncovered.

PubMed

Kaminský, Jakub; Vícha, Jan; Bouř, Petr; Straka, Michal

2017-04-27

Only a single thorium fullerene, Th@C 84 , has been reported to date (Akiyama, K.; et al. J. Nucl. Radiochem. Sci. 2002, 3, 151-154). Although the system was characterized by UV-vis and XANES (X-ray absorption near edge structure) spectra, its structure and properties remain unknown. In this work we used the density functional calculations to identify molecular and electronic structure of the Th@C 84 . Series of molecular structures satisfying the ThC 84 stoichiometric formula were studied comprising 24 IPR and 110 non-IPR Th@C 84 isomers as well as 9 ThC 2 @C 82 IPR isomers. The lowest energy structure is Th@C 84 -C s (10) with the singlet ground state. Its predicted electronic absorption spectra are in agreement with the experimentally observed ones. The bonding between the cage and Th was characterized as polar covalent with Th in formal oxidation state IV. The NMR chemical shifts of Th@C 84 -C s (10) were predicted to guide the future experimental efforts in identification of this compound.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

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

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

[The electron microscopic observation of the effect of monoclonal antibody on the form and structure of mutans streptococci OMZ176].

PubMed

Wen, L; Yue, S

1996-01-01

The effect of monoclonal antibody on the form and structure of Mutans Streptococci OMZ176 was studied. The result showed that a great number of Mutans Streptococci OMZ176 was agglutianated after treating with monoclonal antibody prepared by a cell wall protein antigen (molecular weight 220 kd) of Mutans Streptococci OMZ176. Bacterial cells were swollen obviously. The gap between cell wall and cytoplasmic was widened. The electronic density of cell plasm was greatly decreased.

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

Lawrence R. Sita

Ferrocene-based molecular components for nanoelectronics offer a number of distinct advantages relative to all carbon frameworks due to metal-centered molecular states that should be closer in energy to the Fermi levels of the metal electrodes in metal / molecule / metal heterojunctions. Given this, the overall goal of the project was to investigate the conduction physics of a variety of proposed ferrocene diode / transistor designs in order to address the fundamental question; can electron transport within nm-length scale structures be modulated in a controlled fashion? During the funded period, substantial progress towards achieving this goal was made by surmountingmore » a number of scientific and technical obstacles. More specifically, a concise and general synthetic route to several mono- and diferrocene dithiols and monothiols was achieved that now allows for the directed and controlled assembly of a variety of metal / molecule /metal test structures for the single molecule conductance measurements and the fabrication of self-assembled monolayers (SAMs) on Au(111) that are amenable to quantitative electrochemical characterization of electron-transfer rates. Most importantly, by using an electromigrated test structure, reproducible I/V data for one of the ferrocene dithiol molecules have been collected which exhibit surprisingly high conductance. Exceptional agreement of this result with theory serves to substantiate the original hypothesis that metal-centered states within a molecular bridge can indeed serve to establish higher conductance relative to all-organic molecular bridges. Overall, the successful demonstration of the ability of ferrocene-molecular frameworks to serve as exceptional molecular conductors will play an important role in the continued evolution in design of molecular components for nanoelectronic devices, which in turn, will have a positive impact on the science and potential technologies associated with these systems.« less

Structure and electronic properties of ion pairs accompanying cyclic morpholinium cation and alkylphosphite anion based ionic liquids

NASA Astrophysics Data System (ADS)

Verma, Prakash L.; Singh, Priti; Gejji, Shridhar P.

2017-07-01

Molecular insights for the formation of ion pairs accompanying the cyclic ammonium cation based room temperature ionic liquids (RTILs) composed of alkyl substituted N-methylmorpholinium (RMMor) and alkylphosphite [(Rsbnd O)2PHdbnd O] (Rdbnd ethyl, butyl, hexyl, octyl) anion have been derived from the M06-2x level of theory. Electronic structures, binding energies, and spectral characteristics of the ion pairs underlying these RTILs have been characterized. The ion pair formation is largely governed by Csbnd H⋯O and other intermolecular interactions. Calculated binding energies increase with the increasing alkyl chain on either cation or alkylphosphite anion. The cation-anion binding reveals signature in the frequency down-(red) shift of the characteristic anionic Pdbnd O stretching whereas the Psbnd H stretching exhibits a shift in the opposite direction in vibrational spectra which has further been rationalized through molecular electron density topography. Correlations of measured electrochemical stability with the separation of frontier orbital energies and binding energies in the ion pairs have further been established.

Photoactive layer based on T-shaped benzimidazole dyes used for solar cell: from photoelectric properties to molecular design

NASA Astrophysics Data System (ADS)

Xu, Beibei; Li, Yuanzuo; Song, Peng; Ma, Fengcai; Sun, Mengtao

2017-03-01

Three benzimidazole-based organic dyes, possessing the same triphenylamine donors and cyanoacrylic acid acceptors with the bithiophene π-bridges combined in different nuclear positions of benzimidazole, were investigated in the utility of dye-sensitizer solar cells. The structure, molecular orbital and energy, absorption spectra and some important parameters (such as light harvesting efficiency (LHE), electron injection driving force, the electron injection time, chemical reactivity parameters, vertical dipole moment as well as interaction models of dye-I2) were obtained according to Newns-Anderson model and DFT calculation. The process and strength of charge transfer and separation were visualized with charge different density and index of spatial extent (S, D and Δq). Current work paid attention to the new T-shaped dyes to reveal the relation between the structure and photoelectric performance. Furthermore, nine dyes (substitution of alkyl chains and π-bridges) have been designed and characterized to screen promising sensitizer candidates with excellent photo-electronic properties.

Molecular structure and conformational preferences of gaseous 1-iodo-1-silacyclohexane

NASA Astrophysics Data System (ADS)

Belyakov, A. V.; Baskakov, A. A.; Berger, R. J. F.; Mitzel, N. W.; Oberhammer, H.; Arnason, I.; Wallevik, S. Ò.

2012-03-01

The molecular structure of the axial and equatorial conformers of 1-iodo-1-silacyclohexane, CH2(CH2CH2)2SiH-I, as well as thermodynamic equilibrium between these species were investigated by means of gas-phase electron diffraction (GED) and quantum chemical calculations up to MP2(full)/SDB-AUG-CC-pVTZ level of theory (MP2). According to electron diffraction data, the vapor of this compound comprises a mixture of conformers with chair conformation and Cs symmetry differing in the axial and equatorial position of the Si-I bond (axial = 73(7) mol%/equatorial = 27(7) mol%) at T = 352 K. This corresponds to a free energy difference of A = -0.59(22) kcal mol-1. The observed gas-phase electron diffraction parameters are in good agreement with those obtained from theory. NBO analysis revealed that axial conformer of 1-iodo-1-silacyclohexane is an example for electrostatic stabilization of a conformer which is unfavorable in terms of steric and conjugation interaction.

A mixed valence zinc dithiolene system with spectator metal and reactor ligands.

PubMed

Ratvasky, Stephen C; Mogesa, Benjamin; van Stipdonk, Michael J; Basu, Partha

2016-08-16

Neutral complexes of zinc with N,N'-diisopropylpiperazine-2,3-dithione ( i Pr 2 Dt 0 ) and N,N'-dimethylpiperazine-2,3-dithione (Me 2 Dt 0 ) with chloride or maleonitriledithiolate (mnt 2- ) as coligands have been synthesized and characterized. The molecular structures of these zinc complexes have been determined using single crystal X-ray diffractometry. Complexes recrystallize in monoclinic P type systems with zinc adopting a distorted tetrahedral geometry. Two zinc complexes with mixed-valent dithiolene ligands exhibit ligand-to-ligand charge transfer bands. Optimized geometries, molecular vibrations and electronic structures of charge-transfer complexes were calculated using density functional theory (B3LYP/6-311G+(d,p) level). Redox orbitals are shown to be almost exclusively ligand in nature, with a HOMO based heavily on the electron-rich maleonitriledithiolate ligand, and a LUMO comprised mostly of the electron-deficient dithione ligand. Charge transfer is thus believed to proceed from dithiolate HOMO to dithione LUMO, showing ligand-to-ligand redox interplay across a d 10 metal.

Computational study of the RGD-peptide interactions with perovskite-type BFO-(1 1 1) membranes under aqueous conditions

NASA Astrophysics Data System (ADS)

Li, Hai-long; Bian, Liang; Hou, Wen-ping; Dong, Fa-Qin; Song, Mian-Xin; Zhang, Xiao-yan; Wang, Li-sheng

2016-07-01

We elucidated a number of facets regarding arginine-glycine-aspartate (RGD)-bismuth ferrite (BFO)-(1 1 1) membrane interactions and reactivity that have previously remained unexplored on a molecular level. Results demonstrate the intra-molecular interaction facilitates a ;horseshoe; structure of RGD adsorbed onto the BFO-(1 1 1) membrane, through the electrostatic (Asp-cation-Fe) and water-bridge (Osbnd H2O and H2Osbnd NH2) interactions. The effect of structural and electron-transfer interactions is attributed to the cation-valences, indicating that the divalent cations are electron-acceptors and the monovalent cations as electron-donors. Notably, the strongly bound Ca2+ ion exerts a ;gluing; effect on the Asp-side-chain, indicating a tightly packed RGD-BFO configuration. Thus, modulating the biological response of BFO-(1 1 1) membrane will allow us to design more appropriate interfaces for implantable diagnostic and therapeutic perovskite-type micro-devices.

All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures.

PubMed

Yang, Huayan; Wang, Yu; Huang, Huaqi; Gell, Lars; Lehtovaara, Lauri; Malola, Sami; Häkkinen, Hannu; Zheng, Nanfeng

2013-01-01

Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag44(SR)30 and three Au12Ag32(SR)30 intermetallic nanoclusters stabilized with fluorinated arylthiols (SR=SPhF, SPhF2 or SPhCF3). The nanocluster forms a Keplerate solid of concentric icosahedral and dodecahedral atom shells, protected by six Ag2(SR)5 units. Positive counterions in the crystal indicate a high negative charge of 4(-) per nanoparticle, and density functional theory calculations explain the stability as an 18-electron superatom shell closure in the metal core. Highly featured optical absorption spectra in the ultraviolet-visible region are analysed using time-dependent density functional perturbation theory. This work forms a basis for further understanding, engineering and controlling of stability as well as electronic and optical properties of these novel nanomaterials.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tetrametallic molecular catalysts for photochemical water oxidation.

PubMed

Sartorel, Andrea; Bonchio, Marcella; Campagna, Sebastiano; Scandola, Franco

2013-03-21

Among molecular water oxidation catalysts (WOCs), those featuring a reactive set of four multi-redox transition metals can leverage an extraordinary interplay of electronic and structural properties. These are of particular interest, owing to their close structural, and possibly functional, relationship to the oxygen evolving complex of natural photosynthesis. In this review, special attention is given to two classes of tetrametallic molecular WOCs: (i) M(4)O(4) cubane-type structures stabilized by simple organic ligands, and (ii) systems in which a tetranuclear metal core is stabilized by coordination of two polyoxometalate (POM) ligands. Recent work in this rapidly evolving field is reviewed, with particular emphasis on photocatalytic aspects. Special attention is given to studies addressing the mechanistic complexity of these systems, sometimes overlooked in the rush for oxygen evolving performance. The complementary role of molecular WOCs and their relationship with bulk oxides and heterogeneous catalysis are discussed.

Combined experimental and theoretical studies on the molecular structures, spectroscopy, and inhibitor activity of 3-(2-thienyl)acrylic acid through AIM, NBO,FT-IR, FT-Raman, UV and HOMO-LUMO analyses, and molecular docking

NASA Astrophysics Data System (ADS)

Issaoui, N.; Ghalla, H.; Bardak, F.; Karabacak, M.; Aouled Dlala, N.; Flakus, H. T.; Oujia, B.

2017-02-01

In this work, the molecular structures and vibrational spectral analyses of 3-(2-Theinyl)acrylic acid (3-2TAA) monomer and dimer structures have been reported by using density functional theory calculations at B3LYP/6-311++G(d,p) level of theory. The complete assignments of the fundamental vibrational modes were obtained using potential energy distribution. Intermolecular interactions were analyzed by orbital NBO and topological AIM approaches. The electronic properties have been carried out using TD-DFT approach. Great agreements between experimental and theoretical values were achieved throughout the analysis of structural parameters and spectroscopic features. Inhibitor characteristics on human monoamine oxidase B (MAOB) enzyme of two determined stable conformers of 3-2TAA (β and γ) along with four selective inhibitors, namely safinamide, a coumarin analogue, farnesol, and phenyethylhydrazine were investigated via molecular docking. Moreover, molecular electrostatic potential (MEP) and temperature dependency of thermodynamic functions have been reported.

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Modeling charge transport in organic photovoltaic materials.

PubMed

Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

2009-11-17

The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse-grained structural simulation method. Finally, we quantitatively reproduce the field-effect mobility in disordered C60 films. On the basis of these results, we conclude that all of the necessary building blocks are in place for the predictive simulation of charge transport in macromolecular electronic materials and that such methods can be used as a tool toward the future rational design of functional organic electronic materials.

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.

"Vibrational spectroscopic analysis and molecular docking studies of (E)-4-methoxy-N‧-(4-methylbenzylidene) benzohydrazide by DFT"

NASA Astrophysics Data System (ADS)

Maheswari, R.; Manjula, J.

2016-07-01

(E)-4-methoxy-N‧-(4-methylbenzylidene)benzohydrazide (4MN'MBH) a novel, organic, hydrazone Schiff base compound was synthesized and its structure was characterized by Fourier Transform Infrared (4000-400 cm-1), Fourier Transform Raman (3500-50 cm-1), Ultraviolet-Visible (200-800 nm) and 1H and 13C NMR spectroscopic analysis. Optimized molecular structure, vibrational frequencies and corresponding vibrational assignments regarding 4MN'MBH has become screened tentatively as well as hypothetically utilizing Gaussian09Wprogram package. Potential energy distributions of the normal modes of vibrations connected with vibrations are generally accomplished by applying VEDA program. Natural Bonding Orbital (NBO) assessment was completed with a reason to clarify charge transfer or conjugative interaction, the intra-molecular-hybridization and delocalization of electron density within the molecule. Electronic transitions were studied employing UV-Visible spectrum and the observed values were compared with theoretical values. 1H and13C NMR spectral assessment had been made with choosing structure property relationship by chemical shifts along with magnetic shielding effects of title compound. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4MN'MBH were calculated. The computed first order hyperpolarizability commensurate with the documented worth of very similar structure and could be an interesting thing for more experiments on non linear optics. Molecular docking study has been performed by in silico method to analysis their antituberculosis aspects against Enoyl acyl carrier protein reductase (Mycobacterium tuberculosis InhA) protein.

Molecular Beam Mass Spectrometry With Tunable Vacuum Ultraviolet (VUV) Synchrotron Radiation

PubMed Central

Golan, Amir; Ahmed, Musahid

2012-01-01

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics1-4. Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water1, 5-9. We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline10 located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds1. Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations11, 12. By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species 1, 3. PMID:23149375

Molecular weight dependence of carrier mobility and recombination rate in neat P3HT films

DOE PAGES

Dixon, Alex G.; Visvanathan, Rayshan; Clark, Noel A.; ...

2017-11-02

The microstructure dependence of carrier mobility and recombination rates of neat films of poly 3-hexylthyophene (P3HT) were determined for a range of materials of weight-average molecular weights, Mw, ranging from 14 to 331 kDa. This variation has previously been shown to modify the polymer microstructure, with low molecular weights forming a one-phase, paraffinic-like structure comprised of chain-extended crystallites, and higher molecular weights forming a semicrystalline structure with crystalline domains being embedded in an amorphous matrix. Using Charge Extraction by Linearly Increasing Voltage (CELIV), we show here that the carrier mobility in P3HT devices peaks for materials of Mw = 48more » kDa, and that the recombination rate decreases monotonically with increasing molecular weight. This trend is likely due to the development of a semicrystalline, two-phase structure with increasing Mw, which allows for the spatial separation of holes and electrons into the amorphous and crystalline regions, respectively. This separation leads to decreased recombination.« less

Molecular weight dependence of carrier mobility and recombination rate in neat P3HT films

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

Dixon, Alex G.; Visvanathan, Rayshan; Clark, Noel A.

The microstructure dependence of carrier mobility and recombination rates of neat films of poly 3-hexylthyophene (P3HT) were determined for a range of materials of weight-average molecular weights, Mw, ranging from 14 to 331 kDa. This variation has previously been shown to modify the polymer microstructure, with low molecular weights forming a one-phase, paraffinic-like structure comprised of chain-extended crystallites, and higher molecular weights forming a semicrystalline structure with crystalline domains being embedded in an amorphous matrix. Using Charge Extraction by Linearly Increasing Voltage (CELIV), we show here that the carrier mobility in P3HT devices peaks for materials of Mw = 48more » kDa, and that the recombination rate decreases monotonically with increasing molecular weight. This trend is likely due to the development of a semicrystalline, two-phase structure with increasing Mw, which allows for the spatial separation of holes and electrons into the amorphous and crystalline regions, respectively. This separation leads to decreased recombination.« less

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Electron Mobilities and Effective Masses in InGaAs/InAlAs HEMT Structures with High In Content

NASA Astrophysics Data System (ADS)

Yuzeeva, N. A.; Sorokoumova, A. V.; Lunin, R. A.; Oveshnikov, L. N.; Galiev, G. B.; Klimov, E. A.; Lavruchin, D. V.; Kulbachinskii, V. A.

2016-12-01

InxGa_{1-{x}}As/InyAl_{1-{y}}As HEMT structures {δ}-doped by Si were grown by molecular beam epitaxy on InP substrate. We investigated the influence of the In content on the electron mobilities and effective masses in dimensionally quantized subbands. The electron effective masses were determined by the temperature dependence of the amplitude of the Shubnikov-de Haas effect at 1.6 and 4.2 K. We found that the more the In content in quantum well (QW), the less the electron effective masses. The mobilities are higher in HEMT structures with wider and deeper QW. The energy band diagrams were calculated by using Vegard's law for basic parameters. The calculated band diagrams are in a good agreement with the experimental data of photoluminescence spectra.

A density functional theory study on the structural and electronic properties of PbxSbySez (x + y + z = 2, 3) clusters

NASA Astrophysics Data System (ADS)

Peköz, Rengi˙n; Erkoç, Şaki˙r

2018-01-01

The structural and electronic properties of neutral ternary PbxSbySez clusters (x + y + z = 2, 3) in their ground states have been explored by means of density functional theory calculations. The geometric structures and binding energies are systematically explored and for the most stable configurations of each cluster type vibrational frequencies, charges on atoms, energy difference between highest occupied and lowest unoccupied molecular orbitals, and the possible dissociations channels have been analyzed. Depending on being binary or ternary cluster and composition, the most energetic structures have singlet, doublet or triplet ground states, and trimers prefer to form isosceles, equilateral or scalene triangle structure.

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

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

On-surface formation of one-dimensional polyphenylene through Bergman cyclization.

PubMed

Sun, Qiang; Zhang, Chi; Li, Zhiwen; Kong, Huihui; Tan, Qinggang; Hu, Aiguo; Xu, Wei

2013-06-12

On-surface fabrication of covalently interlinked conjugated nanostructures has attracted significant attention, mainly because of the high stability and efficient electron transport ability of these structures. Here, from the interplay of scanning tunneling microscopy imaging and density functional theory calculations, we report for the first time on-surface formation of one-dimensional polyphenylene chains through Bergman cyclization followed by radical polymerization on Cu(110). The formed surface nanostructures were further corroborated by the results for the ex situ-synthesized molecular product after Bergman cyclization. These findings are of particular interest and importance for the construction of molecular electronic nanodevices on surfaces.

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.

Using Molecular Modeling to Understand Some of the More Subtle Aspects of Aromaticity and Antiaromaticity

ERIC Educational Resources Information Center

Box, Vernon G. S.

2011-01-01

pi-Electron delocalization exerts one of the most significant structure or energy influences in organic chemistry. Apart from determining the shapes of alkenes and alkynes, the planarity of aromatic molecules is a hallmark of pi-electron delocalization. Huckel's rules for aromaticity are easily applied in the teaching of undergraduates, but…

The world as viewed by and with unpaired electrons.

PubMed

Eaton, Sandra S; Eaton, Gareth R

2012-10-01

Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models. Copyright © 2012 Elsevier Inc. All rights reserved.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

[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.

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.

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole

NASA Astrophysics Data System (ADS)

Arjunan, V.; Raj, Arushma; Santhanam, R.; Marchewka, M. K.; Mohan, S.

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. 1H and 13C NMR chemical shifts and the electronic transitions of the molecule are also discussed.

Physics Division annual review, 1 April 1980-31 March 1981

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

Not Available

1982-06-01

Progress in nuclear physics research is reported in the following areas: medium-energy physics (pion reaction mechanisms, high-resolution studies and nuclear structure, and two-nucleon physics with pions and electrons); heavy-ion research at the tandem and superconducting linear accelerator (resonant structure in heavy-ion reactions, fusion cross sections, high angular momentum states in nuclei, and reaction mechanisms and distributions of reaction strengths); charged-particle research; neutron and photonuclear physics; theoretical physics (heavy-ion direct-reaction theory, nuclear shell theory and nuclear structure, nuclear matter and nuclear forces, intermediate-energy physics, microscopic calculations of high-energy collisions of heavy ions, and light ion direct reactions); the superconducting linac; acceleratormore » operations; and GeV electron linac. Progress in atomic and molecular physics research is reported in the following areas: dissociation and other interactions of energetic molecular ions in solid and gaseous targets, beam-foil research and collision dynamics of heavy ions, photoionization- photoelectron research, high-resolution laser rf spectroscopy with atomic and molecular beams, moessbauer effect research, and theoretical atomic physics. Studies on interactions of energetic particles with solids are also described. Publications are listed. (WHK)« less

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

PubMed

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Centrohexaindane: six benzene rings mutually fixed in three dimensions - solid-state structure and six-fold nitration.

PubMed

Kuck, Dietmar; Linke, Jens; Teichmann, Lisa Christin; Barth, Dieter; Tellenbröker, Jörg; Gestmann, Detlef; Neumann, Beate; Stammler, Hans-Georg; Bögge, Hartmut

2016-04-28

The solid-state molecular structure of centrohexaindane (), a unique hydrocarbon comprising six benzene rings clamped to each other in three dimensions around a neopentane core, and the molecular packing in crystals of ·CHCl3 are reported. The molecular Td-symmetry and the Cartesian orientation of the six indane wings of in the solid state have been confirmed. The course and limitation of electrophilic aromatic substitution of are demonstrated for the case of nitration. Based on nitration experiments of a lower congener of , tribenzotriquinacene , the six-fold nitrofunctionalisation of has been achieved in excellent yield, giving four constitutional isomers, two nonsymmetrical ( and ) and two C3-symmetrical ones ( and ), all of which contain one single nitro group in each of the six benzene rings. The relative yields of the four isomers (∼3 : 1 : 1 : 3) point to a random electrophilic attack of the electrophiles at the twelve formally equivalent outer positions of the aromatic periphery of , suggesting electronic independence of its six aromatic π-electron systems. In turn, the pronounced conformational rigidity of the centrohexacyclic framework of enables the unequivocal structural identification of the isomeric hexanitrocentrohexaindanes by (1)H NMR spectroscopy.

Tuning the Rectification Ratio by Changing the Electronic Nature (Open-Shell and Closed-Shell) in Donor-Acceptor Self-Assembled Monolayers.

PubMed

Souto, Manuel; Yuan, Li; Morales, Dayana C; Jiang, Li; Ratera, Imma; Nijhuis, Christian A; Veciana, Jaume

2017-03-29

This Communication describes the mechanism of charge transport across self-assembled monolayers (SAMs) of two donor-acceptor systems consisting of a polychlorotriphenylmethyl (PTM) electron-acceptor moiety linked to an electron-donor ferrocene (Fc) unit supported by ultraflat template-stripped Au and contacted by a eutectic alloy of gallium and indium top contacts. The electronic and supramolecular structures of these SAMs were well characterized. The PTM unit can be switched between the nonradical and radical forms, which influences the rectification behavior of the junction. Junctions with nonradical units rectify currents via the highest occupied molecular orbital (HOMO) with a rectification ratio R = 99, but junctions with radical units have a new accessible state, a single-unoccupied molecular orbital (SUMO), which turns rectification off and drops R to 6.

Electronic structure evolution of fullerene on CH 3NH 3PbI 3

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

Wang, Chenggong; Wang, Congcong; Liu, Xiaoliang

2015-03-19

The thickness dependence of fullerene on CH 3NH 3PbI 3 perovskitefilm surface has been investigated by using ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy(XPS), and inverse photoemission spectroscopy (IPES). The lowest unoccupied molecular orbital and highest occupied molecular orbital (HOMO) can be observed directly with IPES and UPS. It is observed that the HOMO level in fullerene shifts to lower binding energy. The XPS results show a strong initial shift of core levels to lower binding energy in the perovskite, which indicates that electrons transfer from the perovskitefilm to fullerene molecules. Further deposition of fullerene forms C 60 solid, accompaniedmore » by the reduction of the electron transfer. As a result, the strongest electron transfer happened at 1/4 monolayer of fullerene.« less

Electronic structure evolution of fullerene on CH{sub 3}NH{sub 3}PbI{sub 3}

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

Wang, Chenggong; Wang, Congcong; Kauppi, John

2015-03-16

The thickness dependence of fullerene on CH{sub 3}NH{sub 3}PbI{sub 3} perovskite film surface has been investigated by using ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), and inverse photoemission spectroscopy (IPES). The lowest unoccupied molecular orbital and highest occupied molecular orbital (HOMO) can be observed directly with IPES and UPS. It is observed that the HOMO level in fullerene shifts to lower binding energy. The XPS results show a strong initial shift of core levels to lower binding energy in the perovskite, which indicates that electrons transfer from the perovskite film to fullerene molecules. Further deposition of fullerene forms C{submore » 60} solid, accompanied by the reduction of the electron transfer. The strongest electron transfer happened at 1/4 monolayer of fullerene.« less

Excitons in molecular crystals from first-principles many-body perturbation theory: Picene versus pentacene

NASA Astrophysics Data System (ADS)

Cudazzo, Pierluigi; Gatti, Matteo; Rubio, Angel

2012-11-01

By solving the first-principles many-body Bethe-Salpeter equation, we compare the optical properties of two prototype and technological relevant organic molecular crystals: picene and pentacene. Albeit very similar for the structural and electronic properties, picene and pentacene show remarkable differences in their optical spectra. While for pentacene the absorption onset is due to a charge-transfer exciton, in picene it is related to a strongly localized Frenkel exciton. The detailed comparison between the two materials allows us to discuss, on general grounds, how the interplay between the electronic band dispersion and the exchange electron-hole interaction plays a fundamental role in setting the nature of the exciton. It represents a clear example of the relevance of the competition between localization and delocalization in the description of two-particle electronic correlation.

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.

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.

Nonadiabatic one-electron transfer mechanism for the O-O bond formation in the oxygen-evolving complex of photosystem II

NASA Astrophysics Data System (ADS)

Shoji, Mitsuo; Isobe, Hiroshi; Shigeta, Yasuteru; Nakajima, Takahito; Yamaguchi, Kizashi

2018-04-01

The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O-O sigma bond formation.

Electronic structure, transport, and collective effects in molecular layered systems.

PubMed

Hahn, Torsten; Ludwig, Tim; Timm, Carsten; Kortus, Jens

2017-01-01

The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc) and a flourinated copper phthalocyanine-manganese phthalocyanine (F 16 CoPc/MnPc) heterostructure, are investigated by means of density functional theory (DFT) and the non-equilibrium Green's function (NEGF) approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View.

PubMed

López-Rosa, Sheila; Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Soriano-Correa, Catalina; Dehesa, Jésus S

2016-12-05

The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy-like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three-dimensional space (IT-3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT-3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para-aminobenzoic acid than to the theoretically designed analogues. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clays. Role in U and Hg(II) transformations

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

Scherer, Michelle

2016-08-31

During this project, we investigated Fe electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clay minerals. We used selective chemical extractions, enriched Fe isotope tracer experiments, computational molecular modeling, and Mössbauer spectroscopy. Our findings indicate that structural Fe(III) in clay minerals is reduced by aqueous Fe(II) and that electron transfer occurs when Fe(II) is sorbed to either basal planes and edge OH-groups of clay mineral. Findings from highly enriched isotope experiments suggest that up to 30 % of the Fe atoms in the structure of some clay minerals exhanges with aqueous Fe(II). First principles calculations usingmore » a small polaron hopping approach suggest surprisingly fast electron mobility at room temperature in a nontronite clay mineral and are consistent with temperature dependent Mössbauer data Fast electron mobility suggests that electrons may be able to conduct through the mineral fast enough to enable exchange of Fe between the aqueous phase and clay mineral structure. over the time periods we observed. Our findings suggest that Fe in clay minerals is not as stable as previously thought.« less

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.

Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy

PubMed Central

Henderson, Richard; Chen, Shaoxia; Chen, James Z.; Grigorieff, Nikolaus; Passmore, Lori A.; Ciccarelli, Luciano; Rubinstein, John L.; Crowther, R. Anthony; Stewart, Phoebe L.; Rosenthal, Peter B.

2011-01-01

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1–5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy. PMID:21939668

Charge separation in photoredox reactions. Technical progress report, May 1, 1981-May 1, 1984. [N,N,N',N'-tetramethylbenzidine

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

Kevan, L.

1984-05-01

The structural aspects controlling charge separation in molecular photoionization reactions in organized molecular assemblies involving micelles and vesicles are being studied by optical and electron magnetic resonance techniques including the time domain technique of electron spin echo modulation (ESEM). Photoionization of N,N,N',N'-tetramethylbenzidine (TMB) to give the cation radical has been carried out in both liquid and frozen micellar and vesicular solutions. Cation-water interactions have been detected by ESEM analysis and indicate that the cation is localized asymmetrically within these organized molecular assemblies. x-Doxylstearic acid spin probes have been used to determine that the neutral TMB molecule before photoionization is alsomore » localized asymmetrically within such organized molecular assemblies. Electron spin echo detection of laser photogenerated TMB cation in liquid micellar solutions gives a direct measurement of the phase memory magnetic relaxation time which gives additional structural information. The photoionization efficiency has been related to cation-water interactions measured by ESEM. The photoionization efficiency is also dependent on surface charge and is about twofold greater in cationic micelles and vesicles compared to anionic micelles and vesicles. TMB is in a less polar environment in vesicles compared to micelles consistent with ESEM results. The preferential adsorption of metal species at micellar surfaces has been detected by ESEM. Modifications in the micelle surface have been effected by added salts and varying counterions which have been related to cation-water interactions and to the TMB photoionization efficiency. Corresponding changes in the surface and internal micellar structure have been investigated by x-doxylstearic acid spin probes and specifically deuterated surfactants. The decay kinetics of TMB cations in micelles have been interpreted in terms of a time dependent rate constant.« less

Electronic structure of Cr doped Fe3O4 thin films by X-ray absorption near-edge structure spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Chi-Liang; Dong, Chung-Li; Asokan, Kandasami; Chern, G.; Chang, C. L.

2018-04-01

Present study reports the electronic structures of Cr doped Fe3O4 (Fe3-xCrxO4 (0 ≤ x ≤ 3) grown on MgO (100) substrates in the form of thin films fabricated by a plasma-oxygen assisted Molecular Beam Epitaxy (MBE). X-ray absorption near-edge structure (XANES) spectra at Cr & Fe L-, and O K-edges were used to understand the electronic structure: changes in the bonding nature, valence states, and site occupancies. Cr doping in Fe3O4 results in the change of charge transfer, crystal structure, and selective occupation of ions in octahedral and tetrahedral sites. Such change modifies the electrical and magnetic properties due to the covalency of Cr ions. The physical and chemical properties of ferrites are strongly dependent on the lattice site, ion size of dopant, and magnetic nature present at different structural symmetry of the spinel structure.

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.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites

DTIC Science & Technology

2016-06-08

conjugated polymers and composites by analysis of the structural determinants of the mechanical properties. We developed coarse-grained molecular...dynamics simulations that predicted the mechanical properties of conjugated polymers and polymer -fullerene composites. We elucidated the mechanical...We also determined the effect of cyclic stretching on the microstructure and mechanical properties of conjugated polymers . We used many of

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory.

PubMed

Coriani, Sonia; Høst, Stinne; Jansík, Branislav; Thøgersen, Lea; Olsen, Jeppe; Jørgensen, Poul; Reine, Simen; Pawłowski, Filip; Helgaker, Trygve; Sałek, Paweł

2007-04-21

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.