Modelling of energetic molecule-surface interactions

International Nuclear Information System (INIS)

Kerford, M.

2000-09-01

This thesis contains the results of molecular dynamics simulations of molecule-surface interactions, looking particularly at fullerene molecules and carbon surfaces. Energetic impacts of fullerene molecules on graphite create defect craters. The relationship between the parameters of the impacting molecule and the parameters of the crater axe examined and found to be a function of the energy and velocity of the impacting molecule. Less energetic fullerene molecules can be scattered from a graphite surface and the partitioning of energy after a scattering event is investigated. It is found that a large fraction of the kinetic energy retained after impact is translational energy, with a small fraction of rotational energy and a number of vibrational modes. At impact energies where the surface is not broken and at normal incidence, surface waves axe seen to occur. These waves axe used to develop a method of desorbing molecules from a graphite surface without damage to either the surface or the molecules being desorbed. A number of fullerene molecules are investigated and ways to increase the desorption yield are examined. It is found that this is a successful technique for desorbing large numbers of intact molecules from graphite. This technique could be used for desorbing intact molecules into a gas phase for mass spectrometric analysis. (author)

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

Science.gov (United States)

Tribello, Gareth A.; Cuny, Jérôme; Eshet, Hagai; Parrinello, Michele

2011-09-01

A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010), 10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface.

MSINDO quantum chemical modeling study of water molecule adsorption at nano-sized anatase TiO2 surfaces

International Nuclear Information System (INIS)

Wahab, Hilal S.; Bredow, Thomas; Aliwi, Salah M.

2008-01-01

In this work, we studied the adsorption of water molecule onto the (1 0 0), (0 1 0) and (0 0 1) surfaces of nano-sized anatase TiO 2 with semiempirical SCF MO method, MSINDO. The anatase TiO 2 particles are modeled with free clusters (TiO 2 ) n, where n = 20-80. Whereas, the surfaces have been modeled with two saturated clusters, Ti 21 O 58 H 32 and Ti 36 O 90 H 36 . The surface lattice fivefold coordinated titanium atoms (Ti 5C ), which represent the Lewis acid sites, are selected as adsorption centers. We also investigated the effect of TiO 2 cluster size on the computed band gap energy. Results reveal that the electronic properties of a cluster in the lowest excited state differ from that of the ground state. Furthermore, the MSINDO band gap energies of 3.68-3.77 eV for the anatase TiO 2 are in a fair accordance with other literature data. In agreement with other computational and experimental studies, the dissociated form of water molecule adsorption on anatase TiO 2 surfaces is always more stabilized than the molecular form

Controlled Clustering of Gold Nanoparticles using Solid-support for Surface-enhanced Raman Spectroscopic Probes

International Nuclear Information System (INIS)

Chang, Hyejin; Chae, Jinjoo; Jeong, Hong; Kang, Homan; Lee, Yoonsik

2014-01-01

We fabricated small clusters of gold nanoparticles by using solid-supported aggregation of gold nanoparticles. The fabricated Au nanoclusters consisting mainly of dimers showed homogeneous characteristics in cluster size and SERS intensity. The SERS enhancement of 4-ABT molecules in an effective area within 2-nm gap appeared to be approximately 10. Detachment process by ultrasonication was successively carried out in order to use the nanoclusters as SERS probes. The possibility of these clusters as SERS probe was proved in terms of signal and cluster size. Single molecule-level sensitivity of surface-enhanced Raman scattering (SERS) was known approximately fifteen years ago. Ever since there have been many different applications benefiting from the ultra-high sensitivity such as single molecule detection, chemical sensing and bio-molecular probes. Especially, SERS has drawn much attention in bio-multiplexing probes owing to its unique optical characteristics claiming extremely narrow bandwidth, high sensitivity of light signals, and non-bleaching feature

Controlled Clustering of Gold Nanoparticles using Solid-support for Surface-enhanced Raman Spectroscopic Probes

Energy Technology Data Exchange (ETDEWEB)

Chang, Hyejin; Chae, Jinjoo; Jeong, Hong [Department of Chemistry Education, Seoul (Korea, Republic of); Kang, Homan; Lee, Yoonsik [Interdisciplinary Program in Nano-Science and Technology, Pohang (Korea, Republic of)

2014-03-15

We fabricated small clusters of gold nanoparticles by using solid-supported aggregation of gold nanoparticles. The fabricated Au nanoclusters consisting mainly of dimers showed homogeneous characteristics in cluster size and SERS intensity. The SERS enhancement of 4-ABT molecules in an effective area within 2-nm gap appeared to be approximately 10. Detachment process by ultrasonication was successively carried out in order to use the nanoclusters as SERS probes. The possibility of these clusters as SERS probe was proved in terms of signal and cluster size. Single molecule-level sensitivity of surface-enhanced Raman scattering (SERS) was known approximately fifteen years ago. Ever since there have been many different applications benefiting from the ultra-high sensitivity such as single molecule detection, chemical sensing and bio-molecular probes. Especially, SERS has drawn much attention in bio-multiplexing probes owing to its unique optical characteristics claiming extremely narrow bandwidth, high sensitivity of light signals, and non-bleaching feature.

Cluster ions and van der Waals molecules

CERN Document Server

Smirnov, Boris M

1992-01-01

This review discusses current ideas in the physics and chemistry of cluster ions and Van der Waals molecules as well as presenting numerical data on their parameters and the processes involving them. It is also a detailed reference on basic data relating to many species.

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

Science.gov (United States)

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

An algebraic model for three-cluster giant molecules

International Nuclear Information System (INIS)

Hess, P.O.; Bijker, R.; Misicu, S.

2001-01-01

After an introduction to the algebraic U(7) model for three bodies, we present a relation of a geometrical description of three-cluster molecule to the algebraic U(7) model. Stiffness parameters of oscillations between each of two clusters are calculated and translated to the model parameter values of the algebraic model. The model is applied to the trinuclear system l32 Sn+ α + ll6 Pd which occurs in the ternary cold fission of 252 Cf. (Author)

Decoration of carbon nano surfaces with hydrogen and hydrogen rich molecules

International Nuclear Information System (INIS)

Zöttl, S.

2013-01-01

The use of helium nano droplets as a matrix to investigate different atomic and molecular samples is a well established experimental technique. The unique properties of helium allow for different analytical methods and at the same time provide a stable ambient temperature. Cluster growth inside helium nano droplets can be accomplished by repeatedly doping the droplets with sample particles in a controlled environment. The experimental work represented in this thesis was performed using helium nano droplets to create clusters of fullerenes like C 60 and C 70 . The adsorption properties of these fullerene clusters regarding hydrogen and hydrogen rich molecules have been subject to investigation. The observed results suggest that curved carbon nano surfaces offer higher storage densities than planar graphite surfaces. The use of C 60 as a model carbon nano structure provides a well understood molecule for testing and evaluating computational methods to calculate surface properties of various carbon nano materials. The cost effective storage of hydrogen for mobile applications plays a key role in the development of alternatives to fossil fuels. For that reason, the application of carbon nano materials to store hydrogen by adsorption has attracted much scientific attention lately. The insights gained in the presented thesis contribute to the collective efforts and deliver more refined tools to estimate the adsorption properties of future carbon nano materials. In addition to the aforementioned, a time-of-flight mass spectrometer for educational purpose has been designed and constructed in the framework of my PhD thesis. The instrument is successfully used in various lab courses and information on the setup can be found in the Appendix of this work. (author) [de

Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

Science.gov (United States)

Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

2017-09-28

This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe) 34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS 2 - ), carboxylate (-COO - ), and amine (-NH 2 )], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe) 34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

Advances in single-molecule magnet surface patterning through microcontact printing.

Science.gov (United States)

Mannini, Matteo; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M; Speets, Emiel A; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, Bart Jan; Reinhoudt, David N; Sessoli, Roberta; Gatteschi, Dante

2005-07-01

We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing microCP). We describe different approaches of microCP to print stripes of a sulfur-functionalized dodecamanganese (III, IV) cluster on gold surfaces. Comparison by atomic force microscopy profile analysis of the patterned structures confirms the formation of a chemically stable single layer of SMMs. Images based on chemical contrast, obtained by time-of-flight secondary ion mass spectrometry, confirm the patterned structure.

Dimensional scale effects on surface enhanced Raman scattering efficiency of self-assembled silver nanoparticle clusters

International Nuclear Information System (INIS)

Fasolato, C.; Domenici, F.; De Angelis, L.; Luongo, F.; Postorino, P.; Sennato, S.; Mura, F.; Costantini, F.; Bordi, F.

2014-01-01

A study of the Surface Enhanced Raman Scattering (SERS) from micrometric metallic nanoparticle aggregates is presented. The sample is obtained from the self-assembly on glass slides of micro-clusters of silver nanoparticles (60 and 100 nm diameter), functionalized with the organic molecule 4-aminothiophenol in water solution. For nanoparticle clusters at the micron scale, a maximum enhancement factor of 10 9 is estimated from the SERS over the Raman intensity ratio normalized to the single molecule contribution. Atomic force microscopy, correlated to spatially resolved Raman measurements, allows highlighting the connection between morphology and efficiency of the plasmonic system. The correlation between geometric features and SERS response of the metallic structures reveals a linear trend of the cluster maximum scattered intensity as a function of the surface area of the aggregate. On given clusters, the intensity turns out to be also influenced by the number of stacking planes of the aggregate, thus suggesting a plasmonic waveguide effect. The linear dependence results weakened for the largest area clusters, suggesting 30 μm 2 as the upper limit for exploiting the coherence over large scale of the plasmonic response.

Photo-stimulated desorption from water and methane clusters on the surface of solid neon

International Nuclear Information System (INIS)

Arakawa Ichiri; Matsumoto Dairo; Takekuma Shinichi; Tamura Reimi; Miura Takashi

2012-01-01

Photo-stimulated desorption of ions from methane and water heterocluster on the surface of solid neon was studied. The desorption yields of the variety of photo-desorbed species showed strong dependence on the composition and the size of the mother cluster. It was found that the presence of a water molecule in the cluster significantly enhanced, or was almost essential for, the desorption of any species observed. Systematic investigation of the correlation between the cluster size and the desorption yield of each ion has revealed the mother cluster which yields the each desorbed ion.

Individual Magnetic Molecules on Ultrathin Insulating Surfaces

Science.gov (United States)

El Hallak, Fadi; Warner, Ben; Hirjibehedin, Cyrus

2012-02-01

Single molecule magnets have attracted ample interest because of their exciting magnetic and quantum properties. Recent studies have demonstrated that some of these molecules can be evaporated on surfaces without losing their magnetic properties [M. Mannini et al., Nature 468, 417, (2010)]. This remarkable progress enhances the chances of real world applications for these molecules. We present STM imaging and spectroscopy data on iron phthalocyanine molecules deposited on Cu(100) and on a Cu2N ultrathin insulating surface. These molecules have been shown to display a large magnetic anisotropy on another thin insulating surface, oxidized Cu(110) [N. Tsukahara et al., Phys. Rev. Lett. 102, 167203 (2009)]. By using a combination of elastic and inelastic electron tunnelling spectroscopy, we investigate the binding of the molecules to the surface and the impact that the surface has on their electronic and magnetic properties.

Multipole moments of water molecules in clusters and ice Ih from first principles calculations

International Nuclear Information System (INIS)

Batista, E.R.; Xantheas, S.S.; Jonsson, H.

1999-01-01

We have calculated molecular multipole moments for water molecules in clusters and in ice Ih by partitioning the charge density obtained from first principles calculations. Various schemes for dividing the electronic charge density among the water molecules were used. They include Bader close-quote s zero flux surfaces and Voronoi partitioning schemes. A comparison was also made with an induction model including dipole, dipole-quadrupole, quadrupole-quadrupole polarizability and first hyperpolarizability as well as fixed octopole and hexadecapole moments. We have found that the different density partitioning schemes lead to widely different values for the molecular multipoles, illustrating how poorly defined molecular multipoles are in clusters and condensed environments. For instance, the magnitude of the molecular dipole moment in ice Ih ranges between 2.3 D and 3.1 D depending on the partitioning scheme used. Within each scheme, though, the value for the molecular dipole moment in ice is larger than in the hexamer. The magnitude of the molecular dipole moment in the clusters shows a monotonic increase from the gas phase value to the one in ice Ih, with the molecular dipole moment in the water ring hexamer being smaller than the one in ice Ih for all the partitioning schemes used. copyright 1999 American Institute of Physics

Surface-enhanced resonance Raman scattering spectroscopy of single R6G molecules

Institute of Scientific and Technical Information of China (English)

Zhou Zeng-Hui; Liu Li; Wang Gui-Ying; Xu Zhi-Zhan

2006-01-01

Surface-enhanced resonance Raman scattering (SERRS) of Rhodamine 6G (R6G) adsorbed on colloidal silver clusters has been studied. Based on the great enhancement of the Raman signal and the quench of the fluorescence, the SERRS spectra of R6G were recorded for the samples of dye colloidal solution with different concentrations. Spectral inhomogeneity behaviours from single molecules in the dried sample films were observed with complementary evidences, such as spectral polarization, spectral diffusion, intensity fluctuation of vibrational lines and even "breathing" of the molecules. Sequential spectra observed from a liquid sample with an average of 0.3 dye molecules in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1 or 2 molecules. Difference between the SERRS spectra of R6G excited by linearly and circularly polarized light were experimentally measured.

Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation.

Science.gov (United States)

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P; Fang, Yigang; Kostko, Oleg; Ahmed, Musahid; Head-Gordon, Martin

2017-05-23

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C 2 H 2 ) n + , just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4 H 4 + and C 6 H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2 H 2 ) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6 H 6 + isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.

Ab initio dynamics and photoionization mass spectrometry reveal ion–molecule pathways from ionized acetylene clusters to benzene cation

Science.gov (United States)

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; Fang, Yigang; Kostko, Oleg

2017-01-01

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion–molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion–molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM. PMID:28484019

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

Science.gov (United States)

Sørensen, L. K.; Fleig, T.; Olsen, J.

2009-08-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

International Nuclear Information System (INIS)

Soerensen, L K; Fleig, T; Olsen, J

2009-01-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Cluster structures influenced by interaction with a surface.

Science.gov (United States)

Witt, Christopher; Dieterich, Johannes M; Hartke, Bernd

2018-05-30

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Effects of incident cluster size, substrate temperature, and incident energy on bombardment of Ni clusters onto Cu (0 0 1) surface studied using molecular dynamics simulation

International Nuclear Information System (INIS)

Lin, Shiang-Jiun; Wu, Cheng-Da; Fang, Te-Hua; Chen, Guan-Hung

2012-01-01

The bombardment process of a Ni cluster onto a Cu (0 0 1) surface is studied using molecular dynamics (MD) simulations based on the tight-binding second-moment approximation (TB-SMA) many-body potential. The effects of incident cluster size, substrate temperature, and incident energy are evaluated in terms of molecular trajectories, kinetic energy, stress, self-diffusion coefficient, and sputtering yield. The simulation results clearly show that the penetration depth and Cu surface damage increase with increasing incident cluster size for a given incident energy per atom. The self-diffusion coefficient and the penetration depth of a cluster significantly increase with increasing substrate temperature. An incident cluster can be scattered into molecules or atoms that become embedded in the surface after incidence. When the incident energy is increased, the number of volcano-like defects and the penetration depth increase. A high sputtering yield can be obtained by increasing the incident energy at high temperature. The sputtering yield significantly increases with cluster size when the incident energy is above 5 eV/atom.

Clustering and segregation of small vacancy clusters near tungsten (0 0 1) surface

Science.gov (United States)

Duan, Guohua; Li, Xiangyan; Xu, Yichun; Zhang, Yange; Jiang, Yan; Hao, Congyu; Liu, C. S.; Fang, Q. F.; Chen, Jun-Ling; Luo, G.-N.; Wang, Zhiguang

2018-01-01

Nanoporous metals have been shown to exhibit radiation-tolerance due to the trapping of the defects by the surface. However, the behavior of vacancy clusters near the surface is not clear which involves the competition between the self-trapping and segregation of small vacancy clusters (Vn) nearby the surface. In this study, we investigated the energetic and kinetic properties of small vacancy clusters near tungsten (0 0 1) surface by combining molecular statics (MS) calculations and object Kinetic Monte Carlo (OKMC) simulations. Results show that vacancies could be clustered with the reduced formation energy and migration energy of the single vacancy around a cluster as the respective energetic and kinetic driving forces. The small cluster has a migration energy barrier comparable to that for the single vacancy; the migration energy barriers for V1-5 and V7 are 1.80, 1.94, 2.17, 2.78, 3.12 and 3.11 eV, respectively. Clusters and become unstable near surface (0 0 1) and tend to dissociate into the surface. At the operation temperature of 1000 K, the single vacancy, V2, 2 V 3 V3 and V4 were observed to segregate to the surface within a time of one hour. Meanwhile, larger clusters survived near the surface, which could serve as nucleating center for voids near the surface. Our results suggest that under a low radiation dose, surface (0 0 1) could act as a sink for small vacancy clusters, alleviating defect accumulation in the material under a low radiation dose. We also obtained several empirical expressions for the vacancy cluster formation energy, binding energy, and trapping radius as a function of the number of vacancies in the cluster.

Deposition of size-selected atomic clusters on surfaces

International Nuclear Information System (INIS)

Carroll, S.J.

1999-06-01

This dissertation presents technical developments and experimental and computational investigations concerned with the deposition of atomic clusters onto surfaces. It consists of a collection of papers, in which the main body of results are contained, and four chapters presenting a subject review, computational and experimental techniques and a summary of the results presented in full within the papers. Technical work includes the optimization of an existing gas condensation cluster source based on evaporation, and the design, construction and optimization of a new gas condensation cluster source based on RF magnetron sputtering (detailed in Paper 1). The result of cluster deposition onto surfaces is found to depend on the cluster deposition energy; three impact energy regimes are explored in this work. (1) Low energy: n clusters create a defect in the surface, which pins the cluster in place, inhibiting cluster diffusion at room temperature (Paper V). (3) High energy: > 50 eV/atom. The clusters implant into the surface. For Ag 20 -Ag 200 clusters, the implantation depth is found to scale linearly with the impact energy and inversely with the cross-sectional area of the cluster, with an offset due to energy lost to the elastic compression of the surface (Paper VI). For smaller (Ag 3 ) clusters the orientation of the cluster with respect to the surface and the precise impact site play an important role; the impact energy has to be 'focused' in order for cluster implantation to occur (Paper VII). The application of deposited clusters for the creation of Si nanostructures by plasma etching is explored in Paper VIII. (author)

Metal cluster compounds - chemistry and importance; clusters containing isolated main group element atoms, large metal cluster compounds, cluster fluxionality

International Nuclear Information System (INIS)

Walther, B.

1988-01-01

This part of the review on metal cluster compounds deals with clusters containing isolated main group element atoms, with high nuclearity clusters and metal cluster fluxionality. It will be obvious that main group element atoms strongly influence the geometry, stability and reactivity of the clusters. High nuclearity clusters are of interest in there own due to the diversity of the structures adopted, but their intermediate position between molecules and the metallic state makes them a fascinating research object too. These both sites of the metal cluster chemistry as well as the frequently observed ligand and core fluxionality are related to the cluster metal and surface analogy. (author)

Surface Passivation for Single-molecule Protein Studies

Science.gov (United States)

Chandradoss, Stanley D.; Haagsma, Anna C.; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

2014-01-01

Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation. PMID:24797261

Electrons from fixed in space molecules and clusters

International Nuclear Information System (INIS)

Doerner, R.; Jahnke, T.; Czasch, A.; Jagutzki, O.; Schmidt-Boecking; Kreidi, K.; Knapp, A.; Schmidt, L.; Schoeffler, M.; Foucar, L.; Cocke, C.L.; Osipov, T.; Alnaser, A.

2004-01-01

Full text: We use modern multi particle momentum imaging techniques (COLTRIMS) to measure the vector momenta of all charged fragments, ions, photoelectrons and Auger electrons for small molecules excited by synchrotron radiation. These complete images of the fragmentation give an umprecedented detailed insight in the molecular photoionization and Auger process. Also latest results on molecular double ionisation and on cluster fragmentation unveiling interatomic coulomb decay will be presented

Using self-consistent Gibbs free energy surfaces to calculate size distributions of neutral and charged clusters for the sulfuric acid-water binary system

Science.gov (United States)

Smith, J. A.; Froyd, K. D.; Toon, O. B.

2012-12-01

We construct tables of reaction enthalpies and entropies for the association reactions involving sulfuric acid vapor, water vapor, and the bisulfate ion. These tables are created from experimental measurements and quantum chemical calculations for molecular clusters and a classical thermodynamic model for larger clusters. These initial tables are not thermodynamically consistent. For example, the Gibbs free energy of associating a cluster consisting of one acid molecule and two water molecules depends on the order in which the cluster was assembled: add two waters and then the acid or add an acid and a water and then the second water. We adjust the values within the tables using the method of Lagrange multipliers to minimize the adjustments and produce self-consistent Gibbs free energy surfaces for the neutral clusters and the charged clusters. With the self-consistent Gibbs free energy surfaces, we calculate size distributions of neutral and charged clusters for a variety of atmospheric conditions. Depending on the conditions, nucleation can be dominated by growth along the neutral channel or growth along the ion channel followed by ion-ion recombination.

Photochemical dynamics of surface oriented molecules

International Nuclear Information System (INIS)

Ho, W.

1992-01-01

The period 8/01/91-7/31/92 is the first year of a new project titled ''Photochemical Dynamics of Surface Oriented Molecules'', initiated with DOE Support. The main objective of this project is to understand the dynamics of elementary chemical reactions by studying photochemical dynamics of surface-oriented molecules. In addition, the mechanisms of photon-surface interactions need to be elucidated. The strategy is to carry out experiments to measure the translational energy distribution, as a function of the angle from the surface normal, of the photoproducts by time-of-flight (TOF) technique by varying the photon wavelength, intensity, polarization, and pulse duration. By choosing adsorbates with different bonding configuration, the effects of adsorbate orientation on surface photochemical dynamics can be studied

Linear and nonlinear surface spectroscopy of supported size selected metal clusters and organic adsorbates

Energy Technology Data Exchange (ETDEWEB)

Thaemer, Martin Georg

2012-03-08

The spectroscopic investigation of supported size selected metal clusters over a wide wavelength range plays an important role for understanding their outstanding catalytic properties. The challenge which must be overcome to perform such measurements is the difficult detection of the weak spectroscopic signals from these samples. As a consequence, highly sensitive spectroscopic methods are applied, such as surface Cavity Ringdown Spectroscopy and surface Second Harmonic Generation Spectroscopy. The spectroscopic apparatus developed is shown to have a sensitivity which is high enough to detect sub-monolayer coverages of adsorbates on surfaces. In the measured spectra of small supported silver clusters of the sizes Ag{sub 4}2, Ag{sub 2}1, Ag{sub 9}, and Ag atoms a stepwise transition from particles with purely metallic character to particles with molecule-like properties can be observed within this size range.

Vacancy clusters at nanoparticle surfaces

Energy Technology Data Exchange (ETDEWEB)

Xu, J.; Moxom, J.; Somieski, B.; White, C.W. [Oak Ridge National Lab., TN (United States); Mills, A.P. Jr. [Bell Labs., Lucent Technologies, Murray Hill, NJ (United States); Suzuki, R.; Ishibashi, S. [Electrotechnical Lab., Tsukuba, Ibaraki (Japan); Ueda, A.; Henderson, D. [Physics Dept., Fisk Univ., Nashville, TN (United States)

2001-07-01

We detect vacancy clusters at Au nanoparticle surfaces using a combination of positron lifetime spectroscopy, 1- detector, and 2-detector measurements of Doppler broadening of annihilation radiation. Gold nanoparticles are formed by MeV implantation of gold ions into MgO (100) followed by annealing. Clusters of two Mg and two O vacancies (v{sub 4}) are attached to the gold nanoparticle surfaces within the projected range (R{sub p}). (orig.)

Vacancy clusters at nanoparticle surfaces

International Nuclear Information System (INIS)

Xu, J.; Moxom, J.; Somieski, B.; White, C.W.; Mills, A.P. Jr.; Suzuki, R.; Ishibashi, S.; Ueda, A.; Henderson, D.

2001-01-01

We detect vacancy clusters at Au nanoparticle surfaces using a combination of positron lifetime spectroscopy, 1- detector, and 2-detector measurements of Doppler broadening of annihilation radiation. Gold nanoparticles are formed by MeV implantation of gold ions into MgO (100) followed by annealing. Clusters of two Mg and two O vacancies (v 4 ) are attached to the gold nanoparticle surfaces within the projected range (R p ). (orig.)

Ultrafast dynamics of electronically excited molecules and clusters

International Nuclear Information System (INIS)

Lietard, Aude

2014-01-01

This PhD thesis investigated the ultrafast dynamics of photo-chromic molecules and argon clusters in the gas phase at the femtosecond timescale. Pump-probe experiments are performed in a set-up which associates a versatile pulsed molecular beam coupled to a photoelectron/photoion velocity map imager (VMI) and a time-of-flight mass spectrometer (TOF-MS). Theses pump-probe experiments provides the temporal evolution of the electronic distribution for each system of interest. Besides, a modelization has been performed in order to characterize the density and the velocity distribution in the pulsed beam. Regarding the photo-chromic di-thienyl-ethene molecules, parallel electronic relaxation pathways were observed. This contrasts with the observation of sequential relaxation processes in most molecules studied so far. In the present case, the initial wave packet splits in two parts. One part is driven to the ground state at the femtosecond time scale through a conical intersection, and the second part remains for ps in the excited state and experiences oscillations in a suspended well. This study has shed light into the intrinsic dynamics of the molecules under study and a general relaxation mechanism has been proposed, which applies to the whole family of di-thienyl-ethene molecules whatever the state of matter (gas phase or solution) in which they have been investigated. Concerning argon clusters excited at about 14 eV, two behaviors of different time scale have been observed at different time scales. The first one occurs in the first picoseconds of the dynamics. It corresponds to the electronic relaxation of an excitonic state at a rate of 1 eV.ps -1 . The second phenomenon corresponds to the localization of the exciton on the excimer Ar 2 *. This phenomenon is observed 4-5 ps after the excitation. In this study, we also observed the ejection of excited argon atoms, addressing the lifetime of the delocalized excitonic state. This work provide additional informations

Independent center, independent electron approximation for dynamics of molecules and clusters

International Nuclear Information System (INIS)

McGuire, J.H.; Straton, J.C.; Wang, J.; Wang, Y.D.; Weaver, O.L.; Corchs, S.E.; Rivarola, R.D.

1996-01-01

A formalism is developed for evaluating probabilities and cross sections for multiple-electron transitions in scattering of molecules and clusters by charged collision partners. First, the molecule is divided into subclusters each made up of identical centers (atoms). Within each subcluster coherent scattering from identical centers may lead to observable phase terms and a geometrical structure factor. Then, using a mean field approximation to describe the interactions between centers we obtain A I ∼ summation k product ke iδ k I A Ik . Second, the independent electron approximation for each center may be obtained by neglecting the correlation between electrons in each center. The probability amplitude for each center is then a product of single electron transition probability amplitudes, a Ik i , i.e. A Ik ≅ product iaik i . Finally, the independent subcluster approximation is introduced by neglecting the interactions between different subclusters in the molecule or cluster. The total probability amplitude then reduces to a simple product of amplitudes for each subcluster, A≅ product IAI . Limitations of this simple approximation are discussed. copyright 1996 American Institute of Physics

Effects on energetic impact of atomic clusters with surfaces

International Nuclear Information System (INIS)

Popok, V.N.; Vuchkovich, S.; Abdela, A.; Campbell, E.E.B.

2007-01-01

A brief state-of-the-art review in the field of cluster ion interaction with surface is presented. Cluster beams are efficient tools for manipulating agglomerates of atoms providing control over the synthesis as well as modification of surfaces on the nm-scale. The application of cluster beams for technological purposes requires knowledge of the physics of cluster-surface impact. This has some significant differences compared to monomer ion - surface interactions. The main effects of cluster-surface collisions are discussed. Recent results obtained in experiments on silicon surface nanostructuring using keV-energy implantation of inert gas cluster ions are presented and compared with molecular dynamics simulations. (authors)

Interaction of intense electromagnetic fields with SF6 molecules and clusters in supersonic expansion

International Nuclear Information System (INIS)

Airoldi, V.J.T.

1987-01-01

A method of measuring SF 6 cluster formation and inhibition in pulsed supersonic expansion in the presence of intense electromagnetic radiation is presented. The characterization of the expansion of SF 6 molecules was done and, the extension of the collision region was determined. An improved unidimensional theory of supersonic expansion showed good agreement with the experimental results. The spectra of multiphoton absorption of SF 6 molecules in supersonic jet and the average energy absorved by each molecule were determined. The absorption spectra of molecule in the collision region present absorption maxima different from those obtained in the collisionless region. The results, if compared with the literature data, show good agreement, with a small difference in the spetra corresponding to the collisionless region. This difference was observed, for the first time in the multiphoton absorption and is attribuited to cluster formation in the jet. A new technique for measuring cluster formation in the supersonic jet, based on determination of the spatial distribution of the energy of molecules in the jet after passing through a skimmer located in the collision region is shown. The inhibition of cluster formation, due to the incidence of intense electromagnetic radiation from a CO 2 -TEA pulsed laser in the initial collision region of the jet, causes a second expansion in the skimmer. The results obtained show that this method can lead to a new isotope separation process. All the parts of the experimental set up, for example, high vacuum system, pulsed valve and pyroelectric detector, were developed and constructed specially for the experiment. (Author) [pt

Electric dipole moments of nanosolvated acid molecules in water clusters.

Science.gov (United States)

Guggemos, Nicholas; Slavíček, Petr; Kresin, Vitaly V

2015-01-30

The electric dipole moments of (H2O)nDCl (n=3-9) clusters have been measured by the beam-deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at n≈5-6. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular-dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero-point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.

The Role of Molecule Clustering by Hydrogen Bond in Hydrous Ethanol on Laminar Burning Velocity

Directory of Open Access Journals (Sweden)

I Made Suarta

2016-01-01

Full Text Available The role of hydrogen bond molecule clustering in laminar burning velocities was observed. The water in hydrous ethanol can change the interaction between water-ethanol molecules. A certain amount of water can become oxygenated which increases the burning velocity. The hydrogen bond interaction pattern of ethanol and water molecules was modeled. Based on the molecular model, azeotropic behavior emerges from ethanol-water hydrogen bond, which is at a 95.1%v composition. The interaction with water molecule causes the ethanol molecule to be clustered with centered oxygenated compound. So, it supplies extra oxygen and provides intermolecular empty spaces that are easily infiltrated by the air. In the azeotropic composition, the molecular bond chain is the shortest, so hypothetically the burning velocity is anticipated to increase. The laminar burning velocity of ethanol fuel was tested in a cylindrical explosion bomb in lean, stoichiometric, and rich mixtures. The experimental result showed that the maximum burning velocity occurred at hydrous ethanol of 95.5%v composition. This discrepancy is the result of the addition of energy from 7.7% free ethanol molecules that are not clustered. At the rich mixture, the burning velocity of this composition is higher than that of anhydrous ethanol.

Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts.

Science.gov (United States)

Kardash, Maria E; Dzuba, Sergei A

2017-05-25

The clustering of molecules is an important feature of plasma membrane organization. It is challenging to develop methods for quantifying membrane heterogeneities because of their transient nature and small size. Here, we obtained evidence that transient membrane heterogeneities can be frozen at cryogenic temperatures which allows the application of solid-state experimental techniques sensitive to the nanoscale distance range. We employed the pulsed version of electron paramagnetic resonance (EPR) spectroscopy, the electron spin echo (ESE) technique, for spin-labeled molecules in multilamellar lipid bilayers. ESE decays were refined for pure contribution of spin-spin magnetic dipole-dipolar interaction between the labels; these interactions manifest themselves at a nanometer distance range. The bilayers were prepared from different types of saturated and unsaturated lipids and cholesterol (Chol); in all cases, a small amount of guest spin-labeled substances 5-doxyl-stearic-acid (5-DSA) or 3β-doxyl-5α-cholestane (DChl) was added. The local concentration found of 5-DSA and DChl molecules was remarkably higher than the mean concentration in the bilayer, evidencing the formation of lipid-mediated clusters of these molecules. To our knowledge, formation of nanoscale clusters of guest amphiphilic molecules in biological membranes is a new phenomenon suggested only recently. Two-dimensional 5-DSA molecular clusters were found, whereas flat DChl molecules were found to be clustered into stacked one-dimensional structures. These clusters disappear when the Chol content is varied between the boundaries known for lipid raft formation at room temperatures. The room temperature EPR evidenced entrapping of DChl molecules in the rafts.

Desorption of large molecules with light-element clusters: Effects of cluster size and substrate nature

Energy Technology Data Exchange (ETDEWEB)

Delcorte, Arnaud, E-mail: arnaud.delcorte@uclouvain.be [Institute of Condensed Matter and Nanosciences - Bio and Soft Matter, Universite catholique de Louvain, Croix du Sud, 1 bte 3, B-1348 Louvain-la-Neuve (Belgium); Garrison, Barbara J. [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)

2011-07-15

This contribution focuses on the conditions required to desorb a large hydrocarbon molecule using light-element clusters. The test molecule is a 7.5 kDa coil of polystyrene (PS61). Several projectiles are compared, from C{sub 60} to 110 kDa organic droplets and two substrates are used, amorphous polyethylene and mono-crystalline gold. Different aiming points and incidence angles are examined. Under specific conditions, 10 keV nanodrops can desorb PS61 intact from a gold substrate and from a soft polyethylene substrate. The prevalent mechanism for the desorption of intact and 'cold' molecules is one in which the molecules are washed away by the projectile constituents and entrained in their flux, with an emission angle close to {approx}70 deg. The effects of the different parameters on the dynamics and the underlying physics are discussed in detail and the predictions of the model are compared with other published studies.

Desorption of large molecules with light-element clusters: Effects of cluster size and substrate nature

International Nuclear Information System (INIS)

Delcorte, Arnaud; Garrison, Barbara J.

2011-01-01

This contribution focuses on the conditions required to desorb a large hydrocarbon molecule using light-element clusters. The test molecule is a 7.5 kDa coil of polystyrene (PS61). Several projectiles are compared, from C 60 to 110 kDa organic droplets and two substrates are used, amorphous polyethylene and mono-crystalline gold. Different aiming points and incidence angles are examined. Under specific conditions, 10 keV nanodrops can desorb PS61 intact from a gold substrate and from a soft polyethylene substrate. The prevalent mechanism for the desorption of intact and 'cold' molecules is one in which the molecules are washed away by the projectile constituents and entrained in their flux, with an emission angle close to ∼70 deg. The effects of the different parameters on the dynamics and the underlying physics are discussed in detail and the predictions of the model are compared with other published studies.

Molecule scattering from insulator and metal surfaces

International Nuclear Information System (INIS)

Moroz, Iryna; Ambaye, Hailemariam; Manson, J R

2004-01-01

Calculations are carried out and compared with data for the scattering of CH 4 molecules from a LiF(001) surface and for O 2 scattering from Al(111). The theory is a mixed classical-quantum formalism that includes energy and momentum transfers between the surface and projectile for translational and rotational motions as well as internal mode excitation of the projectile molecule. The translational and rotational degrees of freedom couple most strongly to multiphonon excitations of the surface and are treated with classical dynamics. Internal vibrational excitations of the molecules are treated with a semiclassical formalism with extension to arbitrary numbers of modes and arbitrary quantum numbers. Calculations show good agreement for the dependence on incident translational energy, incident beam angle and surface temperature when compared with data for energy-resolved intensity spectra and angular distributions

Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling

Directory of Open Access Journals (Sweden)

Remus Daniela M

2012-11-01

Full Text Available Abstract Background Bacterial cell surface-associated polysaccharides are involved in the interactions of bacteria with their environment and play an important role in the communication between pathogenic bacteria and their host organisms. Cell surface polysaccharides of probiotic species are far less well described. Therefore, improved knowledge on these molecules is potentially of great importance to understand the strain-specific and proposed beneficial modes of probiotic action. Results The Lactobacillus plantarum WCFS1 genome encodes 4 clusters of genes that are associated with surface polysaccharide production. Two of these clusters appear to encode all functions required for capsular polysaccharide formation (cps2A-J and cps4A-J, while the remaining clusters are predicted to lack genes encoding chain-length control functions and a priming glycosyl-transferase (cps1A-I and cps3A-J. We constructed L. plantarum WCFS1 gene deletion mutants that lack individual (Δcps1A-I, Δcps2A-J, Δcps3A-J and Δcps4A-J or combinations of cps clusters (Δcps1A-3J and Δcps1A-3I, Δcps4A-J and assessed the genome wide impact of these mutations by transcriptome analysis. The cps cluster deletions influenced the expression of variable gene sets in the individual cps cluster mutants, but also considerable numbers of up- and down-regulated genes were shared between mutants in cps cluster 1 and 2, as well as between mutant in cps clusters 3 and 4. Additionally, the composition of overall cell surface polysaccharide fractions was altered in each mutant strain, implying that despite the apparent incompleteness of cps1A-I and cps3A-J, all clusters are active and functional in L. plantarum. The Δcps1A-I strain produced surface polysaccharides in equal amounts as compared to the wild-type strain, while the polysaccharides were characterized by a reduced molar mass and the lack of rhamnose. The mutants that lacked functional copies of cps2A-J, cps3A-J or cps4A

Adsorption of metal-phthalocyanine molecules onto the Si(111) surface passivated by δ doping: Ab initio calculations

Science.gov (United States)

Veiga, R. G. A.; Miwa, R. H.; McLean, A. B.

2016-03-01

We report first-principles calculations of the energetic stability and electronic properties of metal-phthalocyanine (MPc) molecules (M = Cr, Mn, Fe, Co, Ni, Cu, and Zn) adsorbed on the δ -doped Si(111)-B (√{3 }×√{3 }) reconstructed surface. (i) It can be seen that CrPc, MnPc, FePc, and CoPc are chemically anchored to the topmost Si atom. (ii) Contrastingly, the binding of the NiPc, CuPc, and ZnPc molecules to the Si (111 ) -B (√{3 }×√{3 }) surface is exclusively ruled by van der Waals interactions, the main implication being that these molecules may diffuse and rearrange to form clusters and/or self-organized structures on this surface. The electronic structure calculations reveal that in point (i), owing to the formation of the metal-Si covalent bond, the net magnetic moment of the molecule is quenched by 1 μB , remaining unchanged in point (ii). In particular, the magnetic moment of CuPc (1 μB ) is preserved after adsorption. Finally, we verify that the formation of ZnPc, CuPc, and NiPc molecular (self-assembled) arrangements on the Si(111)-B (√{3 }×√{3 } ) surface is energetically favorable, in good agreement with recent experimental findings.

Electrostrictive deformations in small carbon clusters, hydrocarbon molecules, and carbon nanotubes

International Nuclear Information System (INIS)

Cabria, I.; Lopez, M. J.; Alonso, J. A.; Amovilli, C.; March, N. H.

2006-01-01

The electrostrictive response of small carbon clusters, hydrocarbon molecules, and carbon nanotubes is investigated using the density functional theory. For ringlike carbon clusters, one can get insight on the deformations induced by an electric field from a simple two-dimensional model in which the positive charge of the carbon ions is smeared out in a circular homogeneous line of charge and the electronic density is calculated for a constant applied electric field within a two-dimensional Thomas-Fermi method. According to the Hellmann-Feynman theorem, this model predicts, for fields of about 1 V/A ring , only a small elongation of the ring clusters in the direction of the electric field. Full three-dimensional density functional calculations with an external electric field show similar small deformations in the ring carbon clusters compared to the simple model. The saturated benzene and phenanthrene hydrocarbon molecules do not experience any deformation, even under the action of relatively intense (1 V/A ring ) electric fields. In contrast, finite carbon nanotubes experience larger elongations (∼2.9%) induced by relatively weak (0.1 V/A ring ) applied electric fields. Both C-C bond length elongation and the deformation of the honeycomb structure contribute equally to the nanotube elongation. The effect of the electric field in hydrogen terminated nanotubes is reduced with respect to the nanotubes with dangling bonds in the edges

Fano-induced spontaneous emission enhancement of molecule placed in a cluster of asymmetrically-arranged metallic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Le, Khai Q., E-mail: khai.lequang@hoasen.edu.vn [Faculty of Science and Technology, Hoa Sen University, Ho Chi Minh (Viet Nam); Department of Electrical Engineering, University of Minnesota, Duluth, MN 55812 (United States); Bai, Jing [Department of Electrical Engineering, University of Minnesota, Duluth, MN 55812 (United States); Nguyen, H.P.T. [Department of Electrical and Computer Engineering, New Jersey Institute of Technology, NJ 07102 (United States)

2016-05-15

We demonstrate that plasmonic Fano resonance significantly boosts spontaneous emission rate of a single emitter, e.g. atom, molecule and quantum dot, over a moderately broad emission spectrum. An emission enhancement of up to 140 times compared to the system with no external inclusion at tunable frequencies is achieved, providing a new complementary enhancement mechanism. Fano resonance is induced in clusters of four asymmetric-arranged nanoparticles with ultra-small inter-particle gaps. It is shown to play a dominant role in light-emitting enhancement, mediated by combined localized surface plasmon resonances.

Single Molecule Raman Detection of Enkephalin on Silver Colloidal Particles

DEFF Research Database (Denmark)

Kneipp, Katrin; Kneipp, Holger; Abdali, Salim

2004-01-01

the Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm-1 can be used as “intrinsic marker” for detecting a single enkephalin molecule...... and for monitoring its diffusion on the surface of the silver colloidal cluster without using a specific label molecule....

Surface processing with ionized cluster beams: computer simulation

International Nuclear Information System (INIS)

Insepov, Z.; Yamada, I.

1999-01-01

Molecular Dynamics (MD) and Monte Carlo (MC) models of energetic gas cluster irradiation of a solid surface have been developed to investigate the phenomena of crater formation, sputtering, surface treatment, and the material hardness evaluation by irradiation with cluster ions. Theoretical estimation of crater dimensions formed with Ar gas cluster ion irradiation of different substrates, based on hydrodynamics and MD simulation, are presented. The atomic scale shock waves arising from cluster impact were obtained by calculating the pressure, temperature and mass-velocity of the target atoms. The crater depth is given as a unique 1/3 dependence on the cluster energy and on the cold material Brinell hardness number (BHN). A new 'true material hardness' scale which can be very useful for example for thin film coatings deposited on a soft substrate, is defined. This finding could be used as a new technique for measuring of a material hardness. Evolution of surface morphology under cluster ion irradiation was described by the surface relaxation equation which contains a term of crater formation at cluster impact. The formation of ripples on a surface irradiated with oblique cluster ion beams was predicted. MD and MC models of Decaborane ion (B 10 H 14 ) implantation into Si and the following rapid thermal annealing (RTA) have been developed

Ion collision-induced chemistry in pure and mixed loosely bound clusters of coronene and C60 molecules.

Science.gov (United States)

Domaracka, Alicja; Delaunay, Rudy; Mika, Arkadiusz; Gatchell, Michael; Zettergren, Henning; Cederquist, Henrik; Rousseau, Patrick; Huber, Bernd A

2018-05-23

Ionization, fragmentation and molecular growth have been studied in collisions of 22.5 keV He2+- or 3 keV Ar+-projectiles with pure loosely bound clusters of coronene (C24H12) molecules or with loosely bound mixed C60-C24H12 clusters by using mass spectrometry. The heavier and slower Ar+ projectiles induce prompt knockout-fragmentation - C- and/or H-losses - from individual molecules and highly efficient secondary molecular growth reactions before the clusters disintegrate on picosecond timescales. The lighter and faster He2+ projectiles have a higher charge and the main reactions are then ionization by ions that are not penetrating the clusters. This leads mostly to cluster fragmentation without molecular growth. However, here penetrating collisions may also lead to molecular growth but to a much smaller extent than with 3 keV Ar+. Here we present fragmentation and molecular growth mass distributions with 1 mass unit resolution, which reveals that the same numbers of C- and H-atoms often participate in the formation and breaking of covalent bonds inside the clusters. We find that masses close to those with integer numbers of intact coronene molecules, or with integer numbers of both intact coronene and C60 molecules, are formed where often one or several H-atoms are missing or have been added on. We also find that super-hydrogenated coronene is formed inside the clusters.

Surface functionalization of aluminosilicate nanotubes with organic molecules

Directory of Open Access Journals (Sweden)

Wei Ma

2012-02-01

Full Text Available The surface functionalization of inorganic nanostructures is an effective approach for enriching the potential applications of existing nanomaterials. Inorganic nanotubes attract great research interest due to their one-dimensional structure and reactive surfaces. In this review paper, recent developments in surface functionalization of an aluminosilicate nanotube, “imogolite”, are introduced. The functionalization processes are based on the robust affinity between phosphate groups of organic molecules and the aluminol (AlOH surface of imogolite nanotubes. An aqueous modification process employing a water soluble ammonium salt of alkyl phosphate led to chemisorption of molecules on imogolite at the nanotube level. Polymer-chain-grafted imogolite nanotubes were prepared through surface-initiated polymerization. In addition, the assembly of conjugated molecules, 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-ylethylphosphonic acid (HT3P and 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-ylethylphosphonic acid 1,1-dioxide (HT3OP, on the imogolite nanotube surface was achieved by introducing a phosphonic acid group to the corresponding molecules. The optical and photophysical properties of these conjugated-molecule-decorated imogolite nanotubes were characterized. Moreover, poly(3-hexylthiophene (P3HT chains were further hybridized with HT3P modified imogolite to form a nanofiber hybrid.

Formation of self-assembled monolayer of curcuminoid molecules on gold surfaces

International Nuclear Information System (INIS)

Berlanga, Isadora; Etcheverry-Berríos, Álvaro; Mella, Andy; Jullian, Domingo; Gómez, Victoria Alejandra; Aliaga-Alcalde, Núria; Fuenzalida, Victor; Flores, Marcos

2017-01-01

Highlights: • Thiophene curcuminoid molecules deposited on a gold surface by immersion. • Molecular dynamic studies of the molecular arrangement approaching the surface. • XPS and STM studies showing different arrangement of the molecules on the surface. • Molecular Interaction with surface depends on the sulfur position in thiophene rings. • Temporal evolution of the molecular arrangement on the surface. - Abstract: We investigated the formation of self-assembled monolayers of two thiophene curcuminoid molecules, 2-thphCCM (1) and 3-thphCCM (2), on polycrystalline gold substrates prepared by immersion of the surfaces in a solution of the molecules during 24 h. The functionalized surfaces were studied by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). Despite the fact that both molecules have the same composition and almost the same structure, these molecules exhibit different behavior on the gold surface, which can be explained by the different positions of the sulfur atoms in the terminal aromatic rings. In the case of molecule 1, the complete formation of a SAM can be observed after 24 h of immersion. In the case of molecule 2, the transition from flat-lying to upright configuration on the surface is still in process after 24 h of immersion. This is attributed to the fact that molecule 2 have the sulfur atoms more exposed than molecule 1.

Formation of self-assembled monolayer of curcuminoid molecules on gold surfaces

Energy Technology Data Exchange (ETDEWEB)

Berlanga, Isadora [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Blanco Encalada 2008, Santiago (Chile); Etcheverry-Berríos, Álvaro; Mella, Andy; Jullian, Domingo [Departamento de Ciencia de los Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Beaucheff 851, Santiago (Chile); Gómez, Victoria Alejandra [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Blanco Encalada 2008, Santiago (Chile); Aliaga-Alcalde, Núria [ICREA (Institució Catalana de Recerca i Estudis Avançats), Passeig Lluís Companys, 23, 08018, Barcelona (Spain); CSIC-ICMAB (Institut de Ciència dels Materials de Barcelona), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra (Spain); Fuenzalida, Victor [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Blanco Encalada 2008, Santiago (Chile); Flores, Marcos, E-mail: mflorescarra@ing.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Av. Blanco Encalada 2008, Santiago (Chile); and others

2017-01-15

Highlights: • Thiophene curcuminoid molecules deposited on a gold surface by immersion. • Molecular dynamic studies of the molecular arrangement approaching the surface. • XPS and STM studies showing different arrangement of the molecules on the surface. • Molecular Interaction with surface depends on the sulfur position in thiophene rings. • Temporal evolution of the molecular arrangement on the surface. - Abstract: We investigated the formation of self-assembled monolayers of two thiophene curcuminoid molecules, 2-thphCCM (1) and 3-thphCCM (2), on polycrystalline gold substrates prepared by immersion of the surfaces in a solution of the molecules during 24 h. The functionalized surfaces were studied by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). Despite the fact that both molecules have the same composition and almost the same structure, these molecules exhibit different behavior on the gold surface, which can be explained by the different positions of the sulfur atoms in the terminal aromatic rings. In the case of molecule 1, the complete formation of a SAM can be observed after 24 h of immersion. In the case of molecule 2, the transition from flat-lying to upright configuration on the surface is still in process after 24 h of immersion. This is attributed to the fact that molecule 2 have the sulfur atoms more exposed than molecule 1.

Low-energy irradiation effects of gas cluster ion beams

International Nuclear Information System (INIS)

Houzumi, Shingo; Takeshima, Keigo; Mochiji, Kozo; Toyoda, Noriaki; Yamada, Isao

2007-01-01

A cluster-ion irradiation system with cluster-size selection has been developed to study the effects of the cluster size for surface processes using cluster ions. A permanent magnet with a magnetic field of 1.2 T is installed for size separation of large cluster ions. Trace formations at HOPG surface by the irradiation with size-selected Ar-cluster ions under acceleration energy of 30 keV were investigated by a scanning tunneling microscopy. Generation behavior of the crater-like traces is strongly affected by the number of constituent atoms (cluster size) of the irradiating cluster ion. When the incident cluster ion is composed of 100-3000 atoms, crater-like traces are observed on the irradiated surfaces. In contrast, such traces are not observed at all with the irradiation of the cluster-ions composed of over 5000 atoms. Such the behavior is discussed on the basis of the kinetic energy per constituent atom of the cluster ion. To study GCIB irradiation effects against macromolecule, GCIB was irradiated on DNA molecules absorbed on graphite surface. By the GCIB irradiation, much more DNA molecules was sputtered away as compared with the monomer-ion irradiation. (author)

Far-Infrared Spectroscopy of Weakly Bound Hydrated Cluster Molecules

DEFF Research Database (Denmark)

Andersen, Jonas

The thermodynamic properties of condensed phases, the functionality of many materials and the molecular organization in biological organisms are all governed by the classes of non-covalent interactions that occur already on the microscopic scale between pairs of molecules. A detailed investigation...... of the intermolecular interactions between prototypical molecular assemblies are valuable for accurate descriptions of larger supramolecular systems such as materials, gas hydrates and biological macromolecules. The aim of this PhD dissertation is to investigate intermolecular interactions fora series of medium...... vibrational bands of the cluster molecules in the challenging far-infrared and terahertz spectral regions.A key parameter in the validation of the performance of theoretical predictions for weak non-covalent intermolecular interactions is the dissociation energy D0 that depends heavily on the class of large...

Formation of clusters composed of C60 molecules via self-assembly in critical fluids

International Nuclear Information System (INIS)

Fukuda, Takahiro; Ishii, Koji; Kurosu, Shunji; Whitby, Raymond; Maekawa, Toru

2007-01-01

Fullerenes are promising candidates for intelligent, functional nanomaterials because of their unique mechanical, electronic and chemical properties. However, it is necessary to invent some efficient but relatively simple methods of producing structures composed of fullerenes for the development of nanomechatronic, nanoelectronic and biochemical devices and sensors. In this paper, we show that various structures such as straight fibres, networks formed by fibres, wide sheets and helical structures, which are composed of C 60 molecules, are created by placing C 60 -crystals in critical ethane, carbon dioxide and xenon even though C 60 molecules do not dissolve or disperse in the above fluids. It is supposed, judging by the intermolecular potentials between C 60 and C 60 , between C 60 and ethane, and between ethane and ethane, that C 60 -clusters grow with the assistance of solvent molecules, which are trapped between C 60 molecules under critical conditions. This room-temperature self-assembly cluster growth process in critical fluids may open up a new methodology of forming structures built up with fullerenes without the need for any ultra-fine processing technologies

Dynamics of photoprocesses induced by femtosecond infrared radiation in free molecules and clusters of iron pentacarbonyl

International Nuclear Information System (INIS)

Kompanets, V. O.; Lokhman, V. N.; Poydashev, D. G.; Chekalin, S. V.; Ryabov, E. A.

2016-01-01

The dynamics of photoprocesses induced by femtosecond infrared radiation in free Fe(CO) 5 molecules and their clusters owing to the resonant excitation of vibrations of CO bonds in the 5-μm range has been studied. The technique of infrared excitation and photoionization probing (λ = 400 nm) by femtosecond pulses has been used in combination with time-of-flight mass spectrometry. It has been found that an infrared pulse selectively excites vibrations of CO bonds in free molecules, which results in a decrease in the yield of the Fe(CO) 5 + molecular ion. Subsequent relaxation processes have been analyzed and the results have been interpreted. The time of the energy transfer from excited vibrations to other vibrations of the molecule owing to intramolecular relaxation has been measured. The dynamics of dissociation of [Fe(CO) 5 ] n clusters irradiated by femtosecond infrared radiation has been studied. The time dependence of the yield of free molecules has been measured under different infrared laser excitation conditions. We have proposed a model that well describes the results of the experiment and makes it possible, in particular, to calculate the profile of variation of the temperature of clusters within the “evaporation ensemble” concept. The intramolecular and intracluster vibrational relaxation rates in [Fe(CO) 5 ] n clusters have been estimated.

Cluster-surface collisions: Characteristics of Xe55- and C20 - Si[111] surface bombardment

International Nuclear Information System (INIS)

Cheng, H.

1999-01-01

Molecular dynamics (MD) simulations are performed to study the cluster-surface collision processes. Two types of clusters, Xe 55 and C 20 are used as case studies of materials with very different properties. In studies of Xe 55 - Si[111] surface bombardment, two initial velocities, 5.0 and 10.0 km/s (normal to the surface) are chosen to investigate the dynamical consequences of the initial energy or velocity in the cluster-surface impact. A transition in the speed of kinetic energy propagation, from subsonic velocities to supersonic velocities, is observed. Energy transfer, from cluster translational motion to the substrate, occurs at an extremely fast rate that increases as the incident velocity increases. Local melting and amorphous layer formation in the surfaces are found via energetic analysis of individual silicon atoms. For C 20 , the initial velocity ranges from 10 to 100 km/s. The clusters are damaged immediately upon impact. Similar to Xe 55 , increase in the potential energy is larger than the increase in internal kinetic energy. However, the patterns of energy distribution are different for the two types of clusters. The energy transfer from the carbon clusters to Si(111) surface is found to be slower than that found in the Xe clusters. Fragmentation of the carbon cluster occurs when the initial velocity is greater than 30 km/s. At 10 km/s, the clusters show recrystallization at later times. The average penetration depth displays a nonlinear dependence on the initial velocity. Disturbance in the surface caused by C 20 is discussed and compared to the damage caused by Xe 55 . Energetics, structures, and dynamics of these systems are fully analyzed and characterized. copyright 1999 American Institute of Physics

Simulation of resonance hyper-Rayleigh scattering of molecules and metal clusters using a time-dependent density functional theory approach.

Science.gov (United States)

Hu, Zhongwei; Autschbach, Jochen; Jensen, Lasse

2014-09-28

Resonance hyper-Rayleigh scattering (HRS) of molecules and metal clusters have been simulated based on a time-dependent density functional theory approach. The resonance first-order hyperpolarizability (β) is obtained by implementing damped quadratic response theory using the (2n + 1) rule. To test this implementation, the prototypical dipolar molecule para-nitroaniline (p-NA) and the octupolar molecule crystal violet are used as benchmark systems. Moreover, small silver clusters Ag 8 and Ag 20 are tested with a focus on determining the two-photon resonant enhancement arising from the strong metal transition. Our results show that, on a per atom basis, the small silver clusters possess two-photon enhanced HRS comparable to that of larger nanoparticles. This finding indicates the potential interest of using small metal clusters for designing new nonlinear optical materials.

Photodissociation of hydrogen iodide on the surface of large argon clusters: The orientation of the librational wave function and the scattering from the cluster cage

International Nuclear Information System (INIS)

Slavicek, Petr; Jungwirth, Pavel; Lewerenz, Marius; Nahler, N. Hendrik; Farnik, Michal; Buck, Udo

2004-01-01

A set of photodissociation experiments and simulations of hydrogen iodide (HI) on Ar n clusters, with an average size =139, has been carried out for different laser polarizations. The doped clusters are prepared by a pick-up process. The HI molecule is then photodissociated by a UV laser pulse and the outgoing H fragment is ionized by resonance enhanced multiphoton ionization in a (2+1) excitation scheme within the same laser pulse at the wavelength of 243 nm. The measured time-of-flight spectra are transformed into hydrogen kinetic energy distributions. They exhibit a strong fraction of caged H atoms at zero-kinetic energy and peaks at the unperturbed cage exit for both spin-orbit channels nearly independent of the polarization. At this dissociation wavelength, the bare HI molecule exhibits a strict state separation, with a parallel transition to the spin-orbit excited state and perpendicular transitions to the ground state. The experimental results have been reproduced using molecular simulation techniques. Classical molecular dynamics was used to estimate the HI dopant distribution after the pick-up procedure. Subsequently, quasi-classical molecular dynamics (Wigner trajectories approach) has been applied for the photodissociation dynamics. The following main results have been obtained: (i) The HI dopant lands on the surface of the argon cluster during the pick-up process, (ii) zero-point energy plays a dominant role for the hydrogen orientation in the ground state of HI-Ar n surface clusters, qualitatively changing the result of the photodissociation experiment upon increasing the number of argon atoms, and, finally, (iii) the scattering of hydrogen atoms from the cage which originate from different dissociation states seriously affects the experimentally measured kinetic energy distributions

Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

Science.gov (United States)

Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

2016-01-01

The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013

Structure and dynamics of molecular clusters. 2. Melting and freezing of CCl4 clusters

International Nuclear Information System (INIS)

Bartell, L.S.; Chen, Jian

1992-01-01

Phase transitions of a 225-molecule cluster of carbon tetrachloride have been studied by a molecular dynamics simulation. A five-site model potential function was developed to reproduce the density and heat of vaporization of the bulk liquid. Computations began with orientationally disordered molecules distributed in fcc lattice sites of a nearly spherical cluster. The cluster was heated from a low temperature to 200 K in 10-deg steps of 50 ps each and then cooled to 10 K. Translational and rotational transitions were monitored by following several indicators including the translational and rotational diffusion and rotational entropies of individual molecules. Melting began at the surface and propagated inward as the temperature increased. Solidification of the molten cluster proceeded from the center to the surface. At the high cooling rate of the simulation, however, molecules were unable to organize into a crystalline array and solidified into a glassy structure instead. Except for spatial order, the indicators of degree of liquefaction exhibited almost the same temperature dependence in the crystsl → liquid as in the liquid → glass transition, a behavior that could be rationalized on the basis of Lindemann's theory of melting. Results were compared with predictions of an illustrative model due to Reiss, Mirabel, and Whetten. Qualitatively, the model included all of the features of the simulation. Quantitatively, the model grossly underestimated the range over which the melting transition took place. 40 refs., 10 figs., 1 tab

Mechanism of Shiga Toxin Clustering on Membranes

DEFF Research Database (Denmark)

Pezeshkian, Weria; Gao, Haifei; Arumugam, Senthil

2017-01-01

between them. The precise mechanism by which this clustering occurs remains poorly defined. Here, we used vesicle and cell systems and computer simulations to show that line tension due to curvature, height, or compositional mismatch, and lipid or solvent depletion cannot drive the clustering of Shiga...... toxin molecules. By contrast, in coarse-grained computer simulations, a correlation was found between clustering and toxin nanoparticle-driven suppression of membrane fluctuations, and experimentally we observed that clustering required the toxin molecules to be tightly bound to the membrane surface...... molecules (several nanometers), and persist even beyond. This force is predicted to operate between manufactured nanoparticles providing they are sufficiently rigid and tightly bound to the plasma membrane, thereby suggesting a route for the targeting of nanoparticles to cells for biomedical applications....

Exactly soluble models for surface partition of large clusters

International Nuclear Information System (INIS)

Bugaev, K.A.; Bugaev, K.A.; Elliott, J.B.

2007-01-01

The surface partition of large clusters is studied analytically within a framework of the 'Hills and Dales Model'. Three formulations are solved exactly by using the Laplace-Fourier transformation method. In the limit of small amplitude deformations, the 'Hills and Dales Model' gives the upper and lower bounds for the surface entropy coefficient of large clusters. The found surface entropy coefficients are compared with those of large clusters within the 2- and 3-dimensional Ising models

Isolated single-molecule magnets on native gold.

Science.gov (United States)

Zobbi, Laura; Mannini, Matteo; Pacchioni, Mirko; Chastanet, Guillaume; Bonacchi, Daniele; Zanardi, Chiara; Biagi, Roberto; Del Pennino, Umberto; Gatteschi, Dante; Cornia, Andrea; Sessoli, Roberta

2005-03-28

The incorporation of thioether groups in the structure of a Mn12 single-molecule magnet, [Mn12(O12)(L)16(H2O)4] with L = 4-(methylthio)benzoate, is a successful route to the deposition of well-separated clusters on native gold surfaces and to the addressing of individual molecules by scanning tunnelling microscopy.

Cluster ion-surface interactions: from meV to MeV energies

Energy Technology Data Exchange (ETDEWEB)

Nordlund, Kai; Meinander, Kristoffer; Jaervi, Tommi T.; Peltola, Jarkko; Samela, Juha [Accelerator Laboratory, University of Helsinki (Finland)

2008-07-01

The nature of cluster ion-surface interactions changes dramatically with the kinetic energy of the incoming cluster species. In this talk I review some of our recent work on the nature of cluster-surface interactions spanning an energy range from a few MeV/cluster to about 1 MeV/cluster and cluster sizes in the range of 10 - 1000 atoms/cluster. In the energy range of a few MeV/cluster ion, the kinetic energy of the incoming ion is insignificant compared to the energy gained when the surface potential energy at the cluster-surface interface is released and partly translated into kinetic energy. Even in this energy regime I show that surprisingly drastic effects can occur. When the energy of the incoming cluster is raised to a few eV/atom, the kinetic energy of the incoming cluster starts to affect the deposition. It will cause the cluster to entirely reform on impact. When the energy is raised to the range of keV's/cluster, the clusters start to penetrate the sample, fairly similar to conventional ion implantation. However, in dense targets the cluster ions may stick close to each other long enough to cause a significant enhancement of the heat spike in the material. Finally, I show that at kinetic energies around 1 MeV/cluster the cluster enhancement of the heat spike may lead to dramatic surface effects.

Conserved water molecules in bacterial serine hydroxymethyltransferases.

Science.gov (United States)

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

2015-10-01

Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Electron attachment to molecules and clusters of atmospheric relevance: oxygen and ozone

International Nuclear Information System (INIS)

Matejcik, S.; Cicman, P.; Skalny, J.; Kiendler, A.; Stampfli, P.; Maerk, T.D.; Illenberger, E.; Chu, Y.; Stamatovic, A.

1996-01-01

Highly monochromatized electrons are used in a crossed beams experiment to investigate electron attachment to oxygen clusters (O 2 )-n at electron energies from approximately zero eV up to 2 eV. At energies close to zero the attachment cross section for the reaction (O 2 ) n + e → O 2 - varies inversely with the electron energy, indicative of s-wave electron capture to (O 2 ) n . Peaks in the attachment cross section present at higher energies can be ascribed to vibrational levels of the oxygen anion. The vibrational spacings observed can be quantitatively accounted for. In addition electron attachment to ozone and mixed oxygen/ozone clusters has been studied in the energy range up to 4 eV. Absolute attachment cross sections for both fragment ions anions, O - and O 2 - , from ozone could be deduced. Moreover, despite the initially large excess of oxygen molecules in the neutral oxygen/ozone clusters the dominant attachment products are un-dissociated cluster ions (O 3 ) m - including the O 3 - monomer while oxygen cluster ions (O 2 ) n appear with comparatively low intensity. (authors)

Light controllable catalytic activity of Au clusters decorated with photochromic molecules

Science.gov (United States)

Guo, Na; Meng Yam, Kah; Zhang, Chun

2018-06-01

By ab initio calculations, we show that when decorated with a photochromic molecule, the catalytic activity of an Au nanocluster can be reversibly controlled by light. The combination of a photochromic thiol-pentacarbonyl azobenzene (TPA) molecule and an Au8 cluster is chosen as a model catalyst. The TPA molecule has two configurations (trans and cis) that can be reversibly converted to each other upon photo-excitation. Our calculations show that when the TPA takes the trans configuration, the combined system (trans-Au8) is an excellent catalyst for CO oxidation. The reaction barrier of the catalyzed CO oxidation is less than 0.4 eV. While, the reaction barrier of CO oxidation catalyzed by cis-Au8 is very high (>2.7 eV), indicating that the catalyst is inactive. These results pave the way for a new class of light controllable nanoscale catalysts.

Cluster Formation of Polyphilic Molecules Solvated in a DPPC Bilayer

Directory of Open Access Journals (Sweden)

Xiang-Yang Guo

2017-10-01

Full Text Available We analyse the initial stages of cluster formation of polyphilic additive molecules which are solvated in a dipalmitoylphosphatidylcholine (DPPC lipid bilayer. Our polyphilic molecules comprise an aromatic (trans-bilayer core domain with (out-of-bilayer glycerol terminations, complemented with a fluorophilic and an alkyl side chain, both of which are confined within the aliphatic segment of the bilayer. Large-scale molecular dynamics simulations (1 μ s total duration of a set of six of such polyphilic additives reveal the initial steps towards supramolecular aggregation induced by the specific philicity properties of the molecules. For our intermediate system size of six polyphiles, the transient but recurrent formation of a trimer is observed on a characteristic timescale of about 100 ns. The alkane/perfluoroalkane side chains show a very distinct conformational distribution inside the bilayer thanks to their different philicity, despite their identical anchoring in the trans-bilayer segment of the polyphile. The diffusive mobility of the polyphilic additives is about the same as that of the surrounding lipids, although it crosses both bilayer leaflets and tends to self-associate.

Ultrahigh-sensitive detection of molecules produced in catalytic reactions by uni-atomic-composition bi-element clusters supported on solid substrate

International Nuclear Information System (INIS)

Yasumatsu, H; Fukui, N

2013-01-01

An apparatus has been developed for measuring catalytic activities of uni-atomic-composition bi-element clusters supported on a solid substrate. The cluster sample is prepared by irradiating a cluster-ion beam having the uni-atomic composition onto the substrate on a soft-landing condition in an ultra-high vacuum. The catalytic activity is measured by temperature-programmed desorption (TPD) mass analysis. Molecules at a density as low as 3 cm −3 have been detected with an ultrahigh-sensitive TPD mass spectrometer consisting of a cylindrical electron gun, a quadrupole mass filter and a micro-channel-plate ion-detector. The high reproducibility has been achieved by careful calibration of the TPD mass spectrometer. As a benchmark example, thermal oxidation of CO catalysed on Pt 30 disks supported on a silicon surface was studied. The CO 2 products have been successfully observed at the Pt 30 density as low as 3 × 10 12 clusters in a circular area of 8 mm in diameter at the ramping rate of the sample temperature as low as 0.3 K s −1 .

Molecular recognition of chromophore molecules to amine terminated surfaces

International Nuclear Information System (INIS)

Flores-Perez, Rosangelly; Ivanisevic, Albena

2007-01-01

We report the design and characterization of quartz surfaces that can bind to three retinal based chromophores. The amine terminated surfaces were engineered in order to mimic the environment of the opsin protein that accommodates binding of chromophore molecules in the human eye. Each surface coupling step was characterized by water contact angle measurements, ellipsometry, atomic force microscopy, X-ray photoelectron spectroscopy, and transmission infrared spectroscopy. The spectroscopic techniques confirmed that the three chromophore molecules can bind to the surface using a Schiff base mode. Our data suggests that the availability of the amine groups on the surface is critical in the accommodation of the binding of different chromophores

Current-induced switching of magnetic molecules on topological insulator surfaces

Science.gov (United States)

Locane, Elina; Brouwer, Piet W.

2017-03-01

Electrical currents at the surface or edge of a topological insulator are intrinsically spin polarized. We show that such surface or edge currents can be used to switch the orientation of a molecular magnet weakly coupled to the surface or edge of a topological insulator. For the edge of a two-dimensional topological insulator as well as for the surface of a three-dimensional topological insulator the application of a well-chosen surface or edge current can lead to a complete polarization of the molecule if the molecule's magnetic anisotropy axis is appropriately aligned with the current direction. For a generic orientation of the molecule a nonzero but incomplete polarization is obtained. We calculate the probability distribution of the magnetic states and the switching rates as a function of the applied current.

Stochastic models for surface diffusion of molecules

Energy Technology Data Exchange (ETDEWEB)

Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)

2014-07-28

We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

Indium tin oxide surface smoothing by gas cluster ion beam

CERN Document Server

Song, J H; Choi, W K

2002-01-01

CO sub 2 cluster ions are irradiated at the acceleration voltage of 25 kV to remove hillocks on indium tin oxide (ITO) surfaces and thus to attain highly smooth surfaces. CO sub 2 monomer ions are also bombarded on the ITO surfaces at the same acceleration voltage to compare sputtering phenomena. From the atomic force microscope results, the irradiation of monomer ions makes the hillocks sharper and the surfaces rougher from 1.31 to 1.6 nm in roughness. On the other hand, the irradiation of CO sub 2 cluster ions reduces the height of hillocks and planarize the ITO surfaces as smooth as 0.92 nm in roughness. This discrepancy could be explained by large lateral sputtering yield of the cluster ions and re-deposition of sputtered particles by the impact of the cluster ions on surfaces.

Interactions between nitrogen molecules and barium atoms on Ru (0001) surface

International Nuclear Information System (INIS)

Zhao Xinxin; Mi Yiming; Xu Hongxia; Wang Lili; Ren Li; Tao Xiangming; Tan Mingqiu

2011-01-01

We had performed first principles calculations on interactions between nitrogen molecules and barium atoms on Ru (0001) surface using density function theory methods. It was shown that effects of barium atoms weakened the bond strength of nitrogen molecules. The bond length of nitrogen molecule increases from 0.113 nm on Ru (001)-N 2 to 0.120 nm on Ru (001)-N 2 /Ba surface. While stretch vibrational frequency of nitrogen molecule decreased from 2222 cm -1 and charge transfer toward nitrogen molecule increased from 0.3 e to 1.1 e. Charge was mainly translated from 6 s orbitals of barium atoms to 4 d orbitals of substrate, which enhanced the hybridization between 4 d and 2 π orbitals and increased the dipole moment of 5 σ and d π orbitals of nitrogen molecule. The molecular dipole moment of nitrogen molecule was increased by -0.136 e Anstrom. It was suggested that barium had some characters to be an electronic promoter on the process of activating nitrogen molecules on Ru (0001) surface. (authors)

Brome isotope selective control of CF3Br molecule clustering by IR laser radiation in gas-dynamic expansion of CF3Br - Ar mixture

Science.gov (United States)

Apatin, V. M.; Lokhman, V. N.; Makarov, G. N.; Ogurok, N.-D. D.; Ryabov, E. A.

2018-02-01

We report the results of research on the experimental control of CF3Br molecule clustering under gas-dynamic expansion of the CF3Br - Ar mixture at a nozzle exit by using IR laser radiation. A cw CO2 laser is used for exciting molecules and clusters in the beam and a time-of-flight mass-spectrometer with laser UV ionisation of particles for their detection. The parameters of the gas above the nozzle are determined (compositions and pressure) at which intensive molecule clustering occurs. It is found that in the case of the CF3Br gas without carrier when the pressure P0 above the nozzle does not exceed 4 atm, molecular clusters actually are not generated in the beam. If the gas mixture of CF3Br with argon is used at a pressure ratio 1 : N, where N >= 3, and the total pressure above the nozzle is P0 >= 2 atm, then there occurs molecule clustering. We study the dependences of the efficiency of suppressing the molecule clustering on parameters of the exciting pulse, gas parameters above the nozzle, and on a distance of the molecule irradiation zone from the nozzle exit section. It is shown that in the case of resonant vibrational excitation of gas-dynamically cooled CF3Br molecules at the nozzle exit one can realise isotope-selective suppression of molecule clustering with respect to bromine isotopes. With the CF3Br - Ar mixtures having the pressure ratio 1 : 3 and 1 : 15, the enrichment factors obtained with respect to bromine isotopes are kenr ≈ 1.05 ± 0.005 and kenr ≈ 1.06 ± 0.007, respectively, under jet irradiation by laser emission in the 9R(30) line (1084.635 cm-1). The results obtained let us assume that this method can be used to control clustering of molecules comprising heavy element isotopes, which have a small isotopic shift in IR absorption spectra.

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

A magnetic nanoparticle-clustering biosensor for blu-ray based optical detection of small-molecules

DEFF Research Database (Denmark)

Yang, Jaeyoung; Donolato, Marco; Antunes, Paula Soares Martins

2014-01-01

MNP-clustering facilitates high-resolution small-molecule assays. For experiments, aptamer-functionalized MNPs (Apt-MNPs) were first incubated with adenosine-5'-triphosphate (ATP) followed by adding MNPs with linker strands (linker-MNPs). The linker hybridizes with a region of aptamer sequences...

Single-molecule conductivity of non-redox and redox molecules at pure and gold-mined Au(111)-electrode surfaces

DEFF Research Database (Denmark)

Zhang, Jingdong; Chi, Qijin; Ulstrup, Jens

The structure, two-dimensional organization, and function of molecules immobilized on solid surfaces can be addressed in a degree of detail that has reached the level of the single-molecule. In this context redox molecules are “smart” molecules adding sophisticated electronic function. Redox meta...

Discrete Visible Luminescence of Helium Atoms and Molecules Desorbing from Helium Clusters: The Role of Electronic, Vibrational, and Rotational Energy Transfer

International Nuclear Information System (INIS)

von Haeften, K.; von Pietrowski, R.; Moeller, T.; Joppien, M.; Moussavizadeh, L.; de Castro, A.R.

1997-01-01

Discrete visible and near-infrared luminescence of a beam of photoexcited helium clusters is reported. The emission lines are attributed to free helium atoms and molecules desorbing from clusters in electronically excited states. Depending on the excitation energy, various atomic and molecular singlet and triplet states are involved in the relaxation process. With increasing cluster size the intensity of molecular transitions becomes dominant. The temperature of ejected molecules could be estimated to T vib ∼2500 K and T rot ∼450 K and is much higher than that of the cluster itself. copyright 1997 The American Physical Society

Low surface brightness galaxies in the Fornax Cluster: automated galaxy surface photometry

International Nuclear Information System (INIS)

Davies, J.I.; Phillipps, S.; Disney, M.J.

1988-01-01

A sample is presented of low surface brightness galaxies (with extrapolated central surface brightness fainter than 22.0 Bμ) in the Fornax Cluster region which has been measured by the APM machine. Photometric parameters, namely profile shape, scale length, central brightness and total magnitude, are derived for the sample galaxies and correlations between the parameters of low surface brightness dwarf galaxies are discussed, with particular reference to the selection limits. Contrary to previous authors we find no evidence for a luminosity-surface brightness correlation in the sense of lower surface brightness galaxies having lower luminosities and scale sizes. In fact, the present data suggest that it is the galaxies with the largest scale lengths which are more likely to be of very low surface brightness. In addition, the larger scale length galaxies occur preferentially towards the centre of the Cluster. (author)

Effects of microwave electric fields on the translational diffusion of dipolar molecules in surface potential: A simulation study

Science.gov (United States)

Kapranov, Sergey V.; Kouzaev, Guennadi A.

2018-01-01

Variations of effective diffusion coefficient of polar molecules exposed to microwave electric fields in a surface potential are studied by solving coupled stochastic differential equations of motion with a deterministic component of the surface force. Being an essential tool for the simulation interpretation, a theoretical approach to effective diffusion in surface potential is first developed. The effective diffusion coefficient is represented as the product of the normal diffusion coefficient and potential-dependent correction function, whose temperature dependence is close to the Arrhenius form. The analytically found zero-diffusion condition defines the state of thermal equilibrium at the surface. The diffusion of a water-like dipole molecule in the potential of graphite surface is simulated in the field-free conditions and in the presence of the alternating electric fields of various magnitude intensities and frequencies. Temperature dependence of the correction function exhibits field-induced variations of the effective Lennard-Jones energy parameter. It demonstrates maximum departure from the zero-field value at certain frequencies and intensities, which is associated with variations in the rotational dynamics. A concept of the amplitude-frequency resonance put forward to interpret the simulation results is explained using a heuristic reasoning and is corroborated by semi-quantitative considerations in terms of the Dissado-Hill cluster theory of dielectric relaxation.

Adsorption Mechanism of Inhibitor and Guest Molecules on the Surface of Gas Hydrates.

Science.gov (United States)

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2015-09-23

The adsorption of guest and kinetic inhibitor molecules on the surface of methane hydrate is investigated by using molecular dynamics simulations. We calculate the free energy profile for transferring a solute molecule from bulk water to the hydrate surface for various molecules. Spherical solutes with a diameter of ∼0.5 nm are significantly stabilized at the hydrate surface, whereas smaller and larger solutes exhibit lower adsorption affinity than the solutes of intermediate size. The range of the attractive force is subnanoscale, implying that this force has no effect on the macroscopic mass transfer of guest molecules in crystal growth processes of gas hydrates. We also examine the adsorption mechanism of a kinetic hydrate inhibitor. It is found that a monomer of the kinetic hydrate inhibitor is strongly adsorbed on the hydrate surface. However, the hydrogen bonding between the amide group of the inhibitor and water molecules on the hydrate surface, which was believed to be the driving force for the adsorption, makes no contribution to the adsorption affinity. The preferential adsorption of both the kinetic inhibitor and the spherical molecules to the surface is mainly due to the entropic stabilization arising from the presence of cavities at the hydrate surface. The dependence of surface affinity on the size of adsorbed molecules is also explained by this mechanism.

Switching behavior of double-decker single molecule magnets on a metal surface

Energy Technology Data Exchange (ETDEWEB)

Fu, Yingshuang; Schwoebel, Joerg; Hoffmann, Germar; Brede, Jens; Wiesendanger, Roland [University of Hamburg, Hamburg (Germany); Dillulo, Andrew [Ohio University, Athens (United States); Klyatskaya, Svetlana [Karlsruhe Institute of Technology, Karlsruhe (Germany); Ruben, Mario [Karlsruhe Institute of Technology, Karlsruhe (Germany); Universite de Strasbourg, Strasbourg (France)

2011-07-01

Single molecule magnets (SMM) are most promising materials for spin based molecular electronics. Due to their large magnetic anisotropy stabilized by inside chemical bonds, SMM can potentially be used for information storage at the single molecule level. For applications, it is of importance to adsorb the SMM onto surfaces and to study their subsequent conformational, electronic and magnetic properties. We have investigated the adsorption behavior of Tb and Dy based double-decker SMM on an Ir(111) surface with low temperature scanning tunneling microscopy and spectroscopy. It is found that Tb double-decker molecules bind tightly to the Ir(111) surface. By resonantly injecting tunneling electrons into its LUMO or HOMO state, the Tb double-decker molecule can be switched from a four-lobed structure to an eight-lobed structure. After switching, energy positions of the HOMO and LUMO states both shift closer to the Fermi level. Dy double-decker molecules also exhibit the same switching properties on the Ir(111) surface. The switching behavior of the molecules is tentatively attributed to a conformational change of the double-decker molecular frame.

Influencing the bonding and assembly of a multiterminal molecule on a metal surface

Energy Technology Data Exchange (ETDEWEB)

Lukas, Maya; Doessel, Kerrin; Fink, Karin; Fuhr, Olaf [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Schramm, Alexandrina; Stroh, Christophe [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); Mayor, Marcel [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); University of Basel, Department of Chemistry, CH-4056 Basel (Switzerland); Loehneysen, Hilbert von [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Karlsruhe Institute of Technology (KIT), Physics Institute and Institute for Solid State Physics, D-76049 Karlsruhe (Germany)

2011-07-01

The bond of a molecule to a metallic electrode is known to have a crucial influence on the molecular conductance. As electronic functionalities are integrated into molecules or several subunits are connected to a three-dimensional multiterminal molecule, it is not obvious that a ''well-known'' chemical linker group will lead to the bonding configuration known from simpler molecules. We investigated a series of tripodal molecules on metal surfaces by STM. The chemical linker groups and the complex connecting the three wire-units are varied. We find that the position of molecules on the surface is governed by a subtle balance of intermolecular and molecule-surface interactions, partly in strong contrast to expectations. This emphasizes the need to characterize the nature of molecule-electrode contacts along with the investigation of the electronic conductance.

Energy redistribution in diatomic molecules on surfaces

International Nuclear Information System (INIS)

Asscher, M.; Somorjai, G.A.

1984-04-01

Translational and internal degrees of freedom of a scattered beam of NO molecules from a Pt(111) single crystal surface were measured as a function of scattering angle and crystal temperature in the range 450 to 1250K. None of the three degrees of freedom were found to fully accommodate to the crystal temperature, the translational degree being the most accommodated and the rotational degree of freedom the least. A precursor state model is suggested to account for the incomplete accommodation of translational and vibrational degrees of freedom as a function of crystal temperature and incident beam energy. The vibrational accommodation is further discussed in terms of a competition between desorption and vibrational excitation processes, thus providing valuable information on the interaction between vibrationally excited molecules and surfaces. Energy transfer into rotational degrees of freedom is qualitatively discussed

Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

International Nuclear Information System (INIS)

Imran, Muhammad; Hussain, Fayyaz; Ullah, Hafeez; Ahmad, Ejaz; Rashid, Muhammad; Ismail, Muhammad; Cai, Yongqing; Javid, M Arshad; Ahmad, S A

2016-01-01

Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results. (paper)

The atomic structure of transition metal clusters

International Nuclear Information System (INIS)

Riley, S.J.

1995-01-01

Chemical reactions are used to probe the atomic (geometrical) structure of isolated clusters of transition metal atoms. The number of adsorbate molecules that saturate a cluster, and/or the binding energy of molecules to cluster surfaces, are determined as a function of cluster size. Systematics in these properties often make it possible to propose geometrical structures consistent with the experimental observations. We will describe how studies of the reactions of cobalt and nickel clusters with ammonia, water, and nitrogen provide important and otherwise unavailable structural information. Specifically, small (less than 20 atoms) clusters of cobalt and nickel atoms adopt entirely different structures, the former having packing characteristic of the bulk and the latter having pentagonal symmetry. These observations provide important input for model potentials that attempt to describe the local properties of transition metals. In particular, they point out the importance of a proper treatment of d-orbital binding in these systems, since cobalt and nickel differ so little in their d-orbital occupancy

Low surface brightness galaxies in the cluster A1367

International Nuclear Information System (INIS)

Davies, J.I.; Phillipps, S.; Disney, M.J.

1989-01-01

We have obtained deep CCD frames of apparently blank regions of sky in the hope of detecting very low surface brightness (LSB) objects in the cluster A1367. We discuss our data reduction, and image detection and selection techniques. If the galaxies detected are actually cluster members then they are dwarfs and the conclusions of a previous paper on the Fornax cluster are essentially confirmed. One area of variance is that the lowest surface brightness galaxies do not appear to be preferentially concentrated towards the cluster centre. This can be explained by there being a much larger density of dwarf galaxies over this bright galaxy-rich region of the universe. We find over our small area approximately four times as many LSB galaxies as would be expected from our Fornax data. We speculate on the possible origin and likely intensity of intergalactic light within clusters. (author)

Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers

DEFF Research Database (Denmark)

Nuermaimaiti, Ajiguli; Schultz-Falk, Vickie; Lind Cramer, Jacob

2016-01-01

Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamel......Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self......-assembly of lamellae structures. From statistical analysis of Scanning Tunnelling Microscopy (STM) data we observe a clear selection of specific conformational states after self-assembly. Using Density Functional Theory (DFT) calculations we rationalise how this selection is correlated to the orientation of the alkyl...

Cluster-surface interaction: from soft landing to implantation

DEFF Research Database (Denmark)

Popok, Vladimir; Barke, Ingo; Campbell, Eleanor E.B.

2011-01-01

applications of keV-energy cluster ion beams. This includes ultra-shallow doping of semiconductors and formation of ultrathin insulating layers. A few examples of MeV-energy cluster implantation, leading to the formation of nanosize hillocks or pillars on the surface as well as to local phase transitions (for...... instance, graphite-to-diamond) are also discussed. The review is finalized by an outlook on the future development of cluster beam research....

Site-specific fragmentation of polystyrene molecule using size-selected Ar gas cluster ion beam

International Nuclear Information System (INIS)

Moritani, Kousuke; Mukai, Gen; Hashinokuchi, Michihiro; Mochiji, Kozo

2009-01-01

The secondary ion mass spectrum (SIMS) of a polystyrene thin film was investigated using a size-selected Ar gas cluster ion beam (GCIB). The fragmentation in the SIM spectrum varied by kinetic energy per atom (E atom ); the E atom dependence of the secondary ion intensity of the fragment species of polystyrene can be essentially classified into three types based on the relationship between E atom and the dissociation energy of a specific bonding site in the molecule. These results indicate that adjusting E atom of size-selected GCIB may realize site-specific bond breaking within a molecule. (author)

Suzaku observations of low surface brightness cluster Abell 1631

Science.gov (United States)

Babazaki, Yasunori; Mitsuishi, Ikuyuki; Ota, Naomi; Sasaki, Shin; Böhringer, Hans; Chon, Gayoung; Pratt, Gabriel W.; Matsumoto, Hironori

2018-06-01

We present analysis results for a nearby galaxy cluster Abell 1631 at z = 0.046 using the X-ray observatory Suzaku. This cluster is categorized as a low X-ray surface brightness cluster. To study the dynamical state of the cluster, we conduct four-pointed Suzaku observations and investigate physical properties of the Mpc-scale hot gas associated with the A 1631 cluster for the first time. Unlike relaxed clusters, the X-ray image shows no strong peak at the center and an irregular morphology. We perform spectral analysis and investigate the radial profiles of the gas temperature, density, and entropy out to approximately 1.5 Mpc in the east, north, west, and south directions by combining with the XMM-Newton data archive. The measured gas density in the central region is relatively low (a few ×10-4 cm-3) at the given temperature (˜2.9 keV) compared with X-ray-selected clusters. The entropy profile and value within the central region (r clusters. These features are also observed in another low surface brightness cluster, Abell 76. The spatial distributions of galaxies and the hot gas appear to be different. The X-ray luminosity is relatively lower than that expected from the velocity dispersion. A post-merger scenario may explain the observed results.

Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

Energy Technology Data Exchange (ETDEWEB)

Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D. [Department of Chemical Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

2015-10-28

We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.

Hydration of a Large Anionic Charge Distribution - Naphthalene-Water Cluster Anions

Science.gov (United States)

Weber, J. Mathias; Adams, Christopher L.

2010-06-01

We report the infrared spectra of anionic clusters of naphthalene with up to three water molecules. Comparison of the experimental infrared spectra with theoretically predicted spectra from quantum chemistry calculations allow conclusions regarding the structures of the clusters under study. The first water molecule forms two hydrogen bonds with the π electron system of the naphthalene moiety. Subsequent water ligands interact with both the naphthalene and the other water ligands to form hydrogen bonded networks, similar to other hydrated anion clusters. Naphthalene-water anion clusters illustrate how water interacts with negative charge delocalized over a large π electron system. The clusters are interesting model systems that are discussed in the context of wetting of graphene surfaces and polyaromatic hydrocarbons.

Thermal ion-molecule reactions in oxygen-containing molecules

International Nuclear Information System (INIS)

Kumakura, Minoru

1981-02-01

The energetics of ions and the thermal ion-molecule reactions in oxygen-containing molecules have been studied with a modified time-of-flight mass spectrometer. It was found that the translational energy of ion can be easily obtained from analysis of the decay curve using the time-of-flight mass spectrometer. The condensation-elimination reactions proceeded via cross- and homo-elimination mechanism in which the nature of intermediate-complex could be correlated with the nature of reactant ion. It was elucidated that behavior of poly-atomic oxygen-containing ions on the condensation-elimination reactions is considerably influenced by their oxonium ion structures having functional groups. In addition, the rate constants of the condensation-elimination reactions have affected with the energy state of reactant ion and the dipole moment and/or the polarizability of neutral molecule. It was clarified that the rate constants of the ion-molecule clustering reactions in poly-atomic oxygen-containing molecules such as cyclic ether of six member rings are very large and the cluster ions are stable owing to the large number of vibrational degree of freedom in the cluster ions. (author)

Surface-confined electroactive molecules for multistate charge storage information.

Science.gov (United States)

Mas-Torrent, M; Rovira, C; Veciana, J

2013-01-18

Bi-stable molecular systems with potential for applications in binary memory devices are raising great interest for device miniaturization. Particular appealing are those systems that operate with electrical inputs since they are compatible with existing electronic technologies. The processing of higher memory densities in these devices could be accomplished by increasing the number of memory states in each cell, although this strategy has not been much explored yet. Here we highlight the recent advances devoted to the fabrication of charge-storage molecular surface-confined devices exhibiting multiple states. Mainly, this goal has been realized immobilizing a variety (or a combination) of electroactive molecules on a surface, although alternative approaches employing non-electroactive systems have also been described. Undoubtedly, the use of molecules with chemically tunable properties and nanoscale dimensions are raising great hopes for the devices of the future in which molecules can bring new perspectives such as multistability.

Metal nanostructures: from clusters to nanocatalysis and sensors

Science.gov (United States)

Smirnov, B. M.

2017-12-01

The properties of metal clusters and nanostructures composed of them are reviewed. Various existing methods for the generation of intense beams of metal clusters and their subsequent conversion into nanostructures are compared. Processes of the flow of a buffer gas with active molecules through a nanostructure are analyzed as a basis of using nanostructures for catalytic applications. The propagation of an electric signal through a nanostructure is studied by analogy with a macroscopic metal. An analysis is given of how a nanostructure changes its resistance as active molecules attach to its surface and are converted into negative ions. These negative ions induce the formation of positively charged vacancies inside the metal conductor and attract the vacancies to together change the resistance of the metal nanostructure. The physical basis is considered for using metal clusters and nanostructures composed of them to create new materials in the form of a porous metal film on the surface of an object. The fundamentals of nanocatalysis are reviewed. Semiconductor conductometric sensors consisting of bound nanoscale grains or fibers acting as a conductor are compared with metal sensors conducting via a percolation cluster, a fractal fiber, or a bunch of interwoven nanofibers formed in superfluid helium. It is shown that sensors on the basis of metal nanostructures are characterized by a higher sensitivity than semiconductor ones, but are not selective. Measurements using metal sensors involve two stages, one of which measures to high precision the attachment rate of active molecules to the sensor conductor, and in the other one the surface of metal nanostructures is cleaned from the attached molecules using a gas discharge plasma (in particular, capillary discharge) with a subsequent chromatography analysis for products of cleaning.

Multilayer Choline Phosphate Molecule Modified Surface with Enhanced Cell Adhesion but Resistance to Protein Adsorption.

Science.gov (United States)

Chen, Xingyu; Yang, Ming; Liu, Botao; Li, Zhiqiang; Tan, Hong; Li, Jianshu

2017-08-22

Choline phosphate (CP), which is a new zwitterionic molecule, and has the reverse order of phosphate choline (PC) and could bind to the cell membrane though the unique CP-PC interaction. Here we modified a glass surface with multilayer CP molecules using surface-initiated atom-transfer radical polymerization (SI-ATRP) and the ring-opening method. Polymeric brushes of (dimethylamino)ethyl methacrylate (DMAEMA) were synthesized by SI-ATRP from the glass surface. Then the grafted PDMAEMA brushes were used to introduce CP groups to fabricate the multilayer CP molecule modified surface. The protein adsorption experiment and cell culture test were used to evaluate the biocompatibility of the modified surfaces by using human umbilical veinendothelial cells (HUVECs). The protein adsorption results demonstrated that the multilayer CP molecule decorated surface could prevent the adsorption of fibrinogen and serum protein. The adhesion and proliferation of cells were improved significantly on the multilayer CP molecule modified surface. Therefore, the biocompatibility of the material surface could be improved by the modified multilayer CP molecule, which exhibits great potential for biomedical applications, e.g., scaffolds in tissue engineering.

Single atom and-molecules chemisorption on solid surfaces

International Nuclear Information System (INIS)

Anda, E.V.; Ure, J.E.; Majlis, N.

1981-01-01

A simplified model for the microscopic interpretation of single atom and- molecules chemisorption on metallic surfaces is presented. An appropriated hamiltonian for this problem is resolved, through the Green's function formalism. (L.C.) [pt

Single DNA molecules as probes for interrogating silica surfaces after various chemical treatments

International Nuclear Information System (INIS)

Liu Xia; Wu Zhan; Nie Huagui; Liu Ziling; He Yan; Yeung, E.S.

2007-01-01

We examined the adsorption of single YOYO-1-labeled λ-DNA molecules at glass surfaces after treatment with various chemical cleaning methods by using total internal reflection fluorescence microscopy (TIRFM). The characteristics of these surfaces were further assessed using contact angle (CA) measurements and atomic force microscopy (AFM). By recording the real-time dynamic motion of DNA molecules at the liquid/solid interface, subtle differences in adsorption affinities were revealed. The results indicate that the driving force for adsorption of DNA molecules on glass surfaces is mainly hydrophobic interaction. We also found that surface topography plays a role in the adsorption dynamics

Three exciting areas of experimental physical sciences : high temperature superconductors, metal clusters and super molecules of carbon

International Nuclear Information System (INIS)

Rao, C.N.

1992-01-01

The author has narrated his experience in carrying out research in three exciting areas of physical sciences. These areas are : high temperature superconductors, metal clusters and super molecules of carbon. (M.G.B.)

Nanocoating of titanium implant surfaces with organic molecules. Polysaccharides including glycosaminoglycans

DEFF Research Database (Denmark)

Gurzawska, Katarzyna Aleksandra; Svava, Rikke; Jørgensen, Niklas Rye

2012-01-01

Long-term stability of titanium implants are dependent on a variety of factors. Nanocoating with organic molecules is one of the method used to improve osseointegration. Nanoscale modification of titanium implants affects surface properties, such as hydrophilicity, biochemical bonding capacity...... and roughness. This influences cell behaviour on the surface such as adhesion, proliferation and differentiation of cells as well as the mineralization of the extracellular matrix at the implant surfaces. The aim of the present systematic review was to describe organic molecules used for surface nanocoating...... nanocoatings. The included in vivo studies, showed improvement of bone interface reactions measured as increased Bone-to-Implant Contact length and Bone Mineral Density adjacent to the polysaccharide coated surfaces. Based on existing literature, surface modification with polysaccharide and glycosaminoglycans...

Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

Science.gov (United States)

Kildgaard, Jens; Mikkelsen, Kurt V; Bilde, Merete; Elm, Jonas

2018-05-09

We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algo- rithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in 9 different orientations. To allow the sam- pling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond and a water molecule is placed in between in three different ori- entations. Generated redundant structures are eliminated based on minimizing the root mean square distance (RMSD) of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density func- tional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm we study the hydration of sulfuric acid with up to 15 water molecules. We find that the additions of the first four water molecules "saturate" the sulfuric acid molecule and are more thermodynamically favourable than the addition of water molecule 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91 and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimates the binding energies compared to cou- pled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.

DNA origami as biocompatible surface to match single-molecule and ensemble experiments

Science.gov (United States)

Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

2012-01-01

Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

Anchoring of alkyl chain molecules on oxide surface using silicon alkoxide

Energy Technology Data Exchange (ETDEWEB)

Narita, Ayumi, E-mail: narita.ayumi@jaea.go.jp [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki-ken 319-1195 (Japan); Graduate School of Science and Engineering, Ibaraki University, Bunnkyo, Mito-shi, Ibaraki-ken 310-8512 (Japan); Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Hirao, Norie [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki-ken 319-1195 (Japan); Yaita, Tsuyoshi [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki-ken 319-1195 (Japan); Graduate School of Science and Engineering, Ibaraki University, Bunnkyo, Mito-shi, Ibaraki-ken 310-8512 (Japan)

2012-01-01

Chemical states of the interfaces between octadecyl-triethoxy-silane (ODTS) molecules and sapphire surface were measured by X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure (NEXAFS) using synchrotron soft X-rays. The nearly self-assembled monolayer of ODTS was formed on the sapphire surface. For XPS and NEXAFS measurements, it was elucidated that the chemical bond between silicon alkoxide in ODTS and the surface was formed, and the alkane chain of ODTS locates upper side on the surface. As a result, it was elucidated that the silicon alkoxide is a good anchor for the immobilization of organic molecules on oxides.

Suzaku observations of low surface brightness cluster Abell 1631

Science.gov (United States)

Babazaki, Yasunori; Mitsuishi, Ikuyuki; Ota, Naomi; Sasaki, Shin; Böhringer, Hans; Chon, Gayoung; Pratt, Gabriel W.; Matsumoto, Hironori

2018-04-01

We present analysis results for a nearby galaxy cluster Abell 1631 at z = 0.046 using the X-ray observatory Suzaku. This cluster is categorized as a low X-ray surface brightness cluster. To study the dynamical state of the cluster, we conduct four-pointed Suzaku observations and investigate physical properties of the Mpc-scale hot gas associated with the A 1631 cluster for the first time. Unlike relaxed clusters, the X-ray image shows no strong peak at the center and an irregular morphology. We perform spectral analysis and investigate the radial profiles of the gas temperature, density, and entropy out to approximately 1.5 Mpc in the east, north, west, and south directions by combining with the XMM-Newton data archive. The measured gas density in the central region is relatively low (a few ×10-4 cm-3) at the given temperature (˜2.9 keV) compared with X-ray-selected clusters. The entropy profile and value within the central region (r < 0.1 r200) are found to be flatter and higher (≳400 keV cm2). The observed bolometric luminosity is approximately three times lower than that expected from the luminosity-temperature relation in previous studies of relaxed clusters. These features are also observed in another low surface brightness cluster, Abell 76. The spatial distributions of galaxies and the hot gas appear to be different. The X-ray luminosity is relatively lower than that expected from the velocity dispersion. A post-merger scenario may explain the observed results.

Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

Science.gov (United States)

Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

2016-02-18

Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

Advances on the nanostructuration of magnetic molecules on surfaces: the case of single-molecule magnets (SMM).

Science.gov (United States)

Gómez-Segura, Jordi; Veciana, Jaume; Ruiz-Molina, Daniel

2007-09-28

SMMs exhibit slow magnetization relaxation rates characteristic of nanodomain particles whose origin is however on individual molecules. For this reason, they have attracted much interest due to their potential applications in high-density information storage devices and quantum computing applications, where for instance, each molecule can be used as a magnetic bit of information. However, for this to become a reality, several basic studies such as their deposition on surfaces are still highly required. Here we will revise all the experimental approximations that have been so far reported for their addressing, nanostructuration and study on surfaces, from the use of stamps as templates to their anchorage to gold surface through the use of thiol-based ligands. It is also important to emphasize that the results and methodologies described along this review are applicable not only to SMMs but to any molecular material.

Dissociation of N{sub 2}O on anatase TiO{sub 2} (001) surface – The effect of oxygen vacancy and presence of Ag cluster

Energy Technology Data Exchange (ETDEWEB)

Sowmiya, M.; Senthilkumar, K., E-mail: ksenthil@buc.edu.in

2016-12-15

Highlights: • This study elucidates the dissociation of N{sub 2}O on anatase TiO{sub 2} (001) surface. • N{sub 2}O is decomposed into N{sub 2} and O on reduced TiO{sub 2} even in the presence of Ag cluster. • Excess charge in reduced TiO{sub 2} surface is transferred to the adsorbed N{sub 2}O molecule. • The vibrational frequency analysis also performed to study the dissociation of N{sub 2}O. • Anatase TiO{sub 2} with oxygen vacancies is a suitable catalyst for decomposition of N{sub 2}O. - Abstract: The increase in concentration of nitrous oxide (N{sub 2}O) in the atmosphere is one of the major contributors to the greenhouse effect, ozone depletion and climate change. Therefore, it is important to decompose harmful N{sub 2}O molecule into harmless N{sub 2}. In the present work, we have studied the decomposition of N{sub 2}O on anatase TiO{sub 2} (001) surface using first principle calculations. The results indicates that the N{sub 2}O molecule is physisorbed on perfect TiO{sub 2} surface without any dissociation, and is dissociated into N{sub 2} and oxygen on the reduced TiO{sub 2} surface. In addition, it has been found that the interaction between N{sub 2}O and TiO{sub 2} is augmented by the presence of Ag cluster on anatase (001) surface. On the basis of Bader charge analysis and electron density difference plot, it has been found that the excess charge in the reduced anatase TiO{sub 2} (001) surface is transferred to the adsorbed N{sub 2}O molecule, which results the weakening of N–O bond of N{sub 2}O followed by the decomposition of N{sub 2}O into N{sub 2} and O. Vibrational frequency analysis also performed to confirm the decomposition of N{sub 2}O molecule. From the pathway for N{sub 2}O dissociation on reduced TiO{sub 2} and Ag/TiO{sub 2} surfaces, it has been observed that the dissociation reaction of N{sub 2}O on TiO{sub 2} surface is highly exothermic with activation energy barrier of 0.25 eV. The results presented in this work show that the

Electron Scattering From Atoms, Molecules, Nuclei, and Bulk Matter

CERN Document Server

Whelan, Colm T

2005-01-01

Topics that are covered include electron scattering in the scanning TEM; basic theory of inelastic electron imaging; study of confined atoms by electron excitation; helium bubbles created in extreme pressure with application to nuclear safety; lithium ion implantation; electron and positron scattering from clusters; electron scattering from physi- and chemi-absorbed molecules on surfaces; coincidence studies; electron scattering from biological molecules; electron spectroscopy as a tool for environmental science; electron scattering in the presence of intense fields; electron scattering from astrophysical molecules; electon interatctions an detection of x-ray radiation.

Hyperthermal surface ionization mass spectrometry of organic molecules: monoterpenes

International Nuclear Information System (INIS)

Kishi, Hiroshi; Fujii, Toshihiro.

1997-01-01

This paper describes an experimental study on the influence of kinetic energy of fast monoterpene molecules on the surface ionization efficiency and on the mass spectral patterns, using rhenium oxide (ReO 2 ) surface. Molecular kinetic energy, given to the molecules through the acceleration in the seeded supersonic molecular beam, ranged from 1 to 10 eV. Hyperthermal surface ionization mass spectra (HSIMS) were taken for various incident kinetic energies and surface temperatures. The observed mass spectra were interpreted in a purely empirical way, by means of evidence from the previous investigations, and they were compared with conventional EI techniques and with the thermal energy surface ionization technique (SIOMS; Surface Ionization Organic Mass Spectrometry). Ionization efficiency (β) was also studied. Under hyperthermal surface ionization (HSI) conditions, many kinds of fragment ions, including quite abundant odd electron ions (OE +· ) are observed. HSIMS patterns of monoterpenes are different among 6-isomers, contrary to those of SIOMS and EIMS, where very similar patterns for isomers are observed. HSIMS patterns are strongly dependent on the molecular kinetic energies. The surface temperature does not affect much the spectral patterns, but it controls the total amount of ion formation. We conclude from these mass spectral findings, HSI-mechanism contains an impulsive process of ion formation, followed by the fragmentation process as a results of the internal energies acquired through the collision processes. (author)

Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments

DEFF Research Database (Denmark)

List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob

2014-01-01

are specifically motivated by a twofold aim: (i) computation of core excitations in realistic surroundings and (ii) examination of the effect of the differential response of the environment upon excitation solely related to the CC multipliers (herein denoted the J matrix) in computations of excitation energies......We present an extension of a previously reported implementation of a Lanczos-driven coupled-cluster (CC) damped linear response approach to molecules in condensed phases, where the effects of a surrounding environment are incorporated by means of the polarizable embedding formalism. We...... and transition moments of polarizable-embedded molecules. Numerical calculations demonstrate that the differential polarization of the environment due to the first-order CC multipliers provides only minor contributions to the solvatochromic shift for all transitions considered. We thus complement previous works...

2012 Gordon Research Conference On Molecular And Ionic Clusters

International Nuclear Information System (INIS)

McCoy, Anne

2012-01-01

The Gordon Research Conference on 'Molecular and Ionic Clusters' focuses on clusters, which are the initial molecular species found in gases when condensation begins to occur. Condensation can take place solely from molecules interacting with each other, mostly at low temperatures, or when molecules condense around charged particles (electrons, protons, metal cations, molecular ions), producing ion molecule clusters. These clusters provide models for solvation, allow a pristine look at geometric as well as electronic structures of molecular complexes or matter in general, their interaction with radiation, their reactivity, their thermodynamic properties and, in particular, the related dynamics. This conference focuses on new ways to make clusters composed of different kinds of molecules, new experimental techniques to investigate the properties of the clusters and new theoretical methods with which to calculate the structures, dynamical motions and energetics of the clusters. Some of the main experimental methods employed include molecular beams, mass spectrometry, laser spectroscopy (from infrared to XUV; in the frequency as well as the time domain) and photoelectron spectroscopy. Techniques include laser absorption spectroscopy, laser induced fluorescence, resonance enhanced photoionization, mass-selected photodissociation, photofragment imaging, ZEKE photoelectron spectroscopy, etc. From the theoretical side, this conference highlights work on potential surfaces and measurable properties of the clusters. The close ties between experiment, theory and computation have been a hallmark of the Gordon Research Conference on Molecular and Ionic Clusters. In the 2012 meeting, we plan to have sessions that will focus on topics including: (1) The use of cluster studies to probe fundamental phenomena; (2) Finite size effects on structure and thermodynamics; (3) Intermolecular forces and cooperative effects; (4) Molecular clusters as models for solvation; and (5) Studies of

The quantitative analysis of silicon carbide surface smoothing by Ar and Xe cluster ions

Science.gov (United States)

Ieshkin, A. E.; Kireev, D. S.; Ermakov, Yu. A.; Trifonov, A. S.; Presnov, D. E.; Garshev, A. V.; Anufriev, Yu. V.; Prokhorova, I. G.; Krupenin, V. A.; Chernysh, V. S.

2018-04-01

The gas cluster ion beam technique was used for the silicon carbide crystal surface smoothing. The effect of processing by two inert cluster ions, argon and xenon, was quantitatively compared. While argon is a standard element for GCIB, results for xenon clusters were not reported yet. Scanning probe microscopy and high resolution transmission electron microscopy techniques were used for the analysis of the surface roughness and surface crystal layer quality. The gas cluster ion beam processing results in surface relief smoothing down to average roughness about 1 nm for both elements. It was shown that xenon as the working gas is more effective: sputtering rate for xenon clusters is 2.5 times higher than for argon at the same beam energy. High resolution transmission electron microscopy analysis of the surface defect layer gives values of 7 ± 2 nm and 8 ± 2 nm for treatment with argon and xenon clusters.

Controlled enzymatic cutting of DNA molecules adsorbed on surfaces using soft lithography

Science.gov (United States)

Auerbach, Alyssa; Budassi, Julia; Shea, Emily; Zhu, Ke; Sokolov, Jonathan

2013-03-01

The enzyme DNase I was applied to adsorbed and aligned DNA molecules (Lamda, 48.5 kilobase pairs (kbp), and T4, 165.6 kbp), stretched linearly on a surface, by stamping with a polydimethylsiloxane (PDMS) grating. The DNAs were cut by the enzyme into separated, micron-sized segments along the length of the molecules at positions determined by the grating dimensions (3-20 microns). Ozone-treated PDMS stamps were coated with DNase I solutions and placed in contact with surface-adsorbed DNA molecules deposited on a 750 polymethylmethacrylate (PMMA) film spun-cast onto a silicon substrate. The stamps were applied under pressure for times up to 15 minutes at 37 C. The cutting was observed by fluorescence microscopy imaging of DNA labeled with YOYO dye. Cutting was found to be efficient despite the steric hindrance due to surface attachment of the molecules. Methods for detaching and separating the cut segments for sequencing applications will be discussed. Supported by NSF-DMR program.

Surface-enhanced Raman scattering of dipolar molecules by the graphene Fermi surface modulation with different dipole moments

Science.gov (United States)

Zhang, Mingjia; Leng, Yandan; Huang, Jing; Yu, JiaoJiao; Lan, Zhenggang; Huang, Changshui

2017-12-01

We report the modulation of Raman scattering spectrum of chromophore/graphene hybrids by tunning the molecular polarization with different terminal groups (methyl, methoxy, nitrile, and two nitros). Based on the density functional theory, the specific dipole moment values of the chromophore molecules are calculated. An obvious surface-enhanced Raman scattering (SERS) was observed and the scattering intensity of molecule increases with enlarged dipole moment. According to the analysis of G band Raman shifts of graphene, the enhancement of the Raman signal can be attributed to strong electronic coupling between graphene and chromophore, which is closely related with the modulation of graphene Fermi surface by changing the dipole moment of the molecule. Besides, the optimization of the ground state geometry and the binding energy of the hybrids were also calculated with the Density Functional Based Tight Bonding (DFTB) method, which confirms that the enhanced Raman scattering of molecules on graphene arises from the improved energy level matching between graphene Fermi surface and molecular band, further providing a new way to design novel SERS devices.

Theory of the reaction dynamics of small molecules on metal surfaces

Energy Technology Data Exchange (ETDEWEB)

Jackson, Bret [Univ. of Massachusetts, Amherst, MA (United States)

2016-09-09

The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H₂, H₂O and CH₄ on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimental data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C-covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).

Stochastic clustering of material surface under high-heat plasma load

Science.gov (United States)

Budaev, Viacheslav P.

2017-11-01

The results of a study of a surface formed by high-temperature plasma loads on various materials such as tungsten, carbon and stainless steel are presented. High-temperature plasma irradiation leads to an inhomogeneous stochastic clustering of the surface with self-similar granularity - fractality on the scale from nanoscale to macroscales. Cauliflower-like structure of tungsten and carbon materials are formed under high heat plasma load in fusion devices. The statistical characteristics of hierarchical granularity and scale invariance are estimated. They differ qualitatively from the roughness of the ordinary Brownian surface, which is possibly due to the universal mechanisms of stochastic clustering of material surface under the influence of high-temperature plasma.

Automated analysis of organic particles using cluster SIMS

Energy Technology Data Exchange (ETDEWEB)

Gillen, Greg; Zeissler, Cindy; Mahoney, Christine; Lindstrom, Abigail; Fletcher, Robert; Chi, Peter; Verkouteren, Jennifer; Bright, David; Lareau, Richard T.; Boldman, Mike

2004-06-15

Cluster primary ion bombardment combined with secondary ion imaging is used on an ion microscope secondary ion mass spectrometer for the spatially resolved analysis of organic particles on various surfaces. Compared to the use of monoatomic primary ion beam bombardment, the use of a cluster primary ion beam (SF{sub 5}{sup +} or C{sub 8}{sup -}) provides significant improvement in molecular ion yields and a reduction in beam-induced degradation of the analyte molecules. These characteristics of cluster bombardment, along with automated sample stage control and custom image analysis software are utilized to rapidly characterize the spatial distribution of trace explosive particles, narcotics and inkjet-printed microarrays on a variety of surfaces.

Thermal dynamics of silver clusters grown on rippled silica surfaces

Energy Technology Data Exchange (ETDEWEB)

Bhatnagar, Mukul, E-mail: mkbh10@gmail.com [FCIPT, Institute for Plasma Research, Gandhinagar, Gujarat (India); Nirma University, Ahmedabad, Gujarat (India); Ranjan, Mukesh [FCIPT, Institute for Plasma Research, Gandhinagar, Gujarat (India); Nirma University, Ahmedabad, Gujarat (India); Jolley, Kenny; Lloyd, Adam; Smith, Roger [Dept. of Mathematical Sciences, Loughborough University, Leicestershire LE11 3TU (United Kingdom); Mukherjee, Subroto [FCIPT, Institute for Plasma Research, Gandhinagar, Gujarat (India); Nirma University, Ahmedabad, Gujarat (India)

2017-02-15

Highlights: • Low energy oblique angle ion bombardment forms ripple pattern on silicon surface. • The ripple patterns have wavelengths between 20 and 45 nm and correspondingly low height. • Silver nanoparticles have been deposited at an angle of 70° on patterned silicon templates. • The as-deposited np are annealed in vacuo at temperature of 573 K for a time duration of 1 h. • MD simulation is used to model the process and compare the results to the experiment. • Results show that silver clusters grow preferentially along parallel to the rippled surface. • Mobility of silver atoms depends on the site to which they are bonded on this amorphous surface. • MD simulations show contour ordered coalescence which is dependent on ripple periodicity. - Abstract: Silver nanoparticles have been deposited on silicon rippled patterned templates at an angle of incidence of 70° to the surface normal. The templates are produced by oblique incidence argon ion bombardment and as the fluence increases, the periods and heights of the structures increase. Structures with periods of 20 nm, 35 nm and 45 nm have been produced. Moderate temperature vacuum annealing shows the phenomenon of cluster coalescence following the contour of the more exposed faces of the ripple for the case of 35 nm and 45 nm but not at 20 nm where the silver aggregates into larger randomly distributed clusters. In order to understand this effect, the morphological changes of silver nanoparticles deposited on an asymmetric rippled silica surface are investigated through the use of molecular dynamics simulations for different deposition angles of incidence between 0° and 70° and annealing temperatures between 500 K and 900 K. Near to normal incidence, clusters are observed to migrate over the entire surface but for deposition at 70°, a similar patterning is observed as in the experiment. The random distribution of clusters for the periodicity ≈ of 20 nm is linked to the geometry of the silica

Low-energy electron scattering from molecules, biomolecules and surfaces

CERN Document Server

Carsky, Petr

2011-01-01

Since the turn of the 21st century, the field of electron molecule collisions has undergone a renaissance. The importance of such collisions in applications from radiation chemistry to astrochemistry has flowered, and their role in industrial processes such as plasma technology and lighting are vital to the advancement of next generation devices. Furthermore, the development of the scanning tunneling microscope highlights the role of such collisions in the condensed phase, in surface processing, and in the development of nanotechnology.Low-Energy Electron Scattering from Molecules, Biomolecule

Potential energy surface from spectroscopic data in the photodissociation of polyatomic molecules

International Nuclear Information System (INIS)

Kim, Hwa Joong; Kim, Young Sik

2001-01-01

The time-dependent tracking inversion method is studied to extract the potential energy surface of the electronic excited state in the photodissociation of triatomic molecules. Based on the relay of the regularized inversion procedure and time-dependent wave packet propagation, the algorithm extracts the underlying potential energy surface piece by tracking the time-dependent data, which can be synthesized from Raman excitation profiles. We have demonstrated the algorithm to extract the potential energy surface of electronic excited state for NO 2 molecule where the wave packet split on a saddle-shaped surface. Finally, we describe the merits of the time-dependent tracking inversion method compared with the time-dependent inversion method and discussed several extensions of the algorithm

Encaged molecules in external electric fields: A molecular "tug-of-war"

Science.gov (United States)

Gurav, Nalini D.; Gejji, Shridhar P.; Bartolotti, Libero J.; Pathak, Rajeev K.

2016-08-01

Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.

Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

Science.gov (United States)

Gerber, R Benny; Varner, Mychel E; Hammerich, Audrey D; Riikonen, Sampsa; Murdachaew, Garold; Shemesh, Dorit; Finlayson-Pitts, Barbara J

2015-02-17

CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on

Bio-active molecules modified surfaces enhanced mesenchymal stem cell adhesion and proliferation

International Nuclear Information System (INIS)

Mobasseri, Rezvan; Tian, Lingling; Soleimani, Masoud; Ramakrishna, Seeram; Naderi-Manesh, Hossein

2017-01-01

Surface modification of the substrate as a component of in vitro cell culture and tissue engineering, using bio-active molecules including extracellular matrix (ECM) proteins or peptides derived ECM proteins can modulate the surface properties and thereby induce the desired signaling pathways in cells. The aim of this study was to evaluate the behavior of human bone marrow mesenchymal stem cells (hBM-MSCs) on glass substrates modified with fibronectin (Fn), collagen (Coll), RGD peptides (RGD) and designed peptide (R-pept) as bio-active molecules. The glass coverslips were coated with fibronectin, collagen, RGD peptide and R-peptide. Bone marrow mesenchymal stem cells were cultured on different substrates and the adhesion behavior in early incubation times was investigated using scanning electron microscopy (SEM) and confocal microscopy. The MTT assay was performed to evaluate the effect of different bio-active molecules on MSCs proliferation rate during 24 and 72 h. Formation of filopodia and focal adhesion (FA) complexes, two steps of cell adhesion process, were observed in MSCs cultured on bio-active molecules modified coverslips, specifically in Fn coated and R-pept coated groups. SEM image showed well adhesion pattern for MSCs cultured on Fn and R-pept after 2 h incubation, while the shape of cells cultured on Coll and RGD substrates indicated that they might experience stress condition in early hours of culture. Investigation of adhesion behavior, as well as proliferation pattern, suggests R-peptide as a promising bio-active molecule to be used for surface modification of substrate in supporting and inducing cell adhesion and proliferation. - Highlights: • Bioactive molecules modified surface is a strategy to design biomimicry scaffold. • Bi-functional Tat-derived peptide (R-pept) enhanced MSCs adhesion and proliferation. • R-pept showed similar influences to fibronectin on FA formation and attachment.

Structural and electronic properties of single molecules and organic layers on surfaces

NARCIS (Netherlands)

Sotthewes, Kai

2016-01-01

Single molecules and organic layers on well-defined solid surfaces have attracted tremendous attention owing to their interesting physical and chemical properties. The ultimate utility of single molecules or self-assembled monolayers (SAMs) for potential applications is critically dependent on the

Surface single-molecule dynamics controlled by entropy at low temperatures

Science.gov (United States)

Gehrig, J. C.; Penedo, M.; Parschau, M.; Schwenk, J.; Marioni, M. A.; Hudson, E. W.; Hug, H. J.

2017-02-01

Configuration transitions of individual molecules and atoms on surfaces are traditionally described using an Arrhenius equation with energy barrier and pre-exponential factor (attempt rate) parameters. Characteristic parameters can vary even for identical systems, and pre-exponential factors sometimes differ by orders of magnitude. Using low-temperature scanning tunnelling microscopy (STM) to measure an individual dibutyl sulfide molecule on Au(111), we show that the differences arise when the relative position of tip apex and molecule changes by a fraction of the molecule size. Altering the tip position on that scale modifies the transition's barrier and attempt rate in a highly correlated fashion, which results in a single-molecular enthalpy-entropy compensation. Conversely, appropriately positioning the STM tip allows selecting the operating point on the compensation line and modifying the transition rates. The results highlight the need to consider entropy in transition rates of single molecules, even at low temperatures.

Mass spectrometric studies of the cluster formation of radon progeny

Energy Technology Data Exchange (ETDEWEB)

Gong, S L [Toronto Univ., ON (Canada). Dept. of Chemical Engineering and Applied Chemistry

1994-12-31

A new experimental system is developed to study the cluster formation of radon progeny with neutral molecules in the environment, which includes a modified mass spectrometer and a surface barrier detector. With the system, the cluster research is carried out at molecular level at which the mass of individual cluster formed is measured. A theory is also proposed to treat the cluster formation as a discrete process based on the ion-dipole and dipole-dipole interactions. Comparison between the theory and experiment is given. (author). 16 refs., 6 figs.

Mass spectrometric studies of the cluster formation of radon progeny

International Nuclear Information System (INIS)

Gong, S.L.

1993-01-01

A new experimental system is developed to study the cluster formation of radon progeny with neutral molecules in the environment, which includes a modified mass spectrometer and a surface barrier detector. With the system, the cluster research is carried out at molecular level at which the mass of individual cluster formed is measured. A theory is also proposed to treat the cluster formation as a discrete process based on the ion-dipole and dipole-dipole interactions. Comparison between the theory and experiment is given. (author). 16 refs., 6 figs

Efficient Synthesis of Ir-Polyoxometalate Cluster Using a Continuous Flow Apparatus and STM Investigation of Its Coassembly Behavior on HOPG Surface.

Science.gov (United States)

Zhang, Junyong; Chang, Shaoqing; Suryanto, Bryan H R; Gong, Chunhua; Zeng, Xianghua; Zhao, Chuan; Zeng, Qingdao; Xie, Jingli

2016-06-06

Taking advantage of a continuous-flow apparatus, the iridium(III)-containing polytungstate cluster K12Na2H2[Ir2Cl8P2W20O72]·37H2O (1) was obtained in a reasonable yield (13% based on IrCl3·H2O). Compound 1 was characterized by Fourier transform IR, UV-visible, (31)P NMR, electrospray ionization mass spectrometry (ESI-MS), and thermogravimetric analysis measurements. (31)P NMR, ESI-MS, and elemental analysis all indicated 1 was a new polytungstate cluster compared with the reported K14[(IrCl4)KP2W20O72] compound. Intriguingly, the successful isolation of 1 relied on the custom-built flow apparatus, demonstrating the uniqueness of continuous-flow chemistry to achieve crystalline materials. The catalytic properties of 1 were assessed by investigating the activity on catalyzing the electro-oxidation of ruthenium tris-2,2'-bipyridine [Ru(bpy)3](2+/3+). The voltammetric behavior suggested a coupled catalytic behavior between [Ru(bpy)3](3+/2+) and 1. Furthermore, on the highly oriented pyrolytic graphite surface, 1,3,5-tris(10-carboxydecyloxy) benzene (TCDB) was used as the two-dimensional host network to coassemble cluster 1; the surface morphology was observed by scanning tunneling microscope technique. "S"-shape of 1 was observed, indicating that the cluster could be accommodated in the cavity formed by two TCDB host molecules, leading to a TCDB/cluster binary structure.

Bonding in Mercury Molecules Described by the Normalized Elimination of the Small Component and Coupled Cluster Theory

NARCIS (Netherlands)

Cremer, Dieter; Kraka, Elfi; Filatov, Michael

2008-01-01

Bond dissociation energies (BDEs) of neutral HgX and cationic HgX(+) molecules range from less than a kcal mol(-1) to as much as 60 kcal mol(-1). Using NESCICCCSD(T) [normalized elimination of the small component and coupled-cluster theory with all single and double excitations and a perturbative

Webs on surfaces, rings of invariants, and clusters.

Science.gov (United States)

Fomin, Sergey; Pylyavskyy, Pavlo

2014-07-08

We construct and study cluster algebra structures in rings of invariants of the special linear group action on collections of 3D vectors, covectors, and matrices. The construction uses Kuperberg's calculus of webs on marked surfaces with boundary.

Manipulating individual dichlorotin phthalocyanine molecules on Cu(100) surface at room temperature by scanning tunneling microscopy

International Nuclear Information System (INIS)

Li, Chao; Xiang, Feifei; Wang, Zhongping; Liu, Xiaoqing; Jiang, Danfeng; Wang, Li; Wang, Guang; Zhang, Xueao; Chen, Wei

2014-01-01

Single molecule manipulations have been achieved on dichlorotin phthalocyanine(SnCl 2 Pc) molecules adsorbed on Cu (100) at room temperature. Scanning tunneling microscopy observations directly demonstrate that the individual SnCl 2 Pc molecules can be moved along the [100] direction on Cu(100) surface by employing a scanning tunneling microscope tip fixed at the special position of the molecules. The orientation of the molecule can be switched between two angles of ±28° with respect to the [011] surface direction in the same way. Dependences of the probability of molecular motion on the distances between the tip and the molecules reveal that the mechanism for such manipulation of a SnCl 2 Pc molecule is dominated by the repulsive interactions between the tip and the molecules. With the assistance of this manipulation process, a prototype molecular storage array with molecular orientation as information carrier and an artificial hydrogen bonded supramolecular structure have been constructed on the surface. (paper)

Single OR molecule and OR atomic circuit logic gates interconnected on a Si(100)H surface

International Nuclear Information System (INIS)

Ample, F; Joachim, C; Duchemin, I; Hliwa, M

2011-01-01

Electron transport calculations were carried out for three terminal OR logic gates constructed either with a single molecule or with a surface dangling bond circuit interconnected on a Si(100)H surface. The corresponding multi-electrode multi-channel scattering matrix (where the central three terminal junction OR gate is the scattering center) was calculated, taking into account the electronic structure of the supporting Si(100)H surface, the metallic interconnection nano-pads, the surface atomic wires and the molecule. Well interconnected, an optimized OR molecule can only run at a maximum of 10 nA output current intensity for a 0.5 V bias voltage. For the same voltage and with no molecule in the circuit, the output current of an OR surface atomic scale circuit can reach 4 μA.

Detecting edges in the X-ray surface brightness of galaxy clusters

Science.gov (United States)

Sanders, J. S.; Fabian, A. C.; Russell, H. R.; Walker, S. A.; Blundell, K. M.

2016-08-01

The effects of many physical processes in the intracluster medium of galaxy clusters imprint themselves in X-ray surface brightness images. It is therefore important to choose optimal methods for extracting information from and enhancing the interpretability of such images. We describe in detail a gradient filtering edge detection method that we previously applied to images of the Centaurus cluster of galaxies. The Gaussian gradient filter measures the gradient in the surface brightness distribution on particular spatial scales. We apply this filter on different scales to Chandra X-ray observatory images of two clusters with active galactic nucleus feedback, the Perseus cluster and M 87, and a merging system, A 3667. By combining filtered images on different scales using radial filters spectacular images of the edges in a cluster are produced. We describe how to assess the significance of features in filtered images. We find the gradient filtering technique to have significant advantages for detecting many kinds of features compared to other analysis techniques, such as unsharp masking. Filtering cluster images in this way in a hard energy band allows shocks to be detected.

High-intensity X-rays interaction with matter processes in plasmas, clusters, molecules and solids

CERN Document Server

Hau-Riege, Stefan P

2012-01-01

Filling the need for a book bridging the effect of matter on X-ray radiation and the interaction of x-rays with plasmas, this monograph provides comprehensive coverage of the topic. As such, it presents and explains such powerful new X-ray sources as X-ray free-electron lasers, as well as short pulse interactions with solids, clusters, molecules, and plasmas, and X-ray matter interactions as a diagnostic tool. Equally useful for researchers and practitioners working in the field.

Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

Science.gov (United States)

Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

2013-12-01

Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

Bright galaxies in the Fornax cluster. Automated galaxy surface photometry: Pt. 7

International Nuclear Information System (INIS)

Disney, M.J.; Phillipps, S.; Davies, J.L.; Cawson, M.G.M.; Kibblewhite, E.J.

1990-01-01

We have determined surface-brightness profiles for all galaxies down to magnitude B = 16 in the central region of the Fornax cluster. Using existing redshift data, we have determined the distributions of surface brightness for both the whole sample and for cluster disc galaxies only. Although both distributions peak at extrapolated central surface brightness ∼ 21.7B mag/arcsec 2 (the canonical result), it is shown that they are, in fact, consistent with very broad distributions of disc central surface brightness once selection effects and the effects of bulge contamination of the profile are taken into account. (author)

New projectiles: multicharged metal clusters and biopolymers

International Nuclear Information System (INIS)

Della-Negra, S.; Gardes, D.; Le Beyec, Y.; Waast, B.

1991-01-01

Metal clusters and molecules are the one mean to realize simultaneous impacts of several atoms on a reduced surface(∼100A). The interaction characteristics is the non-linearity of energy deposition; the perturbation that the cluster produces, is above than the sum of the perturbation induced by its components, taken separately. The purpose of ORION project is to accelerate these new projectiles at ORSAY Tandem. The considered mass range is from 100 Daltons to 100 000 Daltons and energy range from MeV to GeV

Comparison and combination of "direct" and fragment based local correlation methods: Cluster in molecules and domain based local pair natural orbital perturbation and coupled cluster theories

Science.gov (United States)

Guo, Yang; Becker, Ute; Neese, Frank

2018-03-01

Local correlation theories have been developed in two main flavors: (1) "direct" local correlation methods apply local approximation to the canonical equations and (2) fragment based methods reconstruct the correlation energy from a series of smaller calculations on subsystems. The present work serves two purposes. First, we investigate the relative efficiencies of the two approaches using the domain-based local pair natural orbital (DLPNO) approach as the "direct" method and the cluster in molecule (CIM) approach as the fragment based approach. Both approaches are applied in conjunction with second-order many-body perturbation theory (MP2) as well as coupled-cluster theory with single-, double- and perturbative triple excitations [CCSD(T)]. Second, we have investigated the possible merits of combining the two approaches by performing CIM calculations with DLPNO methods serving as the method of choice for performing the subsystem calculations. Our cluster-in-molecule approach is closely related to but slightly deviates from approaches in the literature since we have avoided real space cutoffs. Moreover, the neglected distant pair correlations in the previous CIM approach are considered approximately. Six very large molecules (503-2380 atoms) were studied. At both MP2 and CCSD(T) levels of theory, the CIM and DLPNO methods show similar efficiency. However, DLPNO methods are more accurate for 3-dimensional systems. While we have found only little incentive for the combination of CIM with DLPNO-MP2, the situation is different for CIM-DLPNO-CCSD(T). This combination is attractive because (1) the better parallelization opportunities offered by CIM; (2) the methodology is less memory intensive than the genuine DLPNO-CCSD(T) method and, hence, allows for large calculations on more modest hardware; and (3) the methodology is applicable and efficient in the frequently met cases, where the largest subsystem calculation is too large for the canonical CCSD(T) method.

Internal state distributions of molecules scattering and desorbing from surfaces

International Nuclear Information System (INIS)

Auerbach, D.J.

1983-01-01

Attempts are made to interpret scattering experiments of NO molecules on Ag(111) where a (rotational) state-specific detector has been used. A model using an anisotropic potential is proposed to explain the observed incoming energy- and angle dependence. The so-called rotational rainbows are explained. It is concluded, that in this way information on intermolecular potentials and the transfer of translational to rotational energy in the dynamics of trapping and sticking of molecules on surfaces can be extracted. (G.Q.)

Stability of Ta-encapsulating Si clusters on Si(111)-(7x7) surfaces

CERN Document Server

Uchida, N; Miyazaki, T; Kanayama, T

2003-01-01

Tantalum containing Si cluster ions TaSi sub 1 sub 0 sub - sub 1 sub 3 H sub x sup + were synthesized in an ion trap and deposited onto Si(111)-(7x7) surfaces with a kinetic energy of 18 eV. Scanning tunnelling microscope observations revealed that the clusters adsorbed on the surface without decomposition, consistent with ab initio calculation results, that predicted the clusters would have stable Si-cage structures with a Ta atom at the centre. (rapid communication)

Probing Enzyme-Surface Interactions via Protein Engineering and Single-Molecule Techniques

Science.gov (United States)

2017-06-26

SECURITY CLASSIFICATION OF: The overall objective of this research was to exploit protein engineering and fluorescence single-molecule methods to...enhance our understanding of the interaction of proteins and surfaces. Given this objective, the specific aims of this research were to: 1) exploit the...incorporation of unnatural amino acids in proteins to introduce single-molecule probes (i.e., fluorophores for fluorescence resonance energy transfer

Density functional studies: First principles and semiempirical calculations of clusters and surfaces

International Nuclear Information System (INIS)

Sinnott, S.B.

1993-01-01

In the research presented here, various theoretical electronic structure techniques are utilized to analyze widely different systems from silicon clusters to transition metal solids and surfaces. For the silicon clusters, first principles density functional methods are used to investigate Si N for N = 2-8. The goal is to understand the different types of bonding that can occur in such small clusters where the coordination of the atoms differs substantially from that of the stable bulk tetrahedral bonding. Such uncoordinated structures can provide a good test of more approximate theories that can be used eventually to model silicon surfaces, of obvious technological importance. For the transition metal systems, non-self-consistent electronic structure methods are used to provide an understanding of the driving force for surface relaxations. An in-depth analysis of the results is presented and the physical basis of surface relaxation within the theory is discussed. In addition, the limitations inherent in calculations of metal surface relaxation are addressed. Finally, in an effort to increase understanding of approximate methods, a novel non-self-consistent density functional electronic structure method is developed that is ∼1000 times faster computationally than more sophisticated methods. This new method is tested for a variety of systems including diatomics, mixed clusters, surfaces and bulk lattices. The strengths and weaknesses of the new theory are discussed in detail, leading to greater understanding of non-self-consistent density functional theories as a whole

Jump rates for surface diffusion of large molecules from first principles

Energy Technology Data Exchange (ETDEWEB)

Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)

2015-04-21

We apply a recently developed stochastic model for the surface diffusion of large molecules to calculate jump rates for 9,10-dithioanthracene on a Cu(111) surface. The necessary input parameters for the stochastic model are calculated from first principles using density functional theory (DFT). We find that the inclusion of van der Waals corrections to the DFT energies is critical to obtain good agreement with experimental results for the adsorption geometry and energy barrier for diffusion. The predictions for jump rates in our model are in excellent agreement with measured values and show a marked improvement over transition state theory (TST). We find that the jump rate prefactor is reduced by an order of magnitude from the TST estimate due to frictional damping resulting from energy exchange with surface phonons, as well as a rotational mode of the diffusing molecule.

Adsorption behavior of sulfur-containing amino acid molecule on transition metal surface studied by S K-edge NEXAFS

International Nuclear Information System (INIS)

Yagi, S.; Matsumura, K.; Nakano, Y.; Ikenaga, E.; Sardar, S.A.; Syed, J.A.; Soda, K.; Hashimoto, E.; Tanaka, K.; Taniguchi, M.

2003-01-01

Adsorption behavior of a sulfur-containing amino acid L-cysteine molecule on transition metal surface have been investigated by S K-edge near-edge X-ray absorption fine structure. The L-cysteine molecule for first adsorption layer was found to dissociate on polycrystalline nickel surface, whereas molecularly adsorbed on copper surface at room temperature. Most of the L-cysteine molecules have been dissociated on nickel surface in annealing condition up to 353 K. On the other hand, the L-cysteine molecule did not dissociate on copper surface and the elongation of the S-C bonding occurred at 353 K

Use of fluorescence to probe the surface dynamics during disorder-to-order transition and cluster formation in dihalonaphthalene-water thin films on Al2O3(0001)

International Nuclear Information System (INIS)

Evans, M.A.; Hoss, D.R.; Howard, K.E.; Louie, A.D.; Bishop, A.J.; Martin, K.A.; Nishimura, A.M.

2006-01-01

Amorphous dihalonaphthalenes that are prepared by vacuum deposition onto a cold Al 2 O 3 surface form electronically excited dimers when optically pumped, and their emission is characteristically red-shifted, broad and featureless compared to the monomeric fluorescence. If the surface is heated, the adlayer undergoes a disorder-to-order transition at a temperature characteristic of the molecule. Since pure crystalline dihalonaphthalenes typically fluoresce and do not exhibit excimeric features, the transition was studied by taking advantage of the changes in the spectral characteristics of the adlayer. These included transmittance, and emission from fluorescence and excimer. The combination of these methods allowed a close look at the surface dynamics of molecules on the surface of Al 2 O 3 as the adlayer was heated from the deposition temperature to desorption. If a bilayer is formed by depositing water onto the surface with the organic adlayer on top, water, with its lower desorption energy, can be made to percolate into the organic layer. The optical probes indicate that the water clearly associates with the organic molecules while the excess water desorbs. By varying the coverage of either the water or the dihalonaphthalene, the stoichiometric composition of the cluster can be determined and are reported here

A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.

Science.gov (United States)

Schneider, Julian; Ciacchi, Lucio Colombi

2011-02-08

The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.

Stabilities of protonated water-ammonia clusters

Science.gov (United States)

Sundén, A. E. K.; Støchkel, K.; Hvelplund, P.; Brøndsted Nielsen, S.; Dynefors, B.; Hansen, K.

2018-05-01

Branching ratios of water and ammonia evaporation have been measured for spontaneous evaporation from protonated mixed clusters H+(H2O)n(NH3)m in the size range 0 ≤ n ≤ 11 and 0 ≤ m ≤ 7. Mixed clusters evaporate water except for clusters containing six or more ammonia molecules, indicating the formation of a stable core of one ammonium ion surrounded by four ammonia molecules and a second shell consisting predominantly of water. We relate evaporative branching ratios to free energy differences between the products of competing channels and determine the free energy differences for clusters with up to seven ammonia molecules. Clusters containing up to five ammonia molecules show a very strong scaling of these free energy differences.

Metallic behavior and negative differential resistance properties of (InAs)n (n = 2 − 4) molecule cluster junctions via a combined non–equilibrium Green's function and density functional theory study

International Nuclear Information System (INIS)

Wang, Qi; Li, Rong; Xu, Yuanlan; Zhang, Jianbing; Miao, Xiangshui; Zhang, Daoli

2014-01-01

In this present work, the geometric structures and electronic transport properties of (InAs) n (n = 2, 3, 4) molecule cluster junctions are comparatively investigated using NEGF combined with DFT. Results indicate that all (InAs) n molecule cluster junctions present metallic behavior at the low applied biases ([−2V, 2V]), while NDR appears at a certain high bias range. Our calculation shows that the current of (InAs) 4 molecule cluster–based junction is almost the largest at any bias. The mechanisms of the current–voltage characteristics of all the three molecule cluster junctions are proposed.

Dependence of surface smoothing, sputtering and etching phenomena on cluster ion dosage

CERN Document Server

Song, J H; Choi, W K

2002-01-01

The dependence of surface smoothing and sputtering phenomena of Si (1 0 0) solid surfaces irradiated by CO sub 2 cluster ions on cluster-ion dosage was investigated using an atomic force microscope. The flux and total ion dosage of impinging cluster ions at the acceleration voltage of 50 kV were fixed at 10 sup 9 ions/cm sup 2 s and were scanned from 5x10 sup 1 sup 0 to 5x10 sup 1 sup 3 ions/cm sup 2 , respectively. The density of hillocks induced by cluster ion impact was gradually increased with the dosage up to 5x10 sup 1 sup 1 ions/cm sup 2 , which caused that the irradiated surface became rough from 0.4 to 1.24 nm in root-mean-square roughness (sigma sub r sub m sub s). At the boundary of the ion dosage of 10 sup 1 sup 2 ions/cm sup 2 , the density of the induced hillocks was decreased and sigma sub r sub m sub s was about 1.21 nm, not being deteriorated further. At the dosage of 5x10 sup 1 sup 3 ions/cm sup 2 , the induced hillocks completely disappeared and the surface became very flat as much as sigma...

Chemical reactions of water molecules on Ru(0001) induced by selective excitation of vibrational modes

Energy Technology Data Exchange (ETDEWEB)

Mugarza, Aitor; Shimizu, Tomoko K.; Ogletree, D. Frank; Salmeron, Miquel

2009-05-07

Tunneling electrons in a scanning tunneling microscope were used to excite specific vibrational quantum states of adsorbed water and hydroxyl molecules on a Ru(0 0 0 1) surface. The excited molecules relaxed by transfer of energy to lower energy modes, resulting in diffusion, dissociation, desorption, and surface-tip transfer processes. Diffusion of H{sub 2}O molecules could be induced by excitation of the O-H stretch vibration mode at 445 meV. Isolated molecules required excitation of one single quantum while molecules bonded to a C atom required at least two quanta. Dissociation of single H{sub 2}O molecules into H and OH required electron energies of 1 eV or higher while dissociation of OH required at least 2 eV electrons. In contrast, water molecules forming part of a cluster could be dissociated with electron energies of 0.5 eV.

Adsorption of ethyl xanthate on ZnS(110) surface in the presence of water molecules: A DFT study

Energy Technology Data Exchange (ETDEWEB)

Long, Xianhao [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Chen, Jianhua, E-mail: jhchen@gxu.edu.cn [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Guangxi Colleges and University Key Laboratory of Minerals Engineering, 530004 (China); Chen, Ye, E-mail: fby18@126.com [College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China)

2016-05-01

Graphical abstract: - Highlights: • Adsorption of water molecules decreases the reactivity of surface Zn atom. • Copper impurities decrease the band gap of ZnS surface. • Copper impurities enhance the adsorption of xanthate on the ZnS surface. • Water molecules have little influence on the properties of Cu-substituted ZnS surface. • The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface. - Abstracts: The interaction of collector with the mineral surface plays a very important role in the froth flotation of sphalerite. The adsorptions occurred at the interface between the mineral surface and waters; however most of DFT simulations are performed in vacuum, without consideration of water effect. Semiconductor surface has an obvious proximity effect, which will greatly influence the surface reactivity. To understand the mechanism of xanthate interacting with sphalerite surface in the presence of water molecules, the ethyl xanthate molecule adsorption on un-activated and Cu-activated ZnS(110) surface in the absence and presence of water molecules were performed using the density functional theory (DFT) method. The calculated results show that the adsorption of water molecules dramatically changes the properties of ZnS surface, resulting in decreasing the reactivity of surface Zn atoms with xanthate. Copper activation of ZnS surface changes the surface properties, leading to the totally different adsorption behaviors of xanthate. The presence of waters has little influence on the properties of Cu-activated ZnS surface. The xanthate S atom can interact with the surface S atom of Cu-substituted ZnS surface, which would result in the formation of dixanthogen.

Anchoring of organic molecules to a metal surface: HtBDC on Cu(110)

DEFF Research Database (Denmark)

Schunack, M.; Petersen, L.; Kuhnle, A.

2001-01-01

The interaction of largish molecules with metal surfaces has been studied by combining the imaging and manipulation capabilities of the scanning tunneling microscope (STM). At the atomic scale, the STM results directly reveal that the adsorption of a largish organic molecule can induce...

Photoionization dynamics of glycine adsorbed on a silicon cluster: ''On-the-fly'' simulations

International Nuclear Information System (INIS)

Shemesh, Dorit; Baer, Roi; Seideman, Tamar; Gerber, R. Benny

2005-01-01

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by ''on-the-fly'' molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering

Single-Molecule Chemistry with Surface- and Tip-Enhanced Raman Spectroscopy.

Science.gov (United States)

Zrimsek, Alyssa B; Chiang, Naihao; Mattei, Michael; Zaleski, Stephanie; McAnally, Michael O; Chapman, Craig T; Henry, Anne-Isabelle; Schatz, George C; Van Duyne, Richard P

2017-06-14

Single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have emerged as analytical techniques for characterizing molecular systems in nanoscale environments. SERS and TERS use plasmonically enhanced Raman scattering to characterize the chemical information on single molecules. Additionally, TERS can image single molecules with subnanometer spatial resolution. In this review, we cover the development and history of SERS and TERS, including the concept of SERS hot spots and the plasmonic nanostructures necessary for SM detection, the past and current methodologies for verifying SMSERS, and investigations into understanding the signal heterogeneities observed with SMSERS. Moving on to TERS, we cover tip fabrication and the physical origins of the subnanometer spatial resolution. Then, we highlight recent advances of SMSERS and TERS in fields such as electrochemistry, catalysis, and SM electronics, which all benefit from the vibrational characterization of single molecules. SMSERS and TERS provide new insights on molecular behavior that would otherwise be obscured in an ensemble-averaged measurement.

Investigation of the Structures and Energy Landscapes of Thiocyanate-Water Clusters

Directory of Open Access Journals (Sweden)

Lewis C. Smeeton

2017-03-01

Full Text Available The Basin Hopping search method is used to find the global minima (GM and map the energy landscapes of thiocyanate-water clusters, (SCN−(H2On with 3–50 water molecules, with empirical potentials describing the ion-water and water-water interactions. (It should be noted that beyond n = 23, the lowest energy structures were only found in 1 out of 8 searches so they are unlikely to be the true GM but are indicative low energy structures. As for pure water clusters, the low energy isomers of thiocyanate-water clusters show a preponderance of fused water cubes and pentagonal prisms, with the weakly solvated thiocyanate ion lying on the surface, replacing two water molecules along an edge of a water polyhedron and with the sulfur atom in lower coordinated sites than nitrogen. However, by comparison with Density Functional Theory (DFT calculations, the empirical potential is found to overestimate the strength of the thiocyanate-water interaction, especially O–H⋯S, with low energy DFT structures having lower coordinate N and (especially S atoms than for the empirical potential. In the case of these finite ion-water clusters, the chaotropic (“disorder-making” thiocyanate ion weakens the water cluster structure but the water molecule arrangement is not significantly changed.

Single molecule detection on the cell membrane with Near-field Scanning Optical Microscopy

NARCIS (Netherlands)

de Bakker, B.I.

2004-01-01

In this research we have developed a dedicated near- field scanning optical microscope (NSOM) for molecular biology and applied it to study the spatial organization of (fluorescently labeled) proteins at the cell surface. For the first time, protein clusters and individual molecules are resolved at

Vascular Cell Adhesion Molecule 1, Intercellular Adhesion Molecule 1, and Cluster of Differentiation 146 Levels in Patients with Type 2 Diabetes with Complications.

Science.gov (United States)

Hocaoglu-Emre, F Sinem; Saribal, Devrim; Yenmis, Guven; Guvenen, Guvenc

2017-03-01

Type 2 diabetes mellitus (T2DM) is a multisystemic, chronic disease accompanied by microvascular complications involving various complicated mechanisms. Intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), and cluster of differentiation-146 (CD146) are mainly expressed by endothelial cells, and facilitate the adhesion and transmigration of immune cells, leading to inflammation. In the present study, we evaluated the levels of soluble adhesion molecules in patients with microvascular complications of T2DM. Serum and whole blood samples were collected from 58 T2DM patients with microvascular complications and 20 age-matched healthy subjects. Levels of soluble ICAM-1 (sICAM-1) and soluble VCAM-1 (sVCAM-1) were assessed using enzyme-linked immunosorbent assay, while flow cytometry was used to determine CD146 levels. Serum sICAM-1 levels were lower in T2DM patients with microvascular complications than in healthy controls (Pmolecule levels were not correlated with the complication type. In the study group, most of the patients were on insulin therapy (76%), and 95% of them were receiving angiotensin-converting enzyme (ACE)-inhibitor agents. Insulin and ACE-inhibitors have been shown to decrease soluble adhesion molecule levels via various mechanisms, so we suggest that the decreased or unchanged levels of soluble forms of cellular adhesion molecules in our study group may have resulted from insulin and ACE-inhibitor therapy, as well as tissue-localized inflammation in patients with T2DM. Copyright © 2017 Korean Endocrine Society

Endocytic pathway rapidly delivers internalized molecules to lysosomes: an analysis of vesicle trafficking, clustering and mass transfer.

Science.gov (United States)

Pangarkar, Chinmay; Dinh, Anh-Tuan; Mitragotri, Samir

2012-08-20

Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion-advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Density functional study of TaSin (n = 1-3, 12) clusters adsorbed to graphene surface

International Nuclear Information System (INIS)

Guo Ping; Zheng Lin; Zheng Jiming; Zhang Ruizhi; Yang Luna; Ren, Zhaoyu

2011-01-01

A plane-wave density functional theory (DFT) calculations have been performed to investigate structural and electronic properties of TaSi n (n = 1-3, 12) clusters supported by graphene surface. The resulting adsorption structures are described and discussed in terms of stability, bonding, and electron transfer between the cluster and the graphene. The TaSi n clusters on graphene surface favor their free-standing ground-state structures. Especially in the cases of the linear TaSi 2 and the planar TaSi 3 , the graphene surface may catalyze the transition of the TaSi n clusters from an isomer of lower dimensionality into the ground-state structure. The adsorption site and configuration of TaSi n on graphene surface are dominated by the interaction between Ta atom and graphene. Ta atom prefers to adsorb on the hollow site of graphene, and Si atoms tend to locate on the bridge site. Further, the electron transfer is found to proceed from the cluster to the surface for n = 1 and 2, while its direction reverses as n > 2. For the case of TaSi, chemisorption is shown to prevail over physisorption as the dominant mode of surface-adsorbate interaction by charge density analysis.

Differential Expression of Osteo-Modulatory Molecules in Periodontal Ligament Stem Cells in Response to Modified Titanium Surfaces

Directory of Open Access Journals (Sweden)

So Yeon Kim

2014-01-01

Full Text Available This study assessed differential gene expression of signaling molecules involved in osteogenic differentiation of periodontal ligament stem cells (PDLSCs subjected to different titanium (Ti surface types. PDLSCs were cultured on tissue culture polystyrene (TCPS, and four types of Ti discs (PT, SLA, hydrophilic PT (pmodPT, and hydrophilic SLA (modSLA with no osteoinductive factor and then osteogenic activity, including alkaline phosphatase (ALP activity, mRNA expression of runt-related gene 2, osterix, FOSB, FRA1, and protein levels of osteopontin and collagen type IA, were examined. The highest osteogenic activity appeared in PDLSCs cultured on SLA, compared with the TCPS and other Ti surfaces. The role of surface properties in affecting signaling molecules to modulate PDLSC behavior was determined by examining the regulation of Wnt pathways. mRNA expression of the canonical Wnt signaling molecules, Wnt3a and β-catenin, was higher on SLA and modSLA than on smooth surfaces, but gene expression of the calcium-dependent Wnt signaling molecules Wnt5a, calmodulin, and NFATc1 was increased significantly on PT and pmodPT. Moreover, integrin α2/β1, sonic hedgehog, and Notch signaling molecules were affected differently by each surface modification. In conclusion, surface roughness and hydrophilicity can affect differential Wnt pathways and signaling molecules, targeting the osteogenic differentiation of PDLSCs.

Metallization of DNA on silicon surface

International Nuclear Information System (INIS)

Puchkova, Anastasiya Olegovna; Sokolov, Petr; Petrov, Yuri Vladimirovich; Kasyanenko, Nina Anatolievna

2011-01-01

New simple way for silver deoxyribonucleic acid (DNA)-based nanowires preparation on silicon surface was developed. The electrochemical reduction of silver ions fixed on DNA molecule provides the forming of tightly matched zonate silver clusters. Highly homogeneous metallic clusters have a size about 30 nm. So the thickness of nanowires does not exceed 30–50 nm. The surface of n-type silicon monocrystal is the most convenient substrate for this procedure. The comparative analysis of DNA metallization on of n-type silicon with a similar way for nanowires fabrication on p-type silicon, freshly cleaved mica, and glass surface shows the advantage of n-type silicon, which is not only the substrate for DNA fixation but also the source of electrons for silver reduction. Images of bound DNA molecules and fabricated nanowires have been obtained using an atomic force microscope and a scanning ion helium microscope. DNA interaction with silver ions in a solution was examined by the methods of ultraviolet spectroscopy and circular dichroism.

Adsorption and dissociation of oxygen molecules on Si(111)-(7×7) surface

International Nuclear Information System (INIS)

Niu, Chun-Yao; Wang, Jian-Tao

2013-01-01

The adsorption and dissociation of O 2 molecules on Si(111)-(7×7) surface have been studied by first-principles calculations. Our results show that all the O 2 molecular species adsorbed on Si(111)-(7×7) surface are unstable and dissociate into atomic species with a small energy barrier about 0.1 eV. The single O 2 molecule adsorption tends to form an ins×2 or a new metastable ins×2* structure on the Si adatom sites and the further coming O 2 molecules adsorb on those structures to produce an ad-ins×3 structure. The ad-ins×3 structure is indeed highly stable and kinetically limited for diving into the subsurface layer to form the ins×3-tri structure by a large barrier of 1.3 eV. Unlike the previous views, we find that all the ad-ins, ins×2, and ad-ins×3 structures show bright images, while the ins×2*, ins×3, and ins×3-tri structures show dark images. The proposed oxidation pathways and simulated scanning tunneling microscope images account well for the experimental results and resolve the long-standing confusion and issue about the adsorption and reaction of O 2 molecules on Si(111) surface

Photochemistry in rare gas clusters

International Nuclear Information System (INIS)

Moeller, T.; Haeften, K. von; Pietrowski, R. von

1999-01-01

In this contribution photochemical processes in pure rare gas clusters will be discussed. The relaxation dynamics of electronically excited He clusters is investigated with luminescence spectroscopy. After electronic excitation of He clusters many sharp lines are observed in the visible and infrared spectral range which can be attributed to He atoms and molecules desorbing from the cluster. It turns out that the desorption of electronically excited He atoms and molecules is an important decay channel. The findings for He clusters are compared with results for Ar clusters. While desorption of electronically excited He atoms is observed for all clusters containing up to several thousand atoms a corresponding process in Ar clusters is only observed for very small clusters (N<10). (orig.)

Photochemistry in rare gas clusters

Energy Technology Data Exchange (ETDEWEB)

Moeller, T.; Haeften, K. von; Pietrowski, R. von [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Hamburger Synchrotronstrahlungslabor; Laarman, T. [Universitaet Hamburg, II. Institut fuer Experimentalphysik, Luruper Chaussee 149, D-22761 Hamburg (Germany)

1999-12-01

In this contribution photochemical processes in pure rare gas clusters will be discussed. The relaxation dynamics of electronically excited He clusters is investigated with luminescence spectroscopy. After electronic excitation of He clusters many sharp lines are observed in the visible and infrared spectral range which can be attributed to He atoms and molecules desorbing from the cluster. It turns out that the desorption of electronically excited He atoms and molecules is an important decay channel. The findings for He clusters are compared with results for Ar clusters. While desorption of electronically excited He atoms is observed for all clusters containing up to several thousand atoms a corresponding process in Ar clusters is only observed for very small clusters (N<10). (orig.)

Cluster-collision frequency. II. Estimation of the collision rate

International Nuclear Information System (INIS)

Amadon, A.S.; Marlow, W.H.

1991-01-01

Gas-phase cluster-collision rates, including effects of cluster morphology and long-range intermolecular forces, are calculated. Identical pairs of icosahedral or dodecahedral carbon tetrachloride clusters of 13, 33, and 55 molecules in two different relative orientations were discussed in the preceding paper [Phys. Rev. A 43, 5483 (1991)]: long-range interaction energies were derived based upon (i) exact calculations of the iterated, or many-body, induced-dipole interaction energies for the clusters in two fixed relative orientations; and (ii) bulk, or continuum descriptions (Lifshitz--van der Waals theory), of spheres of corresponding masses and diameters. In this paper, collision rates are calculated according to an exact description of the rates for small spheres interacting via realistic potentials. Utilizing the interaction energies of the preceding paper, several estimates of the collision rates are given by treating the discrete clusters in fixed relative orientations, by computing rotationally averaged potentials for the discrete clusters, and by approximating the clusters as continuum spheres. For the discrete, highly symmetric clusters treated here, the rates using the rotationally averaged potentials closely approximate the fixed-orientation rates and the values of the intercluster potentials for cluster surface separations under 2 A have negligible effect on the overall collision rates. While the 13-molecule cluster-collision rate differs by 50% from the rate calculated as if the cluster were bulk matter, the two larger cluster-collision rates differ by less than 15% from the macroscopic rates, thereby indicating the transition of microscopic to macroscopic behavior

Friction and diffusion dynamics of adsorbates at surfaces

NARCIS (Netherlands)

Fusco, C.

2005-01-01

A theoretical study of the motion of adsorbates (e. g. atoms, molecules or clusters) on solid surfaces is presented, with a focus on surface diffusion and atomic-scale friction. These two phenomena are inextricably linked, because when an atomic or molecular adsorbate diffuses, or is pulled, it

Simulation of depositions of a Lennard-Jones cluster on a crystalline surface

International Nuclear Information System (INIS)

Saitoh, Kuniyasu; Hayakawa, Hisao

2009-01-01

Depositions of amorphous Lennard-Jones clusters on a crystalline surface are numerically investigated. From the results of the molecular dynamics simulation, we found that the deposited clusters exhibit a transition from multilayered adsorption to monolayered adsorption at a critical incident speed. Employing the energy conservation law, we can explain the behavior of the ratio of the number of atoms adsorbed on the substrate to the cluster size. The boundary shape of the deposited cluster depends strongly on the incident speed, and some unstable modes grow during the spread of the deposited cluster on the substrate. We also discuss the wettability between different Lennard-Jones atoms. (author)

Desorption dynamics of deuterium molecules from the Si(100)-(3x1) dideuteride surface.

Science.gov (United States)

Niida, T; Tsurumaki, H; Namiki, A

2006-01-14

We measured polar angle (theta)-resolved time-of-flight spectra of D2 molecules desorbing from the Si(100)-(3x1) dideuteride surface. The desorbing D2 molecules exhibit a considerable translational heating with mean desorption kinetic energies of approximately 0.25 eV, which is mostly independent of the desorption angles for 0 degreesdynamics of deuterium was discussed along the principle of detailed balance to predict their adsorption dynamics onto the monohydride Si surface.

Observation of the adsorption and desorption of vibrationally excited molecules on a metal surface

Science.gov (United States)

Shirhatti, Pranav R.; Rahinov, Igor; Golibrzuch, Kai; Werdecker, Jörn; Geweke, Jan; Altschäffel, Jan; Kumar, Sumit; Auerbach, Daniel J.; Bartels, Christof; Wodtke, Alec M.

2018-06-01

The most common mechanism of catalytic surface chemistry is that of Langmuir and Hinshelwood (LH). In the LH mechanism, reactants adsorb, become thermalized with the surface, and subsequently react. The measured vibrational (relaxation) lifetimes of molecules adsorbed at metal surfaces are in the range of a few picoseconds. As a consequence, vibrational promotion of LH chemistry is rarely observed, with the exception of LH reactions occurring via a molecular physisorbed intermediate. Here, we directly detect adsorption and subsequent desorption of vibrationally excited CO molecules from a Au(111) surface. Our results show that CO (v = 1) survives on a Au(111) surface for 1 × 10-10 s. Such long vibrational lifetimes for adsorbates on metal surfaces are unexpected and pose an interesting challenge to the current understanding of vibrational energy dissipation on metal surfaces. They also suggest that vibrational promotion of surface chemistry might be more common than is generally believed.

Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface.

Science.gov (United States)

Pawlak, Rémy; Ouyang, Wengen; Filippov, Alexander E; Kalikhman-Razvozov, Lena; Kawai, Shigeki; Glatzel, Thilo; Gnecco, Enrico; Baratoff, Alexis; Zheng, Quanshui; Hod, Oded; Urbakh, Michael; Meyer, Ernst

2016-01-26

The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.

Two-Dimensional Cysteine and Cystine Cluster Networks on Au(111) Disclosed by Voltammetry and in Situ Scanning Tunneling Microscopy

DEFF Research Database (Denmark)

Zhang, Jingdong; Chi, Qijin; Nielsen, Jens Ulrik

2000-01-01

Microscopic structures for molecular monolayers of L-cysteine and L-cystine assembled on Au(111) have been disclosed by employing electrochemistry and in situ scanning tunneling microscopy (STM). HighresolutionSTMimages show that the adlayers of both cyteine and cystine exhibit highly......-ordered networklike clusters with (3x3 6)R30° structure. By combining the surface coverage estimated from voltammetric data, each cluster is demonstrated to include six individual cysteine molecules or three cystine molecules. As a comparison, no cluster structure is observed for the 1-butanethiol adlayer prepared...... and examined under the same conditions as those for cysteine and cystine. This suggests that intermolecular and intramolecular hydrogen bonds among adsorbed cysteine or cystine molecules could be responsible for the origin of the cluster-network structures for the adlayers. Several models are proposed and used...

Desorption dynamics of deuterium molecules from the Si(100)-(3×1) dideuteride surface

OpenAIRE

Niida, T; Tsurumaki, Hiroshi; Namiki, Akira

2006-01-01

We measured polar angle ()-resolved time-of-flight spectra of D2 molecules desorbing from the Si(100)-(3×1) dideuteride surface. The desorbing D2 molecules exhibit a considerable translational heating with mean desorption kinetic energies of 0.25 eV, which is mostly independent of the desorption angles for 0°30°. The observed desorption dynamics of deuterium was discussed along the principle of detailed balance to predict their adsorption dynamics onto the monohydride Si surface.

A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

Science.gov (United States)

Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

2018-05-01

The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

Adsorption of small NaCl clusters on surfaces of silicon nanostructures

International Nuclear Information System (INIS)

Amsler, Maximilian; Alireza Ghasemi, S; Goedecker, Stefan; Neelov, Alexey; Genovese, Luigi

2009-01-01

We have studied possible adsorption geometries of neutral NaCl clusters on the disordered surface of a large silicon model tip used in non-contact atomic force microscopy. The minima hopping method was used to determine low energy model tip configurations as well as ground state geometries of isolated NaCl clusters. The combined system was treated with density functional theory. Alkali halides have proven to be strong structure seekers and tend to form highly stable ground state configurations whenever possible. The favored adsorption geometry for four Na and four Cl atoms was found to be an adsorption of four NaCl dimers due to the formation of Cl-Si bonds. However, for larger NaCl clusters, the increasing energy required to dissociate the cluster into NaCl dimers suggests that adsorption of whole clusters in their isolated ground state configuration is preferred.

Temperature Dependence of Arn+ Cluster Backscattering from Polymer Surfaces: a New Method to Determine the Surface Glass Transition Temperature.

Science.gov (United States)

Poleunis, Claude; Cristaudo, Vanina; Delcorte, Arnaud

2018-01-01

In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to study the intensity variations of the backscattered Ar n + clusters as a function of temperature for several amorphous polymer surfaces (polyolefins, polystyrene, and polymethyl methacrylate). For all these investigated polymers, our results show a transition of the ratio Ar 2 + /(Ar 2 + + Ar 3 + ) when the temperature is scanned from -120 °C to +125 °C (the exact limits depend on the studied polymer). This transition generally spans over a few tens of degrees and the temperature of the inflection point of each curve is always lower than the bulk glass transition temperature (T g ) reported for the considered polymer. Due to the surface sensitivity of the cluster backscattering process (several nanometers), the presented analysis could provide a new method to specifically evaluate a surface transition temperature of polymers, with the same lateral resolution as the gas cluster beam. Graphical abstract ᅟ.

A fitting program for potential energy surfaces of bent triatomic molecules

International Nuclear Information System (INIS)

Searles, D.J.; Nagy-Felsobuki, E.I. von

1992-01-01

A program has been developed in order to fit analytical power series expansions (Dunham, Simon-Parr-Finlan, Ogilvie and their exponential variants) and Pade approximants to discrete ab initio potential energy surfaces of non-linear triatomic molecules. The program employs standard least-squares fitting techniques using the singular decomposition method in order to dampen the higher-order coefficients (if deemed necessary) without significantly degrading the fit. The program makes full use of the symmetry of a triatomic molecule and so addresses the D 3h , C 2v and C S cases. (orig.)

Interface formation between hydrocarbon ring molecules and III-V semiconductor surfaces

Energy Technology Data Exchange (ETDEWEB)

Passmann, Regina

2008-08-15

In this work a systematical study to investigate the adsorption structures of small hydrocarbon ring shaped molecules on III-V semiconductor surfaces with Photo-Emission Spectroscopy (PES), Reflectance Anisotropy Spectroscopy (RAS), Scanning Tunneling Microscopy (STM) as well as Low Electron Energy Diffraction (LEED) was performed. To investigate the influence of the surface structure in detail the surface dimer configuration to the adsorption process of organic molecules GaAs(001) surfaces, the c(4 x 4), the (2 x 4) and the (4 x 2) have been investigated as well as the adsorption of cyclopentene on the InP(001)(2 x 4) reconstructed surface. In the direct comparison it is shown that cyclopentene bonds to the InP(001)(2 x 4) surface via a cycloaddition like reaction. During this adsorption the double bond splits which is in contrast to the adsorption of cyclopentene on the GaAs(001) surfaces. Therefrom it is concluded that the surface geometry has an influence on the resulting adsorption structure. In order to investigate the influence of the intra-molecular double bonds, cyclopentene (one double bond), 1,4-cyclohexadiene (two double bonds) and benzene (three double bonds) were used for the characterization of the interface formation. With the investigations on the GaAs(001) reconstructed surfaces it was shown that a dependency of the bonding configuration on the intra-molecular double bonds exists. During the adsorption of cyclopentene no evidence was found that the double bond has to be involved in the interface formation while during the adsorption of 1,4-cyclohexadiene and benzene the double bonds are involved. Furthermore it was found that a bonding to As atoms of the surface is more likely than a bonding to Ga atoms. (orig.)

Interface formation between hydrocarbon ring molecules and III-V semiconductor surfaces

International Nuclear Information System (INIS)

Passmann, Regina

2008-01-01

In this work a systematical study to investigate the adsorption structures of small hydrocarbon ring shaped molecules on III-V semiconductor surfaces with Photo-Emission Spectroscopy (PES), Reflectance Anisotropy Spectroscopy (RAS), Scanning Tunneling Microscopy (STM) as well as Low Electron Energy Diffraction (LEED) was performed. To investigate the influence of the surface structure in detail the surface dimer configuration to the adsorption process of organic molecules GaAs(001) surfaces, the c(4 x 4), the (2 x 4) and the (4 x 2) have been investigated as well as the adsorption of cyclopentene on the InP(001)(2 x 4) reconstructed surface. In the direct comparison it is shown that cyclopentene bonds to the InP(001)(2 x 4) surface via a cycloaddition like reaction. During this adsorption the double bond splits which is in contrast to the adsorption of cyclopentene on the GaAs(001) surfaces. Therefrom it is concluded that the surface geometry has an influence on the resulting adsorption structure. In order to investigate the influence of the intra-molecular double bonds, cyclopentene (one double bond), 1,4-cyclohexadiene (two double bonds) and benzene (three double bonds) were used for the characterization of the interface formation. With the investigations on the GaAs(001) reconstructed surfaces it was shown that a dependency of the bonding configuration on the intra-molecular double bonds exists. During the adsorption of cyclopentene no evidence was found that the double bond has to be involved in the interface formation while during the adsorption of 1,4-cyclohexadiene and benzene the double bonds are involved. Furthermore it was found that a bonding to As atoms of the surface is more likely than a bonding to Ga atoms. (orig.)

Surface EMG decomposition based on K-means clustering and convolution kernel compensation.

Science.gov (United States)

Ning, Yong; Zhu, Xiangjun; Zhu, Shanan; Zhang, Yingchun

2015-03-01

A new approach has been developed by combining the K-mean clustering (KMC) method and a modified convolution kernel compensation (CKC) method for multichannel surface electromyogram (EMG) decomposition. The KMC method was first utilized to cluster vectors of observations at different time instants and then estimate the initial innervation pulse train (IPT). The CKC method, modified with a novel multistep iterative process, was conducted to update the estimated IPT. The performance of the proposed K-means clustering-Modified CKC (KmCKC) approach was evaluated by reconstructing IPTs from both simulated and experimental surface EMG signals. The KmCKC approach successfully reconstructed all 10 IPTs from the simulated surface EMG signals with true positive rates (TPR) of over 90% with a low signal-to-noise ratio (SNR) of -10 dB. More than 10 motor units were also successfully extracted from the 64-channel experimental surface EMG signals of the first dorsal interosseous (FDI) muscles when a contraction force was held at 8 N by using the KmCKC approach. A "two-source" test was further conducted with 64-channel surface EMG signals. The high percentage of common MUs and common pulses (over 92% at all force levels) between the IPTs reconstructed from the two independent groups of surface EMG signals demonstrates the reliability and capability of the proposed KmCKC approach in multichannel surface EMG decomposition. Results from both simulated and experimental data are consistent and confirm that the proposed KmCKC approach can successfully reconstruct IPTs with high accuracy at different levels of contraction.

A DFT study of arsine adsorption on palladium doped graphene: Effects of palladium cluster size

International Nuclear Information System (INIS)

Kunaseth, Manaschai; Mudchimo, Tanabat; Namuangruk, Supawadee; Kungwan, Nawee; Promarak, Vinich; Jungsuttiwong, Siriporn

2016-01-01

Graphical abstract: The relationship between charge difference and adsorption strength demonstrates that charge migration from Pd_n-SDG to AsH_x significantly enhanced adsorption strength, the Pd_6 clusters doped SDG with a steep slope is recommended as a superior adsorbent material for AsH_3 removal from gas stream. - Highlights: • Pd atom and Pd clusters bind strongly onto the defective graphene surface. • Larger size of Pd cluster adsorbs arsine and its hydrogenated products stronger. • Order of adsorption strength on Pd_n doped graphene: As > AsH > AsH_2 > > AsH_3. • Charge migration characterizes the strong adsorption of AsH_2, AsH, and As. • Pd cluster doped graphene is thermodynamically preferable for arsine removal. - Abstract: In this study, we have investigated the size effects of palladium (Pd) doped single-vacancy defective graphene (SDG) surface to the adsorption of AsH_3 and its dehydrogenated products on Pd using density functional theory calculations. Here, Pd cluster binding study revealed that Pd_6 nanocluster bound strongest to the SDG surface, while adsorption of AsH_x (x = 0–3) on the most stable Pd_n doped SDG showed that dehydrogenated arsine compounds adsorbed onto the surface stronger than the pristine AsH_3 molecule. Charge analysis revealed that considerable amount of charge migration from Pd to dehydrogenated arsine molecules after adsorption may constitute strong adsorption for dehydrogenated arsine. In addition, study of thermodynamic pathways of AsH_3 dehydrogenation on Pd_n doped SDG adsorbents indicated that Pd cluster doping on SDG adsorbent tends to be thermodynamically favorable for AsH_3 decomposition than the single-Pd atom doped SDG. Hence, our study has indicated that Pd_6 clusters doped SDG is more advantageous as adsorbent material for AsH_3 removal.

Charge Transfer Effect on Raman and Surface Enhanced Raman Spectroscopy of Furfural Molecules.

Science.gov (United States)

Wan, Fu; Shi, Haiyang; Chen, Weigen; Gu, Zhaoliang; Du, Lingling; Wang, Pinyi; Wang, Jianxin; Huang, Yingzhou

2017-08-02

The detection of furfural in transformer oil through surface enhanced Raman spectroscopy (SERS) is one of the most promising online monitoring techniques in the process of transformer aging. In this work, the Raman of individual furfural molecules and SERS of furfural-M x (M = Ag, Au, Cu) complexes are investigated through density functional theory (DFT). In the Raman spectrum of individual furfural molecules, the vibration mode of each Raman peak is figured out, and the deviation from experimental data is analyzed by surface charge distribution. In the SERS of furfural-M x complexes, the influence of atom number and species on SERS chemical enhancement factors (EFs) are studied, and are further analyzed by charge transfer effect. Our studies strengthen the understanding of charge transfer effect in the SERS of furfural molecules, which is important in the online monitoring of the transformer aging process through SERS.

Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

International Nuclear Information System (INIS)

Alnemrat, Sufian; Hooper, Joseph P.

2014-01-01

We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O 2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O 2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material

Interaction of Model Inhibitor Compounds with Minimalist Cluster Representations of Hydroxyl Terminated Metal Oxide Surfaces

Directory of Open Access Journals (Sweden)

Christopher D. Taylor

2018-01-01

Full Text Available The computational modeling of corrosion inhibitors at the level of molecular interactions has been pursued for decades, and recent developments are allowing increasingly realistic models to be developed for inhibitor–inhibitor, inhibitor–solvent and inhibitor–metal interactions. At the same time, there remains a need for simplistic models to be used for the purpose of screening molecules for proposed inhibitor performance. Herein, we apply a reductionist model for metal surfaces consisting of a metal cation with hydroxide ligands and use quantum chemical modeling to approximate the free energy of adsorption for several imidazoline class candidate corrosion inhibitors. The approximation is made using the binding energy and the partition coefficient. As in some previous work, we consider different methods for incorporating solvent and reference systems for the partition coefficient. We compare the findings from this short study with some previous theoretical work on similar systems. The binding energies for the inhibitors to the metal hydroxide clusters are found to be intermediate to the binding energies calculated in other work for bare metal vs. metal oxide surfaces. The method is applied to copper, iron, aluminum and nickel metal systems.

Improved density functional calculations for atoms, molecules and surfaces

International Nuclear Information System (INIS)

Fricke, B.; Anton, J.; Fritzsche, S.; Sarpe-Tudoran, C.

2005-01-01

The non-collinear and collinear descriptions within relativistic density functional theory is described. We present results of both non-collinear and collinear calculations for atoms, diatomic molecules, and some surface simulations. We find that the accuracy of our density functional calculations for the smaller systems is comparable to good quantum chemical calculations, and thus this method provides a sound basis for larger systems where no such comparison is possible. (author)

Heat transfer and forces on concave surfaces in free molecule flow.

Science.gov (United States)

Fan, C.

1971-01-01

A Monte Carlo modeling technique is described for mathematically simulating free molecular flows over a concave spherical surface and a concave cylindrical surface of finite length. The half-angle of the surfaces may vary from 0 to 90 degrees, and the incident flow may have an arbitrary speed ratio and an arbitrary angle of attack. Partial diffuse reflection and imperfect energy accommodation for molecules colliding with the surfaces are also considered. Results of heat transfer, drag and lift coefficients are presented for a variety of flow conditions. The present Monte Carlo results are shown to be in very good agreement with certain available theoretical solutions.

Pulsed EPR for studying silver clusters

International Nuclear Information System (INIS)

Michalik, J.; Wasowicz, T.; Sadlo, J.; Reijerse, E.J.; Kevan, L.

1996-01-01

The cationic silver clusters of different nuclearity have been produced by radiolysis of zeolite A and SAPO molecular sieves containing Ag + as exchangeable cations. The pulsed EPR spectroscopy has been applied for studying the local environment of silver cluster in order to understand the mechanism of cluster formation and stabilization. the electron spin echo modulation (ESEM) results on Ag 6 n+ cluster in dehydration zeolite A indicate that the hexameric silver is stabilized only in sodalite cages which are surrounded by α-cages containing no water molecules. Trimeric silver clusters formed in hydrated A zeolites strongly interact with water, thus the paramagnetic center can be considered as a cluster-water adduct. In SAPO-molecular sieves, silver clusters are formed only in the presence of adsorbed alcohol molecules. From ESEM it is determined that Ag 4 n+ in SAPO-42 is stabilized in α cages, where it is directly coordinated by two methanol molecules. Dimeric silver, Ag 2 + in SAPO-5 and SAPO-11 is located in 6-ring channels and interacts with three CH 3 OH molecules, each in different 10 ring or 12 ring channels. The differences of Ag 2 + stability in SAPO-5 and SAPO-11 are also discussed. (Author)

Nickel group cluster anion reactions with carbon monoxide: Rate coefficients and chemisorption efficiency

Science.gov (United States)

Hintz, Paul A.; Ervin, Kent M.

1994-04-01

Reactions of Ni-n(n=3-10), Pd-n(n=3-8), and Pt-n(n=3-7) with CO are studied in a flow tube reactor. Bimolecular rate coefficients are measured for the association reaction of CO adsorbing on the cluster surface. The rate coefficients range from about 10% of the collision rate for the trimer anions to near the collision rate for clusters larger than four atoms. The maximum number of CO molecules that bind to each cluster is determined. Whereas the saturation limits for nickel are typical for an 18 electron transition metal, the limits for platinum are lower, reflecting the electron deficient structures observed in condensed phase chemistry. The CO saturated palladium clusters represent the first examples of saturated binary palladium carbonyl compounds. Comparisons are made to similar studies on metal cation and neutral clusters and also to surface scattering studies of nickel group metals.

Density functional study the interaction of oxygen molecule with defect sites of graphene

Energy Technology Data Exchange (ETDEWEB)

Qi Xuejun [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Guo Xin, E-mail: guoxin@mail.hust.edu.cn [State Key Laboratory of Coal Combustion, Wuhan 430074 (China); Zheng Chuguang [State Key Laboratory of Coal Combustion, Wuhan 430074 (China)

2012-10-15

Highlights: Black-Right-Pointing-Pointer The defect sites existed on the graphite surface create active sites and enhance the reactivity of carbonaceous material. Black-Right-Pointing-Pointer Oxygen molecule more favor chemisorbed on the graphene surface contains defect sites than the perfect surface. Black-Right-Pointing-Pointer The single active oxygen atom adsorbed on the defect surfaces, it completely insert into the surface. - Abstract: The present article reports a theoretical study of oxygen interacted with graphene surface containing defect sites on the atomic level by employing the density functional theory combined with the graphene cluster model. It was founded that oxygen molecule prefers to be chemisorbed on the graphene surface containing defect sites compared to the perfect surface. The adsorption energy of O{sub 2} on the double defect site is about 2.5 times as large as that on the perfect graphene surface. Moreover, the oxygen molecule interacts with S-W defect site gives rise to stable epoxy structure, which pulling the carbon atom outward from the original site in the direction perpendicular to the surface. If the oxygen molecule is adsorbed on the single vacancy site, two C-O bonds are formed on the graphene surface. However, when the oxygen molecule is chemisorbed on the double vacancy site, the oxygen atoms substitute the missing carbon atom's position in the carbon plane and form a hexagonal structure on the graphene network. The results indicate that single active oxygen atom approaches the defect site, it's completely adsorbed in the plane and high energy is released. In all cases, the interaction of an oxygen atom with defect surface involves an exothermic process. The defect site creates active sites on the surface of graphene and produces catalytic effects during the process of oxidation of carbonaceous materials.

Measuring the force of single protein molecule detachment from surfaces with AFM.

Science.gov (United States)

Tsapikouni, Theodora S; Missirlis, Yannis F

2010-01-01

Atomic force microscopy (AFM) was used to measure the non-specific detachment force of single fibrinogen molecules from glass surfaces. The identification of single unbinding events was based on the characteristics of the parabolic curves, recorded during the stretching of protein molecules. Fibrinogen molecules were covalently bound to Si(3)N(4) AFM tips, previously modified with 3-aminopropyl-dimethyl-ethoxysilane, through a homobifunctional poly(ethylene glycol) linker bearing two hydroxysulfosuccinimide esters. The most probable detachment force was found to be 210 pN, when the tip was retracting with a velocity of 1400 nm/s, while the distribution of the detachment distances indicated that the fibrinogen chain can be elongated beyond the length of the physical conformation before detachment. The dependence of the most probable detachment force on the loading rate was examined and the dynamics of fibrinogen binding to the surface were found amenable to the simple expression of the Bell-Evans theory. The theory's expansion, however, by incorporating the concept of the rupture of parallel residue-surface bonds could only describe the detachment of fibrinogen for a small number of such bonds. Finally, the mathematical expression of the Worm-Like Chain model was used to fit the stretching curves before rupture and two interpretations are suggested for the description of the AFM curves with multiple detachment events.

Extracting Galaxy Cluster Gas Inhomogeneity from X-Ray Surface Brightness: A Statistical Approach and Application to Abell 3667

Science.gov (United States)

Kawahara, Hajime; Reese, Erik D.; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi

2008-11-01

Our previous analysis indicates that small-scale fluctuations in the intracluster medium (ICM) from cosmological hydrodynamic simulations follow the lognormal probability density function. In order to test the lognormal nature of the ICM directly against X-ray observations of galaxy clusters, we develop a method of extracting statistical information about the three-dimensional properties of the fluctuations from the two-dimensional X-ray surface brightness. We first create a set of synthetic clusters with lognormal fluctuations around their mean profile given by spherical isothermal β-models, later considering polytropic temperature profiles as well. Performing mock observations of these synthetic clusters, we find that the resulting X-ray surface brightness fluctuations also follow the lognormal distribution fairly well. Systematic analysis of the synthetic clusters provides an empirical relation between the three-dimensional density fluctuations and the two-dimensional X-ray surface brightness. We analyze Chandra observations of the galaxy cluster Abell 3667, and find that its X-ray surface brightness fluctuations follow the lognormal distribution. While the lognormal model was originally motivated by cosmological hydrodynamic simulations, this is the first observational confirmation of the lognormal signature in a real cluster. Finally we check the synthetic cluster results against clusters from cosmological hydrodynamic simulations. As a result of the complex structure exhibited by simulated clusters, the empirical relation between the two- and three-dimensional fluctuation properties calibrated with synthetic clusters when applied to simulated clusters shows large scatter. Nevertheless we are able to reproduce the true value of the fluctuation amplitude of simulated clusters within a factor of 2 from their two-dimensional X-ray surface brightness alone. Our current methodology combined with existing observational data is useful in describing and inferring the

Gold Cluster Diffusion Kinetics on Stoichiometric and Reduced Surfaces of Rutile TiO ₂ (110)

Energy Technology Data Exchange (ETDEWEB)

Goldman, Nir; Browning, Nigel D.

2011-06-16

Gold clusters on rutile TiO₂ are known to serve as efficient oxidation catalysts for pollutants and environmental contaminants. However, the mechanism by which highly mobile small clusters migrate and aggregate into larger species relevant to gold’s catalytic activity remains unresolved. We report herein on ab initio simulations of the diffusion of atomic gold clusters up to the trimer on rutile TiO₂(110) surfaces. We show that, on the stoichiometric surface, both the dimer and the trimer can exhibit relatively low surface mobility due to high energetic barriers for diffusion out of their energetic minima coupled with low barriers for the reverse motion. On the reduced surface, these clusters can diffuse relatively quickly between energetic minima within the oxygen vacancy site due to the large degree of vibrational entropy in their transition states. Our computed diffusion times provide a point of comparison for future experiments and will aid in development of models of gold cluster island sintering.

Cluster beam injection

International Nuclear Information System (INIS)

Bottiglioni, F.; Coutant, J.; Fois, M.

1978-01-01

Areas of possible applications of cluster injection are discussed. The deposition inside the plasma of molecules, issued from the dissociation of the injected clusters, has been computed. Some empirical scaling laws for the penetration are given

Interplay of radiative and nonradiative transitions in surface hopping with radiation-molecule interactions

Energy Technology Data Exchange (ETDEWEB)

Bajo, Juan José [Departamento de Química-Física I, Universidad Complutense de Madrid, 28040 Madrid (Spain); Granucci, Giovanni, E-mail: giovanni.granucci@unipi.it; Persico, Maurizio [Università di Pisa, Dipartimento di Chimica e Chimica Industriale, via Risorgimento 35, 56126 Pisa (Italy)

2014-01-28

We implemented a method for the treatment of field induced transitions in trajectory surface hopping simulations, in the framework of the local diabatization scheme, especially suited for on-the-fly dynamics. The method is applied to a simple one-dimensional model with an avoided crossing and compared with quantum wavepacket dynamics. The results show the importance of introducing a proper decoherence correction to surface hopping, in order to obtain meaningful results. Also the energy conservation policy of standard surface hopping must be revised: in fact, the quantum wavepacket energetics is well reproduced if energy absorption/emission is allowed for in the hops determined by radiation-molecule coupling. To our knowledge, this is the first time the issues of decoherence and energy conservation have been analyzed in depth to devise a mixed quantum-classical method for dynamics with molecule-field interactions.

Atoms, molecules, clusters and synchrotron radiation

International Nuclear Information System (INIS)

Kui Rexi; Ju Xin

1995-01-01

The importance of synchrotron radiation, especially the third generation synchrotron radiation light source, in atomic, molecular and cluster physics is discussed and some views are presented on new methods which may become available for research in the above fields

Modeling of hydrogen desorption from tungsten surface

Energy Technology Data Exchange (ETDEWEB)

Guterl, J., E-mail: jguterl@ucsd.edu [University of California, San Diego, La Jolla, CA 92093 (United States); Smirnov, R.D. [University of California, San Diego, La Jolla, CA 92093 (United States); Krasheninnikov, S.I. [University of California, San Diego, La Jolla, CA 92093 (United States); Nuclear Research National University MEPhI, Moscow 115409 (Russian Federation); Uberuaga, B.; Voter, A.F.; Perez, D. [Los Alamos National Laboratory, Los Alamos, NM 8754 (United States)

2015-08-15

Hydrogen retention in metallic plasma-facing components is among key-issues for future fusion devices. For tungsten, which has been chosen as divertor material in ITER, hydrogen desorption parameters experimentally measured for fusion-related conditions show large discrepancies. In this paper, we therefore investigate hydrogen recombination and desorption on tungsten surfaces using molecular dynamics simulations and accelerated molecular dynamics simulations to analyze adsorption states, diffusion, hydrogen recombination into molecules, and clustering of hydrogen on tungsten surfaces. The quality of tungsten hydrogen interatomic potential is discussed in the light of MD simulations results, showing that three body interactions in current interatomic potential do not allow to reproduce hydrogen molecular recombination and desorption. Effects of surface hydrogen clustering on hydrogen desorption are analyzed by introducing a kinetic model describing the competition between surface diffusion, clustering and recombination. Different desorption regimes are identified and reproduce some aspects of desorption regimes experimentally observed.

A theoretical and experimental investigation of the interaction between gas molecules and cryogenic surfaces

International Nuclear Information System (INIS)

Varlam, M.; Steflea, D.; Chiriloaie, N.

1992-01-01

The cryo-pumping performance of a cryo-surface subjected to the impingement of low-pressure, thermal-velocity air flow is experimentally and theoretically investigated. Our purpose is to determine the angular dependence of capture coefficients for gas molecules incident on a cryogenic surface under conditions closely approximating those prevailing in cryo-pumped high vacuum chambers. The classical model for the interaction of gas atoms and the solid surface - the 'soft-tube' model - is developed and the basic assumption are examined. Starting from this theory we have calculated the capture coefficient of the Ag - N system and these values are discussed in terms of principal parameters considered. Despite the many simplifying assumptions, this model has the important attribute that it yields closed-form expressions for the capture coefficient of gas molecules. The molecular beam technique offers a direct experimental method for determining the capture coefficient for molecules with given angles of incidence by measuring the incident and reflected molecular fluxes. An experimental setup is also designed and the method for determining these coefficients is proposed. (Author)

Adhesion of Model Molecules to Metallic Surfaces, the Implications for Corrosion Protection

International Nuclear Information System (INIS)

De Wit, J. H. W.; Van den Brand, J.; De Wit, F. M.; Mol, J. M. C.

2008-01-01

The majority of the described experimental results deal with relatively pure aluminium. Variations were made in the pretreatment of the aluminum substrates and an investigation was performed on the resulting changes in oxide layer composition and chemistry. Subsequently, the bonding behavior of the surfaces was investigated by using model adhesion molecules. These molecules were chosen to represent the bonding functionality of an organic polymer. They were applied onto the pretreated surfaces as a monolayer and the bonding behavior was studied using infrared reflection absorption spectroscopy. A direct and clear relation was found between the hydroxyl fraction on the oxide surfaces and the amount of molecules that subsequently bonded to the surface. Moreover, it was found that most bonds between the oxide surface and organic functional groups are not stable in the presence of water. The best performance was obtained using molecules, which are capable of chemisorption with the oxide surface. Finally, it was found that freshly prepared relatively pure aluminum substrates, which are left in air, rapidly lose their bonding capacity towards organic functional groups. This can be attributed to the adsorption of contamination and water to the oxide surface. in addition the adhesion of a typical epoxy-coated aluminum system was investigated during exposure to water at different temperatures. The coating was found to quite rapidly lose its adhesion upon exposure to water. This rapid loss of adhesion corresponds well with the data where it was demonstrated that the studied epoxy coating only bonds through physisorptive hydrogen bonding, these bonds not being stable in the presence of water. After the initial loss the adhesion of the coating was however found to recover again and even exceeded the adhesion prior to exposure. The improvement could be ascribed to the growth of a thin oxyhydroxide layer on the aluminum substrate, which forms a new, water-stable and stronger bond

Multivalent adhesion molecule 7 clusters act as signaling platform for host cellular GTPase activation and facilitate epithelial barrier dysfunction.

Directory of Open Access Journals (Sweden)

Jenson Lim

2014-09-01

Full Text Available Vibrio parahaemolyticus is an emerging bacterial pathogen which colonizes the gastrointestinal tract and can cause severe enteritis and bacteraemia. During infection, V. parahaemolyticus primarily attaches to the small intestine, where it causes extensive tissue damage and compromises epithelial barrier integrity. We have previously described that Multivalent Adhesion Molecule (MAM 7 contributes to initial attachment of V. parahaemolyticus to epithelial cells. Here we show that the bacterial adhesin, through multivalent interactions between surface-induced adhesin clusters and phosphatidic acid lipids in the host cell membrane, induces activation of the small GTPase RhoA and actin rearrangements in host cells. In infection studies with V. parahaemolyticus we further demonstrate that adhesin-triggered activation of the ROCK/LIMK signaling axis is sufficient to redistribute tight junction proteins, leading to a loss of epithelial barrier function. Taken together, these findings show an unprecedented mechanism by which an adhesin acts as assembly platform for a host cellular signaling pathway, which ultimately facilitates breaching of the epithelial barrier by a bacterial pathogen.

Molecular dynamics simulations of nucleation and phase transitions in molecular clusters of hexafluorides

International Nuclear Information System (INIS)

Xu, S.

1993-01-01

Molecular dynamics simulations of nucleation and phase transitions in TeF 6 and SeF 6 clusters containing 100-350 molecules were carried out. Simulations successfully reproduced the crystalline structures observed in electron diffraction studies of large clusters (containing about 10 4 molecules) of the same materials. When the clusters were cooled, they spontaneously underwent the same bcc the monoclinic phase transition in simulations as in experiment, despite the million-fold difference in the time scales involved. Other transitions observed included melting and freezing. Several new techniques based on molecular translation and orientation were introduced to identify different condensed phases, to study nucleation and phase transitions, and to define characteristic temperatures of transitions. The solid-state transition temperatures decreased with cluster size in the same way as did the melting temperature, in that the depression of transition temperature was inversely proportional to the cluster radius. Rotational melting temperatures, as inferred from the rotational diffusion of molecules, coincided with those of the solid-state transition. Nucleation in liquid-solid and bcc-monoclinic transitions started in the interior of clusters on cooling, and at the surface on heating. Transition temperatures on cooling were always lower than those on heating due to the barriers to nucleation. Linear growth rates of nuclei in freezing were an order of magnitude lower than those in the bcc-monoclinic transition. Revealing evidence about the molecular behavior associated with phase changes was found. Simulations showed the formation of the actual transition complexes along the transition pathway, i.e., the critical nuclei of the new phase. These nuclei, consisting of a few dozen molecules, were distinguishable in the midst of the surrounding matter

Structure determination by photoelectron diffraction of small molecules on surfaces

International Nuclear Information System (INIS)

Booth, N.A.

1998-05-01

The synchrotron radiation based technique of Photoelectron Diffraction (PhD) has been applied to three adsorption systems. Structure determinations, are presented for each system which involve the adsorption of small molecules on the low index {110} plane of single crystal Cu and Ni substrates. For the NH 3 -Cu(110) system PhD was successful in determining a N-Cu bondlength of 2.05 ± 0.03 A as well as values for the anisotropic vibrational amplitudes of the N and an expansion of the 1st to 2nd Cu substrate layer spacing from the bulk value of 0.08 ± 0.08 A. The most significant and surprising structural parameter determined for this system was that the N atom occupies an asymmetric adsorption site. Rather than being situated in the expected high symmetry atop site the N atom was found to be offset parallel to the surface by 0.37 ± 0.12 A in the [001] azimuth. In studying the glycine-Cu(110) system the adsorption structure of an amino-acid has been quantified. The local adsorption geometries of all the atoms involved in the molecule to surface bond have been determined. The glycine molecule is found to be bonded to the surface via both its amino and carboxylate functional groups. The molecule straddles two [11-bar0] rows of the Cu substrate. The two O atoms are found to be in identical sites both approximately atop Cu atoms on the [11-bar0] rows offset parallel to the surface by 0.80 ± 0.05 A in the [001] azimuth, the O-Cu bondlength was found to be 2.03 ± 0.05 A. The N atom was also found to adsorb in an approximately atop geometry but offset parallel to the surface by 0.24 ± 0.10A in the [11-bar0] direction, the N-Cu bondlength was found to be 2.05± 0.05 A. PhD was unsuccessful in determining the positions of the two C atoms that form a bridge between the two functional groups bonded to the surface due to difficulties in separating the two inequivalent contributions to the final intensity modulation function. For the CN-Ni(110) system both PhD and Near Edge

Electronic properties and assambly of DNA-based molecules on gold surfaces

DEFF Research Database (Denmark)

Salvatore, Princia

, highly base specific voltammetric peak in the presence of spermidine ions. A capacitive origin was attributed to this peak, and a novel route to detection of hybridization and base pair mismatches proposed on the basis of the high sensitivity to base pair mismatches showed by such ON-based monolayers...... as widely employed as Au(111) surfaces). In particular, SERS offered a valuable and rapid way ofcharacterising interactions between the DNA-based molecules and the NP surface, with no need for complex sample preparation....

Spontaneous dissociation of a conjugated molecule on the Si(100) surface

DEFF Research Database (Denmark)

Lin, Rong; Galili, Michael; Quaade, Ulrich

2002-01-01

The adsorption mechanism of alpha-sexithiophene (alpha-6T) on the clean Si(100)-(2x1) surface has been investigated using scanning tunneling microscopy (STM) and first principles electronic structure calculations. We find that at submonolayer coverage, the alpha-6T molecules are not stable and di...

Implanting very low energy atomic ions into surface adsorbed cage molecules: the formation/emission of Cs/C60+

International Nuclear Information System (INIS)

Kolodney, Eli; Kaplan, Andrey; Manor, Yoni; Bekkerman, Anatoly; Tsipinyuk, Boris

2004-01-01

Full Text: We demonstrate the formation of an endo-complex via a collision of energetic ions with molecular overlayers on a surface. An incoming atomic ion is encapsulated inside a very large molecule or cluster by implanting the primary ion into the target species, which then recovers its original structure or rearrange itself around the implanted ion in some stable configuration. Here we describe an experiment resulting in the formation and ejection of an endo-complex, within a single collision. We study the formation and emission of endohedral fullerenes, Cs/C 60 + and Cs/C 70 + , following a single collision of Cs + ion with a sub-monolayer of C 60 (steady state coverage) on gold and silicon surfaces and with a sub-monolayer of C 70 on gold. A continuous low energy (E 0 =35-220 eV) Cs + ion beam hit the Cs + covered surface and the collisional formation and ejection of the endohedral Cs/Cs 60 + complex, within a single Cs + /C 60 collision was observed and characterized. Several experimental observations clearly demonstrate the single collision nature of the combined atom penetration endo-complex ejection event. The fullerene molecule is actually being picked up off the surface by the penetrating Cs + ion. The evidence for the trapping of the Cs + ion inside the fullerene cage is given both by the appearance of the Cs/Cs (602-2n) + (n=1-5) sequence and its termination at Cs/Cs 50 + . Kinetic Energy Distributions (KEDs) of the outgoing Cs/Cs 60 + were measured for two different Cs + impact energies under field-free conditions. The most striking observation is the near independence of the KEDs on the impact energy. Both KEDs peak around 1.2 eV with similar line shapes. A simple model for the formation/ejection/fragmentation dynamics of the endohedral complex is proposed and is found to be in good agreement with the experimental results

Ab-initio perturbed-cluster study of carbon monoxide adsorption at a stepped LiF(001) surface

Science.gov (United States)

Pisani, C.; Corà, F.; Orlando, R.; Nada, R.

1993-02-01

The perturbed-cluster ab-initio Hartree-Fock approach to the study of local defects in crystals [J. Chem. Phys. 92(1990)7448] is applied to the study of CO adsorption at a stepped LiF(001) surface. The step is simulated by a tablet of four ions superimposed on an infinite LiF(001) monolayer. The geometry of the step is first optimized, and corresponds to an important relaxation of cations and anions of the tablet inwards and outwards, respectively. The equilibrium configuration, adsorption energy and vibrational frequency of CO at a corner of the tablet occupied by a lithium cation are calculated. With respect to adsorption at a perfect (100) face, there is a large increase in interaction energy, especially when adsorption occurs via the oxygen atom. This difference is essentially related to modifications of the electrostatic field experienced by the adsorbed molecule.

Properties of clusters in the gas phase: V. Complexes of neutral molecules onto negative ions

International Nuclear Information System (INIS)

Keesee, R.G.; Lee, N.; Castleman, A.W. Jr.

1980-01-01

Ion--molecules association reactions of the form A - (B)/sub n1/-+B=A - (B)/sub n/ were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl - , I - , and NO 2 - with n ranging from one to three or four, and onto SO 2 - and SO 3 - with n equal to one; and (2) carbon dioxide onto Cl - , I - , NO 2 - , CO 3 - , and SO 3 - with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions. For any given ion, the relative order of the addition enthalpies among the neutrals was found to be dependent on the polarizabilities of the neutrals and on the covalency in the ion-neutral bond. Dispersion of charge via covalent bonding was found to affect significantly the succeeding clustering steps

On surface clustering and Pauli principle effects in alpha decay

International Nuclear Information System (INIS)

Holan, S.

1983-01-01

The importance of the correct description of nuclear surface region in alpha decay calculations is pointed out. A model is proposed takinq into account explicitly surface clustering and Pauli principle effects which are essential in this region. A method for solving the main integrodifferential equation of the model by using the oscillator shell basis and the Collatz method is worked out. The first numerical results are obtained for nonlocal potential of the atpha particle-daughter nucleus interaction

Ligand-protected gold clusters: the structure, synthesis and applications

Science.gov (United States)

Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

2015-11-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

Hydrogen spillover on DV (555-777) graphene – vanadium cluster system: First principles study

Energy Technology Data Exchange (ETDEWEB)

Kumar, E. Mathan, E-mail: ranjit.t@res.srmuniv.ac.in, E-mail: mathanranjitha@gmail.com; Thapa, Ranjit, E-mail: ranjit.t@res.srmuniv.ac.in, E-mail: mathanranjitha@gmail.com [SRM Research Institute, SRM University, Kattankulathur, Tamil Nadu - 603203 (India); P, Sabarikirishwaran [Department of Physics and Nanotechnology, SRM University, Kattankulathur, Tamil Nadu - 603203 (India)

2015-06-24

Using dispersion corrected density functional theory (DFT+D), the interaction of Vanadium adatom and cluster with divacancy (555-777) defective graphene sheet has been studied elaborately. We explore the prospect of hydrogen storage on V{sub 4} cluster adsorbed divacancy graphene system. It has been observed that V{sub 4} cluster (acting as a catalyst) can dissociate the H{sub 2} molecule into H atoms with very low barrier energy. We introduce the spillover of the atomic hydrogen throughout the surface via external mediator gallane (GaH{sub 3}) to form a hydrogenated system.

Graphite surface topography induced by Ta cluster impact and oxidative etching

International Nuclear Information System (INIS)

Reimann, C.T.; Olsson, L.; Erlandsson, R.; Henkel, M.; Urbassek, H.M.

1998-01-01

Freshly cleaved highly oriented pyrolytic graphite (HOPG), when baked in air at ∝630 C, forms one-monolayer(ML)-deep circular pits due to oxidation initiated at surface defect sites. We found that the areal density and depths of these pits could be modulated by deliberately introducing surface and sub-surface defects by energetic ion bombardment prior to baking. Bombardment by 555-eV/atom Ta 1 + , Ta 2 + , Ta 4 + , or Ta 9 + , always enhanced the areal density of etch pits, but only bombardment by Ta 4 + , or Ta 9 + significantly enhanced the depths of the pits. We performed molecular dynamics simulations of Ta n cluster bombardment of HOPG (n = 1, 2, 4, and 9) with the aim of characterizing the damage structures induced by the bombardment and correlating them with the experimental data. For Ta 9 + , the simulations showed a high level of damage extending from the surface down to nine MLs, in agreement with the most probable etch pit depth observed. For other cluster species, predicted etch pit depths were deeper than the observed ones. Annealing or steric requirements for initiating oxidation may account for some of the differences between simulations and experimental results. (orig.)

Control of magnetism in dilute magnetic semiconductor (Ga,Mn)As films by surface decoration of molecules

Science.gov (United States)

Wang, Hailong; Wang, Xiaolei; Xiong, Peng; Zhao, Jianhua

2016-03-01

The responses of magnetic moments to external stimuli such as magnetic-field, heat, light and electric-field have been utilized to manipulate the magnetism in magnetic semiconductors, with many of the novel ideas applied even to ferromagnetic metals. Here, we review a new experimental development on the control of magnetism in (Ga,Mn)As thin films by surface decoration of organic molecules: Molecules deposited on the surface of (Ga,Mn)As thin films are shown to be capable of significantly modulating their saturation magnetization and Curie temperature. These phenomena are shown to originate from the carrier-mediated ferromagnetism in (Ga,Mn)As and the surface molecules acting as acceptors or donors depending on their highest occupied molecular orbitals, resembling the charge transfer mechanism in a pn junction in which the equilibrium state is reached on the alignment of Fermi levels.

Control of magnetism in dilute magnetic semiconductor (Ga,MnAs films by surface decoration of molecules

Directory of Open Access Journals (Sweden)

Hailong eWang

2016-03-01

Full Text Available The responses of magnetic moments to external stimuli such as magnetic-field, heat, light and electric-field have been utilized to manipulate the magnetism in magnetic semiconductors, with many of the novel ideas applied even to ferromagnetic metals. Here, we review a new experimental development on the control of magnetism in (Ga,MnAs thin films by surface decoration of organic molecules: Molecules deposited on the surface of (Ga,MnAs thin films are shown to be capable of significantly modulating their saturation magnetization and Curie temperature. These phenomena are shown to originate from the carrier-mediated ferromagnetism in (Ga,MnAs and the surface molecules acting as acceptors or donors depending on their highest occupied molecular orbitals, resembling the charge transfer mechanism in a pn junction in which the equilibrium state is reached on the alignment of Fermi levels.

Scanning tunneling microscopy studies of glucose oxidase on gold surface

International Nuclear Information System (INIS)

Losic, D.; Shapter, J.G.; Gooding, J.J.

2002-01-01

Full text: Three immobilization methods have been used for scanning tunneling microscopy (STM) studies of glucose oxidase (GOD) on gold. They are based on a) physical adsorption from solution, b) microcontact printing and c) covalent bonding onto self-assembled monolayers (SAM) of 3-mercaptopropionic acid (MPA). The STM images are used to provide information about the organization of individual GOD molecules and more densely packed monolayers of GOD on electrode surfaces, thus providing information of the role of interfacial structure on biosensor performance. The use of atomically flat gold substrates enables easy distinction of deposited enzyme features from the flat gold substrate. Microcontact printing is found to be a more reliable method than adsorption from solution for preparing individual GOD molecules on the gold surface STM images of printed samples reveal two different shapes of native GOD molecules. One is a butterfly shape with dimensions of 10 ± 1 nm x 6 ± 1 nm, assigned to the lying position of molecule while the second is an approximately spherical shape with dimensions of 6.5 ± 1 nm x 5 ± 1nm assigned to a standing position. Isolated clusters of 5 to 6 GOD molecules are also observed. With monolayer coverage, GOD molecules exhibit a tendency to organize themselves into a two dimensional array with adequate sample stability to obtain high-resolution STM images. Within these two-dimensional arrays are clearly seen repeating clusters of five to six enzyme molecules in a unit STM imaging of GOD monolayers covalently immobilized onto SAM (MPA) are considerably more difficult than when the enzyme is adsorbed directly onto the metal. Cluster structures are observed both high and low coverage despite the fact that native GOD is a negatively charged molecule. Copyright (2002) Australian Society for Electron Microscopy Inc

Ionization of nitrogen cluster beam

International Nuclear Information System (INIS)

Yano, Katsuki; Be, S.H.; Enjoji, Hiroshi; Okamoto, Kosuke

1975-01-01

A nitrogen cluster beam (neutral particle intensity of 28.6 mAsub(eq)) is ionized by electron collisions in a Bayard-Alpert gauge type ionizer. The extraction efficiency of about 65% is obtained at an electron current of 10 mA with an energy of 50 eV. The mean cluster size produced at a pressure of 663 Torr and temperature of 77.3 K is 2x10 5 molecules per cluster. By the Coulomb repulsion force, multiply ionized cluster ions are broken up into smaller fragments and the cluster ion size reduces to one-fourth at an electron current of 15 mA. Mean neutral cluster sizes depend strongly on the initial degree of saturation PHI 0 and are 2x10 5 , 7x10 4 and 3x10 4 molecules per cluster at PHI 0 's of 0.87, 0.66 and 0.39, respectively. (auth.)

Structure and stability of M6N8 clusters (M = Si, Ge, Sn, Ti).

Science.gov (United States)

Davydova, Elena I; Timoshkin, Alexey Y; Frenking, Gernot

2010-06-10

The structures and stabilities of the M(6)N(8) clusters (M = Si, Ge, Sn, Ti) have been theoretically studied at DFT and ab initio levels of theory. Two new isomers have been considered: cage-like molecules and propeller-like molecules. It is shown that only for M = Si are both isomers true minima on the potential energy surface. The thermodynamics of the dissociation process (1/6)M(6)N(8) --> (1/3)M(3)N(4) is discussed. For each M(3)N(4) molecule, four structures with different multiplicity are considered. The thermodynamic analysis shows that independently of the multiplicity of M(3)N(4) nitrides all M(6)N(8) clusters are stable in the gas phase in a wide temperature range and could be potential intermediates in chemical vapor deposition of the nitride materials.

Hydration dynamics in water clusters via quantum molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

2014-05-28

We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

International Nuclear Information System (INIS)

Fahrendorf, Sarah

2013-01-01

They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

Structures and Spectroscopic Properties of F-(H2O) n with n = 1-10 Clusters from a Global Search Based On Density Functional Theory.

Science.gov (United States)

Shi, Ruili; Wang, Pengju; Tang, Lingli; Huang, Xiaoming; Chen, Yonggang; Su, Yan; Zhao, Jijun

2018-04-05

Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F - (H 2 O) n with n = 1-10. The F - (H 2 O) n clusters prefer structures in which the F - anion remains at the surface of the structure and coordinates with four water molecules, as the F - (H 2 O) n clusters have strong F - -H 2 O interactions as well as strong hydrogen bonds between H 2 O molecules. The strong interaction between the F - anion and adjacent H 2 O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule. The simulated infrared (IR) spectra of the F - (H 2 O) 1-5 clusters obtained via second-order vibrational perturbation theory (VPT2) and including anharmonic effects reproduce the experimental results quite well. The strong interaction between the F - anion and water molecules results in a large redshift (600-2300 cm -1 ) of the adjacent O-H stretching mode. Natural bond orbital (NBO) analysis of the lowest-energy structures of the F - (H 2 O) 1-10 clusters illustrates that charge transfer from the lone pair electron orbital of F - to the antibonding orbital of the adjacent O-H is mainly responsible for the strong interaction between the F - anion and water molecules, which leads to distinctly different geometric and vibrational properties compared with neutral water clusters.

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

Science.gov (United States)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

Analysis of functional organic molecules at noble metal surfaces by means of vibrational spectroscopies

Energy Technology Data Exchange (ETDEWEB)

Leyssner, Felix

2011-10-24

The goal of this work is to optimize the efficiency of photoinduced molecular switching processes on surfaces via controlled variations of the adsorption and electronic properties of the switch. We investigated the influence of external stimuli, i.e. photons and thermal activation, on surface bound molecular switches undergoing trans/cis-isomerizations and ring-opening/closing-reactions, respectively. High resolution electron energy loss spectroscopy (HREELS) and sum-frequency generation (SFG) spectroscopy have been used as the main tools to investigate the adsorption behavior and the molecular switching properties. Two basic concepts of coupling the molecular switch to the surface have been studied: (i) physisorbed or weakly chemisorbed systems deposited on noble metal surfaces under UHV conditions and (ii) molecular switches bound covalently via anchor groups. In the HREELS study following concept (i), we investigated the adsorption geometry and isomerization behavior of various molecular switches on metal substrates which are able to undergo a photoinduced trans/cis-isomerization in solution. We investigated three isoelectronic molecules on Au where we systematically changed the photochemically active group from the diazo-group in an azobenzene-derivative (on Cu(111)) to the imine-group, and the vinylene-group, respectively. Finding the photoisomerization quenched for all systems we observed considerable differences in their thermal isomerization behavior. Comparable we find the photoinduced ring-opening/closing-reaction of spiropyran quenched on Au(111) but a thermally induced ring-opening reaction resulting in the open form being strongly stabilized by the metal. SFG spectroscopy is employed to investigate the reversible, photoinduced trans/cis-isomerization of an azobenzene-functionalized self-assembled monolayer (SAM) on gold using a tripodal linker system. In consequence of the decoupling provided by the tripodal linker, the switching behavior of the

GAS SURFACE DENSITY, STAR FORMATION RATE SURFACE DENSITY, AND THE MAXIMUM MASS OF YOUNG STAR CLUSTERS IN A DISK GALAXY. II. THE GRAND-DESIGN GALAXY M51

International Nuclear Information System (INIS)

González-Lópezlira, Rosa A.; Pflamm-Altenburg, Jan; Kroupa, Pavel

2013-01-01

We analyze the relationship between maximum cluster mass and surface densities of total gas (Σ gas ), molecular gas (Σ H 2 ), neutral gas (Σ H I ), and star formation rate (Σ SFR ) in the grand-design galaxy M51, using published gas data and a catalog of masses, ages, and reddenings of more than 1800 star clusters in its disk, of which 223 are above the cluster mass distribution function completeness limit. By comparing the two-dimensional distribution of cluster masses and gas surface densities, we find for clusters older than 25 Myr that M 3rd ∝Σ H I 0.4±0.2 , whereM 3rd is the median of the five most massive clusters. There is no correlation withΣ gas ,Σ H2 , orΣ SFR . For clusters younger than 10 Myr, M 3rd ∝Σ H I 0.6±0.1 and M 3rd ∝Σ gas 0.5±0.2 ; there is no correlation with either Σ H 2 orΣ SFR . The results could hardly be more different from those found for clusters younger than 25 Myr in M33. For the flocculent galaxy M33, there is no correlation between maximum cluster mass and neutral gas, but we have determined M 3rd ∝Σ gas 3.8±0.3 , M 3rd ∝Σ H 2 1.2±0.1 , and M 3rd ∝Σ SFR 0.9±0.1 . For the older sample in M51, the lack of tight correlations is probably due to the combination of strong azimuthal variations in the surface densities of gas and star formation rate, and the cluster ages. These two facts mean that neither the azimuthal average of the surface densities at a given radius nor the surface densities at the present-day location of a stellar cluster represent the true surface densities at the place and time of cluster formation. In the case of the younger sample, even if the clusters have not yet traveled too far from their birth sites, the poor resolution of the radio data compared to the physical sizes of the clusters results in measuredΣ that are likely quite diluted compared to the actual densities relevant for the formation of the clusters.

Transcriptional analysis of exopolysaccharides biosynthesis gene clusters in Lactobacillus plantarum.

Science.gov (United States)

Vastano, Valeria; Perrone, Filomena; Marasco, Rosangela; Sacco, Margherita; Muscariello, Lidia

2016-04-01

Exopolysaccharides (EPS) from lactic acid bacteria contribute to specific rheology and texture of fermented milk products and find applications also in non-dairy foods and in therapeutics. Recently, four clusters of genes (cps) associated with surface polysaccharide production have been identified in Lactobacillus plantarum WCFS1, a probiotic and food-associated lactobacillus. These clusters are involved in cell surface architecture and probably in release and/or exposure of immunomodulating bacterial molecules. Here we show a transcriptional analysis of these clusters. Indeed, RT-PCR experiments revealed that the cps loci are organized in five operons. Moreover, by reverse transcription-qPCR analysis performed on L. plantarum WCFS1 (wild type) and WCFS1-2 (ΔccpA), we demonstrated that expression of three cps clusters is under the control of the global regulator CcpA. These results, together with the identification of putative CcpA target sequences (catabolite responsive element CRE) in the regulatory region of four out of five transcriptional units, strongly suggest for the first time a role of the master regulator CcpA in EPS gene transcription among lactobacilli.

Surface Chemistry Dependence of Mechanochemical Reaction of Adsorbed Molecules-An Experimental Study on Tribopolymerization of α-Pinene on Metal, Metal Oxide, and Carbon Surfaces.

Science.gov (United States)

He, Xin; Kim, Seong H

2018-02-20

Mechanochemical reactions between adsorbate molecules sheared at tribological interfaces can induce association of adsorbed molecules, forming oligomeric and polymeric products often called tribopolymers). This study revealed the role or effect of surface chemistry of the solid substrate in mechanochemical polymerization reactions. As a model reactant, α-pinene was chosen because it was known to readily form tribopolymers at the sliding interface of stainless steel under vapor-phase lubrication conditions. Eight different substrate materials were tested-palladium, nickel, copper, stainless steel, gold, silicon oxide, aluminum oxide, and diamond-like carbon (DLC). All metal substrates and DLC were initially covered with surface oxide species formed naturally in air or during the oxidative sample cleaning. It was found that the tribopolymerization yield of α-pinene is much higher on the substrates that can chemisorb α-pinene, compared to the ones on which only physisorption occurs. From the load dependence of the tribopolymerization yield, it was found that the surfaces capable of chemisorption give a smaller critical activation volume for the mechanochemical reaction, compared to the ones capable of physisorption only. On the basis of these observations and infrared spectroscopy analyses of the adsorbed molecules and the produced polymers, it was concluded that the mechanochemical reaction mechanisms might be different between chemically reactive and inert surfaces and that the chemical reactivity of the substrate surface greatly influences the tribochemical polymerization reactions of adsorbed molecules.

Ge clusters and wetting layers forming from granular films on the Si(001) surface

International Nuclear Information System (INIS)

Storozhevykh, M S; Arapkina, L V; Yuryev, V A

2016-01-01

The report studies the transformation of a Ge granular film deposited on the Si(001) surface at room temperature into a Ge/Si(001) heterostructure as a result of rapid heating and annealing at 600 °C. As a result of the short-term annealing at 600 °C in conditions of a closed system, the Ge granular film transforms into a usual wetting layer and Ge clusters with multimodal size distribution and Ge oval drops having the highest number density. After the long-term thermal treatment of the Ge film at the same temperature, Ge drops disappear; the large clusters increase their sizes at the expense of the smaller ones. The total density of Ge clusters on the surface drastically decreases. The wetting layer mixed c(4 x 2) + p(2 x 2) reconstruction transforms into a single c(4 x 2) one which is likely to be thermodynamically favoured. Pyramids or domes are not observed on the surface after any annealing. (paper)

Desorption of large organic molecules induced by keV projectiles

International Nuclear Information System (INIS)

Delcorte, A.; Garrison, B.J.

2001-01-01

In order to understand the emission of organic molecules in sputtering, classical molecular dynamics (MD) is used to model the 5 keV Ar atom bombardment of polystyrene oligomers adsorbed on Ag{1 1 1}. The analysis of the results shows that a significant fraction of the trajectories generates high action events in the sample. These events are characterized by the simultaneous motion of several hundreds of substrate atoms and, oftentimes, by high emission yields of substrate atoms, clusters and polystyrene molecules. Collision trees representing the energetic part of the cascades confirm that high sputtering yields of molecules occur when a large portion of the primary particle energy is quickly dissipated in the upper layers of the silver substrate. This class of events where high action occurs in the surface region might explain the ejection of organic species with a mass of several kilodaltons such as biomolecules and synthetic polymers. In the simulation, these events are capable of desorbing polystyrene molecules of ∼2 kDa

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

Science.gov (United States)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

Hut clusters on Ge(001) surfaces studied by STM and synchrotron X-ray diffraction

DEFF Research Database (Denmark)

Nielsen, M.; Smilgies, D.-M.; Feidenhans'l, R.

1996-01-01

Nanoscale hut clusters formed on Ge(001) surfaces by depositing one monolayer of indium and annealing at temperatures between 350 and 500 degrees C were studied by scanning tunnelling microscopy and synchrotron X-ray diffraction. It was found that the hut clusters form regular arrays over...

Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

2014-09-30

Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

SEM visualization of glycosylated surface molecules using lectin-coated microspheres

Science.gov (United States)

Duke, J.; Janer, L.; Campbell, M.

1985-01-01

There are several techniques currently used to localize glycosylated surface molecules by scanning electron microscopy (Grinnell, 1980; Molday, 1976; Linthicum and Sell, 1975; Nicolson, 1974; Lo Buglio, et al, 1972). A simple and rapid method, using a modification of Grinnell's technique is reported here. Essentially, microspheres coated with Concavalin A are used to bind to glycosylated regions of the palatal shelf epithelium and are visualized in the scanning electron microscope (SEM).

A DFT study of arsine adsorption on palladium doped graphene: Effects of palladium cluster size

Energy Technology Data Exchange (ETDEWEB)

Kunaseth, Manaschai, E-mail: manaschai@nanotec.or.th [National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , Pathum Thani 12120 (Thailand); Mudchimo, Tanabat [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190 (Thailand); Namuangruk, Supawadee [National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA) , Pathum Thani 12120 (Thailand); Kungwan, Nawee [Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Promarak, Vinich [Department of Material Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21201 (Thailand); Jungsuttiwong, Siriporn, E-mail: siriporn.j@ubu.ac.th [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190 (Thailand)

2016-03-30

Graphical abstract: The relationship between charge difference and adsorption strength demonstrates that charge migration from Pd{sub n}-SDG to AsH{sub x} significantly enhanced adsorption strength, the Pd{sub 6} clusters doped SDG with a steep slope is recommended as a superior adsorbent material for AsH{sub 3} removal from gas stream. - Highlights: • Pd atom and Pd clusters bind strongly onto the defective graphene surface. • Larger size of Pd cluster adsorbs arsine and its hydrogenated products stronger. • Order of adsorption strength on Pd{sub n} doped graphene: As > AsH > AsH{sub 2} > > AsH{sub 3}. • Charge migration characterizes the strong adsorption of AsH{sub 2}, AsH, and As. • Pd cluster doped graphene is thermodynamically preferable for arsine removal. - Abstract: In this study, we have investigated the size effects of palladium (Pd) doped single-vacancy defective graphene (SDG) surface to the adsorption of AsH{sub 3} and its dehydrogenated products on Pd using density functional theory calculations. Here, Pd cluster binding study revealed that Pd{sub 6} nanocluster bound strongest to the SDG surface, while adsorption of AsH{sub x} (x = 0–3) on the most stable Pd{sub n} doped SDG showed that dehydrogenated arsine compounds adsorbed onto the surface stronger than the pristine AsH{sub 3} molecule. Charge analysis revealed that considerable amount of charge migration from Pd to dehydrogenated arsine molecules after adsorption may constitute strong adsorption for dehydrogenated arsine. In addition, study of thermodynamic pathways of AsH{sub 3} dehydrogenation on Pd{sub n} doped SDG adsorbents indicated that Pd cluster doping on SDG adsorbent tends to be thermodynamically favorable for AsH{sub 3} decomposition than the single-Pd atom doped SDG. Hence, our study has indicated that Pd{sub 6} clusters doped SDG is more advantageous as adsorbent material for AsH{sub 3} removal.

Impact and spreading behavior of cluster atoms bombarding substrates

Energy Technology Data Exchange (ETDEWEB)

Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Kang, Shao-Hui; Liao, Jia-Hung [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

2009-12-15

The purpose of this study is to investigate the behavior of copper cluster atoms bombarding a substrate using molecule dynamics based on tight-binding second moment approximation (TB-SMA) potential. The simulated results show that a crater on the substrate surface was created by the impact of the clusters. The variations of kinetic energy of cluster bombardments can be divided into three stages. At the initial impact level, the kinetic energies of the clusters and the substrate were constant. Then, the system went into a sluggish stage of energy variation, in which the kinetic energy of the clusters reduced. In the final stage, the kinetic energy of the system became stable. The high slip vector region around the crater had a disorder damage zone. The symmetry-like cross-slip occurred beneath the top layer of the substrate along the <1 1 0> orientations. The spreading index, temperature, and potential functions that affect the bombardments are also discussed.

Impact and spreading behavior of cluster atoms bombarding substrates

International Nuclear Information System (INIS)

Fang, Te-Hua; Kang, Shao-Hui; Liao, Jia-Hung

2009-01-01

The purpose of this study is to investigate the behavior of copper cluster atoms bombarding a substrate using molecule dynamics based on tight-binding second moment approximation (TB-SMA) potential. The simulated results show that a crater on the substrate surface was created by the impact of the clusters. The variations of kinetic energy of cluster bombardments can be divided into three stages. At the initial impact level, the kinetic energies of the clusters and the substrate were constant. Then, the system went into a sluggish stage of energy variation, in which the kinetic energy of the clusters reduced. In the final stage, the kinetic energy of the system became stable. The high slip vector region around the crater had a disorder damage zone. The symmetry-like cross-slip occurred beneath the top layer of the substrate along the orientations. The spreading index, temperature, and potential functions that affect the bombardments are also discussed.

Gold cluster carbonyls: saturated adsorption of CO on gold cluster cations, vibrational spectroscopy, and implications for their structures.

Science.gov (United States)

Fielicke, André; von Helden, Gert; Meijer, Gerard; Pedersen, David B; Simard, Benoit; Rayner, David M

2005-06-15

We report on the interaction of carbon monoxide with cationic gold clusters in the gas phase. Successive adsorption of CO molecules on the Au(n)(+) clusters proceeds until a cluster size specific saturation coverage is reached. Structural information for the bare gold clusters is obtained by comparing the saturation stoichiometry with the number of available equivalent sites presented by candidate structures of Au(n)(+). Our findings are in agreement with the planar structures of the Au(n)(+) cluster cations with n < or = 7 that are suggested by ion mobility experiments [Gilb, S.; Weis, P.; Furche, F.; Ahlrichs, R.; Kappes, M. M. J. Chem. Phys. 2001, 116, 4094]. By inference we also establish the structure of the saturated Au(n)(CO)(m)(+) complexes. In certain cases we find evidence suggesting that successive adsorption of CO can distort the metal cluster framework. In addition, the vibrational spectra of the Au(n)(CO)(m)(+) complexes in both the CO stretching region and in the region of the Au-C stretch and the Au-C-O bend are measured using infrared photodepletion spectroscopy. The spectra further aid in the structure determination of Au(n)(+), provide information on the structure of the Au(n)(+)-CO complexes, and can be compared with spectra of CO adsorbates on deposited clusters or surfaces.

Selective on site separation and detection of molecules in diluted solutions with super-hydrophobic clusters of plasmonic nanoparticles

KAUST Repository

Gentile, Francesco T.; Coluccio, Maria Laura; Proietti Zaccaria, Remo; Francardi, Marco; Cojoc, Gheorghe; Perozziello, Gerardo; Raimondo, Raffaella; Candeloro, Patrizio; Di Fabrizio, Enzo M.

2014-01-01

Super-hydrophobic surfaces are bio-inspired interfaces with a superficial texture that, in its most common evolution, is formed by a periodic lattice of silicon micro-pillars. Similar surfaces reveal superior properties compared to conventional flat surfaces, including very low friction coefficients. In this work, we modified meso-porous silicon micro-pillars to incorporate networks of metal nano-particles into the porous matrix. In doing so, we obtained a multifunctional-hierarchical system in which (i) at a larger micrometric scale, the super-hydrophobic pillars bring the molecules dissolved in an ultralow-concentration droplet to the active sites of the device, (ii) at an intermediate meso-scale, the meso-porous silicon film adsorbs the low molecular weight content of the solution and, (iii) at a smaller nanometric scale, the aggregates of silver nano-particles would measure the target molecules with unprecedented sensitivity. In the results, we demonstrated how this scheme can be utilized to isolate and detect small molecules in a diluted solution in very low abundance ranges. The presented platform, coupled to Raman or other spectroscopy techniques, is a realistic candidate for the protein expression profiling of biological fluids. © 2014 the Partner Organisations.

Vacancy Clusters on Surfaces of Au Nanoparticles Embedded in MgO

International Nuclear Information System (INIS)

Xu, Jun; Mills, A. P. Jr.; Ueda, A.; Henderson, D. O.; Suzuki, R.; Ishibashi, S.

1999-01-01

MeV implantation of gold ions into MgO(100) followed by annealing is a method to form gold nanoparticles for obtaining modified optical properties. We show from variable-energy positron spectroscopy that clusters of 2 Mg and 2 O vacancies (v 4 ) are attached to the gold nanoparticle surfaces within the projected range (R p ) . We also find that v 4 vacancy clusters are created at depths less than R p , and extend into the region greater than R p due to damage induced by knock-on collisions. (c) 1999 The American Physical Society

Beam broadening of polar molecules and clusters in deflection experiments.

Science.gov (United States)

Bulthuis, J; Kresin, V V

2012-01-07

A beam of rotating dipolar particles (molecules or clusters) will broaden when passed through an electric or magnetic field gradient region. This broadening, which is a common experimental observable, can be expressed in terms of the variance of the distribution of the resulting polarization orientation (the direction cosine). Here, the broadening for symmetric-top and linear rotors is discussed. These two types of rotors have qualitatively different low-field orientation distribution functions, but behave similarly in a strong field. While analytical expressions for the polarization variance can be derived from first-order perturbation theory, for experimental guidance it is important to identify the applicability and limitations of these expressions, and the general dependence of the broadening on the experimental parameters. For this purpose, the analytical results are compared with the full diagonalization of the rotational Stark-effect matrices. Conveniently for experimental estimations, it is found that for symmetric tops, the dependence of the broadening parameter on the rotational constant, the axial ratio, and the field strength remains similar to the analytical expression even outside of the perturbative regime. Also, it is observed that the shape envelope, the centroid, and the width of the orientation distribution function for a symmetric top are quite insensitive to the value of its rotational constant (except at low rotational temperatures).

B and R CCD surface photometry of selected low surface brightness galaxies in the region of the Fornax cluster

International Nuclear Information System (INIS)

Davies, J.I.; Phillipps, S.; Disney, M.J.

1990-01-01

The recent discoveries of large numbers of low surface brightness (LSB) galaxies in clusters and of the extreme LSB giant galaxy Malin 1 are changing our view of the galactic contents of the Universe. In this paper we describe B and R band CCD photometry of a sample of LSB galaxies previously identified from photographic plates of the Fornax cluster. This sample contains some of the lowest surface brightness galaxies known, one having the same central surface brightness as Main 1. The objects in this sample have a wide range of morphologies, and galaxies of similar appearance may have very different (B-R) colours. The range of (B-R) colours for this sample (almost all of which would have been described as dE from their B band morphology alone) is as large as that of the entire Hubble sequence. (author)

Performance improvement of haptic collision detection using subdivision surface and sphere clustering.

Directory of Open Access Journals (Sweden)

A Ram Choi

Full Text Available Haptics applications such as surgery simulations require collision detections that are more precise than others. An efficient collision detection method based on the clustering of bounding spheres was proposed in our prior study. This paper analyzes and compares the applied effects of the five most common subdivision surface methods on some 3D models for haptic collision detection. The five methods are Butterfly, Catmull-Clark, Mid-point, Loop, and LS3 (Least Squares Subdivision Surface. After performing a number of experiments, we have concluded that LS3 method is the most appropriate for haptic simulations. The more we applied surface subdivision, the more the collision detection results became precise. However, it is observed that the performance becomes better until a certain threshold and degrades afterward. In order to reduce the performance degradation, we adopted our prior work, which was the fast and precise collision detection method based on adaptive clustering. As a result, we obtained a notable improvement of the speed of collision detection.

Surface self-diffusion behavior of individual tungsten adatoms on rhombohedral clusters

International Nuclear Information System (INIS)

Yang Jianyu; Hu Wangyu; Tang Jianfeng

2011-01-01

The diffusion of single tungsten adatoms on the surfaces of rhombohedral clusters is studied by means of molecular dynamics and the embedded atom method. The energy barriers for the adatom diffusing across and along the step edge between a {110} facet and a neighboring {110} facet are calculated using the nudged elastic band method. We notice that the tungsten adatom diffusion across the step edge has a much higher barrier than that for face-centered cubic metal clusters. The result shows that diffusion from the {110} facet to a neighboring {110} facet could not take place at low temperatures. In addition, the calculated energy barrier for an adatom diffusing along the step edge is lower than that for an adatom on the flat (110) surface. The results show that the adatom could diffuse easily along the step edge, and could be trapped by the facet corner. Taking all of this evidence together, we infer that the {110} facet starts to grow from the facet corner, and then along the step edge, and finally toward the {110} facet center. So the tungsten rhombohedron can grow epitaxially along the {110} facet one facet at a time and the rhombohedron should be the stable structure for both large and small tungsten clusters. (paper)

Comparison between selenium and tellurium clusters

International Nuclear Information System (INIS)

Benamar, A.; Rayane, D.; Tribollet, B.; Broyer, M.; Melinon, P.

1991-01-01

Selenium and tellurium clusters are produced by the inert gas condensation technique. The mass spectra of both species are completely different and reveal different properties. In selenium, a periodicity of 6-7 is observed and may be interpreted by the binding energy between small cyclic molecules. Moreover, it was very difficult to obtained large clusters probably because the binding energy between these molecules is very small. In tellurium, these periodic structures do not exist and large clusters are easily obtained in nucleation conditions where only small selenium clusters are present. These results are discussed and a simple nucleation model is used to illustrate this different behavior. Finally these clusters properties are correlated to the bulk structure of both materials. (orig.)

Toward single-molecule detection with sensors based on propagating surface plasmons

Czech Academy of Sciences Publication Activity Database

Kvasnička, Pavel; Chadt, Karel; Vala, Milan; Bocková, Markéta; Homola, Jiří

2012-01-01

Roč. 37, č. 2 (2012), s. 163-165 ISSN 0146-9592 R&D Projects: GA AV ČR KAN200670701; GA MŠk OC09058; GA MŠk(CZ) LH11102 Institutional research plan: CEZ:AV0Z20670512 Keywords : optical biosenzor * single molecule * surface plasmon microscopy Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.385, year: 2012

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

Science.gov (United States)

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.

Surface chemical reactions induced by molecules electronically-excited in the gas

DEFF Research Database (Denmark)

Petrunin, Victor V.

2011-01-01

and alignment are taking place, guiding all the molecules towards the intersections with the ground state PES, where transitions to the ground state PES will occur with minimum energy dissipation. The accumulated kinetic energy may be used to overcome the chemical reaction barrier. While recombination chemical...... be readily produced. Products of chemical adsorption and/or chemical reactions induced within adsorbates are aggregated on the surface and observed by light scattering. We will demonstrate how pressure and spectral dependencies of the chemical outcomes, polarization of the light and interference of two laser...... beams inducing the reaction can be used to distinguish the new process we try to investigate from chemical reactions induced by photoexcitation within adsorbed molecules and/or gas phase photolysis....

Influences of excluded volume of molecules on signaling processes on the biomembrane.

Directory of Open Access Journals (Sweden)

Masashi Fujii

Full Text Available We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by i monotonically increasing; ii increasing then decreasing in a bell-shaped curve; or iii increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor.

Ligand-protected gold clusters: the structure, synthesis and applications

International Nuclear Information System (INIS)

Pichugina, D A; Kuz'menko, N E; Shestakov, A F

2015-01-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Au n with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au 15 and Au 25 ) and on anchorage to a support surface (Au 25 /SiO 2 , Au 20 /C, Au 10 /FeO x ) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR) n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters M x Au n L m (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR) x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active

Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

Energy Technology Data Exchange (ETDEWEB)

Fahrendorf, Sarah

2013-01-24

They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

Physisorption of three amine terminated molecules (TMBDA, BDA, TFBDA) on the Au(111) Surface: The Role of van der Waals Interaction

Science.gov (United States)

Aminpour, Maral; Le, Duy; Rahman, Talat S.

2012-02-01

Recently, the electronic properties and alignment of tetramethyl-1,4-benzenediamine (TMBDA), 1,4-benzenediamine (BDA) and tetrafluro-1,4-benzenediamine (TFBDA) molecules were studied experimentally. Discrepancies were found for both the binding energy and the molecule tilt angle with respect to the surface, when results were compared with density functional theory calculations [1]. We have included the effect of vdW interactions both between the molecules and the Au(111) surface and find binding energies which are in very good agreement with experiments. We also find that at low coverages each of these molecules would adsorb almost parallel to the surface. N-Au bond lengths and charge redistribution on adsorption of the molecules are also analyzed. Our calculations are based on DFT using vdW-DF exchange correlation functionals. For BDA (since we are aware of experimental data), we show that for higher coverage, inclusion of intermolecular van der Waals interaction leads to tilting of the molecules with respect to the surface and formation of line structures. Our results demonstrate the central role played by intermolecular interaction in pattern formation on this surface.[4pt] [1] M. Dell'Angela et al, Nano Lett. 2010, 10, 2470; M. Kamenetska et al, J. Phys. Chem. C, 2011, 115, 12625

Electron-induced chemistry in microhydrated sulfuric acid clusters

Science.gov (United States)

Lengyel, Jozef; Pysanenko, Andriy; Fárník, Michal

2017-11-01

We investigate the mixed sulfuric acid-water clusters in a molecular beam experiment with electron attachment and negative ion mass spectrometry and complement the experiment by density functional theory (DFT) calculations. The microhydration of (H2SO4)m(H2O)n clusters is controlled by the expansion conditions, and the electron attachment yields the main cluster ion series (H2SO4)m(H2O)nHSO4- and (H2O)nH2SO4-. The mass spectra provide an experimental evidence for the onset of the ionic dissociation of sulfuric acid and ion-pair (HSO4- ṡ ṡ ṡ H3O+) formation in the neutral H2SO4(H2O)n clusters with n ≥ 5 water molecules, in excellent agreement with the theoretical predictions. In the clusters with two sulfuric acid molecules (H2SO4)2(H2O)n this process starts as early as n ≥ 2 water molecules. The (H2SO4)m(H2O)nHSO4- clusters are formed after the dissociative electron attachment to the clusters containing the (HSO4- ṡ ṡ ṡ H3O+) ion-pair structure, which leads to the electron recombination with the H3O+ moiety generating H2O molecule and the H-atom dissociation from the cluster. The (H2O)nH2SO4- cluster ions point to an efficient caging of the H atom by the surrounding water molecules. The electron-energy dependencies exhibit an efficient electron attachment at low electron energies below 3 eV, and no resonances above this energy, for all the measured mass peaks. This shows that in the atmospheric chemistry only the low-energy electrons can be efficiently captured by the sulfuric acid-water clusters and converted into the negative ions. Possible atmospheric consequences of the acidic dissociation in the clusters and the electron attachment to the sulfuric acid-water aerosols are discussed.

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

Energy Technology Data Exchange (ETDEWEB)

Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

2017-02-03

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach

Energy Technology Data Exchange (ETDEWEB)

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H., E-mail: xuehuma@dlut.edu.cn [Liaoning Provincial Key Laboratory of Clean Utilization of Chemical Resources, Institute of Chemical Engineering, Dalian University of Technology, Dalian 116024 (China)

2015-02-07

Heterogeneous nucleation of water droplet on surfaces with different solid-liquid interaction intensities is investigated by molecular dynamics simulation. The interaction potentials between surface atoms and vapor molecules are adjusted to obtain various surface free energies, and the nucleation process and wetting state of nuclei on surfaces are investigated. The results indicate that near-constant contact angles are already established for nano-scale nuclei on various surfaces, with the contact angle decreasing with solid-liquid interaction intensities linearly. Meanwhile, noticeable fluctuation of vapor-liquid interfaces can be observed for the nuclei that deposited on surfaces, which is caused by the asymmetric forces from vapor molecules. The formation and growth rate of nuclei are increasing with the solid-liquid interaction intensities. For low energy surface, the attraction of surface atoms to water molecules is comparably weak, and the pre-existing clusters can depart from the surface and enter into the bulk vapor phase. The distribution of clusters within the bulk vapor phase becomes competitive as compared with that absorbed on surface. For moderate energy surfaces, heterogeneous nucleation predominates and the formation of clusters within bulk vapor phase is suppressed. The effect of high energy particles that embedded in low energy surface is also discussed under the same simulation system. The nucleation preferably initiates on the high energy particles, and the clusters that formed on the heterogeneous particles are trapped around their original positions instead of migrating around as that observed on smooth surfaces. This feature makes it possible for the heterogeneous particles to act as fixed nucleation sites, and simulation results also suggest that the number of nuclei increases monotonously with the number of high energy particles. The growth of nuclei on high energy particles can be divided into three sub-stages, beginning with the formation

Superfluid response of two-dimensional parahydrogen clusters in confinement

Energy Technology Data Exchange (ETDEWEB)

Idowu, Saheed; Boninsegni, Massimo [Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E7 (Canada)

2015-04-07

We study by computer simulations the effect of confinement on the superfluid properties of small two-dimensional (2D) parahydrogen clusters. For clusters of fewer than twenty molecules, the superfluid response in the low temperature limit is found to remain comparable in magnitude to that of free clusters, within a rather wide range of depth and size of the confining well. The resilience of the superfluid response is attributable to the “supersolid” character of these clusters. We investigate the possibility of establishing a bulk 2D superfluid “cluster crystal” phase of p-H{sub 2}, in which a global superfluid response would arise from tunnelling of molecules across adjacent unit cells. The computed energetics suggests that for clusters of about ten molecules, such a phase may be thermodynamically stable against the formation of the equilibrium insulating crystal, for values of the cluster crystal lattice constant possibly allowing tunnelling across adjacent unit cells.

A theoretical investigation on optimal structures of ethane clusters (C2H6)n with n ≤ 25 and their building-up principle.

Science.gov (United States)

Takeuchi, Hiroshi

2011-05-01

Geometry optimization of ethane clusters (C(2)H(6))(n) in the range of n ≤ 25 is carried out with a Morse potential. A heuristic method based on perturbations of geometries is used to locate global minima of the clusters. The following perturbations are carried out: (1) the molecule or group with the highest energy is moved to the interior of a cluster, (2) it is moved to stable positions on the surface of a cluster, and (3) orientations of one and two molecules are randomly modified. The geometry obtained after each perturbation is optimized by a quasi-Newton method. The global minimum of the dimer is consistent with that previously reported. The putative global minima of the clusters with 3 ≤ n ≤ 25 are first proposed and their building-up principle is discussed. Copyright © 2010 Wiley Periodicals, Inc.

Covalent attachment of pyridine-type molecules to glassy carbon surfaces by electrochemical reduction of in situ generated diazonium salts. Formation of ruthenium complexes on ligand-modified surfaces

International Nuclear Information System (INIS)

Yesildag, Ali; Ekinci, Duygu

2010-01-01

In this study, pyridine, quinoline and phenanthroline molecules were covalently bonded to glassy carbon (GC) electrode surfaces for the first time using the diazonium modification method. Then, the complexation ability of the modified films with ruthenium metal cations was investigated. The derivatization of GC surfaces with heteroaromatic molecules was achieved by electrochemical reduction of the corresponding in situ generated diazonium salts. X-ray photoelectron spectroscopy (XPS) was used to confirm the attachment of heteroaromatic molecules to the GC surfaces and to determine the surface concentration of the films. The barrier properties of the modified GC electrodes were studied in the presence of redox probes such as Fe(CN) 6 3- and Ru(NH 3 ) 6 3+ by cyclic voltammetry. Additionally, the presence of the resulting organometallic films on the surfaces was verified by XPS after the chemical transformation of the characterized ligand films to the ruthenium complex films. The electrochemical behavior of these films in acetonitrile solution was investigated using voltammetric methods, and the surface coverage of the organometallic films was determined from the reversible metal-based Ru(II)/Ru(III) oxidation waves.

Physisorption of helium on a TiO{sub 2}(110) surface: Periodic and finite cluster approaches

Energy Technology Data Exchange (ETDEWEB)

Lara-Castells, Maria Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Fisica Fundamental (C.S.I.C.), Serrano 123, E-28006 Madrid (Spain); Aguirre, Nestor F. [Instituto de Fisica Fundamental (C.S.I.C.), Serrano 123, E-28006 Madrid (Spain); Mitrushchenkov, Alexander O. [Universite Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France)

2012-05-03

Graphical abstract: The physisorption of helium on the TiO{sub 2}(110) surface is explored by using finite cluster and periodic approaches (see left panel). Once the basis set is specifically tailored to minimize the BSSE (rigth panel), DFT periodic calculations using the PBE functional (left panel) yield interaction potentials in good agreement with those obtained using post-HF methods as the LMP2 treatment (see left panel). Highlights: Black-Right-Pointing-Pointer He/TiO{sub 2}(110) is a simplest example of physisorption on transition-metal oxide surfaces. Black-Right-Pointing-Pointer Optimized basis sets that minimize the BSSE are better suited for physisorption problems. Black-Right-Pointing-Pointer FCI benchmarks on the He{sub 2} bound-state assess the Counterpoise scheme reliability. Black-Right-Pointing-Pointer Periodic DFT-PBE and post-HF results on H-saturated clusters compare satisfactorily. Black-Right-Pointing-Pointer Correlation energies by using embedded and H-saturated clusters agree well. - Abstract: As a proto-typical case of physisorption on an extended transition-metal oxide surface, the interaction of a helium atom with a TiO{sub 2}(110) - (1 Multiplication-Sign 1) surface is studied here by using finite cluster and periodic approaches and both wave-function-based (post-Hartree-Fock) quantum chemistry methods and density functional theory. Both classical and advanced finite cluster approaches, based on localized Wannier orbitals combined with one-particle embedding potentials, are applied to provide (reference) coupled-cluster and second-order Moeller-Plesset interaction energies. It is shown that, once the basis set is specifically tailored to minimize the basis set superposition error, periodic calculations using the Perdew-Burke-Ernzerhof functional yield short and medium-range interaction potentials in very reasonable agreement with those obtained using the correlated wave-function-based methods, while small long-range dispersion corrections

On determination of the dynamics of hydrocarbon molecules on catalyst's surfaces by means of neutron scattering

International Nuclear Information System (INIS)

Stockmeyer, R.

1976-01-01

The intensity distribution of slow neutrons scattered by adsorbed hydrocarbon molecules contains information on the dynamics of the molecules. In this paper the scattering law for incoherently scattering molecules is derived taking into account the very different mobility perpendicular and parallel to the surface. In contrast to the well known scattering law of threedimensionally diffusing particles the scattering law for twodimensional diffusion diverges logarithmically at zero energy transfer. Conclusions relevant to the interpretation of neutron scattering data are discussed. (orig.) [de

Interface properties of organic molecules on metal surfaces; Grenzflaecheneigenschaften organischer Molekuele auf Metalloberflaechen

Energy Technology Data Exchange (ETDEWEB)

Karacuban, Hatice

2010-01-28

In this work, the growth of the archetype molecules CuPc and PTCDA was investigated on Cu(111). PTCDA was also studied on NaCl/Cu(111). The main experiments were carried out with a scanning tunneling microscope. Structural analysis of CuPc on Cu (111) is only possible at low temperatures, since at room temperature the molecules exhibit a high surface mobility. For the investigation of these structures and especially to enable scanning tunneling spectroscopy, a low-temperature scanning tunneling microscope was developed. Using this home built STM the experiments could be carried out at about 10 K. After the adsorption of CuPc on Cu (111) a substrate-induced symmetry reduction of the molecules can be observed in scanning tunneling microscopy. When the occupied states of the molecules are imaged, a switching between two distinct levels is found. These modifications are determined by the adsorption geometry of the molecules. Based on high resolution STM data, an on-top adsorption geometry of the CuPc-molecules on Cu (111)-substrate can be deducted. At low temperatures, two new superstructures of PTCDA on Cu(111) are observed. The molecules within these superstructures are tilted with respect to the substrate. Intermolecular interactions may be the crucial factor for the realignment of the molecules. If PTCDA molecules are adsorbed on a NaCl/Cu (111) substrate, at room temperature, also two new superstructures on the copper substrate were found. They indicate the formation of a metall-organic-complex. On top of the NaCl layer the molecules exclusively grow at polar NaCl step edges. This is an indication for electrostatic interaction between the PTCDA molecules and the NaCl layer. When the molecule density is further increased, a Vollmer-Weber growth sets in. If both molecules PTCDA and CuPc are present on the sample at the same time, local spectroscopy provides information on the metal-organic interface in direct comparison. The STS-results of CuPc/PTCDA on Cu (111

Effect of concentration and pH on the surface-enhanced Raman scattering of captopril on nano-colloidal silver surface

Science.gov (United States)

Gao, Junxiang; Gu, Huaimin; Liu, Fangfang; Dong, Xiao; Xie, Min; Hu, Yongjun

2011-07-01

In this report, Raman and surface-enhanced Raman scattering (SERS) spectra of captopril are studied in detail. Herein, the Raman bands are assigned by the density functional theory (DFT) calculations and potential energy distributions (PED) based on internal coordinates of the molecule, which are found to be in good agree with the experimental values. Furthermore, the concentration and pH dependence of the SERS intensity of the molecule is discussed. By analyzing the intensities variation of SERS bands of the different concentrations of captopril solution, it can be concluded that the molecules orientation adsorbed on the silver nanoparticles surface change with the change of the concentrations. The variation of SERS spectra of captopril with the change of pH suggests that the interaction among the adsorbates with Ag cluster depend on the protonated state of the adsorbate and the aggregation of silver nanoparticles.

Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

Science.gov (United States)

Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

2017-01-21

Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

Variable surface composition and radial interface formation in self-assembled free, mixed Ar/Xe clusters

International Nuclear Information System (INIS)

Tchaplyguine, M.; Maartensson, N.; Lundwall, M.; Oehrwall, G.; Feifel, R.; Svensson, S.; Bjoerneholm, O.; Gisselbrecht, M.; Sorensen, S.

2004-01-01

Using photoelectron spectroscopy, we demonstrate how the self-assembling process of cluster formation in an adiabatic expansion leads to radial segregation and layering as well as to variable surface composition for binary Ar/Xe clusters. The radial structuring can be qualitatively understood from the different interatomic bonding strengths of the two components

Modification on surface oxide layer structure and surface morphology of niobium by gas cluster ion beam treatments

International Nuclear Information System (INIS)

Wu, A.T.; Swenson, D.R.; Insepov, Z.

2010-01-01

Recently, it was demonstrated that significant reductions in field emission on Nb surfaces could be achieved by means of a new surface treatment technique called gas cluster ion beam (GCIB). Further study as shown in this paper revealed that GCIB treatments could modify surface irregularities and remove surface asperities leading to a smoother surface finish as demonstrated through measurements using a 3D profilometer, an atomic force microscope, and a scanning electron microscope. These experimental observations were supported by computer simulation via atomistic molecular dynamics and a phenomenological surface dynamics. Measurements employing a secondary ion mass spectrometry found that GCIB could also alter Nb surface oxide layer structure. Possible implications of the experimental results on the performance of Nb superconducting radio frequency cavities treated by GCIB will be discussed. First experimental results on Nb single cell superconducting radio frequency cavities treated by GCIB will be reported.

Cluster ion beam facilities

International Nuclear Information System (INIS)

Popok, V.N.; Prasalovich, S.V.; Odzhaev, V.B.; Campbell, E.E.B.

2001-01-01

A brief state-of-the-art review in the field of cluster-surface interactions is presented. Ionised cluster beams could become a powerful and versatile tool for the modification and processing of surfaces as an alternative to ion implantation and ion assisted deposition. The main effects of cluster-surface collisions and possible applications of cluster ion beams are discussed. The outlooks of the Cluster Implantation and Deposition Apparatus (CIDA) being developed in Guteborg University are shown

Production of molecules on a surface under plasma exposure: example of NO on pyrex

International Nuclear Information System (INIS)

Marinov, D; Guaitella, O; Rousseau, A; Ionikh, Y

2010-01-01

We propose a new experimental approach to the study of surface-catalysed nitric oxide production under plasma exposure. Stable nitrogen species are grafted to the surface of a pyrex discharge tube during N 2 plasma pretreatment. These species are trapped by surface active sites and on being exposed to O 2 plasma, they initiate the production of NO molecules, which are detected using tunable diode laser absorption spectroscopy. Supposing that nitrogen species are adsorbed N atoms, we estimate the initial surface coverage as [N ads ] = 3 x 10 13 cm -2 . This gives an assessment of the lower boundary of the density of surface active sites.

Blu-ray based optomagnetic aptasensor for detection of small molecules

DEFF Research Database (Denmark)

Yang, Jaeyoung; Donolato, Marco; Pinto, Alessandro

2016-01-01

This paper describes an aptamer-based optomagnetic biosensor for detection of a small molecule based on target binding-induced inhibition of magnetic nanoparticle (MNP) clustering. For the detection of a target small molecule, two mutually exclusive binding reactions (aptamer-target binding...... the hydrodynamic size distribution of MNPs and their clusters. A commercial Blu-ray optical pickup unit is used for optical signal acquisition, which enables the establishment of a low-cost and miniaturized biosensing platform. Experimental results show that the degree of MNP clustering correlates well...

The specificity of targeted vaccines for APC surface molecules influences the immune response phenotype.

Directory of Open Access Journals (Sweden)

Gunnveig Grødeland

Full Text Available Different diseases require different immune responses for efficient protection. Thus, prophylactic vaccines should prime the immune system for the particular type of response needed for protection against a given infectious agent. We have here tested fusion DNA vaccines which encode proteins that bivalently target influenza hemagglutinins (HA to different surface molecules on antigen presenting cells (APC. We demonstrate that targeting to MHC class II molecules predominantly induced an antibody/Th2 response, whereas targeting to CCR1/3/5 predominantly induced a CD8(+/Th1 T cell response. With respect to antibodies, the polarizing effect was even more pronounced upon intramuscular (i.m delivery as compared to intradermal (i.d. vaccination. Despite these differences in induced immune responses, both vaccines protected against a viral challenge with influenza H1N1. Substitution of HA with ovalbumin (OVA demonstrated that polarization of immune responses, as a consequence of APC targeting specificity, could be extended to other antigens. Taken together, the results demonstrate that vaccination can be tailor-made to induce a particular phenotype of adaptive immune responses by specifically targeting different surface molecules on APCs.

In-situ Evaluation of Soil Organic Molecules: Functional Group Chemistry Aggregate Structures, Metal and Surface Complexation Using Soft X-Ray

International Nuclear Information System (INIS)

Myneni, Satish C.

2008-01-01

Organic molecules are common in all Earth surface environments, and their composition and chemistry play an important role in a variety of biogeochemical reactions, such as mineral weathering, nutrient cycling and the solubility and transport of contaminants. However, most of what we know about the chemistry of these molecules comes from spectroscopy and microscopy studies of organic molecules extracted from different natural systems using either inorganic or organic solvents. Although all these methods gave us clues about the composition of these molecules, their composition and structure change with the extraction and the type of ex-situ analysis, their true behavior is less well understood. The goal of this project is to develop synchrotron instrumentation for studying natural organics, and to apply these recently developed synchrotron X-ray spectroscopy and microscopy techniques for understanding the: (1) functional group composition of naturally occurring organic molecules; (2) macromolecular structures of organic molecules; and (3) the nature of interactions of organic molecules with mineral surfaces in different environmental conditions.

Study of Si wafer surfaces irradiated by gas cluster ion beams

International Nuclear Information System (INIS)

Isogai, H.; Toyoda, E.; Senda, T.; Izunome, K.; Kashima, K.; Toyoda, N.; Yamada, I.

2007-01-01

The surface structures of Si (1 0 0) wafers subjected to gas cluster ion beam (GCIB) irradiation have been analyzed by cross-sectional transmission electron microscopy (XTEM) and atomic force microscopy (AFM). GCIB irradiation is a promising technique for both precise surface etching and planarization of Si wafers. However, it is very important to understand the crystalline structure of Si wafers after GCIB irradiation. An Ar-GCIB used for the physically sputtering of Si atoms and a SF 6 -GCIB used for the chemical etching of the Si surface are also analyzed. The GCIB irradiation increases the surface roughness of the wafers, and amorphous Si layers are formed on the wafer surface. However, when the Si wafers are annealed in hydrogen at a high temperature after the GCIB irradiation, the surface roughness decreases to the same level as that before the irradiation. Moreover, the amorphous Si layers disappear completely

A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Kimori, Yoshitaka [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502 (Japan); Oguchi, Yosuke [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Ichise, Norihiko [Department of Visual Communication, Komazawa Women' s University, Inagi, Tokyo 206-8511 (Japan); Baba, Norio [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Katayama, Eisaku [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)]. E-mail: ekatayam@ims.u-tokyo.ac.jp

2007-01-15

Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the 'Structural analysis of single molecules', we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.

A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy

International Nuclear Information System (INIS)

Kimori, Yoshitaka; Oguchi, Yosuke; Ichise, Norihiko; Baba, Norio; Katayama, Eisaku

2007-01-01

Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the 'Structural analysis of single molecules', we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application

Using Force to Probe Single-Molecule Receptor-Cytoskeletal Anchoring Beneath the Surface of a Living Cell

DEFF Research Database (Denmark)

Evans, Evan; Kinoshita, Koji

2007-01-01

-cytoskeletal unbinding increased exponentially with the level of force, suggesting disruption at a site of single-molecule interaction. Since many important enzymes and signaling molecules are closely associated with a membrane receptor-cytoskeletal linkage, pulling on a receptor could alter interactions among its......The ligation of cell surface receptors often communicates a signal that initiates a cytoplasmic chemical cascade to implement an important cell function. Less well understood is how physical stress applied to a cell surface adhesive bond propagates throughout the cytostructure to catalyze...... or trigger important steps in these chemical processes. Probing the nanoscale impact of pulling on cell surface bonds, we discovered that receptors frequently detach prematurely from the interior cytostructure prior to failure of the exterior adhesive bond [Evans, E., Heinrich, V., Leung, A., and Kinoshita...

Molecules in stars

International Nuclear Information System (INIS)

Tsuji, T.

1986-01-01

Recently, research related to molecules in stars has rapidly expanded because of progress in related fields. For this reason, it is almost impossible to cover all the topics related to molecules in stars. Thus, here the authors focus their attention on molecules in the atmospheres of cool stars and do not cover in any detail topics related to circumstellar molecules originating from expanding envelopes located far from the stellar surface. However, the authors do discuss molecules in quasi-static circumstellar envelopes (a recently discovered new component of circumstellar envelopes) located near the stellar surface, since molecular lines originating from such envelopes show little velocity shift relative to photospheric lines, and hence they directly affect the interpretation and analysis of stellar spectra

Automated detection of very Low Surface Brightness galaxies in the Virgo Cluster

Science.gov (United States)

Prole, D. J.; Davies, J. I.; Keenan, O. C.; Davies, L. J. M.

2018-04-01

We report the automatic detection of a new sample of very low surface brightness (LSB) galaxies, likely members of the Virgo cluster. We introduce our new software, DeepScan, that has been designed specifically to detect extended LSB features automatically using the DBSCAN algorithm. We demonstrate the technique by applying it over a 5 degree2 portion of the Next-Generation Virgo Survey (NGVS) data to reveal 53 low surface brightness galaxies that are candidate cluster members based on their sizes and colours. 30 of these sources are new detections despite the region being searched specifically for LSB galaxies previously. Our final sample contains galaxies with 26.0 ≤ ⟨μe⟩ ≤ 28.5 and 19 ≤ mg ≤ 21, making them some of the faintest known in Virgo. The majority of them have colours consistent with the red sequence, and have a mean stellar mass of 106.3 ± 0.5M⊙ assuming cluster membership. After using ProFit to fit Sérsic profiles to our detections, none of the new sources have effective radii larger than 1.5 Kpc and do not meet the criteria for ultra-diffuse galaxy (UDG) classification, so we classify them as ultra-faint dwarfs.

Covalent attachment of pyridine-type molecules to glassy carbon surfaces by electrochemical reduction of in situ generated diazonium salts. Formation of ruthenium complexes on ligand-modified surfaces

Energy Technology Data Exchange (ETDEWEB)

Yesildag, Ali [Department of Chemistry, Faculty of Sciences, Atatuerk University, 25240 Erzurum (Turkey); Ekinci, Duygu, E-mail: dekin@atauni.edu.t [Department of Chemistry, Faculty of Sciences, Atatuerk University, 25240 Erzurum (Turkey)

2010-09-30

In this study, pyridine, quinoline and phenanthroline molecules were covalently bonded to glassy carbon (GC) electrode surfaces for the first time using the diazonium modification method. Then, the complexation ability of the modified films with ruthenium metal cations was investigated. The derivatization of GC surfaces with heteroaromatic molecules was achieved by electrochemical reduction of the corresponding in situ generated diazonium salts. X-ray photoelectron spectroscopy (XPS) was used to confirm the attachment of heteroaromatic molecules to the GC surfaces and to determine the surface concentration of the films. The barrier properties of the modified GC electrodes were studied in the presence of redox probes such as Fe(CN){sub 6}{sup 3-} and Ru(NH{sub 3}){sub 6}{sup 3+} by cyclic voltammetry. Additionally, the presence of the resulting organometallic films on the surfaces was verified by XPS after the chemical transformation of the characterized ligand films to the ruthenium complex films. The electrochemical behavior of these films in acetonitrile solution was investigated using voltammetric methods, and the surface coverage of the organometallic films was determined from the reversible metal-based Ru(II)/Ru(III) oxidation waves.

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

Science.gov (United States)

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

Electron-induced chemistry in microhydrated sulfuric acid clusters

Directory of Open Access Journals (Sweden)

J. Lengyel

2017-11-01

Full Text Available We investigate the mixed sulfuric acid–water clusters in a molecular beam experiment with electron attachment and negative ion mass spectrometry and complement the experiment by density functional theory (DFT calculations. The microhydration of (H2SO4m(H2On clusters is controlled by the expansion conditions, and the electron attachment yields the main cluster ion series (H2SO4m(H2OnHSO4− and (H2OnH2SO4−. The mass spectra provide an experimental evidence for the onset of the ionic dissociation of sulfuric acid and ion-pair (HSO4−  ⋅  ⋅  ⋅  H3O+ formation in the neutral H2SO4(H2On clusters with n ≥ 5 water molecules, in excellent agreement with the theoretical predictions. In the clusters with two sulfuric acid molecules (H2SO42(H2On this process starts as early as n ≥ 2 water molecules. The (H2SO4m(H2OnHSO4− clusters are formed after the dissociative electron attachment to the clusters containing the (HSO4−  ⋅  ⋅  ⋅  H3O+ ion-pair structure, which leads to the electron recombination with the H3O+ moiety generating H2O molecule and the H-atom dissociation from the cluster. The (H2OnH2SO4− cluster ions point to an efficient caging of the H atom by the surrounding water molecules. The electron-energy dependencies exhibit an efficient electron attachment at low electron energies below 3 eV, and no resonances above this energy, for all the measured mass peaks. This shows that in the atmospheric chemistry only the low-energy electrons can be efficiently captured by the sulfuric acid–water clusters and converted into the negative ions. Possible atmospheric consequences of the acidic dissociation in the clusters and the electron attachment to the sulfuric acid–water aerosols are discussed.

Microscopic solvation of a lithium atom in water-ammonia mixed clusters: solvent coordination and electron localization in presence of a counterion.

Science.gov (United States)

Pratihar, Subha; Chandra, Amalendu

2008-07-14

The microsolvation structures and energetics of water-ammonia mixed clusters containing a lithium atom, i.e., Li(H(2)O)(n)(NH(3)), n = 1-5, are investigated by means of ab initio theoretical calculations. Several structural aspects such as the solvent coordination to the metal ion and binding motifs of the free valence electron of the metal are investigated. We also study the energetics aspects such as the dependence of vertical ionization energies on the cluster size, and all these structural and energetics aspects are compared to the corresponding results of previously studied anionic water-ammonia clusters without a metal ion. It is found that the Li-O and Li-N interactions play a very important role in stabilizing the lithium-water-ammonia clusters, and the presence of these metal ion-solvent interactions also affect the characteristics of electron solvation in these clusters. This is seen from the spatial distribution of the singly occupied molecular orbital (SOMO) which holds the ejected valence electron of the Li atom. For very small clusters, SOMO electron density is found to exist mainly at the vicinity of the Li atom, whereas for larger clusters, it is distributed outside the first solvation shell. The free dangling hydrogens of water and ammonia molecules are involved in capturing the SOMO electron density. In some of the conformers, OH{e}HO and OH{e}HN types of interactions are found to be present. The presence of the metal ion at the center of the cluster ensures that the ejected electron is solvated at a surface state only, whereas both surface and interiorlike states were found for the free electron in the corresponding anionic clusters without a metal ion. The vertical ionization energies of the present clusters are found to be higher than the vertical detachment energies of the corresponding anionic clusters which signify a relatively stronger binding of the free electron in the presence of the positive metal counterion. The shifts in different

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts.

Science.gov (United States)

Verkhoturov, Stanislav V; Gołuński, Mikołaj; Verkhoturov, Dmitriy S; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A

2018-04-14

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C 60 2+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H) - , emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H) - from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ∼30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts

Science.gov (United States)

Verkhoturov, Stanislav V.; Gołuński, Mikołaj; Verkhoturov, Dmitriy S.; Geng, Sheng; Postawa, Zbigniew; Schweikert, Emile A.

2018-04-01

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C602+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H)-, emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H)- from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ˜30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of

Analytic Morse/long-range potential energy surfaces and "adiabatic-hindered-rotor" treatment for a symmetric top-linear molecule dimer: A case study of CH3F-H2

Science.gov (United States)

Zhang, Xiao-Long; Ma, Yong-Tao; Zhai, Yu; Li, Hui

2018-03-01

A first effective six-dimensional ab initio potential energy surface (PES) for CH3F-H2 which explicitly includes the intramolecular Q3 stretching normal mode of the CH3F monomer is presented. The electronic structure computations have been carried out at the explicitly correlated coupled cluster level of theory [CCSD(T)-F12a] with an augmented correlation-consistent triple zeta basis set. Five-dimensional analytical intermolecular PESs for ν3(CH3F) = 0 and 1 are then obtained by fitting the vibrationally averaged potentials to the Morse/Long-Range (MLR) potential function form. The MLR function form is applied to the nonlinear molecule-linear molecule case for the first time. These fits to 25 015 points have root-mean-square deviations of 0.74 cm-1 and 0.082 cm-1 for interaction energies less than 0.0 cm-1. Using the adiabatic hindered-rotor approximation, three-dimensional PESs for CH3F-paraH2 are generated from the 5D PESs over all possible orientations of the hydrogen monomer. The infrared and microwave spectra for CH3F-paraH2 dimer are predicted for the first time. These analytic PESs can be used for modeling the dynamical behavior in CH3F-(H2)N clusters, including the possible appearance of microscopic superfluidity.

A multi purpose source chamber at the PLEIADES beamline at SOLEIL for spectroscopic studies of isolated species: cold molecules, clusters, and nanoparticles.

Science.gov (United States)

Lindblad, Andreas; Söderström, Johan; Nicolas, Christophe; Robert, Emmanuel; Miron, Catalin

2013-11-01

This paper describes the philosophy and design goals regarding the construction of a versatile sample environment: a source capable of producing beams of atoms, molecules, clusters, and nanoparticles in view of studying their interaction with short wavelength (vacuum ultraviolet and x-ray) synchrotron radiation. In the design, specific care has been taken of (a) the use standard components, (b) ensuring modularity, i.e., that swiftly switching between different experimental configurations was possible. To demonstrate the efficiency of the design, proof-of-principle experiments have been conducted by recording x-ray absorption and photoelectron spectra from isolated nanoparticles (SiO2) and free mixed clusters (Ar/Xe). The results from those experiments are showcased and briefly discussed.

Electronic structure of the BiSI cluster

Energy Technology Data Exchange (ETDEWEB)

Audzijonis, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Gaigalas, G. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Institute of Theoretical Physics and Astronomy, Vilnius University, A. Gostauto 12, LT-01108 Vilnius (Lithuania); Zigas, L. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania)]. E-mail: kkol@vpu.lt; Pauliukas, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Zaltauskas, R. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Cerskus, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Narusis, J. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Institute of Theoretical Physics and Astronomy, Vilnius University, A. Gostauto 12, LT-01108 Vilnius (Lithuania); Kvedaravicius, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania)

2007-03-15

The energy levels of valence bands (VB) and core levels (CL) of the BiSI crystals have been investigated theoretically. The molecular model of this crystal was used for calculation of VB and CL by the unrestricted Hartree-Fock method using GAMESS program, with Hw and MINI basis set. The molecular cluster consisting of 20 molecules of BiSI was used for calculations of averaged total density of states including atom vibrations. The spectra of averaged total density of states from VB of BiSI cluster has been compared with experimental X-ray photoelectron spectra (XPS) of VB of SbSI crystal. The results clarify that the atomic vibrations is one of possible reasons for the smoother appearance of the experimental XPS. The investigation of vibrational spectrum reveals new experimental information about the reflection spectrum of BiSI crystals. The cluster model calculations have shown that the splitting of the CL in the BiSI may be caused by the photoelectron emission from the atoms at the surface that is in different valence states. The cluster model calculation showed that splitting energy of CL depends on difference of ionic charges of the same atoms at the edges of BiSI cluster.

Electronic structure of the BiSI cluster

International Nuclear Information System (INIS)

Audzijonis, A.; Gaigalas, G.; Zigas, L.; Pauliukas, A.; Zaltauskas, R.; Cerskus, A.; Narusis, J.; Kvedaravicius, A.

2007-01-01

The energy levels of valence bands (VB) and core levels (CL) of the BiSI crystals have been investigated theoretically. The molecular model of this crystal was used for calculation of VB and CL by the unrestricted Hartree-Fock method using GAMESS program, with Hw and MINI basis set. The molecular cluster consisting of 20 molecules of BiSI was used for calculations of averaged total density of states including atom vibrations. The spectra of averaged total density of states from VB of BiSI cluster has been compared with experimental X-ray photoelectron spectra (XPS) of VB of SbSI crystal. The results clarify that the atomic vibrations is one of possible reasons for the smoother appearance of the experimental XPS. The investigation of vibrational spectrum reveals new experimental information about the reflection spectrum of BiSI crystals. The cluster model calculations have shown that the splitting of the CL in the BiSI may be caused by the photoelectron emission from the atoms at the surface that is in different valence states. The cluster model calculation showed that splitting energy of CL depends on difference of ionic charges of the same atoms at the edges of BiSI cluster

Mobility of chemisorbed molecules and surface regeneration of active centers during dehydration of isopropanol on aluminium oxide and aluminosilicate

International Nuclear Information System (INIS)

Makhlis, L.A.; Vasserberg, V.Eh.

1976-01-01

By a differential isotope method involving 14 C the authors have investigated the surface mobility of chemisorbed molecules of isopropanol during its dehydration in an adsorption layer on aluminium oxide and aluminosilicate. The chemisorbed alcohol molecules possess marked surface mobility which plays a decisive part in the mechanism of surface regeneration of the active catalyst centers in the process of dehydration. The cessation of the reaction long before the adsorbed alcohol is completely used up is explained by the hypothesis that there is local overpopulation of the active sectors by water formed by the reaction; this hinders further surface regeneration and repetition of the elementary events of dehydration

Pronounced cluster-size effects: gas-phase reactivity of bare vanadium cluster cations V(n)+ (n = 1-7) toward methanol.

Science.gov (United States)

Feyel, Sandra; Schröder, Detlef; Schwarz, Helmut

2009-05-14

Mass spectrometric experiments are used to examine the size-dependent interactions of bare vanadium cluster cations V(n)(+) (n = 1-7) with methanol. The reactivity patterns exhibit enormous size effects throughout the range of clusters investigated. For example, dehydrogenation of methanol to produce V(n)OC(+) is only brought about by clusters with n > or = 3. Atomic vanadium cation V(+) also is reactive, but instead of dehydrogenation of the alcohol, expulsions of either methane or a methyl radical take place. In marked contrast, the reaction efficiency of the dinuclear cluster V(2)(+) is extremely low. For the cluster cations V(n)(+) (n = 3-7), complete and efficient dehydrogenation of methanol to produce V(n)OC(+) and two hydrogen molecules prevails. DFT calculations shed light on the mechanism of the dehydrogenation of methanol by the smallest reactive cluster cation V(3)(+) and propose the occurrence of chemisorption concomitant with C-O bond cleavage rather than adsorption of an intact carbon monoxide molecule by the cluster.

The clustered nucleus-cluster structures in stable and unstable nuclei

International Nuclear Information System (INIS)

Freer, Martin

2007-01-01

The subject of clustering has a lineage which runs throughout the history of nuclear physics. Its attraction is the simplification of the often uncorrelated behaviour of independent particles to organized and coherent quasi-crystalline structures. In this review the ideas behind the development of clustering in light nuclei are investigated, mostly from the stand-point of the harmonic oscillator framework. This allows a unifying description of alpha-conjugate and neutron-rich nuclei, alike. More sophisticated models of clusters are explored, such as antisymmetrized molecular dynamics. A number of contemporary topics in clustering are touched upon; the 3α-cluster state in 12 C, nuclear molecules and clustering at the drip-line. Finally, an understanding of the 12 C+ 12 C resonances in 24 Mg, within the framework of the theoretical ideas developed in the review, is presented

GOLD CLUSTER LABELS AND RELATED TECHNOLOGIES IN MOLECULAR MORPHOLOGY.

Energy Technology Data Exchange (ETDEWEB)

HAINFELD,J.F.; POWELL,R.D.

2004-02-04

Although intensely colored, even the largest colloidal gold particles are not, on their own, sufficiently colored for routine use as a light microscopy stain: only with very abundant antigens or with specialized illumination methods can bound gold be seen. Colloidal gold probes were developed primarily as markers for electron microscopy, for which their very high electron density and selectivity for narrow size distributions when prepared in different ways rendered them highly suited. The widespread use of gold labeling for light microscopy was made possible by the introduction of autometallographic enhancement methods. In these processes, the bound gold particles are exposed to a solution containing metal ions and a reducing agent; they catalyze the reduction of the ions, resulting in the deposition of additional metal selectively onto the particles. On the molecular level, the gold particles are enlarged up to 30-100 nm in diameter; on the macroscale level, this results in the formation of a dark stain in regions containing bound gold particles, greatly increasing visibility and contrast. The applications of colloidal gold have been described elsewhere in this chapter, we will focus on the use of covalently linked cluster complexes of gold and other metals. A gold cluster complex is a discrete molecular coordination compound comprising a central core, or ''cluster'' of electron-dense metal atoms, ligated by a shell of small organic molecules (ligands), which are linked to the metal atoms on the surface of the core. This structure gives clusters several important advantages as labels. The capping of the metal surface by ligands prevents non-specific binding to cell and tissue components, which can occur with colloidal gold. Cluster compounds are more stable and may be used under a wider range of conditions. Unlike colloidal gold, clusters do not require additional macromolecules such as bovine serum albumin or polyethylene glycol for

Amphiphilic Bio-molecules/ZnO Interface: Enhancement of Bio-affinity and Dispersibility

International Nuclear Information System (INIS)

Meng Xiu-Qing; Fang Yun-Zhang; Wu Feng-Min

2012-01-01

The dispersibility of bio-molecules such as lecithins on the surface of ZnO nanowires are investigated for biosensor applications. Lecithins can be absorbed on an as-synthesized ZnO nanowire surface in the form of sub-micro sized clusters, while scattering well on those annealed under oxygen atmosphere. Wettability analysis reveals that the as-synthesized ZnO nanowires bear a super-hydrophobic surface, which convents to superhydrophilic after oxygen annealing. First-principles calculations indicate that the adsorption energy of ZnO with water is about 0.2 eV at a distance of 2 Å when it is superhydrophilic, suggesting that lecithin can be absorbed on the hydrophilic surface stably at this distance and the bio-affinity can be enhanced under this condition. (condensed matter: structure, mechanical and thermal properties)

Thermodynamic properties of water solvating biomolecular surfaces

Science.gov (United States)

Heyden, Matthias

Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

Angstrom-Resolution Magnetic Resonance Imaging of Single Molecules via Wave-Function Fingerprints of Nuclear Spins

Science.gov (United States)

Ma, Wen-Long; Liu, Ren-Bao

2016-08-01

Single-molecule sensitivity of nuclear magnetic resonance (NMR) and angstrom resolution of magnetic resonance imaging (MRI) are the highest challenges in magnetic microscopy. Recent development in dynamical-decoupling- (DD) enhanced diamond quantum sensing has enabled single-nucleus NMR and nanoscale NMR. Similar to conventional NMR and MRI, current DD-based quantum sensing utilizes the "frequency fingerprints" of target nuclear spins. The frequency fingerprints by their nature cannot resolve different nuclear spins that have the same noise frequency or differentiate different types of correlations in nuclear-spin clusters, which limit the resolution of single-molecule MRI. Here we show that this limitation can be overcome by using "wave-function fingerprints" of target nuclear spins, which is much more sensitive than the frequency fingerprints to the weak hyperfine interaction between the targets and a sensor under resonant DD control. We demonstrate a scheme of angstrom-resolution MRI that is capable of counting and individually localizing single nuclear spins of the same frequency and characterizing the correlations in nuclear-spin clusters. A nitrogen-vacancy-center spin sensor near a diamond surface, provided that the coherence time is improved by surface engineering in the near future, may be employed to determine with angstrom resolution the positions and conformation of single molecules that are isotope labeled. The scheme in this work offers an approach to breaking the resolution limit set by the "frequency gradients" in conventional MRI and to reaching the angstrom-scale resolution.

Possibility of 1-nm level localization of a single molecule with gap-mode surface-enhanced Raman scattering

International Nuclear Information System (INIS)

Choi, Han Kyu; Kim, Zee Hwan

2015-01-01

The electromagnetic (EM) enhancement mechanism of surface-enhanced Raman scattering (SERS) has been well established through 30 years of extensive investigation: molecules adsorbed on resonantly driven silver or gold nanoparticles (NPs) experience strongly enhanced field and thus show enhanced Raman scattering. Even stronger SERS enhancement is possible with a gap structure in which two or more NPs form assemblies with gap sizes of 1 nm or less. We have theoretically shown that the measurement of SERS angular distribution can reveal the position of a single molecule near the gap with 1-nm accuracy, even though the spatial extent of the enhanced field is ~10 nm. Real implementation of such experiment requires extremely well-defined (preferably a single crystal) dimeric junctions. Nevertheless, the experiment will provide spatial as well as frequency domain information on single-molecule dynamics at metallic surfaces

Adsorption of a cationic dye molecule on polystyrene microspheres in colloids: effect of surface charge and composition probed by second harmonic generation.

Science.gov (United States)

Eckenrode, Heather M; Jen, Shih-Hui; Han, Jun; Yeh, An-Gong; Dai, Hai-Lung

2005-03-17

Nonlinear optical probe, second harmonic generation (SHG), of the adsorption of the dye molecule malachite green (MG), in cationic form at pH polystyrene microspheres in aqueous solution is used to study the effect of surface charge and composition on molecular adsorption. Three types of polystyrene microspheres with different surface composition are investigated: (1) a sulfate terminated, anionic surface, (2) a neutral surface without any functional group termination, and (3) an amine terminated, cationic surface. The cationic dye was found to adsorb at all three surfaces, regardless of surface charge. The adsorption free energies, DeltaG's, measured for the three surfaces are -12.67, -12.39, and -10.46 kcal/mol, respectively, with the trend as expected from the charge interactions. The adsorption density on the anionic surface, where attractive charge-charge interaction dominates, is determined by the surface negative charge density. The adsorption densities on the neutral and cationic surfaces are on the other hand higher, perhaps as a result of a balance between minimizing repulsive charge interaction and maximizing attractive molecule-substrate and intermolecular interactions. The relative strength of the SH intensity per molecule, in combination of a model calculation, reveals that the C(2) axis of the MG molecule is nearly perpendicular to the surface on the anionic surface and tilts away from the surface norm when the surface is neutral and further away when cationic. Changing the pH of the solution may alter the surface charge and subsequently affect the adsorption configuration and SH intensity.

Self-diffusion dynamic behavior of atomic clusters on Re(0 0 0 1) surface

Energy Technology Data Exchange (ETDEWEB)

Liu Fusheng [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu Wangyu, E-mail: wangyuhu2001cn@yahoo.com.cn [Department of Applied Physics, Hunan University, Changsha 410082 (China); Deng Huiqiu; Luo Wenhua; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)

2009-08-15

Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of rhenium atomic clusters up to seven atoms on Re(0 0 0 1) surface have been studied in the temperature ranges from 600 K to 1900 K. The simulation time varies from 20 ns to 200 ns according to the cluster sizes and the temperature. The heptamer and trimer are more stable comparing to other neighboring non-compact clusters. The diffusion coefficients of clusters are derived from the mean square displacement of cluster's mass-center, and diffusion prefactors D{sub 0} and activation energies E{sub a} are derived from the Arrhenius relation. It is found that the Arrhenius relation of the adatom can be divided into two parts at different temperature range. The activation energy of clusters increases with the increasing of the atom number in clusters. The prefactor of the heptamer is 2-3 orders of magnitude higher than a usual prefactor because of a large number of nonequivalent diffusion processes. The trimer and heptamer are the nuclei at different temperature range according to the nucleation theory.

What do we want from computer simulation of SIMS using clusters?

International Nuclear Information System (INIS)

Webb, R.P.

2008-01-01

Computer simulation of energetic cluster interactions with surfaces has provided much needed insight into some of the complex processes which occur and are responsible for the desirable as well as undesirable effects which make the use of clusters in SIMS both useful and challenging. Simulations have shown how cluster impacts can cause meso-scale motion of the target material which can result in the relatively gentle up-lift of large intact molecules adsorbed on the surface in contrast to the behaviour of single atom impacts which tend to create discrete motion in the surface often ejecting fragments of adsorbed molecules instead. With the insight provided from simulations experimentalists can then improve their equipment to best maximise the desired effects. The past 40 years has seen great progress in simulation techniques and computer equipment. 40 years ago simulations were performed on simple atomic systems of around 300 atoms employing only simple pair-wise interaction potentials to times of several hundred femtoseconds. Currently simulations can be performed on large organic materials employing many body potentials for millions of atoms for times of many picoseconds. These simulations, however, can take several months of computation time. Even with the degree of realism introduced with these long time simulations they are still not perfect are often not capable of being used in a completely predictive way. Computer simulation is reaching a position where by any more effort to increase its realism will make it completely intractable to solution in a reasonable time frame and yet there is an increasing demand from experimentalists for something that can help in a predictive way to help in experiment design and interpretation. This paper will discuss the problems of computer simulation and what might be possible to achieve in the short term, what is unlikely ever to be possible without a major new break through and how we might exploit the meso-scale effects in

Asymmetric Top Rotors in Superfluid Para-Hydrogen Nano-Clusters

Science.gov (United States)

Zeng, Tao; Li, Hui; Roy, Pierre-Nicholas

2012-06-01

We present the first simulation study of bosonic clusters doped with an asymmetric top molecule. A variation of the path-integral Monte Carlo method is developed to study a para-water (pH_2O) impurity in para-hydrogen (pH_2) clusters. The growth pattern of the doped clusters is similar in nature to that of the pure clusters. The pH_2O molecule appears to rotate freely in the cluster due to its large rotational constants and the lack of adiabatic following. The presence of pH_2O substantially quenches the superfluid response of pH_2 with respect to the space fixed frame. We also study the behaviour of a sulphur dioxide (32S16O_2) dopant in the pH_2 clusters. For such a heavy rotor, the adiabatic following of the pH_2 molecules is established and the superfluid renormalization of the rotational constants is observed. The rotational structure of the SO_2-p(H_2)_N clusters' ro-vibrational spectra is predicted. The connection between the superfluid response respect to the external boundary rotation and the dopant rotation is discussed.

Hydrogen-bonded clusters of 1, 1'-ferrocenedicarboxylic acid on Au(111) are initially formed in solution

Science.gov (United States)

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

2015-03-01

Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.

Electronic structure and dynamics of ordered clusters with ME or RE ions on oxide surface

Energy Technology Data Exchange (ETDEWEB)

Kulagin, N.A., E-mail: nkulagin@bestnet.kharkov.u [Kharkiv National University for Radio Electronics, Avenue Shakespeare 6-48, 61045 Kharkiv (Ukraine)

2011-03-15

Selected data of ab initio simulation of the electronic structure and spectral properties of either cluster with ions of iron, rare earth or actinium group elements have been presented here. Appearance of doped Cr{sup +4} ions in oxides, Cu{sup +2} in HTSC, Nd{sup +2} in solids has been discussed. Analysis of experimental data for plasma created ordered structures of crystallites with size of about 10{sup -9} m on surface of separate oxides are given, too. Change in the spectroscopic properties of clusters and nano-structures on surface of strontium titanate crystals discussed shortly using the X-ray line spectroscopy experimental results. - Research highlights: External influence and variation of technology induce changes in valence of nl ions in compounds. Wave function of cluster presented as anti-symmetrical set of ions wave functions. The main equation describes the self-consistent field depending on state of all electrons of cluster. Level scheme of Cr{sup 4+} ions in octo- and tetra-site corresponds to doped oxides spectra after treatment. Plasma treatment effects in appearance of systems of unit crystallites with size of about 10{sup -6}-10{sup -9} m.

Electronic structure and dynamics of ordered clusters with ME or RE ions on oxide surface

International Nuclear Information System (INIS)

Kulagin, N.A.

2011-01-01

Selected data of ab initio simulation of the electronic structure and spectral properties of either cluster with ions of iron, rare earth or actinium group elements have been presented here. Appearance of doped Cr +4 ions in oxides, Cu +2 in HTSC, Nd +2 in solids has been discussed. Analysis of experimental data for plasma created ordered structures of crystallites with size of about 10 -9 m on surface of separate oxides are given, too. Change in the spectroscopic properties of clusters and nano-structures on surface of strontium titanate crystals discussed shortly using the X-ray line spectroscopy experimental results. - Research highlights: → External influence and variation of technology induce changes in valence of nl ions in compounds. → Wave function of cluster presented as anti-symmetrical set of ions wave functions. → The main equation describes the self-consistent field depending on state of all electrons of cluster. → Level scheme of Cr 4+ ions in octo- and tetra-site corresponds to doped oxides spectra after treatment. → Plasma treatment effects in appearance of systems of unit crystallites with size of about 10 -6 -10 -9 m.

Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

International Nuclear Information System (INIS)

Wopperer, P.; Dinh, P.M.; Reinhard, P.-G.; Suraud, E.

2015-01-01

There are various ways to analyze the dynamical response of clusters and molecules to electromagnetic perturbations. Particularly rich information can be obtained from measuring the properties of electrons emitted in the course of the excitation dynamics. Such an analysis of electron signals covers observables such as total ionization, Photo-Electron Spectra (PES), Photoelectron Angular Distributions (PAD), and ideally combined PES/PAD. It has a long history in molecular physics and was increasingly used in cluster physics as well. Recent progress in the design of new light sources (high intensity, high frequency, ultra short pulses) opens new possibilities for measurements and thus has renewed the interest on these observables, especially for the analysis of various dynamical scenarios, well beyond a simple access to electronic density of states. This, in turn, has motivated many theoretical investigations of the dynamics of electronic emission for molecules and clusters up to such a complex and interesting system as C 60 . A theoretical tool of choice is here Time-Dependent Density Functional Theory (TDDFT) propagated in real time and on a spatial grid, and augmented by a Self-Interaction Correction (SIC). This provides a pertinent, robust, and efficient description of electronic emission including the detailed pattern of PES and PAD. A direct comparison between experiments and well founded elaborate microscopic theories is thus readily possible, at variance with more demanding observables such as for example fragmentation or dissociation cross sections. The purpose of this paper is to describe the theoretical tools developed on the basis of real-time and real-space TDDFT and to address in a realistic manner the analysis of electronic emission following irradiation of clusters and molecules by various laser pulses. After a general introduction, we shall present in a second part the available experimental results motivating such studies, starting from the simplest

Clusters in nuclei

CERN Document Server

Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is today one of those domains of heavy-ion nuclear physics that faces the greatest challenges, yet also contains the greatest opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physicists has decided to collaborate in producing a comprehensive collection of lectures and tutorial reviews covering the field. This third volume follows the successful Lect. Notes Phys. 818 (Vol. 1) and 848 (Vol. 2), and comprises six extensive lectures covering the following topics:  - Gamma Rays and Molecular Structure - Faddeev Equation Approach for Three Cluster Nuclear Reactions - Tomography of the Cluster Structure of Light Nuclei Via Relativistic Dissociation - Clustering Effects Within the Dinuclear Model : From Light to Hyper-heavy Molecules in Dynamical Mean-field Approach - Clusterization in Ternary Fission - Clusters in Light N...

Excess electrons in methanol clusters: Beyond the one-electron picture

Science.gov (United States)

Pohl, Gábor; Mones, Letif; Turi, László

2016-10-01

We performed a series of comparative quantum chemical calculations on various size negatively charged methanol clusters, ("separators=" CH 3 OH ) n - . The clusters are examined in their optimized geometries (n = 2-4), and in geometries taken from mixed quantum-classical molecular dynamics simulations at finite temperature (n = 2-128). These latter structures model potential electron binding sites in methanol clusters and in bulk methanol. In particular, we compute the vertical detachment energy (VDE) of an excess electron from increasing size methanol cluster anions using quantum chemical computations at various levels of theory including a one-electron pseudopotential model, several density functional theory (DFT) based methods, MP2 and coupled-cluster CCSD(T) calculations. The results suggest that at least four methanol molecules are needed to bind an excess electron on a hydrogen bonded methanol chain in a dipole bound state. Larger methanol clusters are able to form stronger interactions with an excess electron. The two simulated excess electron binding motifs in methanol clusters, interior and surface states, correlate well with distinct, experimentally found VDE tendencies with size. Interior states in a solvent cavity are stabilized significantly stronger than electron states on cluster surfaces. Although we find that all the examined quantum chemistry methods more or less overestimate the strength of the experimental excess electron stabilization, MP2, LC-BLYP, and BHandHLYP methods with diffuse basis sets provide a significantly better estimate of the VDE than traditional DFT methods (BLYP, B3LYP, X3LYP, PBE0). A comparison to the better performing many electron methods indicates that the examined one-electron pseudopotential can be reasonably used in simulations for systems of larger size.

Reaction dynamics of small molecules at metal surfaces

International Nuclear Information System (INIS)

Samson, P.A.

1999-09-01

The dissociation-desorption dynamics of D 2 upon the Sn/Pt(111) surface alloy are dependent on the surface concentration of Sn. The p(2 x 2) Sn/Pt(111) alloy surface (Θ Sn = 0.25 ML), is initially ∼30 times less reactive towards D 2 adsorption than clean Pt(111). On the (√3 x √3) R30 deg Sn/Pt(111) alloy surface (Θ Sn = 0.33 ML), increased inhibition of D 2 adsorption is reported, with S o ∼ 10 -5 at low energy, coinciding with the loss of stable Pt 3 hollow sites and a significant reduction in the D atom binding energy. Sticking on the √3 alloy is activated with an increased energy threshold of ∼280 meV, with no evidence that vibration enhances dissociation. The barrier to dissociation remains in the entrance channel before the D 2 bond begins to stretch. Vibrational excitation is, however, observed in nitrogen desorption from the catalytic reaction of NO + H 2 over Pd(110). For a surface at 600 K, N 2 vibrational state population ratios of P(v=1/v=0) = 0.50 ± 0.05 and P(v=2/v=0) = 0.60 ± 0.20 are reported. Desorption occurs via the N(ad) + N(ad) recombination channel with little energy released into translation and rotation. The translational energy release observed is dependent on the N 2 vibrational state, with translational temperatures of 425 K, 315 K and 180 K reported for the v=0, 1 and 2 states respectively. Sub-thermal energy releases and normally directed angular distributions suggest the influence of a trapping mechanism, recombining molecules scattering through a molecularly adsorbed state, with a transition state of large d NN responsible for the product vibrational excitation. Although N 2 dissociation on Fe(100) forms a simple overlayer structure, on Fe(110), molecular chemisorption does not occur at or above room temperature and the sticking is extremely small (∼10 -6 to 10 -7 ). Activated nitrogen bombardment can be used to prepare a 'surface nitride' with a structure related to the geometry of bulk Fe 4 N. Scanning tunnelling

Tapping mode AFM study on the surface dynamics of a single glucose oxidase molecule on a Au(1 1 1) surface in water with implication for a surface-induced unfolding pathway

International Nuclear Information System (INIS)

Otsuka, Ichiro; Yaoita, Masashi; Higano, Michi; Nagashima, Seiiichi; Kataoka, Ryoichi

2004-01-01

We have investigated a surface-induced unfolding dynamics of a single glucose oxidase (GO) molecule on Au(1 1 1) in air-saturated water, using tapping mode atomic force microscopy (TMAFM). We followed the unfolding process by measuring the maximum height of a well-isolated GO molecule on a terrace near a step-edge of the surface as a function of contact time. We find three linear portions with two intersections in a power-law fit to the selected values of the observed heights. The kinetic TMAFM result implies that there exist at least two distinct dynamic regimes in the unfolding

GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells.

Science.gov (United States)

Paladino, Simona; Lebreton, Stéphanie; Lelek, Mickaël; Riccio, Patrizia; De Nicola, Sergio; Zimmer, Christophe; Zurzolo, Chiara

2017-12-01

Spatio-temporal compartmentalization of membrane proteins is critical for the regulation of diverse vital functions in eukaryotic cells. It was previously shown that, at the apical surface of polarized MDCK cells, glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are organized in small cholesterol-independent clusters of single GPI-AP species (homoclusters), which are required for the formation of larger cholesterol-dependent clusters formed by multiple GPI-AP species (heteroclusters). This clustered organization is crucial for the biological activities of GPI-APs; hence, understanding the spatio-temporal properties of their membrane organization is of fundamental importance. Here, by using direct stochastic optical reconstruction microscopy coupled to pair correlation analysis (pc-STORM), we were able to visualize and measure the size of these clusters. Specifically, we show that they are non-randomly distributed and have an average size of 67 nm. We also demonstrated that polarized MDCK and non-polarized CHO cells have similar cluster distribution and size, but different sensitivity to cholesterol depletion. Finally, we derived a model that allowed a quantitative characterization of the cluster organization of GPI-APs at the apical surface of polarized MDCK cells for the first time. Experimental FRET (fluorescence resonance energy transfer)/FLIM (fluorescence-lifetime imaging microscopy) data were correlated to the theoretical predictions of the model. © 2017 The Author(s).

SASP. Contributions to the 13. Symposium on atomic and surface physics and related topics

Energy Technology Data Exchange (ETDEWEB)

Scheier, P; Maerk, T [eds.

2002-07-01

The XIII symposium on Atomic and Surface Physics and related Topics (SASP) is devoted to cover the research of interactions between ions, electrons, photons, atoms, molecules and clusters and their interaction with surfaces. This year there was a special session dedicated to proton transfer reaction mass spectrometry covering its applications in different fields and a mini symposium on the radiation action on bio-molecules such as uracil. The contributions included in the proceeding correspond to invited lectures and poster sessions, consisting of short and extended abstracts as well as short articles. (nevyjel)

SASP. Contributions to the 13. Symposium on atomic and surface physics and related topics

International Nuclear Information System (INIS)

Scheier, P.; Maerk, T.

2002-01-01

The XIII symposium on Atomic and Surface Physics and related Topics (SASP) is devoted to cover the research of interactions between ions, electrons, photons, atoms, molecules and clusters and their interaction with surfaces. This year there was a special session dedicated to proton transfer reaction mass spectrometry covering its applications in different fields and a mini symposium on the radiation action on bio-molecules such as uracil. The contributions included in the proceeding correspond to invited lectures and poster sessions, consisting of short and extended abstracts as well as short articles. (nevyjel)

Determination of surface concentrations of individual molecule-layers used in nanoscale biosensors by in situ ATR-FTIR spectroscopy

KAUST Repository

Punzet, Manuel; Baurecht, Dieter; Varga, Franz; Karlic, Heidrun; Heitzinger, Clemens

2012-01-01

formation of typical functionalization protocols and to determine the respective molecule surface concentrations. BSA, anti-TNF-α and anti-PSA antibodies were bound via 3-(trimethoxy)butylsilyl aldehyde linkers to silicon-oxide surfaces in order

Theoretical studies of molecule surface scattering: Rotationally inelastic diffraction and dissociative dynamics of H2 on metals

International Nuclear Information System (INIS)

Cruz Pol, A.J.

1993-01-01

The interaction of H 2 and its isotopes with metal surfaces has been the subject of many investigations. The scattering experiments provide data such as the final rotational state distribution, sticking coefficients, kinetic energy distribution, and diffraction data. In the first study of this thesis the author implemented a model for looking at the rotationally inelastic diffraction probabilities for H 2 , HD, and D 2 , as a function of surface temperature. The surface is treated in a quantum mechanical fashion using a recently developed formalism. The center of mass translational motion is treated semiclassically using Gaussian wave packets, and the rotations are described quantum mechanically. The phonon summed rotation-diffraction probabilities as well as the probability distribution for a scattering molecule exchanging an amount of energy ΔE with the surface were computed. In the second and third study of this thesis the author implemented a mixed quantum-classical model to compute the probability for dissociation and rotational excitation for H 2 , HD, and D 2 scattered from Ni(100) dimensionally in dynamics simulations. Of the six degrees of freedom for the dissociative adsorption of a diatomic molecule on a static surface, the author treats Z,d the center of mass distance above the surface plan, r, the internuclear separation, θ, the polar orientation angle, quantum mechanically. The remaining three degrees of freedom, X and Y, the center of mass position on the surface plane, and oe, the azimuthal orientation angle, are treated classically. Probabilities for dissociation and ro-vibrational excitation are computed as a function of incident translational energy. Two sudden approximations are tested, in which either the center of mass translation parallel to the surface or the azimuthal orientation of the molecule are frozen. Comparisons are made between low and high dimensionality results and with fully classical results

Scaling properties of adsorption energies for hydrogen-containing molecules on transition-metal surfaces

DEFF Research Database (Denmark)

Abild-Pedersen, Frank; Greeley, Jeffrey Philip; Studt, Felix

2007-01-01

Density functional theory calculations are presented for CHx, x=0,1,2,3, NHx, x=0,1,2, OHx, x=0,1, and SHx, x=0,1 adsorption on a range of close-packed and stepped transition-metal surfaces. We find that the adsorption energy of any of the molecules considered scales approximately with the adsorp...

Multiple atomic scale solid surface interconnects for atom circuits and molecule logic gates

International Nuclear Information System (INIS)

Joachim, C; Martrou, D; Gauthier, S; Rezeq, M; Troadec, C; Jie Deng; Chandrasekhar, N

2010-01-01

The scientific and technical challenges involved in building the planar electrical connection of an atomic scale circuit to N electrodes (N > 2) are discussed. The practical, laboratory scale approach explored today to assemble a multi-access atomic scale precision interconnection machine is presented. Depending on the surface electronic properties of the targeted substrates, two types of machines are considered: on moderate surface band gap materials, scanning tunneling microscopy can be combined with scanning electron microscopy to provide an efficient navigation system, while on wide surface band gap materials, atomic force microscopy can be used in conjunction with optical microscopy. The size of the planar part of the circuit should be minimized on moderate band gap surfaces to avoid current leakage, while this requirement does not apply to wide band gap surfaces. These constraints impose different methods of connection, which are thoroughly discussed, in particular regarding the recent progress in single atom and molecule manipulations on a surface.

Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

Energy Technology Data Exchange (ETDEWEB)

Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, 116023 Dalian (China); Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany)

2015-10-28

Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

Phase transition temperatures of 405-725 K in superfluid ultra-dense hydrogen clusters on metal surfaces

International Nuclear Information System (INIS)

Holmlid, Leif; Kotzias, Bernhard

2016-01-01

Ultra-dense hydrogen H(0) with its typical H-H bond distance of 2.3 pm is superfluid at room temperature as expected for quantum fluids. It also shows a Meissner effect at room temperature, which indicates that a transition point to a non-superfluid state should exist above room temperature. This transition point is given by a disappearance of the superfluid long-chain clusters H_2_N(0). This transition point is now measured for several metal carrier surfaces at 405 - 725 K, using both ultra-dense protium p(0) and deuterium D(0). Clusters of ordinary Rydberg matter H(l) as well as small symmetric clusters H_4(0) and H_3(0) (which do not give a superfluid or superconductive phase) all still exist on the surface at high temperature. This shows directly that desorption or diffusion processes do not remove the long superfluid H_2_N(0) clusters. The two ultra-dense forms p(0) and D(0) have different transition temperatures under otherwise identical conditions. The transition point for p(0) is higher in temperature, which is unexpected.

Adsorption of small gas molecules on B36 nanocluster

Indian Academy of Sciences (India)

B36 cluster; Adsorption; Density functional theory; Gas molecules. 1. Introduction ... tural and chemical properties of boron clusters by com- putational methods and ..... systems in which the interaction is physical adsorption. (R>2 Å) are the ...

Experimental study of cluster formation in binary mixture of H2O and H2SO4 vapors in the presence of an ionizing radiation source

Science.gov (United States)

Singh, J. J.; Smith, A. C.; Yue, G. K.

1980-01-01

Molecular clusters formed in pure nitrogen containing H2O and H2SO4 vapors and exposed to a 3 mCi Ni63 beta source were studied in the mass range 50 to 780 amu using a quadrupole mass spectrometer. Measurements were made under several combinations of relative humidity and relative acidity ranging from 0.7 to 7.5 percent and 0.00047 to 0.06333 percent, respectively. The number of H2SO4 molecules in the clusters observed ranged from 1 to 7 whereas the number of H2O molecules ranged from 1 to 16. The experimental cluster spectra differ considerably from those calculated using the classical nucleation theory. First order calculations using modified surface tension values and including the effects of multipole moments of the nucleating molecules indicate that these effects may be enough to explain the difference between the measured and the calculated spectra.

Theoretical Study On The Interaction Between Xenon And Positive Silver Clusters In Gas Phase And On The (001) Chabazite Surface

International Nuclear Information System (INIS)

Hunter, D.

2009-01-01

A systematic study on the adsorption of xenon on silver clusters in the gas phase and on the (001) surface of silver-exchanged chabazite is reported. Density functional theory at the B3LYP level with the cluster model was employed. The results indicate that the dominant part of the binding is the σ donation, which is the charge transfer from the 5p orbital of Xe to the 5s orbital of Ag and is not the previously suggested d π -d π back-donation. A correlation between the binding energy and the degree of σ donation is found. Xenon was found to bind strongly to silver cluster cations and not to neutral ones. The binding strength decreases as the cluster size increases for both cases, clusters in the gas-phase and on the chabazite surface. The Ag + cation is the strongest binding site for xenon both in gas phase and on the chabazite surface with the binding energies of 73.9 and 14.5 kJ/mol, respectively. The results also suggest that the smaller silver clusters contribute to the negative chemical shifts observed in the 129 Xe NMR spectra in experiments.

Long-term surface EMG monitoring using K-means clustering and compressive sensing

Science.gov (United States)

Balouchestani, Mohammadreza; Krishnan, Sridhar

2015-05-01

In this work, we present an advanced K-means clustering algorithm based on Compressed Sensing theory (CS) in combination with the K-Singular Value Decomposition (K-SVD) method for Clustering of long-term recording of surface Electromyography (sEMG) signals. The long-term monitoring of sEMG signals aims at recording of the electrical activity produced by muscles which are very useful procedure for treatment and diagnostic purposes as well as for detection of various pathologies. The proposed algorithm is examined for three scenarios of sEMG signals including healthy person (sEMG-Healthy), a patient with myopathy (sEMG-Myopathy), and a patient with neuropathy (sEMG-Neuropathr), respectively. The proposed algorithm can easily scan large sEMG datasets of long-term sEMG recording. We test the proposed algorithm with Principal Component Analysis (PCA) and Linear Correlation Coefficient (LCC) dimensionality reduction methods. Then, the output of the proposed algorithm is fed to K-Nearest Neighbours (K-NN) and Probabilistic Neural Network (PNN) classifiers in order to calclute the clustering performance. The proposed algorithm achieves a classification accuracy of 99.22%. This ability allows reducing 17% of Average Classification Error (ACE), 9% of Training Error (TE), and 18% of Root Mean Square Error (RMSE). The proposed algorithm also reduces 14% clustering energy consumption compared to the existing K-Means clustering algorithm.

Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA.

Science.gov (United States)

Velagapudi, Sai Pradeep; Luo, Yiling; Tran, Tuan; Haniff, Hafeez S; Nakai, Yoshio; Fallahi, Mohammad; Martinez, Gustavo J; Childs-Disney, Jessica L; Disney, Matthew D

2017-03-22

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.

Formation of transition metal cluster adducts on the surface of single-walled carbon nanotubes: HRTEM studies

KAUST Repository

Kalinina, Irina V.

2014-01-01

We report the formation of chromium clusters on the outer walls of single-walled carbon nanotubes (SWNTs). The clusters were obtained by reacting purified SWNTs with chromium hexacarbonyl in dibutyl ether at 100°C. The functionalized SWNTs were characterized by thermogravimetic analysis, XPS, and high-resolution TEM. The curvature of the SWNTs and the high mobility of the chromium moieties on graphitic surfaces allow the growth of the metal clusters and we propose a mechanism for their formation. © 2014 Taylor and Francis Group, LLC.

PREFACE: Nuclear Cluster Conference; Cluster'07

Science.gov (United States)

Freer, Martin

2008-05-01

The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

Surface-Enhanced Raman Spectroscopy of Dye and Thiol Molecules Adsorbed on Triangular Silver Nanostructures: A Study of Near-Field Enhancement, Localization of Hot-Spots, and Passivation of Adsorbed Carbonaceous Species

Directory of Open Access Journals (Sweden)

Manuel R. Gonçalves

2012-01-01

Full Text Available Surface-enhanced Raman spectroscopy (SERS of thiols and dye molecules adsorbed on triangular silver nanostructures was investigated. The SERS hot-spots are localized at the edges and corners of the silver triangular particles. AFM and SEM measurements permit to observe many small clusters formed at the edges of triangular particles fabricated by nanosphere lithography. Finite-element calculations show that near-field enhancements can reach values of more than 200 at visible wavelengths, in the gaps between small spherical particles and large triangular particles, although for the later no plasmon resonance was found at the wavelengths investigated. The regions near the particles showing strong near-field enhancement are well correlated with spatial localization of SERS hot-spots done by confocal microscopy. Silver nanostructures fabricated by thermal evaporation present strong and fast fluctuating SERS activity, due to amorphous carbon contamination. Thiols and dye molecules seem to be able to passivate the undesired SERS activity on fresh evaporated silver.

Ion emission in solids bombarded with Aun+ (n = 1 - 9) clusters accelerated within the 0.15 - 1.25 MeV energy range

International Nuclear Information System (INIS)

Wehbe, Nimer

2006-06-01

This experimental work is devoted to the study of the ion emission in solids at the impact of gold clusters of energies within 0.15 to 1.25 MeV range. The physics of ion-solid collisions and the theoretical models of sputtering of solids under ion bombardment are presented in the first chapter. The chapter no. 2 deals with the description of the experimental setup. The study of a gold target allowed to evidence the role of the size and energy of the clusters in determining the emission intensity and the mass distribution of the ions. The 4. chapter gives results from the study of cesium iodide in which the intense emission of CsI clusters could be investigated quantitatively due to multiplicity measurements. Finally, the chapter no. 5 was devoted to the study of a biologic molecule, the phenylalanine, and of a pesticide molecule, chlorosulfuron. This work evidenced the importance of clusters for surface analyses by mass spectrometry

Isotope separation using vibrationally excited molecules

International Nuclear Information System (INIS)

Woodroffe, J.A.; Keck, J.C.

1979-01-01

Vibrational excitation of molecules having components of a selected isotope type is used to produce a conversion from vibrational to translational excitation of the molecules by collision with the molecules of a heavy carrier gas. The resulting difference in translaton between the molecules of the selected isotope type and all other molecules of the same compound permits their separate collection. When applied to uranium enrichment, a subsonic cryogenic flow of molecules of uranium hexafluoride in combination with an argon carrier gas is directed through a cooled chamber that is illuminated by laser radiaton tuned to vibrationally excite the uranium hexafluoride molecules of a specific uranium isotope. The excited molecules collide with carrier gas molecules, causing a conversion of the excitation energy into a translation of the excited molecule, which results in a higher thermal energy or diffusivity than that of the other uranium hexafluoride molecules. The flowing molecules including the excited molecules directly enter a set of cryogenically cooled channels. The higher thermal velocity of the excited molecules increases the probability of their striking a collector surface. The molecules which strike this surface immediately condense. After a predetermined thickness of molecules is collected on the surface, the flow of uranium hexafluoride is interrupted and the chamber heated to the point of vaporization of the collected hexafluoride, permitting its removal. (LL)

Threshold electron impact ionization of molecules (CF4, CHF3, CH4, C3H8) and clusters (Ar, Ne, H2, D2), dissociative electron attachment to hydrogen and surface induced reactions of fullerenes (Cn, n=50-60)

International Nuclear Information System (INIS)

Fiegele, T.

2001-02-01

After many years of research the accurate determination and interpretation of threshold energies at which a molecule is ionized by electron impact remains still difficult. The reasons for this are a number of technical obstacles like preparing electrons with a high energy resolution and a complicated physical situation in the reaction complex involving a quantum mechanical many body system. The use of photoionization sometimes appears to be less difficult but nevertheless the values obtained by this technique are not directly comparable to those obtained by electron impact studies. With the use of a newly constructed hemispherical electron monochromator the interaction of electrons under high energy resolution (up to 30 meV) with atoms, molecules and clusters was investigated. In the present study two new techniques have been invoked to obtain more information about the energy resolution of the electrons. Up to now it was only possible to determine the electron energy resolution with the help of s-wave attachment cross sections, e.g. the Cl-/CCl4 resonance at 0 eV. The new techniques allow the investigation at higher energies (at about 12 up to about 58 eV) and by using positive ions. Especially in the case of measuring threshold energies of positive ions the new methods have the advantage that there is no need to change between positive and negative ions. Additionally one gets information about the calibration and the linearity of the energy scale. The value at which the resolution is determined lies also in the range of the threshold. The results show that the resolution is constant over a large electron energy range. Due to low ion signals at the threshold regions the used electron energy resolution was set at about 120 meV for most of the present measurements. In the present work it was for the first time possible to measure accurately the appearance energies for rare gas cluster ions (Ar, Ne) and for hydrogen cluster ions. There are two important observations

Dependence of partial molecules surface area on the third component in lyotropic liquid crystals

International Nuclear Information System (INIS)

Badalyan, H.G.; Ghazaryan, Kh.M.; Yayloyan, S.M.

2015-01-01

Free surface of one amphiphilic molecule head of a lyotropic liquid crystal has been investigated by X-Ray diffraction method, at small and large angles, in the presence of the third component. The pentadecilsulphonat-water system in the presence of cholesterol as well as the lecithin-water system in the presence of decanol were investigated. It is shown that the above mentioned free surface decreases if the cholesterol concentration increases, while this surface increases in the case of water concentration increase. However, it increases slower than in the case of the two-component system. The same is observed for the lecithin-water-decanol system

Molecule-surface interaction processes of relevance to gas blanket type fusion device divertor design

Energy Technology Data Exchange (ETDEWEB)

Snowdon, K.J. [Newcastle Univ. (United Kingdom). Dept. of Physics; Tawara, H.

1997-01-01

The mechanisms which may lead to the departure of molecular species from surfaces exposed to low energy (0.1-100 eV) particle or photon and electron irradiation are reviewed. Where possible, the charge and electronic state, angular, translational and internal energy distributions of the departing molecules are described and the physical origin of the nature of those distributions identified. The consequences, for the departing molecules, of certain material choices become apparent from such an analysis. Such information may help guide the choice of appropriate materials for plasma facing components of gas-blanket type divertors such as that recently proposed for the International Thermonuclear Experimental Reactor (ITER). (author). 71 refs.

Adsorption of organic molecules on mineral surfaces studied by first-principle calculations: A review.

Science.gov (United States)

Zhao, Hongxia; Yang, Yong; Shu, Xin; Wang, Yanwei; Ran, Qianping

2018-04-09

First-principle calculations, especially by the density functional theory (DFT) methods, are becoming a power technique to study molecular structure and properties of organic/inorganic interfaces. This review introduces some recent examples on the study of adsorption models of organic molecules or oligomers on mineral surfaces and interfacial properties obtained from first-principles calculations. The aim of this contribution is to inspire scientists to benefit from first-principle calculations and to apply the similar strategies when studying and tailoring interfacial properties at the atomistic scale, especially for those interested in the design and development of new molecules and new products. Copyright © 2017. Published by Elsevier B.V.

State selective dynamics of molecules, clusters, and nanostructures

Energy Technology Data Exchange (ETDEWEB)

Keto, John W. [Univ. of Texas, Austin, TX (United States)

2005-06-01

Early objectives of this grant were: (1) Measure two-photon excitation of even parity excitons in liquid an solid xenon, (2) Study state-to-state energy transver between two-photon laser excited states or rare-gas atoms to other rare has atoms, (3) study reactive half-collisions between xenon and chlorine leading to the XeCl* B state, (4) measure the spectra of ro-vibrational states of cluster ions and radicals formed in high-pressure discharges and to study their dynamics, (5) measure the surface and bulk electronic states of nanoparticles produced by a unique method of synthesis--laser ablation of microspheres (LAM). Using near-field and microluminescence techniques, we obtained spectra of single nanocrystals to compare with spectra obtained in a supersonic jet apparatus using resonance excitation followed by photoionization (REMPI) with time-of-flight mass analysis. These materials combine the functional advantages obtained from the size-tunable properties of nanocomposite materials with the fabrication and direct-write advantages of NPs manufactured by LAM. We demostrated that CdSe nanoparticles produced by LAM were efficiient fluorescers, even when deposited dry on sapphire substrates. Si nanoparticles were fluorescent when captured in ethylene glycol. We also obtiained efficient fluorescence from Er doped phosphate glass nanopartiicles which have application to gain wafeguides in integrated optics or to nanoslush lasers. We used a femptosecond laser to study the nonlinear spectra of NC composites. We are currently measuring fluorescence and second and third-order susceptibilities of composites of Ag, Si, and GaN nanoparticles encapsulated within thin films of sapphire or SiO ₂.

State selective dynamics of molecules, clusters, and nanostructures

International Nuclear Information System (INIS)

John W. Keto

2005-01-01

Early objectives of this grant were: (1) Measure two-photon excitation of even parity excitons in liquid an solid xenon, (2) Study state-to-state energy transfer between two-photon laser excited states or rare-gas atoms to other rare has atoms, (3) study reactive half-collisions between xenon and chlorine leading to the XeCl* B state, (4) measure the spectra of ro-vibrational states of cluster ions and radicals formed in high-pressure discharges and to study their dynamics, (5) measure the surface and bulk electronic states of nanoparticles produced by a unique method of synthesis--laser ablation of microspheres (LAM). Using near-field and microluminescence techniques, we obtained spectra of single nanocrystals to compare with spectra obtained in a supersonic jet apparatus using resonance excitation followed by photoionization (REMPI) with time-of-flight mass analysis. These materials combine the functional advantages obtained from the size-tunable properties of nanocomposite materials with the fabrication and direct-write advantages of NPs manufactured by LAM. We demonstrated that CdSe nanoparticles produced by LAM were efficient fluorescers, even when deposited dry on sapphire substrates. Si nanoparticles were fluorescent when captured in ethylene glycol. We also obtained efficient fluorescence from Er doped phosphate glass nanoparticles which have application to gain waveguides in integrated optics or to nanoslush lasers. We used a femptosecond laser to study the nonlinear spectra of NC composites. We are currently measuring fluorescence and second and third-order susceptibilities of composites of Ag, Si, and GaN nanoparticles encapsulated within thin films of sapphire or SiO2

A new experimental setup for high-pressure catalytic activity measurements on surface deposited mass-selected Pt clusters

International Nuclear Information System (INIS)

Watanabe, Yoshihide; Isomura, Noritake

2009-01-01

A new experimental setup to study catalytic and electronic properties of size-selected clusters on metal oxide substrates from the viewpoint of cluster-support interaction and to formulate a method for the development of heterogeneous catalysts such as automotive exhaust catalysts has been developed. The apparatus consists of a size-selected cluster source, a photoemission spectrometer, a scanning tunneling microscope (STM), and a high-pressure reaction cell. The high-pressure reaction cell measurements provided information on catalytic properties in conditions close to practical use. The authors investigated size-selected platinum clusters deposited on a TiO 2 (110) surface using a reaction cell and STM. Catalytic activity measurements showed that the catalytic activities have a cluster-size dependency.

Microassay for measurement of binding of radiolabelled ligands to cell surface molecules

International Nuclear Information System (INIS)

Woof, J.M.; Burton, D.R.

1988-01-01

An improved technique for measuring the binding of radiolabelled ligands to cell surface molecules has been developed by modification of a procedure using centrifugation through a water-immiscible oil to separate free and cell-bound ligand. It maximises the percentage of ligand bound since cell-bound and free ligand can be separated easily and reproducibly even when very small reaction volumes are used. This permits low levels of ligand radiolabelling and relatively low numbers of cells to be used

Phase transition temperatures of 405-725 K in superfluid ultra-dense hydrogen clusters on metal surfaces

Energy Technology Data Exchange (ETDEWEB)

Holmlid, Leif, E-mail: holmlid@chem.gu.se [Atmospheric Science, Department of Chemistry, University of Gothenburg, SE-412 96 Göteborg (Sweden); Kotzias, Bernhard [Airbus DS, Department Mechanical Engineering, D28199 Bremen (Germany)

2016-04-15

Ultra-dense hydrogen H(0) with its typical H-H bond distance of 2.3 pm is superfluid at room temperature as expected for quantum fluids. It also shows a Meissner effect at room temperature, which indicates that a transition point to a non-superfluid state should exist above room temperature. This transition point is given by a disappearance of the superfluid long-chain clusters H{sub 2N}(0). This transition point is now measured for several metal carrier surfaces at 405 - 725 K, using both ultra-dense protium p(0) and deuterium D(0). Clusters of ordinary Rydberg matter H(l) as well as small symmetric clusters H{sub 4}(0) and H{sub 3}(0) (which do not give a superfluid or superconductive phase) all still exist on the surface at high temperature. This shows directly that desorption or diffusion processes do not remove the long superfluid H{sub 2N}(0) clusters. The two ultra-dense forms p(0) and D(0) have different transition temperatures under otherwise identical conditions. The transition point for p(0) is higher in temperature, which is unexpected.

Introduction to cluster dynamics

CERN Document Server

Reinhard, Paul-Gerhard

2008-01-01

Clusters as mesoscopic particles represent an intermediate state of matter between single atoms and solid material. The tendency to miniaturise technical objects requires knowledge about systems which contain a ""small"" number of atoms or molecules only. This is all the more true for dynamical aspects, particularly in relation to the qick development of laser technology and femtosecond spectroscopy. Here, for the first time is a highly qualitative introduction to cluster physics. With its emphasis on cluster dynamics, this will be vital to everyone involved in this interdisciplinary subje

The influence of internal degrees of freedom on the unimolecular decay of the molecule-cluster compound Au8+CH3OH

Science.gov (United States)

Vogel, M.; Hansen, K.; Herlert, A.; Schweikhard, L.; Walther, C.

2002-06-01

Time-resolved photodissociation measurements of the sequential reaction Au8+CH3OH→Au8+→Au7+ and the direct reaction Au8+→Au7+ have been performed for several excitation energies. The production rates and yields of the final state Au7+ in the sequential process are strongly influenced by the excitation energy deposited into the evaporated methanol molecule during the initial fragmentation step. Both the rate constants and yields can be fitted with a single parameter, the cluster-methanol binding energy.

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

2017-11-28

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO₂ and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO₂ nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO₂ nanoparticle surfaces by using ultrafast single-molecule

Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

Energy Technology Data Exchange (ETDEWEB)

Hatter, Nino

2016-12-14

In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

The effect of oxygen molecule adsorption on lead iodide perovskite surface by first-principles calculation

Science.gov (United States)

Ma, Xia-Xia; Li, Ze-Sheng

2018-01-01

Oxygen molecule has a negative effect on perovskite solar cells, which has been investigated experimentally. However, detailed theoretical research is still rare. This study presents a microscopic view to reveal the interaction mechanism between O2 and perovskite based on the first-principles calculation. The results show that O2 is adsorbed on the (100) surface of MAPbI3 perovskite mainly by Van der Waals force. O2 adsorption makes the MAPbI3 surface generate a small number of positive charges, which leads to the increase of the work function of the MAPbI3 surface. This is in agreement with the experimental measurement. And increased work function of MAPbI3 surface is not beneficial to electron transfer from perovskite to electronic extraction layer (such as TiO2). Comparison of the density of states (DOS) of the clean (100) surface and the adsorbed system shows that an in-gap state belonging to O2 appears, which can explain the phenomenon observed from experiments that electron transfers from the surface of perovskite to O2 to form superoxide. The theoretical power conversion efficiency of the system with and without O2 adsorption is evaluated, and it turns out that the power conversion efficiency of the system with O2 adsorption is slightly lower than that of the system without O2 adsorption. This result indicates that avoiding the introduction of O2 molecules between perovskite and electronic extraction layer is beneficial to the perovskite solar cell.

Nanometer-scale discernment of field emission from tungsten surface with single carbon monoxide molecule

Science.gov (United States)

Matsunaga, Soichiro; Suwa, Yuji; Katagiri, Souichi

2017-12-01

Unusual quantized beam fluctuations were found in the emission current from a cold-field emitter (CFE) operating in an extremely high vacuum of 10-10 Pa. To clarify the microscopic mechanism behind these fluctuations, we developed a new calculation method to evaluate the field emission from a heterogeneous surface under a strong electric field of 4 × 109 V/m by using the local potential distribution obtained by a first-principles calculation, instead of by using the work function. As a result of the first-principles calculations of a single molecule adsorbed on a tungsten surface, we found that dissociative adsorption of a carbon monoxide (CO) molecule enhances the emission current by changing the potential barrier in the area surrounding the C and O adatoms when these two atoms are placed at their most stable positions. It is also found that the migration of the O atom from the most stable position reduces the emission current. These types of enhancement and reduction of the emission current quantitatively explain the observed quantized fluctuations of the CFE emission current.

Bonding and vibrational dynamics of a large π-conjugated molecule on a metal surface

International Nuclear Information System (INIS)

Temirov, R; Soubatch, S; Lassise, A; Tautz, F S

2008-01-01

The interplay between the substrate bonding of a large π-conjugated semiconductor molecule and the dynamical properties of the metal-organic interface is studied, employing the prototypical PTCDA/Ag(111) monolayer as an example. Both the coupling of molecular vibrations to the electron-hole-pair continuum of the metal surface and the inelastic scattering of tunnelling electrons by the molecular vibrations on their passage through the molecule are considered. The results of both types of experiment are consistent with the findings of measurements which probe the geometric and electronic structure of the adsorbate-substrate complex directly; generally speaking, they can be understood in the framework of standard theories for the electron-vibron coupling. While the experiments reported here in fact provide additional qualitative insights into the substrate bonding of our π-conjugated model molecule, their detailed quantitative understanding would require a full calculation of the dynamical interface properties, which is currently not available

Coupling of carbon monoxide molecules over oxygen-defected UO2(111) single crystal and thin film surfaces.

Science.gov (United States)

Senanayake, S D; Waterhouse, G I N; Idriss, H; Madey, Theodore E

2005-11-22

While coupling reactions of carbon-containing compounds are numerous in organometallic chemistry, they are very rare on well-defined solid surfaces. In this work we show that the reductive coupling of two molecules of carbon monoxide to C2 compounds (acetylene and ethylene) could be achieved on oxygen-defected UO2(111) single crystal and thin film surfaces. This result allows in situ electron spectroscopic investigation of a typical organometallic reaction such as carbon coupling and extends it to heterogeneous catalysis and solids. By using high-resolution photoelectron spectroscopy (HRXPS) it was possible to track the changes in surface states of the U and O atoms as well as identify the intermediate of the reaction. Upon CO adsorption U cations in low oxidation states are oxidized to U4+ ions; this was accompanied by an increase of the O-to-U surface ratios. The HRXPS C 1s lines show the presence of adsorbed species assigned to diolate species (-OCH=CHO-) that are most likely the reaction intermediate in the coupling of two CO molecules to acetylene and ethylene.

Coupling of Carbon Monoxide Molecules over Oxygen Defected UO2 (111) Single Crystal and Thin Film Surfaces

International Nuclear Information System (INIS)

Senanayake, S.; Waterhouse, G.; Idriss, H.; Madey, T.

2005-01-01

While coupling reactions of carbon-containing compounds are numerous in organometallic chemistry, they are very rare on well-defined solid surfaces. In this work we show that the reductive coupling of two molecules of carbon monoxide to C 2 compounds (acetylene and ethylene) could be achieved on oxygen-defected UO 2 (111) single crystal and thin film surfaces. This result allows in situ electron spectroscopic investigation of a typical organometallic reaction such as carbon coupling and extends it to heterogeneous catalysis and solids. By using high-resolution photoelectron spectroscopy (HRXPS) it was possible to track the changes in surface states of the U and O atoms as well as identify the intermediate of the reaction. Upon CO adsorption U cations in low oxidation states are oxidized to U 4+ ions; this was accompanied by an increase of the O-to-U surface ratios. The HRXPS C 1s lines show the presence of adsorbed species assigned to diolate species (-OCH=CHO-) that are most likely the reaction intermediate in the coupling of two CO molecules to acetylene and ethylene

Epitaxially Grown Films of Standing and Lying Pentacene Molecules on Cu(110) Surfaces

Science.gov (United States)

2011-01-01

Here, it is shown that pentacene thin films (30 nm) with distinctively different crystallographic structures and molecular orientations can be grown under essentially identical growth conditions in UHV on clean Cu(110) surfaces. By X-ray diffraction, we show that the epitaxially oriented pentacene films crystallize either in the “thin film” phase with standing molecules or in the “single crystal” structure with molecules lying with their long axes parallel to the substrate. The morphology of the samples observed by atomic force microscopy shows an epitaxial alignment of pentacene crystallites, which corroborates the molecular orientation observed by X-ray diffraction pole figures. Low energy electron diffraction measurements reveal that these dissimilar growth behaviors are induced by subtle differences in the monolayer structures formed by slightly different preparation procedures. PMID:21479111

In Situ Detection of Organic Molecules on the Martian Surface With the Mars Organic Molecule Analyzer (MOMA) on Exomars 2018

Science.gov (United States)

Li, Xiang; Brinckerhoff, William B.; Pinnick, Veronica T; van Amerom, Friso H. W.; Danell, Ryan M.; Arevalo, Ricardo D., Jr.; Getty, Stephanie; Mahaffy, Paul R.

2015-01-01

The Mars Organic Molecule Analyzer (MOMA) investigation on the 2018 ExoMars rover will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. The MOMA instrument is centered around a miniaturized linear ion trap (LIT) that facilitates two modes of operation: i) pyrolysisgas chromatography mass spectrometry (pyrGC-MS); and, ii) laser desorptionionization mass spectrometry (LDI-MS) at ambient Mars pressures. The LIT also enables the structural characterization of complex molecules via complementary analytical capabilities, such as multi-frequency waveforms (i.e., SWIFT) and tandem mass spectrometry (MSMS). When combined with the complement of instruments in the rovers Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds.

Properties of ammonium ion-water clusters: analyses of structure evolution, noncovalent interactions, and temperature and humidity effects.

Science.gov (United States)

Pei, Shi-Tu; Jiang, Shuai; Liu, Yi-Rong; Huang, Teng; Xu, Kang-Ming; Wen, Hui; Zhu, Yu-Peng; Huang, Wei

2015-03-26

Although ammonium ion-water clusters are abundant in the biosphere, some information regarding these clusters, such as their growth route, the influence of temperature and humidity, and the concentrations of various hydrated clusters, is lacking. In this study, theoretical calculations are performed on ammonium ion-water clusters. These theoretical calculations are focused on determining the following characteristics: (1) the pattern of cluster growth; (2) the percentages of clusters of the same size at different temperatures and humidities; (3) the distributions of different isomers for the same size clusters at different temperatures; (4) the relative strengths of the noncovalent interactions for clusters of different sizes. The results suggest that the dipole moment may be very significant for the ammonium ion-water system, and some new stable isomers were found. The nucleation of ammonium ions and water molecules is favorable at low temperatures; thus, the clusters observed at high altitudes might not be present at low altitudes. High humidity can contribute to the formation of large ammonium ion-water clusters, whereas the formation of small clusters may be favorable under low-humidity conditions. The potential energy surfaces (PES) of these different sized clusters are complicated and differ according to the distribution of isomers at different temperatures. Some similar structures are observed between NH4(+)(H2O)n and M(H2O)n (where M represents an alkali metal ion or water molecule); when n = 8, the clusters begin to form the closed-cage geometry. As the cluster size increases, these interactions become progressively weaker. The successive binding energy at the DF-MP2-F12/VDZ-F12 level is better than that at the PW91PW91/6-311++G(3df, 3pd) level and is consistent with the experimentally determined values.

Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks

Directory of Open Access Journals (Sweden)

Keitel Cervantes-Salguero

2015-02-01

Full Text Available Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics.

Detection of Surface-Linked Polychlorinated Biphenyls using Surface-Enhanced Raman Scattering Spectroscopy

DEFF Research Database (Denmark)

Rindzevicius, Tomas; Barten, Jan; Vorobiev, Mikhail

2017-01-01

We present an improved procedure for analytical detection of toxic polychlorinated biphenyls (PCB) using surface-enhanced Raman scattering (SERS) spectroscopy. A gold-capped silicon nanopillar substrate was utilized to concentrate PCB molecules within an area of high electromagnetic fields through...... formation of microsized nanopillar clusters, and consequently, so-called “hot spots” can be formed. In order to improve PCB detection limit, 3,3',4,4'-tetrachlorobiphenyl (PCB77) compounds were chemically modified with a – SCH3 (PCB77-SCH3) group. Experimental and numerical analysis of vibrational modes...

Control of the interparticle spacing in superparamagnetic iron oxide nanoparticle clusters by surface ligand engineering

Science.gov (United States)

Dan, Wang; Bingbing, Lin; Taipeng, Shen; Jun, Wu; Fuhua, Hao; Chunchao, Xia; Qiyong, Gong; Huiru, Tang; Bin, Song; Hua, Ai

2016-07-01

Polymer-mediated self-assembly of superparamagnetic iron oxide (SPIO) nanoparticles allows modulation of the structure of SPIO nanocrystal cluster and their magnetic properties. In this study, dopamine-functionalized polyesters (DA-polyester) were used to directly control the magnetic nanoparticle spacing and its effect on magnetic resonance relaxation properties of these clusters was investigated. Monodisperse SPIO nanocrystals with different surface coating materials (poly(ɛ-caprolactone), poly(lactic acid)) of different molecular weights containing dopamine (DA) structure (DA-PCL2k, DA-PCL1k, DA-PLA1k)) were prepared via ligand exchange reaction, and these nanocrystals were encapsulated inside amphiphilic polymer micelles to modulate the SPIO nanocrystal interparticle spacing. Small-angle x-ray scattering (SAXS) was applied to quantify the interparticle spacing of SPIO clusters. The results demonstrated that the tailored magnetic nanoparticle clusters featured controllable interparticle spacing providing directly by the different surface coating of SPIO nanocrystals. Systematic modulation of SPIO nanocrystal interparticle spacing can regulate the saturation magnetization (M s) and T 2 relaxation of the aggregation, and lead to increased magnetic resonance (MR) relaxation properties with decreased interparticle spacing. Project supported by the National Key Basic Research Program of China (Grant No. 2013CB933903), the National Key Technology R&D Program of China (Grant No. 2012BAI23B08), and the National Natural Science Foundation of China (Grant Nos. 20974065, 51173117, and 50830107).

Coupling between diffusion and orientation of pentacene molecules on an organic surface.

Science.gov (United States)

Rotter, Paul; Lechner, Barbara A J; Morherr, Antonia; Chisnall, David M; Ward, David J; Jardine, Andrew P; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor

2016-04-01

The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems.

Organizing and addressing magnetic molecules.

Science.gov (United States)

Gatteschi, Dante; Cornia, Andrea; Mannini, Matteo; Sessoli, Roberta

2009-04-20

Magnetic molecules ranging from simple organic radicals to single-molecule magnets (SMMs) are intensively investigated for their potential applications in molecule-based information storage and processing. The goal of this Article is to review recent achievements in the organization of magnetic molecules on surfaces and in their individual probing and manipulation. We stress that the inherent fragility and redox sensitivity of most SMM complexes, combined with the noninnocent role played by the substrate, ask for a careful evaluation of the structural and electronic properties of deposited molecules going beyond routine methods for surface analysis. Detailed magnetic information can be directly obtained using X-ray magnetic circular dichroism or newly emerging scanning probe techniques with magnetic detection capabilities.

Spinterface between tris(8-hydroxyquinoline)metal(III) molecules and magnetic surfaces: a first-principles study

Science.gov (United States)

Jiang, W.; Wang, Jingying; Dougherty, Daniel; Liu, Feng; Feng Liu Team; Daniel Dougherty Team

Using first-principles calculations, we have systematically investigated the hybridization between tris(8-hydroxyquinoline)metal(III) (Mq3, M = Fe, Cr, Al) molecules and magnetic substrates (Co and Cr). Mq3 with different central metal elements but the same organic framework has dramatically different interaction with different magnetic substrates, which affect the interface state significantly. AFM coupling was observed between magnetic Mq3 molecules and ferromagnetic (Co) as well as antiferromagnetic (Cr) substrate, manifested with a superexchange and direct exchange interaction, respectively. Such strong magnetic interfacial coupling may open a gap around the Fermi level and significantly change interface transport properties. Nonmagnetic Alq3 molecule was found to enhance the interface spin polarization due to hybridization between the lowest unoccupied molecular orbitals (LUMO) of Alq3 and metallic surface state. These findings will help better understand spinterface and shed new light on future application of Mq3 molecules in spintronics devices. This work was support by NSF-MRSEC (DMR-1121252) and DOE-BES (DE-FG02-04ER46148).

Bimetallic Ag-Pt Sub-nanometer Supported Clusters as Highly Efficient and Robust Oxidation Catalysts

Energy Technology Data Exchange (ETDEWEB)

Negreiros, Fabio R. [CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, Pisa Italy; Halder, Avik [Materials Science Division, Argonne National Laboratory, Lemont IL USA; Yin, Chunrong [Materials Science Division, Argonne National Laboratory, Lemont IL USA; Singh, Akansha [Harish-Chandra Research Institute, HBNI, Chhatnag Road Jhunsi Allahabad 211019 India; Barcaro, Giovanni [CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, Pisa Italy; Sementa, Luca [CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, Pisa Italy; Tyo, Eric C. [Materials Science Division, Argonne National Laboratory, Lemont IL USA; Pellin, Michael J. [Materials Science Division, Argonne National Laboratory, Lemont IL USA; Bartling, Stephan [Institut für Physik, Universität Rostock, Rostock Germany; Meiwes-Broer, Karl-Heinz [Institut für Physik, Universität Rostock, Rostock Germany; Seifert, Sönke [X-ray Science Division, Argonne National Laboratory, Lemont IL USA; Sen, Prasenjit [Harish-Chandra Research Institute, HBNI, Chhatnag Road Jhunsi Allahabad 211019 India; Nigam, Sandeep [Chemistry Division, Bhabha Atomic Research Centre, Trombay Mumbai- 400 085 India; Majumder, Chiranjib [Chemistry Division, Bhabha Atomic Research Centre, Trombay Mumbai- 400 085 India; Fukui, Nobuyuki [East Tokyo Laboratory, Genesis Research Institute, Inc., Ichikawa Chiba 272-0001 Japan; Yasumatsu, Hisato [Cluster Research Laboratory, Toyota Technological Institute: in, East Tokyo Laboratory, Genesis Research Institute, Inc. Ichikawa, Chiba 272-0001 Japan; Vajda, Stefan [Materials Science Division, Argonne National Laboratory, Lemont IL USA; Nanoscience and Technology Division, Argonne National Laboratory, Lemont IL USA; Institute for Molecular Engineering, University of Chicago, Chicago IL USA; Fortunelli, Alessandro [CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, Pisa Italy; Materials and Process Simulation Center, California Institute of Technology, Pasadena CA USA

2017-12-29

A combined experimental and theoretical investigation of Ag-Pt sub-nanometer clusters as heterogeneous catalysts in the CO -> CO2 reaction (COox) is presented. Ag9Pt2 and Ag9Pt3 clusters are size-selected in the gas phase, deposited on an ultrathin amorphous alumina support, and tested as catalysts experimentally under realistic conditions and by first-principles simulations at realistic coverage. Insitu GISAXS/TPRx demonstrates that the clusters do not sinter or deactivate even after prolonged exposure to reactants at high temperature, and present comparable, extremely high COox catalytic efficiency. Such high activity and stability are ascribed to a synergic role of Ag and Pt in ultranano-aggregates, in which Pt anchors the clusters to the support and binds and activates two CO molecules, while Ag binds and activates O-2, and Ag/Pt surface proximity disfavors poisoning by CO or oxidized species.

Surface Collisions of Small Cluster Ions at Incident Energies 10-102 eV

Czech Academy of Sciences Publication Activity Database

Herman, Zdeněk

2004-01-01

Roč. 233, - (2004), s. 361-371 ISSN 1387-3806 R&D Projects: GA MŠk ME 561 Grant - others:XE(CZ) EURATOM-IPP.CR Institutional research plan: CEZ:AV0Z4040901 Keywords : surface collisions * cluster ions * unimolecular dissociation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.235, year: 2004

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria

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Muscariello Lidia

2006-05-01

Full Text Available Abstract Background Genomes of gram-positive bacteria encode many putative cell-surface proteins, of which the majority has no known function. From the rapidly increasing number of available genome sequences it has become apparent that many cell-surface proteins are conserved, and frequently encoded in gene clusters or operons, suggesting common functions, and interactions of multiple components. Results A novel gene cluster encoding exclusively cell-surface proteins was identified, which is conserved in a subgroup of gram-positive bacteria. Each gene cluster generally has one copy of four new gene families called cscA, cscB, cscC and cscD. Clusters encoding these cell-surface proteins were found only in complete genomes of Lactobacillus plantarum, Lactobacillus sakei, Enterococcus faecalis, Listeria innocua, Listeria monocytogenes, Lactococcus lactis ssp lactis and Bacillus cereus and in incomplete genomes of L. lactis ssp cremoris, Lactobacillus casei, Enterococcus faecium, Pediococcus pentosaceus, Lactobacillius brevis, Oenococcus oeni, Leuconostoc mesenteroides, and Bacillus thuringiensis. These genes are neither present in the genomes of streptococci, staphylococci and clostridia, nor in the Lactobacillus acidophilus group, suggesting a niche-specific distribution, possibly relating to association with plants. All encoded proteins have a signal peptide for secretion by the Sec-dependent pathway, while some have cell-surface anchors, novel WxL domains, and putative domains for sugar binding and degradation. Transcriptome analysis in L. plantarum shows that the cscA-D genes are co-expressed, supporting their operon organization. Many gene clusters are significantly up-regulated in a glucose-grown, ccpA-mutant derivative of L. plantarum, suggesting catabolite control. This is supported by the presence of predicted CRE-sites upstream or inside the up-regulated cscA-D gene clusters. Conclusion We propose that the CscA, CscB, CscC and Csc

Br2(X) microsolvation in helium clusters: effect of the interaction on the quantum solvent density distribution.

Science.gov (United States)

Di Paola, Cono; Gianturco, Franco A; López-Durán, David; de Lara-Castells, Maria Pilar; Delgado-Barrio, Gerardo; Villarreal, Pablo; Jellinek, Julius

2005-07-11

The Born-Oppenheimer potential energy surface for the Br2(X) molecule interacting with a varying number of 4He bosons is constructed following two different schemes which employ either a full ab initio evaluation of the Br2-He interaction forces or an estimate of the latter through an empirical model. Both descriptions are employed by carrying out diffusion Monte Carlo (DMC) calculations of the ground-state energies and quantum wavefunctions for Br2-(He)n clusters with n up to 24. The results clearly indicate, for both interactions, the occurrence of the full solvation of the molecular dopant within the quantum bosonic "solvent" but also show differences between the two models in terms of the expected density distributions of the surrounding particles within the shorter-range region that makes up the clusters with smaller n values. Our calculations also show that such differences become insignificant for the larger 4He clusters surrounding the Br2 molecule, where density profiles and bulk behaviour are chiefly driven by the solvent structure, once n values reach the region of 15-20 adatoms.

Ion bombardment modification of surfaces

International Nuclear Information System (INIS)

Auciello, O.

1984-01-01

An historical overview of the main advances in the understanding of bombardment-induced surface topography is presented. The implantation and sputtering mechanisms which are relevant to ion bombardment modification of surfaces and consequent structural, electronic and compositional changes are described. Descriptions of plasma and ion-beam sputtering-induced film formation, primary ion-beam deposition, dual beam techniques, cluster of molecule ion-beam deposition, and modification of thin film properties by ion bombardment during deposition are presented. A detailed account is given of the analytical and computational modelling of topography from the viewpoint of first erosion theory. Finally, an account of the possible application and/or importance of textured surfaces in technologies and/or experimental techniques not considered in previous chapters is presented. refs.; figs.; tabs

FY 2000 report on the results of the research and development project for new industry creation type industrial science technologies. Cluster ion beam process technology; 2000 nendo shinki sangyo soshutsugata sangyo kagaku gijutsu kenkyu kaihatsu seido seika hokokusho. Cluster ion beam process technology

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NONE

2001-03-01

Described herein are the FY 2000 results of development of cluster ion beams. This technology generates the strong ion beams of atom and molecule clusters, and irradiate them onto the solid surfaces, to create new materials or treat materials. It allows the nano-level treatment. The program for high-current cluster ion beam generation/irradiation technology for industrial purposes attains the target high-current beam of 500{mu}m. It is necessary to establish the optimum cluster size, irradiated energy and ion species for the highly functional surface treatment, for which applicable technologies, e.g., those related to time of flight and molecular dynamics, are developed. Studies on high-current, large-area irradiation technologies are started. The program for material processing technologies involves evaluation of crystalline defects formed during the beam implantation by photoluminescence spectroscopy, and studies on semiconductor surface processing technologies. The surface smoothening technology is investigated to reduce crystalline defects and stress-induced strains for difficult-to-process materials, e.g., SiC and diamond, and the good results are produced. The program for development of superflat/superhard thin film formation technology involves irradiation of the Ar ion beams during the deposition of C{sub 60}(fullerene), to produce the superhard thin film. (NEDO)

Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

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Galvão, B R L; Rodrigues, S P J; Varandas, A J C

2008-07-28

A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

Effect of Water Clustering on the Activity of Candida antarctica Lipase B in Organic Medium

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Sindrila Dutta Banik

2017-07-01

Full Text Available The effect of initial water activity of MTBE (methyl tert-butyl ether medium on CALB (Candida antarctica lipase B catalyzed esterification reaction is investigated using experimental methods and classical molecular dynamics (MD simulations. The experimental kinetic studies show that the initial reaction rate of CALB-catalyzed esterification reaction between butyric acid and ethanol decreases with increasing initial water activity of the medium. The highest rate of esterification is observed at the lowest water activity studied. MD simulations were performed to gain a molecular insight on the effect of initial water activity on the rate of CALB-catalyzed reaction. Our results show that hydration has an insignificant effect on the structure and flexibility of CALB. Rather, it appears that water molecules bind to certain regions (“hot spots” on the CALB surface and form clusters. The size of the water clusters at these hot spot regions gradually increase and expand with increasing water activity. Consequently, the surface area of CALB covered by the water molecules also increases. Specifically, our results indicate that a particular water cluster located close to the active site partially cover the binding pocket of substrate at high water activity. As a consequence, the effective concentration of substrate at the catalytic site decreases. Therefore, the reaction rate slows down with increasing water activity, which correlates well with the observed decrease in the experimentally determined initial reaction rate.

The three-cluster structures in 7Li

International Nuclear Information System (INIS)

Beck, R.; Krivec, R.; Mihailovic, M.V.; Kernforschungszentrum Karlsruhe G.m.b.H.

1981-01-01

A cluster model for the description of light nuclei is investigated which includes the interplay of three-cluster structures with the two-cluster ones and allows molecule-like vibrations of clusters. It is applied to the nucleus 7 Li in order to study the influence of the trhee-cluster structures of the type ( 4 He- 2 H-n) on the low-lying states previously described by two-cluster structures ( 4 He- 3 H) and ( 6 Li-n). An effective central interaction is used in the calculation. The structure of the nucleus 7 Li is described by the two-cluster configuration ( 4 He- 3 H) and the three-cluster configurations ( 4 He- 2 H(Isub(d))-n), with Isub(d) = 0, 1, and the total spin I = 1/2, 3/2. In the wave function of three-cluster structure the pair of values L 1 = 0, L 2 = 1 only is included. The effective nuclear potential V2 of Volkov is used in the calculation. The energy of the ground state described by a single configuration of the two-cluster structure ( 4 He- 3 H) is lowered by 0.66 MeV when this configuration is coupled to two three-cluster configurations and the molecule-like vibration is allowed through solving the Hill-Wheeler equation. Both mechanism have approximately equal effects. The ground-state energy (-38.14 MeV) is 0.3 MeV lower than in the model which describes the 7 Li by a superposition of two-cluster structures ( 4 He- 3 H) and ( 6 Li-n). (orig./HSI)

Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

Science.gov (United States)

Vysotsky, Yu B; Kartashynska, E S; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Miller, R

2015-11-21

Using the quantum chemical semi-empirical PM3 method it is shown that aliphatic alcohols favor the spontaneous clusterization of vaporous alkanes at the water surface due to the change of adsorption from the barrier to non-barrier mechanism. A theoretical model of the non-barrier mechanism for monolayer formation is developed. In the framework of this model alcohols (or any other surfactants) act as 'floats', which interact with alkane molecules of the vapor phase using their hydrophobic part, whereas the hydrophilic part is immersed into the water phase. This results in a significant increase of contact effectiveness of alkanes with the interface during the adsorption and film formation. The obtained results are in good agreement with the existing experimental data. To test the model the thermodynamic and structural parameters of formation and clusterization are calculated for vaporous alkanes C(n)H(2n+2) (n(CH3) = 6-16) at the water surface in the presence of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K. It is shown that the values of clusterization enthalpy, entropy and Gibbs' energy per one monomer of the cluster depend on the chain lengths of corresponding alcohols and alkanes, the alcohol molar fraction in the monolayers formed, and the shift of the alkane molecules with respect to the alcohol molecules Δn. Two possible competitive structures of mixed 2D film alkane-alcohol are considered: 2D films 1 with single alcohol molecules enclosed by alkane molecules (the alcohols do not form domains) and 2D films 2 that contain alcohol domains enclosed by alkane molecules. The formation of the alkane films of the first type is nearly independent of the surfactant type present at the interface, but depends on their molar fraction in the monolayer formed and the chain length of the compounds participating in the clusterization, whereas for the formation of the films of the second type the interaction between the hydrophilic parts of the surfactant is

Assessment of structures and stabilities of defect clusters and surface energies predicted by nine interatomic potentials for UO{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Taller, Stephen A. [School of Nuclear Engineering, Purdue University, West Lafayette, IN 47907 (United States); Bai, Xian-Ming, E-mail: xianming.bai@inl.gov [Fuels Modeling and Simulation Department, Idaho National Laboratory, Idaho Falls, ID 83415 (United States)

2013-11-15

The irradiation in nuclear reactors creates many point defects and defect clusters in uranium dioxide (UO{sub 2}) and their evolution severely degrades the thermal and mechanical properties of the nuclear fuels. Previously many empirical interatomic potentials have been developed for modeling defect production and evolution in UO{sub 2}. However, the properties of defect clusters and extended defects are usually not fitted into these potentials. In this work nine interatomic potentials for UO{sub 2} are examined by using molecular statics and molecular dynamics to assess their applicability in predicting the properties of various types of defect clusters in UO{sub 2}. The binding energies and structures for these defect clusters have been evaluated for each potential. In addition, the surface energies of voids of different radii and (1 1 0) flat surfaces predicted by these potentials are also evaluated. It is found that both good agreement and significant discrepancies exist for these potentials in predicting these properties. For oxygen interstitial clusters, these potentials predict significantly different defect cluster structures and stabilities; For defect clusters consisting of both uranium and oxygen defects, the prediction is in better agreement; The surface energies predicted by these potentials have significant discrepancies, and some of them are much higher than the experimentally measured values. The results from this work can provide insight on interpreting the outcome of atomistic modeling of defect production using these potentials and may provide guidelines for choosing appropriate potential models to study problems of interest in UO{sub 2}.

Biomimetic Nanoarchitectures for the Study of T Cell Activation with Single-Molecule Control

Science.gov (United States)

Cai, Haogang

organized into a stereotypic geometric structure, known as the immunological synapse, between T cell and antigen-presenting cell. Novel bifunctionalization schemes were developed to better mimic the antigen-presenting surfaces. Nanoarrays were functionalized by single molecules of UCHT1 Fab', and served as individual T cell receptor binding sites. The adhesion molecule ICAM-1 was bound to either static PEG background, or a mobile supported lipid bilayer. The minimum geometric requirements (receptor clustering, spacing and stoichiometry) for T cell activation was probed by systematic variation of the nanoarray spacing and cluster size. Out-of-plane spatial control of the two key molecules by way of nanopillar arrays was used to adjust the membrane bending and steric effects, which were essential for the investigation of molecular segregation in T cell activation. The results provide insights into the complicated T cell activation mechanism, with translational implications toward adoptive immunotherapies for cancer and other diseases. This single-molecule platform serves as a novel and powerful tool for molecular and cellular biology, e.g., receptor-mediated signaling/adhesion, especially when multiple ligands or membrane deformation are involved.

Effect of nontronite smectite clay on the chemical evolution of several organic molecules under simulated Mars surface UV radiation conditions

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Poch, Olivier; Dequaire, Tristan; Stalport, Fabien; Jaber, Maguy; Lambert, Jean-François; Szopa, Cyril; Coll, Patrice

2015-04-01

The search for organic carbon-containing molecules at the surface of Mars, as clues of past habitability or remnants of life, is a major scientific goal for Mars exploration. Several lines of evidence, including the detection of phyllosilicates, suggest that early Mars offered favorable conditions for long-term sustaining of water. As a consequence, we can assume that in those days, endogenous chemical processes, or even primitive life, may have produced organic matter on Mars. Moreover, exogenous delivery from small bodies or dust particles is likely to have brought fresh organic molecules to the surface of Mars up today. Organic matter is therefore expected to be present at the surface/subsurface of the planet. But the current environmental conditions at the surface - UV radiation, oxidants and energetic particles - generate physico-chemical processes that may affect organic molecules. On the other hand, on Earth, phyllosilicates are known to accumulate and preserve organic matter. But are phyllosilicates efficient at preserving organic molecules under the current environmental conditions at the surface of Mars? We have monitored the qualitative and quantitative evolutions of glycine, urea and adenine interacting with the Fe3+-smectite clay nontronite, one of the most abundant phyllosilicates present at the surface of Mars, under simulated Martian surface ultraviolet light (190-400 nm), mean temperature (218 ± 2 K) and pressure (6 ± 1 mbar) in a laboratory simulation setup. We have tested organic-rich samples which may be representative of the evaporation of a warm little pond of liquid water having concentrated organics on Mars. For each molecule, we have observed how the nontronite influences the quantum efficiency of its photodecomposition and the nature of its solid evolution products. The results reveal a pronounced photoprotective effect of nontronite on the evolution of glycine and adenine: their efficiencies of photodecomposition are reduced by a factor

First-principles analysis of C2H2 molecule diffusion and its dissociation process on the ferromagnetic bcc-Fe(110) surface

International Nuclear Information System (INIS)

Ikeda, Minoru; Yamasaki, Takahiro; Kaneta, Chioko

2010-01-01

Using the projector-augmented plane wave method, we study diffusion and dissociation processes of C 2 H 2 molecules on the ferromagnetic bcc-Fe(110) surface and investigate the formation process of graphene created by C 2 H 2 molecules. The most stable site for C 2 H 2 on the Fe surface is a hollow site and its adsorption energy is - 3.5 eV. In order to study the diffusion process of the C 2 H 2 molecule, the barrier height energies for the C atom, C 2 -dimer and CH as well as the C 2 H 2 molecule are estimated using the nudged elastic band method. The barrier height energy for C 2 H 2 is 0.71 eV and this indicates that the C 2 H 2 diffuses easily on this FM bcc-Fe(110) surface. We further investigate the two step dissociation process of C 2 H 2 on Fe. The first step is the dissociation of C 2 H 2 into C 2 H and H, and the second step is that of C 2 H into C 2 and H. Their dissociation energies are 0.9 and 1.2 eV, respectively. These energies are relatively small compared to the dissociation energy 7.5 eV of C 2 H 2 into C 2 H and H in the vacuum. Thus, the Fe surface shows catalytic effects. We further investigate the initial formation process of graphene by increasing the coverage of C 2 H 2 . The formation process of the benzene molecule on the FM bcc(110) surface is also discussed. We find that there exists a critical coverage of C 2 H 2 which characterizes the beginning of the formation of the graphene.

First-principles analysis of C2H2 molecule diffusion and its dissociation process on the ferromagnetic bcc-Fe110 surface.

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Ikeda, Minoru; Yamasaki, Takahiro; Kaneta, Chioko

2010-09-29

Using the projector-augmented plane wave method, we study diffusion and dissociation processes of C(2)H(2) molecules on the ferromagnetic bcc-Fe(110) surface and investigate the formation process of graphene created by C(2)H(2) molecules. The most stable site for C(2)H(2) on the Fe surface is a hollow site and its adsorption energy is - 3.5 eV. In order to study the diffusion process of the C(2)H(2) molecule, the barrier height energies for the C atom, C(2)-dimer and CH as well as the C(2)H(2) molecule are estimated using the nudged elastic band method. The barrier height energy for C(2)H(2) is 0.71 eV and this indicates that the C(2)H(2) diffuses easily on this FM bcc-Fe(110) surface. We further investigate the two step dissociation process of C(2)H(2) on Fe. The first step is the dissociation of C(2)H(2) into C(2)H and H, and the second step is that of C(2)H into C(2) and H. Their dissociation energies are 0.9 and 1.2 eV, respectively. These energies are relatively small compared to the dissociation energy 7.5 eV of C(2)H(2) into C(2)H and H in the vacuum. Thus, the Fe surface shows catalytic effects. We further investigate the initial formation process of graphene by increasing the coverage of C(2)H(2). The formation process of the benzene molecule on the FM bcc(110) surface is also discussed. We find that there exists a critical coverage of C(2)H(2) which characterizes the beginning of the formation of the graphene.

Clusters in nuclei. Vol. 1

International Nuclear Information System (INIS)

Beck, Christian

2010-01-01

Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is presently one of the domains of heavy-ion nuclear physics facing both the greatest challenges and opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physics decided to team up in producing a comprehensive collection of lectures and tutorial reviews covering the field. This first volume, gathering seven extensive lectures, covers the follow topics: - Cluster Radioactivity - Cluster States and Mean Field Theories - Alpha Clustering and Alpha Condensates - Clustering in Neutron-rich Nuclei - Di-neutron Clustering - Collective Clusterization in Nuclei - Giant Nuclear Molecules By promoting new ideas and developments while retaining a pedagogical nature of presentation throughout, these lectures will both serve as a reference and as advanced teaching material for future courses and schools in the fields of nuclear physics and nuclear astrophysics. (orig.)

Colliding holes in Riemann surfaces and quantum cluster algebras

Science.gov (United States)

Chekhov, Leonid; Mazzocco, Marta

2018-01-01